Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Follicular Lymphoma 2013 - Malek

ABSTRACT:

A cohort of follicular lymphoma cases had tumor cells purified from tissue samples after informed consent using flow cytometry. DNA was extracted from the cells, and samples were subjected to solution-based exome capture using the Illumina TruSeq Exome Enrichment Kit and the Illumina HiSeq 2000 platform.

PROVIDER: phs000729 | dbGaP |

SECONDARY ACCESSION(S): PRJNA242450PRJNA242449

REPOSITORIES: dbGaP

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GapExchange_phs000729.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs000729.FollicularLymphoma.v1.p1.MULTI.pdf	Pdf
	manifest_phs000729.FollicularLymphoma.v1.p1.c1.DS-LYM-MDS.pdf	Pdf
	datadict_v2.xsl	Other

Items per page:

1 - 5 of 15

Similar Datasets

RNA-seqs of SRSF3 and hnRNPK depleted C2C12 cells

Project description:Total RNA was extracted from C2C12 cells transfected with the indicated siRNA using TRIZOL (Thermo Fisher Scientific), and was further purified with Quick-RNA Miniprep Kit (Zymo research) according to the manufacturer’s instructions. The extracted RNA was subjected to RNA-seq at Macrogen, Japan. Briefly, a sequencing library was prepared using the TruSeq Stranded mRNA kit (Illumina), and the library was read on Illumina NovaSeq 6000 (150 bp paired-end reads).

2021-07-20 | GSE161601 | GEO

Transcriptional profiling of wildtype versus Themis2-deficient follicular B cells

Project description:This RNA-seqexperiment was designed to find transciptional differences between wildtype and Themis2-deficient B cells either directly ex-vivo or stimulated for 6 h with various stimuli in vitro. It is part of a larger study on the function of Themis2 in B cells. Therefore splenic, live, B220+ CD93- IgM+ CD23+ follicular B cells were sorted by flow cytometry from wildtype or Themis2-deficient (Themis2KO/KO) C57BL/6J mice. Unstimulated samples were were lysed directly after the sort. Stimulated samples were stimulated in vitro for 6 h at 37 degree Celsius at a concentration of 3 million cells/mL with either 10 microgram/mL anti-IgM or 10 microgram/mL LPS or 1 microgram/mL CD40L with 0.1 microgram/mL IL-4 and then lysed. RNA was extracted using Trizol reagent (Life Technologies) and cleaned up using the RNEasy Mini Kit (Quiagen). Single end, unstranded, poly-A-enriched libraries were made using the TruSeq RNA sample preparation kit (Illumina). Samples were analysed with an Illumina HiSeq 2000, collecting 13.2 to 76.1 million reads of 75 bases per sample.

2014-06-10 | E-MTAB-2499 | biostudies-arrayexpress

Gene expression profiling of CD4+ T-cell subsets in follicular lymphoma.

2013-11-21 | GSE52561 | GEO

Follicular B (FoB) cells purified from miR-17-92 transgenic mice, stimulated with LPS/IL-4 for 13.5 or 25.5 hours

Project description:We have generated a miR-17-92 transgenic allele (termed miR-17-92 Tg) whose expression can be turned on conditionally by Cre recombinase (Xiao et al, Nature Immunology, 9:405-14, 2008). The mice were crossed to CD19-Cre mice to turn on the transgene expression specifically in B cells. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 Tg/Tg mice (TG1, TG2, TG3) and miR-17~92 Tg/Tg mice (WT1, WT2, WT3) by MACS depletion of cells positive for CD5, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 13.5hr or 25.5hr. The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

2014-04-01 | E-GEOD-56377 | biostudies-arrayexpress

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

2015-05-11 | GSE57392 | GEO

Total RNA sequencing of IFN-stimulated and HIV-1-infected macrophages

Project description:Monocyte-derived macrophages were stimulated with 25 ng/ml of the indicated IFNs or infected with HIV-1-BaL-HSA. Total RNA was isolated 18 h following stimulation/infection using RNeasy minikit (Qiagen). Intact poly(A) RNA was purified from total RNA samples (100 to 500 ng) with oligo(dT) magnetic beads, and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation kit (catalog no. RS-122-2101 and RS-122-2102). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (catalog no. 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant kit (catalog no. KK4824). Individual libraries were normalized to 10 nM, and equal volumes were pooled in preparation for Illumina sequence analysis. Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single-read flow cell using an Illumina cBot system. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR cluster kit v4-cBot (catalog no. GD-401-4001). Following transfer of the flow cell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50-cycle single-read sequence run was performed using HiSeq SBS kit v4 sequencing reagents (catalog no. FC-401-4002).

2020-10-02 | GSE158434 | GEO

Follicular B (FoB) cells purified from miR-17-92 transgenic mice

Project description:We have generated a miR-17-92 transgenic allele (termed miR-17-92 Tg) whose expression can be turned on conditionally by Cre recombinase (Xiao et al, Nature Immunology, 9:405-14, 2008). The mice were crossed to CD19-Cre mice to turn on the transgene expression specifically in B cells. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 Tg/Tg mice (FoBtg1, FoBtg2, FoBtg3) and miR-17~92 Tg/Tg mice (FoBwt1, FoBwt2, FoBwt3) by MACS depletion of cells positive for CD5, CD43, and CD93 (also known as AA4.1). The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

2011-07-21 | E-GEOD-30877 | biostudies-arrayexpress

Follicular B (FoB) cells purified from miR-17-92 tKO mice

Project description:We have generated a miR-17~92 fl/fl allele whose expression can be turned off conditionally by Cre recombinase in the miR-106a-363-/-;miR-106b-25-/- background. The mice were crossed to CD19-Cre mice to turn off the expression of miR-17~92 specifically in B cells. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 fl/fl;miR-106a-363;miR-106b~25 mice (tKO1, tKO2, tKO3) and CD19-cre (Control1, Control2, Control3) by MACS depletion of cells positive for CD9, CD43, and CD93 (also known as AA4.1). The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

2014-04-01 | E-GEOD-56376 | biostudies-arrayexpress

Gene expression profiling of CD4+ T-cell subsets in follicular lymphoma.

Project description:CD4+ T-cells from three follicular lymphoma tumors were sorted by flow cytometry into three subsets based on high (hi), intermediate (int), or low (lo) levels of PD-1 and CXCR5 expression and whole genome gene expression profiling was performed. This set contains three samples for PD-1hiCXCR5hiCD4+ T cells, two samples for PD-1intCXCR5intCD4+ T cells, and three samples for PD-1loCXCR5loCD4+ T cells.

2013-11-21 | E-GEOD-52561 | biostudies-arrayexpress

Follicular B (FoB) cells purified from miR-17-92 tKO mice, stimulated with LPS/IL-4, 13.5hr

Project description:We have generated a miR-17~92 fl/fl allele whose expression can be turned off conditionally by Cre recombinase in the miR-106a-363-/-;miR-106b-25-/- background. The mice were crossed to CD19-Cre mice to turn off the expression of miR-17~92 specifically in B cells and stimulated LPS/IL-4 for 13.5hr. Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 fl/fl;miR-106a-363;miR-106b~25 mice (TKO1, TKO2, TKO3) and WT (WT1, WTl2, WT3) by MACS depletion of cells positive for CD9, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 13.5hr in B cell media. The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

2014-04-01 | E-GEOD-56378 | biostudies-arrayexpress