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| # Use this template for a NimbleGen genomic submissions. If the array has been previously submitted to GEO, the platform sections are optional. If it is a new array, the platform section MUST be completed. | |||||||||||||||||||||||||||
| # Include descriptive information and protocols for the overall experiment, individual Samples, and Platform in this Metadata worksheet. | |||||||||||||||||||||||||||
| # Click the Metadata Example tab below to view a completed worksheet. | |||||||||||||||||||||||||||
| # Field names (in blue on this page) should not be edited. Hover over cells containing field names to view field content guidelines or, | |||||||||||||||||||||||||||
| # CLICK HERE for Field Content Guidelines Web page. | |||||||||||||||||||||||||||
| # Include your Platform annotation columns and processed Sample data in the accompanying Matrix worksheet (click Matrix tab below). | |||||||||||||||||||||||||||
| # NOTE: If your row count exceeds the capacity of Excel, then skip the Matrix worksheet and provide Platform annotation columns and processed data as an external file(s) in plain text, tab-delimited format: | |||||||||||||||||||||||||||
| # either as a matrix containing both Platform Columns and multiple Samples -or- as individual files for the Platform Columns and each of the Samples. | |||||||||||||||||||||||||||
| # Any external file(s) must contain an ID_REF column (e.g., based on the PROBE_ID column of the .ndf file). | |||||||||||||||||||||||||||
| # Reference any external file name(s) under the 'processed data file' and 'Platform Columns file' headers below. | |||||||||||||||||||||||||||
| SERIES | |||||||||||||||||||||||||||
| # This section describes the overall experiment | |||||||||||||||||||||||||||
| title | |||||||||||||||||||||||||||
| summary | |||||||||||||||||||||||||||
| summary | |||||||||||||||||||||||||||
| overall design | |||||||||||||||||||||||||||
| contributor | |||||||||||||||||||||||||||
| contributor | |||||||||||||||||||||||||||
| SEEK Project | Project | ||||||||||||||||||||||||||
| Experiment Class (assay Type) | transcripomics | ||||||||||||||||||||||||||
| Experiment Design type | ExperimentDesignType | ||||||||||||||||||||||||||
| Technology type | microarray | ||||||||||||||||||||||||||
| quality control type | QualityControlDescriptionType | ||||||||||||||||||||||||||
| SAMPLES | |||||||||||||||||||||||||||
| # The Sample names in the first column are arbitrary but they must match the column headers of the matrix table. | |||||||||||||||||||||||||||
| # CLICK HERE to find the platform accession number (GPLxxxx). | |||||||||||||||||||||||||||
| Sample name | title | processed data file | ch1: source name | ch1: raw data file | ch1: organism | ch1:characteristics:NCBI_ID | ch1:characteristics:Strain | ch1:characteristics:Genotype | ch1:characteristics:Phenotype | ch1: characteristics: tag | ch1: molecule | ch1: label | ch1: growth protocol | ch1: treatment protocol | ch2: source name | ch2: raw data file | ch2: organism | ch2:characteristics:NCBI_ID | ch2:characteristics:Strain | ch2:characteristics:Genotype | ch2:characteristics:Phenotype | ch2: characteristics: tag | ch2: molecule | ch2: label | ch2: growth protocol | ch2: treatment protocol | description |
| Sample 1 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 2 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 3 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 4 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 5 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 6 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 7 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 8 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample 9 | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| Sample X | organism | MaterialType | LabelCompound | organism | MaterialType | LabelCompound | |||||||||||||||||||||
| PROTOCOLS | |||||||||||||||||||||||||||
| # This section includes protocols and fields which are common to all Samples. | |||||||||||||||||||||||||||
| # Protocols which are applicable to specific Samples or specific channels should be included in additional columns of the SAMPLES section instead. | |||||||||||||||||||||||||||
| extract protocol | |||||||||||||||||||||||||||
| label protocol | |||||||||||||||||||||||||||
| hyb protocol | |||||||||||||||||||||||||||
| scan protocol | |||||||||||||||||||||||||||
| data processing | |||||||||||||||||||||||||||
| value definition | |||||||||||||||||||||||||||
| PLATFORM | |||||||||||||||||||||||||||
| # If your array is not deposited in GEO, please include platform annotation columns in your Matrix worksheet (see example) and complete the fields below. | |||||||||||||||||||||||||||
| title | |||||||||||||||||||||||||||
| technology | in situ oligonucleotide | ||||||||||||||||||||||||||
| distribution | |||||||||||||||||||||||||||
| organism | |||||||||||||||||||||||||||
| manufacturer | NimbleGen | ||||||||||||||||||||||||||
| manufacture protocol | |||||||||||||||||||||||||||
| description | Genome build information | ||||||||||||||||||||||||||
| description | |||||||||||||||||||||||||||
| native array description file | .ndf | ||||||||||||||||||||||||||
| native array description file | .pos | ||||||||||||||||||||||||||
| Platform Columns file | |||||||||||||||||||||||||||
| # Platform Column Definitions: describe the contents of each platform column in the Matrix worksheet or in an external file | |||||||||||||||||||||||||||
| SEQUENCE | Sequence of oligo | ||||||||||||||||||||||||||
| Chromosome | Chromosomal location | ||||||||||||||||||||||||||
| RANGE_START | Chromosomal start position of oligo | ||||||||||||||||||||||||||
| LENGTH | Oligo length | ||||||||||||||||||||||||||
| RANGE_END | Chromosomal end position of oligo | ||||||||||||||||||||||||||
| etc… |
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| # Use this template for a NimbleGen genomic submission based on an array not represented in GEO. | ||||||||||||||||||||
| # Include Platform annotation columns (ID_REF, SEQUENCE, etc.) and processed Sample data used to draw the conclusions from your study, for example: | ||||||||||||||||||||
| # scaled, probe-level log2 ratio (IP fraction/input DNA) data for Chip-chip Samples. | ||||||||||||||||||||
| # Loess- or qspline-normalized, probe-level log2 ratio (test/ref) data for aCGH Samples. | ||||||||||||||||||||
| # scaled, probe-level log2 ratio (MeDIP fraction/input DNA) data for DNA methylation Samples. | ||||||||||||||||||||
| # The ID_REF column must contain unique identifiers, e.g., based on the PROBE_ID column of the .ndf file (PROBE_IDs are NimbleGen probe identifiers). | ||||||||||||||||||||
| # The sample header names in the Matrix must match the Sample name in the SAMPLES section of the Metadata file. | ||||||||||||||||||||
| # Values that should be disregarded may either be left blank or labeled as "null". | ||||||||||||||||||||
| # NOTE: If your row count exceeds the capacity of Excel, then skip this Matrix worksheet and provide Platform annotation columns and processed data as an external file(s) in plain text, tab-delimited format: | ||||||||||||||||||||
| # either as a matrix containing Platform Columns and multiple Samples -or- as individual files for the Platform Columns and each of the Samples. | ||||||||||||||||||||
| # Any external file(s) must contain an ID_REF column (e.g., based on the PROBE_ID column of the .ndf file). | ||||||||||||||||||||
| # Reference any external file name(s) under the 'processed data file' and 'Platform Columns file' headers of the Metadata worksheet. | ||||||||||||||||||||
| ID_REF | SEQUENCE | Chromosome | RANGE_START | LENGTH | RANGE_END | Sample 1 | Sample 2 | Sample 3 | Sample 4 | Sample 5 | Sample 6 | Sample 7 | Sample 8 | Sample 9 | Sample X | |||||
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| # This is a Metadata example for a NimbleGen genomic submission based on an array not represented in GEO. | |||||||||||||||||||||||||
| SERIES | |||||||||||||||||||||||||
| title | Chip-chip from pro-B cells with H3K4me3, H3K4me2 and H3K9ac | ||||||||||||||||||||||||
| summary | The transcription factor Pax5 represses B-lineage-inappropriate genes and activates B-cell-specific genes in B-lymphocytes. Conditional mutagenesis demonstrated that the Pax5-regulated genes require continuous Pax5 activity for normal expression in pro-B and mature B cells. | ||||||||||||||||||||||||
| summary | Chromatin immunoprecipitation (ChIP) of Pax5 together with chromatin profiling by ChIP-on-chip analysis demonstrated that Pax5 directly activates the chromatin at promoters or putative enhancers of Pax5 target genes. | ||||||||||||||||||||||||
| overall design | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells | ||||||||||||||||||||||||
| contributor | Jane, Doe | ||||||||||||||||||||||||
| contributor | John,A,Smith | ||||||||||||||||||||||||
| SAMPLES | |||||||||||||||||||||||||
| Sample name | title | processed data file | ch1: source name | ch1: raw data file | ch1: organism | ch1: characteristics: Genotype | ch1: characteristics: Cell type | ch1: characteristics: Strain | ch1: characteristics: ChIP Antibody | ch1: molecule | ch1: label | ch1: growth protocol | ch1: treatment protocol | ch2: source name | ch2: raw data file | ch2: organism | ch2: characteristics: Genotype | ch2: characteristics: Cell type | ch2: characteristics: Strain | ch2: characteristics: ChIP Antibody | ch2: molecule | ch2: label | ch2: growth protocol | ch2: treatment protocol | description |
| Sample 1 | RAG H3K4me2 | RAG H3K4me2.txt | H3K4me2 ChIP DNA from Rag2-/- pro-B cells | RAG_H3K4me2_Cy5.pair | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | H3K4me2 | genomic DNA | Cy5 | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Input DNA from Rag2-/- pre-B cells | RAG_H3K4me2_Cy3.pair | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Chip-chip Rag2-/- pro-B cells H3K4me2 |
| Sample 2 | RAG H3K4me3 | RAG H3K4me3.txt | H3K4me3 ChIP DNA from Rag2-/- pro-B cells | RAG_H3K4me3_Cy5.pair | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | H3K4me3 | genomic DNA | Cy5 | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Input DNA from Rag2-/- pro-B cells | RAG_H3K4me3_Cy3.pair | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Chip-chip Rag2-/- pro-B cells H3K4me3 |
| Sample 3 | RAG H3K9ac | RAG H3K9ac.txt | H3K9ac ChIP DNA from Pax5-/- Rag2-/- pro-B cells | RAG_H3K9ac_Cy5.pair | Mus musculus | Pax5-/- Rag2-/- | pro-B cells | C57BL/6J | H3K9ac | genomic DNA | Cy5 | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Pax5-/- Rag2-/- pro-B cells are an established cell line | Input DNA from Pax5-/- Rag2-/- pro-B cells | RAG_H3K9ac_Cy3.pair | Mus musculus | Pax5-/-Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Pax5-/- Rag2-/- pro-B cells are an established cell line | Chip-chip Pax5-/-Rag2-/- pro-B cells H3K9ac |
| Sample 4 | P5R2 H3K4me3 | P5R2 H3K4me3.txt | H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells | P5R2_H3K4me3_Cy5.pair | Mus musculus | Pax5-/- Rag2-/- | pro-B cells | C57BL/6J | H3K4me3 | genomic DNA | Cy5 | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Pax5-/- Rag2-/- pro-B cells are an established cell line | Input DNA from Pax5-/- Rag2-/- pro-B cells | P5R2_H3K4me3_Cy3.pair | Mus musculus | Pax5-/-Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Pax5-/- Rag2-/- pro-B cells are an established cell line | Chip-chip Pax5-/-Rag2-/- pro-B cells H3K4me3 |
| Sample 5 | P5R2 H3K4me2 | P5R2 H3K4me2.txt | H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells | P5R2_H3K4me2_Cy5.pair | Mus musculus | Pax5-/- Rag2-/- | pro-B cells | C57BL/6J | H3K4me2 | genomic DNA | Cy5 | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Pax5-/- Rag2-/- pro-B cells are an established cell line | Input DNA from Pax5-/- Rag2-/- pro-B cells | P5R2_H3K4me2_Cy3.pair | Mus musculus | Pax5-/-Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Pax5-/- Rag2-/- pro-B cells are an established cell line | Chip-chip Pax5-/-Rag2-/- pro-B cells H3K4me2 |
| Sample 6 | RAG H3K9ac | RAG H3K9ac.txt | H3K9ac ChIP DNA from Rag2-/- pro-B cells | RAG_H3K9ac_Cy5.pair | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | H3K9ac | genomic DNA | Cy5 | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice | Input DNA from Rag2-/- pre-B cells | RAG_H3K9ac_Cy3.pair | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice | Chip-chip Rag2-/- pro-B cells H3K9ac |
| PROTOCOLS | |||||||||||||||||||||||||
| extract protocol | 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation. | ||||||||||||||||||||||||
| label protocol | 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). | ||||||||||||||||||||||||
| hyb protocol | The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html) | ||||||||||||||||||||||||
| scan protocol | Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). | ||||||||||||||||||||||||
| data processing | Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. | ||||||||||||||||||||||||
| value definition | scaled, log2 (ChIP/Input) ratio | ||||||||||||||||||||||||
| PLATFORM | |||||||||||||||||||||||||
| title | |||||||||||||||||||||||||
| technology | in situ oligonucleotide | ||||||||||||||||||||||||
| distribution | custom-commercial | ||||||||||||||||||||||||
| organism | Mus musculus | ||||||||||||||||||||||||
| manufacturer | NimbleGen | ||||||||||||||||||||||||
| manufacture protocol | see manufacturer's web site www.nimblegen.com | ||||||||||||||||||||||||
| description | Annotation in this record based on NCBI mouse build 34. | ||||||||||||||||||||||||
| description | Genomic regions of potential pax5 target genes from mm6, isothermal tiling oligos at 100bp | ||||||||||||||||||||||||
| native array description file | 2006-07-18_mm6.ndf | ||||||||||||||||||||||||
| native array description file | 2006-07-18_mm6.pos | ||||||||||||||||||||||||
| Platform Columns file | GEO_Platform_file.txt | ||||||||||||||||||||||||
| # Platform Column Definitions | |||||||||||||||||||||||||
| SEQUENCE | Sequence of oligo | ||||||||||||||||||||||||
| Chromosome | Chromosomal location of oligo (NCBI mouse build 34) | ||||||||||||||||||||||||
| RANGE_START | Chromosomal start position of oligo (NCBI mouse build 34) | ||||||||||||||||||||||||
| LENGTH | Oligo length | ||||||||||||||||||||||||
| RANGE_END | Chromosomal end position of oligo (NCBI mouse build 34) |
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| # This is a truncated Matrix worksheet for a NimbleGen genomic submission based on an array not represented in GEO. | |||||||||||||||||
| # Include Platform annotation columns (e.g., ID_REF, SEQUENCE, etc.) and processed Sample data (e.g., scaled log2 ChIP/Input ratios) used to draw the conclusions from your study. | |||||||||||||||||
| # The ID_REF column must contain unique identifiers, e.g., based on the PROBE_ID column of the .ndf file. | |||||||||||||||||
| # The sample header names in the matrix must match the Sample name in the SAMPLES section of the Metadata file. | |||||||||||||||||
| # Values that should be disregarded may either be left blank or labeled as "null". | |||||||||||||||||
| ID_REF | SEQUENCE | Chromosome | RANGE_START | LENGTH | RANGE_END | Sample 1 | Sample 2 | Sample 3 | Sample 4 | Sample 5 | Sample 6 | ||||||
| MB1_0680_0216 | AAAATGAGGCAACAGGGATAAGAGCCATCCAACTGGAAGTCAAGC | chr1 | 172488822 | 50 | 172488871 | -0.8 | -1.17 | -0.38 | -0.76 | -1.29 | -0.83 | ||||||
| MB1_0451_0165 | ATGTGGGCCCTGCCTTTAGAACCCAGTCTGACCTTACATTTCTCT | chr1 | 172488922 | 50 | 172488971 | -0.11 | -0.01 | 0.02 | 0.21 | -0.55 | -0.26 | ||||||
| MB1_0584_0692 | CTTCCCTGGCTCAGATTGTCTCAACAGCTCTGTTTTCCTCTTTGC | chr1 | 172489102 | 50 | 172489151 | 0.66 | 1.28 | 1.12 | 1.61 | -0.24 | 1.03 | ||||||
| MB1_0678_0926 | CTGCAGCAGAGGGTCCGCTTTGCAGCCTCAGACCCCAGCCAGTAC | chr1 | 172489202 | 70 | 172489271 | -0.04 | -1.16 | -1.02 | -1.01 | -0.68 | -0.39 | ||||||
| MB1_0433_0701 | GCCGGGTGAAGAAGACCACCATGGCCACCAGGAAGGTCATTGTCA | chr1 | 172489302 | 70 | 172489371 | 0.14 | 0.8 | 0.63 | 0.15 | -0.26 | -0.2 | ||||||
| MB1_0152_0242 | AAGTGCAGATTGGCTGCTGTGAGCCTGGCTCAGGCTTTTGGCTGC | chr1 | 172489402 | 70 | 172489471 | -0.3 | -0.81 | 0.26 | -0.12 | -0.85 | -0.32 | ||||||
| MB1_0456_0598 | GGACGGAAGGCCACATGTCAAAGGGCAACGATGTGGTGCTGAAGT | chr1 | 172489502 | 55 | 172489556 | 0.38 | 1.12 | 1.08 | 1.37 | -0.08 | 0.96 | ||||||
| MB1_0388_0570 | GCACAGTCACCCCTACCGAGCTGGGGCTTACCACTCACAGCACAG | chr1 | 172489602 | 60 | 172489661 | -0.19 | 0.42 | 0 | 0.8 | -0.75 | 0.49 | ||||||
| MB1_0501_0519 | GAGGGGGCCCAGCCGAGGGAGAGTGAAAAACAGTTATGGGATTGG | chr1 | 172489702 | 62 | 172489763 | -0.12 | 0.37 | -0.43 | 0.15 | 0.35 | 0.1 | ||||||
| MB1_0468_0238 | GGAAACCTGCTTTAGAATATCCTGTCTTACAGGGCTTCCTTCTGC | chr2 | 24952389 | 65 | 24952453 | 0.35 | 0.5 | 1.01 | 0.36 | 2.39 | 1.75 | ||||||
| MB1_0367_0749 | GTAACTTGAAGAGAGCTTTAGTAGCAGCCAGGATTGGGAGAGGAG | chr2 | 24952489 | 65 | 24952553 | 0.63 | 0.24 | 0.72 | 0.83 | 1.94 | 0.83 | ||||||
| MB1_0016_0344 | AAGGCTATCAGAGAGAGAAGGGACTGCCCTATACTCTGGACTAAAA | chr2 | 24952589 | 65 | 24952653 | 1.33 | 3.68 | 1.21 | 1.2 | 2.72 | 3.88 | ||||||
| MB1_0252_0608 | TTTGGCTCTTGGCCTCTAGAGAAACATTCAGATGCTTATAGTAGAATTCTCTGAGTG | chr2 | 24953081 | 65 | 24953145 | -0.38 | -0.13 | 0.25 | -0.64 | -0.55 | 0.22 | ||||||
| MB1_0305_0951 | TATATCTGAAAATCTGGACAGTTTCATTTAGATCTAATGTGGGCTCTGACCCTACCAC | chr2 | 24953237 | 70 | 24953306 | -0.79 | -0.01 | -0.98 | -0.23 | -0.14 | -0.5 | ||||||
| MB1_0026_1000 | CCCTGGTGTCACCTAACTGACATAAAACACAGCAGGTGTCCCTAT | chr2 | 24953337 | 70 | 24953406 | -0.17 | -0.08 | -0.56 | -0.61 | -0.31 | -0.79 | ||||||
| MB1_0648_0436 | TTATACATGGGACGGCCTCTTAGGTCATTTGCTACCCGGAGTGTG | chr2 | 24953437 | 70 | 24953506 | -0.81 | -0.17 | -0.44 | -0.43 | -1.02 | -0.42 | ||||||
| MB1_0013_0885 | TCCCCCCCCCATTCCCAACCAAACACATTATTCTGCTCTCCCCCA | chr2 | 24953537 | 70 | 24953606 | 0.01 | -0.01 | 0.06 | -0.42 | -0.38 | -0.13 | ||||||
| MB1_0149_0899 | ACAGTTTCATCTGGAAACCGGGAGATCGTATGGGCCCTGGTCATC | chr2 | 24953916 | 75 | 24953990 | 0 | 0.34 | 0.02 | 0.06 | -0.6 | -0.3 | ||||||
| MB1_0126_0180 | CTGTTTAATGCTATATGACATTTCCCAGTCCCAGCATTTCACCGTTTAAACGTGT | chr2 | 24954016 | 75 | 24954090 | -0.39 | -0.17 | 0.06 | -0.04 | 0.32 | -0.88 | ||||||
| MB1_0342_0038 | ACTGATTCATCTCTTGGGCGAGAAGATCTTAGGCAGTCTCCAGCA | chr2 | 24954116 | 75 | 24954190 | 1.33 | 0.89 | 0.69 | 0.62 | 1.67 | 2.1 | ||||||
| MB1_0278_0784 | GAATGCACTGCCCCACCCTTCCCCTTGCAGAGCATTGTGGGATAC | chr2 | 24954216 | 75 | 24954290 | -0.09 | -0.6 | -0.22 | 0.09 | 0.36 | -0.55 | ||||||
| MB1_0110_0164 | TTAAGGAGGGCTTAGATTTTTAACAGTGTCAGCGTATTTTGCCAAGCTATGTCTCAACA | chr2 | 24954316 | 50 | 24954365 | 0.13 | -0.42 | -0.08 | 0.99 | 0.45 | 0.34 | ||||||
| MB1_0213_0253 | GTTTAGAAAGAGGAAACAGGATGAGGCCTCTGGAAGAGTGGTACA | chr2 | 24954416 | 50 | 24954465 | -0.01 | 0.32 | 0.63 | 1.14 | -0.62 | 0.86 | ||||||
| MB1_0068_0014 | TGTGGGTATCAGGGACTAACACTCTACCCCAGCTTGTATGCTTTC | chr2 | 24954516 | 50 | 24954565 | 1.14 | 0.02 | 0.98 | 0 | 1.49 | 0.36 | ||||||
| MB1_0154_0270 | ACTGCCTTCTTTCCCTGAATCCCACAGATATGAGAGCTCTGATATTG | chr2 | 24954616 | 50 | 24954665 | -0.48 | -0.53 | -0.2 | -0.85 | -0.57 | 0.12 | ||||||
| MB1_0719_0731 | TACTGGTTTATACTTGTCCGTGCCTGTGGTCCTCCCGACCTGTTC | chr2 | 24954716 | 50 | 24954765 | -0.29 | -0.12 | -0.03 | -0.3 | -0.3 | -0.15 | ||||||
| MB1_0377_0745 | CCCTCTGCATATTTACATCTGAGACTGGTGTACTGACCTGAGTGTTT | chr2 | 24954816 | 55 | 24954870 | 0.68 | 1.14 | 0.86 | 1.92 | 0.09 | 0.84 | ||||||
| MB1_0555_0057 | TACATCTGCACAGCCCTTGAGATGTGCTTTAAGCCATCACTTCTACAT | chr2 | 24955143 | 55 | 24955197 | 0.09 | 0.42 | 0.29 | 0.56 | -0.69 | 0.33 | ||||||
| MB1_0112_0550 | TAGGAACAGTAGTCTGGAAATGTTCCAAAATCTGAAAATGTCAGAACTCCACCACACT | chr2 | 24955274 | 52 | 24955325 | -0.02 | 0.19 | -1.09 | -0.26 | 0.68 | 0.08 | ||||||
| MB1_0412_0818 | TCCACAGCCTGCCTTTCATCTATCCTCATCTTTACTCTTCAGAGG | chr2 | 24955374 | 65 | 24955438 | 1.04 | 1.33 | 0.51 | 0.73 | 1.24 | 0.94 | ||||||
| MB1_0030_0342 | CTGCTGTAGCACGCCAGTGTATGTGGCTGTCACTCCTGTCCTGTC | chr2 | 24955841 | 55 | 24955895 | -1.1 | 0.08 | -0.08 | 0.08 | 0.48 | -0.38 | ||||||
| MB1_0013_0753 | ATCCCCTATCCCCTTCCCCACAAAAATTTTCGTTACTGTGTTTTGGC | chr2 | 24955941 | 65 | 24956005 | 0.69 | 0.63 | -0.14 | 0.11 | 0.34 | 1 | ||||||
| MB1_0286_0098 | TCTGATTTCATGATTGCTGGCTATAACTAGCTACATTTCATTGTTCCTGGCAAACAACTTTGAC | chr2 | 24956045 | 60 | 24956104 | 0.04 | -0.4 | -0.02 | -0.18 | -0.17 | -0.34 | ||||||
| MB1_0417_0287 | ATTTATTAGCACATATAATCCCCCAGAAAAATACTGCTTTGTGGTCTGCTGGGAAGGA | chr2 | 24956155 | 60 | 24956214 | -0.04 | -0.07 | -0.29 | 0.09 | 0.37 | -0.56 |
