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| Status |
Public on Apr 24, 2022 |
| Title |
Case1_gDNA_LCL_ATAC |
| Sample type |
SRA |
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| Source name |
human lymphoblastoid cell line
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| Organism |
Homo sapiens |
| Characteristics |
phenotype: affected
condition: experimental control - ATAC performed on genomic DNA
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| Growth protocol |
LCLs derived from ATR-X patients and healthy controls were incubated with RPMI medium supplemented with 15% FCS, 1% PenStrep and 1% glutamine at 37°C and 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-100000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). As experimental controls, ATAC-Seq was also performed on genomic DNA (instead of isolated nuclei).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Genome-wide library of tagmented fragments
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| Data processing |
Library Strategy: ATAC-seq
Mapping : bowtie2, hg19
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments
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| Submission date |
Jan 09, 2022 |
| Last update date |
Apr 24, 2022 |
| Contact name |
Julia Truch |
| Organization name |
University of Oxford
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| Department |
RDM - WIMM
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| Lab |
GIBBONS/HIGGS
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| Street address |
John Radcliffe Hospital, Headley Way, Headington
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| City |
Oxford |
| ZIP/Postal code |
Oxford OX3 9DS |
| Country |
United Kingdom |
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| Platform ID |
GPL18573 |
| Series (1) |
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| Relations |
| BioSample |
SAMN24776738 |
| SRA |
SRX13811142 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5791929_Case1_gDNA_LCL_ATAC_per100M.bw |
174.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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