title: Hxk2, GFP-tagged, rep3

value: GFP polyclonal antibody (Takara:cat # 632592)


title: Tape_stripped_skin_replicate_WT_2

status: Public on Feb 13 2024

type: SRA

city: Boston

first: Manuel

last: Leyva-Castillo

state: MA

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
Run metrics, read alignment and detection of on-target transcripts was done using Torrent Suite Software 5.12.1 according to standard analysis procedures
CHP files were generated using Ion AmpliSeq RNA plug-in
N/A
N/A
N/A
Assembly: mm9
Supplementary files format and content: CHP format. Processed data files (.chp) contain normalized counts (read per million) .
Supplementary files format and content: N/A

molecule: total RNA

organism: Mus musculus

source_name: skin

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) and RNA was retrotranscribed using SuperScript VILO cDNA Synthesis Kit (ThermoFisher Scientific)
cDNA libraries were prepare using Ion AmpliSeqTM Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit in the the Ion Chef System

treatment_protocol: Skin samples were stored in RNAlater and store at -80 C until RNA extraction

tag: tissue

value: skin

tag: genotype

value: WT Balb/c

tag: treatment

value: Tape stripped


title: Tape_stripped_skin_replicate_WT_1


title: Hxk2, GFP-tagged, rep1

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

library_source: genomic

data_processing:
CUT&RUN analysis workflow (doi:10.3791/63655)
FastQ quality check with FastQC version 0.11.9
Adapter trimming with cutadapt version 3.5
Alignment to Candida albicans genome assembly 21 using Bowtie2 version 2.4.4
Remove PCR duplicated reads using MarkDuplicates function of Picard version 2.26.6
Filter reads less than 20 bp and greater than 120 bp in length using SamTools version 1.14
Subsample reads from GFP or IgG samples based on E. coli read count in each paired sample using SamTools version 1.14
Peaks were called using Macs2 version 2.2.7.1
Assembly: ASM18296v3
Supplementary files format and content: narrowPeak files  generated using from Macs2 version 2.2.7.1 during peak calling step
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Candida albicans

source_name: planktonic

growth_protocol: Precultured GFP-tagged Hxk1 and GFP-tagged Hxk2 strains in SC (synthetic complete) + glycerol (3%) overnight at 30°C. After 16 hours, transfered the cells to fresh SC glycerol with an OD of 0.3. Added 2% glucose to cells when cells were OD = 1.0. Collected cells after 20 minutes.

extract_protocol:
Nuclei isolation using zymolyase. TF-DNA complex were isolated with antibody.
Libraries were prepared using the NEBNextUltra II DNA Library Prepkit. Briefly, DNA was end-repaired and adapter ligated. After a DNA clean-up without size-selection, PCR enrichment of adapter-ligated samples was performed. After a second round of DNA clean-up, libraries are size selected by Polyacrylamide Gel Electrophoresis and cleaned up for sequencing.

tag: cell type

value: planktonic

tag: strain

tag: cut&run antibody


title: D19, OA, 24h

type: genomic

city: Leiden

first: Thomas

middle: B

last: Kuipers

address: Einthovenweg 20

country: Netherlands

institute: LUMC

description: Resting CD4+ T cells (non activated)

hyb_protocol: Genomic DNA was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research, Orange, CA, USA) according to the manufacturer’s procedure.

scan_protocol: Subsequent methylation analysis was performed on an Illumina (San Diego, CA, USA) iScan platform using the Infinium MethylationEPIC BeadChip according to standard protocols provided by Illumina. This consisted of a whole genome amplification step using 4 µl of each bisulfite converted sample, followed by enzymatic fragmentation and application of the samples to BeadChips (Illumina). The arrays were fluorescently stained and scanned. GenomeStudio software version 2011.1 with Methylation Module version 1.9.0 was used for initial quality control of assay performance and for generation of methylation data export files.

data_processing:
Following receipt of the methylation data as IDAT files, preprocessing and quality control (QC) followed the DNAmArray pipeline. Briefly, sample quality was assessed using visualizations, including MethylAid plots. The data underwent functional normalization, followed by removal of outlying or unreliable values, including those based on low bead number (0.16%), intensity (0.03%), or that were not substantially distinguishable from background noise (0.42%). Additionally, cross-reactive and polymorphic probes were omitted, along with those on sex chromosomes. The resulting dataset contained DNA methylation data at 738,991 CpGs for 90 samples, and this was annotated using the IlluminaHumanMethylationEPIC manifest (v1.0b2). Linear models were fitted to each probe using the limma package in R, with DNA methylation as the independent and stimulation status as the dependent variable. Timepoint and donor ID were adjusted for, and the effect of stimulation status was allowed to vary by timepoint using an interaction term. P-values were adjusted for multiple testing using FDR, with a 5% significance threshold.
The data underwent functional normalization, followed by removal of outlying or unreliable values, including those based on low bead number (0.16%), intensity (0.03%), or that were not substantially distinguishable from background noise (0.42%). Additionally, cross-reactive and polymorphic probes were omitted, along with those on sex chromosomes.

label: Biotin or dinitrophenyl (DNP)

organism: Homo sapiens

source_name: CD4+ T cell, OA, 24h

label_protocol: Standard Illumina Protocol

growth_protocol: CD4+ T cells were isolated from a buffy coat using magnetic beads and rested for 24h in DMEM supplemented with 5% fetal calf serum (FCS), pen/strep, glutamax, and IL-2 in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol: DNA was harvested using Zymo Quick-DNA/RNA Microprep Plus Kit (Zymo). 500ng of total DNA was sent for 850k DNA methylation array.

treatment_protocol: After 24h resting, the cells were exposed to either 30μg/mL oleic acid diluted in ethanol and dissolved in DMEM supplmented with 2% fatty acid free (FAF) bovine serum albumin (BSA), pen/strep, and glutamax or to the control, ethanol dissolved in DMEM supplmented with 2% FAF BSA, pen/strep, and glutamax for either 30min, 3 hours, 24 hours, 48 hours, or 72 hours.

value: Oleic Acid

tag: donor

value: Donor 19

tag: time

value: CD4+ T cells

value: Buffy Coat

tag: plate

value: Plate 1

tag: well

tag: sentrix barcode

tag: sentrix position


title: D19, OA, 72h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 72h


title: Hxk1, IgG control, rep3

value: Rabbit IgG negative control antibody (Epicypher:cat# 13-0042)


title: D19, OA, 3h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 3h


title: D19, OA, 48h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 48h


title: Hxk1, IgG control, rep2


title: D19, OA, 30m

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 30m


title: Tape_stripped_skin_replicate_IL22KO_1

value: IL22 deficient


title: Hxk1, GFP-tagged, rep3


title: Hxk1, GFP-tagged, rep1


title: D19, EtOH, 48h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 48h

value: Ethanol


title: D19, EtOH, 3h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 3h


title: Hxk1, IgG control, rep1


title: D19, EtOH, 72h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 72h

value: Plate 2


title: D19, EtOH, 24h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 24h


title: D19, EtOH, 30m

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 30m


title: ProQ CLIP_SPI2_plusCL_rep3

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
Adapter removal and read pair merging performed with SeqPrep (https://github.com/jstjohn/SeqPrep)
Read mapping performed with bowtie 1.2.2 allowing for 1 mismatch and one match per read
Mapped reads were converted to strand separated bedgraph files with samtools and bedtools genomecov.
Bedgraph files converted to Wig file format (www.encodeproject.org/software/bedgraphtobigwig/)
Assembly: NC_016810.1
Supplementary files format and content: Strand separated bigWig files for viewing mapping coverage in genome browsers.

organism: Salmonella enterica

growth_protocol: SPI2-medium to OD600 of 0.3

extract_protocol:
CLIP
NEBNext Small RNA Prep Kit


title: ProQ CLIP_SPI2_minusCL_rep3


title: D17, OA, 48h

description: Resting CD4+ T cells (non activated)

value: Donor 17


title: ProQ CLIP_SPI2_plusCL_rep2


title: D17, OA, 72h

description: Resting CD4+ T cells (non activated)


title: Hxk2, GFP-tagged, rep2


title: D17, OA, 24h

description: Resting CD4+ T cells (non activated)


title: D17, OA, 3h

description: Resting CD4+ T cells (non activated)


title: ProQ CLIP_SPI2_minusCL_rep2


title: D17, OA, 30m

description: Resting CD4+ T cells (non activated)


title: D17, EtOH, 72h

description: Resting CD4+ T cells (non activated)


title: D17, EtOH, 48h

description: Resting CD4+ T cells (non activated)


title: Donor 3; Sivelestat_High; 30 min

type: protein

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: After blocking non-specific binding sites on the array, an incubation chamber is mounted onto the microarray to permit the loading of 2 samples side by side on the same chip and prevent mixing of the samples. Following sample incubation, unbound proteins are washed away and the array is then probed with anti-biotin antibody that is labelled with a proprietary fluorescent dye combination.

scan_protocol: Each array produces a pair of 16-bit images, which are captured with a Perkin-Elmer ScanArray Reader laser array scanner (Waltham, MA).

data_processing: Signal quantification is performed with ImaGene 9.0 from BioDiscovery (El Segundo, CA) with predetermined settings for spot segmentation and background correction. The background-corrected raw intensity data are logarithmically transformed with base 2.

label: biotin

molecule: protein

source_name: Human islets

label_protocol: Proteins were covalently labeled with biotin. Free biotin molecules are then removed at the completion of labeling reactions by gel filtration.

growth_protocol: Human islets were obtained by Prodo Lab or IIDP. Upon receipt, human islets were cultured in Miami Media at 37 C 5% CO2. After overnight incubation, 150/200 size-matched IEQs per condition were hand-picked for the following procedure

extract_protocol: Total proteins were harvested from islets lysates using M-PER protein extraction reagent (Thermo Fisher, USA) supplemented with proteinase and phosphatase inhibitors  (Sigma, USA) according to standard protocol.

treatment_protocol: Human islets were starved in Final Wash media for 3 hours. After, IEQs were treated with DMSO, telaprevir (1 and 100 µg/ml), tebipenem (1 and 100 µg/ml), sivelestat (100 µg/ml), 5-IT (1 µM), Ovalbumin (1 µg/ml) and SerpinB1 (1 µg/ml) for 10 or 30 minutes. At the end of the incubation, islets were collected and washed once in PBS. Finally islet pellet was snap-frozen in liquid nitrogen.

tag: diabetes status

value: Non-diabetic

tag: unos id/rrid

tag: date of treatment


title: Donor 3; Telaprevir_Low; 30 min


title: Donor 3; Telaprevir_High; 30 min


title: D17, EtOH, 30m

description: Resting CD4+ T cells (non activated)


title: D16, OA, 48h

description: Resting CD4+ T cells (non activated)

value: Donor 16


title: D17, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: Hxk1, GFP-tagged, rep2

value: GFP polyclonal antibody (Takara:cat # 632592)


title: D16, OA, 72h

description: Resting CD4+ T cells (non activated)


title: Donor 3; DMSO; 30 min


title: D17, EtOH, 3h

description: Resting CD4+ T cells (non activated)


title: Donor 3; Sivelestat_High; 10 min


title: D16, OA, 24h

description: Resting CD4+ T cells (non activated)


title: D16, OA, 30m

description: Resting CD4+ T cells (non activated)


title: Donor 3; Telaprevir_Low; 10 min


title: D16, EtOH, 72h

description: Resting CD4+ T cells (non activated)


title: D16, EtOH, 48h

description: Resting CD4+ T cells (non activated)


title: Donor 3; DMSO; 10 min


title: D16, OA, 3h

description: Resting CD4+ T cells (non activated)


title: Donor 3; Telaprevir_High; 10 min


title: Donor 2; Sivelestat_High; 30 min


title: D16, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: D16, EtOH, 3h

description: Resting CD4+ T cells (non activated)


title: D16, EtOH, 30m

description: Resting CD4+ T cells (non activated)


title: Donor 2; Telaprevir_Low; 30 min


title: Donor 2; DMSO; 30 min


title: Donor 2; Telaprevir_Low; 10 min


title: D15, OA, 72h

description: Resting CD4+ T cells (non activated)

value: Donor 15


title: Donor 2; Sivelestat_High; 10 min


title: Donor 2; DMSO; 10 min


title: D15, OA, 48h

description: Resting CD4+ T cells (non activated)


title: Donor 2; Telaprevir_High; 10 min


title: D15, OA, 30m

description: Resting CD4+ T cells (non activated)


title: D15, OA, 3h

description: Resting CD4+ T cells (non activated)


title: D15, OA, 24h

description: Resting CD4+ T cells (non activated)


title: Donor 2; Telaprevir_High; 30 min


title: Donor 1; Sivelestat_High; 30 min


title: Donor 1; Telaprevir_Low; 30 min


title: D15, EtOH, 72h

description: Resting CD4+ T cells (non activated)


title: Donor 1; DMSO; 30 min


title: R20019483-YX5

city: Beijijng

first: Xingbo

last: Long

address: No 1, Dongdan Dahua Road, Dongcheng District

department: Urology

country: China

institute: Beijing Hospital

description:
10× Genomics scRNA-seq
Single-cell RNA sequencing

data_processing:
1) For 10× Genomics scRNA-seq technology. Reads were mapped to the human reference genome (build GRCh38 with ensemble version 92 gene annotation) using CellRanger V 3.1.0 (10× Genomics); 2) For Singleron scRNA-seq technology. Reads were mapped to GRCh38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2) . Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 files include count values for each Sample

source_name: Prostate transitional zone

extract_protocol:
1) Four samples were submitted to droplet-based scRNA-seq: the Chromium Single-cell 3′-Library, Gel Bead & Multiplex Kit and Chip Kit (10× Genomics, Pleasanton, CA, USA) were employed to construct a chromium single-cell 3′-library according to the manufacturer’s instructions. Cell suspensions were loaded onto a chromium single-cell chip along with reverse transcription (RT) master mix and single-cell 3′-gel beads, attempting to obtain 2000–8000 single cells per reaction. The samples were processed using 10× Genomics V2 barcoding chemistry kits. Following cell lysis, first-strand cDNA synthesis and amplification were carried out according to the manufacturer’s instructions with cDNA amplification set for 12 cycles. Libraries were sequenced on an Illumina HiSeq X Ten system. 2) Two samples were submitted to Singleron scRNA-seq: Single-cell suspensions with a concentration of 1×105 cells/mL  in PBS (HyClone) were prepared. Single-cell suspensions were then loaded onto microfluidic devices, and scRNA-seq libraries were constructed according to the Singleron GEXSCOPETM protocol by the GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4 nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X system.
1) Four samples were submitted to droplet-based scRNA-seq: the Chromium Single-cell 3′-Library, Gel Bead & Multiplex Kit and Chip Kit (10× Genomics, Pleasanton, CA, USA) were employed to construct a chromium single-cell 3′-library according to the manufacturer’s instructions. Cell suspensions were loaded onto a chromium single-cell chip along with reverse transcription (RT) master mix and single-cell 3′-gel beads, attempting to obtain 2000–8000 single cells per reaction. The samples were processed using 10× Genomics V2 barcoding chemistry kits. Following cell lysis, first-strand cDNA synthesis and amplification were carried out according to the manufacturer’s instructions with cDNA amplification set for 12 cycles. Libraries were sequenced on an Illumina HiSeq X Ten system. 2) Two samples were submitted to Singleron scRNA-seq: Single-cell suspensions with a concentration of 1×105 cells/mL  in PBS (HyClone) were prepared. Single-cell suspensions were then loaded onto microfluidic devices, and scRNA-seq libraries were constructed according to the Singleron GEXSCOPETM protocol by the GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4 nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X system.
10× Genomics scRNA-seq/Singleron scRNA-seq

treatment_protocol: No treatment

value: prostate


title: D15, EtOH, 48h

description: Resting CD4+ T cells (non activated)


title: Donor 1; Sivelestat_High; 10 min


title: W.raw

description:
Singleron scRNA-seq
Single-cell RNA sequencing

source_name: Prostate peripheral zone


title: D15, EtOH, 30m

description: Resting CD4+ T cells (non activated)


title: Y.raw


title: D15, EtOH, 3h

description: Resting CD4+ T cells (non activated)


title: Donor 1; Telaprevir_Low; 10 min


title: Donor 1; Telaprevir_High; 10 min


title: Donor 1; DMSO; 10 min


title: R20019482-WZ5


title: D14, OA, 72h

description: Resting CD4+ T cells (non activated)

value: Donor 14


title: Donor 1; Telaprevir_High; 30 min


title: D14, OA, 3h

description: Resting CD4+ T cells (non activated)


title: D14, OA, 48h

description: Resting CD4+ T cells (non activated)


title: D15, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: D14, EtOH, 72h

description: Resting CD4+ T cells (non activated)


title: PW_S1


title: D14, OA, 24h

description: Resting CD4+ T cells (non activated)


title: D14, EtOH, 48h

description: Resting CD4+ T cells (non activated)


title: D14, OA, 30m

description: Resting CD4+ T cells (non activated)


title: D14, EtOH, 3h

description: Resting CD4+ T cells (non activated)


title: D14, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: TFH_M2

city: Laval

first: Simona

last: Stager

state: Quebec

address: 531 Boul. des Prairies

department: Centre Armand-Frappier

country: Canada

institute: INRS

description:
Harvested 21 days post infection
DESEQ_LC_M_vs_TFH_M.tsv
STAR_Genes_TPM_LC_M_TFH_M.stranded.tsv

data_processing:
Basecalls performed using Illumina RTA 2.11.3.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version M25 (based on Ensembl 100)
DESeq2 version 1.30.1 was used to normalize gene readcounts and perform differential expression analysis
Assembly: GRCm38
Supplementary files format and content: Readcounts: Tab-delimited file as returned by STAR where columns are: Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: DESeq2: Tab-delimited matrix file where the first column is the Ensembl gene identifier followed by columns corresponding to a standard DESeq2 output including normalized read counts for all 12 samples
Supplementary files format and content: STAR-TPM: Tab-delimited matrix file where the first column is the Ensembl gene identifier followed by gene TPM values calculated based on the STAR readcounts for the 12 samples, and the last 4 columns containing additional gene annotations

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: Spleens were harvested from day 21 infected mice and CD4 T cells were isolated by magnetic activated cell sorting (MACS). Isolated CD4 T cells were then stained and the LAG-3+ CXCR5+ PD-1lo/int cells and Tfh cells were sorted using BD FACSAria IIu cell sorter and used for RNA extraction.

value: Spleen

value: T follicular helper cells

value: Leishmania donovani infected


title: TFH_M3


title: TFH_M4


title: TFH_M5


title: D14, EtOH, 30m

description: Resting CD4+ T cells (non activated)

value: CD4+ T cells


title: TFH_M6


title: D13, OA, 72h

description: Resting CD4+ T cells (non activated)

value: Oleic Acid

value: Donor 13

value: Buffy Coat


title: TFH_M1


title: LC_M5

value: LAG-3+ CXCR5+ PD-1lo/int CD4 T cells


title: LC_M6


title: D13, OA, 24h

description: Resting CD4+ T cells (non activated)

value: Plate 1


title: LC_M4


title: D13, OA, 48h

description: Resting CD4+ T cells (non activated)

value: Plate 2


title: LC_M3


title: D13, OA, 30m

description: Resting CD4+ T cells (non activated)


title: D13, EtOH, 72h

description: Resting CD4+ T cells (non activated)

value: Ethanol


title: LC_M2


title: LC_M1


title: D13, OA, 3h

description: Resting CD4+ T cells (non activated)


title: PY_S1


title: D13, EtOH, 48h

description: Resting CD4+ T cells (non activated)


title: posterior mesoderm, Sall4 cKO, rep2

city: Minneapolis

first: Matthew

last: Pappas

address: 321 Church St. SE

institute: University of Minnesota

data_processing:
Reads were trimmed using TrimGalore (0.6.0) and mapped to the GRCm38 genome using bwa mem (v 0.7.17).
Mapped reads were sorted with samtools (v1.9). Duplicates were marked with Picard MarkDuplicates (2.18.16).
ATAC peaks were identified with MACS (v2.1.1.20160309) using the following command line options: callpeak --broad -q 0.05 --nomodel --shift -100 --extsize 20.
Assembly: mm10
Supplementary files format and content: bigwig, read coverage file

source_name: posterior mesoderm

extract_protocol:
E9.5-E9.75 embryonic tissues posterior to the boundary of PSM and the somite were collected and the neural tube removed. The remaining tissue (the posterior mesoderm tissue) was dissociated by TrypLE (Invitrogen) at 37°C for 5min, neutralized by DMEM + 10% FBS, and collected by low-speed centrifugation. Tissues were washed with cold 1x PBS buffer, lysed, and pelleted. Pellets were resuspended in a reaction mixture with Nextera Tn5 transposase according to manufacturer spectifications.Transposed DNA was purified by Qiagen MinElute PCR purification kit.
Libraries were created using dual indexed Nextera reagent kits according to manufacturer specifications.

value: posterior mesoderm

value: Sall4 cKO


title: D13, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: posterior mesoderm, Sall4 cHet, rep3

value: Sall4 cHet


title: D13, EtOH, 3h

description: Resting CD4+ T cells (non activated)


title: posterior mesoderm, Sall4 cHet, rep2


title: posterior mesoderm, Sall4 cHet, rep1


title: D12, OA, 48h

description: Resting CD4+ T cells (non activated)

value: Donor 12


title: D12, OA, 24h

description: Resting CD4+ T cells (non activated)


title: D12, OA, 72h

description: Resting CD4+ T cells (non activated)


title: D12, OA, 3h

description: Resting CD4+ T cells (non activated)


title: Colon IBD RI0065 [T_20171006MN1_H04P1_Run1]

city: New York

first: Mohammad

last: Arifuzzaman

state: NY

address: 413 E 69th Street, 7th Floor

department: Department of Medicine

institute: Weill Cornell Medicine

description: generated from colon biopsies from a pan-colitic IBD patient

data_processing:
Reads were demultiplexed using Illumina’s CASAVA (v1.8.2), adapter-trimmed using FLEXBAR v2.4 (Dodt et al., 2012), and aligned to the human reference genome (NCBI GRC GRCg38-95) using STAR aligner v2.3.0 (Dobin et al., 2013) with default parameters.
Read counts per gene (RefSeq annotation) were determined using the Rsubread R package v3.10 I (Liao et al., 2019).
Normalization and differential expression analysis were performed using DESeq2 version 1.38.3 (Love et al., 2014).
Assembly: GRCg38-95
Supplementary files format and content: Excel file includes normalized counts for each Sample

source_name: Colon

extract_protocol:
Colonic biopsies from five non-IBD healthy controls and five pan-colitic IBD patients were digested into single cell suspensions and checked for quality control.
RNA-seq libraries were prepared from the single cell suspensions by Bristol Myers Squibb.  Libraries were sequenced on an Illumina HiSeq 2500, generating 2x50 bp paired-end reads.

value: Colon

tag: disease state

value: pan-colitic IBD


title: D12, EtOH, 72h

description: Resting CD4+ T cells (non activated)


title: Colon IBD RI0469 [T_20171006MN1_G05P1_Run1]


title: D12, OA, 30m

description: Resting CD4+ T cells (non activated)


title: posterior mesoderm, Sall4 cKO, rep1


title: D12, EtOH, 48h

description: Resting CD4+ T cells (non activated)


title: D12, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: D12, EtOH, 3h

description: Resting CD4+ T cells (non activated)


title: Colon IBD RI0416 [T_20171006MN1_F05P1_Run1]


title: D12, EtOH, 30m

description: Resting CD4+ T cells (non activated)


title: Colon non-IBD RI0360 [T_20171006MN1_F04P1_Run1]

description: generated from colon biopsies from a non-IBD healthy control

value: non-IBD healthy control


title: D11, OA, 48h

description: Resting CD4+ T cells (non activated)

value: Donor 11


title: D13, EtOH, 30m

description: Resting CD4+ T cells (non activated)


title: Colon non-IBD RI0351 [T_20171006MN1_D07P1_Run1]


title: D11, OA, 24h

description: Resting CD4+ T cells (non activated)


title: Neurofibroma, patient number 126

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 according to the manufacturer's instructions.

data_processing: Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software (v1.4.1.46, HTA-2.0_0.r3 library files).

source_name: Patient number 126

label_protocol: 100 ng total RNA was amplified, fragmented and labeled according to the GeneChip Whole Transcript (WT) PLUS Reagent Kit User Manual.

extract_protocol: Total RNA was isolated from tissue samples using either the Qiagen AllPrep DNA/RNA/miRNA Universal kit or a standard Trizol extraction method.

value: Neurofibroma tissue sample

tag: patient number

tag: tumor type

value: Neurofibroma

tag: specific location

tag: location group


title: Neurofibroma, patient number 125

source_name: Patient number 125

tag: tissue


title: Neurofibroma, patient number 122

source_name: Patient number 122


title: Neurofibroma, patient number 123

source_name: Patient number 123


title: Colon non-IBD RI0103 [T_20171006MN1_C06P1_Run1]


title: D11, EtOH, 48h

description: Resting CD4+ T cells (non activated)

tag: treatment

tag: cell type

value: CD4+ T cells


title: D11, OA, 72h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 72h

value: Oleic Acid

tag: donor


title: Colon IBD RI0380 [T_20171006MN1_B06P1_Run1]


title: Colon non-IBD RI0123 [T_20171006MN1_H05P1_Run1]


title: D11, EtOH, 30m

description: Resting CD4+ T cells (non activated)

tag: time

value: Buffy Coat


title: D11, OA, 3h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 3h

tag: plate


title: Colon non-IBD RI0278 [T_20171006MN1_G06P1_Run1]


title: Colon IBD RI0098-02 [T_20171006MN1_C05P1_Run1]


title: D11, EtOH, 3h

description: Resting CD4+ T cells (non activated)

tag: well


title: D11, EtOH, 72h

description: Resting CD4+ T cells (non activated)

tag: sentrix barcode


title: D10, OA, 72h

description: Resting CD4+ T cells (non activated)

value: Donor 10

tag: sentrix position


title: D11, EtOH, 24h

description: Resting CD4+ T cells (non activated)


title: PECs+CSF-1, sh T24H, time 24 hours

city: Hospitalet de Llobregat

first: ANNA

last: SOLA

state: --- Select One ---

address: Pavelló de Govern, Avda Mare de Déu de Bellvitge, Lab 4120

country: Spain

institute: IDIBELL

data_processing:
Samples were processed using the publicly available nf- core/RNA-seq pipeline v1.4.2 with the command nextflow run nf-core/rnaseq -profile conda -c ../multi/slurm.conFigure --reads '*.fastq.gz' --genome GRCh38 --singleEnd –aligner hisat2 --skipTrimming --skipQC --max_memory 64.GB --max_cpus 16 —skipBiotypeQC.
Briefly, fastq file were aligned to reference genome GRCh38 using HISAT2 parametrized with the command hisat2 -x <inde> -U <input_bam> -F --known-splicesite-infile <splice_site_file> --un-gz <unmapped_output_file> --met-stderr --new-summary --dta -- summary-file <ouput_summary_file> | samtools view -bS -F 4 -F 256 - > <output.bam>.
Gene-level assignment was then conducted using featureCounts parametrized with the command  featureCounts  -a  <gtf_fiile>  -g  'gene_id’  -t  ‘exon'  -o <ouput_gene.featureCounts.txt> —extraAttributes gene_name -s 1 <input.bam>.
Assembly: GRCh38
Supplementary files format and content: Read count matrix (genes as rows, samples as columns)

source_name: kidney

growth_protocol: Parietal epithelial cells were maintained in EGM-MV medium supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37ºC

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit (Invitrogen)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (96 samples ref. 20020595 or 48 samples ref. 20020594) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.

treatment_protocol: PECs cells (>80% CD133+ and CD24+)  were incubated with 50 ng/ml of CSF-1 protein (Prospect) during 24 hours

value: kidney

tag: cell line

value: primary

value: renal parietal epithelial cells

tag: genotype

value: WT

value: CSF-1 administration


title: D10, OA, 48h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 48h

value: Plate 1


title: Neurofibroma, patient number 119

source_name: Patient number 119


title: D10, OA, 24h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 24h


title: PECs, sh CTL, time 0

description: Control

value: non-treatment


title: D11, OA, 30m

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, OA, 30m


title: Neurofibroma, patient number 117

source_name: Patient number 117


title: D10, OA, 3h

description: Resting CD4+ T cells (non activated)


title: Neurofibroma, patient number 121

source_name: Patient number 121


title: Neurofibroma, patient number 115

source_name: Patient number 115


title: D10, EtOH, 72h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 72h

value: Ethanol

value: Plate 2


title: D10, EtOH, 24h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 24h


title: Neurofibroma, patient number 108

source_name: Patient number 108


title: D10, EtOH, 48h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 48h


title: double resistant, PPS-ICBR

city: Notre Dame

first: Dailin

last: Gan

address: Holy Cross Dr.

institute: University of Notre Dame

data_processing:
The raw reads are aligned to the Mouse reference genome build mm10, using Tophat RNASeq alignment software. The aligned reads verified for quality using FASTQC software. HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.The raw counts are normalized and differential expression analysis is performed on contrasts of interest using the DEseq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and RPKM values for each sample

source_name: PPS-ICBR

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). The quantity and quality of each sample were measured using an Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA sequencing was performed at Sequencing and Microarray Facility at MD Anderson Cancer Center using standard stranded RNA-seq protocol on an Illumina HiSeq 4000 (76nt pair-end).

value: PPS-ICBR


title: D10, OA, 30m

description: Resting CD4+ T cells (non activated)


title: Neurofibroma, patient number 107

source_name: Patient number 107


title: D10, EtOH, 30m

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 30m


title: D10, EtOH, 3h

description: Resting CD4+ T cells (non activated)

source_name: CD4+ T cell, EtOH, 3h


title: anti-CTLA4 resistant, PPS-CTLA4R


title: Neurofibroma, patient number 116

source_name: Patient number 116


title: anti-PD1 resistant, PPS-PD1R


title: Neurofibroma, patient number 114

source_name: Patient number 114


title: PPS-6239


title: Neurofibroma, patient number 105

source_name: Patient number 105


title: T111 GBM cells after TMZ treatment

city: København Nv

first: Inès

middle: CN

last: Avenel

address: Ole Maaløes Vej 5

country: Denmark

institute: BRIC

data_processing:
Bowtie2 version 2.1.0 and Tophat2 version 2.0.10 with default parameters were used to align the RNA-seq reads against the human transcriptome and genome. The output files were indexed using Samtools version 0.1.19, and Cufflinks version 2.1.1 was used for sample transcriptome assembly, transcript isoform identification and abundance estimation. Differential gene expression analysis on known UCSC genes was done using the edgeR R-package (version 3.4.2), from the R version 3.0.2 open source-environment.
Assembly: UCSC hg19
Supplementary files format and content: Excel matrix showing cpms
Supplementary files format and content: Text file showing cpms

source_name: Primary GBM

growth_protocol: Cells were grown in Neurobasal media supplemented with FGF; EGF; N2 and B27 and maintained at 37˚C in a humidified atmosphere of 5% CO2

extract_protocol:
Treated and untreated cells in suspension were harvested, and RNA extraction was performed using the RNeasy Mini Kit (Qiagen).
RNA was converted to ds cDNA using the TrueSeq Stranded Total RNA Gold Kit (Illumina), and the ds cDNA pools were sequenced using the HiSeq 1500 System (Illumina)

treatment_protocol: 4 million T78, T86 and T111 cells were treated with 50 μM of temozolomide (Sigma-Aldrich) or a DMSO (Sigma-Aldrich) control for 48 hours, after which the media was removed, and the cells were grown in NB + all media for a week

value: Primary GBM

value: T111 (patient derived)

value: Primary GBM tumor cells

value: 50 μM TMZ


title: XX Fetal Gonad, minusKTS KO, replicate 1

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Gonad

extract_protocol:
E12 (23±3ts) gonads from wild-type, -KTS KO and +KTS KO mice were enzymatically dissociated for 10 min at 37°C using trypsin-EDTA 0.05% (Gibco, Fisher Scientific, Hampton, NH).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Gonad

tag: developmental stage

value: Fetal

tag: age

tag: Sex

value: female

value: minusKTS KO

tag: replicate


title: T86 GBM cells after TMZ treatment

value: T86 (patient derived)


title: Control T78 GBM cells

value: T78 (patient derived)

value: DMSO


title: T111 Control cells


title: T86 control cells


title: T78 GBM cells afer TMZ treatment


title: XX Fetal Gonad, minusKTS KO, replicate 2

description: 10x Genomics


title: Neurofibroma, patient number 103

source_name: Patient number 103

value: Neurofibroma tissue sample

tag: patient number

tag: tumor type

value: Neurofibroma (Plexiformed)

tag: specific location


title: MPNST, patient number 100

source_name: Patient number 100

tag: tissue

value: MPNST tissue sample

value: MPNST primary

value: gluteal

tag: location group

value: Extremities


title: Neurofibroma, patient number 1

source_name: Patient number 1

value: Neurofibroma


title: XX Fetal Gonad, plusKTS KO, replicate 2

description: 10x Genomics

value: plusKTS KO


title: Donor13, Oleic Acid, 24h

description:
Passed QC
D13-OA-24h

data_processing:
FastQC v0.11.9 was used for checking raw read QC
Adapter clipping was performed using Cutadapt v2.10
RNAseq reads were aligned to human reference genome GRCh38 using Ensembl v99 & star v2.7.5a
Gene quantification was then performed using htseq-count v0.12.4
Assembly: GRCh38
Supplementary files format and content: TSV, gene raw count

source_name: Buffy Coat

extract_protocol:
RNA was harvested using Zymo Quick-DNA/RNA Microprep Plus Kit (Zymo). 1μg of total RNA was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared from 200ng RNA using the Illumina Truseq stranded mRNA library prep (Illumina, 20020595) after depletion of ribosomal RNA with Ribo Zero Gold (Illumina, 20037135)

value: Buffy Coat

tag: cell type

value: CD4+ T cell

tag: treatment

value: Oleic Acid

tag: donor

value: Donor 13

tag: batch

value: batch 1


title: XY Fetal Gonad, plusKTS KO, replicate 2

description: 10x Genomics

value: Gonad

value: Fetal

value: male


title: Donor13, Oleic Acid, 48h

description:
Passed QC
D13-OA-48h

tag: time


title: Donor13, Oleic Acid, 3h

description:
Passed QC
D13-OA-3h


title: MPNST, patient number 98

source_name: Patient number 98

value: lower leg


title: XX Fetal Gonad, plusKTS KO, replicate 1

description: 10x Genomics

value: female


title: Donor13, Ethanol, 72h

description:
Passed QC
D13-EtOH-72h

value: Ethanol


title: 80hpf

city: Bad Nauheim

first: Noah

last: Knoppik

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max-Planck-Institute for Heart and Lung Research

description: 10x Genomics

data_processing:
Reads were aligned against the zebrafish genome and counted by StarSolo.
Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore, we filtered genes if they were detected in less than 30 cells.
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: DanRer11
Supplementary files format and content: starsolo outputs

organism: Danio rerio

source_name: heart

extract_protocol:
Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without Calcium and Magnesium and with 0.04% BSA.
Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3,1 (10xGenomics).  scRNA-seq library preparation was done using a standard protocol, and sequencing was done on a Nextseq2000

value: heart

value: wild type


title: XY Fetal Gonad, plusKTS KO, replicate 1

description: 10x Genomics


title: Donor13, Oleic Acid, 30m

description:
Passed QC
D13-OA-30m


title: MPNST, patient number 99

source_name: Patient number 99

value: MPNST tissue sample

value: MPNST primary

value: headneck

value: Non-extremities


title: Aorta, A+S, DHT5

city: Lexington

first: Xufang

last: Mu

state: KY

address: 900 S. Limestone St

institute: University of Kentucky

data_processing:
Illumina BaseSpace Sequencing Hub
RNA-seq Alignment App v. 1.1
STAR aligner to map sequences
Cufflinks 2 to do FPKM count normalization
DESeq2 to test for differentially abundant mRNAs
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: aorta

growth_protocol: 10-month-old C57BL/6 male mice were housed in animal facilities with a 14:10 light dark cycle and free access to food and drinking water

extract_protocol:
Aortas were harvested, stored and cleaned in RNAlater. Total RNA was extracted using RNeasy fibrous tissue mini kit (Qiagen)
The polyA enrichment library preparation procedure is used to construct 250-300 bp insert cDNA library.

treatment_protocol: Mice were first subjected to orchiectomy or sham-operation. After two weeks recovery, mice were administered with aldosterone (200 ug/kg/d) via osmotic minipump and high salt in drinking water (0.9% NaCl + 0.2% KCl) for seven days with or without DHT pellet to orchiectomized mice

value: aorta

tag: strain

value: WT

value: orchiectomy with DHT

value: Aldo-salt

value: Day 7


title: Donor13, Ethanol, 48h

description:
Passed QC
D13-EtOH-48h

value: Buffy Coat

value: CD4+ T cell

value: Donor 13

value: batch 1


title: XX Fetal Gonad, WT, replicate 2

description: 10x Genomics

value: Gonad

value: Fetal

value: female


title: 50hpf

description: 10x Genomics

value: heart

value: wild type


title: Donor13, Ethanol, 24h

description:
Passed QC
D13-EtOH-24h

value: Ethanol


title: MPNST, patient number 97

source_name: Patient number 97

value: MPNST tissue sample

value: MPNST primary

value: thigh

value: Extremities


title: Donor13, Ethanol, 3h

description:
Passed QC
D13-EtOH-3h


title: MPNST, patient number 95

source_name: Patient number 95

value: upper trunk

value: Non-extremities


title: Aorta, A+S, DHT4

value: aorta

value: WT

value: orchiectomy with DHT

value: Aldo-salt

value: Day 7


title: MPNST, patient number 94

source_name: Patient number 94

value: MPNST second primary

value: lower trunk


title: Donor13, Ethanol, 30m

description:
Passed QC
D13-EtOH-30m

value: Buffy Coat

value: CD4+ T cell

value: Donor 13

value: batch 1


title: XY Fetal Gonad, WT, replicate 2

description: 10x Genomics

value: Gonad

value: Fetal

value: male


title: Aorta, A+S, DHT3


title: XY Fetal Gonad, minusKTS KO, replicate 1

description: 10x Genomics

value: minusKTS KO


title: Donor12, Oleic Acid, 72h

description:
Passed QC
D12-OA-72h

value: Oleic Acid

value: Donor 12


title: XY Fetal Gonad, minusKTS KO, replicate 2

description: 10x Genomics


title: Aorta, A+S, DHT2

value: aorta


title: MPNST, patient number 93

source_name: Patient number 93

value: MPNST tissue sample

value: MPNST primary

value: thigh

value: Extremities


title: Aorta, A+S, orx5

value: WT

value: orchiectomy

value: Aldo-salt

value: Day 7


title: MPNST, patient number 90

source_name: Patient number 90

value: sacrum

value: Non-extremities


title: Donor12, Oleic Acid, 24h

description:
Passed QC
D12-OA-24h

value: Buffy Coat

value: CD4+ T cell

value: batch 1


title: XY Fetal Gonad, WT, replicate 1

description: 10x Genomics

value: Gonad

value: Fetal

value: male


title: MPNST, patient number 88

source_name: Patient number 88

value: MPNST relapse

value: kneepit


title: MPNST, patient number 87

source_name: Patient number 87

value: MPNST tissue sample

value: MPNST primary

value: leg


title: Aorta, A+S, orx4

value: aorta

value: WT


title: Aorta, A+S, orx3

value: orchiectomy

value: Aldo-salt


title: Donor12, Oleic Acid, 30m

description:
Passed QC
D12-OA-30m

value: Oleic Acid

value: Donor 12


title: T cell mouse2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

description: DNA barcode

data_processing:
Library strategy: Amplicon-seq
NA
Genome_build: NA
Supplementary_files_format_and_content: Barcode sequences and counts

source_name: T cells

extract_protocol:
HSCs isolated from bone marrow from C57BL/6 mice were cultured ex vivo. Five days after plating, cultured HSCs were infected with barcoding lentivirus pBC008 in HSC culture medium. Two days after infection, medium was refreshed with HSC culture medium. Four days after infection, the infected HSCs were detached and GFP+LinSca1+cKit+ cells were sorted using a FACS Aria IIIa instrument and mixed with CD45.2+ LincKit+Sca1- cells as rescue cells. Five-week-old recipient CD45.2 male mice were irradiated with a dose of 9 Gy to the whole body and were intravenously injected with 2x10e4 GFP+LSK and 10e5 rescue cells per mouse. Two months later, peripheral blood, hearts, and kidneys were isolated. Then the sorted cells were lysed in buffer RLT plus (QIAGEN) and the genomic DNA was extracted from these samples by using AllPrep DNA/RNA Mini Kit (QIAGEN).
Barcode sequences incorporated into genomic DNA were PCR amplified by NEBNext Ultra II Q5 Master Mix (NEB) with the following primers: 5’-TCT TTC CCT ACA CGA CGC TCT TCC GAT CTT AAC TTA CGG AGT CGC TCT ACG-3’ and 5’-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TGG ATG GGA TTC TTT AGG TCC TG-3’. The cycling protocol was 98 °C, 30 sec; then 18 cycles of 98 °C, 10 sec, 60 °C, 10 sec, 72 °C, 30 sec; then 72 °C, 5 min. The PCR amplicons were amplified with NEBNext Multiplex Oligos (NEB) at 9-11 cycles to generate sequencing libraries.

value: T cells


title: T cell mouse1

description: DNA barcode


title: Donor12, Ethanol, 72h

description:
Passed QC
D12-EtOH-72h

value: Buffy Coat

value: CD4+ T cell

value: Ethanol


title: Aorta, A+S, orx2

value: Day 7


title: Donor12, Oleic Acid, 48h

description:
Passed QC
D12-OA-48h

value: batch 1


title: MPNST, patient number 84

source_name: Patient number 84

value: Extremities


title: XX Fetal Gonad, WT, replicate 1

description: 10x Genomics

source_name: Gonad

value: Gonad

value: Fetal

value: female


title: MPNST, patient number 83

source_name: Patient number 83

value: MPNST tissue sample

value: MPNST primary

value: foot


title: MPNST, patient number 85

source_name: Patient number 85

value: thorax

value: Non-extremities


title: Aorta, A+S, DHT1

value: aorta

value: WT

value: orchiectomy with DHT

value: Aldo-salt


title: Neutrophil mouse3

description: DNA barcode

source_name: Neutrophils

value: Neutrophils


title: T cell mouse3

description: DNA barcode

value: T cells


title: Aorta, A+S, con5

value: control

value: Day 7


title: Aorta, A+S, orx1

value: orchiectomy


title: Donor12, Ethanol, 24h

description:
Passed QC
D12-EtOH-24h

source_name: Buffy Coat

value: Buffy Coat

value: CD4+ T cell

value: Ethanol

value: Donor 12

value: batch 1


title: Donor12, Ethanol, 3h

description:
Passed QC
D12-EtOH-3h


title: Donor12, Oleic Acid, 3h

description:
Passed QC
D12-OA-3h

value: Oleic Acid


title: Aorta, A+S, con4


title: Monocyte mouse3

description: DNA barcode

source_name: Monocytes

value: Monocytes


title: MPNST, patient number 81

source_name: Patient number 81

value: MPNST tissue sample

value: MPNST relapse

value: gluteus

value: Extremities


title: MPNST, patient number 80

source_name: Patient number 80

value: back

value: Non-extremities


title: MPNST, patient number 79

source_name: Patient number 79

value: thigh


title: MPNST, patient number 76

source_name: Patient number 76


title: MPNST, patient number 78

source_name: Patient number 78

value: MPNST primary


title: Donor12, Ethanol, 48h

description:
Passed QC
D12-EtOH-48h


title: Donor11, Oleic Acid, 72h

description:
Passed QC
D11-OA-72h

value: Donor 11


title: MPNST, patient number 82

source_name: Patient number 82

value: leg


title: Aorta, A+S, con2

source_name: aorta

value: aorta

value: WT

value: control

value: Aldo-salt

value: Day 7


title: Neutrophil mouse2

description: DNA barcode

value: Neutrophils


title: Monocyte mouse1

description: DNA barcode

value: Monocytes


title: Renal M2 macrophage mouse3

description: DNA barcode

source_name: Renal M2 macrophages

value: Renal M2 macrophages


title: Neutrophil mouse1

description: DNA barcode


title: Aorta, A+S, con1


title: Donor11, Oleic Acid, 48h

description:
Passed QC
D11-OA-48h

value: Buffy Coat

value: CD4+ T cell

value: Oleic Acid

value: batch 1


title: Donor11, Oleic Acid, 24h

description:
Passed QC
D11-OA-24h


title: IVD, WT_INTACT3

city: Philadelphia

first: Ken

last: Chen

state: Pennsylvania

address: 3701 Chestnut Street, Apt 1136

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
RNA Library Preparation and Sequencing was performed by Azenta US (South Plainfield, NJ). Specifically, RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Assembly: GRCm38
Supplementary files format and content: TPM file containing the TPM-normalized values of each gene in each sample

source_name: IVD

extract_protocol:
From each mouse tail,  Co3/4, 4/5,5/6 and Co6/7 IVDs were shaved off the cartilaginous endplate with a scalpel under a dissecting microscope (VistaVision, VWR International, Radnor, PA). The IVD tissues were from all 4 coccygeal IVDs of each animal were isolate, and immersed in RNALater (Ambion, Foster City, CA) overnight and preserved at -80°C until extraction. Total cellular RNA was isolated by the Trizol method. Specifically, RNALater was eliminated, and the tissues were rapidly frozen with liquid Nitrogen before being transferred into Trizol (Invitrogen, Carlsbad, CA). Subsequently, the tissues were homogenized using a homogenizer equipped with disposable OmniTip probes designed for hard tissue (Omni International, Kennesaw, GA). RNA was then precipitated with 70% ethanol and further purified using a RNeasy Micro Kit (Qiagen).
RNA Library Preparation and Sequencing was performed by Azenta US (South Plainfield, NJ). Specifically, RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

value: IVD

value: type

value: INTACT


title: Renal M2 macrophage mouse2

description: DNA barcode


title: Donor12, Ethanol, 30m

description:
Passed QC
D12-EtOH-30m

value: Ethanol

value: Donor 12


title: Donor11, Oleic Acid, 3h

description:
Passed QC
D11-OA-3h

value: Donor 11


title: IVD, WT_INTACT2


title: Renal M2 macrophage mouse1

description: DNA barcode


title: Aorta, A+S, con3

value: aorta

value: WT


title: Renal M1 macrophage mouse3

description: DNA barcode

source_name: Renal M1 macrophages

value: Renal M1 macrophages


title: MPNST, patient number 73

source_name: Patient number 73

value: MPNST tissue sample

value: MPNST primary

value: leg

value: Extremities


title: MPNST, patient number 72

source_name: Patient number 72

value: MPNST relapse

value: hand


title: Donor11, Ethanol, 72h

description:
Passed QC
D11-EtOH-72h

value: Buffy Coat

value: CD4+ T cell


title: IVD, WT_INTACT1

value: IVD


title: IVD, WT_INJURED4

value: type

value: INJURED


title: MPNST, patient number 69

source_name: Patient number 69

value: thigh


title: MPNST, patient number 71

source_name: Patient number 71


title: MPNST, patient number 70

source_name: Patient number 70


title: Renal M1 macrophage mouse2

description: DNA barcode


title: Donor11, Ethanol, 48h

description:
Passed QC
D11-EtOH-48h

source_name: Buffy Coat

value: Ethanol

value: batch 1


title: IVD, WT_INJURED3


title: Donor11, Ethanol, 24h

description:
Passed QC
D11-EtOH-24h

value: Donor 11


title: IVD, WT_INJURED2


title: Renal M1 macrophage mouse1

description: DNA barcode


title: Cardiac Ccr2lo macrophage mouse3

description: DNA barcode

source_name: Cardiac Ccr2lo macrophages

value: Cardiac Ccr2lo macrophages


title: IVD, WT_INJURED1


title: Donor11, Oleic Acid, 30m

description:
Passed QC
D11-OA-30m

value: Oleic Acid


title: Donor11, Ethanol, 30m

description:
Passed QC
D11-EtOH-30m


title: Donor11, Ethanol, 3h

description:
Passed QC
D11-EtOH-3h


title: IVD, MUT_INTACT4

value: INTACT


title: Cardiac Ccr2lo macrophage mouse2

description: DNA barcode


title: Cardiac Ccr2lo macrophage mouse1

description: DNA barcode


title: MPNST, patient number 67

source_name: Patient number 67

value: MPNST tissue sample

value: MPNST primary


title: MPNST, patient number 68

source_name: Patient number 68

value: forearm

value: Extremities


title: Donor10, Oleic Acid, 72h

description:
Passed QC
D10-OA-72h

value: Donor 10


title: MPNST, patient number 65

source_name: Patient number 65

value: gluteus


title: MPNST, patient number 66

source_name: Patient number 66


title: Cardiac Ccr2hi macrophage mouse3

description: DNA barcode

source_name: Cardiac Ccr2hi macrophages

value: Cardiac Ccr2hi macrophages


title: MPNST, patient number 63

source_name: Patient number 63


title: MPNST, patient number 62

source_name: Patient number 62

value: MPNST relapse


title: Donor10, Oleic Acid, 48h

description:
Passed QC
D10-OA-48h

value: Buffy Coat

value: CD4+ T cell


title: IVD, MUT_INTACT3

value: IVD


title: Cardiac Ccr2hi macrophage mouse2

description: DNA barcode


title: IVD, MUT_INTACT2


title: Donor10, Oleic Acid, 24h

description:
Passed QC
D10-OA-24h


title: IVD, MUT_INTACT1


title: IVD, MUT_INJURED5

value: INJURED


title: Cardiac Ccr2hi macrophage mouse1

description: DNA barcode


title: Donor10, Oleic Acid, 30m

description:
Passed QC
D10-OA-30m

value: batch 1


title: B cell mouse3

description: DNA barcode

source_name: B cells

value: B cells


title: Donor10, Oleic Acid, 3h

description:
Passed QC
D10-OA-3h


title: IVD, MUT_INJURED3

source_name: IVD


title: IVD, MUT_INJURED4


title: B cell mouse2

description: DNA barcode


title: MPNST, patient number 59

source_name: Patient number 59

value: shoulder


title: B cell mouse1

description: DNA barcode


title: Donor10, Ethanol, 48h

description:
Passed QC
D10-EtOH-48h

value: Ethanol


title: U87MG OFF_3

city: Lille

first: Mohamed

last: Elati

address: Bd du Professeur Jules Leclercq

institute: University of Lille

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: hg38
Supplementary files format and content: tsv

extract_protocol:
RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA, USA), according to manufacturer’s instructions. Briefly, following purification with poly-T oligo-attached magnetic beads, the mRNA was fragmented using divalent cations at 94 °C for 2 min. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second-strand cDNA synthesis using DNA Polymerase I and RNase H.
Following addition of a single ‘A’ base and subsequent ligation of the adapter on double-stranded cDNA fragments, the products were purified and enriched with PCR (30 s at 98 °C; (10 s at 98 °C, 30 s at 60 °C, 30 s at 72 °C) × 12 cycles; 5 min at 72 °C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter, Villepinte, France), and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Libraries were then sequenced on an Illumina HiSeq4000 system as single-end 1 × 50 base reads.

tag: cell line

value: TMZ-resistant cells with interrupted treatment


title: U87MG OFF_2


title: IVD, MUT_INJURED1

tag: genotype


title: Donor10, Ethanol, 24h

first: Thomas

last: Kuipers

address: Einthovenweg 20

institute: LUMC

description:
Passed QC
D10-EtOH-24h


title: Donor10, Ethanol, 3h

description:
Passed QC
D10-EtOH-3h


title: MPNST, patient number 56

source_name: Patient number 56

value: MPNST tissue sample

value: leg


title: MPNST, patient number 54

source_name: Patient number 54

value: MPNST primary

value: thigh


title: MPNST, patient number 57

source_name: Patient number 57

value: arm

value: Extremities


title: MPNST, patient number 60

source_name: Patient number 60


title: MPNST, patient number 55

source_name: Patient number 55


title: Inner ear organoids,scRNA-seq,D21,GFP low signal

city: Ann Arbor

first: Joerg

last: Waldhaus

state: MI

address: Medical Sciences I Building, 1150 West Medical Center Drive

department: Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute

institute: University of Michigan

description: single-nuclei gene expression data

data_processing:
Sequencing reads were demultiplexed and aligned against the mm10 mouse genome reference using 10X CellRanger v6.1.0 for scRNA-seq samples
From filtered counts Seurat version 4.0.6 was used to process the single cell data including normalization, integration, dimension reduction, UMAP visualization.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with filtered_gene_bc_matrices.

source_name: Inner ear organoids

extract_protocol:
Whole inner ear organoids from day 16 to 21 of the Atoh1-nGFP ESC line were dissected, dissociated and flow sorted based on GFP expression. Cells were then loaded on 10X Genomics chip for scRNA-seq library preparation following the manufacturer's instructions.
RNA libraries were prepared using standard 10X genomics protocols

value: Inner ear organoids

value: otic lineage

tag: days in vitro (div)


title: MPNST, patient number 53

source_name: Patient number 53

value: MPNST relapse


title: U87MG OFF_1


title: Donor10, Ethanol, 30m

city: Leiden

description:
Passed QC
D10-EtOH-30m

source_name: Buffy Coat

value: Buffy Coat

value: CD4+ T cell

value: Donor 10


title: Donor10, Ethanol, 72h

description:
Passed QC
D10-EtOH-72h

value: batch 1


title: MPNST, patient number 52

source_name: Patient number 52


title: SHEP.tet21n Dox siSNRPD3 #2_rep3

city: Randwick

first: Daniel

last: Carter

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

data_processing:
RNA-seq reads (FASTQ) were aligned against the hg38 genome using STAR (v2.5.0a) two pass alignment with the parameters; --twopassMode Basic --runMode alignReads --genomeLoad NoSharedMemory --sjdbOverhang 100 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin --outSAMtype BAM Unsorted
Aligned read (BAM) files were sorted and indexed using samtools (v1.3.1)
leafcutter junction files were generated using the bam2junc.sh script and then parsed into the leafcutter_cluster.py script for intron clustering
leafcutter differential analysis was performed using the leafcutter_ds.R script with the parameters -i 3 -g 3 -f 0.05 and a resulting statistics table was constructed using a custom R script
quanitifcation of leafcutter PSI counts was calculated using the leafcutter_quantify_psi.R script found here https://github.com/davidaknowles/leafcutter/blob/psi_2019/scripts/leafcutter_quantify_psi.R
Assembly: hg38
Supplementary files format and content: leafcutter_psi.txt (percent spliced in for each intron in every sample)
Supplementary files format and content: stats_table.txt (FDR + deltaPSI for all paired sample comparisons for each cluster - FDR refers to differential test for each cluster, deltaPSI refers to difference in each introns percent spliced in value)

source_name: SHEP.tet21n cells

growth_protocol: SHEP21n maintained in Dulbecco’s Modified Eagle Medium / 10% FCS in in an incubator with a humidified atmosphere of 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using the PureLink RNA kit (Life Technologies)
RNA-seq libraries were prepared using TruSeq Stranded mRNA-seq (Illumina)

treatment_protocol: 2 μg/mL doxycycline was added to the media every 72 hours

value: DOX

tag: sirna

tag: ID


title: SHEP.tet21n Dox siSNRPD3 #2_rep2


title: Inner ear organoids,scRNA-seq,D20

description: single-nuclei gene expression data


title: U87MG R50_2

value: TMZ-resistant cells with continuous TMZ treatment


title: U87MG R50_3


title: U87MG R50_1


title: Inner ear organoids,scRNA-seq,D21,GFP high signal

description: single-nuclei gene expression data


title: Inner ear organoids,scRNA-seq,D16

description: single-nuclei gene expression data


title: IVD, MUT_INJURED2

value: IVD

value: INJURED


title: SHEP.tet21n Dox siSNRPD3 #2_rep1


title: SHEP.tet21n Dox siSNRPD3 #1_rep3


title: Tnrc6a Trim71-/-_3

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

description:
Trim71-/-_3
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Upf1-/-
TruSeq Illumina Total RNA-seq (stranded - high input)

data_processing:
Base calling and quality scoring is performed using RTA software (v3.4.4), demultiplexing with bcl2fastq2 v2.20.
Alignment was performed as follows: Samples were aligned against the GRCm38 mouse genome assembly from GENCODE (Frankish et al., 2021), primary assembly from release M24).(Rosenbloom et al., 2015) Alignments were performed using STAR version 2.7.3a with settings --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1(Gaidatzis et al., 2015). These settings follow ENCODE guidelines and report a single randomly selected alignment for reads that map to the genome no more than 20 times(Langmead et al., 2009) Gene annotations were also obtained from GENCODE release M24, transforming the gtf file into a Bioconductor TxDb object using the makeTxDbFromGFF function from the GenomicFeatures package (version 1.44.0, (Lawrence et al., 2013). Gene-level read counts were obtained by summing the counts from the union of all exons per gene, using the qCount function from the QuasR package (version 1.32.0, (Gaidatzis et al., 2015)) with the created TxDb and parameters orientation = “opposite”.
Assembly: mm10
Supplementary files format and content: csv: First column contains ENSEMBL transcript ID, second column contains ENSEMBL gene ID,  third column contains ENTREZ gene ID, fourth column contains gene symbol (Ensembl identifiers), fifth column contains gene nams (EMSENBL), sixth column contains summed width of exons per gene (quasr package),  columns named 'raw.count' contain raw counts of reads overlapping each gene for each sample, columns named 'rpkm' contain rpkm read counts overlapping each gene for each sample.

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.

tag: overexpression

tag: group

value: Experiment 3

value: Mouse embryonic stem cells


title: U87MG_3

value: control


title: MPNST, patient number 49

source_name: Patient number 49

value: MPNST tissue sample

tag: patient number

tag: tumor type

value: back

value: Non-extremities


title: Tnrc6a Trim71-/-_2

description:
Trim71-/-_2
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Upf1-/-
TruSeq Illumina Total RNA-seq (stranded - high input)


title: MPNST, patient number 44

source_name: Patient number 44

tag: tissue

value: MPNST primary

tag: specific location

value: thigh

value: Extremities


title: MPNST, patient number 51

source_name: Patient number 51

tag: location group


title: MPNST, patient number 43

source_name: Patient number 43

value: retroperitoneum


title: U87MG_1

tag: cell type


title: Tnrc6a Trim71-/-_1

description:
Trim71-/-_1
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Upf1-/-
TruSeq Illumina Total RNA-seq (stranded - high input)


title: SHEP.tet21n Dox siSNRPD3 #1_rep2

tag: treatment


title: MPNST, patient number 25

source_name: Patient number 25

value: arm


title: U2OS cells S2P IR batch 2 rep 2

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

library_source: other

data_processing:
mNET-Seq: adapter trimming with Cutadapt v. 1.8.3 in paired end mode
mNET-Seq: data mapping with STAR to hg38
extraction of properly mapped, properly paired reads with SAMTools
Extraction of most 3' nucleotide of Read 2, strandedness of Read 1
Creation of bigwig files using DeepTools BamCoverage
Assembly: hg38
Supplementary files format and content: RNA Pol II density across gene body of each gene excluding proximal promoter region
Library strategy: mNET-Seq

molecule: other

source_name: Bone

growth_protocol: cells were cultured in Dulbecco's modified Eagle complete medium (DMEM, Sigma) with 10% fetal bovine serum (Life Technologies) at 37°C and 5% CO2

extract_protocol:
Nascent RNA was isolated using immunopurification of mammalian nascent elongating transcripts (mNET-IP) as described in Nojima 2016.
Libraries were prepared as described in Nojima 2016; small RNA-seq library

treatment_protocol: DNA double-strand breaks were induced with 10 Gy irradiation for 10 mins

value: Bone

value: osteosarcoma

value: WT

value: S2P IR  batch 2 rep 2


title: SHEP.tet21n Dox siSNRPD3 #1_rep1

value: DOX


title: SHEP.tet21n DMSO siSNRPD3 #2_rep2

value: DMSO


title: Tnrc6a Ctrl_2

description:
Ctrl_2
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-
TruSeq Illumina Total RNA-seq (stranded - high input)

value: Experiment 3


title: Tnrc6a Ctrl_1

description:
Ctrl_1
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-
TruSeq Illumina Total RNA-seq (stranded - high input)

value: Mouse embryonic stem cells


title: U2OS cells Y1P IR batch 2 rep 2

value: Y1P IR  batch 2 rep 2


title: Tnrc6a Ctrl_3

description:
Ctrl_3
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-
TruSeq Illumina Total RNA-seq (stranded - high input)


title: SHEP.tet21n DMSO siSNRPD3 #2_rep3


title: U87MG_2

value: control


title: U2OS cells S5P IR batch 2 rep 2

value: S5P IR  batch 2 rep 2


title: SHEP.tet21n DMSO siSNRPD3 #2_rep1


title: SHEP.tet21n DMSO siSNRPD3 #1_rep3


title: Cas9 Trim71-/-_3

description:
Trim71-/-_3
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a
TruSeq Illumina Total RNA-seq (stranded - high input)


title: U2OS cells S5P no IR batch 2 rep 2

value: S5P no IR batch 2 rep 2


title: MPNST, patient number 24

source_name: Patient number 24

value: MPNST tissue sample

value: MPNST relapse

value: shoulder


title: MPNST, patient number 23

source_name: Patient number 23

value: MPNST primary

value: retroperitoneum

value: Non-extremities


title: Cas9 Trim71-/-_2

description:
Trim71-/-_2
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a
TruSeq Illumina Total RNA-seq (stranded - high input)


title: U2OS cells S2P no IR batch 2 rep 2

value: Bone

value: osteosarcoma

value: S2P no IR  batch 2 rep 2


title: MPNST, patient number 21

source_name: Patient number 21

value: thigh

value: Extremities


title: MPNST, patient number 19

source_name: Patient number 19

value: arm


title: SHEP.tet21n DMSO siSNRPD3 #1_rep2

value: DMSO


title: MPNST, patient number 22

source_name: Patient number 22

value: mediastinum


title: MPNST, patient number 20

source_name: Patient number 20


title: SHEP.tet21n DMSO siSNRPD3 #1_rep1


title: Cas9 Trim71-/-_1

description:
Trim71-/-_1
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a
TruSeq Illumina Total RNA-seq (stranded - high input)

value: Experiment 3

value: Mouse embryonic stem cells


title: SHEP.tet21n Dox siControl_rep3

value: DOX

value: siControl


title: SHEP.tet21n Dox siControl_rep2


title: U2OS cells Y1P IR batch 2 rep 1

value: WT

value: Y1P IR  batch 2 rep 1


title: Cas9 Ctrl_3

description:
Ctrl_3
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)
TruSeq Illumina Total RNA-seq (stranded - high input)


title: U2OS cells S5P IR batch 2 rep 1

value: S5P IR  batch 2 rep 1


title: U2OS cells S2P IR batch 2 rep 1

value: S2P IR  batch 2 rep 1


title: Cas9 Ctrl_2

description:
Ctrl_2
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)
TruSeq Illumina Total RNA-seq (stranded - high input)


title: Cas9 Ctrl_1

description:
Ctrl_1
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
Input RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)
TruSeq Illumina Total RNA-seq (stranded - high input)


title: Monocyte mouse2

description: DNA barcode

source_name: Monocytes

value: Monocytes


title: SHEP.tet21n Dox siControl_rep1


title: U2OS cells S5P no IR batch 2 rep 1

value: Bone

value: S5P no IR  batch 2 rep 1


title: Experiment 4: HA-Tnrc6a_Upf1KO_IP_3

description: Experiment 4

data_processing:
Base calling and quality scoring is performed using RTA software (v3.4.4), demultiplexing with  bcl2fastq2 v2.20.
Alignment was performed as follows: Samples were aligned against the GRCm38 mouse genome assembly from GENCODE (Frankish et al., 2021), primary assembly from release M24).(Rosenbloom et al., 2015) Alignments were performed using STAR version 2.7.3a with settings --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1(Gaidatzis et al., 2015). These settings follow ENCODE guidelines and report a single randomly selected alignment for reads that map to the genome no more than 20 times(Langmead et al., 2009) Gene annotations were also obtained from GENCODE release M24, transforming the gtf file into a Bioconductor TxDb object using the makeTxDbFromGFF function from the GenomicFeatures package (version 1.44.0, (Lawrence et al., 2013). Gene-level read counts were obtained by summing the counts from the union of all exons per gene, using the qCount function from the QuasR package (version 1.32.0, (Gaidatzis et al., 2015)) with the created TxDb and parameters orientation = “opposite”.
Assembly: mm10
Supplementary files format and content: csv: First column contains ENSEMBL transcript ID, second column contains ENSEMBL gene ID,  third column contains ENTREZ gene ID, fourth column contains gene symbol (Ensembl identifiers), fifth column contains gene nams (EMSENBL), sixth column contains summed width of exons per gene (quasr package),  columns named 'raw.count' contain raw counts of reads overlapping each gene for each sample, columns named 'rpkm' contain rpkm read counts overlapping each gene for each sample.

source_name: embryonic stem cells

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)

value: GFP_5xT71BS, HA-AVI-Tnrc6a,Upf1-/-

value: IP

value: embryonic stem cells


title: SHEP.tet21n DMSO siControl_rep3


title: Experiment 4: HA-Tnrc6a_Upf1KO_IP_2

description: Experiment 4


title: U2OS cells Y1P no IR batch 2 rep 2

value: osteosarcoma

value: Y1P no IR  batch 2 rep 2


title: U2OS cells S2P no IR batch 2 rep 1

value: S2P no IR  batch 2 rep 1


title: SHEP.tet21n DMSO siControl_rep2

value: DMSO


title: MPNST, patient number 17

source_name: Patient number 17

value: MPNST tissue sample

value: MPNST primary

value: leg

value: Extremities


title: MPNST, patient number 18

source_name: Patient number 18

value: buttock


title: U2OS cells Y1P no IR batch 2 rep 1

value: WT

value: Y1P no IR  batch 2 rep 1


title: MPNST, patient number 16

source_name: Patient number 16

value: thigh


title: MPNST, patient number 13

source_name: Patient number 13


title: MPNST, patient number 15

source_name: Patient number 15


title: MPNST, patient number 12

source_name: Patient number 12

value: lower trunk

value: Non-extremities


title: Experiment 4: HA-Tnrc6a_Upf1KO_IP_1

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a,Upf1-/-


title: MPNST, patient number 11

source_name: Patient number 11


title: SHEP.tet21n DMSO siControl_rep1

source_name: SHEP.tet21n cells

value: siControl


title: U2OS cells S2P IR batch 1 rep 2

source_name: Bone

value: Bone

value: S2P IR  batch 1 rep 2


title: U2OS cells S5P IR batch 1 rep 2

value: osteosarcoma

value: S5P IR  batch 1 rep 2


title: Experiment 4: HA-Tnrc6a_IP_3

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a

value: IP

value: embryonic stem cells


title: MDA-MB-231 cells - siCNT

city: Suwon-si

first: Jongsu

last: Kim

address: 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, Republic of Korea (16419)

country: South Korea

institute: Sungkyunkwan university

description: Sample 1

data_processing:
Ilumina NovaSeq 6000 reads were trimmed in Trimmomatic v0.38.
Quality check was performed though FastQC v0.11.7.
High throughput sequencing data mapped to GRCh37 genomic reference using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1.
FPKM and TPM were calculated using StringTie version 2.1.3b.
Assembly: They were aligned to reference genotype (GRCh37.p13, gencode release 19)
Supplementary files format and content: Expression_Profile.GRCh37.gene.txt: Tab-delimited text file includes read counts, FPKMs and TPMs for each sample.
Supplementary files format and content: Tab file includes FPKMs and TPMs for each sample

source_name: breast; mammary gland

growth_protocol: MDA-MB-231 human breast cancer cell line was maintained in Dulbecco’s modiﬁed Eagle’s medium (DMEM, 10-013-CVR, Corning, NY, USA) supplemented with 10% FBS and 1% antibiotics (penicillin 10,000 U/mL, streptomycin 10,000 µg/mL). Cells were incubated at 37 °C in a humidiﬁed atmosphere with 5% CO2. For experiments, we used MDA-MB 231 at 70–90% conﬂuence.

extract_protocol:
RNA was harvested using Rneasy Mini Kit (QIAGEN, Cat. No. 74106). Illumina TruSeq Stranded Total RNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA) was used with 1ug of total RNA for each sample for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded totalRNA ribo-zero kit

treatment_protocol: Cells in serum-free medium were treated with kahweol (50 µM) for 48 h.

value: epithelial cell

value: breast; mammary gland

tag: transfection

value: control

value: untreated


title: Experiment 4: HA-Tnrc6a_Ago2KO_IP_3

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a,Ago2-/-


title: Experiment 4: HA-Tnrc6a_Ago2KO_IP_2

description: Experiment 4


title: U2OS cells S2P no IR batch 1 rep 2

value: WT

value: S2P no IR  batch 1 rep 2


title: MDA-MB-231 cells - siCTGF+KW

description: Sample 4

value: MDA-MB-231 human breast cancer cell line

value: CTGF siRNA

value: kahweol (50 µM) for 48 h


title: U2OS cells S5P no IR batch 1 rep 2

value: Bone

value: S5P no IR batch 1 rep 2


title: Experiment 4: HA-Tnrc6a_IP_2

description: Experiment 4


title: MDA-MB-231 cells - siCNT+KW

description: Sample 2


title: Experiment 4: HA-Tnrc6a_Ago2KO_IP_1

description: Experiment 4


title: Mock-Infection-3

city: Hong Kong

first: Peng

last: Luo

address: 21 Sassoon Rd

institute: The University of Hong Kong

data_processing:
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp. Low Quality is defined as:i.Reads with more than 5% unknown bases (“N”)，ii.Reads having more than 50% of bases with quality value <= 11
i.STAR Version 2.5.2: Alignment(https://github.com/alexdobin/STAR)
ii.RSEM Version 1.2.31: Quantify expression(https://deweylab.github.io/RSEM/)
iii.EBSeq Version 1.18.0: Identify differentially expressed genes(http://bioconductor.org/packages/release/bioc/html/EBSeq.html)
Assembly: Human Genome GRCh38

source_name: lung

extract_protocol:
The samples were extracted by a modified Folch extraction procedure. Specifically, 4.9 ml of a Chloroform/Methanol solution (2:1, v/v) was added to the cells. The mixture was subjected to two cycles of sonication at 10 microns for 20 seconds on ice, followed by a 10 second pause. Subsequently, the mixture was centrifuged at 4000 rpm for 5 minutes, resulting in the formation of a clear supernatant. To this, 2.5 ml of the supernatant was combined with 0.5 ml of NaCl/Water (0.73%, w/v) and vortexed for 30 seconds. The resulting aqueous layer was discarded, and the organic layer was washed twice with 0.5 ml of Methanol/Water (1:1, v/v) without mixing. The aqueous layer was again discarded, and the organic layer was dried under a gentle stream of nitrogen at 45°C. For esterification, the dried sample was dissolved in a mixture of 0.1 ml of chloroform, 1 ml of methanol, and 50 µl of concentrated hydrochloric acid (35%, w/w). The solution was then covered with nitrogen and the tube was tightly closed. After vortexing, the tube was heated at 100°C for 1 hour. Once the solution cooled to room temperature, 1 ml of hexane and 1 ml of water were added for extraction of fatty acid methyl esters (FAMEs). The tube was vortexed, and after phase separation, up to 1 µl of the hexane phase was injected for GC-MS analysis.
Sequencing libraries were constructed and sequenced in the Proteomics and Metabolomics Core (LKS Faculty of Medicine, The University of Hong Kong). After filtering the low-quality reads, clean reads were mapped to reference sequences using HISAT/Bowtie2. The DEGs in treated samples were submitted to DAVID server for pathway enrichment and cluster analysis. Gene Ontology (GO) enrichment analysis of DEGs was implemented using the GOseq R package. KOBAS software was used to examine the statistical enrichment of DEGS in The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.

value: lung

value: adenocarcinomicepithelial cells

value: PBS treatment


title: U2OS cells Y1P IR batch 1 rep 2

value: osteosarcoma

value: Y1P IR  batch 1 rep 2


title: MPNST, patient number 10

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

institute: Institute for Cancer Research, Oslo University Hospital

data_processing: Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software (v1.4.1.46, HTA-2.0_0.r3 library files).

source_name: Patient number 10

extract_protocol: Total RNA was isolated from tissue samples using either the Qiagen AllPrep DNA/RNA/miRNA Universal kit or a standard Trizol extraction method.

value: MPNST tissue sample

value: MPNST primary

value: upper trunk

value: Non-extremities


title: Experiment 4: HA-Tnrc6a_IP_1

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a

value: IP

value: embryonic stem cells


title: Mock-Infection-2


title: MDA-MB-231 cells - siCTGF

description: Sample 3

value: MDA-MB-231 human breast cancer cell line

value: epithelial cell

value: breast; mammary gland

value: untreated


title: U2OS cells Y1P no IR batch 1 rep 2

value: Bone

value: WT

value: Y1P no IR  batch 1 rep 2


title: Experiment 4: untagged control_IP_3

description: Experiment 4

value: GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)


title: U2OS cells S5P IR batch 1 rep 1

value: osteosarcoma

value: S5P IR  batch 1 rep 1


title: MPNST, patient number 8

source_name: Patient number 8

value: MPNST tissue sample

value: pelvis


title: MPNST, patient number 7

source_name: Patient number 7

value: MPNST primary

value: thigh

value: Extremities


title: MPNST, patient number 4

source_name: Patient number 4


title: MPNST, patient number 5

source_name: Patient number 5

value: lower trunk

value: Non-extremities


title: MPNST, patient number 9

source_name: Patient number 9

value: retroperitoneal


title: Mock-Infection-1

value: lung

value: adenocarcinomicepithelial cells

value: PBS treatment


title: Experiment 4: untagged control_IP_2

description: Experiment 4

source_name: embryonic stem cells

value: IP

value: embryonic stem cells


title: U2OS cells S2P IR batch 1 rep 1

value: Bone

value: WT

value: S2P IR  batch 1 rep 1


title: PPSR ICB BHB treated Cell Line 2

first: Xin

last: Lu

state: IN

address: 109 Galvin Life Science Center

department: Biological Sciences

data_processing:
PolyA selection for mRNA species (eukaryotic)
STAR Transcripts were generated

source_name: PPS-ICBR

extract_protocol:
Zymo Research Miniprep was used to extract the RNA of the cels
Samples were sent to GeneWiz

value: PPS-ICBR

value: Immunotherapy and Castration Resistant Prostate Cancer Cell Line

value: PTEN/P53/SMAD4 Knock Out

value: 3mM Beta-hydroxybutyrate 18 Hours


title: U2OS cells Y1P IR batch 1 rep 1

value: osteosarcoma

value: Y1P IR  batch 1 rep 1


title: PPSR ICB BHB treated Cell Line 1


title: H1N1-PBS-3


title: MPNST, patient number 1

source_name: Patient number 1

value: MPNST tissue sample

value: MPNST primary


title: U2OS cells S5P no IR batch 1 rep 1

value: S5P no IR  batch 1 rep 1


title: Experiment 4: HA-Tnrc6a_Upf1KO_input_2

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a, Upf1-/-

value: input


title: H1N1-PBS-1

value: lung

value: adenocarcinomicepithelial cells

value: PBS treatment


title: H1N1-Mannose-3

value: 25mM mannose treatment


title: MPNST, patient number 3

source_name: Patient number 3

value: thigh

value: Extremities


title: U2OS cells S2P no IR batch 1 rep 1

value: Bone

value: WT

value: S2P no IR  batch 1 rep 1


title: PPSR ICB Untreated Cell Line 2

value: PPS-ICBR

value: Immunotherapy and Castration Resistant Prostate Cancer Cell Line

value: PTEN/P53/SMAD4 Knock Out

value: No Treatent


title: AS78_CD8CCR4

city: Bellinzona

first: Veronica

last: Martini

state: Ticino

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine

description: Patient with active AS under TNFi therapy

data_processing:
RNA sequencing reads were aligned with the STAR-aligner. The Ensembl human genome build GRCh38 was used as reference. Gene expression values were computed with the function featureCounts from the R package Rsubread while gene expression analysis was performed using the BigOmics platform.
Assembly: GRCh38
Supplementary files format and content: xlsx format, counts and related gene description

source_name: blood

extract_protocol:
After sorting, CD8+CCR4+ T-cells were stored in TRIzol Reagent (15596026, Life Technologies) at -80°C until RNA extraction was performed. Total RNA was extracted with Zymo-Spin IC Columns (C1004-50, Zymo Research) and Direct-zol RNA MiniPrep Kit (R2050, Zymo Research) according to manufacturer’s instructions.
NEBNext Ultra Directional RNA Library Prep for Illumina (New England BioLabs Inc.) and the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) kits were then used for library and cDNA synthesis and addition of barcode sequences, as per manufacturer’s instruction.

value: blood

value: CD8+ CCR4+ T cells


title: Experiment 4: HA-Tnrc6a_Ago2KO_input_3

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-

value: embryonic stem cells


title: AS43_CD8CCR4


title: U2OS cells Y1P no IR batch 1 rep 1

value: osteosarcoma

value: Y1P no IR  batch 1 rep 1


title: Experiment 4: HA-Tnrc6a_Upf1KO_input_1

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a, Upf1-/-

value: input


title: H1N1-Mannose-1

value: lung

value: adenocarcinomicepithelial cells

value: 25mM mannose treatment


title: AS51_CD8CCR4


title: Experiment 4: HA-Tnrc6a_Ago2KO_input_2

description: Experiment 4


title: Experiment 4: HA-Tnrc6a_Ago2KO_input_1

description: Experiment 4


title: TLE-nonHS patient3

city: shanghai

first: che

last: che

state: - None -

address: ruijin second road, No 197, huangpu district，shanghai

institute: ruijin hospital

data_processing:
Raw data were processed through Seqtk. In this step, the raw data were cleaned by removing reads containing adaptors, contaminants, and low-quality reads. Additionally, the Q30, and GC content were calculated to estimate the quality of clean reads. Next, the clean reads were aligned to the reference genome (GRCh38) using HISAT2.
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet file includes raw counts for each sample
Supplementary files format and content: Excel spreadsheet file includes FPKM values for each sample

source_name: brain

extract_protocol:
The total RNA was extracted using miRNeasy Micro Kit (Cat#217084, Qiagen), and RNA quality was checked using an Agilent Bioanalyzer 4200 (Agilent technologies, Santa Clara, CA, US).
Sequencing libraries were generated using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (NR604, Vazyme, Nanjing, China) according to the manufacturer’s instructions.

value: brain


title: Ribo_4A2KO_PP242_10uM

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

source_name: HEK293 T-REx

growth_protocol: DMEM + GlutaMAX-I with 10% FBS at 5% CO2, 37°C

extract_protocol:
Cells were directly lysed in lysis buffer on culture dishes.
For ribosome profiling (Ribo), RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq (RNA), RNA extraction and TruSeq Stranded mRNA Library Prep Kit (Illumina). For RNA pulldown-Seq (RIP), pulldown by streptavidin beads, elution by biotin, RNA extraction, and TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: PP242 treatment was performed for 30 min at 37°C. siRNAs transfection was performed using the TransIT-X2 Dynamic Delivery System for 72 h.

value: HEK293 T-REx

value: EIF4A2 KO


title: Ribo_4A2KO_DMSO_rep2

value: DMSO


title: HDB_CD8CCR4

description: Healthy donor


title: AS58_CD8CCR4

description: Patient with inactive AS under TNFi therapy


title: Experiment 4: HA-Tnrc6a_Upf1KO_input_3

description: Experiment 4


title: Experiment 4: untagged control_IP_1

description: Experiment 4

value: GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)

value: IP


title: H1N1-PBS-2

value: PBS treatment


title: H1N1-Mannose-2


title: Ribo_4A2KO_DMSO_rep1


title: TLE-HS patient3


title: HDA_CD8CCR4

description: Healthy donor

value: blood

value: CD8+ CCR4+ T cells


title: Ribo_4A2KO_PP242_1uM

value: PP242 1 µM


title: RIP_4A2_pulldown_rep2

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts


title: Experiment 4: HA-Tnrc6a_input_1

description: Experiment 4

value: GFP_5xT71BS, HA-AVI-Tnrc6a

value: embryonic stem cells


title: Experiment 4: HA-Tnrc6a_input_2

description: Experiment 4


title: TLE-HS patient2


title: TLE-nonHS patient2


title: TLE-HS patient1


title: Experiment 4: untagged control_input_2

description: Experiment 4


title: TLE-nonHS patient1


title: Experiment 4: HA-Tnrc6a_input_3

description: Experiment 4


title: DM_34

city: NEW DELHI

last: Chopra

state: DELHI

address: Dr BRA-IRCH AIIMS

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Science

data_processing:
Quality check by FastQC
Trimming of adaptors by Trimmomatic 0.33
Alignment through TopHat2 2.1.1
Assemblies of samples and DEG analysis through Cufflinks package.
GSEA through DAVID data base
Assembly: hg38
Supplementary files format and content: Normalized FPKM values in a text matrix

source_name: Blood

extract_protocol:
RNA was isolated from patient samples by the TRIzol method.
Illumina Truseq total RNA sample preparation kit

value: Blood

value: PBMC

tag: disease state


title: RIP_4A2_input_rep2


title: Experiment 4: untagged control_input_1

description: Experiment 4

value: input


title: Experiment 4: untagged control_input_3

description: Experiment 4


title: DM_33


title: HD37_CD8CCR4

description: Healthy donor


title: RNA_4A1KO_rep2

value: EIF4A1 KO


title: HD38_CD8CCR4

description: Healthy donor


title: DM_32


title: Experiment 3: HA-Tnrc6a_Upf1KO_IP_3

description: Experiment 3

value: GFP_5xT71BS, HA-AVI-Tnrc6a,Upf1-/-


title: RNA_4A1KO_rep1


title: RIP_4A2_pulldown_rep1


title: AS93_CD8CCR4

description: Patient with inactive AS not under TNFi therapy


title: DM_35


title: DM_31


title: AS50_CD8CCR4

description: Patient with active AS not under TNFi therapy


title: HD21_CD8CCR4

description: Healthy donor


title: Experiment 3: HA-Tnrc6a_Upf1KO_IP_1

description: Experiment 3


title: Experiment 3: HA-Tnrc6a_Upf1KO_IP_2

description: Experiment 3


title: RNA_naive_rep1

value: Naive


title: DC_30


title: Donor19, Oleic Acid, 72h

description:
Passed QC
D19-OA-72h

data_processing:
FastQC v0.11.9 was used for checking raw read QC
Adapter clipping was performed using Cutadapt v2.10
RNAseq reads were aligned to human reference genome GRCh38 using Ensembl v99 & star v2.7.5a
Gene quantification was then performed using htseq-count v0.12.4
Assembly: GRCh38
Supplementary files format and content: TSV, gene raw count

source_name: Buffy Coat

extract_protocol:
RNA was harvested using Zymo Quick-DNA/RNA Microprep Plus Kit (Zymo). 1μg of total RNA was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared from 200ng RNA using the Illumina Truseq stranded mRNA library prep (Illumina, 20020595) after depletion of ribosomal RNA with Ribo Zero Gold (Illumina, 20037135)

value: Buffy Coat

value: CD4+ T cell

value: Oleic Acid

tag: donor

value: Donor 19

tag: time

tag: batch

value: batch 2


title: Experiment 3: HA-Tnrc6a_Ago2KO_IP_3

description: Experiment 3

tag: genotype

value: GFP_5xT71BS, HA-AVI-Tnrc6a,Ago2-/-

value: IP


title: DC_29


title: Donor19, Oleic Acid, 48h

description:
Passed QC
D19-OA-48h


title: Experiment 3: HA-Tnrc6a_Ago2KO_IP_2

description: Experiment 3