title: Fadu_EGF_w_EpEX 6h_3

status: Public on Oct 26 2022

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: raw gene counts for every gene and every sample

source_name: hypopharynx

growth_protocol: Kyse30 and FaDu (ATCC, Manassas, VA, USA) were passaged in DMEM or RPMI, 10% FCS, 1% penicillin/streptomycin, 5% CO2 atmosphere at 37°C. Treatment with EGF (PromoCell PromoKine, Heidelberg, Germany), EpEX-Fc (Pan et al. PMID: 30261040) were conducted under serum-free conditions for 6h and 72h.

extract_protocol:
total RNA was extracted from cell pellets using the Qiagen AllPrep DNA/RNA Micro Kit according to the kit manual.
RNA libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina kit following the manufacturer's instructions.

treatment_protocol: Treatements were all performed under serum-starvation conditions. Cells were plated in FCS-containing medium and were serum-starved 24h later for additional 24h before adding EGF or EpEX-Fc. EGF and EpEX-Fc treatment was performed for 6h and 72h before collecting samples.

value: Fadu

value: hypopharyngeal carcinoma


title: 18-ary memory T cells rep 1 (RNA-seq)

status: Public on Nov 17 2022

type: SRA

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Adapters and low-quality segments were trimmed with Trimmomatic
Filtered reads were aligned to the mouse genome GRCm38 using Hisat2 and the count matrix was generated using featureCounts
All subsequent gene expression data analyses were done within the R software
Lowly expressed genes were filtered using the filterByExpr function and TMM normalized in edgeR.
Differentially expressed genes were determined using limma. The RNA-Seq samples were sequenced in two batches. Genes were considered significantly different if logFC >1 and FDR <0.05.
Assembly: mm10
Supplementary files format and content: csv files containing raw counts and TMM-normalized lcpm values (Samples Naïve 4, Naïve 5, and Naïve 6were the only samples used in the analysis.)

molecule: total RNA

organism: Mus musculus

source_name: Spleen and Lymph Nodes

extract_protocol:
N-specific memory T cells were isolated and FACS-sorted from the spleen using an H-2Kb/N52-59 tetramer
Naïve samples 1-3, Primary, Tertiary, and 27° samples were prepared with the Takara/Clontech Stranded Total RNA-Seq Kit v1 - Pico Input Mammalian reagents following manufacturer's instructions. All other samples were prepared with the Takara/Clontech Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian reagents following manufacturer's instructions.

treatment_protocol: CD45.1+ C57Bl/6 female mice were immunized with three heterologous prime boost immunizations (VSV-NJ VV-N, VSV-Ind) at >= 60 day intervals. H-2Kb/N52-59+ CD45.1+ tertiary memory CD8 T cells were sorted from spleen and lymph nodes and 1x10^5 cells were transferred to congenic CD45.2 recipients, which subsequently received three immunizations (VSV-Ind, VV-N, VSV-NJ) at 60+d intervals. Transfer & boost scheme was repeated until 45 immunizations were reached.

tag: tissue

value: Spleen and Lymph Nodes

tag: cell type

value: T cells

tag: strain

value: B6 CD45.1 (B6.SJL-Ptprca Pepcb/BoyJ)

tag: genotype

value: wild type

tag: treatment

value: 18 immunizations

tag: cohort


title: Fadu_EpEX 6h_3

organism: Homo sapiens

tag: cell line

value: EpEX

tag: timepoint


title: Kyse_EGF_w_EpEX 6h_4

source_name: esophagus

value: Kyse

value: esophageal squamous cell carcinoma


title: Healthy heart 3676-JB-2 VDJ

status: Public on Sep 22 2022

city: Nashville

first: Margaret

middle: L

last: Axelrod

state: TN

address: 2200 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt University

description:
Healthy heart
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
CD45+ cells were FACS sorted and prepapred as single cell suspensions
Library was performed according to the manufacter’s instructions (single cell 5’ RNA + VDJ protocol, 10x Genomics).
scRNA-seq and scTCR-seq

value: Heart

value: C57BL6 WT

tag: age

value: 4 weeks old


title: Kyse_EpEX 6h_4


title: Healthy heart 3676-JB-2

description:
Healthy heart
10x Genomics

library_source: transcriptomic single cell


title: Myocaritids heart 3676-JB-1 VDJ

description:
Myocaritids heart
10x Genomics


title: Non-tumor brain #5 [BC08]

status: Public on Sep 12 2022

city: London

first: Rober

last: Abdo

state: ON

address: 1151 Richmond St

department: Pathology

country: Canada

institute: The University of Western Ontario

data_processing:
GeoMx® DSP counts from each AOI were scaled to the 75th percentile of expression
Assembly: hg38
Supplementary files format and content: tab-delimited text files include 75th percentile of expression values for each Sample
Library strategy: GeoMx Seq

source_name: non-tumor brain

extract_protocol:
Lung FFPE tissues were processed following the GeoMx® DSP slide prep user manual (MAN-10087-04). Before being deparaffinized and hydrated by Leica Biosystems BOND RX, the slides were baked in oven at 60°C for at least 3 hours. And then proteinase K was added to digest the proteins.
Oligoes from PanCK+ and PanCK- regions were collected separately by UV-cleavage. The oligoes then were uniquely indexed using Illumina’s i5 x i7 dual-indexing system. PCR reactions were purified and libraries were paired-end sequenced (2x75) on a NextSeq550.

value: non-tumor brain


title: Non-tumor brain #4 [BC07]


title: Myocaritids heart 3676-JB-1

description:
Myocaritids heart
10x Genomics


title: Primary memory T cells rep 3 (RNA-seq)

value: 1 immunizations

value: Primary


title: Non-tumor brain #2 [BC04]


title: Non-tumor brain #1 [BC03]


title: Non-tumor brain #3 [BC06]


title: Patient 40 [LB40]

source_name: Metastatic lung cancer in the brain

value: Metastatic lung cancer in the brain


title: Patient 37 [L37]

source_name: primary lung cancer

value: primary lung cancer


title: Patient 37 [LB37]


title: Patient 44 [LB44]


title: Patient 35 [TIME-L35]

source_name: tumor immune microenviroment in the primary lung cancer


title: Patient 44 [L44]


title: Patient 35 [LB35]


title: Patient 30 [TIME-L30]

value: tumor immune microenviroment in the primary lung cancer


title: Patient 35 [TIME-B35]

source_name: tumor immune microenviroment in the metastatic brain


title: Patient 35 [L35]


title: Naive T cells rep 6 (RNA-seq)

description: Naïve 6

value: Spleen and Lymph Nodes

value: 0 immunizations

value: Naive


title: Non-tumor brain #6 [BC09]


title: Patient 43 [L43]


title: Patient 31 [LB31]


title: Patient 31 [TIME-B31]

value: tumor immune microenviroment in the metastatic brain


title: Patient 43 [TIME-L43]


title: Patient 34 [LB34]


title: Patient 32 [L32]


title: Patient 40 [TIME-L40]


title: Patient 32 [TIME-L32]


title: Patient 29 [L29]


title: Patient 29 [TIME-L29]


title: Patient 34 [L34]


title: Patient 40 [L40]


title: Patient 24 [TIME-L24b]


title: Patient 27 [TBME27]

source_name: tumor brain microenviroment in metastatic brain


title: Patient 12 [TIME-B12]


title: Patient 26 [L26]


title: Patient 24 [TIME-L24a]


title: Patient 26 [TIME-L26]


title: Patient 24 [L24]


title: Patient 24 [LB24]


title: Patient 30 [L30]


title: Patient 18 [LB18]


title: Patient 18 [TIME-L18]


title: Patient 22 [TBME22]

value: tumor brain microenviroment in metastatic brain


title: Patient 19 [TBME19]


title: Patient 18 [L18]


title: Patient 22 [L22]


title: Patient 21 [LB21]


title: Patient 12 [TIME-L12b]


title: Patient 21 [L21]


title: Patient 15 [TBME15b]


title: Patient 11 [TBME11]


title: Patient 19 [TIME-B19]


title: Patient 3 [L03]


title: Patient 19 [TIME-L19]


title: Patient 3 [LB03]


title: Patient 15 [LB15]


title: Patient 15 [TIME-B15]


title: Patient 20 [TIME-B20]


title: Patient 20 [L20]


title: Patient 20 [LB20]


title: Patient 20 [mLN20]

source_name: Metastatic lung cancer in a lymph node

value: Metastatic lung cancer in a lymph node


title: Patient 20 [TBME20]


title: Patient 18 [TBME18]


title: Patient 17 [TBME17]


title: Patient 19 [L19]


title: Patient 15 [L15]


title: Patient 17 [L17]


title: Patient 19 [LB19]


title: Patient 15 [TBME15a]


title: Patient 14 [L14]


title: Patient 16 [LB16]


title: Non-tumor brain #7 [BC10]


title: Patient 14 [TIME-B14]


title: Patient 17 [LB17]


title: Patient 16 [L16]


title: Patient 14 [mLN14]


title: Patient 13 [TBME13]


title: Patient 13 [L13]


title: Patient 14 [LB14]


title: Patient 13 [LB13]


title: Patient 12 [L12]


title: Patient 12 [TIME-L12a]


title: Patient 12 [LB12]


title: Patient 11 [mLN11]


title: Patient 10 [LB10]


title: Patient 11 [L11]


title: Patient 10 [TBME10]


title: Patient 16 [TBME16]


title: Patient 10 [mLN10]


title: Patient 9 [L09]


title: Patient 9 [mLN09]


title: Patient 15 [TIME-L15]


title: Patient 9 [LB09]


title: Patient 9 [TBME09]


title: Patient 8 [LB08]


title: Patient 7 [mLN07]


title: Patient 7 [LB07]


title: Patient 7 [TBME07]


title: Patient 6 [LB06]


title: Patient 7 [L07]


title: Patient 6 [mLN06]


title: Patient 5 [TIME-L05]


title: Patient 6 [TBME06]


title: Patient 12 [mLN12]


title: Patient 5 [L05]


title: Patient 5 [TBME05]


title: Patient 5 [TIME-B05]


title: Patient 5 [LB05]


title: Patient 4 [LB04]


title: Patient 3 [mLN03]


title: Patient 4 [TBME04]


title: Patient 4 [mLN04]


title: Patient 2 [L02]


title: Patient 2 [TBME02]


title: Patient 2 [mLN02]


title: Patient 3 [TBME03]


title: Patient 1 [mLN01]


title: Patient 1 [L01]


title: Patient 1 [LB01]


title: Patient 1 [TBME01]


title: CK-2

status: Public on Sep 07 2022

city: Jinan

first: Panpan

last: Li

address: Daxue Road 3501

country: China

institute: Qilu University of Technology

description: KN5585 maize inbred line

data_processing:
After QC, the raw reads are filtered into clean reads, which are aligned to the reference sequence. The alignment data was used to calculate the distribution and alignment rate of reads on the reference gene.
In order to avoid the influence of gene length and sequencing depth on expression level, the method of RPKM (Reads per kilobases per million mapped reads) was used to normalize the sequencing data
Differentially expressed genes (DEGs) were determined using DEseq2.
Further, we also can perform deep analysis based on DEGs (We use 'FDR >= 0.001 and the absolute value of Log2Ratio >= 1' as the threshold to judge the significance of gene expression difference), including Gene Ontology (GO) enrichment analysis, pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.

organism: Zea mays

source_name: kernal

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Takara). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kernal

value: 10 days after pollination

value: plant cell

value: normal


title: CK-1

description: KN5585 maize inbred line


title: Patient 5 [mLN05]


title: Patient 2 [LB02]


title: T-1

description: KN5585 maize inbred line

value: ZmSUS1 transgenic


title: CK-3

description: KN5585 maize inbred line


title: Patient 4 [L04]


title: OS152, nuclei, m6dA methylated, rep4

status: Public on Aug 08 2022

city: San Francisco

first: Arjun

middle: S

last: Nanda

state: California

address: 1700 Owens St

department: Gladstone Institute for Data Science & Biotechnology

institute: Gladstone Institutes / UCSF

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR30_plusM

library_source: genomic

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular consensus sequences (CCS) using ccs (v6.4.0) with kinetic information
Extracting kinetic information from CCS reads using the SAMOSA-ChAAT computational pipeline
Aligning CCS reads to a modified version of the hg38 reference genome with the contaminant contig KI270752.1 removed using pbmm2 (v.1.9.0)
Assembly: hg38
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Supplementary files format and content: *_zmwinfo.pickle: Python pickle containing a  dataframe with length, # of  passes, and mean IPD per base per CCS read
Library strategy: SMRT-Tag Library Preparation

molecule: genomic DNA

source_name: OS152 cell line

growth_protocol: OS152 cells were cultured in standard 1x DMEM supplemented with 10% Fetal Bovine Serum and 1% 100x Penicillin-Streptomycin-Glutamine.

extract_protocol:
Tagmented nuclei were pre-treated with 10uL RNaseA at 37°C for 15 minutes, then purified with 2.5uL Proteinase K (20mg/mL), 2.5uL 10% SDS, and 2.5uL 0.5mM EDTA at 60°C for 1-2 hours with continuous shaking at 1000 rpm. DNA was extracted with 2x SPRI bead cleanup.
Tagmented fragments were gap-repaired using Phusion DNA polymerase and Taq Ligase, or T4 DNA polymerase and Ampligase, at 37ºC for 1hr, digested with Exonuclease III at 37ºC for 1hr, then cleaned up using Ampure PB. Library quality was assessed with Qubit 1x High Sensitivity DNA Assay and Agilent Bioanalyzer High Sensitivity DNA kit.

treatment_protocol:
Isolated OS152 nuclei were methylated (10uL EcoGII per 1-2e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 1.16mM (NEB) after 15 minutes.
Isolated nuclei (methylated or unmethylated) were tagmented with H-Tn5-R27S,E54K,L372P (QB3 MarcoLab) at 55°C for 1hr.

tag: Sex

value: F

value: OS152 cell line

value: metastatic osteosarcoma cell line

value: MYC amplified, CN40

value: m6dA methylated


title: OS152, nuclei, unmethylated, rep1

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR12_minusM

value: umethylated


title: OS152, nuclei, unmethylated, rep2

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR30_minusM


title: T-2

description: KN5585 maize inbred line


title: T-3

description: KN5585 maize inbred line


title: OS152, nuclei, m6dA methylated, rep6

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR32_plusM


title: OS152, nuclei, m6dA methylated, rep8

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR34_plusM


title: OS152, nuclei, m6dA methylated, rep2

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR28_plusM


title: OS152, nuclei, m6dA methylated, rep1

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR27_plusM


title: OS152, nuclei, unmethylated, rep3

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR31_minusM


title: Spleen_Chronic_D5_CD8_TetNeg_rep1_tcr

status: Public on Jul 25 2022

city: Stanford

first: Ansuman

middle: T

last: Satpathy

state: CA

address: 300 Pasteur Drive

institute: Stanford University

description: TCR library (10X Genomics)

data_processing:
Processed with cellranger pipeline, version 3.1.0
Assembly: mm10

molecule: polyA RNA

source_name: CD8+ gp33- T cells from spleen 5 dpi with LCMV-c13

extract_protocol: 10X Genomics Single Cell 5' Library & Gel Bead Kit (v1.1 Chemistry)

value: CD8+ gp33- T cells


title: Spleen_Chronic_D5_CD8_TetPos_rep2_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from spleen 5 dpi with LCMV-c13

value: CD8+ gp33+ T cells


title: Spleen_Chronic_D8_CD8_TetNeg_tcr

description: TCR library (10X Genomics)

data_processing:
Processed with cellranger pipeline, version 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA_LCMV.mtx, scRNA_LCMV_barcodes.tsv, scRNA_LCMV_features.tsv, scRNA_LCMV_metadata.tsv.

source_name: CD8+ gp33- T cells from spleen 8 dpi with LCMV-c13

extract_protocol: 10X Genomics Single Cell 5' Library & Gel Bead Kit (v1.1 Chemistry).


title: OS152, nuclei, m6dA methylated, rep7

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR33_plusM


title: Spleen_Chronic_D5_CD8_TetPos_rep1_tcr

description: TCR library (10X Genomics)


title: Spleen_Chronic_D8_CD8_TetPos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from spleen 8 dpi with LCMV-c13


title: Spleen_Acute_D8_CD8_TetPos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from spleen 8 dpi with LCMV-Armstrong


title: OS152, nuclei, m6dA methylated, rep3

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR29_plusM


title: Spleen_Acute_D21_CD8_TetPos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from spleen 21 dpi with LCMV-Armstrong


title: OS152, nuclei, m6dA methylated, rep5

description:
OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF
OS152_PR31_plusM


title: Spleen_Acute_D8_CD8_TetNeg_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33- T cells from spleen 8 dpi with LCMV-Armstrong


title: Spleen_Acute_D21_CD8_TetNeg_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33- T cells from spleen 21 dpi with LCMV-Armstrong


title: Lung_Chronic_D21_CD8_TetPos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from lung 21 dpi with LCMV-c13


title: Spleen_Chronic_D21_CD8_TetPos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from spleen 21 dpi with LCMV-c13


title: Liver_Chronic_D21_CD8_TetNeg_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33- T cells from liver 21 dpi with LCMV-c13


title: Spleen_Chronic_D21_CD8_TetPos_rep1_tcr

description: TCR library (10X Genomics)


title: Liver_Chronic_D21_CD8_TetPos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33+ T cells from liver 21 dpi with LCMV-c13


title: 80ng NA12878, 5-letter seq, Rep2

status: Public on Jul 24 2022

city: Cambridge

first: Páidí

last: Creed

address: B400, The Trinity Building Chesterford Business Park, Saffron Walden

country: United Kingdom

institute: biomodal limited

data_processing:
Downsampling to 550M PE reads: seqtk v1.3  Adapter and quality trimming: fastp v0.20.1  Read resolution: proprietary Python package  Alignment:  bwa v0.7.17  Sorting and Indexing: samtools v1.15  Merging BAMs across lanes: bamtools v2.5  Duplicate Marking: Picard MarkDuplicates v2.23.8  BAM splitting: samtools v1.15  Methylation quantification: proprietary Python package
supplementary_files_format_and_content: quant.tsv.gz: TSV file with methylation quantification data
Assembly: GRCh38
Library strategy: 5-letter sequencing

source_name: Blood

extract_protocol:
Genomic DNA was obtained from the Coriell Institute (https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA12878)
80ng of sonicated genomic DNA was processed by either 5-Letter Seq (Cambridge Epigenetix), EM-Seq (Cat#E7120, New England Biolabs) or EpiTect Plus DNA Bisulphite kit (Cat#59124, Qiagen). 5-Letter seq and 6-Letter seq was performed with kits available from Cambridge Epigenetix.

value: Blood

value: B-Lymphocyte


title: Spleen_Chronic_D5_CD8_TetNeg_rep2_tcr

description: TCR library (10X Genomics)


title: Spleen_Chronic_D21_CD8_TetNeg_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33- T cells from spleen 21 dpi with LCMV-c13


title: 80ng NA12878, 5-letter seq, Rep1


title: Spleen_Chronic_D21_CD8_CX3CR1Neg_Slamf6Pos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ CX3CR1- SLAMF6+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1- SLAMF6+ T cells


title: Th17-Spleen_Lymph_nodes, untreated

status: Public on Jul 19 2022

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

institute: Helmholtz-Centre for Infection Research

data_processing:
Illumina RTA3 was used for basecalling.
All libraries have been assessed for sufficient sequencing quality and potential adapter contamination using programs FastQC (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trim_galore and cutadapt. To avoid potential methylation bias due to insufficient end-repair reaction, from both reads (R1/R2) the first 10 bases at the 5' as well as the 3' end have been trimmed after adapter removal and trimming of low-quality ends with a Phred score below 20. Reads, which are shorter than 20 nucleotides after trimming have been discarded.
Quality controlled libraries have been mapped against the mouse reference genome (version: GRCm38, w/o gonosomes) using the bisulfite short read mapping software BSMAP. In order to accurately measure the methylation levels of cytosines inside CpG context genome-wide and obtain corresponding coverage information, methylation level calling has taken only properly paired unique read pair mappings (methratio.py parameters: --unique, --paired,--remove-duplicate) into account.
The reliable detection of DMRs even in the absence of replicates was performed with the software tool metilene. We considered for the detection process only CpG motifs with a coverage of at least five that are present in at least one sample. In addition, a DMR has to contain at least three CpG's with a distance between two CpGs of at most 200 nucleotides and a total length of the region of at least 300. Further on, to be classified as DMR, the difference in mean methylation (i.e., mean over all CpG's of a region) of a region between two compared samples/conditions has to be greater or equal 25 percent and the adjusted P-value from the 2D-KS test has to be at most 0.1
Assembly: GRCm38 (mm10)
Supplementary files format and content: *,methout.gz: CSV formatted file with methylation values for all CpGs for each sample as generated by  BSMAp/methratio.py; *metilene_DMRs.csv.gz: Differentially methylated regions for each pairwise comparison (generated by metilene)

source_name: spleen, lymph node

extract_protocol:
Spleen and lymph nodes were removed and meshed through a sieve. Genomic DNA was prepared from Th1, Th2 or Th17 cells sorted by FACS. Genomic DNA was converted by bisulfite and subjected to library preparation.
The bisulfite converted DNA was fragmented by sonication and served as input for library preparation by using the Accel-NGS Methyl-Seq DNA Library Kit.

value: RORc(gt)-GfpTG-Foxp3-IRES-mRFP mice

value: pooled male and female

value: spleen, lymph node

value: CD4+ memory T cell

tag: marker


title: Spleen_Chronic_D21_CD8_CX3CR1Pos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ CX3CR1+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1+ T cells


title: Th2-Spleen_Lymph_nodes, untreated


title: Th1-Spleen_Lymph_nodes, untreated


title: Spleen_Chronic_D21_CD8_TetMid_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33 mid T cells from spleen 21 dpi with LCMV-c13

value: CD8+ gp33 mid T cells


title: mESC_H3K27me3_HiChIP

status: Public on May 13 2022

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

description:
H3K27me3 HiChIP library
7B_K27ME3-TGGGTTTC-GGGCCGGT_S2_L001

data_processing:
library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: mm10,hg38
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

source_name: mESC

growth_protocol: Cells were maintained in Knockout DMEM (Gibco #10829-018) supplemented with LIF on CD1 feeder cells.

extract_protocol:
HiChIP libraries were generated as described previously (PMID: 27643841).
Nextera

value: mouse embryonic stem cells (mESCs)

tag: chip antibody

value: H3K27me3 (Millipore-Sigma #07-449)


title: Normal endothelial cells (NECs)

status: Public on Jun 10 2022

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description: 10x Genomics

data_processing:
The FASTQ files were mapped using CellRanger pipeline (10X Genomics) to generate a count matrix. The matrix generated by cell ranger pipeline was imported into Seurat R package for performing the additional QC and in-depth analysis. In summary, cells that had low RNA counts (<200 genes) were filtered out. The cells were also filtered based on <10% mitochondrial genes. The data was normalized after removing unwanted cells (immune cells, pericytes, smooth muscle cells, and epithelial cells) from the dataset by employing a global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell by the total expression. The highly variable (highly expressed in some cells, and lowly expressed in others) top 4,000 genes were used for downstream analysis. Random permutated subsets of the data (1% by default) were used to rerun the PCA and to construct a ‘null distribution’ of feature scores to identify number of PCs to consider for performing the clustering analysis. The FindNeighbors and FindClusters functions were used from the Seurat object. The FindNeighbors function works by calculating the neighborhood overlap (Jaccard index) between every cell and its k.param nearest neighbors. The FindClusters uses a graph-based clustering approach and a Louvain algorithm. Non-linear dimensionality reduction (UMAP/tSNE) was used to explore and visualize the clusters.
Assembly: mm10
Supplementary files format and content: Normal_counts.csv

source_name: E0771 mammary

extract_protocol: For EC sorting, tissues were minced into small pieces and added to a GentleMACs C tube (Miltenyi) and dissociated using the Miltenyi Tissue Dissociator (Miltenyi). The homogenized tissues were incubated for 60 min at 37 °C in a dissociation buffer containing 2 mg/ml of collagenase type I (Worthington), 1 mg /ml of DNase (Worthington), and 2.5 units/ml of neural protease (Worthington). The digested tissues were then separated into a single-cell suspension by passing through a 100 mM cell strainer. The cell pellet was washed three times at 1,200 rpm for 5 minutes and resuspended in Pharmlyse B (BD Pharmingen) for 5 mins at room temperature. After removing the Pharmlyse B by centrifugation, cells were washed in FACS buffer, and then stained with Live dye (Live-or-Dye™ Fixable Viability Staining Kits, Biotium). For Fc blocking, cells were incubated with mouse FcR blocking reagent (Miltenyi) for 10 min. Cells were then stained with PE-conjugated CD31 (1:50) and APC-conjugated CD45 antibodies (1:50) (BD Pharmingen) for 30 min on ice. After incubation, cells were washed three times at 1,200 rpm for 5 min and then sorted by an Influx Cell Sorter (Becton Dickinson).

value: Endothelial cells (TECs)

value: E0771 mammary

value: 6-8 weeks old


title: mESC_H3K27ac_HiChIP

description:
H3K27ac HiChIP library
7A_K27AC_WT-GTGTGGTG-GGGCCGGT_S1_L001

value: H3K27ac (Active Motif #39133)


title: Bdm14

status: Public on Apr 19 2022

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

data_processing:
Illumina NextSeq Control Software v. 1.4.1.2 / RTA v. 2.4.6
Quality control: Reads were aligned against Zv9/danRer7 using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against Zv9/danRer7 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
Read mapping and quantification: RSEM v. 1.2.15  rsem-calculate-expression command was used with the following flags:  -p 5 --output-genome-bam --paired-end --calc-ci --bowtie-chunkmbs 1024 against the Zv9/danRer7 genome assembly and ENSEMBL 70 annotation (bowtie v. 1.0.1).
Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

organism: Danio rerio

source_name: Co-dissected ventricles and outflow tracts

extract_protocol:
Sibling control and ltbp1-/-; ltbp3-/- larvae on 5 days post-fertilization were anesthetized in standard embryo   media containing 0.4% tricaine (ethyl 3-aminobenzoate methanesulfonate, MS222;   Sigma) (Westerfield, 2000). Their hearts, including both the ventricle and OFT, were   manually dissected from the animals using fine forceps and micro scissors (Fine Science   Tools) and placed in cold 1XPBS (Westerfield, 2000). After 10 hearts were collected per   biological replicate, they were centrifuged at 4°C for 5 minutes at maximum speed   before being resuspended in TRIzol Reagent (Thermo Fisher Scientific) and flash frozen   in liquid nitrogen. Total RNA was isolated using the Direct-zol, RNA MicroPrep (Zymo   Research, Catolog number R2062) Kit, according to the manufacturer’s instructions.   RNA was eluted with 30µl water.
RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument (Agilent   Technologies). Only samples with RIN scores greater than 8 were used for cDNA library   preparation. Approximately 400-500ng of RNA per sample were used to prepare   sequencing libraries with the low-input RNA NeoPrep Library Prep System (Illumina).

value: laboratory

value: 5 days post-fertilization


title: Bdm7

value: Co-dissected ventricles and outflow tracts


title: Spleen_Chronic_D21_CD8_TetNeg_rep1_tcr

description: TCR library (10X Genomics)

value: CD8+ gp33- T cells


title: Bdm5


title: Bdm3


title: Lung_Chronic_D21_CD8_TetNeg_tcr

description: TCR library (10X Genomics)

source_name: CD8+ gp33- T cells from lung 21 dpi with LCMV-c13


title: Tumor endothelial cells (TECs)

status: Public on May 02 2022

data_processing:
The FASTQ files were mapped using CellRanger pipeline (10X Genomics) to generate a count matrix. The matrix generated by cell ranger pipeline was imported into Seurat R package for performing the additional QC and in-depth analysis. In summary, cells that had low RNA counts (<200 genes) were filtered out. The cells were also filtered based on <10% mitochondrial genes. The data was normalized after removing unwanted cells (immune cells, pericytes, smooth muscle cells, and epithelial cells) from the dataset by employing a global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell by the total expression. The highly variable (highly expressed in some cells, and lowly expressed in others) top 4,000 genes were used for downstream analysis. Random permutated subsets of the data (1% by default) were used to rerun the PCA and to construct a ‘null distribution’ of feature scores to identify number of PCs to consider for performing the clustering analysis. The FindNeighbors and FindClusters functions were used from the Seurat object. The FindNeighbors function works by calculating the neighborhood overlap (Jaccard index) between every cell and its k.param nearest neighbors. The FindClusters uses a graph-based clustering approach and a Louvain algorithm. Non-linear dimensionality reduction (UMAP/tSNE) was used to explore and visualize the clusters.
Genome_build: mm10
Supplementary_files_format_and_content: Tumor_counts.csv

source_name: E0771 mammary tumors

value: E0771 mammary tumors

value: Tumor endothelial cells (TECs)


title: Bdm4


title: Spleen_Chronic_D21_CD8_PD1Pos_tcr

description: TCR library (10X Genomics)

source_name: CD8+ PD1+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ PD1+ T cells


title: Sib11

value: sibing


title: Spleen_Chronic_D21_CD8_CX3CR1Neg_tcr

description: TCR library (10X Genomics)

source_name: CD8+ CX3CR1- T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1- T cells


title: Bdm2


title: Sib1


title: Sib8


title: Sib10


title: VML_D42_3mm

status: Public on Apr 04 2022

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

data_processing:
Base calling, alignment, filtering, barcode counting, and UMI counting: 10x CellRanger v2.0.0 software’s mkfastq and count commands were run with default parameters except expect-cells=10000. Alignment was performed to the mm10 reference genome.
ata filtering and quality control: Matrix files were imported into R using the Seurat package. Genes expressed in less than 200 cells or cells expressing less than 3 genes were removed. Seurat objects were merged and cells with >10% mitochondrial gehes or over 75000 reads were deemed low quality and removed. Libraries were normalized and scaled using default parameters.
Batch correction: Technical batch effects were regressed out using Seurat v3’s FindIntegrationAnchors and Integrate data functions.
Dimension reduction and community detection: Dimensional reduction was performed in Seurat using UMAP followed by community detection using the louvain algorithm. Cluster markergenes were determined in Seurat using the Wilcoxon sum-rank test.
Celltype annotation: Cell types were annotated using scCATCH to compare with mouse muscle databases in combination with markergene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Large Seurat object containing merged, processed matrix file as well as raw counts, normalized data, integrated data, scaled data, variable features, metadata (condition, timepoint, defect size,  seurat clusters, celltypes), and reductions (PCA and UMAP).

source_name: Quadriceps muscle

extract_protocol:
Mouse quadriceps were extracted, and separately weighed using sterile surgical tools and placed into separate petri dishes containing ice-cold PBS. Using surgical scissors, muscle tissues were minced and collagenase type II (Gibco 17101015, 0.2%) and dispase II (Sigma D4693, 2.5U/mL) were added to 10mL of DMEM (Gibco-Invitrogen Cat#10569010) per mouse. Samples were placed on rocker in a 37˚C incubator for 1 hour and mixed by pipette every 30 minutes. The enzymes within the slurry were then inactivated by addition of 20% heat-inactivated fetal bovine serum (HI-FBS) in Ham’s F10 media (Gibco-Invitrogen # 11550-043). The solution was passed through a 70um cell strainers, centrifuged, washed, and counted. Cells were then divided for fluorescent activated cell sorting (FACS) enrichment of viable cells and removal of debris
Freshly isolated cells were briefly stained with Propidium Iodide (PI)and FACS sorted to remove dead cells (PI positive) and debris. 10,000-16,000 cells were loaded into the 10x Genomics chromium single cell controller and single cells were captured into nanoliter-scale gel bead-in-emulsions (GEMs). cDNAs were prepared using the single cell 3′ Protocol as per manufacturer’s instructions and sequenced on a NovaSeq 6000 flow cell (Illumina) with 26 bases for read1 and 98x8 bases for read2.

treatment_protocol: C57BL/6 wild-type female and male mice were obtained from Jackson Laboratories. All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and the Institutional Animal Care and Committee and were in accordance with the U.S. National Institute of Health (NIH). Young mice (3-4 months) were first anesthetized with 1.5% isoflurane and administered 10mg/kg buprenorphine. Hair was removed from the hindlimbs using clippers, followed by Nair hair removal cream. The surgical area was wiped with proprium iodide followed by 70% ethanol three times to sterilize. A 1cm incision was made in the skin on the anterior side of each quadricep, followed by the removal of a 2mm or 3mm full depth muscle section from the medial quadricep from the distal half of the muscle. A suture was placed in the muscle to identify the location of the injury, and the skin was sutured closed. Dermal sutures were removed 7 days post-surgery.

value: Quadriceps muscle

tag: defect

tag: gender

value: male

tag: timepoint (days post injury)


title: Uninjured_R2

value: Uninjured

value: female


title: VML_D28_2mm

data_processing:
Base calling, alignment, filtering, barcode counting, and UMI counting: 10x CellRanger v2.0.0 software's mkfastq and count commands were run with default parameters except expect-cells=10000. Alignment was performed to the mm10 reference genome.
Data filtering and quality control: Matrix files were imported into R using the Seurat package. Genes expressed in less than 200 cells or cells expressing less than 3 genes were removed. Seurat objects were merged and cells with >10% mitochondrial gehes or over 75000 reads were deemed low quality and removed. Libraries were normalized and scaled using default parameters.
Batch correction: Technical batch effects were regressed out using Seurat v3s FindIntegrationAnchors and Integrate data functions.
Dimension reduction and community detection: Dimensional reduction was performed in Seurat using UMAP followed by community detection using the louvain algorithm with a resolution of 0.2. Cluster markergenes were determined in Seurat using the Wilcoxon sum-rank test.
Celltype annotation: Cell types were annotated using scCATCH to compare with mouse muscle databases in combination with markergene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Large Seurat object containing merged, processed matrix file as well as raw counts, scaled data, variable features, metadata (condition, timepoint, defect size, mitochondrial gene fraction, seurat clusters, celltypes), and reductions (iNMF and umap).

value: pooled male and female


title: VML_D7_3mm_M


title: VML_D14_3mm


title: VML_D7_3mm_F


title: VML_D14_2mm


title: VML_D7_2mm


title: scRNAseq DIA WT 12months

status: Public on Mar 14 2022

city: CRETEIL

first: Valentina

last: TAGLIETTI

address: RUE GENERAL SERRAIL

country: France

institute: INSERM

description: scRNAseq

data_processing:
Sequence analysis with Cell Ranger Single Cell Software Suite 3.0.2 by 10X Genomics
Raw base call files were demultiplexed with the cellranger mkfastq pipeline into library specific FASTQ files
The FASTQ files for each library were then processed independently with the cellranger count pipeline.
Assembly: rn6
Supplementary files format and content: For each sample, set of 3 files in format 10X (list of cell barcodes, list of genes and expression matrix (raw counts))

organism: Rattus norvegicus

source_name: Diaphragm, muscle

extract_protocol:
muscle enzymatic digestion - 10x Genomics Chromium Next GEM Single Cell 3' V3.1
Chromium Next GEM Single Cell 3' Library kit v3.1

tag: disease status

value: wild-type

value: 12 months

tag: cell types

value: Total cells from diaphragm


title: VML_D28_3mm

tag: tissue


title: Uninjured


title: scRNAseq DIA DMD 12months

description: scRNAseq

value: Duchenne muscular dystrophy (DMD)


title: MZsox19bspg2-dome

status: Public on Jan 07 2022

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

description:
MZsox19bspg_dome_peak_summits.txt
MZsox19bspg_dome_bw.bigwig

data_processing:
Library strategy: Omni-ATAC-seq
Novaseq 6000 base calling software RTA3
Trimming: FASTQ paired 150bp files were trimmed for adapter sequence.  Low quality reads (Q<30), unpaired reads and reads less than 25 bp were removed, the rest was cropped to 30 bp from the start of the read. All the operations were done using   Trimmomatics software on the european Galaxy server.
Mapping: The paired reads were mapped with Bowtie2  on the european Galaxy server, with the option "allow mate dovetailing". The maximum fragment length for valid paired-end alignment was set to 1000 bp. Raw files in our submission come from this step.
Filtering: BAM files were filtered using BAMtools on the european Galaxy server  with the parameters {'filters': [{'id': '1', 'isProperPair': 'true', 'isDuplicate': 'false', 'reference': '!chrM', 'mapQuality': '>=30'}]}. Then the fragment ends were shifted as appropriate for ATAC-seq, and only the paired reads with the length less the 110bp ( less than one nucleosome) were kept for further processing . This step was  using the "alighmentsieve" program from deeptools suite on the european Galaxy server.
Peak calling:  The peaks were called using MACS2 program in the european Galaxy server with the  parameters extension size 200, shift size -100,--call-summits. Peak calling was performed for each filtered BAM file. In addition, the peaks were called from merged and filtered BAM files for all replicates from one stage and genotype. Only the peaks present in all replicates and merged file were kept for further analysis. The resulting peak summits for each stage and genotype are supplied as processed files
Generation of bigwig files for visualization and scoring:   BAM files for all replicates from one stage and genotype were merged using  Picard merge command and filtered.  Bigwig files were generated with BAM coverage utility ( deeptools), with the parameters bin size =10, normalization method RPKM.
Genome_build: danrer11
Supplementary_files_format_and_content: peak text files (chr,start,end,name, MACS2 score), bigwig files

source_name: whole embryo

growth_protocol: embryos were obrained from the natural matings and incubated at 28.5° until the desired stage

extract_protocol:
Chorions were removed by 15 - min. incubation in Pronase E. 3. 30 embryos were deyolked manually with an  eyebrow needle in Danieaus medium, centrifuged (500 x g, 5 min, 4°C), resuspended in 100 µl ice-cold PBS and centrifuged again. The cells were resuspended by pipetting  in 50 µl ice-cold lysis buffer: (ATAC-RSB (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2), with 0.1% NP40, 0.1% Tween20, and 0.01% digitonin)) and incubated on ice for 5 minutes, then diluted with dilution buffer (1 ml, ATAC-RSB containing 0.1% Tween-20). Nuclei were pelleted at 500 x g, 10 min, 4°C, and resuspended in 16.5 µl PBST.
Tagmentation reaction was assembled according to the manufacturer instructions for Illumina small Tn5 buffer and enzyme kit in 50µl volume and incubated in a thermomixer for 30 min, 37°C, 800 RPM. The samples were purified  using Qiagen PCR MinElute Purification kit. The purified transposed mix was pre-amplified  for 5 cycles using NEBNext 2x Master Mix (NEB) and Nextera adapters and put on ice. To determine the number of  additional cycles, 5 µl of the pre-amplified mixture was used  to run a 15 ml qPCR. The amplified libraries were purified using SPRI beads (Beckmann) according to the manufacturer instructions.

treatment_protocol: no treatment

tag: developmental stage

value: blastula, dome, 4.3 hpf

value: MZsox19bspg m793, m1434


title: MZsox19bspg3-dome


title: MZspg2-dome

description:
MZspg_dome_peak_summits.txt
MZspg_dome_bw.bigwig

value: MZspg m793


title: MZsox19bspg1-dome


title: MZspg3-dome


title: MZsox19bspg4-dome


title: WT3-dome

description:
WT_dome_peak_summits.txt
WT_dome_bw.bigwig

value: wild-type AB/TL strain


title: MZspg1-dome


title: MZsox19b1-dome

description:
MZsox19b_dome_peak_summits.txt
MZsox19b_dome_bw.bigwig

value: MZsox19b m1434


title: WT1-dome


title: MZsox19b2-dome


title: WT2-dome


title: MZsox19b3-dome


title: MZsox19bspg1-oblong

description:
MZsox19bspg_oblong_peak_summits.txt
MZsox19bspg_oblong_bw.bigwig

value: blastula, oblong, 3.7 hpf


title: MZspg2-oblong

description:
MZspg_oblong_peak_summits.txt
MZspg_oblong_bw.bigwig


title: MZspg1-oblong


title: MZsox19b2-oblong

description:
MZsox19b_oblong_peak_summits.txt
MZsox19b_oblong_bw.bigwig


title: TT_FBS_3

status: Public on Jan 17 2022

type: RNA

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description:
Total cellular input RNA.
Total cellular RNA extracted from cells grown in standard FBS culture, RNA input sample for the immunoprecipitation.

hyb_protocol: Cy3 labeled cRNA was hybridised onto a custom Agilent oligo microarray at 65⁰C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: Differential expression was determined using the Bayesian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R. Data was annotated using Gencode v21 / Ensembl 77 (GRCh38).

source_name: LNCaP prostate cancer cell line

label_protocol: RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: LNCaP cells were cultured in phenol-red free RPMI-1640 medium + 5% FBS at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was extracted using the RNeasy Micro Kit (Qiagen #74004) according to the manufacturer’s protocol, including DNase-I treatment.

value: LNCaP

tag: cell type

value: Prostate cancer cell line

tag: condition

value: FBS

tag: antibody


title: TT_FBS_2


title: TT_FBS_1


title: YBX1-IP_FBS_1

type: other

description:
RNA co-immunoprecipitated with YB-1 antibody.
RNA bound in YB-1 containing RNP granules was co-immunoprecipitated from cells grown in standard FBS culture using an N-terminal antibody against YB-1.

molecule: other


title: SC_2

description:
Non-targeting siRNA control.
Cells were seeded at a density of 10,000 cells/cm2, transfected 24 hrs after seeding with non-targeting All-Stars negative control siRNA (Qiagen #1027281) using Lipofectamine RNAiMax at a final dilution of 1:690 (Life Technologies #13778150) and harvested at 48 hrs past transfection.

tag: sirna

value: Non-targeting


title: WT3-oblong

description:
WT_oblong_peak_summits.txt
WT_oblong_bw.bigwig

tag: genotype


title: YBX1-SI_2

description:
YBX1 siRNA induced knock down.
Cells were seeded at a density of 10,000 cells/cm2, transfected 24 hrs after seeding with 10 nM FlexiTube siRNA targeting YBX1 (Qiagen YBX1-SI SI03019191) using Lipofectamine RNAiMax at a final dilution of 1:690 (Life Technologies #13778150) and harvested at 48 hrs past transfection.

tag: cell line


title: MZsox19b1-oblong


title: YBX1-SI_3


title: WT1-oblong


title: WT2-oblong


title: MDA-MB-231 WT DSM OE_2

status: Public on Dec 24 2021

city: Gainesville

first: Daiqing

last: Liao

state: FL

address: 2033 Mowry Rd

department: Anatomy and Cell Biology

institute: University of Florida

data_processing:
Briefly, fastq files were aligned to Genome Reference Consortium Human Build 38 (GRCh38) using HISAT2; the transcripts assembling was performed using StringTie with RefSeq as transcripts ID; and the normalized counts (by FPKM) was called using Ballgown. The differential expression analysis was performed using R package limma; and the pathway enrichment analysis was performed using ingenuity pathway analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNAseq data final.xlsx

source_name: Triple negative breast cancer

growth_protocol: The panel of MDA_MB-231 derived cell lines (control DAXX  KD, and WT DAXX OE) were cultured in complete DMEM.

extract_protocol: Extraction of total RNA with the RNeasy mini kit was performed according to the manufacturer's instructions.

treatment_protocol: Stable expression of cDNA and shRNA was established through lentiviral transduction of MDA-MB-231 cell line and puromycin (2 µg/mL) selection. Scrambled control shRNA-transfected MDA-MB-231 cells were applying as control. Control MDA-MB-231 cells, Stable DAXX knockdown, and DAXX overexpression cell lines were seeded with 2 x 10^5 cells at 10 cm culture plate. Triplicates cell culture were conducted.

value: Triple negative breast cancer

value: DSM Overexpression


title: MZsox19bspg2-oblong


title: YBX1-IP_FBS_3


title: SC_3


title: MDA-MB-231 DAXX KD_2

value: DAXX Knockdown


title: MDA-MB-231 DAXX KD_1


title: MDA-MB-231 WT DAXX OE_1

value: DAXX Overexpression


title: MDA-MB-231 shControl_1

value: Control


title: MDA-MB-231 WT DAXX OE_2


title: MDA-MB-231 shControl_2


title: YBX1-SI_1


title: MOC1E1_invitro_RNA_rep2

status: Public on Dec 01 2021

city: Boston

first: Ravindra

last: Uppaluri

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
MOC1E1_invitro_RNA_rep2
bulk RNA
MOC1_MOC1E_inVITRO.csv

data_processing:
The raw sequencing data were processed with Cell Ranger 3.0.2 software
Filtered gene-barcode matrix files were further parsed with Seurat 3.0.01 for fine-grain quality control and downstream analyses
Paired read data was adapted and quality trimmed using Trimmomatic v0.36
Trimmed reads were quantified by pseudoalignment against mm10 using Kallisto v0.46.0
Differential expression analysis was performed using DESeq2
Genome_build: GRCH38
Supplementary_files_format_and_content: txt, csv containg raw counts and scTCR

source_name: in vitro cultured cell line MOC1E1

growth_protocol: Mouse oral squamous cell carcinoma models, MOC1, MOC1esc1, and MOC22 were maintained as previously described [35-37] in IMDM/Hams-F12 (2:1) supplemented with 5% heat inactivated FBS, 100 U/ml penicillin streptomycin, 5 ng/ml EGF (Millipore), 400 ng/ml hydrocortisone (Sigma Aldrich), and 5 mg/ml insulin (Sigma Aldrich). Cell lines were routinely tested for mycoplasma every 6 months.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (QIAGEN) according to manufacturer’s protocol. Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen)
WES Library construction was performed using the Agilent Sure Select Whole Exome Capture and captured using the Agilent SureSelect XT Mouse All Exon probe sets according to the manufacturer protocol.For bulk RNAseq, standard mRNA library preparation kit (RS-122-2101, Illumina) was used for library preparation. The single-cell RNA-seq libraries were processed using ChromiumTM single-cell 5’ library & gel bead kit and coupled TCR-seq libraries were obtained using ChromiumTM single-cell V(D)J enrichment kit (10x Genomics).
RNA-seq, genomic DNA-seq, scRNA-seq&TCRseq

treatment_protocol: isotype, antiPD1, and antiCTLA4 antibodies were ip injected on Day 3, 6, 9 post tumor inoculation

tag: strain

value: Tumor

tag: treatment

value: no treatment


title: SC_1


title: MOC1_invitro_RNA_rep2

description:
MOC1_invitro_RNA_rep2
bulk RNA
MOC1_MOC1E_inVITRO.csv

source_name: in vitro cultured cell line MOC1


title: YBX1-IP_FBS_2


title: MOC1_invitro_RNA_rep3

description:
MOC1_invitro_RNA_rep3
bulk RNA
MOC1_MOC1E_inVITRO.csv


title: MOC1_Whole_Exome_Seq

description:
MOC1_Whole_Exome_Seq
WES

data_processing:
Library strategy: whole exome-seq
The raw sequencing data were processed with Cell Ranger 3.0.2 software
Filtered gene-barcode matrix files were further parsed with Seurat 3.0.01 for fine-grain quality control and downstream analyses
Paired read data was adapted and quality trimmed using Trimmomatic v0.36
Trimmed reads were quantified by pseudoalignment against mm10 using Kallisto v0.46.0
Differential expression analysis was performed using DESeq2
Genome_build: GRCH38
Supplementary_files_format_and_content: txt, csv containg raw counts and scTCR


title: MOC1E1_invitro_RNA_rep1

description:
MOC1E1_invitro_RNA_rep1
bulk RNA
MOC1_MOC1E_inVITRO.csv


title: MOC1_invitro_RNA_rep1

description:
MOC1_invitro_RNA_rep1
bulk RNA
MOC1_MOC1E_inVITRO.csv


title: MOC1e1_Whole_Exome_Seq

description:
MOC1e1_Whole_Exome_Seq
WES


title: MOC1E1_invitro_RNA_rep3

description:
MOC1E1_invitro_RNA_rep3
bulk RNA
MOC1_MOC1E_inVITRO.csv


title: scTCR-seq of mus musculus: tumor infiltrating immune cells [MOC1_scTCR_aCTLA4]

description: single cell TCR

data_processing:
The raw sequencing data were processed with Cell Ranger 3.0.2 software
Filtered gene-barcode matrix files were further parsed with Seurat 3.0.01 for fine-grain quality control and downstream analyses
Paired read data was adapted and quality trimmed using Trimmomatic v0.36
Trimmed reads were quantified by pseudoalignment against mm10 using Kallisto v0.46.0
Differential expression analysis was performed using DESeq2
Genome_build: MM10
Supplementary_files_format_and_content: txt, csv containg raw counts and scTCR

source_name: MOC1 bearing mice received antiCTLA4 treatment

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (QIAGEN) according to manufacturer’s protocol. Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen)
WES Library construction was performed using the Agilent Sure Select Whole Exome Capture and captured using the Agilent SureSelect XT Mouse All Exon probe sets according to the manufacturer protocol.For bulk RNAseq, standard mRNA library preparation kit (RS-122-2101, Illumina) was used for library preparation. The single-cell RNA-seq libraries were processed using ChromiumTM single-cell 5’ library & gel bead kit and coupled TCR-seq libraries were obtained using ChromiumTM single-cell V(D)J enrichment kit (10x Genomics).


title: scTCR-seq of mus musculus: tumor infiltrating immune cells [MOC1_scTCR_ctrl]

description: single cell TCR

source_name: MOC1 bearing mice received isotype control treatment

value: isotype control


title: MOC1E1_bulktumor_RNA_rep2

description:
MOC1E1_bulktumor_RNA_rep2
bulk RNA
MOC1_MOC1E_bulk tumor.csv

source_name: MOC1E1 bearing mice


title: scTCR-seq of mus musculus: tumor infiltrating immune cells [MOC1_scTCR_aPD1]

description: single cell TCR

source_name: MOC1 bearing mice received antiPD1 treatment


title: MOC1_bulktumor_RNA_rep3

description:
MOC1_bulktumor_RNA_rep3
bulk RNA
MOC1_MOC1E_bulk tumor.csv

source_name: MOC1 bearing mice


title: MOC1E1_bulktumor_RNA_rep3

description:
MOC1E1_bulktumor_RNA_rep3
bulk RNA
MOC1_MOC1E_bulk tumor.csv


title: MOC1_bulktumor_RNA_rep1

description:
MOC1_bulktumor_RNA_rep1
bulk RNA
MOC1_MOC1E_bulk tumor.csv


title: MOC1_bulktumor_RNA_rep2

description:
MOC1_bulktumor_RNA_rep2
bulk RNA
MOC1_MOC1E_bulk tumor.csv


title: MOC22_scTCR_aPD1

description:
scTCR-seq of mus musculus: tumor infiltrating T cells
single cell TCR
MOC22_Control_TCR.csv

source_name: MOC22 bearing mice received antiPD1 treatment


title: MOC1E1_scTCR_aPD1

description:
scTCR-seq of mus musculus: tumor infiltrating immune cells
single cell TCR
MOC1_PD1_TCR.csv

source_name: MOC1E1 bearing mice received antiPD1 treatment


title: MOC1E1_scTCR_aCTLA4

description:
scTCR-seq of mus musculus: tumor infiltrating immune cells
single cell TCR
MOC1_CTLA4_TCR.csv

source_name: MOC1E1 bearing mice received antiCTLA4 treatment


title: MOC1E1_scRNA_ctrl

description:
scRNA-seq of mus musculus: tumor infiltrating immune cells
single cell RNA
MOC1E_scRNA_counts.txt

source_name: MOC1E1 bearing mice received isotype control treatment


title: MOC1E1_scRNA_aCTLA4


title: MOC22_scRNA_aPD1

description:
scRNA-seq of mus musculus: tumor infiltrating T cells
single cell RNA
MOC22_scRNA_counts.txt


title: MOC1E1_scRNA_aPD1


title: MOC22_scTCR_ctrl

description:
scTCR-seq of mus musculus: tumor infiltrating T cells
single cell TCR
MOC22_PD1_TCR.csv

source_name: MOC22 bearing mice received isotype control treatment


title: MOC22_scRNA_ctrl


title: scRNA-seq, dura mater leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion

status: Public on Nov 26 2021

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

description:
stroke_dura_24h
single-cell RNA seq data of dura mater leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v6.0)
Read alignments and transcript counting were done individually for each sample using the cellranger count pipeline with standard parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CD45iv-CD45+ leukocytes from dura mater

extract_protocol:
Mice were injected (intravenously; iv) with fluorochrome coupled anti-mouse CD45 antibody (clone 30-11F, Biolegend, 3 µg/mouse). Five minutes later, animals were intracardially perfused with cold PBS with 10 U/ml heparin under deep ketamine/xylazine anesthesia. During perfusion, blood was collected and transferred into a tube. To separate different CNS compartments, the forebrain and cerebellum were dissected from mice. Under binoculars, the dura was dissected from the calvaria and the pia was dissected from the brain parenchyma. All choroid plexuses were removed from the ventricles of the brain. Brain tissue was cut into pieces and digested with collagenase D (2.5 mg/ml, Roche Diagnostics) and DNase I (0.05 mg/ml, Sigma) at 37 °C for 20 min. Pia, dura, and CP were digested in medium containing 1 mg/ml Collagenase D (Roche) for 45 min at 37°C. Afterwards, digested tissue was passed through a 70 μm cell strainer. The parenchyma was centrifuged on a 70%/37% percoll gradient. The interphase was removed, washed and re-suspended in PBS with 2% FCS. Cells extracted from the CNS, pia and dura were sorted for CD45+CD45iv- cells.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit with v2 and 3 chemistry (both from 10X Genomics, #1000128, #1000157). Sample processing and library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter, A63881). Sequencing was carried out on a Illumina Novaseq using NovaSeq 6000 S4 Reagent Kit (300 Cycles, #20028312) the a 150-8-8-150 read setup.
scRNA-seq

value: dura mater

value: CD45iv-CD45+ tissue-resident leukocytes (TRL)

value: transient middle cerebral artery occlusion 24h


title: scRNA-seq, pia mater leukocytes from  C57BL/J mice 24h after transient middle cerebral artery occlusion

description:
stroke_pia_24h
single-cell RNA seq data of pia mater leukocytes from  C57BL/J mice 24h after transient middle cerebral artery occlusion

source_name: CD45iv-CD45+ leukocytes from pia mater

value: pia mater


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion, rep2

description:
stroke_cns_24h_2
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion

source_name: CD45iv-CD45+ leukocytes from brain parenchyma

value: brain parenchyma


title: MDSCs_CD11b+_CD11c+_rep_3 [638_9]

status: Public on Oct 05 2021

city: Biberach (Riss)

first: Katrin

last: Fundel-Clemens

address: Birkendorferstr. 65

department: gCBDS

institute: Boehringer Ingelheim Pharma GmbH&Co KG

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using Ensembl 70 mouse reference genome.
Gene expression levels were quantified by Cufflinks v2.2.1 (Trapnell et al., 2013) to get Reads per kilobase per million mapped reads (RPKM) as well as FeatureCounts (Liao et al., 2014) to get read counts
Illumina reads were converted to FASTQ files and aligned to the mouse reference genomes from Ensembl 70 (http://www.ensembl.org) using the STAR v2.5.2 program on default settings (Dobin et al., 2013).  SAM files were converted by samtools v0.1.18 (Li et al., 2009) to BAM files.   Sequenced read quality was checked with FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and alignment quality metrics were calculated using the RNASeQC v1.1.8 (DeLuca et al., 2012). Duplication rates were assessed with bamUtil v1.0.11 (Jun et al., 2015) and dupRadar v1.4. (Sayols et al., 2016).  Gene expression levels were quantified by Cufflinks v2.2.1 (Trapnell et al., 2013) to get Reads per kilobase per million mapped reads (RPKM) as well as FeatureCounts (Liao et al., 2014) to get read counts.  Differential expression analysis was performed based on voom normalized (Law et al., 2014) read counts as input for the Bioconductor R package LIMMA (Ritchie et al., 2015). The batch number was used as a factor in the LIMMA linear regression model. P-values were corrected for multiple testing by Benjamini–Hochberg.
Genome_build: ENSEMBL mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: MDSCs were generated in vitro by incubating freshly isolated bone marrow (BM) cells with 250 U/mL murine GM-CSF for 4 days at 37°C in an atmosphere with 7.5% CO2. 9x106 – 1x107 BM cells were cultured in α-minimum essential medium (Lonza, Switzerland), 10% fetal calf serum (Sigma Aldrich), 2 mM l-glutamine (Gibco), 1 mM sodium-pyruvate (Gibco), 100 U/mL penicillin-streptomycin (Gibco), and 0.05 mM 2-mercaptoethanol (Gibco,) in Ø 15 cm culture dishes “Cell+” (Sarstedt, Germany).

extract_protocol:
FACS-sorted CD11b+CD11c+ and CD11b+CD11c- MDSCs were collected in RLT buffer supplemented with beta-mercaptoethanol followed by RNA extraction using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions adding an on-column DNA digestion step. Total RNA was quantitatively and qualitatively assessed using the absorbance-based Take3 micro-volume plate system on a Cytation 5 instrument (BioTek) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 12-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 310 ng/µl while RIN values ranged from 8.6 to 10, with an average of 9.8.
MDSC-derived RNA samples were normalized and a RNA input of 100 ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEXNext Multiplex Oligos for Illumina #E7600 downstream (New England Biolabs). Ampure XP beads (Beckman Coulter) were used for double-stranded cDNA purification. mRNA sequencing libraries were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 134 nM. Final library size distribution was assessed (smear analysis of 364 bp average and adapter dimer presence <0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 12-channel Fragment Analyzer (Agilent). All sequencing libraries passed quality check, were normalized, pooled and spiked in with PhiX Control v3 (Illumina). The library pool was subsequently clustered with the HiSeq 3000/4000 SR Cluster Kit on a cBot; and sequenced on a HiSeq 3000 Sequencing System (Illumina) with single index, single read at 85 bp length (Read parameters: Rd1: 85, Rd2: 8), reaching an average depth of 29 million Pass-Filter reads per sample (11% CV).

treatment_protocol: Isolation of CD11b+CD11c+ and CD11b+CD11c- MDSCs:  CD11b+CD11c+ MDSCs were positively isolated by magnetic activated cell sorting using anti-CD11c MicroBeads (Miltenyi, Germany) according to manufacturer´s protocol. CD11b+CD11c- MDSCs were isolated from the flow-through of CD11c isolation by loading the flow through on a depleting LD column (Miltenyi). Purity of both MDSC subpopulations ranged between 85-99 %.

value: myeloid-derived supressor cells (MDSCs)

tag: subpopulation


title: MDSCs_CD11b+_CD11c+_rep_1 [638_7]


title: MDSCs_CD11b+_CD11c+_rep_4 [638_10]


title: MDSCs_CD11b+_CD11c+_rep_2 [638_8]


title: MDSCs_CD11b+_CD11c-_rep_6 [638_6]


title: MDSCs_CD11b+_CD11c+_rep_6 [638_12]


title: MDSCs_CD11b+_CD11c-_rep_5 [638_5]


title: MOC1E1_bulktumor_RNA_rep1

description:
MOC1E1_bulktumor_RNA_rep1
bulk RNA
MOC1_MOC1E_bulk tumor.csv


title: MDSCs_CD11b+_CD11c-_rep_4 [638_4]


title: MOC1E1_scTCR_ctrl

description:
scTCR-seq of mus musculus: tumor infiltrating immune cells
single cell TCR
MOC1_Control_TCR.csv


title: MDSCs_CD11b+_CD11c-_rep_1 [638_1]


title: S02: WT_GFP-

status: Public on Sep 19 2021

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

data_processing:
bowtie2 (v2.2.6) was used for mapping.
Output sam files were converted to bam files and then trimed with "-q 2" and "1 2 3 4 5" parameters in samtools (v0.1.19) to remove mitochondrial and chloroplast sequence.
Output bam files were treated with picard MarkDuplicates (2.25.5) to remove duplicated reads. Then, output files were passed through samtools view again, to obtain 40 M reads (targeted) for further analysis.
bigWig files were generated by bamCoverage in deepTools (v3.5.1) from bam files with 10bp bin size.
bam files were converted to TagDirectory by homer (v4.10.3), and peak calling were done by findPeaks in homer with "-region -minDist 150" option
Genome_build: Arabidopsis TAIR 10 (Arabidopsis_thaliana.TAIR10.28.dna.toplevel.fa)
Supplementary_files_format_and_content: bigWig files are generated from 40M reads bam files for coverage tracks.
Supplementary_files_format_and_content: Peak text files

organism: Arabidopsis thaliana

source_name: seedling nuclei

growth_protocol: Arabidopsis were grown on 1/2 MS agar plate for three weeks in long days (8h light 16h dark, constant 21°C).

extract_protocol:
Approximately 1 g of Arabidopsis seedlings were collected in a 60 mm petri dish and thoroughly chopped using a razor blade for five minutes in nucleus isolation buffer (1x NIB Sigma-Aldrich, #CELLYTPN1) supplemented with 10µg/ml Hoechst 33342 (Sigma-Aldrich, #B2261) as the final concentration. Next, the samples were incubated 15 minutes in a dark cold room while gently shaking. After the incubation, petri dishes were washed with additional 1 ml of NIB to properly clean the plate. Using wide-bored pipet tips, the nucleus suspension was applied to a 50 µm nylon-mesh filter (Sysmex, #04-004-2327) mounted into a 30 µm nylon-mesh filter (Sysmex, #04-004-2326) at the top, both inserted into 2 ml Protein LoBind tubes (Eppendorf #0030108132). The filtered material was passed through a 5 ml Round Bottom Polystyrene FACS tube (Corning, #352235). 15,000 nuclei for each sample were then sorted into a DNA LoBind tubes (Eppendorf) with 300 µL collection buffer (15 mM TRIS-HCl ph 7.5, 20 mM NaCl, 80 mM KCl, 0,1 % Triton) by a BD FACSAriaTM IIIu cell sorter using a 100 µm sort nozzle and a 30kHz drop drive frequency according to their GFP signal levels. The gate for GFP + nuclei was set using a WT Col as reference. Next, samples were centrifuged at 3000 g for 10 minutes at 4 degrees. The supernatant was partially removed and the nuclei resuspended in 300 µL Tris-Mg buffer (Tris HCl pH8 10mM, MgCl2 5mM). A second washing step was performed using centrifugation at 1000 g for 10 minutes at 4 degrees and the supernatant was removed completely. For tagmentation, the TDE1 (Nextera Tn5 Transposase) Tagment DNA Enzyme (Illumina kit #20034198) was immediately applied to the samples by resuspending the nuclei in the transposition reaction mix and the suspension was incubated for 30 minutes at 37 degrees while gently shaking.
The samples were then purified (NEB, Monarch Nucleic Acid Purification Kit #20034198), and 12 µl of transposed DNA was amplified by PCR (8 µl H2O, 2.5 µl 25µM Custom Nextera PCR primer 1 (Buenrostro et al., 2013), 2.5 µl 25 µM Custom Nextera PCR Primer 2 and 25 µl NEB Next High Fidelity 2x PCR Master Mix(NEB, #M0541) with 1 cycle of (72°C for 5 min, 98°C for 30 sec) and 16 cycles of (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). Library was cleaned up using the Coulter Agencourt AMPure XP kit (Beckman-Coulter, #10136224) applying a 1:1 vol:vol (PCR product:beads) and eluted in 15 µl 15 mM Tris.

tag: ecotype

value: Wild type

tag: cell population

value: GFP negative (SMXL5pro:H4-GFP)

value: seedling nuclei


title: S05: smxl4smxl5_GFP+

value: GFP positive (SMXL5pro:H4-GFP)


title: MDSCs_CD11b+_CD11c+_rep_5 [638_11]


title: MDSCs_CD11b+_CD11c-_rep_2 [638_2]


title: MDSCs_CD11b+_CD11c-_rep_3 [638_3]


title: CELLLHNAID40

status: Public on Jun 30 2021

city: Ulm

first: Johannes

last: Bloehdorn

address: Albert-Einstein-Allee 23

institute: University of Ulm

description: gene expression data CD19- fraction of mononuclear cells

hyb_protocol: Array hybridization was performed at 45°C for 16-18h in the Affymetrix GeneChip® Hybridization Oven 640, arrays were subsequently washed in the Fluidics Station 450.

scan_protocol: Arrays were scanned on the GeneChip scanner 3000 7G.

data_processing: Raw Affymetrix Human Exon array (HuEx-1_0-st-v2) data files have been normalized using the RMA algorithm using aroma.affymetrix

label: biotin

source_name: peripheral blood mononuclear cells

label_protocol: Samples were analyzed for mRNA expression using the Affymetrix GeneChip® Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The experiment was conducted according to the manufacturer’s protocol. In brief, 250 ng RNA per sample were amplified, transcribed to cDNA, fragmented and subsequently labeled with Biotin.

growth_protocol: Celllines or mononuclear cells.

extract_protocol: Total RNA for mRNA profiling was extracted from cell lysates according to the Allprep DNA/RNA mini kit (Qiagen). Quality control was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip (Agilent Technologies). RNA for gene expression profiling had a RIN of at least 7.

treatment_protocol: Ficoll density gradient centrifugation for isolation of mononuclear cells with or without subsequent immunomagnetic tumor cell enrichment via CD19.

tag: sample type

value: chronic lymphocytic leukaemia


title: CELLLHNAID42


title: CELLLHNAID6

description: gene expression data from celllines

source_name: celllines

value: celllines


title: CELLLHNAID29

description: gene expression data from healthy donor b cells

source_name: peripheral blood b cells

value: healthy donor


title: CELLLHNAID43


title: CELLLHNAID8

description: gene expression data from celllines


title: CELLLHNAID33


title: CELLLHNAID27

description: gene expression data from celllines


title: CELLLHNAID41


title: CELLLHNAID3

description: gene expression data from celllines


title: CELLLHNAID36


title: CELLLHNAID30


title: CELLLHNAID2

description: gene expression data from celllines


title: CELLLHNAID5

description: gene expression data from celllines


title: CELLLHNAID34


title: CELLLHNAID37


title: CELLLHNAID35


title: CELLLHNAID7

description: gene expression data from celllines


title: CELLLHNAID12

description: gene expression data from celllines


title: CELLLHNAID28

description: gene expression data from celllines


title: CELLLHNAID31


title: CELLLHNAID26

description: gene expression data from celllines


title: CELLLHNAID23

description: gene expression data from celllines


title: CELLLHNAID32


title: CELLLHNAID25

description: gene expression data from celllines


title: CELLLHNAID18

description: gene expression data from celllines


title: CELLLHNAID19

description: gene expression data from celllines


title: CELLLHNAID39


title: CELLLHNAID38


title: CELLLHNAID22

description: gene expression data from celllines


title: CELLLHNAID21

description: gene expression data from celllines


title: CELLLHNAID16

description: gene expression data from celllines


title: CELLLHNAID24

description: gene expression data from celllines


title: CELLLHNAID15

description: gene expression data from celllines


title: CELLLHNAID13

description: gene expression data from celllines


title: CELLLHNAID10

description: gene expression data from celllines


title: CELLLHNAID20

description: gene expression data from celllines


title: CELLLHNAID1

description: gene expression data from celllines


title: CELLLHNAID17

description: gene expression data from celllines


title: CELLLHNAID9

description: gene expression data from celllines


title: CELLLHNAID11

description: gene expression data from celllines


title: CELLLHNAID14

description: gene expression data from celllines


title: CELLLHNAID4

description: gene expression data from celllines


title: CLLCCAID2821

description: Gene expression data from CLL sample

label: Biotin

label_protocol: Samples from CLL patients were analyzed for mRNA expression using the Affymetrix GeneChip® Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The experiment was conducted according to the manufacturer’s protocol. In brief, 250 ng RNA per sample were amplified, transcribed to cDNA, fragmented and subsequently labeled with Biotin.

growth_protocol: Peripheral blood mononuclear cells were collected from CLL patients before initiation of treatment on randomized trial with fludarabine and cyclophosphomide +/- rituximab.

extract_protocol: Total RNA for mRNA profiling was extracted from whole cell lysates of CLL patient samples according to the Allprep DNA/RNA mini kit (Qiagen). Quality control was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip (Agilent Technologies). RNA for gene expression profiling had a RIN of at least 7.

tag: disease state

tag: prognostic association with gep signature

value: aggressive GEP signature

tag: antibody pretreatment

value: Rituximab-naive

tag: sensitivity to chemotherapy

value: Fludarabine untreated/sensitive

tag: ecog

tag: clinical course

value: early progression


title: CLLCCAID2815

description: Gene expression data from CLL sample

value: indolent GEP signature

value: intermediate/late progression


title: CLLCCAID2823

description: Gene expression data from CLL sample


title: CLLCCAID2822

description: Gene expression data from CLL sample


title: CLLCCAID2818

description: Gene expression data from CLL sample


title: CLLCCAID2824

description: Gene expression data from CLL sample


title: CLLCCAID2816

description: Gene expression data from CLL sample


title: CLLCCAID2819

description: Gene expression data from CLL sample


title: CLLCCAID2820

description: Gene expression data from CLL sample


title: MDA-MB-231 WT DSM OE_1

source_name: Triple negative breast cancer

tag: tissue

value: Triple negative breast cancer

value: DSM Overexpression


title: CLLCCAID2813

description: Gene expression data from CLL sample


title: CLLCCAID2812

description: Gene expression data from CLL sample


title: CLLCCAID2814

description: Gene expression data from CLL sample


title: CLLCCAID2808

description: Gene expression data from CLL sample


title: CLLCCAID2805

description: Gene expression data from CLL sample


title: CLLCCAID2817

description: Gene expression data from CLL sample


title: CLLCCAID2802

description: Gene expression data from CLL sample


title: CLLCCAID2810

description: Gene expression data from CLL sample


title: CLLCCAID2800

description: Gene expression data from CLL sample


title: CLLCCAID2806

description: Gene expression data from CLL sample


title: CLLCCAID2807

description: Gene expression data from CLL sample


title: CLLCCAID2803

description: Gene expression data from CLL sample


title: CLLCCAID2809

description: Gene expression data from CLL sample


title: CLLCCAID2797

description: Gene expression data from CLL sample


title: CLLCCAID2799

description: Gene expression data from CLL sample


title: CLLCCAID2804

description: Gene expression data from CLL sample


title: CLLCCAID2798

description: Gene expression data from CLL sample


title: CLLCCAID2811

description: Gene expression data from CLL sample


title: CLLCCAID2801

description: Gene expression data from CLL sample


title: CLLCCAID2794

description: Gene expression data from CLL sample


title: CLLCCAID2795

description: Gene expression data from CLL sample


title: CLLCCAID2791

description: Gene expression data from CLL sample


title: CLLCCAID2792

description: Gene expression data from CLL sample


title: CLLCCAID2793

description: Gene expression data from CLL sample


title: CLLCCAID2796

description: Gene expression data from CLL sample


title: CLLCCAID2788

description: Gene expression data from CLL sample


title: CLLCCAID2787

description: Gene expression data from CLL sample


title: CLLCCAID2789

description: Gene expression data from CLL sample


title: CLLCCAID2790

description: Gene expression data from CLL sample


title: CLLCCAID2783

description: Gene expression data from CLL sample


title: CLLCCAID2786

description: Gene expression data from CLL sample


title: CLLCCAID2785

description: Gene expression data from CLL sample


title: CLLCCAID2781

description: Gene expression data from CLL sample


title: CLLCCAID2782

description: Gene expression data from CLL sample


title: CLLCCAID2784

description: Gene expression data from CLL sample


title: CLLCCAID2779

description: Gene expression data from CLL sample


title: CLLCCAID3064

description: Gene expression data from CLL sample


title: CLLCCAID3065

description: Gene expression data from CLL sample


title: CLLCCAID2777

description: Gene expression data from CLL sample


title: CLLCCAID3058

description: Gene expression data from CLL sample


title: CLLCCAID3059

description: Gene expression data from CLL sample


title: CLLCCAID3062

description: Gene expression data from CLL sample


title: CLLCCAID3055

description: Gene expression data from CLL sample


title: CLLCCAID2780

description: Gene expression data from CLL sample


title: CLLCCAID3056

description: Gene expression data from CLL sample


title: CLLCCAID3051

description: Gene expression data from CLL sample


title: CLLCCAID3050

description: Gene expression data from CLL sample


title: CLLCCAID2778

description: Gene expression data from CLL sample


title: CLLCCAID3060

description: Gene expression data from CLL sample


title: CLLCCAID3053

description: Gene expression data from CLL sample


title: CLLCCAID3054

description: Gene expression data from CLL sample


title: CLLCCAID3057

description: Gene expression data from CLL sample


title: CLLCCAID3049

description: Gene expression data from CLL sample


title: CLLCCAID3061

description: Gene expression data from CLL sample


title: CLLCCAID3063

description: Gene expression data from CLL sample


title: CLLCCAID3047

description: Gene expression data from CLL sample


title: CLLCCAID3044

description: Gene expression data from CLL sample


title: CLLCCAID3048

description: Gene expression data from CLL sample


title: CLLCCAID3052

description: Gene expression data from CLL sample


title: CLLCCAID3045

description: Gene expression data from CLL sample


title: CLLCCAID3043

description: Gene expression data from CLL sample


title: CLLCCAID3046

description: Gene expression data from CLL sample


title: CLLCCAID3042

description: Gene expression data from CLL sample


title: CLLCCAID3041

description: Gene expression data from CLL sample


title: CLLCCAID3040

description: Gene expression data from CLL sample


title: CLLCCAID3035

description: Gene expression data from CLL sample


title: CLLCCAID3039

description: Gene expression data from CLL sample


title: CLLCCAID3038

description: Gene expression data from CLL sample


title: CLLCCAID3027

description: Gene expression data from CLL sample


title: CLLCCAID3033

description: Gene expression data from CLL sample


title: CLLCCAID3030

description: Gene expression data from CLL sample


title: CLLCCAID3032

description: Gene expression data from CLL sample


title: CLLCCAID3037

description: Gene expression data from CLL sample


title: CLLCCAID3031

description: Gene expression data from CLL sample


title: CLLCCAID3023

description: Gene expression data from CLL sample


title: CLLCCAID3036

description: Gene expression data from CLL sample


title: CLLCCAID3028

description: Gene expression data from CLL sample


title: CLLCCAID3024

description: Gene expression data from CLL sample


title: CLLCCAID3025

description: Gene expression data from CLL sample


title: CLLCCAID3026

description: Gene expression data from CLL sample


title: CLLCCAID3034

description: Gene expression data from CLL sample


title: CLLCCAID3016

description: Gene expression data from CLL sample


title: CLLCCAID3020

description: Gene expression data from CLL sample


title: CLLCCAID3014

description: Gene expression data from CLL sample


title: CLLCCAID3017

description: Gene expression data from CLL sample


title: CLLCCAID3015

description: Gene expression data from CLL sample


title: CLLCCAID3021

description: Gene expression data from CLL sample


title: CLLCCAID3018

description: Gene expression data from CLL sample


title: CLLCCAID3019

description: Gene expression data from CLL sample


title: CLLCCAID3013

description: Gene expression data from CLL sample


title: CLLCCAID3022

description: Gene expression data from CLL sample


title: CLLCCAID3012

description: Gene expression data from CLL sample


title: CLLCCAID3011

description: Gene expression data from CLL sample


title: CLLCCAID3007

description: Gene expression data from CLL sample


title: CLLCCAID3008

description: Gene expression data from CLL sample


title: CLLCCAID2995

description: Gene expression data from CLL sample


title: CLLCCAID3003

description: Gene expression data from CLL sample


title: CLLCCAID3006

description: Gene expression data from CLL sample


title: CLLCCAID3010

description: Gene expression data from CLL sample


title: CLLCCAID2992

description: Gene expression data from CLL sample


title: CLLCCAID3000

description: Gene expression data from CLL sample


title: CLLCCAID2998

description: Gene expression data from CLL sample


title: CLLCCAID3002

description: Gene expression data from CLL sample


title: CLLCCAID3009

description: Gene expression data from CLL sample


title: CLLCCAID2994

description: Gene expression data from CLL sample


title: CLLCCAID2986

description: Gene expression data from CLL sample


title: CLLCCAID2987

description: Gene expression data from CLL sample


title: CLLCCAID2985

description: Gene expression data from CLL sample


title: CLLCCAID2983

description: Gene expression data from CLL sample


title: CLLCCAID3005

description: Gene expression data from CLL sample


title: CLLCCAID2990

description: Gene expression data from CLL sample


title: CLLCCAID3004

description: Gene expression data from CLL sample


title: CLLCCAID2996

description: Gene expression data from CLL sample


title: CLLCCAID2984

description: Gene expression data from CLL sample


title: CLLCCAID2988

description: Gene expression data from CLL sample


title: CLLCCAID2999

description: Gene expression data from CLL sample


title: CLLCCAID2982

description: Gene expression data from CLL sample


title: CLLCCAID2997

description: Gene expression data from CLL sample


title: CLLCCAID2989

description: Gene expression data from CLL sample


title: CLLCCAID2991

description: Gene expression data from CLL sample


title: CLLCCAID2980

description: Gene expression data from CLL sample


title: CLLCCAID3001

description: Gene expression data from CLL sample


title: CLLCCAID2993

description: Gene expression data from CLL sample


title: CLLCCAID2981

description: Gene expression data from CLL sample


title: CLLCCAID2976

description: Gene expression data from CLL sample


title: CLLCCAID2975

description: Gene expression data from CLL sample


title: CLLCCAID2977

description: Gene expression data from CLL sample


title: CLLCCAID2969

description: Gene expression data from CLL sample


title: CLLCCAID2974

description: Gene expression data from CLL sample


title: CLLCCAID2973

description: Gene expression data from CLL sample


title: CLLCCAID2968

description: Gene expression data from CLL sample


title: CLLCCAID2963

description: Gene expression data from CLL sample


title: CLLCCAID2966

description: Gene expression data from CLL sample


title: CLLCCAID2964

description: Gene expression data from CLL sample


title: CLLCCAID2972

description: Gene expression data from CLL sample


title: CLLCCAID2962

description: Gene expression data from CLL sample


title: CLLCCAID2967

description: Gene expression data from CLL sample


title: CLLCCAID3029

description: Gene expression data from CLL sample


title: CLLCCAID2961

description: Gene expression data from CLL sample


title: CLLCCAID2979

description: Gene expression data from CLL sample


title: CLLCCAID2978

description: Gene expression data from CLL sample


title: CLLCCAID2960

description: Gene expression data from CLL sample


title: CLLCCAID2965

description: Gene expression data from CLL sample


title: CLLCCAID2959

description: Gene expression data from CLL sample


title: CLLCCAID2958

description: Gene expression data from CLL sample


title: CLLCCAID2956

description: Gene expression data from CLL sample


title: CLLCCAID2955

description: Gene expression data from CLL sample


title: CLLCCAID2970

description: Gene expression data from CLL sample


title: CLLCCAID2953

description: Gene expression data from CLL sample


title: CLLCCAID2950

description: Gene expression data from CLL sample


title: CLLCCAID2971

description: Gene expression data from CLL sample


title: CLLCCAID2948

description: Gene expression data from CLL sample


title: CLLCCAID2951

description: Gene expression data from CLL sample


title: CLLCCAID2949

description: Gene expression data from CLL sample


title: CLLCCAID2945

description: Gene expression data from CLL sample


title: CLLCCAID2940

description: Gene expression data from CLL sample


title: CLLCCAID2954

description: Gene expression data from CLL sample


title: CLLCCAID2943

description: Gene expression data from CLL sample


title: CLLCCAID2942

description: Gene expression data from CLL sample


title: CLLCCAID2947

description: Gene expression data from CLL sample


title: CLLCCAID2952

description: Gene expression data from CLL sample


title: CLLCCAID2944

description: Gene expression data from CLL sample


title: CLLCCAID2933

description: Gene expression data from CLL sample


title: CLLCCAID2946

description: Gene expression data from CLL sample


title: CLLCCAID2934

description: Gene expression data from CLL sample


title: CLLCCAID2935

description: Gene expression data from CLL sample


title: CLLCCAID2936

description: Gene expression data from CLL sample


title: CLLCCAID2927

description: Gene expression data from CLL sample


title: CLLCCAID2939

description: Gene expression data from CLL sample


title: CLLCCAID2931

description: Gene expression data from CLL sample


title: CLLCCAID2937

description: Gene expression data from CLL sample


title: CLLCCAID2932

description: Gene expression data from CLL sample


title: CLLCCAID2928

description: Gene expression data from CLL sample


title: CLLCCAID2941

description: Gene expression data from CLL sample


title: CLLCCAID2926

description: Gene expression data from CLL sample


title: CLLCCAID2930

description: Gene expression data from CLL sample


title: CLLCCAID2929

description: Gene expression data from CLL sample


title: CLLCCAID2938

description: Gene expression data from CLL sample


title: CLLCCAID2924

description: Gene expression data from CLL sample


title: CLLCCAID2925

description: Gene expression data from CLL sample


title: CLLCCAID2923

description: Gene expression data from CLL sample


title: CLLCCAID2922

description: Gene expression data from CLL sample


title: CLLCCAID2920

description: Gene expression data from CLL sample


title: CLLCCAID2921

description: Gene expression data from CLL sample


title: CLLCCAID2912

description: Gene expression data from CLL sample


title: CLLCCAID2918

description: Gene expression data from CLL sample


title: CLLCCAID2915

description: Gene expression data from CLL sample


title: CLLCCAID2910

description: Gene expression data from CLL sample


title: CLLCCAID2917

description: Gene expression data from CLL sample


title: CLLCCAID2911

description: Gene expression data from CLL sample


title: CLLCCAID2919

description: Gene expression data from CLL sample


title: CLLCCAID2909

description: Gene expression data from CLL sample


title: CLLCCAID2907

description: Gene expression data from CLL sample


title: CLLCCAID2914

description: Gene expression data from CLL sample


title: CLLCCAID2908

description: Gene expression data from CLL sample


title: CLLCCAID2906

description: Gene expression data from CLL sample


title: CLLCCAID2905

description: Gene expression data from CLL sample


title: CLLCCAID2899

description: Gene expression data from CLL sample


title: CLLCCAID2913

description: Gene expression data from CLL sample


title: CLLCCAID2900

description: Gene expression data from CLL sample


title: CLLCCAID2903

description: Gene expression data from CLL sample


title: CLLCCAID2916

description: Gene expression data from CLL sample


title: CLLCCAID2898

description: Gene expression data from CLL sample


title: CLLCCAID2902

description: Gene expression data from CLL sample


title: CLLCCAID2897

description: Gene expression data from CLL sample


title: CLLCCAID2901

description: Gene expression data from CLL sample


title: CLLCCAID2896

description: Gene expression data from CLL sample


title: CLLCCAID2893

description: Gene expression data from CLL sample


title: CLLCCAID2891

description: Gene expression data from CLL sample


title: CLLCCAID2904

description: Gene expression data from CLL sample


title: CLLCCAID2888

description: Gene expression data from CLL sample


title: CLLCCAID2889

description: Gene expression data from CLL sample


title: CLLCCAID2890

description: Gene expression data from CLL sample


title: CLLCCAID2894

description: Gene expression data from CLL sample


title: CLLCCAID2882

description: Gene expression data from CLL sample


title: CLLCCAID2884

description: Gene expression data from CLL sample


title: CLLCCAID2892

description: Gene expression data from CLL sample


title: CLLCCAID2887

description: Gene expression data from CLL sample


title: CLLCCAID2881

description: Gene expression data from CLL sample


title: CLLCCAID2880

description: Gene expression data from CLL sample


title: CLLCCAID2895

description: Gene expression data from CLL sample


title: CLLCCAID2879

description: Gene expression data from CLL sample


title: CLLCCAID2883

description: Gene expression data from CLL sample


title: CLLCCAID2878

description: Gene expression data from CLL sample


title: CLLCCAID2886

description: Gene expression data from CLL sample


title: CLLCCAID2877

description: Gene expression data from CLL sample


title: CLLCCAID2885

description: Gene expression data from CLL sample


title: CLLCCAID2873

description: Gene expression data from CLL sample


title: CLLCCAID2876

description: Gene expression data from CLL sample


title: CLLCCAID2871

description: Gene expression data from CLL sample


title: CLLCCAID2870

description: Gene expression data from CLL sample


title: CLLCCAID2872

description: Gene expression data from CLL sample


title: CLLCCAID2869

description: Gene expression data from CLL sample


title: CLLCCAID2868

description: Gene expression data from CLL sample


title: CLLCCAID2866

description: Gene expression data from CLL sample


title: CLLCCAID2865

description: Gene expression data from CLL sample


title: CLLCCAID2863

description: Gene expression data from CLL sample


title: CLLCCAID2875

description: Gene expression data from CLL sample


title: CLLCCAID2861

description: Gene expression data from CLL sample


title: CLLCCAID2860

description: Gene expression data from CLL sample


title: CLLCCAID2859

description: Gene expression data from CLL sample


title: CLLCCAID2867

description: Gene expression data from CLL sample


title: CLLCCAID2858

description: Gene expression data from CLL sample


title: CLLCCAID2856

description: Gene expression data from CLL sample


title: CLLCCAID2848

description: Gene expression data from CLL sample


title: CLLCCAID2864

description: Gene expression data from CLL sample


title: CLLCCAID2852

description: Gene expression data from CLL sample


title: CLLCCAID2850

description: Gene expression data from CLL sample


title: CLLCCAID2855

description: Gene expression data from CLL sample


title: CLLCCAID2857

description: Gene expression data from CLL sample


title: CLLCCAID2853

description: Gene expression data from CLL sample


title: CLLCCAID2851

description: Gene expression data from CLL sample


title: CLLCCAID2854

description: Gene expression data from CLL sample


title: CLLCCAID2846

description: Gene expression data from CLL sample


title: CLLCCAID2843

description: Gene expression data from CLL sample


title: CLLCCAID2839

description: Gene expression data from CLL sample


title: CLLCCAID2847

description: Gene expression data from CLL sample


title: CLLCCAID2844

description: Gene expression data from CLL sample


title: CLLCCAID2840

description: Gene expression data from CLL sample


title: CLLCCAID2849

description: Gene expression data from CLL sample


title: CLLCCAID2842

description: Gene expression data from CLL sample


title: CLLCCAID2841

description: Gene expression data from CLL sample


title: CLLCCAID2837

description: Gene expression data from CLL sample


title: CLLCCAID2874

description: Gene expression data from CLL sample


title: CLLCCAID2838

description: Gene expression data from CLL sample


title: CLLCCAID2836

description: Gene expression data from CLL sample


title: CLLCCAID2833

description: Gene expression data from CLL sample


title: CLLCCAID2832

description: Gene expression data from CLL sample


title: CLLCCAID2835

description: Gene expression data from CLL sample


title: CLLCCAID2830

description: Gene expression data from CLL sample


title: CLLCCAID2831

description: Gene expression data from CLL sample


title: CLLCCAID2829

description: Gene expression data from CLL sample


title: CLLCCAID2774

description: Gene expression data from CLL sample


title: CLLCCAID2825

description: Gene expression data from CLL sample


title: CLLCCAID2827

description: Gene expression data from CLL sample


title: CLLCCAID2775

description: Gene expression data from CLL sample


title: CLLCCAID2828

description: Gene expression data from CLL sample


title: CLLCCAID2826

description: Gene expression data from CLL sample


title: CLLCCAID2834

description: Gene expression data from CLL sample


title: CLLCCAID2770

description: Gene expression data from CLL sample


title: CLLCCAID2764

description: Gene expression data from CLL sample


title: CLLCCAID2766

description: Gene expression data from CLL sample


title: CLLCCAID2769

description: Gene expression data from CLL sample


title: CLLCCAID2761

description: Gene expression data from CLL sample


title: CLLCCAID2776

description: Gene expression data from CLL sample


title: CLLCCAID2767

description: Gene expression data from CLL sample


title: CLLCCAID2771

description: Gene expression data from CLL sample


title: CLLCCAID2763

description: Gene expression data from CLL sample


title: CLLCCAID2768

description: Gene expression data from CLL sample


title: CLLCCAID2765

description: Gene expression data from CLL sample


title: CLLCCAID2760

description: Gene expression data from CLL sample


title: CLLCCAID2773

description: Gene expression data from CLL sample


title: CLLCCAID2762

description: Gene expression data from CLL sample


title: CLLCCAID2759

description: Gene expression data from CLL sample


title: CLLCCAID2758

description: Gene expression data from CLL sample


title: CLLCCAID2772

description: Gene expression data from CLL sample


title: CLLCCAID2755

description: Gene expression data from CLL sample


title: CLLCCAID2752

description: Gene expression data from CLL sample


title: CLLCCAID2957

description: Gene expression data from CLL sample


title: CLLCCAID2753

description: Gene expression data from CLL sample


title: CLLCCAID2756

description: Gene expression data from CLL sample


title: CLLCCAID2757

description: Gene expression data from CLL sample


title: CLLCCAID2751

description: Gene expression data from CLL sample


title: CLLCCAID2749

description: Gene expression data from CLL sample


title: CLLCCAID2754

description: Gene expression data from CLL sample


title: CLLCCAID2750

description: Gene expression data from CLL sample


title: CLLCCAID2748

description: Gene expression data from CLL sample


title: CLLCCAID2745

description: Gene expression data from CLL sample


title: CLLCCAID2743

description: Gene expression data from CLL sample


title: CLLCCAID2742

description: Gene expression data from CLL sample


title: CLLCCAID2746

description: Gene expression data from CLL sample


title: CLLCCAID2741

description: Gene expression data from CLL sample


title: CLLCCAID2862

description: Gene expression data from CLL sample


title: CLLCCAID2738

description: Gene expression data from CLL sample


title: CLLCCAID2747

description: Gene expression data from CLL sample


title: CLLCCAID2739

description: Gene expression data from CLL sample


title: CLLCCAID2740

description: Gene expression data from CLL sample


title: CLLCCAID2732

description: Gene expression data from CLL sample


title: CLLCCAID2736

description: Gene expression data from CLL sample


title: CLLCCAID2733

description: Gene expression data from CLL sample