|
| Status |
Public on Sep 15, 2022 |
| Title |
H1963_sgBAP1_1_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
NCI-H1963
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: small cell lung cancer
passages: Low passages (6-10)
cell line: H1963_sgBAP1_1_Rep2
genotype: normal cells
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium containing 10% FBS (Sigma)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
cells transduced with BAP1 specific sgRNA #1 Replication 2
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9 for single-end or bwa version 0.7.12 for paired-end. Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 or Star version 2.5.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Lu Wang |
| E-mail(s) |
lu.wang1@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
Lu Wang
|
| Street address |
303 E. Superior Street Simpson Querrey 7-414
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE196860 |
MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer |
|
| Relations |
| BioSample |
SAMN25996002 |
| SRA |
SRX14203294 |
