title: HEK293T siTRMT61A RNA-seq rep2

description:
NA
DESeq2_RNAseq_HEK293T_siTRMT61AvsCtrl.csv

data_processing: kallisto v0.46.1 was used with paired-end and stranded mode to quantify reads to human GRCh38 Refseq Transcripts (from NCBI Human Genome Resources). Differential gene expression analysis was carried out by DESeq2 after tximport to convert estimated counts from kallisto to gene-level analysis.

source_name: HEK293T siTRMT61A RNA

extract_protocol:
Total RNAs was extracted from cell lines by TRIzol Reagent (Invitrogen #15596018) and Direct-zol RNA Miniprep Plus Kit with on-column DNase treatment (ZYMO #R2071).
Total RNAs (0.1-1 μg) were poly-A selected by NEBNext poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and followed by NEBNext UltraII Directional RNA Kit (NEB #7765).


title: 459s_I24_S216_L006_

status: Public on Feb 09 2022

type: SRA

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

library_source: transcriptomic

data_processing:
The Genome Analyzer Analysis Pipeline (Illumina, USA) was used to process the sequencing files of raw reads in the FASTQ format
Sequenced reads were trimmed for low-quality using Trimmomatic (default parameters)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 (default parameters)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq-count values for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Cells within chimeric heart slices were isolated by dissociation using 20 U/ml papain (Worthington Biochemical, USA). Single cells were collected using FACSAria III (Becton Dickinson)  into individual wells of 384-well plates containing Smart-Seq2 cell lysis buffer.
RNAseq libraries were prepared using compatible Tn5 and Nextera index primers (Illumina, USA) after complementary deoxyribonucleic acid (cDNA) synthesis using Smart-Seq2 protocol.

tag: cell type

value: hESC-derived ventricular progenitors

tag: cell line

tag: time

value: 24h after RFA injury

tag: genotype

tag: age


title: 459s_J10_S226_L006_


title: Wild type_Stem cells_DMSO-2

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description:
GEO_RSEM_normalised_data.txt.gz
WT3-DMSO

data_processing:
The RSEM package (version 1.2.31) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm38 release 89  transcriptome
Normalization of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.16.1)  within the R programming environment (version 3.4.1)
Genome_build: GRCm38 release 89
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

organism: Mus musculus

source_name: Organoids

growth_protocol: Cultured in WENR medium

extract_protocol:
Colon crypts were isloated with 2mM EDTA wash. Crypts embedded in matrigel were cultured in stem cell enrichment media containing Wnt-3A, Noggin, Rspondin-1 and EGF. RNA was extracted from organoids and quantified with Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO for 4hours or 5nM FICZ for 4 hours

value: Wild type

tag: treatment

value: DMSO for 4 hours

tag: tissue

value: Colon

tag: sample type

value: Organoids


title: 459s_I6_S198_L006_


title: Wild type_Stem cells_5nMFICZ-3

description:
GEO_RSEM_normalised_data.txt.gz
WT3-5nMFICZ

value: 5nM FICZ for 4 hours


title: HEK293T siTRMT61A RNA-seq rep1

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

country: USA

institute: University of Alabama

molecule: polyA RNA

growth_protocol: Cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles medium with L-glutamine (GE #SH30081.01) plus 10% fetal bovine serum (Gibco #10437028) and 1% penicillin/streptomycin (Gibco #15140122).

treatment_protocol: 10 nM final total concentration of siRNA (Dharmacon ON-TARGETplus, TRMT6: #L-017324-02-0005, TRMT61A: #L-015870-01-0005) was transfected twice with Lipofectamine RNAiMax (Thermo Fisher #13778150) and collected 96 hrs post first transfection (48 hrs post second transfection). Non-targeting control siRNA (Dharmacon #D-001810-10-20) was used as negative control.


title: HEK293T siCtrl RNA-seq rep2

source_name: HEK293T siCtrl RNA

value: siCtrl


title: 459s_I22_S214_L006_


title: 459s_I19_S211_L006_


title: 459s_I18_S210_L006_


title: 459s_I4_S196_L006_


title: HEK293T siCtrl RNA-seq rep1


title: 459s_I2_S194_L006_


title: 459s_I16_S208_L006_


title: 459s_I15_S207_L006_


title: 459s_I12_S204_L006_


title: 459s_I11_S203_L006_


title: 459s_I10_S202_L006_


title: 459s_H5_S173_L006_


title: 459s_I20_S212_L006_


title: 459s_H3_S171_L006_


title: 459s_H7_S175_L006_


title: 459s_H6_S174_L006_


title: 459s_H8_S176_L006_


title: 459s_I17_S209_L006_


title: 459s_H2_S170_L006_


title: 459s_H4_S172_L006_


title: 459s_H23_S191_L006_


title: 459s_H22_S190_L006_


title: 459s_H24_S192_L006_


title: 459s_H1_S169_L006_


title: 459s_H20_S188_L006_


title: 459s_H18_S186_L006_


title: 459s_I14_S206_L006_


title: 459s_H19_S187_L006_


title: 7_E2a-/-Lef1F/F_545_Cre

type: RNA

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

hyb_protocol: GeneChip Hybridization, Wash and Stain kit Affymetrix

scan_protocol: GeneChip Scanner 3000 Affymetrix

data_processing: CEL files were normalized using the RMA function in the R Bioconductor pacage oligo

label: biotin

source_name: E2a-/-Lef1F/F leukemia, MigR1-Cre

label_protocol: GeneChip 3' IVT Express kit Affymetrix

growth_protocol: OPTI-MEM with 10%FBS, 50mM mercaptoethanol

extract_protocol: RNA was extracted in Trizol Reagent

treatment_protocol: Retroviral infection 72 hours before havest

tag: strain

value: FVB/NJ

tag: retrovirus

tag: phenotype

value: GFP+


title: 5_E2a-/-Lef1F/F_545_MigR1

source_name: E2a-/-Lef1F/F  leukemia, MigR1


title: 8_E2a-/-Lef1F/F_545_Cre


title: 1_E2a-/-_708_MigR1

source_name: E2a-/- leukemia, MigR1


title: 6_E2a-/-Lef1F/F_545_MigR1

source_name: E2a-/-Lef1F/F leukemia, MigR1


title: 3_E2a-/-_708_Cre

source_name: E2a-/- leukemia, MigR1-Cre


title: 459s_H17_S185_L006_


title: 2_E2a-/-_708_MigR1


title: 459s_H16_S184_L006_


title: 4_E2a-/-_708_Cre


title: 459s_H15_S183_L006_


title: 459s_H13_S181_L006_


title: 459s_H21_S189_L006_


title: 459s_G8_S152_L006_


title: 459s_G7_S151_L006_


title: 459s_G9_S153_L006_


title: 459s_G4_S148_L006_


title: 459s_G3_S147_L006_


title: 459s_G6_S150_L006_


title: 459s_H10_S178_L006_


title: 459s_G2_S146_L006_


title: 459s_G23_S167_L006_


title: 459s_H11_S179_L006_


title: 459s_G5_S149_L006_


title: 459s_H12_S180_L006_


title: 459s_G22_S166_L006_


title: 459s_G21_S165_L006_


title: 459s_G20_S164_L006_


title: 459s_G1_S145_L006_


title: 459s_G19_S163_L006_


title: 459s_H14_S182_L006_


title: 459s_G14_S158_L006_


title: 459s_G17_S161_L006_


title: 459s_G16_S160_L006_


title: 459s_G11_S155_L006_


title: 459s_G10_S154_L006_


title: 459s_F7_S127_L006_


title: 459s_G24_S168_L006_


title: 459s_F8_S128_L006_


title: 459s_F4_S124_L006_


title: 459s_F6_S126_L006_


title: 459s_F5_S125_L006_


title: 459s_F2_S122_L006_


title: 459s_F22_S142_L006_


title: 459s_F1_S121_L006_


title: 459s_F23_S143_L006_


title: 459s_G18_S162_L006_


title: 459s_F19_S139_L006_


title: 459s_F3_S123_L006_


title: 459s_F20_S140_L006_


title: 459s_F21_S141_L006_


title: 459s_F17_S137_L006_


title: 459s_F24_S144_L006_


title: 459s_G12_S156_L006_


title: 459s_F16_S136_L006_


title: 459s_F18_S138_L006_


title: 459s_F9_S129_L006_


title: 459s_F14_S134_L006_


title: 459s_F13_S133_L006_


title: 459s_F11_S131_L006_


title: 459s_G13_S157_L006_


title: 459s_F12_S132_L006_


title: 459s_E8_S104_L006_


title: 459s_F10_S130_L006_


title: 459s_E9_S105_L006_


title: 459s_E7_S103_L006_


title: 459s_E6_S102_L006_


title: 459s_E2_S98_L006_


title: 459s_E4_S100_L006_


title: 459s_E3_S99_L006_


title: 459s_E22_S118_L006_


title: 459s_E23_S119_L006_


title: 459s_E17_S113_L006_


title: 459s_E20_S116_L006_


title: 459s_F15_S135_L006_


title: 459s_E16_S112_L006_


title: 459s_E18_S114_L006_


title: StageI-0809

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description: fpkm.csv

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Genome_build: hg19
Supplementary_files_format_and_content: .csv (comma separated values) file containing FPKM values of each gene in each sample.

source_name: human somatic cells during chemical reprogramming stage I

growth_protocol: Human CiPS cells and hES cells (H1 and H9) were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) and human adult skin fibroblasts (hASFs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7775). Fragmented and randomly primed 2 x150 bp pairedend libraries were sequenced using Illumina HiSeq X Ten.

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.


title: StageII-0809

description: fpkm.csv

source_name: human somatic cells during chemical reprogramming stage II


title: 459s_E1_S97_L006_


title: 459s_E14_S110_L006_


title: 459s_E21_S117_L006_


title: 459s_E12_S108_L006_


title: 459s_E15_S111_L006_


title: 459s_E13_S109_L006_


title: 459s_E10_S106_L006_


title: StageII-0618

description: fpkm.csv


title: StageIII-0618

description: fpkm.csv

source_name: human somatic cells during chemical reprogramming stage III


title: StageII-0127

description: fpkm.csv


title: StageI-0127

description: fpkm.csv


title: 459s_E11_S107_L006_


title: StageI-0618

description: fpkm.csv


title: 459s_D9_S81_L006_


title: 459s_E5_S101_L006_


title: 459s_E24_S120_L006_


title: 459s_D8_S80_L006_


title: StageIII-0330

description: fpkm.csv


title: 459s_D7_S79_L006_


title: StageII-0330

description: fpkm.csv


title: 459s_D6_S78_L006_


title: 459s_D4_S76_L006_


title: 459s_D5_S77_L006_


title: HEFs-0127-2

description: fpkm.csv

source_name: human embryonic fibroblasts


title: StageI-0330

description: fpkm.csv


title: 459s_D2_S74_L006_


title: HEFs-0330

description: fpkm.csv


title: HEFs-1117

description: fpkm.csv


title: 459s_D22_S94_L006_


title: 459s_D24_S96_L006_


title: 459s_D23_S95_L006_


title: HEFs-0928

description: fpkm.csv


title: HEFs-0127

description: fpkm.csv


title: 459s_D1_S73_L006_


title: hCiPSCs-1117-3

description: fpkm.csv

source_name: human chemically induced pluripotent stem cells


title: 459s_D18_S90_L006_


title: hCiPSCs-1117-1

description: fpkm.csv


title: hCiPSCs-0928-2

description: fpkm.csv


title: 459s_D19_S91_L006_


title: 459s_D20_S92_L006_


title: hCiPSCs-1117-2

description: fpkm.csv


title: hCiPSCs-0127-4

description: fpkm.csv


title: hCiPSCs-0928-1

description: fpkm.csv


title: hCiPSCs-0127-3

description: fpkm.csv


title: 459s_D17_S89_L006_


title: 459s_D16_S88_L006_


title: 459s_D14_S86_L006_


title: hCiPSCs-1230-4

description: fpkm.csv


title: 459s_D12_S84_L006_


title: 459s_D11_S83_L006_


title: hCiPSCs-0408-2

description: fpkm.csv


title: 459s_D10_S82_L006_


title: hCiPSCs-1217-2

description: fpkm.csv


title: 459s_C9_S57_L006_


title: hCiPSCs-1217-1

description: fpkm.csv


title: 459s_C8_S56_L006_


title: hCiPSCs-0408-1

description: fpkm.csv


title: hCiPSCs-0118-2

description: fpkm.csv


title: 459s_C7_S55_L006_


title: 459s_C6_S54_L006_


title: hCiPSCs-1003

description: fpkm.csv


title: hCiPSCs-0118-1

description: fpkm.csv


title: 459s_C5_S53_L006_


title: 459s_C2_S50_L006_


title: 459s_C3_S51_L006_


title: 459s_C24_S72_L006_


title: 459s_C22_S70_L006_


title: hCiPSCs-0809-1

description: fpkm.csv


title: hASFs-1230

description: fpkm.csv

source_name: human adult skin fibroblasts


title: hASFs-0408

description: fpkm.csv


title: hADSCs-0618

description: fpkm.csv

source_name: adult human adipose derived mesenchymal stromal cells


title: hCiPSCs-0809-3

description: fpkm.csv


title: hADSCs-1217

description: fpkm.csv


title: 459s_C21_S69_L006_


title: 459s_C20_S68_L006_


title: hADSCs-0118

description: fpkm.csv


title: 459s_C1_S49_L006_


title: hADSCs-1003

description: fpkm.csv


title: H9

description: fpkm.csv

source_name: hES cells H9


title: hADSCs-0809

description: fpkm.csv


title: 459s_C18_S66_L006_


title: H1

description: fpkm.csv

source_name: hES cells H1


title: 459s_C17_S65_L006_


title: 459s_C4_S52_L006_


title: 459s_C19_S67_L006_


title: Mist1_MTMG3

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

description: single index

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table.
NextSeq: Technical read: read1 - 3' end - the oligo barcodes are TruDrop which is positioned exactly as in (Klein et al., 2015) Biological read: read2 -UMI/cell barcode
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: colon

growth_protocol: primary cells

extract_protocol:
Human epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015. MARIS libraries are generated according to Chen et al., 2021.
CEL-Seq linear amplification of using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index)

tag: sample preparation

value: Flowsorted - MARIS - bulk

value: colon


title: 459s_C23_S71_L006_


title: hADSCs-0809-2

description: fpkm.csv


title: Mist1_MTMG2

description: single index


title: 459s_C14_S62_L006_


title: Mist1_MTMG1

description: single index


title: 459s_C13_S61_L006_


title: Mist1_YFP

description: single index


title: WT_3655_S2

description: single index

value: inDrop scRNA-seq

value: WT


title: 459s_C11_S59_L006_


title: 459s_B9_S33_L006_


title: mist_tumor2

description: single index


title: WT_2558_S2

description: single index


title: 459s_C10_S58_L006_


title: WT_3655_S1

description: single index


title: 459s_B8_S32_L006_


title: mist_tumor1

description: single index


title: 459s_B7_S31_L006_


title: lrig_tumor3

description: single index

value: Lrig1creERT2; Apcfl/fl


title: 459s_C16_S64_L006_


title: 459s_B6_S30_L006_


title: 459s_C15_S63_L006_


title: lrig_tumor1

description: single index


title: DSS_recovered2

description: single index


title: 459s_B5_S29_L006_


title: 459s_B2_S26_L006_


title: 459s_B3_S27_L006_


title: DSS_recovered3

description: single index


title: 459s_B4_S28_L006_


title: 459s_B22_S46_L006_


title: lrig_tumor2

description: single index


title: DSS_recovered1

description: single index


title: 459s_B23_S47_L006_


title: WT_2489_S1

description: single index


title: TUM_782

city: PARIS

first: Christine

last: Perret

address: 24, rue du faubourg Saint-Jacques

department: DRC

country: France

institute: Institut Cochin

data_processing:
Alignment with STAR v2.7.6a: STAR --genomeDir $reference_dir --sjdbGTFfile $reference_GTF --runThreadN 20 --readFilesIn $fq1 $fq2 --outFileNamePrefix $echantillon --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
Count with RSEM v1.3.1: rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_RSEM $resultats_RSEM
Genome_build: GRCm38, Ensembl database, Release 101
Supplementary_files_format_and_content: RSEM count

extract_protocol:
Colon tissue and colorectal tumors were removed and washed in PBS. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal tumor

value: KO

value: AOM/DSS treated

tag: disease state

value: Colorectal tumors


title: TUM_785

value: wild type


title: 459s_C12_S60_L006_

value: hESC-derived ventricular progenitors

value: 24h after RFA injury


title: 459s_B24_S48_L006_


title: 459s_B21_S45_L006_


title: 459s_B1_S25_L006_


title: TUM_775


title: 459s_B20_S44_L006_


title: 459s_B19_S43_L006_


title: TUM_768


title: AV_671

source_name: Water_WT_untreated mice

value: Untreated

value: No disease


title: 459s_B18_S42_L006_


title: TUM_767


title: 459s_B17_S41_L006_


title: AV_669

source_name: Water_KO_untreated mice


title: 459s_B16_S40_L006_


title: AV_668


title: TUM_781


title: AV_666

source_name: D7_KO_DSS treated mice

value: DSS-treated, sacrificed at D7

value: DSS-induced colitis


title: AV_665

source_name: D7_WT_DSS treated mice


title: AV_664


title: AV_663


title: AV_643


title: AV_654

source_name: D13_WT_DSS treated mice

value: DSS-treated, sacrificed at D13


title: AV_640


title: AV_670


title: AV_639

source_name: D13_KO_DSS treated mice


title: AV_637


title: 459s_B14_S38_L006_


title: 459s_B11_S35_L006_


title: 459s_B13_S37_L006_


title: 459s_A6_S6_L006_


title: 459s_B10_S34_L006_


title: 459s_A8_S8_L006_


title: 459s_B12_S36_L006_


title: 459s_A5_S5_L006_


title: 459s_A9_S9_L006_


title: AV_628


title: AV_638


title: 459s_A7_S7_L006_


title: 459s_A4_S4_L006_


title: 459s_A3_S3_L006_


title: 459s_B15_S39_L006_


title: AV_627


title: 459s_A2_S2_L006_


title: AV_624


title: AV_621


title: 459s_A24_S24_L006_


title: 459s_A23_S23_L006_


title: P02E02_587_mono_191

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
base calling: Casava
alignment: BWA MEM
transcript count: HT-seq
Genome_build: mm10

source_name: monocytes

growth_protocol: Cells were isolated from B6Tg(MMTV-PyMT)634Mul/Lellj mice bearing late stage tumors (upto 24mm diameter) or from aged matched  C57BL/6JCrl controls

extract_protocol:
Cells were sorted into 96 well place containing 2 ul of lysis buffer in each well
as per Smart-seq2 protocol (Picelli et al 2013)

treatment_protocol: 40µL of blood containing x µl 0.5M EDTA was lysed 400µL RBC lysis buffer (Biolegend), cells washed in excess 10% FCS/PBS, and lysis repeated. Cells were then blocked with 20 µL block and stained with antibodies in 30µL FACS buffer and individual live, single CD11b+ CD45+ CD115+ CD3- CD19-NK1.1- cells were FACS sorted into 96 well plates containing 2 ul of the lysis buffer (0.2% Triton X100 containing 1:20 RNASE inhibitor) per well.

value: peripheral blood


title: P02E02_587_mono_190


title: P02E02_587_mono_192


title: 459s_A21_S21_L006_


title: 459s_A1_S1_L006_


title: 459s_A20_S20_L006_


title: P02E02_587_mono_189


title: P02E02_587_mono_187


title: 459s_A19_S19_L006_


title: P02E02_587_mono_188


title: P02E02_587_mono_186


title: 459s_A17_S17_L006_


title: 459s_A16_S16_L006_


title: P02E02_587_mono_182


title: P02E02_587_mono_185


title: 459s_A18_S18_L006_


title: 459s_A11_S11_L006_


title: 459s_A13_S13_L006_


title: P02E02_587_mono_184


title: P02E02_587_mono_180


title: P02E02_587_mono_183


title: 454s_P9_S369_L006_


title: P02E02_587_mono_179


title: P02E02_587_mono_178


title: 459s_A10_S10_L006_


title: 454s_P6_S366_L006_


title: 459s_A22_S22_L006_


title: P02E02_587_mono_176


title: P02E02_587_mono_181


title: 454s_P2_S362_L006_


title: P02E02_587_mono_174


title: 454s_P23_S383_L006_


title: 454s_P24_S384_L006_


title: P02E02_587_mono_171


title: P02E02_587_mono_173


title: P02E02_587_mono_170


title: P02E02_587_mono_169


title: 454s_P7_S367_L006_


title: P02E02_587_mono_172


title: P02E02_587_mono_168


title: 454s_P18_S378_L006_


title: P02E02_587_mono_166


title: 454s_P19_S379_L006_


title: 454s_P21_S381_L006_


title: P02E02_587_mono_165


title: P02E02_587_mono_164


title: 454s_P22_S382_L006_


title: P02E02_587_mono_167


title: P02E02_587_mono_177


title: 454s_P12_S372_L006_


title: 454s_P4_S364_L006_


title: 454s_P13_S373_L006_


title: 454s_P17_S377_L006_


title: 454s_P5_S365_L006_


title: 454s_P1_S361_L006_


title: P02E02_587_mono_175


title: 454s_P3_S363_L006_


title: 454s_P10_S370_L006_


title: 454s_O6_S342_L006_


title: 454s_O5_S341_L006_


title: P02E02_587_mono_155


title: P02E02_587_mono_159


title: 454s_O24_S360_L006_


title: P02E02_587_mono_156


title: P02E02_587_mono_161


title: P02E02_587_mono_157


title: P02E02_587_mono_162


title: P02E02_587_mono_158


title: 454s_O4_S340_L006_


title: P02E02_587_mono_154


title: 454s_O22_S358_L006_


title: 454s_O23_S359_L006_


title: 454s_O1_S337_L006_


title: P02E02_587_mono_153


title: P02E02_587_mono_152


title: 454s_O21_S357_L006_


title: P02E02_587_mono_163


title: P02E02_587_mono_151


title: P02E02_587_mono_150


title: 454s_O18_S354_L006_


title: 454s_O16_S352_L006_


title: P02E02_587_mono_149


title: 454s_O17_S353_L006_


title: 454s_O15_S351_L006_


title: P02E02_587_mono_160


title: P02E02_587_mono_148


title: 454s_O2_S338_L006_


title: 454s_O14_S350_L006_


title: P02E02_587_mono_147


title: 454s_O20_S356_L006_


title: P02E02_587_mono_146


title: 454s_O13_S349_L006_


title: 454s_O12_S348_L006_


title: 454s_N9_S321_L006_


title: 454s_O10_S346_L006_


title: P02E02_587_mono_142


title: P02E02_587_mono_143


title: P02E02_587_mono_141


title: 454s_N5_S317_L006_


title: 454s_N4_S316_L006_


title: 454s_N6_S318_L006_


title: P02E02_587_mono_139


title: 454s_N7_S319_L006_


title: 454s_N3_S315_L006_


title: P02E02_587_mono_140


title: Mouse melanoma - HCmel12 - Biological replicate 2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from in vitro cultured HCmel12 mouse melanoma cells, replicate 2.

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

growth_protocol: WT31 and RET cells were maintained in RPMI 1640 media (Thermo Fisher Scientific, MA, USA) with 10 % (v/v) fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin at 37°C, 5 % CO2. HCmel12 cells were cultured in RPMI with 10 % (v/v) FCS, Hepes, ß-Mercaptoethanol, 1 % L-glutamine, 100 U/ml penicillin/streptomycin, 1 % Natrium Pyruvate and 1 % NEAA. D4M cells were maintained in Advanced DMEM/F-12 (Thermo Fisher Scientific, MA, USA) with 5 % (v/v) FCS, 100 U/ml penicillin/streptomycin and glutamine. After thawing the cells were not passaged more than three times and maximum culture time prior to RNA extraction was one week.

extract_protocol:
Total RNA from sub-confluent (50 %), cultured melanoma cells was extracted with innuPREP RNA Mini Kit (845-KS-2080250, Analytik Jena, Germany), then treated with TURBO DNA-free Kit (AM1907, Invitrogen, USA).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Cultured melanoma cells were not treated by any drugs.

value: melanoma


title: Mouse melanoma - HCmel12 - Biological replicate 5

description: Gene expression data from in vitro cultured HCmel12 mouse melanoma cells, replicate 5.


title: Mouse melanoma - HCmel12 - Biological replicate 3

description: Gene expression data from in vitro cultured HCmel12 mouse melanoma cells, replicate 3.


title: Mouse melanoma - D4M - Biological replicate 5

description: Gene expression data from in vitro cultured D4M mouse melanoma cells, replicate 5.


title: Mouse melanoma - HCmel12 - Biological replicate 1

description: Gene expression data from in vitro cultured HCmel12 mouse melanoma cells, replicate 1.


title: P02E02_587_mono_138


title: Mouse melanoma - HCmel12 - Biological replicate 4

description: Gene expression data from in vitro cultured HCmel12 mouse melanoma cells, replicate 4.


title: Mouse melanoma - D4M - Biological replicate 4

description: Gene expression data from in vitro cultured D4M mouse melanoma cells, replicate 4.


title: 454s_N2_S314_L006_


title: P02E02_587_mono_137


title: P02E02_587_mono_145


title: Mouse melanoma - D4M - Biological replicate 2

description: Gene expression data from in vitro cultured D4M mouse melanoma cells, replicate 2.


title: Mouse melanoma - D4M - Biological replicate 3

description: Gene expression data from in vitro cultured D4M mouse melanoma cells, replicate 3.


title: P02E02_587_mono_144


title: 454s_N24_S336_L006_


title: P02E02_587_mono_136


title: P02E02_587_mono_135


title: Mouse melanoma - RET - Biological replicate 4

description: Gene expression data from in vitro cultured RET mouse melanoma cells, replicate 4.

source_name: RET

value: RET


title: Mouse melanoma - D4M - Biological replicate 1

description: Gene expression data from in vitro cultured D4M mouse melanoma cells, replicate 1.


title: Mouse melanoma - RET - Biological replicate 3

description: Gene expression data from in vitro cultured RET mouse melanoma cells, replicate 3.


title: 454s_N23_S335_L006_


title: 454s_N21_S333_L006_


title: Mouse melanoma - RET - Biological replicate 2

description: Gene expression data from in vitro cultured RET mouse melanoma cells, replicate 2.


title: P02E02_587_mono_133


title: P02E02_587_mono_134


title: P02E02_587_mono_132


title: Mouse melanoma - WT31 - Biological replicate 5

description: Gene expression data from in vitro cultured WT31 mouse melanoma cells, replicate 5.


title: Mouse melanoma - WT31 - Biological replicate 1

description: Gene expression data from in vitro cultured WT31 mouse melanoma cells, replicate 1.


title: Mouse melanoma - WT31 - Biological replicate 2

description: Gene expression data from in vitro cultured WT31 mouse melanoma cells, replicate 2.


title: Mouse melanoma - B16F10 luc 2 - Biological replicate 5

description: Gene expression data from in vitro cultured B16F10 luc2 mouse melanoma cells, replicate 5.


title: 454s_N19_S331_L006_


title: P02E02_587_mono_131


title: 454s_N18_S330_L006_


title: P02E02_587_mono_130


title: Mouse melanoma - B16F10 luc 2 - Biological replicate 4

description: Gene expression data from in vitro cultured B16F10 luc2 mouse melanoma cells, replicate 4.


title: 454s_N22_S334_L006_


title: Mouse melanoma - RET - Biological replicate 5

description: Gene expression data from in vitro cultured RET mouse melanoma cells, replicate 5.


title: Mouse melanoma - WT31 - Biological replicate 3

description: Gene expression data from in vitro cultured WT31 mouse melanoma cells, replicate 3.


title: 454s_N17_S329_L006_


title: Mouse melanoma - B16F10 luc 2 - Biological replicate 3

description: Gene expression data from in vitro cultured B16F10 luc2 mouse melanoma cells, replicate 3.


title: P02E02_587_mono_129


title: 454s_N16_S328_L006_


title: NHP_459s_L13_S277_L006_

organism: Macaca fascicularis

source_name: NHP cells

value: left ventricle heart slices

value: NHP cells


title: 454s_N20_S332_L006_


title: Mouse melanoma - B16F10 luc 2 - Biological replicate 1

description: Gene expression data from in vitro cultured B16F10 luc2 mouse melanoma cells, replicate 1.


title: NHP_459s_L11_S275_L006_


title: P02E02_587_mono_127


title: 454s_N15_S327_L006_


title: Mouse melanoma - WT31 - Biological replicate 4

description: Gene expression data from in vitro cultured WT31 mouse melanoma cells, replicate 4.


title: NHP_459s_L12_S276_L006_


title: Mouse melanoma - RET - Biological replicate 1

description: Gene expression data from in vitro cultured RET mouse melanoma cells, replicate 1.


title: Mouse melanoma - B16F10 luc 2 - Biological replicate 2

description: Gene expression data from in vitro cultured B16F10 luc2 mouse melanoma cells, replicate 2.


title: NHP_459s_K9_S249_L006_


title: 454s_N13_S325_L006_


title: NHP_459s_L10_S274_L006_


title: NHP_459s_K7_S247_L006_


title: 454s_N11_S323_L006_


title: NHP_459s_K8_S248_L006_


title: NHP_459s_K6_S246_L006_


title: NHP_459s_K5_S245_L006_


title: 454s_N12_S324_L006_


title: P02E02_587_mono_126


title: 454s_N10_S322_L006_


title: P02E02_587_mono_124


title: NHP_459s_K3_S243_L006_


title: P02E02_587_mono_123


title: P02E02_587_mono_128


title: NHP_459s_K2_S242_L006_


title: NHP_459s_K23_S263_L006_


title: P02E02_587_mono_122


title: NHP_459s_K22_S262_L006_


title: 454s_M8_S296_L006_


title: 454s_M7_S295_L006_


title: P02E02_587_mono_121


title: P02E02_587_mono_120


title: NHP_459s_K24_S264_L006_


title: P02E02_587_mono_119


title: 454s_M4_S292_L006_


title: NHP_459s_K20_S260_L006_


title: NHP_459s_K21_S261_L006_


title: NHP_459s_K1_S241_L006_


title: 454s_M5_S293_L006_


title: NHP_459s_K19_S259_L006_


title: NHP_459s_K18_S258_L006_


title: P02E02_587_mono_125


title: NHP_459s_K17_S257_L006_


title: 454s_M2_S290_L006_


title: NHP_459s_K4_S244_L006_


title: NHP_459s_K15_S255_L006_


title: P02E02_587_mono_118


title: NHP_459s_K16_S256_L006_


title: 454s_M24_S312_L006_


title: P02E02_587_mono_117


title: 454s_M23_S311_L006_


title: NHP_459s_K14_S254_L006_


title: NHP_459s_K13_S253_L006_


title: NHP_459s_K12_S252_L006_


title: P02E02_587_mono_116


title: P02E02_587_mono_115


title: 454s_M22_S310_L006_


title: NHP_459s_K11_S251_L006_


title: NHP_459s_K10_S250_L006_


title: NHP_459s_J9_S225_L006_


title: P02E02_587_mono_114


title: 454s_M1_S289_L006_


title: 454s_M20_S308_L006_


title: NHP_459s_J6_S222_L006_


title: NHP_459s_J8_S224_L006_


title: NHP_459s_J5_S221_L006_


title: P02E02_587_mono_113


title: NHP_459s_J4_S220_L006_


title: 454s_M19_S307_L006_


title: NHP_459s_J24_S240_L006_


title: 454s_M18_S306_L006_


title: P02E02_587_mono_111


title: NHP_459s_J3_S219_L006_


title: P02E02_587_mono_112


title: NHP_459s_J22_S238_L006_


title: NHP_459s_J20_S236_L006_


title: P02E02_587_mono_110


title: 454s_M17_S305_L006_


title: P02E02_587_mono_109


title: NHP_459s_J19_S235_L006_


title: NHP_459s_J1_S217_L006_


title: 454s_M16_S304_L006_


title: NHP_459s_J18_S234_L006_


title: NHP_459s_J17_S233_L006_


title: NHP_459s_J15_S231_L006_


title: NHP_459s_J16_S232_L006_


title: NHP_459s_J14_S230_L006_


title: P02E02_587_mono_107


title: P02E02_587_mono_108


title: 454s_M12_S300_L006_


title: NHP_459s_J12_S228_L006_


title: NHP_459s_J11_S227_L006_


title: P02E02_587_mono_106


title: 454s_M11_S299_L006_


title: P02E02_587_mono_105


title: NHP_459s_I9_S201_L006_


title: NHP_459s_I6_S198_L006_


title: NHP_459s_I8_S200_L006_


title: P02E02_587_mono_104


title: 454s_M10_S298_L006_


title: NHP_459s_I3_S195_L006_


title: NHP_459s_I5_S197_L006_


title: P02E02_587_mono_103


title: NHP_459s_I2_S194_L006_


title: P02E02_587_mono_102


title: 460s_M9_S297_L007_

value: 48h after RFA injury


title: NHP_459s_J10_S226_L006_


title: 454s_M15_S303_L006_


title: NHP_459s_I21_S213_L006_


title: P02E02_587_mono_101


title: 454s_M13_S301_L006_


title: NHP_459s_I19_S211_L006_


title: 460s_M8_S296_L007_


title: NHP_459s_I18_S210_L006_


title: NHP_459s_I16_S208_L006_


title: P02E02_587_mono_100


title: NHP_459s_I13_S205_L006_


title: 460s_N9_S321_L007_


title: 460s_M5_S293_L007_


title: NHP_459s_I11_S203_L006_


title: 460s_M2_S290_L007_


title: NHP_459s_I10_S202_L006_


title: NHP_459s_H9_S177_L006_


title: P02E02_587_mono_098


title: P02E02_587_mono_097


title: NHP_459s_I24_S216_L006_


title: 460s_N20_S332_L007_


title: NHP_459s_H8_S176_L006_


title: P02E02_587_mono_095


title: NHP_459s_H7_S175_L006_


title: NHP_459s_H4_S172_L006_


title: NHP_459s_H6_S174_L006_


title: 460s_M20_S308_L007_


title: 460s_M12_S300_L007_


title: 460s_M1_S289_L007_


title: P02E02_587_mono_099


title: NHP_459s_H22_S190_L006_


title: NHP_459s_H3_S171_L006_


title: NHP_459s_H5_S173_L006_


title: 460s_L5_S269_L007_


title: P02E02_587_mono_094


title: NHP_459s_I15_S207_L006_


title: NHP_459s_H2_S170_L006_


title: NHP_459s_H24_S192_L006_


title: 460s_L9_S273_L007_


title: 460s_M3_S291_L007_


title: NHP_459s_H17_S185_L006_


title: NHP_459s_H16_S184_L006_


title: 460s_L2_S266_L007_


title: P02E02_587_mono_090


title: NHP_459s_H23_S191_L006_


title: NHP_459s_H15_S183_L006_


title: P02E02_587_mono_092


title: 460s_L20_S284_L007_


title: 460s_L8_S272_L007_


title: NHP_459s_H21_S189_L006_


title: NHP_459s_H20_S188_L006_


title: P02E02_587_mono_096


title: NHP_459s_H11_S179_L006_


title: NHP_459s_H10_S178_L006_


title: P02E02_587_mono_091


title: NHP_459s_H1_S169_L006_


title: NHP_459s_H18_S186_L006_


title: 460s_L3_S267_L007_


title: P02E02_587_mono_093


title: P02E02_587_mono_089


title: NHP_459s_H12_S180_L006_


title: P02E02_587_mono_086


title: NHP_459s_G7_S151_L006_


title: P02E02_587_mono_088


title: NHP_459s_G4_S148_L006_


title: P02E02_587_mono_087


title: 460s_K2_S242_L007_


title: 460s_K9_S249_L007_


title: 460s_K8_S248_L007_


title: 460s_K20_S260_L007_


title: NHP_459s_G8_S152_L006_


title: 460s_K3_S243_L007_


title: NHP_459s_G9_S153_L006_


title: P02E02_587_mono_083


title: 460s_K1_S241_L007_


title: NHP_459s_G6_S150_L006_


title: P02E02_587_mono_084


title: P02E02_587_mono_085


title: P02E02_587_mono_082


title: 460s_K16_S256_L007_


title: NHP_459s_G3_S147_L006_


title: NHP_459s_G2_S146_L006_


title: NHP_459s_G22_S166_L006_


title: NHP_459s_G21_S165_L006_


title: NHP_459s_G20_S164_L006_


title: P02E02_587_mono_081


title: 460s_K12_S252_L007_


title: NHP_459s_G1_S145_L006_


title: NHP_459s_G5_S149_L006_


title: 460s_J9_S225_L007_


title: NHP_459s_G19_S163_L006_


title: P02E02_587_mono_079


title: NHP_459s_G18_S162_L006_


title: NHP_459s_G17_S161_L006_


title: NHP_459s_G24_S168_L006_


title: 460s_J8_S224_L007_


title: NHP_459s_G23_S167_L006_


title: NHP_459s_G16_S160_L006_


title: NHP_459s_G15_S159_L006_


title: P02E02_587_mono_078


title: NHP_459s_G12_S156_L006_


title: P02E02_587_mono_077


title: 460s_J2_S218_L007_


title: P02E02_587_mono_076


title: NHP_459s_F9_S129_L006_


title: NHP_459s_G11_S155_L006_


title: P02E02_587_mono_075


title: NHP_459s_G14_S158_L006_


title: 460s_J1_S217_L007_


title: P02E02_587_mono_080


title: NHP_459s_F7_S127_L006_


title: NHP_459s_F6_S126_L006_


title: P02E02_587_mono_074


title: 460s_I9_S201_L007_


title: 460s_I2_S194_L007_


title: NHP_459s_F4_S124_L006_


title: P02E02_587_mono_073


title: NHP_459s_F3_S123_L006_


title: NHP_459s_F24_S144_L006_


title: 460s_I1_S193_L007_


title: 460s_J12_S228_L007_


title: P02E02_587_mono_072


title: NHP_459s_G10_S154_L006_


title: P02E02_587_mono_070


title: NHP_459s_F23_S143_L006_


title: P02E02_587_mono_071


title: NHP_459s_F20_S140_L006_


title: 460s_I18_S210_L007_


title: P02E02_587_mono_069


title: NHP_459s_F19_S139_L006_


title: NHP_459s_F18_S138_L006_


title: NHP_459s_F1_S121_L006_


title: 460s_C19_S67_L007_


title: NHP_459s_F22_S142_L006_


title: P02E02_587_mono_068


title: NHP_459s_F17_S137_L006_


title: NHP_459s_F5_S125_L006_


title: NHP_459s_F21_S141_L006_


title: 460s_A8_S8_L007_


title: 458s_M9_S297_L008_


title: NHP_459s_F2_S122_L006_


title: P02E02_587_mono_067


title: NHP_459s_F15_S135_L006_


title: P02E02_587_mono_066


title: NHP_459s_F16_S136_L006_


title: 460s_I20_S212_L007_


title: 460s_I16_S208_L007_


title: NHP_459s_F13_S133_L006_


title: NHP_459s_F11_S131_L006_


title: NHP_459s_F10_S130_L006_


title: NHP_459s_F12_S132_L006_


title: 458s_M8_S296_L008_


title: NHP_459s_E9_S105_L006_


title: P02E02_587_mono_064


title: 458s_M7_S295_L008_


title: NHP_459s_E6_S102_L006_


title: 458s_M6_S294_L008_


title: NHP_459s_E8_S104_L006_


title: 458s_M5_S293_L008_


title: P02E02_587_mono_063


title: NHP_459s_E2_S98_L006_


title: P02E02_587_mono_062


title: NHP_459s_E23_S119_L006_


title: P02E02_587_mono_061


title: NHP_459s_E5_S101_L006_


title: 458s_M4_S292_L008_


title: NHP_459s_E21_S117_L006_


title: P02E02_587_mono_060


title: NHP_459s_E1_S97_L006_


title: NHP_459s_E20_S116_L006_


title: 458s_M2_S290_L008_


title: NHP_459s_E18_S114_L006_


title: P02E02_587_mono_065


title: P02E02_587_mono_059


title: NHP_459s_E17_S113_L006_


title: NHP_459s_E16_S112_L006_


title: P02E02_587_mono_058


title: 458s_M24_S312_L008_


title: NHP_459s_E15_S111_L006_


title: P02E02_587_mono_057


title: NHP_459s_E12_S108_L006_


title: NHP_459s_E14_S110_L006_


title: 458s_M22_S310_L008_


title: NHP_459s_E3_S99_L006_


title: P02E02_587_mono_056


title: NHP_459s_E11_S107_L006_


title: NHP_459s_E10_S106_L006_


title: P02E02_587_mono_055


title: NHP_459s_D7_S79_L006_


title: NHP_459s_D8_S80_L006_


title: NHP_459s_D6_S78_L006_


title: 458s_M1_S289_L008_


title: P02E02_587_mono_053


title: 458s_M23_S311_L008_


title: 458s_M19_S307_L008_


title: NHP_459s_D3_S75_L006_


title: P02E02_587_mono_052


title: NHP_459s_D2_S74_L006_


title: P02E02_587_mono_051


title: 458s_M17_S305_L008_


title: NHP_459s_D24_S96_L006_


title: NHP_459s_D23_S95_L006_


title: NHP_459s_D22_S94_L006_


title: 458s_M21_S309_L008_


title: P02E02_587_mono_054


title: P02E02_587_mono_050


title: 458s_M16_S304_L008_


title: 458s_M15_S303_L008_


title: NHP_459s_D20_S92_L006_


title: NHP_459s_D19_S91_L006_


title: NHP_459s_D18_S90_L006_


title: NHP_459s_D5_S77_L006_


title: 458s_M3_S291_L008_


title: P02E02_587_mono_048


title: NHP_459s_D4_S76_L006_


title: NHP_459s_D17_S89_L006_


title: 458s_M13_S301_L008_


title: P02E02_587_mono_047


title: 458s_M12_S300_L008_


title: NHP_459s_D14_S86_L006_


title: P02E02_587_mono_046


title: NHP_459s_D13_S85_L006_


title: NHP_459s_D16_S88_L006_


title: NHP_459s_D9_S81_L006_


title: 458s_M11_S299_L008_


title: NHP_459s_D12_S84_L006_


title: P02E02_587_mono_045


title: 458s_M14_S302_L008_


title: P02E02_587_mono_049


title: NHP_459s_D1_S73_L006_


title: NHP_459s_D10_S82_L006_


title: P02E02_587_mono_044


title: 458s_L8_S272_L008_


title: 458s_L5_S269_L008_


title: P02E02_587_mono_042


title: NHP_459s_D21_S93_L006_


title: NHP_459s_C7_S55_L006_


title: NHP_459s_C8_S56_L006_


title: 458s_L4_S268_L008_


title: P02E02_587_mono_043


title: NHP_459s_C9_S57_L006_


title: NHP_459s_C5_S53_L006_


title: NHP_459s_C6_S54_L006_


title: NHP_459s_C4_S52_L006_


title: P02E02_587_mono_041


title: NHP_459s_C3_S51_L006_


title: 458s_L24_S288_L008_


title: P02E02_587_mono_040


title: 458s_L2_S266_L008_


title: NHP_459s_C2_S50_L006_


title: NHP_459s_D11_S83_L006_


title: 458s_L23_S287_L008_


title: 458s_L22_S286_L008_


title: P02E02_587_mono_039


title: P02E02_587_mono_038


title: NHP_459s_C24_S72_L006_


title: Patient11

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for 20 hours as described in the manufacturer’s protocol.

data_processing:
Samples are loaded onto the nCounter Prep Station for further purification and immobilization onto the sample cartridge. After transfer to the Digital Analyzer (MAX Analysis System, Brightcore, VUB) absolute counts are quantified.
For quality control the nSolver_analysis_software_4.0 was used. Raw counts were processed in R and normalized using the RUVSeq method adjusted for NanoString analysis. The DESeq R-package was used for differential expression analysis.
RCC files are imported in Rstudio, Normalization using RUVSeq, Statistic analysis using DESeq2

source_name: Breast cancer specimen

extract_protocol:
Total RNA extraction ocurred as described in Locy et al, 2021
After RNA quality and quantity control, 50 ng of total RNA was mixed 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the nCounter PanCancer Immune Panel.

tag: tumor grade

value: Grade 1

tag: molecular subtype

value: Luminal A-like


title: NHP_459s_C21_S69_L006_


title: P02E02_587_mono_037


title: NHP_459s_C20_S68_L006_


title: 458s_L21_S285_L008_


title: Patient12

value: Grade 2


title: NHP_459s_C22_S70_L006_


title: Patient10

value: HER2- Luminal B-like


title: 458s_L20_S284_L008_

value: hESC-derived ventricular progenitors


title: Patient9


title: 458s_L19_S283_L008_


title: 458s_L1_S265_L008_


title: Patient8


title: NHP_459s_C19_S67_L006_


title: P02E02_587_mono_036


title: P02E02_587_mono_035


title: P02E02_587_mono_033


title: Patient7


title: 458s_L18_S282_L008_


title: P02E02_587_mono_034


title: Patient5

value: Grade 3

value: TNBC


title: P02E02_587_mono_032


title: NHP_459s_C1_S49_L006_


title: NHP_459s_C18_S66_L006_


title: Patient4

value: HER2+ non-luminal


title: Patient6

value: HER2+ Luminal B-like


title: NHP_459s_C16_S64_L006_


title: 458s_L17_S281_L008_


title: P02E02_587_mono_031


title: P02E02_587_mono_030


title: 458s_L16_S280_L008_


title: NHP_459s_C14_S62_L006_


title: NHP_459s_C15_S63_L006_


title: 458s_L15_S279_L008_


title: 458s_L14_S278_L008_


title: P02E02_587_mono_029


title: MΔχ3,4_Sample3

city: Vari

first: Dimitris

middle: L.

last: Kontoyiannis

state: Attiki

address: 34 Fleming

department: Institute for Fundamental Biomedical Research

country: Greece

institute: BSRC "Alexander Fleming"

data_processing:
Sequencing on an Agilent 2100 Bioanalyzer, version 2.6
The raw .fastq files were mapped with TopHat2 version 2.1.1 against the mm10 mouse reference genome (Mus_musculus.GRCm38.p6).
Bedtools was used to convert unmapped reads .bam files to .fastq files and unmapped reads were additionally mapped with Bowtie2 version 2.3.2
The final 3’ UTR read counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq2 after removing areas that had zero counts over all the Quant-Seq samples. Differential RNA abundance analysis was performed with metaseqR2 (v.1.3.14) Bioconductor package. The raw bam files, one for each RNA-Seq sample, were summarized to a 3’UTR read counts table, using the Bioconductor package GenomicRanges. Transcripts presenting any of the following were excluded from further analysis: i) transcripts with length less than 500bp (2910 genes), ii) transcripts whose average numbers of reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp,  iii) transcripts with read counts below the median read counts of the total normalized count distribution (19325 transcripts with cutoff value 3 normalized read counts), iv) transcripts whose biotype matched the following: rRNA, IG_V_pseudogene, TR_V_pseudogene (54 transcripts), v) transcripts which in 50% of samples did not exceed 5 counts (41343 transcripts) condition-wise.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab delimited) files containing results of metaseqR2 (Bioconductor package) analysis including expression per replicate, fold changes, RPGMs (RPKs), TPMs and gene lenghts.

source_name: Mus musculus BMDM

growth_protocol: Bone Marrow Derived Macrophages from Control and MΔχ3,4 were differentiated in RPMI 1640 medium supplemented with 5% FBS, 1% penicillin/streptomycin , 1% L-glutamine  and 10% L-medium (produced by L929 cells) incubated for 10 days at 37oC with 5% CO2.

extract_protocol:
Total RNAs were extracted from cells using TRI Reagent (MRC, TR 118) according to the manufacturer’s protocol.
RNA samples were processed for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™, Vienna, Austria), according to manufacturer’s instructions.

treatment_protocol: BMDMs were activated with LPS (100ng/ml) for 4 hours.

value: LysCre+hnRNPDfl/fl

value: bone marrow derived macrophages

value: LPS 4h

tag: volume

value: 25 microls


title: MΔχ3,4_Sample2


title: P02E02_587_mono_028

value: peripheral blood


title: 458s_L10_S274_L008_


title: NHP_459s_C12_S60_L006_

value: left ventricle heart slices


title: NHP_459s_C13_S61_L006_

value: NHP cells


title: Patient3


title: NHP_459s_C11_S59_L006_


title: Patient2


title: 458s_K9_S249_L008_

value: 48h after RFA injury


title: P02E02_587_mono_026


title: P02E02_587_mono_027


title: NHP_459s_C10_S58_L006_


title: Patient1


title: MΔχ3,4_Sample1


title: 458s_K4_S244_L008_


title: Control_Sample3

value: hnRNPDfl/fl


title: P02E02_587_mono_025


title: 458s_K24_S264_L008_


title: NHP_459s_B9_S33_L006_


title: 458s_K23_S263_L008_


title: Control_Sample2


title: P02E02_587_mono_024


title: NHP_459s_B8_S32_L006_


title: 458s_L11_S275_L008_


title: Control_Sample1


title: NHP_459s_B6_S30_L006_


title: 458s_K22_S262_L008_


title: P02E02_587_mono_023


title: ESB6_28

first: Gitta

institute: The Francis Crick Institute

data_processing:
Sequence reads were mapped with TopHat to mouse mm9 genome aswell as to Ensembl transcriptome.
After the alignment, the number of reads that mapped to each gene were summarized using HTSEQ-count tool
Genome_build: GRCh37
Supplementary_files_format_and_content: read_counts_with_gene_names

source_name: spleen and lymph nodes

growth_protocol: Naïve CD4 T cells (CD4+CD25-CD44lo) were isolated from C57BL/6 mice and the cells were sort-purified (average purity 99.9.%) with MoFlo flow cytometer (Beckman Coulter) and cultured in IMDM (Sigma-Aldrich) supplemented with 5% FCS, 2x10-3 M L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 5x10-5 M β-mercaptoethanol (all Sigma) in the presence of plate-bound αCD3 (0.5 µg/ml; 2C11) and plate-bound αCD28 (5 µg/ml; 37.51; both from Large Scale Facility, Medical Research Council National Institute for Medical Research). Th17 differentiation was induced by culturing the cells in the presence of TGFβ (1 ng/ml), IL6 (20 ng/ml), IL21 (20 ng/ml) and IL1β (10 ng/ml) (R&D Systems). Part of the cells was cultured without any polarizing cytokines, in “Th0” conditions.

extract_protocol:
RNA was isolated (RNeasy Mini Kit, QIAGEN) and DNase treated (RNase-Free Dnase Set; QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three biological replicates of samples were collected at 0, 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 hours time points.

tag: culture conditions

value: IL6, TGFb, IL1b, IL21

tag: timepoint


title: NHP_459s_B5_S29_L006_

tag: cell type

tag: cell line


title: ESB6_27

value: IL6, TGFb, IL21


title: 458s_K21_S261_L008_

tag: time

tag: genotype


title: NHP_459s_B4_S28_L006_


title: NHP_459s_B3_S27_L006_


title: 458s_K1_S241_L008_

tag: age


title: P02E02_587_mono_020

tag: tissue


title: ESB6_25


title: P02E02_587_mono_019


title: NHP_459s_B2_S26_L006_


title: 458s_K19_S259_L008_


title: ESB6_24


title: ESB6_23

value: IL6, TGFb, IL1b


title: NHP_459s_B24_S48_L006_


title: 458s_K18_S258_L008_

value: hESC-derived ventricular progenitors


title: NHP_459s_B23_S47_L006_


title: ESB6_22


title: P02E02_587_mono_016


title: P02E02_587_mono_017


title: NHP_459s_B22_S46_L006_


title: ESB6_21


title: P02E02_587_mono_022


title: ESB6_26


title: 458s_K20_S260_L008_


title: NHP_459s_B20_S44_L006_


title: P02E02_587_mono_021


title: ESB6_20


title: P02E02_587_mono_014


title: 458s_K17_S257_L008_


title: NHP_459s_B1_S25_L006_


title: 458s_M20_S308_L008_


title: P02E02_587_mono_018


title: P02E02_587_mono_013


title: NHP_459s_B19_S43_L006_


title: ESB6_18


title: P02E02_587_mono_012


title: 458s_J9_S225_L008_


title: ESB6_19


title: 458s_K15_S255_L008_


title: 458s_J8_S224_L008_


title: P02E02_587_mono_011


title: ESB6_17


title: P02E02_587_mono_015


title: ESB6_16


title: NHP_459s_B17_S41_L006_


title: 458s_J7_S223_L008_


title: P02E02_587_mono_010


title: NHP_459s_B16_S40_L006_


title: NHP_459s_B18_S42_L006_


title: 458s_J5_S221_L008_


title: ESB6_15


title: NHP_459s_B15_S39_L006_


title: 458s_K14_S254_L008_


title: 458s_K12_S252_L008_


title: ESB6_14


title: P02E02_587_mono_009


title: 458s_J3_S219_L008_


title: P02E02_587_mono_008


title: NHP_459s_B13_S37_L006_


title: P02E02_587_mono_007


title: 458s_J2_S218_L008_


title: ESB6_13


title: 458s_J24_S240_L008_


title: NHP_459s_B12_S36_L006_


title: P02E02_587_mono_006


title: ESB6_12


title: NHP_459s_B11_S35_L006_


title: 458s_J23_S239_L008_


title: ESB6_11


title: P02E02_587_mono_005


title: 458s_J22_S238_L008_


title: ESB6_10


title: P02E02_587_mono_004


title: NHP_459s_A9_S9_L006_


title: NHP_459s_B10_S34_L006_


title: NHP_459s_A8_S8_L006_


title: ESB6_9


title: 458s_J21_S237_L008_


title: P02E02_587_mono_003


title: P02E02_587_mono_002


title: NHP_459s_A7_S7_L006_


title: ESB6_8


title: 458s_J1_S217_L008_


title: 458s_J18_S234_L008_


title: NHP_459s_A6_S6_L006_


title: P02E02_587_mono_001


title: ESB6_7


title: 458s_J19_S235_L008_


title: P02E02_585_mono_192


title: NHP_459s_A3_S3_L006_


title: ESB6_5


title: 458s_J17_S233_L008_


title: 458s_J16_S232_L008_


title: ESB6_4


title: P02E02_585_mono_191


title: 458s_J15_S231_L008_


title: P02E02_585_mono_190


title: ESB6_3


title: NHP_459s_A22_S22_L006_


title: 458s_J12_S228_L008_


title: ESB6_2


title: P02E02_585_mono_189


title: P02E02_585_mono_188


title: ESB6_1


title: 458s_I9_S201_L008_


title: ESB5_28


title: ESB6_6


title: NHP_459s_A1_S1_L006_


title: NHP_459s_A4_S4_L006_


title: NHP_459s_A20_S20_L006_


title: NHP_459s_A19_S19_L006_


title: ESB5_27


title: NHP_459s_A17_S17_L006_


title: P02E02_585_mono_185


title: ESB5_26


title: 458s_I7_S199_L008_


title: P02E02_585_mono_184


title: NHP_459s_A16_S16_L006_


title: NHP_459s_A21_S21_L006_


title: 458s_I6_S198_L008_


title: NHP_459s_A13_S13_L006_


title: ESB5_24


title: P02E02_585_mono_182


title: P02E02_585_mono_187


title: 458s_I24_S216_L008_


title: 458s_I23_S215_L008_


title: ESB5_23


title: 458s_I8_S200_L008_


title: NHP_454s_P9_S369_L006_


title: P02E02_585_mono_180


title: P02E02_585_mono_186


title: ESB5_22


title: P02E02_585_mono_181


title: 458s_I22_S214_L008_


title: P02E02_585_mono_179


title: NHP_454s_P8_S368_L006_


title: 458s_I21_S213_L008_


title: ESB5_25


title: 458s_I2_S194_L008_


title: 458s_I20_S212_L008_


title: NHP_454s_P4_S364_L006_


title: P02E02_585_mono_183


title: NHP_454s_P6_S366_L006_


title: P02E02_585_mono_178


title: ESB5_21


title: 458s_I19_S211_L008_


title: NHP_459s_A10_S10_L006_


title: ESB5_19


title: ESB5_18


title: ESB5_20


title: 458s_I17_S209_L008_


title: NHP_454s_P2_S362_L006_


title: P02E02_585_mono_177


title: ESB5_17


title: 458s_I16_S208_L008_


title: P02E02_585_mono_176


title: P02E02_585_mono_175


title: P02E02_585_mono_174


title: 458s_I14_S206_L008_


title: 458s_I15_S207_L008_


title: NHP_454s_P23_S383_L006_


title: ESB5_15


title: ESB5_16


title: P02E02_585_mono_173


title: NHP_454s_P20_S380_L006_


title: ESB5_14


title: 458s_I13_S205_L008_


title: ESB5_13


title: P02E02_585_mono_172


title: NHP_454s_P19_S379_L006_


title: NHP_454s_P1_S361_L006_


title: P02E02_585_mono_171


title: NHP_454s_P18_S378_L006_


title: 458s_I11_S203_L008_


title: ESB5_11


title: 458s_I10_S202_L008_


title: NHP_454s_P3_S363_L006_


title: 458s_I12_S204_L008_


title: P02E02_585_mono_169


title: ESB5_12


title: NHP_454s_P17_S377_L006_


title: NHP_454s_P24_S384_L006_


title: P02E02_585_mono_170


title: ESB5_10


title: P02E02_585_mono_168


title: NHP_454s_P16_S376_L006_


title: 458s_H3_S171_L008_


title: ESB5_9


title: ESB5_8


title: P02E02_585_mono_167


title: P02E02_585_mono_166


title: NHP_454s_P12_S372_L006_


title: 458s_H24_S192_L008_


title: ESB5_7


title: P02E02_585_mono_165


title: P02E02_585_mono_164


title: 458s_H23_S191_L008_


title: NHP_454s_P11_S371_L006_


title: NHP_454s_P10_S370_L006_


title: ESB5_5


title: 458s_H21_S189_L008_


title: P02E02_585_mono_162


title: ESB5_3


title: NHP_454s_O6_S342_L006_


title: 458s_H20_S188_L008_


title: NHP_454s_O9_S345_L006_


title: 458s_H19_S187_L008_


title: 458s_H2_S170_L008_


title: P02E02_585_mono_161


title: ESB5_2


title: 458s_H6_S174_L008_


title: 458s_H22_S190_L008_


title: P02E02_585_mono_163


title: P02E02_585_mono_160


title: NHP_454s_O24_S360_L006_


title: NHP_454s_P15_S375_L006_


title: ESB5_1


title: 458s_H18_S186_L008_


title: NHP_454s_O23_S359_L006_


title: P02E02_585_mono_158


title: 458s_H17_S185_L008_


title: ESB4_28


title: ESB5_4


title: 458s_H16_S184_L008_


title: NHP_454s_O22_S358_L006_


title: ESB4_24


title: ESB4_23


title: 458s_H13_S181_L008_


title: ESB4_25


title: NHP_454s_O1_S337_L006_


title: NHP_454s_O20_S356_L006_


title: P02E02_585_mono_153


title: ESB4_26


title: P02E02_585_mono_155


title: P02E02_585_mono_157


title: 458s_H12_S180_L008_


title: P02E02_585_mono_156


title: NHP_454s_O16_S352_L006_


title: NHP_454s_O19_S355_L006_


title: ESB4_27


title: P02E02_585_mono_152


title: ESB4_22


title: NHP_454s_O15_S351_L006_


title: 458s_H11_S179_L008_


title: ESB4_21


title: P02E02_585_mono_159


title: 460s_H9_S177_L007_

value: D3 (without RFA)


title: 460s_L1_S265_L007_


title: P02E02_585_mono_151


title: ESB5_6


title: NHP_454s_O8_S344_L006_


title: P02E02_585_mono_154


title: NHP_454s_O17_S353_L006_


title: 460s_M16_S304_L007_


title: 460s_H8_S176_L007_


title: P02E02_585_mono_150


title: P02E02_585_mono_149


title: NHP_454s_O11_S347_L006_


title: NHP_454s_O10_S346_L006_


title: ESB4_20


title: 460s_H7_S175_L007_


title: NHP_454s_O12_S348_L006_


title: 460s_H4_S172_L007_


title: NHP_454s_N9_S321_L006_


title: ESB4_18


title: ESB4_17


title: 460s_H5_S173_L007_


title: NHP_454s_N8_S320_L006_


title: 460s_H3_S171_L007_


title: P02E02_585_mono_147


title: 460s_H2_S170_L007_


title: ESB4_15


title: ESB4_19


title: NHP_454s_N4_S316_L006_


title: P02E02_585_mono_148


title: ESB4_16


title: P02E02_585_mono_146


title: NHP_454s_N6_S318_L006_


title: ESB4_14


title: P02E02_585_mono_144


title: 460s_H23_S191_L007_


title: P02E02_585_mono_145


title: 460s_H24_S192_L007_


title: NHP_454s_N3_S315_L006_


title: P02E02_585_mono_143


title: 460s_H22_S190_L007_


title: ESB4_13


title: NHP_454s_N24_S336_L006_


title: ESB4_11


title: P02E02_585_mono_142


title: ESB4_12


title: P02E02_585_mono_141


title: NHP_454s_N2_S314_L006_


title: ESB4_10


title: NHP_454s_N23_S335_L006_


title: 460s_H19_S187_L007_


title: NHP_454s_N22_S334_L006_


title: 460s_H18_S186_L007_


title: P02E02_585_mono_140


title: ESB4_9


title: 460s_H15_S183_L007_


title: NHP_454s_N20_S332_L006_


title: P02E02_585_mono_138


title: P02E02_585_mono_139


title: ESB4_8


title: NHP_454s_N1_S313_L006_


title: 460s_H13_S181_L007_


title: ESB4_7


title: P02E02_585_mono_137


title: NHP_454s_N19_S331_L006_


title: ESB4_6


title: 460s_G8_S152_L007_


title: P02E02_585_mono_136


title: ESB4_5


title: P02E02_585_mono_135


title: NHP_454s_N18_S330_L006_


title: 460s_G7_S151_L007_


title: NHP_454s_N16_S328_L006_


title: 460s_G3_S147_L007_


title: 460s_H16_S184_L007_


title: 460s_G5_S149_L007_


title: NHP_454s_N15_S327_L006_


title: ESB4_4


title: P02E02_585_mono_134


title: ESB4_3


title: NHP_454s_N17_S329_L006_


title: P02E02_585_mono_133


title: NHP_454s_N13_S325_L006_


title: ESB4_1


title: P02E02_585_mono_132


title: 460s_G2_S146_L007_


title: 460s_G24_S168_L007_


title: NHP_454s_N12_S324_L006_


title: 460s_G23_S167_L007_


title: P02E02_585_mono_130


title: ESB3_19

value: IL6, TGFb


title: ESB3_18

value: no cytokines


title: P02E02_585_mono_129


title: NHP_454s_N11_S323_L006_


title: NHP_454s_N10_S322_L006_


title: 460s_G21_S165_L007_


title: ESB3_17


title: P02E02_585_mono_128


title: ESB4_2


title: NHP_454s_M9_S297_L006_


title: P02E02_585_mono_127


title: ESB3_16


title: P02E02_585_mono_131


title: 460s_G1_S145_L007_


title: ESB3_15


title: NHP_454s_M8_S296_L006_


title: P02E02_585_mono_126


title: 460s_G17_S161_L007_


title: NHP_454s_M4_S292_L006_


title: NHP_454s_M3_S291_L006_


title: 460s_G16_S160_L007_


title: 460s_G19_S163_L007_


title: P02E02_585_mono_124


title: 460s_G22_S166_L007_


title: P02E02_585_mono_123


title: ESB3_12


title: NHP_454s_M2_S290_L006_


title: ESB3_11


title: P02E02_585_mono_122


title: P02E02_585_mono_121


title: 460s_G13_S157_L007_


title: NHP_454s_M23_S311_L006_


title: NHP_454s_M24_S312_L006_


title: ESB3_9


title: ESB3_10


title: NHP_454s_M22_S310_L006_


title: 460s_G10_S154_L007_


title: P02E02_585_mono_120


title: 460s_G12_S156_L007_


title: P02E02_585_mono_125


title: ESB3_13


title: ESB3_14


title: NHP_454s_M21_S309_L006_


title: NHP_454s_M6_S294_L006_


title: ESB3_8


title: P02E02_585_mono_119


title: P02E02_585_mono_118


title: NHP_454s_M20_S308_L006_


title: 460s_F5_S125_L007_


title: ESB3_7


title: 460s_F6_S126_L007_


title: ESB3_6


title: P02E02_585_mono_117


title: ESB3_5


title: NHP_454s_M1_S289_L006_


title: 460s_G15_S159_L007_


title: P02E02_585_mono_116


title: P02E02_585_mono_115


title: 460s_F24_S144_L007_


title: NHP_454s_M18_S306_L006_


title: ESB3_4


title: NHP_454s_M19_S307_L006_


title: 460s_F4_S124_L007_


title: P02E02_585_mono_114


title: 460s_F21_S141_L007_


title: ESB3_3


title: ESB3_2


title: P02E02_585_mono_113


title: NHP_454s_M17_S305_L006_


title: 460s_F20_S140_L007_


title: 460s_F1_S121_L007_


title: NHP_454s_M16_S304_L006_


title: ESB3_1


title: P02E02_585_mono_111


title: ESB2_18


title: NHP_454s_M15_S303_L006_


title: P02E02_585_mono_112


title: NHP_454s_M12_S300_L006_


title: ESB2_17


title: 460s_F18_S138_L007_


title: NHP_454s_M11_S299_L006_


title: ESB2_16


title: NHP_459s_L9_S273_L006_


title: P02E02_585_mono_110


title: P02E02_585_mono_109


title: 460s_F17_S137_L007_


title: 460s_F16_S136_L007_


title: NHP_454s_M10_S298_L006_


title: 460s_F19_S139_L007_


title: P02E02_585_mono_107


title: 460s_F14_S134_L007_


title: 460s_F11_S131_L007_


title: 460s_F12_S132_L007_


title: P02E02_585_mono_106


title: ESB2_14


title: NHP_459s_L7_S271_L006_


title: ESB2_13


title: ESB2_19


title: P02E02_585_mono_105


title: 460s_F10_S130_L007_


title: NHP_459s_L6_S270_L006_


title: NHP_459s_L23_S287_L006_


title: P02E02_585_mono_103


title: P02E02_585_mono_102


title: NHP_459s_L8_S272_L006_


title: NHP_459s_L24_S288_L006_


title: 460s_E9_S105_L007_


title: 460s_E2_S98_L007_


title: 460s_G20_S164_L007_


title: 460s_E8_S104_L007_


title: P02E02_585_mono_108


title: ESB2_10


title: NHP_459s_L22_S286_L006_


title: P02E02_585_mono_100


title: ESB2_9


title: P02E02_585_mono_104


title: 460s_E24_S120_L007_


title: ESB2_8


title: NHP_459s_L19_S283_L006_


title: ESB2_15


title: ESB2_7


title: P02E02_585_mono_101


title: ESB2_11


title: NHP_459s_L20_S284_L006_


title: P02E02_585_mono_099


title: 460s_E23_S119_L007_


title: NHP_459s_L18_S282_L006_


title: 460s_E22_S118_L007_


title: 460s_E20_S116_L007_


title: ESB2_6


title: 460s_E19_S115_L007_


title: NHP_459s_L16_S280_L006_


title: NHP_459s_L17_S281_L006_


title: ESB2_5


title: P02E02_585_mono_096


title: NHP_459s_L21_S285_L006_


title: 460s_E18_S114_L007_


title: P02E02_585_mono_095


title: P02E02_585_mono_097


title: ESB2_12


title: P02E02_585_mono_093


title: 460s_E16_S112_L007_


title: ESB2_3


title: P02E02_585_mono_092


title: S-1

first: Weijian

last: YAO

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

department: Renal division

institute: Peking university first hospital

data_processing:
The standard Chromium’s Cell Ranger pipeline (version 3.1.0) to align the raw sequence reads according to the reference genome (mm10-2.1.0) using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: cell barcode files
Supplementary_files_format_and_content: gene files
Supplementary_files_format_and_content: gene-barcode counts

source_name: Spleen

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA.Cells were resuspended to a final cell concentration of 700~1200 cells/μl with more than 85% viability. 8,000-12,000 cells were captured in droplets. After the reverse transcription step, emulsions were broken and barcoded-cDNA was purified with Dynabeads, followed by PCR amplification (at 98°C for 45 sec; at 98°C for 20 sec, 67°C for 30 sec, 72°C for 1 min with 13-18 cycles; at 72°C for 1 min). Amplified cDNA was then used for 3’ gene expression library construction.
RNA libraries were prepared with Chromium Single cell v2 or v3 Kits according to the manufacturer's protocol

tag: treatment

value: unilateral ischemia-reperfusion renal injury (uIRI) 1day

value: Spleen

tag: genptype

value: Wild type


title: P02E02_585_mono_094

tag: strain


title: P02E02_585_mono_098


title: ESB2_2


title: 460s_E17_S113_L007_


title: NHP_459s_L14_S278_L006_


title: ESB2_1


title: ESB2_4


title: S-3

value: unilateral ischemia-reperfusion renal injury (uIRI) 3day


title: 460s_E15_S111_L007_


title: ESB1_19


title: ESB1_18


title: S-0

value: untreated


title: P02E02_585_mono_091

value: peripheral blood


title: NHP_459s_L15_S279_L006_

value: left ventricle heart slices


title: ESB1_17


title: P02E02_585_mono_089


title: 460s_E11_S107_L007_


title: 460s_E13_S109_L007_


title: KM-1

source_name: Kidney

value: Kidney


title: P02E02_585_mono_088


title: KM-3


title: 460s_E10_S106_L007_


title: KM-0


title: 460s_D8_S80_L007_


title: ESB1_13


title: ESB1_14


title: ESB1_15


title: 460s_E14_S110_L007_


title: 460s_D6_S78_L007_


title: P02E02_585_mono_087


title: 460s_D2_S74_L007_


title: P02E02_585_mono_090


title: ESB1_12


title: P02E02_585_mono_085


title: KSHV lytic t24 rep2 [Trex24_2BF]

city: Leeds

first: Adrian

last: Whitehouse

address: Leeds

department: 1School of Molecular and Cellular Biology

institute: University of Leeds

data_processing:
Quality filtered (Q < 20), and adapter trimmed reads (Trimmomatic v0.39) [59] were aligned to the GRCh38/hg38 assembly of the human genome using Bowtie2 (V 2.4.2).
The counts in different genomic features were generated using HTSeq (v0.11.1) [62] on human microRNA annotations (miRbase.org).
Expression levels were normalised by “counts per million” (CPM).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include per microRNA counts for each sample.

source_name: KSHV lytic t24

growth_protocol: TREx-BCBL1-Rta cells were cultured in RPMI1640 with glutamine (Gibco), supplemented with 10% Foetal Bovine Serum (FBS) (Gibco), 1% P/S (Gibco) and 100 µg/mL hygromycin B (ThermoFisher)

extract_protocol:
Total RNA was extracted from TREx-BCBL-1s at 0, 16 and 24 hours post lytic induction.
Small RNA libraries were prepared using the TruSeq Small RNA Library Prep Kit (Illumina).

treatment_protocol: TREx-BCBL1-RTA cells, a B cell lymphoma cell line latently infected with KSHV engineered to contain a doxycycline inducible myc-RTA. Virus lytic replication was induced via addition of 2 µg/mL doxycycline hyclate (Sigma-Aldrich)

value: B-lymphocyte

value: KSHV-latently infected

value: KSHV lytic rep 24

tag: molecule subtype

value: small RNA


title: KSHV lytic t24 rep1 [Trex24_1BF]


title: KSHV lytic t24 rep3 [Trex24_3BF]


title: ESB1_16


title: KSHV lytic t16 rep3 [Trex16_3BF]

source_name: KSHV lytic t16

value: KSHV lytic rep 16


title: ESB1_11


title: P02E02_585_mono_084


title: 460s_D22_S94_L007_

value: hESC-derived ventricular progenitors


title: ESB1_10


title: P02E02_585_mono_083


title: KSHV lytic t16 rep2 [Trex16_2BF]


title: ESB1_9


title: P02E02_585_mono_082


title: KSHV lytic t16 rep1 [Trex16_1BF]


title: P02E02_585_mono_086


title: 460s_D21_S93_L007_

value: D3 (without RFA)


title: ESB1_8


title: 460s_D1_S73_L007_


title: ESB1_7

value: IL6, TGFb


title: KSHV lytic t0 rep3 [Trex0_3BF]

source_name: KSHV lytic t0

value: KSHV lytic rep 0


title: 460s_D17_S89_L007_


title: P02E02_585_mono_080


title: KSHV lytic t0 rep2 [Trex0_2BF]


title: 460s_D15_S87_L007_


title: ESB1_6

value: no cytokines


title: KSHV lytic t0 rep1 [Trex0_1BF]


title: P02E02_585_mono_078


title: 460s_D14_S86_L007_


title: 460s_D13_S85_L007_


title: P02E02_585_mono_079


title: P02E02_585_mono_077


title: P02E02_585_mono_076


title: ESB1_3


title: 460s_D24_S96_L007_


title: P02E02_585_mono_081


title: 460s_D12_S84_L007_


title: 460s_C9_S57_L007_


title: ESB1_2


title: 460s_C8_S56_L007_


title: ESB1_1


title: P02E02_585_mono_074


title: 460s_C4_S52_L007_


title: ESB1_4


title: P02E02_585_mono_072


title: P02E02_585_mono_073


title: 460s_C3_S51_L007_


title: P02E02_585_mono_071


title: 460s_D11_S83_L007_


title: P02E02_585_mono_075


title: gastric DLBCL, case 7 sensitive to HPET

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

country: Taiwan

institute: National Taiwan University

description: Gene expression at the time of diagnosis, before treatment

hyb_protocol: 1.5 ug of Cy3-labelled linearly amplified cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 microliter containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 microliter of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (Agilent G4858A-039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SurScan Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent).
Normalized signal intensity according to the GeneSpring GX program (Agilent)

source_name: stomach, gastric lymphoma, pretreatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: not appicable

extract_protocol: Total RNA was extracted from formain-fixed paraffin-embedded tissue blocks with the Trizol method, and quantitaetd with a Nanodrop spectrophotometer.

treatment_protocol: not appicable

value: gastric DLBCL

tag: phenotype

value: sensitive to HPET


title: 460s_C24_S72_L007_


title: P02E02_585_mono_070


title: 460s_C23_S71_L007_


title: 3hr post-neomycin

city: Kansas City

first: Tatjana

last: Piotrowski

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome (GRCz10), ensembl release 91, using the Cell Ranger (version 2.1.1) pipeline from 10x genomics using the default settings.
Genome_build: danRer10
Supplementary_files_format_and_content: h5 files contain the UMI counts for each cell.

organism: Danio rerio

source_name: neuromast

extract_protocol:
Presumptive neuromast cells (GFP+) were isolated by FACS.
Standard 10x genomics scRNA-seq protocol using v2 chemistry
Droplet based scRNA-seq

value: neuromast

tag: treatment/time point

value: 3hr post-neomycin


title: 1hr post-neomycin

value: 1hr post-neomycin


title: 10hr post-neomycin

value: 10hr post-neomycin


title: 5hr post-neomycin

value: 5hr post-neomycin


title: 30min post-neomycin

value: 30min post-neomycin


title: P02E02_585_mono_069

value: peripheral blood


title: gastric DLBCL, case 8 sensitive to HPET


title: P02E02_585_mono_068


title: P02E02_585_mono_067


title: 0min post-neomycin

value: 0min post-neomycin


title: homeo

value: homeo


title: gastric DLBCL, case 5 sensitive to HPET


title: gastric DLBCL, case 2 sensitive to HPET


title: 460s_C22_S70_L007_


title: 460s_C21_S69_L007_


title: gastric DLBCL, case 3 sensitive to HPET


title: gastric DLBCL, case 1 sensitive to HPET


title: gastric DLBCL, case 8 resistant to HPET

value: resistant to HPET


title: gastric DLBCL, case 7 resistant to HPET


title: P02E02_585_mono_066


title: 460s_C20_S68_L007_

value: hESC-derived ventricular progenitors


title: gastric DLBCL, case 6 resistant to HPET


title: 460s_C18_S66_L007_

value: D3 (without RFA)


title: 460s_C1_S49_L007_


title: P02E02_585_mono_065


title: P02E02_585_mono_064


title: gastric DLBCL, case 5 resistant to HPET


title: ESB1_5

value: IL6, TGFb


title: P02E02_585_mono_063


title: TCR-seq of homo sapiens:HD15_S4_beta

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Joining R1 and R2 reads from the paired end sequencing
Demultiplexing of the sequencing results according to the barcodes used for samples multiplexing
Analysis of the TCR clonotypes was carried out using the MiXCR software (version 3.0.5)

source_name: Healthy donor PBMCs:HD15

extract_protocol:
Complementarity determining region (CDR) 3 sequences of TCR alpha and beta chains were amplified by using a modified RACE approach
Total RNA extracted from WT1-specific T cell cultures was reverse transcribed and amplified using primers specific for α/β chain constant regions and for the template switching sequence added during cDNA synthesis. A double barcoded strategy was used: each individual sample was unequivocally tagged with a barcoded fusion primer specific for the constant TCR genes in addition to the barcoded template switching primer used during cDNA synthesis. PCR amplicons were purified using the AmPure beads (Beckman Coulter) and sequenced with the Illumina MiSeq_600v3.
Illumina MiSeq_600v3: paired end

treatment_protocol: WT1-specific T cells were collected at different time points over the co-culture time frame and RNA was extracted by using the Arcturus Pico Pure RNA extraction kit (Life Technology).

tag: time point

value: 4 stimulations with WT1 pool


title: 460s_C15_S63_L007_

first: Gianluca

institute: Klinikum rechts der Isar – Technical University Munich


title: P02E02_585_mono_062


title: T cells-Naïve-rep2

city: San Diego

first: John

last: Sedy

state: CA

address: 10770 Wateridge Cir

institute: AnaptysBio

data_processing:
Illumina HiSeq 1500 was used to process  RNA samples and generate fastq files
Raw fastq files were indexed with Mus_mus GRC_m38 using Salmon (Patro, et al., 2017. Nature Methods) to generate quant.sf files
Indexed quant.sf files were further collated and analyzed using DESeq2
Genome_build: Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: quant.sf files generated using Salmon

source_name: CD4+ T cells

extract_protocol:
Cells were harvested for total RNA using Qiagen RNAeasy miniprep kit and frozen for later construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Purified lymphocytes were stimulated with primary activation antibodies (anti-CD3 or anti-IgM/G), soluble IFNb, or aldehyde sulfate beads coupled to primary stimulus and Ctrl Ig or anti-Btla for 18 hours.

tag: immunization

tag: activation

value: CD4+ T cells


title: P02E02_585_mono_061


title: gastric DLBCL, case 6 sensitive to HPET

value: gastric DLBCL


title: gastric DLBCL, case 4 resistant to HPET


title: U2932 transfected with miR-200c

description: Gene expression in U2932 transfected with a miR-200c expressing EGFP+ vector

hyb_protocol: 1.5 μg of Cy3-labelled linearly amplified cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 microliter containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 microliter of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (Agilent G4858A-039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent).
The raw data was used directly in our manuscript, so the raw data and the processed data are identical.

source_name: B-cell lymphoma cell line U2932

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: U2932 cells were grown with RPMI160 medium.

extract_protocol: Total RNA was extracted with the Trizol method, and quantitated with a Nanodrop spectrophotometer.

treatment_protocol: For transfection experiments, 20-40 μg of EGFP-expressing plasmid was electroporated into the cells, followed by selection with G418 until greater than 90% were positive for EGFP.

value: cell line derived from diffuse large B-cell lymphoma

value: transfected with miR-200c


title: 460s_C14_S62_L007_

last: Santamaria

data_processing:
The Genome Analyzer Analysis Pipeline (Illumina, USA) was used to process the sequencing files of raw reads in the FASTQ format
Sequenced reads were trimmed for low-quality using Trimmomatic (default parameters)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 (default parameters)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq-count values for each Sample

extract_protocol:
Cells within chimeric heart slices were isolated by dissociation using 20 U/ml papain (Worthington Biochemical, USA). Single cells were collected using FACSAria III (Becton Dickinson)  into individual wells of 384-well plates containing Smart-Seq2 cell lysis buffer.
RNAseq libraries were prepared using compatible Tn5 and Nextera index primers (Illumina, USA) after complementary deoxyribonucleic acid (cDNA) synthesis using Smart-Seq2 protocol.


title: U2932 transfected with miR-200a

description: Gene expression in U2932 transfecetd with a miR-200a expressing EGFP+ vector

value: B-cell lymphoma cell line U2932

value: transfected with miR-200a


title: U2932 transfected with miR-200b

description: Gene expression in U2932 transfecetd with a miR-200b expressing EGFP+ vector

value: transfected with miR-200b


title: gastric DLBCL, case 3 resistant to HPET


title: gastric DLBCL, case 1 resistant to HPET


title: TCR-seq of homo sapiens:HD14_S8_beta

source_name: Healthy donor PBMCs:HD14

value: 8 stimulations with WT1 pool


title: T cells-Naïve-rep1


title: P02E02_585_mono_060

source_name: monocytes


title: TCR-seq of homo sapiens:HD14_S5_beta

value: 5 stimulations with WT1 pool


title: 460s_C12_S60_L007_


title: T cells-Naïve-rep3-2


title: 460s_C16_S64_L007_


title: 460s_C13_S61_L007_


title: T cells-Naïve-rep3-1


title: 460s_C11_S59_L007_


title: TCR-seq of homo sapiens:HD13_S6_beta

source_name: Healthy donor PBMCs:HD13

value: 6 stimulations with WT1 pool


title: P02E02_585_mono_059

value: peripheral blood


title: TCR-seq of homo sapiens:HD14_S4_beta


title: P02E02_585_mono_058


title: U2932 transfected with an empty vector

description: Gene expression in U2932 trasnfected with an EGFP vector

value: transfected with an empty vector


title: T cells-Naïve+anti-CD3+CtrlIg+IFNb-rep2

value: IFNb


title: gastric DLBCL, case 2 resistant to HPET

value: resistant to HPET


title: TCR-seq of homo sapiens:HD13_S5_beta


title: P02E02_585_mono_057


title: 460s_B9_S33_L007_

value: hESC-derived ventricular progenitors

value: D3 (without RFA)


title: T cells-Naïve+anti-CD3+CtrlIg+IFNb-rep1


title: 460s_B8_S32_L007_


title: P02E02_585_mono_056


title: 460s_B5_S29_L007_


title: TCR-seq of homo sapiens:HD12_S4_beta

source_name: Healthy donor PBMCs:HD12

value: 4 stimulations with WT1 pool


title: T cells-Naïve+anti-CD3+CtrlIg+IFNb-rep3-2

value: CD4+ T cells


title: 460s_B2_S26_L007_


title: T cells-Naïve+anti-CD3+CtrlIg+IFNb-rep3-1


title: P02E02_585_mono_054


title: TCR-seq of homo sapiens:HD10_S6_beta

source_name: Healthy donor PBMCs:HD10


title: P02E02_585_mono_053


title: 460s_B24_S48_L007_


title: 460s_B23_S47_L007_


title: T cells-Naïve+anti-CD3+CtrlIg-rep3-2


title: TCR-seq of homo sapiens:HD7A_S6_beta

source_name: Healthy donor PBMCs:HD7


title: T cells-Naïve+anti-CD3+CtrlIg-rep3-1


title: 460s_B22_S46_L007_


title: TCR-seq of homo sapiens:HD7B_S7_beta

value: 7 stimulations with WT1 pool


title: P02E02_585_mono_052


title: T cells-Naïve+anti-CD3+CtrlIg-rep2


title: T cells-Naïve+anti-CD3+CtrlIg-rep1


title: P02E02_585_mono_051


title: 460s_B21_S45_L007_


title: TCR-seq of homo sapiens:HD12_S6_beta


title: 460s_B1_S25_L007_


title: T cells-Naïve+anti-CD3+anti-Btla+IFNb-rep3-1

value: anti-Btla


title: P02E02_585_mono_049


title: TCR-seq of homo sapiens:HD6_S3_beta

source_name: Healthy donor PBMCs:HD6

value: 3 stimulations with WT1 pool


title: T cells-Naïve+anti-CD3+anti-Btla+IFNb-rep3-2


title: 460s_B19_S43_L007_


title: TCR-seq of homo sapiens:HD7_S4_beta


title: P02E02_585_mono_055


title: TCR-seq of homo sapiens:HD7_S3_beta


title: P02E02_585_mono_048


title: 460s_B18_S42_L007_


title: gastric DLBCL, case 4 sensitive to HPET

value: gastric DLBCL

value: sensitive to HPET


title: P02E02_585_mono_047


title: TCR-seq of homo sapiens:HD5_S5_beta

source_name: Healthy donor PBMCs:HD5


title: T cells-Naïve+anti-CD3+anti-Btla+IFNb-rep1


title: P02E02_585_mono_046


title: P02E02_585_mono_050


title: TCR-seq of homo sapiens:HD4B_S6_beta

source_name: Healthy donor PBMCs:HD4


title: P02E02_585_mono_045


title: T cells-Naïve+anti-CD3+anti-Btla-rep3-2


title: TCR-seq of homo sapiens:HD6_S6_beta


title: T cells-Naïve+anti-CD3+anti-Btla-rep3-1


title: P02E02_585_mono_044


title: 460s_B15_S39_L007_


title: P02E02_585_mono_043


title: P02E02_585_mono_042


title: TCR-seq of homo sapiens:HD4A_S6_beta


title: T cells-Naïve+anti-CD3+anti-Btla-rep2


title: 460s_B13_S37_L007_


title: 460s_B10_S34_L007_


title: T cells-Naïve+anti-CD3+anti-Btla-rep1


title: TCR-seq of homo sapiens:HD4B_S7_beta


title: P02E02_585_mono_041


title: T cells-Naïve+anti-CD3+anti-Btla+IFNb-rep2-1


title: 460s_B17_S41_L007_


title: TCR-seq of homo sapiens:HD3_S10_beta

source_name: Healthy donor PBMCs:HD3

value: 10 stimulations with WT1 pool


title: T cells-Naïve+anti-CD3+anti-Btla+IFNb-rep2-2


title: 460s_B16_S40_L007_


title: T cells-EAE-rep3-2

value: EAE


title: 460s_A9_S9_L007_


title: TCR-seq of homo sapiens:HD3_S6_beta


title: T cells-EAE-rep3-1


title: TCR-seq of homo sapiens:HD3_S5_beta

value: 5 stimulations with WT1 pool


title: 460s_A6_S6_L007_


title: P02E02_585_mono_040


title: TCR-seq of homo sapiens:HD4A_S7_beta


title: T cells-EAE-rep2


title: P02E02_585_mono_039


title: TCR-seq of homo sapiens:HD1_S11_beta

source_name: Healthy donor PBMCs:HD1

value: 11 stimulations with WT1 pool


title: TCR-seq of homo sapiens:HD4_S4_beta


title: 460s_A4_S4_L007_


title: 460s_B14_S38_L007_


title: P02E02_585_mono_038

value: peripheral blood


title: P02E02_585_mono_037


title: T cells-EAE-rep1


title: 460s_A2_S2_L007_


title: TCR-seq of homo sapiens:HD15_S4_alpha


title: T cells-EAE+anti-CD3+CtrlIg+IFNb-rep2


title: 460s_A24_S24_L007_


title: P02E02_585_mono_034


title: 460s_A21_S21_L007_


title: P02E02_585_mono_036


title: TCR-seq of homo sapiens:HD14_S8_alpha

value: 8 stimulations with WT1 pool


title: TCR-seq of homo sapiens:HD14_S5_alpha


title: T cells-EAE+anti-CD3+CtrlIg-rep3


title: T cells-EAE+anti-CD3+CtrlIg+IFNb-rep3

value: IFNb


title: 460s_A23_S23_L007_


title: T cells-EAE+anti-CD3+CtrlIg+IFNb-rep1


title: P02E02_585_mono_035


title: P02E02_585_mono_033


title: TCR-seq of homo sapiens:HD14_S4_alpha


title: TCR-seq of homo sapiens:HD13_S6_alpha

value: 6 stimulations with WT1 pool


title: 460s_A20_S20_L007_

value: hESC-derived ventricular progenitors


title: 460s_A1_S1_L007_

value: D3 (without RFA)


title: P02E02_585_mono_032


title: P02E02_585_mono_031


title: TCR-seq of homo sapiens:HD13_S5_alpha


title: 460s_A19_S19_L007_


title: TCR-seq of homo sapiens:HD1_S9_beta

value: 9 stimulations with WT1 pool


title: T cells-EAE+anti-CD3+CtrlIg-rep1

value: CD4+ T cells


title: T cells-EAE+anti-CD3+anti-Btla-rep3


title: 460s_A18_S18_L007_


title: P02E02_585_mono_030


title: TCR-seq of homo sapiens:HD12_S6_alpha


title: T cells-EAE+anti-CD3+anti-Btla+IFNb-rep3


title: 460s_A17_S17_L007_


title: TCR-seq of homo sapiens:HD12_S4_alpha

value: 4 stimulations with WT1 pool


title: TCR-seq of homo sapiens:HD10_S6_alpha


title: 460s_A13_S13_L007_


title: P02E02_585_mono_028


title: T cells-EAE+anti-CD3+anti-Btla+IFNb-rep1

value: anti-Btla


title: T cells-EAE+anti-CD3+CtrlIg-rep2


title: T cells-EAE+anti-CD3+anti-Btla+IFNb-rep2


title: P02E02_585_mono_029


title: P02E02_585_mono_027


title: 460s_A11_S11_L007_


title: TCR-seq of homo sapiens:HD7A_S6_alpha


title: T cells-EAE+anti-CD3+anti-Btla-rep1


title: P02E02_585_mono_025


title: TCR-seq of homo sapiens:HD7B_S7_alpha

value: 7 stimulations with WT1 pool


title: T cells-EAE+anti-CD3+anti-Btla-rep2


title: B Cells-EAE+anti-IgM/G+anti-Btla+IFNb-rep3

source_name: B cells

value: anti-IgM/G

value: B cells


title: P02E02_585_mono_026


title: P02E02_585_mono_024


title: B Cells-EAE+anti-IgM/G+anti-Btla-rep3


title: SGs_9_T

city: Guildford

first: Nicolas

last: Locker

state: Surrey

address: Faculty of Health and Medical Sciences

department: School of Biosciences and Medicine

institute: University of Surrey

description:
Paracrine
CountsMatrix.csv

data_processing:
Quality checks were performed via FastQC (version 0.11.4). Trimmomatic tool (version 0.32) was used for quality trimming and clipping of adapters and repeated sequences.
Reads were mapped to the human genome annotation (Gencode Human GRCh38.p12 assembly genome and comprehensive gene annotation, release 29) using the RNA-seq aligner STAR (version 2.5.5b).
The function featureCounts from the R package Rsubread (version 1.30.9) was used to assign mapped sequencing reads to genomic features. Genomic features were defined by the tool’s in-built NCBI RefSeq annotations for the hg38 genome.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: CountsMatrix.csv: Matrix of raw counts in comma separated values (CSV) file format. Columns corresponding to samples and rows corresponding to genes. Row names are Entrez IDs.

source_name: U2OS cells, osteosarcoma

extract_protocol:
G3BP1-GFP- U20S cells were grown O/N on 15cm dishes 80-90% confluent and incubated with 8ml of virus free supernatant for 1h, then washed twice with warm DMEM and scraped out and spun down at 1,500g 10 min. The cell pellet was either snap freeze or resuspended in 1ml of lysis buffer (50mM Tris HCl pH 7.4, 100mM Potassium Acetate, 2mM Magnesium Acetate, 0.5mM DTT, 0.5% NP40, 1 complete mini EDTA free protease inhibitor tablet/ 50ml of lysis buffer) and syringe lysis using 25G 5/8 needle on ice seven time and spun at 300g, for 5min at 4C. The supernatant was transferred and centrifuged again at 18000g for 20min at 4C. The supernatant was discarded the pellet was resuspend pellet in 1ml of SG lysis buffer and spun again at 18000g for 20min at 4C. The pellet was resuspended in 300ul lysis buffer (granule-enriched fraction). The RNA was extracted with Trizol following the manufactural procedure.
The precipitated RNA was used by Novogene to constitute the cDNA library using oligo(dT) beads, then was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. The Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and quantifying by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were fed into Illumina machines according to activity and expected data volume.

treatment_protocol: One replicated was treated with the virus free supernatant for 1h.

value: GFP-G3BP1 U2OS

value: Treated

tag: fraction

value: Granule RNAs


title: SGs_6_T

description:
Paracrine
CountsMatrix.csv


title: TCR-seq of homo sapiens:HD6_S6_alpha


title: P02E02_585_mono_023


title: SGs_3_T

description:
Paracrine
CountsMatrix.csv


title: P02E02_585_mono_022


title: TCR-seq of homo sapiens:HD5_S5_alpha

value: 5 stimulations with WT1 pool


title: B Cells-EAE+anti-IgM/G+CtrlIg-rep3

value: EAE


title: TCR-seq of homo sapiens:HD7_S4_alpha


title: BJAB transfected with miR-155

description: Gene expression in BJAB transfected with a miR-155 expressing EGFP+ vector

source_name: B-cell lymphoma cell line BJAB

growth_protocol: BJAB cells were grown with RPMI160 medium.

value: B-cell lymphoma cell line BJAB

value: cell line derived from diffuse large B-cell lymphoma

value: transfected with miR-155


title: P02E02_585_mono_021

value: peripheral blood


title: TCR-seq of homo sapiens:HD4B_S7_alpha


title: B Cells-EAE+anti-IgM/G+anti-Btla+IFNb-rep2

value: IFNb


title: B Cells-EAE-rep3


title: SGs_4_C

description: CountsMatrix.csv

value: Untreated


title: P02E02_585_mono_020


title: BJAB transfected with an empty vector

description: Gene expression in BJAB transfected with an EGFP vector

value: transfected with an empty vector


title: TCR-seq of homo sapiens:HD4B_S6_alpha

value: 6 stimulations with WT1 pool


title: T_9_T

description:
Paracrine
CountsMatrix.csv

value: Total RNA


title: SGs_1_C

description: CountsMatrix.csv


title: TCR-seq of homo sapiens:HD7_S3_alpha

value: 3 stimulations with WT1 pool


title: TCR-seq of homo sapiens:HD4A_S7_alpha

value: 7 stimulations with WT1 pool


title: P02E02_585_mono_018


title: P02E02_585_mono_017


title: T_6_T

description:
Paracrine
CountsMatrix.csv


title: T_3_T

description:
Paracrine
CountsMatrix.csv


title: B Cells-EAE+anti-IgM/G+CtrlIg+IFNb-rep2

value: anti-IgM/G

value: B cells


title: B Cells-EAE+anti-IgM/G+CtrlIg+IFNb-rep3


title: SGs_7_C

description: CountsMatrix.csv

value: GFP-G3BP1 U2OS


title: B Cells-EAE+anti-IgM/G+CtrlIg-rep2


title: TCR-seq of homo sapiens:HD4A_S6_alpha


title: P02E02_585_mono_016


title: TCR-seq of homo sapiens:HD4_S4_alpha

value: 4 stimulations with WT1 pool


title: B Cells-EAE-rep2


title: TCR-seq of homo sapiens:HD3_S10_alpha

value: 10 stimulations with WT1 pool


title: P02E02_585_mono_015


title: B Cells-EAE+anti-IgM/G+anti-Btla+IFNb-rep1

value: EAE

value: anti-Btla


title: B Cells-EAE+anti-IgM/G+anti-Btla-rep2


title: P02E02_585_mono_019


title: T_7_C

description: CountsMatrix.csv


title: TCR-seq of homo sapiens:HD3_S6_alpha


title: P02E02_585_mono_014


title: B Cells-EAE+anti-IgM/G+anti-Btla-rep1


title: TCR-seq of homo sapiens:HD3_S5_alpha

value: 5 stimulations with WT1 pool


title: P02E02_585_mono_013


title: T_1_C

description: CountsMatrix.csv


title: LZ GC B cells, CD22 KO, rep3

city: Edmonton

first: Jhon

last: Enterina

state: AB

address: 6-020 KATZ Group Centre

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

data_processing:
Galaxy platform for processing the raw sequencing files
Raw sequencing files were trimmed for adaptor sequence and mapped to mm10 whole genome using HISAT2. Quality of unaligned and aligned reads were validated using FastQC v0.11.2. Aligned reads were counted using Htseq-count and annotated using Gencode M25. Read count normalization and differnetial expression analysis were performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA were extracted from approximately 40,000-50,000 cells using Qiagen RNeasy Plus micro kit (cat#74034) following manufacturer's recommended protocol.
RNA libraries were prepared for sequencing using SMART-Seq Stranded kit (cat#634442) following the manufacturer's recommnded protocol.

treatment_protocol: WT and CD22 KO mice were immunized with 1mM of chicken ovalbumin-displaying liposomes. Spleens from these mice were harvested at day 14 post-immunization and B220+CD19+IgDlowGL7+CXCR4highCD86low DZ GC B cells were sorted and B220+CD19+IgDlowGL7+CXCR4lowCD86high LZ GC B cells were sorted.

value: spleen

value: Day 14

value: light zone GC B cells

value: CD22 knockout


title: P02E02_585_mono_011

value: peripheral blood


title: TCR-seq of homo sapiens:HD1_S11_alpha

value: 11 stimulations with WT1 pool


title: P02E02_585_mono_010


title: TCR-seq of homo sapiens:HD1_S9_alpha

value: 9 stimulations with WT1 pool


title: B Cells-EAE-rep1


title: LZ GC B cells, CD22 KO, rep2


title: LZ GC B cells, CD22 KO, rep1


title: P02E02_585_mono_009


title: PD

city: Pittsburgh

first: Lin

last: Zhang

state: Pennsylvania

address: 5117 Centre Ave, Hillman Cancer Ctr Rm2.42a, 5117 Centre Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
Sample quality was assessed by HTSeq v0.6.1 to count the read numbers mapped of each gene.
Data quality was ensured by the percentage of bases with a sequencing quality score above Q30.
FPKM (fragments per kilobase of transcript per million mapped reads) of each gene was calculated based on the length of a gene and read counts mapped to this gene.
Differential expression analysis was performed using the DESeq R package (2_1.6.3).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cancer cells

growth_protocol: HCT116 cells were growth in T75, plated at 20-30%, and left to grow 24 hours prior to treatment.

extract_protocol:
HCT116 cells with or without treatment were collected, and RNA was harvested using the Quick-RNA Kit.
RNA libraries were prepared for sequencing using the Illumina HiSeq platform.

treatment_protocol: HCT116 cells were treated with 1uM palbociclib or transfected with CDK4 siRNA for 24 hours.

value: Cells treated with palbociclib


title: LZ GC B cells, WT, rep3

value: wildtype


title: B Cells-Naïve+anti-IgM/G+anti-Btla+IFNb-rep3

value: anti-IgM/G

value: IFNb


title: T_4_C

description: CountsMatrix.csv

value: GFP-G3BP1 U2OS

value: Untreated

value: Total RNA


title: CDK4_KD

value: Cells with CDK4 siRNA transfection


title: P02E02_585_mono_008


title: B Cells-Naïve+anti-IgM/G+anti-Btla-rep3

value: anti-Btla

value: B cells


title: Untreat

value: Untreated cells


title: TCR-seq of homo sapiens:HD6_S3_alpha

value: 3 stimulations with WT1 pool


title: LZ GC B cells, WT, rep1

value: spleen

value: Day 14

value: light zone GC B cells


title: B Cells-Naïve+anti-IgM/G+CtrlIg+IFNb-rep3


title: LZ GC B cells, WT, rep2


title: P02E02_585_mono_006

value: peripheral blood


title: P02E02_585_mono_007


title: B Cells-EAE+anti-IgM/G+CtrlIg+IFNb-rep1

value: EAE


title: B Cells-Naïve+anti-IgM/G+CtrlIg-rep3


title: DZ GC B cells, CD22 KO, rep3

value: Dark zone GC B cells

value: CD22 knockout


title: B Cells-EAE+anti-IgM/G+CtrlIg-rep1

value: anti-IgM/G


title: MV4-11 day 18

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

data_processing:
Illumina nova 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: Leukemia cells

extract_protocol:
Total RNA was extracted with TRIZOL. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus. Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MV4-11 cells (with FLT3-ITD mutation) were treated with 10nM sorafenib for 24 days.MV4-11 cells were collected in Trizol for RNA-Sequence at Day 0, Day 6,Day 12,Day 18,Day 24.

value: treated with 10nM sorafenib for 18 days

tag: mutations

value: existing FLT3-ITD mutation

tag: cell l ine


title: MV4-11 day 24

value: treated with 10nM sorafenib for 24 days


title: B Cells-Naïve-rep3

tag: cell type


title: P02E02_585_mono_005

data_processing:
base calling: Casava
alignment: BWA MEM
transcript count: HT-seq
Genome_build: mm10

extract_protocol:
Cells were sorted into 96 well place containing 2 ul of lysis buffer in each well
as per Smart-seq2 protocol (Picelli et al 2013)


title: DZ GC B cells, CD22 KO, rep2


title: MV4-11 day 12

value: treated with 10nM sorafenib for 12 days


title: DZ GC B cells, CD22 KO, rep1


title: B Cells-Naïve+anti-IgM/G+anti-Btla+IFNb-rep2

value: IFNb


title: MV4-11 day 6

value: treated with 10nM sorafenib for 6 days


title: P02E02_585_mono_002


title: B Cells-Naïve+anti-IgM/G+anti-Btla-rep2

value: anti-Btla

value: B cells


title: DZ GC B cells, WT, rep3

value: wildtype


title: MV4-11 day 0

value: untreated


title: P02E02_585_mono_001


title: DZ GC B cells, WT, rep2

value: spleen

value: Day 14


title: B Cells-Naïve+anti-IgM/G+CtrlIg+IFNb-rep2


title: B Cells-Naïve+anti-IgM/G+CtrlIg-rep2


title: DZ GC B cells, WT, rep1