|
| Status |
Public on Feb 19, 2024 |
| Title |
GCB_BK_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: GCB cell
genotype: BCL+K_het_KO
|
| Treatment protocol |
Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before collecting CBs and CCs. Mice (BCL2, BCL2+C, BCL2+K, BCL+CK) were immunized with SRBC once every 3 weeks (starting at 56 days post-BMT) to induce continuous GC formation and lymphomagenesis, GC B cells were sorted at day 235 post BMT.
|
| Growth protocol |
Human OCI-Ly7 cell lines were cultured in IMDM supplemented with 15% FBS, 1% L-Glutamine and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from sorted mouse cell suspensions using TRIzol LS Reagent (Invitrogen) or from human OCI-Ly7 cells using Rneasy mini plus kit (Qiagen) following the manufacturer’s instructions.
Libraries were made using the Illumina TruSeq stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
D235_KHET_R3
ck_bcl2_gcb_featurecounts.merged.counts.tsv
|
| Data processing |
nfcore RNA version 2.0
Assembly: mm10 and hg38
Supplementary files format and content: Combined gene count table
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Christopher Russell Chin |
| E-mail(s) |
chc2077@med.cornell.edu
|
| Phone |
3393640514
|
| Organization name |
Weill Cornell
|
| Lab |
Melnick Lab
|
| Street address |
413 E 69th Street, Belfer Building, BB-1462
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE224465 |
Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas [RNA-Seq] |
| GSE224513 |
Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas. |
|
| Relations |
| BioSample |
SAMN33054175 |
| SRA |
SRX19275169 |
