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| # Use this template for ChIP-chip submissions and the array is NOT represented in GEO. If the array has already been submitted, the platform section is optional | |||||||||||||||||||||||||||
| # An accompanying matrix table example is included in the second worksheet. Click on the Matrix tab below. | |||||||||||||||||||||||||||
| # Most fields in this template must be completed. | |||||||||||||||||||||||||||
| # 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. | |||||||||||||||||||||||||||
| 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 | ChIP-on-chip | ||||||||||||||||||||||||||
| 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. | |||||||||||||||||||||||||||
| # If you have more than one raw data file for each Sample, include additional "raw data file" columns. | |||||||||||||||||||||||||||
| # CLICK HERE to find the platform accession number (GPLxxxx). | |||||||||||||||||||||||||||
| Sample name | title | raw data file | raw data file | ch1: source name | 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: 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 table (see example) and complete the fields below. | |||||||||||||||||||||||||||
| title | |||||||||||||||||||||||||||
| technology | |||||||||||||||||||||||||||
| distribution | |||||||||||||||||||||||||||
| organism | |||||||||||||||||||||||||||
| manufacturer | |||||||||||||||||||||||||||
| manufacture protocol | |||||||||||||||||||||||||||
| # Platform Column Definitions: describe the contents of each platform column of the matrix table | |||||||||||||||||||||||||||
| header 1 | header 1 definition | ||||||||||||||||||||||||||
| header 2 | header 2 definition | ||||||||||||||||||||||||||
| header 3 | header 3 definition | ||||||||||||||||||||||||||
| etc… |
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| # Example of a matrix table for a dual channel submission. Only column headers are shown. | |||||||||||||
| # The identifiers in the ID_REF column must match the identifiers in the ID column of the referenced platform (GPLxxxx). | |||||||||||||
| # The matrix table should contain normalized log ratio (test/reference) data that are comparable across rows and Samples. | |||||||||||||
| # Values that should be disregarded may either be left blank or labeled as "null". | |||||||||||||
| ID_REF | Header 1 | Header 2 | Header 3 | Sample 1 | Sample 2 | Sample 3 | Sample 4 | Sample 5 | Sample 6 | Sample 7 | Sample 8 | Sample 9 | Sample X |
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| SERIES | ||||||||||||||||||||||||
| # This section describes the overall experiment | ||||||||||||||||||||||||
| 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, Smith | |||||||||||||||||||||||
| SAMPLES | ||||||||||||||||||||||||
| # The Sample names in the first column are arbitrary but they must match the column headers of the matrix table. | ||||||||||||||||||||||||
| # If you have more than one raw data file for each Sample, include additional "raw data file" columns. | ||||||||||||||||||||||||
| # CLICK HERE to find the platform accession number (GPLxxxx). | ||||||||||||||||||||||||
| Sample name | title | raw data file | raw data file | ch1: source name | ch1: organism | ch1: characteristics: Genotype | ch1: characteristics: Cell type | ch1: characteristics: Strain | ch1: characteristics: ChIP Antibody | ch1: molecule | ch1: label | ch1: treatment protocol | ch1: growth protocol | ch2: source name | ch2: organism | ch2: characteristics: Genotype | ch2: characteristics: Cell type | ch2: characteristics: Strain | ch2: characteristics: ChIP Antibody | ch2: molecule | ch2: label | ch2: treatment protocol | ch2: growth protocol | description |
| Sample 1 | RAG H3K4me2 | RAG_H3K4me2_Cy5.pair | RAG_H3K4me2_Cy3.pair | H3K4me2 ChIP DNA from Rag2-/- pro-B cells | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | H3K4me2 | genomic DNA | Cy5 | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | Input DNA from Rag2-/- pre-B cells | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells |
| Sample 2 | RAG H3K4me3 | RAG_H3K4me3_Cy5.pair | RAG_H3K4me3_Cy3.pair | H3K4me3 ChIP DNA from H3K9ac ChIP DNA from Rag2-/- pro-B cells | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | H3K4me3 | genomic DNA | Cy5 | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | Input DNA from Rag2-/- pro-B cells | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice. | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells. | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells |
| Sample 3 | RAG H3K9ac | RAG_H3K9ac_Cy5.pair | RAG_H3K9ac_Cy3.pair | H3K9ac ChIP DNA from Pax5-/- Rag2-/- pro-B cells | Mus musculus | Pax5-/- Rag2-/- | pro-B cells | C57BL/6J | H3K9ac | genomic DNA | Cy5 | Pax5-/- Rag2-/- pro-B cells are an established cell line | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Input DNA from Pax5-/- Rag2-/- pro-B cells | Mus musculus | Pax5-/-Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Pax5-/- Rag2-/- pro-B cells are an established cell line | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells |
| Sample 4 | P5R2 H3K4me3 | P5R2_H3K4me3_Cy5.pair | P5R2_H3K4me3_Cy3.pair | H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells | Mus musculus | Pax5-/- Rag2-/- | pro-B cells | C57BL/6J | H3K4me3 | genomic DNA | Cy5 | Pax5-/- Rag2-/- pro-B cells are an established cell line | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Input DNA from Pax5-/- Rag2-/- pro-B cells | Mus musculus | Pax5-/-Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Pax5-/- Rag2-/- pro-B cells are an established cell line | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells |
| Sample 5 | P5R2 H3K4me2 | P5R2_H3K4me2_Cy5.pair | P5R2_H3K4me2_Cy3.pair | H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells | Mus musculus | Pax5-/- Rag2-/- | pro-B cells | C57BL/6J | H3K4me2 | genomic DNA | Cy5 | Pax5-/- Rag2-/- pro-B cells are an established cell line | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | Input DNA from Pax5-/- Rag2-/- pro-B cells | Mus musculus | Pax5-/-Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Pax5-/- Rag2-/- pro-B cells are an established cell line | Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells |
| Sample 6 | RAG H3K9ac | RAG_H3K9ac_Cy5.pair | RAG_H3K9ac_Cy3.pair | H3K9ac ChIP DNA from Rag2-/- pro-B cells | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | H3K9ac | genomic DNA | Cy5 | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells | Input DNA from Rag2-/- pre-B cells | Mus musculus | Rag2-/- | pro-B cells | C57BL/6J | none, input DNA | genomic DNA | Cy3 | Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice | Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells | comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells |
| 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 | 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 | |||||||||||||||||||||||
| 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. | |||||||||||||||||||||||
| scan protocol | Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol | |||||||||||||||||||||||
| data processing | The value is log2R normalized using loess | |||||||||||||||||||||||
| value definition | normalized log2 ratios (Cy5/Cy3) | |||||||||||||||||||||||
| PLATFORM | ||||||||||||||||||||||||
| # If your array is not deposited in GEO, please include platform annotation columns in your matrix table (see example) and complete the fields below. | ||||||||||||||||||||||||
| title | NRCC Mouse BCELL v. 1.0 | |||||||||||||||||||||||
| technology | in situ oligonucleotide | |||||||||||||||||||||||
| distribution | non-commercial | |||||||||||||||||||||||
| organism | Mus musculus | |||||||||||||||||||||||
| manufacturer | National Research Council Canada - Biotechnology Research Institute | |||||||||||||||||||||||
| manufacture protocol | The oligonucleotide microarray is composed of 21987 of 50 mer oligonucleotides from the Sigma Geneosys oligo DNA library. Oligonucleotides were printed by Hitachi Software Engineering. | |||||||||||||||||||||||
| # Platform Column Definitions: describe the contents of each platform column of the matrix table | ||||||||||||||||||||||||
| header 1 | CHROMOSOME | |||||||||||||||||||||||
| header 2 | RANGE_GB (Accession Version of NCBI Mouse Build 34) | |||||||||||||||||||||||
| header 3 | RANGE_START | |||||||||||||||||||||||
| header 4 | RANGE_END | |||||||||||||||||||||||
| header 5 | SEQUENCE |
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| ID_REF | CHROMOSOME | RANGE_GB | RANGE_START | RANGE_END | SEQUENCE | Sample 1 | Sample 2 | Sample 3 | Sample 4 | Sample 5 | Sample 6 |
| MB1_0001_0031 | chr1 | NC_000067.2 | 21447200 | 21447250 | CCTTCTTCTGAGGCAGTCTCAGAGTCTGTTCATCTGAAGGAGAAA | -0.8 | -1.17 | -0.38 | -0.76 | -1.29 | -0.83 |
| MB1_0001_0065 | chr1 | NC_000067.2 | 21447660 | 21447710 | AGTTATGCACTGATAGGAAAGCCTACAGTTACACACACACACACTCATAAATGTACAGAACAT | -0.11 | -0.01 | 0.02 | 0.21 | -0.55 | -0.26 |
| MB1_0001_0129 | chr1 | NC_000067.2 | 21448590 | 21448640 | CCAATTGAACAACTACATCATATCTCATCTACATCCCTCACTATTGGGGTACACA | 0.66 | 1.28 | 1.12 | 1.61 | -0.24 | 1.03 |
| MB1_0001_0151 | chr1 | NC_000067.2 | 21448922 | 21448972 | GCGAATTCCTTAACTCCTGGGGCTATCTTATTTTTGTTGCATCTTGGGTAATTGA | -0.04 | -1.16 | -1.02 | -1.01 | -0.68 | -0.39 |
| MB1_0001_0185 | chr1 | NC_000067.2 | 21449056 | 21449106 | TGGGGAAAGGGCTCCATTATAACACATGGTGGTTTATGATCAATTACAAGTGATGTCTT | 0.14 | 0.8 | 0.63 | 0.15 | -0.26 | -0.2 |
| MB1_0001_0197 | chr1 | NC_000067.2 | 21449156 | 21449206 | ATTTAGGGGAGGCAGAAACTACTCCCTGATGAGCTCTGGAAAGTC | -0.3 | -0.81 | 0.26 | -0.12 | -0.85 | -0.32 |
| MB1_0001_0203 | chr1 | NC_000067.2 | 21449256 | 21449306 | AGGATCATGGGCACAGGTGTAAGCTGTGTCTCATTGGTTGAGGGA | 0.38 | 1.12 | 1.08 | 1.37 | -0.08 | 0.96 |
| MB1_0001_0247 | chr1 | NC_000067.2 | 21449356 | 21449406 | ACCAGAGCAGAAGTCTTATTTGGAATCTAAGCAGCTGAGGGCATAG | -0.19 | 0.42 | 0 | 0.8 | -0.75 | 0.49 |
| MB1_0001_0269 | chr1 | NC_000067.2 | 21449483 | 21449533 | TGGAGTTATGAGATGGGAGATAGTGTCTGCATGATACAAGAGGTAAAGATTAAACCTC | -0.12 | 0.37 | -0.43 | 0.15 | 0.35 | 0.1 |
| MB1_0001_0293 | chr1 | NC_000067.2 | 21449611 | 21449661 | TCAAAACACTAGATCACACACTCCTTGCTTTTTCTTTAGACTTGCATCCTTACCAATGGA | 0.35 | 0.5 | 1.01 | 0.36 | 2.39 | 1.75 |
| MB1_0001_0315 | chr1 | NC_000067.2 | 21449842 | 21449892 | TTTTCATTATTTTTAATTGTGTGTGTGTGTGGGGGGGGTGTACACATCATTGTGAGTG | 0.63 | 0.24 | 0.72 | 0.83 | 1.94 | 0.83 |
| MB1_0001_0353 | chr1 | NC_000067.2 | 21449942 | 21449992 | TCTTTCCAGCTTTTCCAGCTATGTAAAGTCTCCCCCCTCCCCCCT | 1.33 | 3.68 | 1.21 | 1.2 | 2.72 | 3.88 |
| MB1_0001_0355 | chr1 | NC_000067.2 | 21450092 | 21450142 | GCCCCTTACTAGGAAATGGACTGTTGAAGTTAAGTGTCTCAGTCCAT | -0.38 | -0.13 | 0.25 | -0.64 | -0.55 | 0.22 |
| MB1_0001_0375 | chr1 | NC_000067.2 | 21450312 | 21450362 | TATGGTTTTCAAGTTGCTGTGAAAATGCCTTTATATAGCCTTACATCATCATCATGTTCAGGGCA | -0.79 | -0.01 | -0.98 | -0.23 | -0.14 | -0.5 |
| MB1_0001_0379 | chr1 | NC_000067.2 | 21450431 | 21450481 | ACTTTCTTTTCTCCAGCCTTTAGTAAGATCATGCCTATTGGTTAACTCCACCCAA | -0.17 | -0.08 | -0.56 | -0.61 | -0.31 | -0.79 |
| MB1_0001_0389 | chr1 | NC_000067.2 | 21450532 | 21450582 | TAATGTTTGACATTCTAATGCATGGTATTTGGGTTTCAGTTACAGCTTTCTTCCTGGCCA | -0.81 | -0.17 | -0.44 | -0.43 | -1.02 | -0.42 |
| MB1_0001_0399 | chr1 | NC_000067.2 | 21450632 | 21450682 | GCCTGCTGGTCTAGTTGCAGGCTTAAGGTAAGAGCCCTTCTGATC | 0.01 | -0.01 | 0.06 | -0.42 | -0.38 | -0.13 |
| MB1_0001_0407 | chr1 | NC_000067.2 | 21451197 | 21451247 | TATTATGATAAGTATTAGCATAGCAGACTTAAGCCACCATAGACTCAGTCTTTGGTGTGACAATG | 0 | 0.34 | 0.02 | 0.06 | -0.6 | -0.3 |
| MB1_0001_0415 | chr1 | NC_000067.2 | 21451323 | 21451373 | AAGAGTTAAGTTCTCCTTCAGTTGGCTTATCCACTGGTAGCAGTAAATTCATCTAGG | -0.39 | -0.17 | 0.06 | -0.04 | 0.32 | -0.88 |
| MB1_0001_0445 | chr1 | NC_000067.2 | 21452371 | 21452421 | AATGTTTCTAATTCCTCCTGGAAGCTGTTCTTGTGTGTTGAAAGACACAAACATCTCC | 1.33 | 0.89 | 0.69 | 0.62 | 1.67 | 2.1 |
| MB1_0001_0447 | chr1 | NC_000067.2 | 21452725 | 21452775 | CTGTGGCAATAAACAAGATGGAAATATTTCAAGCATCAGTAGTATTTTGCCCTGGGCTATA | -0.09 | -0.6 | -0.22 | 0.09 | 0.36 | -0.55 |
| MB1_0001_0449 | chr1 | NC_000067.2 | 21452848 | 21452898 | TATCTTGTGTAGTGATATTTGTTTGTATGGAGTAGTGCCAATGACAACTTTGAAGCTCTGTCC | 0.13 | -0.42 | -0.08 | 0.99 | 0.45 | 0.34 |
| MB1_0001_0473 | chr1 | NC_000067.2 | 21453257 | 21453307 | CTTGACCAGGCCTTCCCAGTGGCTCATCTTCAGTCGCTGTTGGAA | -0.01 | 0.32 | 0.63 | 1.14 | -0.62 | 0.86 |
| MB1_0001_0481 | chr1 | NC_000067.2 | 21453357 | 21453407 | CAGCAGGTTTGCTTTCTCTCATCTGTTCAGGGAATATTTTCAAGTTGCATCTG | 1.14 | 0.02 | 0.98 | 0 | 1.49 | 0.36 |
| MB1_0001_0517 | chr1 | NC_000067.2 | 21453557 | 21453607 | TCCTGTGACTCAGCCTCATGATGATCCTGAGACTTGTGCTGCTGC | -0.48 | -0.53 | -0.2 | -0.85 | -0.57 | 0.12 |
| MB1_0001_0565 | chr1 | NC_000067.2 | 21453825 | 21453875 | TCCTGCTCTTTAATGCATTGTTACTGCTCATTCCCTTTGTCTCTTTATATCTGGAAATTGG | -0.29 | -0.12 | -0.03 | -0.3 | -0.3 | -0.15 |
| MB1_0001_0591 | chr1 | NC_000067.2 | 21453925 | 21453975 | TGAGTGAAATAAGTTAAATAAGTTAACTGCATCCTGTCAGACAATGGGATTCCTGTCGTG | 0.68 | 1.14 | 0.86 | 1.92 | 0.09 | 0.84 |
| MB1_0001_0593 | chr1 | NC_000067.2 | 21454028 | 21454078 | GGGGTTTTATTTGTATTATTGGGGGTGGGGCAGGTTTGCATAGAAGGAATT | 0.09 | 0.42 | 0.29 | 0.56 | -0.69 | 0.33 |
| MB1_0001_0595 | chr1 | NC_000067.2 | 21454181 | 21454231 | CTCAATCACTCAATCGTTTAGGCTGTAACATGTTCTTTAGTAGTGAAAAGGATGTCAGG | -0.02 | 0.19 | -1.09 | -0.26 | 0.68 | 0.08 |
| MB1_0001_0623 | chr1 | NC_000067.2 | 21454281 | 21454331 | TCTCTCTGTCCCCCACACGCCTGTGAGACCACACGCCATGTGAAG | 1.04 | 1.33 | 0.51 | 0.73 | 1.24 | 0.94 |
| MB1_0001_0643 | chr1 | NC_000067.2 | 21454381 | 21454431 | AGACCCCTGCCTATTTCCAATGTCTGCTATGGTCTCTGGGAAACC | -1.1 | 0.08 | -0.08 | 0.08 | 0.48 | -0.38 |
| MB1_0001_0691 | chr1 | NC_000067.2 | 21454481 | 21454531 | TAGCTTGCCCTCCAAGGTAGCAGGCTCACAGTTTCAGTCCTTCAG | 0.69 | 0.63 | -0.14 | 0.11 | 0.34 | 1 |
| MB1_0001_0715 | chr1 | NC_000067.2 | 21454581 | 21454631 | GGTAGGCAGGAGGACTTACCCTCTTGTTAGTGCAAGCGGGATGCT | 0.04 | -0.4 | -0.02 | -0.18 | -0.17 | -0.34 |
| MB1_0001_0783 | chr1 | NC_000067.2 | 21454686 | 21454736 | GGAAACCCATACAAACTTTGTTAGTGTGCTCTCAATGATGCCCTTCTTAAAAGGACA | -0.04 | -0.07 | -0.29 | 0.09 | 0.37 | -0.56 |
| MB1_0001_0793 | chr1 | NC_000067.2 | 21454786 | 21454836 | CATCAGCTGGACTAGAAATGGCAGGTGGTTTGCTTTCTTGACAACA | -0.2 | 0.24 | -0.22 | 0.19 | -0.9 | 0.01 |
| MB1_0001_0815 | chr1 | NC_000067.2 | 21454886 | 21454936 | GCGGTTGGTTGTAGAAACACTTGCTGTATCTGGAAGATACCCCAG | 0.79 | 0.34 | 0.89 | 0.39 | 1.21 | 1.13 |
| MB1_0001_0831 | chr1 | NC_000067.2 | 21455073 | 21455123 | TGTTGAGCTTTCATTTTTAACCTTTGAGGGTGAGCAAGATGGCTCAGCAAGT | -0.14 | -0.04 | -0.77 | -0.25 | -0.8 | 0.24 |
| MB1_0001_0833 | chr1 | NC_000067.2 | 21455365 | 21455415 | CTACGCATGCACAACCACACTCACACATGTGCACACCCACAAATA | -0.35 | -0.39 | 0.02 | -0.28 | -0.55 | 0.01 |
| MB1_0001_0845 | chr1 | NC_000067.2 | 21455465 | 21455515 | GACTCCTGCTTGGGTTTTCTGGACTCACTCTTGGCAGCATGTTTC | -0.65 | -0.55 | -0.36 | -0.37 | -1.19 | -0.7 |
| MB1_0001_0897 | chr1 | NC_000067.2 | 21455848 | 21455898 | AGGTGCAGTGTTTGTCTTTAATTGAGTATGAAACCCTGTAAAGAGCAGGTTCCAATG | 0.21 | -1.04 | 0.75 | 0.03 | -0.37 | 0.08 |
| MB1_0001_0917 | chr1 | NC_000067.2 | 21455948 | 21455998 | AAACAAAAGCAAACAGTGTGAGTATGGAAGTGGACTTGTAGGGAGGAG | 1.24 | 0.69 | 0.64 | 0.33 | 2.58 | 1.45 |
| MB1_0001_0921 | chr1 | NC_000067.2 | 21456182 | 21456232 | TTATGTAATCATTTGTAGCTGAGTCAAATTAGCTCCTTGTGTTTCTCTTCAAGCTGCAAGTGTCA | 0.67 | 1.31 | 0.78 | 1.53 | 0.2 | 0.96 |
| MB1_0001_0929 | chr1 | NC_000067.2 | 21456282 | 21456332 | GAGTGCCACTTTCCACACTGCTGAGACAGAGCACCGATTCCCTTG | -1.38 | -0.28 | -0.5 | -0.18 | -0.02 | -0.64 |
| MB1_0001_0955 | chr1 | NC_000067.2 | 21456637 | 21456687 | TTAAAAATTAGCTTTGTAGATCTACCTGCCTCTGATTGTAGTGTATGTGAGACATCAGTCTGAG | -0.09 | 0.28 | 0.26 | 0.87 | 0.6 | 0.99 |
| MB1_0001_0981 | chr1 | NC_000067.2 | 21456737 | 21456787 | CAATGTGTATTGTAAACAGAGAAAGGAAGCCATGCAAAGCAAGCAGAGGACA | -0.23 | -0.51 | -0.49 | 0.18 | -0.88 | -0.1 |
| MB1_0001_1017 | chr1 | NC_000067.2 | 21456837 | 21456887 | TAGCAGGAGGTTGCCTTTAAGGGTATGCTGAAATCTCATTATACACCAAGGT | 2.13 | -0.12 | 1 | 0.91 | 2.47 | 1.01 |
| MB1_0002_0002 | chr1 | NC_000067.2 | 21456937 | 21456987 | TTTCAGTGCATATGGCACCTGACCTGTGGGGAGGAGAGTCGCTCC | 0.16 | -0.37 | -0.08 | 0.03 | -0.36 | -0.54 |
| MB1_0002_0030 | chr1 | NC_000067.2 | 21457037 | 21457087 | TGGTCTCATTTTCTATTGATCCAGTAGCTCTAGGTTCACCTTGTCATGGC | 1.82 | 4.24 | 3.09 | 5.32 | 3.33 | 4.09 |
| MB1_0002_0154 | chr1 | NC_000067.2 | 21457303 | 21457353 | TGAGTTTGAGTTGCTAGTACAACCCACATATCAGAGCAGCAACTACTTTCTCTAATTCTTCTA | 0.03 | 0.14 | -0.48 | 0.01 | 0.29 | 0.16 |
