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| Status |
Public on Jan 27, 2018 |
| Title |
E12.5_Forebrain_scATAC_Rep1_Rep2 |
| Sample type |
SRA |
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| Source name |
mouse forebrain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6NCrl
developmental stage: embryonic day 12.5
barcodes: Set_1 for Replicate 1; Set_2 for Replicate 2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from snap frozen forebrain tissues or GM12878 cells. Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination. After pooling, 25 nuclei were sorted into 384 or 96 wells and a second barcode wqas introduced by PCR.
Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination (p7 and p5 barcodes). After pooling, 25 nuclei were sorted into 384 or 96 wells and a second barcode (i7 and i5 barcodes) was introduced by PCR. In general, libraries were sequenced on a HiSeq2500 with following read lengths: 50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). The human mouse mixtures was sequenced on a Miseq with this read lengths: 44 + 43 + 37 + 44 (Read1 + Index1 + Index2 + Read2). The first 8 bp of Index1 correspond to the p7 barcode and the last 8 bp to the i7 barcode. The first 8 bp of Index2 correspond to the i5 barcode and the last 8 bp to the p5 barcode. PLease note that the barcode information was integrated into the read name.
combinatorial ATAC-seq
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Alignment: reads were mapped to the mm10 genome assembly using BWA in pair-end mode with default parameters. Alignment filtering: non-uniquely mapped (MAPQ < 10) and improperly paired (flag = 1804) alignments were filtered. Barcode correction: every barcode combination has 4 indexes (i7, p7, p5, i5) with length of 8 bp for each. Reads with barcode combination containing more than 1 mismatch for any index were filtered. Barcodes with allowed mismatches were changed to its closest barcode. Split Reads: Reads were separated into individual cell based on the barcode combination. Mark and remove PCR duplication: for individual cell, we sorted reads based on the genomic coordinates using “samtools sort”, then marked and removed PCR duplication using Picard tools (MarkDuplicate). Remove mitochondria reads: for each cell, reads mapped to mitochondria sequence were filtered. Tn5 insertion position adjustment: all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the - strand were offset -5 bp. Calculate coverage of active promoters (promoters overlapping with aggregate scATAC-seq peaks), coverage of distal elements and “reads in peaks” ratio for each cell. Cell selection: we kept cells that passed our threshold (1) active promoter coverage > 5%; 2) number of reads > 1,000; 3) reads in peak ratio greater than corresponding bulk ATAC-seq level. Selected cells were separated into two replicates based on barcode combination. Insert size distribution was estimated by Picard (CollectInsertSizeMetrics).
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: .mat: binary accessible matrix; xgi: row names for the matrix representing cell barcodes; ygi: column names for the matrix representing genomic elements (features); .qc: Quality metrics for cells that passed quality filtering (column 1: cell barcodes, column 2: number of reads, column 3: promoter coverage, column 4: fraction of reads in peaks.
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| Submission date |
Jun 14, 2017 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Rongxin Fang |
| E-mail(s) |
r3fang@ucsd.edu
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| Organization name |
Ludwig Institute for Cancer Research
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| Lab |
Ren Lab
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| Street address |
9500 Gilman Dr #3080
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE100033 |
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation |
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| Relations |
| BioSample |
SAMN07237046 |
| SRA |
SRX3739247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2668118_e12.5.nchrM.merge.sel_cell.mat.gz |
2.8 Mb |
(ftp)(http) |
MAT |
| GSM2668118_e12.5.nchrM.merge.sel_cell.qc.txt.gz |
23.6 Kb |
(ftp)(http) |
TXT |
| GSM2668118_e12.5.nchrM.merge.sel_cell.xgi.txt.gz |
4.7 Kb |
(ftp)(http) |
TXT |
| GSM2668118_e12.5.nchrM.merge.sel_cell.ygi.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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