|
| Status |
Public on Mar 23, 2020 |
| Title |
RNA-seq_HC5_mouse_proB-Setd2-ko_REP3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse proB cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: primary proB cells
timepoint: 8 weeks
treatment: no treatment
genetic alteration: Setd2 knockout
seqbatch: 171124
|
| Treatment protocol |
no treatment
|
| Growth protocol |
proB cells were sorted from bone marrow of 8 week old mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 75bp, single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
STAR (Version 2.5.1)
--genomeDir <path to reference data (mm10)>
--readFilesIn ${ID}.fastq
--runThreadN 20
--outFilterMultimapScoreRange 1
--outFilterMultimapNmax 20
--outFilterMismatchNmax 10
--alignIntronMax 500000
--alignMatesGapMax 1000000
--sjdbScore 2
--alignSJDBoverhangMin 1
--genomeLoad NoSharedMemory
--limitBAMsortRAM 0
--readFilesCommand <bzcat|cat|zcat>
--outFilterMatchNminOverLread 0.33
--outFilterScoreMinOverLread 0.33
--sjdbOverhang 100
--outSAMstrandField intronMotif
--outSAMattributes NH HI NM MD AS XS
--outSAMunmapped Within
--outSAMtype BAM SortedByCoordinate
--outSAMheaderHD @HD VN:1.4
--outSAMattrRGline <formatted RG line provided by wrapper>
TRUST (Version 3.0.1)
trust -f [PATH]$FILENAME.bam -g mm10 -B -c -o [PATH]BCR_H/
trust -f [PATH]$FILENAME.bam -g mm10 -B -L -c -o [PATH]BCR_L/
Genome_build: mm10
Supplementary_files_format_and_content: TXT of TRUST output of assembled CDR3s for heavy and light chain locus
|
| |
|
| Submission date |
May 21, 2019 |
| Last update date |
Mar 23, 2020 |
| Contact name |
Charlie Hatton |
| E-mail(s) |
Charles_Hatton@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Scott Armstrong/CPCT
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE131588 |
H3K36 methyltransferase SETD2 regulates lymphoid and neural development [RNA-seq] |
| GSE131690 |
H3K36 methyltransferase SETD2 regulates NHEJ during lymphoid and neural development |
|
| Relations |
| BioSample |
SAMN11809191 |
| SRA |
SRX5879594 |
