title: Cancer stem cells isolated from HT29 (Group HT29) 2

type: RNA

city: Delhi

first: Janvie

last: Manhas

state: Delhi

address: Ansari Nagar

department: Biochemistry

country: India

institute: All India Institute of Medical Sciences

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cancer stem cells isolated from HT29 (Group HT29) Replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the One-Color Low total RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol reagent. The protocol includes brief pipetting and vorteing, followed by phase seperation by chloroform and precipitation using iso-propanol. This was followed by washing by 75% ethanol and elution in nuclease-free waster. Total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Single cell suspensions were stained with anti-CD44 and anti-CD166 antibodies and FACS was done to isolate CD44CD166 dual positive and CD44CD166 dual negative populations for downstream assays.

value: HT29 colorectal cancer cell line

tag: gender

value: Female

value: cancer stem cells


title: (4) 50:50 sperm to blood cell count

status: Public on Nov 07 2023

type: genomic

city: Provo

first: Timothy

last: Jenkins

state: UT

address: LSB

department: Cell Biology

country: USA

institute: Brigham Young University

description:
GSM16
50:50 sperm to blood ce

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R Minfi Package

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: individual 16

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from sperm and blood using Qiagen DNeasy Kit according to standard instructions

value: Male

tag: sample type

value: 50:50 sperm to blood cell count

tag: disease state


title: (3) 50:50 sperm to blood cell count

description:
GSM12
50:50 sperm to blood ce

source_name: individual 12


title: CD8 TRM_RNA seq#4 Donor10-treatment3_48h

status: Public on Nov 06 2023

type: SRA

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
75 cycle
D10_T3_48h

library_source: transcriptomic

data_processing:
Reads were aligned to human genome by STAR2
Raw read counts were conducted by HTSeq-count
Digintal expression normalization was done with DEseq2
Assembly: hg38
Supplementary files format and content: Raw read count in tab-delimited text format

molecule: total RNA

source_name: PBMC

growth_protocol: All cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
RNA was extracted using the Qiagen AllPrep DNA/RNA 96-well system
Libraries were generated using ThruPLEX DNA-Seq Library Preparation Kit (Takara Bio, USA)

tag: tissue

value: PBMC

tag: cell line

value: Primary

tag: cell type

tag: genotype

tag: treatment

value: OKT3 + MAdCAM + RA + TGFβ


title: CD8 TRM_RNA seq#4 Donor10-treatment2_48h

description:
75 cycle
D10_T2_48h

value: OKT3 + MAdCAM + RA


title: CD8 TRM_RNA seq#3 Donor8-treatment3_48h

description:
75 cycle
D8_T3_48h


title: Cancer stem cells isolated from HT29 (Group HT29) 1

source_name: Cancer stem cells isolated from HT29 (Group HT29) Replicate 1


title: seedlings, Col0_rep1

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
The reads for each sample were aligned to the TAIR10 A. thaliana genome from ensembl (release v29) using HISAT2 (v2.0.4) with the following command-line parameters: --fr --rna-strandness RF --known-splicesite-infile.
Mapped reads were sorted using samtools sort (v1.1).
Reads were counted with htseq-count (v0.6.0) and the following command-line parameters: -a 0 -s reverse using Araport11 gene annotation (release 201604).
Assembly: TAIR10
Supplementary files format and content: raw counts

organism: Arabidopsis thaliana

source_name: 14-day-old seedlings

growth_protocol: Seeds were surface-sterilized with 30% bleach/0.02% Triton-X100 solution and stratified for 2 days at 4°C on half-strength MS (Murashige and Skoog, 1962) basal salt medium supplemented with 1% (w/v) sucrose and 0.3% phytagel (Sigma-Aldrich). Seddlings were grown in Percival growth chambers at 22/19°C on a 16-h-light and 8-h-dark (long-day) photoperiod.

extract_protocol:
Total RNA was isolated from 14-day-old seedlings using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal (Plant Leaf).

value: wild type (Col-0)

value: 14-day-old seedlings


title: (3) pure blood

description:
GSM10
pure blood

source_name: individual 10

value: pure blood


title: CD8 TRM_RNA seq#3 Donor8-treatment2_48h

description:
75 cycle
D8_T2_48h


title: (3) 50:50 sperm to blood DNA

description:
GSM11
50:50 sperm to blood DNA

source_name: individual 11

value: 50:50 sperm to blood DNA


title: (4) pure sperm

description:
GSM13
pure sperm

source_name: individual 13

value: pure sperm


title: (4) 50:50 sperm to blood DNA

description:
GSM15
50:50 sperm to blood DNA

source_name: individual 15


title: Cancer stem cells isolated from HCT116 (Group HCT116) 2

source_name: Cancer stem cells isolated from HCT116 (Group HCT116) Replicate 2

value: HCT 116 colorectal cancer cell line


title: (4) pure blood

description:
GSM14
pure blood

source_name: individual 14


title: Non-cancer stem cells isolated from HT29 (Group HT29) 1

source_name: Non-cancer stem cells isolated from HT29 (Group HT29) Replicate 1

value: non-cancer stem cells


title: CD8 TRM_RNA seq#3 Donor8-treatment1_48h

description:
75 cycle
D8_T1_48h


title: CD8 TRM_RNA seq#3 Donor7-treatment1_48h

description:
75 cycle
D7_T1_48h


title: CD8 TRM_RNA seq#2 Donor6-treatment3_48h

description:
75 cycle
D6_T3_48h


title: Non-cancer stem cells isolated from HT29 (Group HT29) 2

source_name: Non-cancer stem cells isolated from HT29 (Group HT29) Replicate 2


title: CD8 TRM_RNA seq#2 Donor6-treatment2_48h

description:
75 cycle
D6_T2_48h


title: Cancer stem cells isolated from HCT116 (Group HCT116) 1

source_name: Cancer stem cells isolated from HCT116 (Group HCT116) Replicate 1


title: Non- cancer stem cells isolated from HCT116 (Group HCT116) 2

source_name: Non- cancer stem cells isolated from HCT116 (Group HCT116) Replicate 2


title: (2) 50:50 sperm to blood cell count

description:
GSM8
50:50 sperm to blood cell

source_name: individual 8


title: Non- cancer stem cells isolated from HCT116 (Group HCT116) 1

source_name: Non- cancer stem cells isolated from HCT116 (Group HCT116) Replicate 1


title: CD8 TRM_RNA seq#2 Donor4-treatment2_48h

description:
75 cycle
D4_T2_48h


title: (2) 50:50 sperm to blood DNA

description:
GSM7
50:50 sperm to blood DNA

source_name: individual 7


title: (3) pure sperm

description:
GSM9
pure sperm

source_name: individual 9


title: CD8 TRM_RNA seq#2 Donor4-treatment1_48h

description:
75 cycle
D4_T1_48h

source_name: PBMC


title: (2) pure sperm

description:
GSM5
pure sperm

source_name: individual 5


title: CD8 TRM_RNA seq#2 Donor6-treatment1_48h

description:
75 cycle
D6_T1_48h


title: siScramble_Pool2

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

data_processing:
Fastq files were then aligned using STAR algorithm (version 2.7.6a)
quality control of the alignment realized with Picard tools (version 2.8.1)
Reads were then count using RSEM (v1.3.1)
the statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0)
Assembly: Ensembl Homo sapiens GRCm38 reference,  release 101
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: KGN

growth_protocol: KGN cells were maintained in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA extraction was performed 30 hours after transfection, following the TRI-reagent supplier’s instructions (MRC)
1 ug of high quality total RNA sample (RIN >8.8) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions.

treatment_protocol: KGN cells were transiently transfected in 6-well plates (same conditions as above) with 30 pmoles of a pool of 3 different siRNAs against FOXL2 for RNA-seq experiments (Dharmacon, ON-TARGETplus siRNAs, pool KD1: J-009075-06-005, J-009075-07-005, J-009075-08-005, KD2: J-009075-06-005, J-009075-07-005, J-009075-09-005 and KD3: J-009075-06-005, J-009075-08-005, J-009075-09-) or an equal amount of the control/scrambled siRNA (Dharmacon, D-001810-10-05) using Lipofectamine RNAiMax (Thermo Fisher Scientific).

value: KGN

value: Granulosa cell line

value: FOXL2 WT/WT

value: siRNA scramble


title: siScramble_Pool1


title: Peripheral blood mononuclear cells from Patient 8 after 3 months acupuncture therapy

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

description:
Human_AP_P8_3M
Gene expression data from RA patient after 3 months AP therapy.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).
Raw data Affymetrix .CEL files were pre-processed using mas5 in the affy R package.
SupplementaryTables-mRNA-human-1.1_FullAnon.xls: Excel file includes the differential and functional analysis.
Clinical_patients_data_20220831_FullAnon.xlsx: Excel file includes clinical data.

label: biotin

source_name: Human peripheral blood mononuclear cells, AP, 3 months therapy

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin-labeled cRNA.

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were freshly isolated on Ficoll gradient (Histopaque®-1077, Sigma Aldrich, USA) according to the manufacturer's procedures. Separated cells were maintained in RNAlater (Ambion, USA) at -80ºC until the end of the study and then processed in a whole batch for the following extraction.
Total RNA was extracted and purified using Norgen Biotek kit (#47800) then checked for the RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: Blood sampling was carried out before any therapy in both AP and MTX groups, then after 2 weeks and 3 months in AP group and after 3 months only in MTX group.

value: peripheral blood mononuclear cells

value: rheumatoid arthritis

value: female

tag: age

tag: treatment group

value: acupuncture+methotrexate

tag: time point

value: after 3 months therapy

tag: patient id


title: siScramble_Pool3


title: Peripheral blood mononuclear cells from Patient 4 after 3 months MTX therapy

description:
Human_MTX_P4_3M
Gene expression data from RA patient after 3 months MTX therapy.

source_name: Human peripheral blood mononuclear cells, MTX, 3 months therapy

value: methotrexate


title: siFOXL2_Pool3

value: siRNA against FOXL2


title: MDA-MB-157, LG1

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

data_processing:
We used the R/Bioconductor package edgeR to generate CPM_TMM normalized counts. Briefly, starting with the data in the raw count file, any gene that did not have a CPM value of 0.5 in two or more samples was filtered out. calcNormFactors was then used to calculate the normalization factors for the remaining genes using the TMM normalization method. CPM was then calculated while using the TMM normalization factors for these remaining genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes CPM_TMM normalized values for each Sample

source_name: Breast cancer cell line

growth_protocol: Breast cancer cells (MDA-MB-157) were cultured under low (5mM) and high glucose (25mM)

extract_protocol:
RNA isolation was done using RNeasy Plus Mini Kits from Qiagen. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies) and  sequencing was performed on an Illumina HiSeq machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For each experimental group there were four replicates.  In brief, 5×10^5cells in a T25 flask were treated with low or high glucose for 48 hrs before RNA was isolated.

value: breast cancer cell

tag: er status

value: ER negative

value: low glucose


title: siFOXL2_Pool2


title: Peripheral blood mononuclear cells from Patient 9 after 3 months acupuncture therapy

description:
Human_AP_P9_3M
Gene expression data from RA patient after 3 months AP therapy.


title: Peripheral blood mononuclear cells from Patient 2 after 3 months acupuncture therapy

description:
Human_AP_P2_3M
Gene expression data from RA patient after 3 months AP therapy.


title: Peripheral blood mononuclear cells from Patient 7 after 3 months MTX therapy

description:
Human_MTX_P7_3M
Gene expression data from RA patient after 3 months MTX therapy.


title: Peripheral blood mononuclear cells from Patient 5 after 3 months MTX therapy

description:
Human_MTX_P5_3M
Gene expression data from RA patient after 3 months MTX therapy.


title: Peripheral blood mononuclear cells from Patient 6 after 3 months acupuncture therapy

description:
Human_AP_P6_3M
Gene expression data from RA patient after 3 months AP therapy.


title: (1) pure blood

description:
GSM2
pure blood

source_name: individual 1

value: Male

value: pure blood


title: siFOXL2_Pool1


title: (1) 50:50 sperm to blood DNA

description:
GSM3
50:50 sperm to blood DNA

value: 50:50 sperm to blood DNA


title: RWPE1-ERG, PABPC1 ChIP

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

institute: Indiana University

library_source: genomic

data_processing:
Previously published input data sets were used for RWPE1 (SRA accession number SRR13438519) and RWPE1-ERG (SRA Accession Number SRR13438521).
Reads were aligned to the human reference genome hg19 using Bowtie2.
Duplicates were removed using samtools, and blacklisted regions were removed using bedtools.
Peaks were called using MACS2 (Version 2.1.2), with a p-value cutoff of 0.001.
Assembly: hg19
Supplementary files format and content: MACS2 Peak files

growth_protocol: Keratinocyte Serum Free media containing Bovine Pituitary Extract and Human Recombinant EGF, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico waterbath sonicator (Diagenode).
Illumina TruSeq barcode adapters were ligated to repaired ends of sheared fragments. Adapter-ligated fragments were PCR amplified and purified with Ampure XP beads and size selection from a 2% agarose gel to remove adapter dimer contamination. Libraries were pooled and validated using the Agilent D1000 TapeStation.

value: Human Normal Immortalized Protate Epithelium

tag: group

value: ERG

tag: chip antibody

value: PABPC1 (Santa Cruz, SC-166027)


title: RWPE1-Empty Vector, PABPC1 ChIP

value: Empty Vector


title: Peripheral blood mononuclear cells from Patient 1 after 2 weeks acupuncture therapy

description:
Human_AP_P1_2W
Gene expression data from RA patient after 2 weeks AP therapy.

source_name: Human peripheral blood mononuclear cells, AP, 2 weeks therapy

value: peripheral blood mononuclear cells

value: after 2 weeks therapy


title: (2) pure blood

description:
GSM6
pure blood

source_name: individual 6


title: Peripheral blood mononuclear cells from MTX group, Patient 5 before therapy

description:
Human_MTX_P5_T0
Gene expression data from RA patient before MTX therapy.

source_name: Human peripheral blood mononuclear cells, MTX, before therapy

value: rheumatoid arthritis

value: female

value: before therapy


title: (1) 50:50 sperm to blood cell count

description:
GSM4
50:50 sperm to blood cell

value: 50:50 sperm to blood cell count


title: Peripheral blood mononuclear cells from Patient 3 after 2 weeks acupuncture therapy

description:
Human_AP_P3_2W
Gene expression data from RA patient after 2 weeks AP therapy.

value: acupuncture+methotrexate


title: Peripheral blood mononuclear cells from MTX group, Patient 7 before therapy

description:
Human_MTX_P7_T0
Gene expression data from RA patient before MTX therapy.

value: methotrexate


title: 4 day-old Kn-0 seedlings 3-h ABA treatment rep2

city: Oeiras

first: Alba

last: Rodríguez Díez

state: Lisboa

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

description:
Processed data refers to control vs aba
kn_DESeq2_res.txt
kn_rMATS.xlsx

data_processing:
genome_build/assembly: Kn-0 genome assembly (https://doi.org/10.1038/nature10414)
Genome indexes were generated and reads were mapped using STAR
Count lists were generated using featureCounts
Differential gene expression analysis was conducted using DESeq2
Alternative splicing quantification was conducted using rMATS-turbo
Supplementary files format and content: col_DESeq2_res.txt Tab-delimited text file containing the DESeq2 output quantifying the differential gene expression between Col-0 control and ABA-treated samples
Supplementary files format and content: kn_DESeq2_res.txt Tab-delimited text file containing the DESeq2 output quantifying the differential gene expression between Kn-0 control and ABA-treated samples
Supplementary files format and content: col_rMATS.xlsx Excel workbook file containing the rMATS-turbo output quantifying the differential alternative splicing events between Col-0 control and ABA-treated samples
Supplementary files format and content: kn_rMATS.xlsx Excel workbook file containing the rMATS-turbo output quantifying the differential alternative splicing events between Kn-0 control and ABA-treated samples

molecule: polyA RNA

source_name: whole seedling

growth_protocol: Stratified seeds were grown on filter paper in control medium under continuous light for 4 days

extract_protocol:
Total RNA was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA Kit (Analytik Jena)
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4 day-old seedlings were transferred to control or 5µM-ABA medium for 3 hours

value: whole seedling

tag: genetic background

tag: developmental stage

value: 4 day-old

value: 3 h ABA


title: 4 day-old Kn-0 seedlings 3-h ABA treatment rep3


title: Peripheral blood mononuclear cells from Patient 1 after 3 months acupuncture therapy

description:
Human_AP_P1_3M
Gene expression data from RA patient after 3 months AP therapy.

tag: gender

value: after 3 months therapy


title: 4 day-old Kn-0 seedlings 3-h mock treatment rep3

value: 3 h mock


title: 4 day-old Kn-0 seedlings 3-h ABA treatment rep1


title: CD8 TRM_RNA seq#2 Donor4-treatment3_48h

description:
75 cycle
D4_T3_48h

value: PBMC

value: Primary

value: OKT3 + MAdCAM + RA + TGFβ


title: 4 day-old Kn-0 seedlings 3-h mock treatment rep1


title: E 13.5 trachea Epithelium control 3

city: Cincinnati

first: Debora

last: Sinner

state: OH

address: 3333 Burnet Ave

department: Neonatology and Pulmonary Biology

institute: CCHMC

data_processing:
FASTQ files were trimmed using TrimGalore and aligned using Bowtie2 to mouse reference genome mm10.
RNAseq Normalized gene expressions were generated using Cufflinks.
RNAseq Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the RNAseq raw gene counts and calculate differentially expressed genes
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Mus musculus

source_name: embryonic trachea

extract_protocol:
RNA was isolated using trizol according to manufacturer’s instructions
SMART-Seq v4 Ultra Low Input Kit for Sequencing. Illumina Nextera XT library was used for sequencing library preparation

treatment_protocol:
e13.5 tracheas were dissected out of  γSMAeGFP  embryos and tracheal cells isolated by FACS.
Embryonic tracheal tissue was cut into small pieces and enzymatically treated with TrypLE express for 15 minutes to generate a single-cell suspension. Afterward, cells were stained with Epcam APC antibody, filtered, and sorted using FACS.

value: embryonic trachea

value: Embryonic epithelial and mesenchymal

tag: cell type (sorted)

value: Epithelium

value: Bmp4 f/f; gamma SMA eGFP


title: 4 day-old Kn-0 seedlings 3-h mock treatment rep2


title: Peripheral blood mononuclear cells from MTX group, Patient 4 before therapy

description:
Human_MTX_P4_T0
Gene expression data from RA patient before MTX therapy.

value: peripheral blood mononuclear cells

tag: disease state

value: rheumatoid arthritis

value: female


title: E 13.5 trachea Epithelium control 2

tag: tissue


title: E 13.5 trachea Epithelium control 1


title: E13.5 trachea Muscle control 3

value: Muscle


title: 4 day-old Col-0 seedlings 3-h ABA treatment rep3

description:
Processed data refers to control vs aba
col_DESeq2_res.txt
col_rMATS.xlsx

data_processing:
genome_build/assembly: Col-0 TAIR10 v.50
Genome indexes were generated and reads were mapped using STAR
Count lists were generated using featureCounts
Differential gene expression analysis was conducted using DESeq2
Alternative splicing quantification was conducted using rMATS-turbo
Supplementary files format and content: col_DESeq2_res.txt Tab-delimited text file containing the DESeq2 output quantifying the differential gene expression between Col-0 control and ABA-treated samples
Supplementary files format and content: kn_DESeq2_res.txt Tab-delimited text file containing the DESeq2 output quantifying the differential gene expression between Kn-0 control and ABA-treated samples
Supplementary files format and content: col_rMATS.xlsx Excel workbook file containing the rMATS-turbo output quantifying the differential alternative splicing events between Col-0 control and ABA-treated samples
Supplementary files format and content: kn_rMATS.xlsx Excel workbook file containing the rMATS-turbo output quantifying the differential alternative splicing events between Kn-0 control and ABA-treated samples


title: E13.5 trachea Muscle control 2


title: 4 day-old Col-0 seedlings 3-h ABA treatment rep2


title: 4 day-old Col-0 seedlings 3-h mock treatment rep3


title: E13.5 trachea Muscle control 1


title: 4 day-old Col-0 seedlings 3-h mock treatment rep2


title: d6 p.i. LCMV Arm P14, rep 1

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

library_source: transcriptomic single cell

data_processing:
Illumina bcl2fastq2 Conversion Software 2.20. Quality score is encoded in a +33 offset ASCII (Sanger like)
The raw sequencing reads were filtered, demultiplexed and aligned to the mouse genome and transcriptome (mm10, refdata-gex-mm10-2020-A) using the 10x Genomics Cell Ranger pipeline (version 5.0.1). The cellranger count function was used with default parameters (i.e. --include-introns=FALSE), except for d4 cells where the parameter --force-cells=3399 was provided. A total of 20169 cells were called by the Cell Ranger pipeline
Assembly: mm10
Supplementary files format and content: For each library, the 3 processed files correspond to the output generated by the Cell Ranger pipeline (version 5.0.1). The matrix.mtx file contains the raw counts per cell (in columns) per gene (in rows). The corresponding cell barcode names are in the barcodes.tsv file, and the corresponding genes are in the features.tsv file.

source_name: splenocyte

extract_protocol:
Cell droplet encapsulation, lysis and RNA capture was performed using 10x Chromium Controller (10x Genomics) and the Chromium Single Cell 3′ v3 Reagent Kit according to the manufacturer’s protocol. One cDNA library per time point post infection was generated and further sequenced (paired-end) on a HiSeq4000 device (Ilumina)
10x genomics Single Cell 3' v3 chemistry

treatment_protocol: Tcf7gfp P14 cells (CD45.2) purified from the spleen of naive mice were adoptively transferred into C57BL/6 (B6)  mice (CD45.1) one day prior to infection with LCMV Armstrong (Arm). Total P14 cells sorted from the spleen of recipient mice at d2, d3, d4 and d6 post infection (p.i) or from the spleen of naive mice (d0), were subjected to scRNA-Seq analysis.

value: splenocyte

value: CD8 T cells expressing a P14 TCR and a Tcf7gfp reporter

tag: strain

value: d6 p.i. LCMV Arm


title: 4 day-old Col-0 seedlings 3-h ABA treatment rep1

value: whole seedling

value: 4 day-old

value: 3 h ABA


title: d4 p.i. LCMV Arm P14, rep 1

tag: cell type

value: d4 p.i. LCMV Arm


title: Peripheral blood mononuclear cells from AP group, Patient 9 before therapy

description:
Human_AP_P9_T0
Gene expression data from RA patient before AP therapy.

source_name: Human peripheral blood mononuclear cells, AP, before therapy

value: acupuncture+methotrexate

value: before therapy


title: Peripheral blood mononuclear cells from AP group, Patient 6 before therapy

description:
Human_AP_P6_T0
Gene expression data from RA patient before AP therapy.


title: Peripheral blood mononuclear cells from AP group, Patient 3 before therapy

description:
Human_AP_P3_T0
Gene expression data from RA patient before AP therapy.


title: Peripheral blood mononuclear cells from AP group, Patient 8 before therapy

description:
Human_AP_P8_T0
Gene expression data from RA patient before AP therapy.


title: Peripheral blood mononuclear cells from AP group, Patient 2 before therapy

description:
Human_AP_P2_T0
Gene expression data from RA patient before AP therapy.


title: d0, Naive P14, rep 1

tag: genotype


title: 4 day-old Col-0 seedlings 3-h mock treatment rep1

tag: treatment

value: 3 h mock


title: d2 p.i. LCMV Arm P14, rep 1

value: d2 p.i. LCMV Arm


title: d8 P14, Klrg1+ Tcf7-, rep 3

description: d8_KLRG1pos_Tcf7neg_shift_bampe_peaks.broadPeak

data_processing:
Illumina bcl2fastq2 Conversion Software 2.20. Quality score is encoded in a +33 offset ASCII (Sanger like)
For each file, the fastq files of the 4 separate lanes were concatenated into a single fastq file. The sequencing files were processed using the “atac” method of the bcbio-nextgen pipeline (v1.2.4). The pipeline first started by trimming sequencing adapters (Illumina and TruSeq) and low quality ends using Atropos (v1.1.28) (Didion et al., 2017), with arguments --overlap 8, --minimum-length 25, --quality-cutoff 5 and --no-default-adapters.
The quality-filtered and trimmed reads were aligned to the mouse genome (mm10, 2018-10-10 94) using the bwa mem algorithm (v0.7.17-r1188) (https://arxiv.org/abs/1303.3997), with arguments -c 250 and -M. Sequence alignment map (sam) files were sorted and converted to binary (bam) files using biobambam2 (v2.0.87) (https://gitlab.com/german.tischler/biobambam2) and indexed using samtools (v1.9) (Li et al., 2009).
To correct for the 9-bp duplication created by DNA repair of the nick by the Tn5 transposase, the aligned reads were shifted using alignmentSieve (deepTools3 v3.5.0) (Ramirez et al., 2016) with the --ATACshift and --minMappingQuality arguments. Samtools and sambamba (v0.7.1) (Tarasov et al., 2015) were used with the shifted aligned reads as input to remove reads aligning to the mitochondrial genome, unmapped reads or reads not forming proper pairs, as well as duplicate reads.
Finally, using the bam files of the 3 replicates per cell population, peaks were called using the callpeak function of Macs2 (v2.2.7.1) (Zhang et al., 2008b), with arguments -g ‘mm’, --keep-dup all, --broad and -q 0.05.
Assembly: mm10
Supplementary files format and content: All processed files are broadPeak files output by Macs2. One broadPeak file was generated per cell population by providing the bam files of the 3 replicates to the callpeak function. The location of the called peaks is indicated in the first 3 columns, with chromosome location and start and stop position

extract_protocol:
ATAC-seq was performed as described (Buenrostro et al., 2015). Briefly, 50,000 flow-sorted CD8+ T cells were washed with cold 1x PBS and resuspended in 50 µl of ice-cold lysis buffer (10mM Tris-Cl, pH 7.4, 10nM NaCl, 3mM MgCl2 and 0.1% (v/v) of NP-40. Cells were centrifuged immediately and the resulting pellet (nuclei) was resuspended in 50 µl of transposase reaction mix (25 µl 2xTD buffer (Illumina), 25 µl Tn5 transposase (Illumina) and 22.5 µl of nuclease-free water), followed by incubation at 37ºC for 30 min (while gently shacking). Tagmented DNA was cleaned using QIAGEN MinElute PCR Purification kit as described in the kit’s protocol
Library preparation was performed using Illumina’s Unique Dual (UD) Indexes (R#20027213) and NEBNext High-Fidelity 2x PCR Master Mix (M0541), using the following program: 5 min 72ºC, 30s 98ºC; 10 cycles: 10s 98ºC, 30s 63ºC, 1 min 72ºC: Hold 4ºC. The sequencing libraries were sequenced on 4 lanes of an Illumina HiSeq 4000 device (paired-end, 150 read length) .

treatment_protocol: Tcf7GFP P14 cells (CD45.2) purified from the spleen of naive mice were adoptively transferred into C57BL/6 (B6)  mice (CD45.1) one day prior to infection with LCMV Armstrong (Arm). At d4 and d8 post infection, Tcf7GFP+, Tcf7GFP- Klrg1- and Tcf7GFP- Klrg1+ P14 cells were flow sorted from the spleens of infected recipient mice. CD8+ CD44- CD62L+ cells were flow sorted from the spleen of naive P14 mice (d0). The sorted cells were subjected to bulk ATACseq analysis.

value: CD8 T cells expressing a P14 TCR and Tcf7GFP reporter

value: d8 p.i. LCMV Arm


title: BMDC.IV RRBS

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: all live cells were used at the indicated day

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome (mm9) using Bismark with the Bowtie2 option.  Binary Alignment Map (BAM) files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages (available upon request)  Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Genome_build: mm9
Supplementary_files_format_and_content: Count matrix of methylaed and unmethylated reads for each CpG covered by a minimum of 10 reads within each group.  For each CpG there is the chromosome location and for each sample there are three columns of data containing the sample name followed by the following extensions: ".meth", % of reads methylated; ".u", number of reads unmethylated; ".m", number of reads methylated.

source_name: Day 7 Bone-marrow Derived Dendritic cells (BMDC)

growth_protocol: BM cells were cultured in RPMI supplemented with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U penicillin-streptomycin, 0.05 mM 2-ME, and 20% of Flt3L containing supernatant, secreted by an SP2/0 transfected cell line for the indicated number of days.

extract_protocol:
Genomic DNA was isolated by phenol-chloroform extraction followed by ethanol precipitation.
Two aliquots of DNA were separately digested with either TaqI or MspI restriction enzymes over night and subsequently pooled for all downstream processing.  Digested DNA was end-repaired, A-tailed, and adapters containing methylated cytosines ligated on using the KAPA HyperPrep kit according to the manufacturers instructions.  Adapter-ligated DNA was bisulfite converted over using the EpiTech Bisulfite kit (Qiagen, Inc).  Bisulfite treated libraries were PCR amplified using indexed primers and the HiFi HotStart Uracil+ polymerase (KAPA Biosystems).

tag: Sex

value: male

tag: time in culture (days)

value: bone marrow

value: Bone-marrow Derived Dendritic Cell (BMDC)


title: BMDC.I RRBS


title: CMP.II RRBS

source_name: Day 4 Common Myeloid Progenitors (CMP)

value: Common Myeloid Progenitor (CMP)


title: CMP.I RRBS


title: BMDC.IV RNA-seq

data_processing:
Raw RNA sequencing reads were mapped to the mm9 version of the Mus musculus genome using TopHat-v2.0.13
Per gene coverage from each sample were counted using the samtools-v1.1 into a single file.  Next, for each gene the raw read counts were normalized to Reads Per Kilobase of transcript per Million mapped reads (Rpkm) for all samples.
Genome_build: mm9
Supplementary_files_format_and_content: File containing rpkm values for all genes.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy MiniPrep kit.
cDNA libraries were prepared using the SMARTer v3 Ultra Low Input RNA Kit (Takara Bio), followed by NexteraXT DNA Library Preparation Kit (Illumina) as per the manufacturer’s instructions.


title: BM.III.D0 RRBS

source_name: bone-marrow cells


title: d4 P14, Klrg1+ Tcf7-, rep 2

description: d4_KLRG1pos_Tcf7neg_shift_bampe_peaks.broadPeak

value: splenocyte


title: d3 p.i. LCMV Arm P14, rep 1

value: CD8 T cells expressing a P14 TCR and a Tcf7gfp reporter

value: d3 p.i. LCMV Arm


title: d4 P14, Klrg1+ Tcf7-, rep 3


title: BMDC.III RNA-seq


title: d4 P14, Klrg1+ Tcf7-, rep 1


title: d8 P14, Klrg1- Tcf7-, rep 2

description: d8_KLRG1neg_Tcf7neg_shift_bampe_peaks.broadPeak


title: d8 P14, Klrg1- Tcf7-, rep 1


title: d8 P14, Klrg1+ Tcf7-, rep 1


title: d8 P14, Klrg1- Tcf7-, rep 3


title: BM.III.D0 RNA-seq


title: BM.II.D0 RNA-seq


title: d8 P14, Klrg1+ Tcf7-, rep 2


title: BM.II.D0 RRBS


title: d4 P14, Klrg1- Tcf7-, rep 3

description: d4_KLRG1neg_Tcf7neg_shift_bampe_peaks.broadPeak


title: (1) pure sperm

description:
GSM1
pure sperm

value: Male

tag: sample type

value: pure sperm


title: SCR6: SW480 CONTROL

city: New Haven

first: Vasilis

last: Vasiliou

address: 60 College St

institute: Yale university

data_processing:
Partek® Flow platform (Partek, St. Louis, MO, USA)
Raw fastq files were trimmed (quality score >20 and read length >25) and aligned to the reference genome list (human genome hg38) following the Bowtie algorithm
The reads per million (RPM) values of genes were normalized and used for downstream analyses.
Statistical analyses and heatmap visualization were performed using the Qlucore Omics Explorer platform (Qlucore AB, Lund, Sweden)
Assembly: human genome hg38
Supplementary files format and content: normalised data in txt format

source_name: COLON

extract_protocol:
using 0.25% trypsin-EDTA (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA) and brought to a final concentration of 106 cells/ml in cell medium.
strand-specific sequencing libraries

value: COLON

tag: cell line

value: COLON CANCER CELLS

value: WT


title: d4 P14, Klrg1- Tcf7-, rep 2

value: d4 p.i. LCMV Arm


title: SCR5: SW480 CONTROL


title: SCR4: SW480 CONTROL


title: CMP.II RNA-seq


title: CMP.I RNA-seq


title: d8 P14, Klrg1- Tcf7+, rep 3

description: d8_KLRG1neg_Tcf7pos_shift_bampe_peaks.broadPeak


title: d4 P14, Klrg1- Tcf7-, rep 1


title: d8 P14, Klrg1- Tcf7+, rep 2


title: KD5: SW480 KD

value: ALDH1B1 KD


title: KD6: SW480 KD


title: d4 P14, Klrg1- Tcf7+, rep 3

description: d4_KLRG1neg_Tcf7pos_shift_bampe_peaks.broadPeak


title: KD4: SW480 KD


title: Naive P14, rep 3

description: d0_CD8pos_CD44neg_CD62Lpos_shift_bampe_peaks.broadPeak


title: SCP1-tfcp2-wt-r8

city: Heidelberg

first: Claudia

last: Scholl

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center (DKFZ)

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 8

data_processing:
alignment using STAR v2.5.3a
duplicate marking using sambamba v0.6.5
read quantification using subread/featureCounts v1.5.1 and GENCODE19 as gene model
Assembly: hs37d5 + PhiX
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

source_name: bone marrow

extract_protocol:
RNA was isolated using the RNeasy Mini Plus Kit (Qiagen). cDNA synthesis from 1.5 or 2 μg RNA was performed using the High Capacity cDNA RT Kit (Applied Biosystems).
TruSeq RNA Sample Preparation Kit v2 (Illumina)
RNA-Seq, paired-end, strand-specific

value: mesenchymal stem cell of the bone marrow

value: Case


title: d4 P14, Klrg1- Tcf7+, rep 2

value: CD8 T cells expressing a P14 TCR and Tcf7GFP reporter


title: SCP1-tfcp2-wt-r7

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 7


title: SCP1-tfcp2-wt-r3

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 3


title: SCP1-tfcp2-wt-r5

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 5


title: Naive P14, rep 1


title: SCP1-tfcp2-wt-r6

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 6


title: d8 P14, Klrg1- Tcf7+, rep 1

value: d8 p.i. LCMV Arm


title: TRAP-Day30-rep4

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

institute: Universitätsklinikum Hamburg-Eppendorf

description:
30_TRAP_rep4
raw_counts.tsv
norm_counts.tsv

data_processing:
Alignment with STAR (v2.5.2b)
Counting by featureCounts (v1.5.1)
Analysis with DESeq2 (v1.36.0)
Assembly: ensemble.mouse.GRCm38r79
Supplementary files format and content: Files represent raw counts, norm counts. Rows represent genes, columns represent samples

source_name: Cervical spinal cord

extract_protocol:
Translating ribosome affinity purification (TRAP)
NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs)

value: Cervical spinal cord

value: Spinal motor neurons

tag: mouse strain

value: Chat bacTRAP line DW167

value: EAE day 30


title: d4 P14, Klrg1- Tcf7+, rep 1

value: splenocyte


title: TRAP-Day30-rep3

description:
30_TRAP_rep3
raw_counts.tsv
norm_counts.tsv


title: SCP1-tfcp2-wt-r2

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 2

value: bone marrow


title: SCP1-tfcp2-wt-r9

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 9


title: SC-Day30-rep5

description:
30_SC_rep5
raw_counts.tsv
norm_counts.tsv

value: All spinal cord cells


title: Naive P14, rep 2

value: CD8 T cells expressing a P14 TCR


title: SCP1-tfcp2-wt-r1

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 1


title: TRAP-Day30-rep5

description:
30_TRAP_rep5
raw_counts.tsv
norm_counts.tsv


title: SCP1-tfcp2-wt-r4

description: RNA-Seq of SCP-1 cells transduced with wild-type TFCP2, replicate 4


title: SC-Day30-rep3

description:
30_SC_rep3
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-wt-r5

description: RNA-Seq of SCP-1 cells transduced with wild-type FUS, replicate 5


title: SC-Day30-rep1

description:
30_SC_rep1
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-wt-r4

description: RNA-Seq of SCP-1 cells transduced with wild-type FUS, replicate 4


title: SCP1-fus-wt-r2

description: RNA-Seq of SCP-1 cells transduced with wild-type FUS, replicate 2


title: SCP1-fus-wt-r3

description: RNA-Seq of SCP-1 cells transduced with wild-type FUS, replicate 3


title: SCP1-fus-wt-r1

description: RNA-Seq of SCP-1 cells transduced with wild-type FUS, replicate 1


title: TRAP-Day20-rep5

description:
20_TRAP_rep5
raw_counts.tsv
norm_counts.tsv

value: EAE day 20


title: TRAP-Day20-rep4

description:
20_TRAP_rep4
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-tfcp2-r9

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 9

value: SCP-1 cells transduced with FUS-TFCP2


title: SCP1-fus-tfcp2-r8

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 8


title: TRAP-Day20-rep1

description:
20_TRAP_rep1
raw_counts.tsv
norm_counts.tsv


title: TRAP-Day20-rep3

description:
20_TRAP_rep3
raw_counts.tsv
norm_counts.tsv


title: SC-Day20-rep4

description:
20_SC_rep4
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-tfcp2-r7

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 7


title: SCP1-fus-wt-r6

description: RNA-Seq of SCP-1 cells transduced with wild-type FUS, replicate 6


title: SCP1-fus-tfcp2-r6

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 6


title: SC-Day20-rep5

description:
20_SC_rep5
raw_counts.tsv
norm_counts.tsv


title: SC-Day20-rep2

description:
20_SC_rep2
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-tfcp2-r5

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 5


title: SCP1-fus-tfcp2-r3

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 3


title: TRAP-Day15-rep5

description:
15_TRAP_rep5
raw_counts.tsv
norm_counts.tsv

value: EAE day 15


title: SC-Day30-rep2

description:
30_SC_rep2
raw_counts.tsv
norm_counts.tsv


title: SC-Day30-rep4

description:
30_SC_rep4
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-tfcp2-r4

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 4


title: SC-Day20-rep1

description:
20_SC_rep1
raw_counts.tsv
norm_counts.tsv


title: TRAP-Day15-rep3

description:
15_TRAP_rep3
raw_counts.tsv
norm_counts.tsv


title: SCP1-fus-tfcp2-r2

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 2


title: TRAP-Day15-rep4

description:
15_TRAP_rep4
raw_counts.tsv
norm_counts.tsv


title: SCP1-ewsr1-wt-r3

description: RNA-Seq of SCP-1 cells transduced with wild-type EWSR1, replicate 3


title: SCP1-ewsr1-wt-r2

description: RNA-Seq of SCP-1 cells transduced with wild-type EWSR1, replicate 2


title: TRAP-Day15-rep2

description:
15_TRAP_rep2
raw_counts.tsv
norm_counts.tsv


title: SCP1-ewsr1-wt-r1

description: RNA-Seq of SCP-1 cells transduced with wild-type EWSR1, replicate 1


title: SC-Day15-rep5

description:
15_SC_rep5
raw_counts.tsv
norm_counts.tsv


title: SCP1-ewsr1-tfcp2-r2

description: RNA-Seq of SCP-1 cells transduced with EWSR1-TFCP2, replicate 2

value: SCP-1 cells transduced with EWSR1-TFCP2


title: TRAP-Day15-rep1

description:
15_TRAP_rep1
raw_counts.tsv
norm_counts.tsv


title: SC-Day15-rep4

description:
15_SC_rep4
raw_counts.tsv
norm_counts.tsv


title: SC-Day15-rep3

description:
15_SC_rep3
raw_counts.tsv
norm_counts.tsv


title: SCP1-ewsr1-tfcp2-r1

description: RNA-Seq of SCP-1 cells transduced with EWSR1-TFCP2, replicate 1


title: SC-Day20-rep3

description:
20_SC_rep3
raw_counts.tsv
norm_counts.tsv


title: SC-Day15-rep2

description:
15_SC_rep2
raw_counts.tsv
norm_counts.tsv


title: SCP1-ev-r8

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 8

value: Control


title: SCP1-fus-tfcp2-r1

description: RNA-Seq of SCP-1 cells transduced with FUS-TFCP2, replicate 1

value: mesenchymal stem cell of the bone marrow


title: SCP1-ev-r7

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 7


title: SC-Day15-rep1

description:
15_SC_rep1
raw_counts.tsv
norm_counts.tsv


title: SCP1-ev-r4

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 4


title: TRAP-Day8-rep3

description:
08_TRAP_rep3
raw_counts.tsv
norm_counts.tsv

value: EAE day 8


title: TRAP-Day8-rep2

description:
08_TRAP_rep2
raw_counts.tsv
norm_counts.tsv


title: TRAP-Day8-rep4

description:
08_TRAP_rep4
raw_counts.tsv
norm_counts.tsv


title: SCP1-ev-r5

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 5


title: TRAP-Day8-rep1

description:
08_TRAP_rep1
raw_counts.tsv
norm_counts.tsv


title: SCP1-ev-r2

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 2


title: SCP1-ewsr1-tfcp2-r3

description: RNA-Seq of SCP-1 cells transduced with EWSR1-TFCP2, replicate 3

value: Case


title: SCP1-ev-r3

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 3


title: SCP1-ev-r1

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 1


title: SC-Day8-rep4

description:
08_SC_rep4
raw_counts.tsv
norm_counts.tsv


title: MCF10A-tfcp2-wt-r3

description: RNA-Seq of MCF10A cells transduced with wild-type TFCP2, replicate 3

source_name: breast

value: breast

value: mammary gland cell line


title: MCF10A-tfcp2-wt-r2

description: RNA-Seq of MCF10A cells transduced with wild-type TFCP2, replicate 2


title: SC-Day8-rep5

description:
08_SC_rep5
raw_counts.tsv
norm_counts.tsv

value: Cervical spinal cord


title: SC-Day8-rep2

description:
08_SC_rep2
raw_counts.tsv
norm_counts.tsv

value: Chat bacTRAP line DW167


title: SCP1-ev-r9

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 9


title: MCF10A-tfcp2-wt-r1

description: RNA-Seq of MCF10A cells transduced with wild-type TFCP2, replicate 1


title: SC-Day8-rep1

description:
08_SC_rep1
raw_counts.tsv
norm_counts.tsv


title: MCF10A-fus-wt-r3

description: RNA-Seq of MCF10A cells transduced with wild-type FUS, replicate 3


title: TRAP-Day0-rep4

description:
00_TRAP_rep4
raw_counts.tsv
norm_counts.tsv

value: Spinal motor neurons

value: Healthy, not immunized


title: TRAP-Day8-rep5

description:
08_TRAP_rep5
raw_counts.tsv
norm_counts.tsv


title: MCF10A-fus-wt-r1

description: RNA-Seq of MCF10A cells transduced with wild-type FUS, replicate 1


title: TRAP-Day0-rep2

description:
00_TRAP_rep2
raw_counts.tsv
norm_counts.tsv


title: SCP1-ev-r6

description: RNA-Seq of SCP-1 cells transduced with empty vector, replicate 6

value: bone marrow


title: MCF10A-fus-tfcp2-r2

description: RNA-Seq of MCF10A cells transduced with FUS-TFCP2, replicate 2

value: MCF10A cells transduced with FUS-TFCP2


title: TRAP-Day0-rep3

description:
00_TRAP_rep3
raw_counts.tsv
norm_counts.tsv


title: MCF10A-fus-wt-r2

description: RNA-Seq of MCF10A cells transduced with wild-type FUS, replicate 2


title: MCF10A-fus-tfcp2-r1

description: RNA-Seq of MCF10A cells transduced with FUS-TFCP2, replicate 1


title: SC-Day0-rep5

description:
00_SC_rep5
raw_counts.tsv
norm_counts.tsv

value: All spinal cord cells


title: MCF10A-ewsr1-wt-r3

description: RNA-Seq of MCF10A cells transduced with wild-type EWSR1, replicate 3


title: SC-Day0-rep3

description:
00_SC_rep3
raw_counts.tsv
norm_counts.tsv


title: MCF10A-ewsr1-wt-r2

description: RNA-Seq of MCF10A cells transduced with wild-type EWSR1, replicate 2


title: SC-Day8-rep3

description:
08_SC_rep3
raw_counts.tsv
norm_counts.tsv


title: SC-Day0-rep4

description:
00_SC_rep4
raw_counts.tsv
norm_counts.tsv


title: SC-Day0-rep2

description:
00_SC_rep2
raw_counts.tsv
norm_counts.tsv


title: TRAP-Day0-rep1

description:
00_TRAP_rep1
raw_counts.tsv
norm_counts.tsv


title: MCF10A-fus-tfcp2-r3

description: RNA-Seq of MCF10A cells transduced with FUS-TFCP2, replicate 3


title: MCF10A-ewsr1-tfcp2-r3

description: RNA-Seq of MCF10A cells transduced with EWSR1-TFCP2, replicate 3


title: MCF10A-ewsr1-tfcp2-r2

description: RNA-Seq of MCF10A cells transduced with EWSR1-TFCP2, replicate 2


title: MCF10A-ewsr1-wt-r1

description: RNA-Seq of MCF10A cells transduced with wild-type EWSR1, replicate 1


title: MCF10A-ewsr1-tfcp2-r1

description: RNA-Seq of MCF10A cells transduced with EWSR1-TFCP2, replicate 1


title: Cohort2_miRAP_Healthy_rep2

description:
Cohort2_Hip2
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv

data_processing:
Oasis 2.0 (https://oasis.ims.bio/)
Analysis with DESeq2 (v1.36.0)
Supplementary files format and content: Files represent raw counts, norm counts.  Rows represent miRNAs, columns represent samples

extract_protocol:
miRNA tagging and affinity-purification (miRAP)
TruSeq Small RNA Library Prep Kit (Illumina)

tag: cohort

value: R26-LSL-tAgo2 x Chat-IRES-Cre


title: Cohort2_miRAP_Healthy_rep3

description:
Cohort2_Hip3
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv


title: Cohort2_miRAP_Healthy_rep4

description:
Cohort2_Hip4
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv


title: MCF10A-ev-r3

description: RNA-Seq of MCF10A cells transduced with empty vector, replicate 3


title: MCF10A-ev-r2

description: RNA-Seq of MCF10A cells transduced with empty vector, replicate 2


title: Cohort2_miRAP_EAE_rep4

description:
Cohort2_Eip4
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv

value: EAE day 12


title: Cohort2_miRAP_EAE_rep3

description:
Cohort2_Eip3
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv


title: Cohort2_miRAP_EAE_rep2

description:
Cohort2_Eip2
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv


title: Cohort1_miRAP_Healthy_rep5

description:
Cohort1_Hip5
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Cohort2_miRAP_EAE_rep1

description:
Cohort2_Eip1
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv


title: Cohort1_miRAP_Healthy_rep3

description:
Cohort1_Hip3
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: SC-Day0-rep1

description:
00_SC_rep1
raw_counts.tsv
norm_counts.tsv


title: Cohort1_miRAP_Healthy_rep4

description:
Cohort1_Hip4
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_12_3

city: Tucson

first: Megha

last: Padi

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

description: normalized_counts_cpm1filter_nooutliers.txt

data_processing:
Reads were mapped to a transcriptome index generated from the hg19 human reference genome, using Tophat 2.0.4 and Bowtie1 with all default parameters except for the following: --no-novel-juncs --transcriptome-only -p 6.
Counts were quantified using HTSeq with default bam file parameters, except the following: -s no.
Samples with low read counts were removed from further analysis.  Additionally, outliers were identified using principle component analysis and were subsequenty removed from further analysis.  Samples that were excluded are: TLT_8_1 (low read count), TLT_8_2 (low read count), TLT_40_1 (low read count), TLT_20_1,  and GFP_4_1 (outlier).
Raw counts were then normalized and log-transformed using edgeR.
Genes with average counts-per-million less than 1 were excluded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with normalized counts-per-million for included genes and samples

source_name: IMR90 human lung embryonic fibroblast

growth_protocol: IMR90 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Cellgro) supplemented with 1% Pen-Strep (Gibco), 1% Glutamax (Gibco), 1% non-essential amino acids (Gibco) and 15% fetal bovine serum (FBS) (Sigma).

extract_protocol:
Total RNA was purified using RNeasy Plus Mini Kit (Qiagen).
Sequencing libraries were prepared with NEBNext mRNA library Prep Master Mix Set for Illumina (New England BioLabs), passed Qubit, Bioanalyzer and qPCR QC analyses, and were subsequently sequenced on HiSeq 2000 system (Illumina).

treatment_protocol: Dox-inducible IMR90 lines expressing ST, ER, TLT or GFP were seeded in 6 cm dishes 24 hours before initiation of timecourse with normal media (no dox). At time zero, cells were refed with dox-containing media.  Time zero cells did not receive dox treatment.  Cells were harvested every 4 hours for the first 24 hours, then every 8 for the next 24 hours.  Cells were not refed after the initial addition of dox-containing media.

value: lung embryonic fibroblast

tag: vector

value: ER

tag: time point (hours)

tag: replicate


title: ER_16_1


title: GFP_8_3

value: GFP


title: Activated CD4+ Tcell - 2divisions - rep2

city: Basel

first: Denis

last: Seyres

address: Hebelstrasse 20

institute: UniversitatSpital Basel

data_processing:
Preprocessing of A-seq2 libraries: We first perform quality analysis and read trimming of A-seq2 read libraries with fastp (v.0.19.7) and the following parameters: minimum length required (-l) = 15,  UMIs were integrated by enabling -U, placed in the read 1 (--umi_loc)=read1 and formed of first 7 bases of each reads (--umi_len=7) and finally max N number  limit was set to 2 (--n_base_limit). Mapping of the trimmed reads on mm10 genome was achieved with STAR (Dobin et al., 2013) (v.2.7.3) by asking end to end alignment (--alignEndsType EndToEnd) and no multi mapped reads (--outFilterMultimapNmax 1). Finally, we used UMIs to remove duplicated reads with umi_tools (v.1.0.0)(Smith, Heger and Sudbery, 2017) dedup (--umi-separator=":" --extract-umi-method="read_id" --method="directional")
Poly(A) site quantification and genomic annotation: Read enriched regions (“peaks”) were called using Fseq (v.1.84) (Boyle et al., 2008) with fragment size (-f) of 50, feature length (-l) of 150 and threshold (-t) of 6. Bins around peaks with less than 10 reads were removed to refine peaks. Within each condition, peaks from each replicates were intersected using BEDTools (v.2.27.1) (Quinlan and Hall, 2010) and resulting intersected peak sets were combined into a master set of peaks using DiffBind R package (v.2.16.2)(Ross-Innes et al., 2012) and a minimum overlap of 1 (peaks need to be present in at least one intersected peakset). Master set of peaks was then sloped by 200bp both sides and overlapped with Poly(A) sites from the PolyAsite resource for mouse version r2.0 (https://www.polyasite.unibas.ch/atlas) (Herrmann et al., 2019). We filtered out peaks with a size greater than 2000bp and smaller than 10bp. A-seq2 reads were quantified using featureCounts function from Rsubread package (v.2.4.3) (Liao, Smyth and Shi, 2019). Peaks were categorized based on their genomic locations (5’UTR, 3’UTR, Exon, Intron, Intergenic) using Gencode VM25 annotations (https://www.gencodegenes.org/mouse/release_M25.html).
Event identification and filtering: To identify events (shortening or lengthening), we used PolyA-miner (https://github.com/LiuzLab/PolyA-miner) (Yalamanchili et al., 2020). Parameters were set as follows: polyA annotations file (-pa) contained the sites identified above, reference fasta sequence (-fasta) was downloaded from Ensembl (http://ftp.ensembl.org/pub/release-94/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) and reference genes bed file (-bed) was created from Ensembl gff3 file (v94). The types of events were stringently defined to fulfill two conditions: transcript is shortened if sample B proximal projection was greater than sample A proximal projection and if sample B distal projection was smaller than sample A distal projection. The opposite conditions identified as a lengthened gene. Events were then filtered on FDR (5%). For each pairwise comparison, MaxAPASwitch position from PolyA-miner output was retained as the most used position on condition B whereas the most covered position was considered as the most used APA site in condition A. This was done according to type of event and strand. The DNA sequence between sites from condition A and B was further used for miRNA and RBP binding/motif analysis.
Functional annotation of APA genes: Functional annotation was carried out using the gprofiler2 R package (v.0.2.0)(Raudvere et al., 2019), model organism was set to "mmusculus", "fdr" correction method and the following sources were interrogated: GO:BP, GO:MF, GO:CC, KEGG, REAC, MIRNA, CORUM and WP. A 5% FDR threshold was applied and the top 5 annotations within each of the sources were plotted.
Genome_build: mm10

source_name: Activated CD4+ Tcell - 2divisions

extract_protocol:
Isolated cells were quickly processed and washed with cold PBS before resuspension in 1ml Trizol. Samples were left at room temperature for 5 min and frozen at -20°C. For RNA extraction, Trizol samples were thawed on ice and 100 µl 1-Bromo-3-Chloropropane was added before mixing and incubation for 15 min at RT. Samples were centrifuged for 15 min at 12000g, 4°C and the aqueous phase was transferred to a fresh tube before mixing with 1 volume isopropanol and a subsequent incubation of 10 min at RT. Samples were then centrifuged for 15 min at 12000g, 4°C and the RNA pellet was washed with 1 ml ethanol followed by a centrifugation for 30 min at 12000g, 4°C. The supernatant was discarded and the pellets briefly dried before the RNA dissolve in dH2O and stored at -80°C.
Briefly, poly(A)+ RNAs were isolated from RNA samples and fragmented by alkaline hydrolysis. Next, adaptors were ligated to the 5' end of enriched poly(A)+ RNAs and reverse transcription was carried out with a bio-dU-dT(25) RT-primer. After USER-enzyme digestion and purification, a second adaptor was ligated to 5' ends of the resulting cDNA. Both adaptors were finally used to PCR-amplify libraries with barcoded primers and used for RNA sequencing (Gruber et al., 2016; Martin et al., 2017).

treatment_protocol: Spleens and lymph nodes were isolated from male C57BL/6N mice at an age of 6-10 weeks. Animal work was done in accordance with the federal and cantonal laws of Switzerland. All organs were collected on ice in complete T cell medium (RPMI 1640 (Sigma), 10% heat-inactivated FCS (Atlanta Biologicals), 2mM Glutamax (Gibco), 50μM β-mercaptoethanol (Gibco), 10mM HEPES (Sigma) and non-essential amino acids (Gibco)) and organs were mashed with a syringe plunger through 45µm filters in medium under sterile conditions. Cell suspensions were transferred to 15 ml tubes and centrifuged for 5 min at 400 g, 4°C. Red blood cell lysis was performed with ACK buffer for 5 min at RT and stopped by addition of medium. Naïve CD4+ T cells were isolated with EasySep Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL Technologies Inc) according to manufacturer’s recommendations. For naïve T cell activation 12 well plates (Corning) were coated with 1ml monoclonal anti-CD3 (2µg/ml, 2C11, BioXcell) in 500 µl PBS for 2 hours at 37°C, 5% CO2. Purified naïve CD4+ T cells were labelled with 2µl CellTracerViolet dye (CTV; in DMSO) in 2ml PBS for 20 min at 37°C and labelling reaction was stopped by addition of 10 ml complete medium. Cells were plated in a density of 4 x 106 CTV-labeled naïve T cells per coated 12 well or 6 well plates in 2 ml or 4 ml, respectively, plus anti-CD28 antibodies (1µg/ml, PV-1, BioXcell) and incubated at 37°C with 5% CO2 for 48 hours. 4-6 x 106 purified naïve CD4+ T cells were resuspended in Trizol on the day of T cell purification (day 0). After 48 hours of cell culture cells were harvested and stained with 1µg/ml propidium iodine briefly before sorting. Cells were sorted by their distinct proliferation peaks (peak 0, peak 1 and peak 2) on FACS-Aria and Influx Cell Sorters (BD Biosciences). Cells were kept on ice and after washing with cold PBS were immediately resuspended in Trizol for RNA extraction. One portion of the cells were used for surface phenotype staining with the fluorochrome-conjugated mAbs: anti-CD4 (clone RM4-5), anti-CD25 (PC61), CD62L (MEL-14), CD44 (IM7), CD69 (H1.2F3), CD16/32 (93, all Biolegend). Cells were measured on a LSR-Fortessa (BD Biosciences) and data was analyzed using FlowJo (Treestar). For time course stimulations purified naïve T cells were incubated under stimulatory conditions for 4, 8, 16, 24, and 48 hours at 37°C with 5% CO2, harvested on the respective time-points, washed in cold PBS and resuspended in Trizol for RNA extraction.

value: CD4+ CD62L- CTV peak 2

value: untreated


title: Cohort1_miRAP_Healthy_rep2

description:
Cohort1_Hip2
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_12_1


title: ER_12_2


title: Cohort1_SC_Healthy_rep5

description:
Cohort1_Hin5
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Activated CD4+ Tcell - 2divisions - rep1


title: Cohort1_miRAP_Healthy_rep1

description:
Cohort1_Hip1
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Cohort1_SC_Healthy_rep4

description:
Cohort1_Hin4
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Activated CD4+ Tcell - 1division - rep2

source_name: Activated CD4+ Tcell - 1division

value: CD4+ CD62L- CTV peak 1


title: Cohort1_SC_Healthy_rep3

description:
Cohort1_Hin3
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Activated CD4+ Tcell - 1division - rep1


title: ER_8_3


title: Cohort2_miRAP_Healthy_rep1

description:
Cohort2_Hip1
raw_counts_cohort2.tsv
norm_counts_cohort2.tsv


title: Cohort1_miRAP_EAE_rep5

description:
Cohort1_Eip5
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Cohort1_SC_Healthy_rep2

description:
Cohort1_Hin2
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_8_2


title: Activated CD4+ Tcell - 0division - rep2

source_name: Activated CD4+ Tcell - 0division

value: CD4+ CD62L- CTV peak 0


title: Cohort1_miRAP_EAE_rep4

description:
Cohort1_Eip4
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_8_1


title: Activated CD4+ Tcell - 0division - rep1


title: Cohort1_miRAP_EAE_rep2

description:
Cohort1_Eip2
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_4_3


title: Cohort1_miRAP_EAE_rep1

description:
Cohort1_Eip1
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_4_2


title: Cohort1_SC_EAE_rep5

description:
Cohort1_Ein5
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Cohort1_SC_EAE_rep3

description:
Cohort1_Ein3
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: ER_4_1


title: Cohort1_SC_EAE_rep2

description:
Cohort1_Ein2
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Cohort1_SC_EAE_rep1

description:
Cohort1_Ein1
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv


title: Naive CD4+ Tcell - rep2

source_name: Naive CD4+ Tcell


title: yuhan-con5

city: Seoul

first: Dongkwon

last: Kim

address: Yonsei ro 50-1

country: South Korea

institute: Yonsei university

data_processing:
Sequnceing and data processing was done by MACROGEN according to MACROGEN protocol.
Briefly, After preprocessing (removing artifacts such as duplicates), reads are mapped to the reference genome using the HISAT2 program, and the transcript assembly is carried out through the StringTie program.
FPKM/RPKM, which is a normaIization value that considers read count, transcript length, and depth of coverage, and TPM values were generated.
Assembly: mm10
Supplementary files format and content: Excel file with FPKM, read counts, TPM

source_name: Tumor

extract_protocol:
We treated YH29407, anti-PD-1 to MC38 tumor bearing mouse and collected tumor and analysis
RNA prepared with SureSelectXT RNA Direct Library Preparation kit and followed SureSelect XT RNA Direct Protocol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tumor

value: Colon cell

tag: strain background

value: WT

value: Non


title: Naive CD4+ Tcell - rep1


title: Naive CD4+ Tcell - rep3


title: Cohort1_SC_Healthy_rep1

description:
Cohort1_Hin1
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv

value: Cervical spinal cord

value: Healthy, not immunized


title: yuhan-con3


title: yuhan-aPD-1_4


title: GFP_8_2

description: normalized_counts_cpm1filter_nooutliers.txt


title: Regulatory CD4+ Tcell - rep2

source_name: Regulatory CD4+ Tcell


title: yuhan-aPD-1_3


title: ER_0_2


title: YH100-com_4


title: Cohort1_miRAP_EAE_rep3

description:
Cohort1_Eip3
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv

value: Spinal motor neurons


title: YH100-com_3


title: MCF10A-ev-r1

description: RNA-Seq of MCF10A cells transduced with empty vector, replicate 1

value: breast

value: mammary gland cell line

value: Control


title: ER_0_1

value: lung embryonic fibroblast


title: Naive CD4+ Tcell - rep4


title: Cohort1_SC_EAE_rep4

description:
Cohort1_Ein4
raw_counts_cohort1.tsv
norm_counts_cohort1.tsv

value: All spinal cord cells

value: R26-LSL-tAgo2 x Chat-IRES-Cre

value: EAE day 12


title: YH100-com_2


title: Memory CD4+ Tcell - rep2

source_name: Memory CD4+ Tcell

value: untreated


title: TLT_48_2

value: TLT


title: YH-100_3


title: YH-100_4


title: TLT_48_1


title: Memory CD4+ Tcell - rep1


title: ER_0_3

value: ER


title: TLT_40_2


title: TLT_40_3


title: N2_AbaPep#07 [HaliPep07]

city: Guangzhou

first: Qiangqiang

last: Wang

email: wqq@whu.edu.cn, fewqq@mail.scut.edu.cn

state: Guangdong

address: Waihuan East Road, No. 381

department: School of Food Science and Engineering

country: China

institute: South China University of Technology

data_processing:
The raw sequencing data was subjected to quality control with SOAPnuke (v1.5.2) software. The clean reads were aligned to the C. elegans reference genome WBcel235 using HISAT2 (v2.0.4). Ericscript (v0.5.5) was subsequently used to detect fusion genes, and rMATS (v3.2.5) was used to identify differential splicing genes. Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and the expression level of genes was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using PossionDis with a significance threshold of false discovery rate ≤ 0.05 and fold change ≥ 2 (i.e. |log2(fold change)| ≥ 1).
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text file include raw Read Count, TPM and FPKM for each Sample.

organism: Caenorhabditis elegans

source_name: Whole nematodes

growth_protocol: Wild-type N2 nematodes were cultured in S medium with E. coli NA22 as food in a shaking incubator at 20°C and 120 rpm.

extract_protocol:
Total RNA was extracted from whole nematodes using TRIzol kit (Invitrogen).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Wild-type N2 nematodes with or without 2 mM of AbaPep#07 treatment from L4 stage were collected at day 10 of adulthood, washed with M9 buffer at least 3 times, and immediately flash-frozen in liquid nitrogen.

value: Whole nematodes

value: Wild-type

value: 2 mM AbaPep#07


title: bladder, Dimethylarsinic Acid, 2years, BT1

city: Osaka

first: Tomoki

last: Yamamoto

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

description:
BT-1
SE75

data_processing:
Raw information detailing single-end 75bp sequencing reads generated by Illumina sequencing (using NextSeq 500) is contained within FASTQ files.
First, Illumina adapter sequence is trimmed from the reads. Then, a custom script is used to trim additional bases that are added during the library creation process to facilitate sequencing.
The resulting reads are then mapped to the genome using RRBSMAP using default settings (12bp seed length, max number of mismatches = 0.08 x read length); only unique alignments are kept (if a fragment maps to more than one location, it is discarded).
Another custom script is then used to remove any PCR duplicates based on a randomized 6-mer barcode; if more than one fragment has the same start and end coordinates as well as the same barcode, all but one are discarded. Alignment data is generated by RRBSMAP. The data were aligned to the rat (rn6) genome.
The differential methylation analysis is generated using DMAP. The resulting regions are then annotated using the HOMER software package. Processed data files contain methylation percentages of genes. These data are generated using the software package GBSA 2.0.
Assembly: Rn6.0
Supplementary files format and content: Tab-delimited text files.

organism: Rattus norvegicus

source_name: bladder tumor

growth_protocol: 10-week-old F344/DuCrj rats were randomly allocated to two groups each based on their body weights (measured just before starting DMA treatment).

extract_protocol:
Samples were digested by Proteinase K at 55⁰C overnight and genomic DNA was extracted using the Quick-gDNA MiniPrep kit (Zymo Research). Genomic DNA (100ng) was digested with TaqaI at 65⁰C for 2h followed by MspI at 37⁰C overnight. Following enzymatic digestion, samples were used for library generation using the Ovation RRBS Methyl-Seq System (Tecan). In brief, digested DNA was randomly ligated, and following fragment end repair, bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen). After conversion and clean-up, samples were amplified resuming the Ovation RRBS Methyl-Seq System protocol for library amplification and purification. Libraries were measured using Agilent 2200 TapeStation System and quantified using the KAPA Library Quant Kit ABI Prism qPCR Mix (Roche).
Libraries were measured using Agilent 2200 TapeStation System and quantified using the KAPA Library Quant Kit ABI Prism qPCR Mix (Roche KK4835). Libraries were sequenced on a NextSeq 500 at SE75.

treatment_protocol: Rats were given drinking water containing 0 and 200 ppm DMA for 104 weeks.

value: bladder tumor

value: dimethylarsinic acid

tag: treatment duration

value: 2 years


title: bladder, control, 2years, C3

description:
C3
SE75

source_name: bladder urothelium

value: bladder urothelium

value: control


title: bladder, Dimethylarsinic Acid, 2years, BT5

description:
BT-5
SE75


title: bladder, Dimethylarsinic Acid, 2years, BT2

description:
BT-2
SE75


title: N2_Untreated [Control]

value: Untreated


title: bladder, Dimethylarsinic Acid, 2years, BT4

description:
BT-4
SE75


title: bladder, Dimethylarsinic Acid, 2years, BT3

description:
BT-3
SE75


title: bladder, control, 2years, C2

description:
C2
SE75


title: bladder, control, 2years, C1

description:
C1
SE75


title: TLT_40_1

description: removed from analysis


title: Il_C3_F

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Dr

department: Radiology

institute: Stanford Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence,
Then mapped to rat genome Rattus Norvegicus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: Colon

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

value: SD

value: Control


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 1, library 15_6_shallow, library 23_2_deep

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

country: United Kingdom

institute: University of Exeter

description: SPLiT-seq

data_processing:
Barcode processing and adapter trimming were made using SPLiT-seq toolbox (https://github.com/RebekkaWegmann/splitseq_toolbox), CutAdapt  v2.8 (https://github.com/marcelm/cutadapt), pairfq makepairs (https://github.com/sestaton/Pairfq) and Picard v2.21.1-SNAPSHOT (https://github.com/broadinstitute/picard)
Genome mapping was made with STAR-2.7.3a (https://github.com/alexdobin/STAR/releases/tag/2.7.3a)
Assembly: Genome assembly will be available on planmine (https://planmine.mpibpc.mpg.de/planmine/genome.do)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Schmidtea mediterranea

source_name: Whole-body

extract_protocol:
We used ACME dissociation to dissociate whole animals into fixed and permeable cell suspensions. Dissociated cells were proccessed using a SPLiT-seq protocol (we sorted singlets by FACS during SPLiT-seq, right before the cell lysis step).
We followed the SPLiT-seq library construction pipeline (Dynabeads cDNA purification, template switching, PCR amplification, size selection, tagmentation, indexed-PCR amplification and second size selection). Size selection was performed using Roche KAPA Pure Beads at 0.6X-0.8X ratios. Tagmentation was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer´s instructions.

value: Whole-body

value: WT


title: Regulatory CD4+ Tcell - rep1

value: untreated


title: LC_C3_F


title: RC_C3_F


title: TLT_32_3

value: lung embryonic fibroblast

value: TLT


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 1, library 15_5_shallow, library 23_1_deep

description: SPLiT-seq


title: TLT_32_2


title: LC_C2_F


title: OG1RF without mannose_biol rep3 [NONWT3_S16]

city: Singapore

first: Casandra

last: Tan

address: 60 Nanyang Drive

country: Singapore

institute: SCELSE

description:
rawcounts_withoutMannose.txt
normalisedCountsCPM_mannose.txt

data_processing:
Raw reads were quality and adapter trimmed using bbduk from BBMap tools (Version 39.79).
Trimmed reads were then mapped using bwa-mem of BWA (Version 0.7.17-r1188) with default options against E. faecalis OG1RF (NCBI accession: CP002621) reference genomes.
Reads mapped to predicted open reading frames were quantified using htseq-count of HTSeq (Version 0.12.4) with option “-m intersection-strict”.
Ribosomal sequences were manually removed from all data sets.
Differential gene expression analysis was performed in R using edgeR (Version 3.28.1).
Assembly: E. faecalis OG1RF (NCBI accession: CP002621)
Supplementary files format and content: Raw counts from HTSeq in .txt format.
Supplementary files format and content: Normalized counts using edgeR for every comparsion made in .txt format.
Supplementary files format and content: Sample metadata csv file used in DGE analysis in edgeR.

organism: Enterococcus faecalis

growth_protocol: Overnight cultures of OG1RF and ∆mptD were sub-cultured to OD600 of 0.01 in a 24-well microtiter plate with containing 1 mL of TSBd supplemented with or without mannose at 37ᵒC.

extract_protocol:
Bacteria were harvested at late log/early stationary phase in RNAprotect™ Bacteria Reagent and incubated at room temperature for 5 min before centrifuging at 10,000 g for 10 min. The supernatant was decanted and bacteria pellets collected were subjected to total RNA extraction using Qiagen RNeasy® Mini Kit with slight modifications. Briefly, cell pellets were resuspended in TE buffer containing 20 mg/mL lysozyme, further supplemented with 20 µL proteinase K and incubated at 37 °C for 1 h. Subsequent RNA extraction steps were performed according to manufacturer’s protocol. The extracted RNA samples were treated with DNase for removal of genome DNA before it was purified using Monarch® RNA cleanup kit.
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instructions but without the oligo dT purification.

treatment_protocol: OG1RF and ∆mptD were grown in TSBd with and without mannose supplementation.

value: wild-type

value: without mannose


title: OG1RF without mannose_biol rep1 [NONWT1_S24]


title: GFP_8_1

value: GFP


title: ∆mptD without mannose_biol rep3 [NONDEL3_S4]

value: mptD deletion


title: TLT_24_3


title: OG1RF without mannose_biol rep2 [NONWT2_S20]


title: YH-100_1

value: Tumor

value: Colon cell


title: ∆mptD without mannose_biol rep1 [NONDEL1_S12]


title: ∆mptD without mannose_biol rep2 [NONDEL2_S8]


title: OG1RF in mannose_biol rep3 [MNEWT3_S23]

description:
rawcounts_withMannose.txt
normalisedCountsCPM_mannose.txt

value: with mannose


title: TLT_24_2


title: TLT_24_1


title: OG1RF in mannose_biol rep2 [MNEWT2_S27]


title: TLT_20_3


title: ∆mptD in mannose_biol rep2 [MNEDEL2_S15]


title: IL_C2_F


title: OG1RF in mannose_biol rep1 [MNEWT1_S30]


title: RC_C1_F


title: LC_C1_F


title: ∆mptD in mannose_biol rep3 [MNEDEL3_S11]


title: ∆mptD in mannose_biol rep1 [MNEDEL1_S19]


title: TLT_20_2


title: LC_C3_M

value: DSS


title: IL_C1_F


title: inoculum_biol rep1 [ino1_S1]

description:
rawcounts_inoculum.txt
normcounts.txt

extract_protocol:
A 1 × 1 cm of mouse skin encompassing the wound site was excised into 2 mL of RNAlater stabilization solution and incubated overnight at 4 °C. The mouse skin was then transferred into 1 mL of TRIzol and cut into smaller pieces. The entire suspension was transferred into Lysing Matrix B 2-mL tubes and homogenized using a FastPrep-24 tissue grinder for 2 rounds of 40 s at 6.0 m/s with 2 min rest on ice in between. To each sample, 200 µL of chloroform was added, vortexed vigorously for 30 s and centrifuged at 12,000 x g for 10 min at 4 °C. The top layer (aqueous phase) containing RNA was transferred to 1.5 mL tubes containing 500 µL of ice-cold ethanol and shaken vigorously before loading into the RNeasy Mini spin columns. Subsequent RNA extraction steps were performed according to manufacturer’s protocol of the RNeasy Mini Kit. Briefly, samples were washed once with Buffer RW1, followed by 2 washes with Buffer RPE and elution of RNA with RNase-free water.
Library preparation was done using the Ribo-Zero Plus rRNA depletion kit as per manufacturer's instructions.

value: inoculum


title: TLT_20_1

description: removed from analysis


title: inoculum_biol rep2 [ino8_S4]

description:
rawcounts_inoculum.txt
normcounts.txt


title: RC_C3_M

value: Colon


title: inoculum_biol rep4 [ino11_S10]

description:
rawcounts_inoculum.txt
normcounts.txt


title: inoculum_biol rep3 [ino10_S7]

description:
rawcounts_inoculum.txt
normcounts.txt


title: RC_C2_F

value: SD


title: TLT_16_3


title: 8h post-infection_biol rep4 [8hpi5_S22]

description:
rawcounts_8hpi.txt
normcounts.txt

value: 8h post-infection


title: 8h post-infection_biol rep3 [8hpi4_S19]

description:
rawcounts_8hpi.txt
normcounts.txt


title: TLT_16_2


title: 8h post-infection_biol rep2 [8hpi3_S16]

description:
rawcounts_8hpi.txt
normcounts.txt


title: RC_C2_M


title: LC_C2_M


title: TLT_16_1


title: TLT_12_3


title: IL_C2_M


title: RC_C1_M


title: S2 day 5 NT Donor 2

city: Stanford

first: Victor

last: Tieu

state: CA California

address: 290 Jane Stanford Way

department: Bioengineering

institute: Stanford University

data_processing:
Transcript abundance was quantified from raw reads via kallisto pseudo-alignment with n = 100 bootstraps.
Assembly: Homo sapiens (GRCh38.p14)
Supplementary files format and content: Transcript abundances in tsv format via kallisto pseudo-alignment (for DE analysis using sleuth, please see supplementary tables in linked publication).

source_name: primary human T cells

extract_protocol:
Total RNA was extracted from approximately 5E6 primary human T cells on day 10 of culture using the RNEasy Plus kit (QIAGEN) according to the manufacturer’s protocol using additional 2-mercaptoethanol.
Total RNA was sent to Novogene (Davis, CA) for cDNA library preparation for mRNA sequencing (polyA capture).
150bp paired-end read (Illumina PE150).

value: primary human T cells


title: S2 day 5 B2M Donor 1


title: S2 day 5 B2M Donor 2


title: TLT_12_1


title: GFP_4_3


title: IL_C1_M


title: 6 day 10 HA NT Donor 2


title: TLT_8_3


title: 6 day 10 HA 4KO Donor 2


title: TLT_12_2


title: 6 day 10 HA AAVS1 Donor 1


title: S2 day 5 NT Donor 1


title: 6 day 10 HA GLY Donor 2


title: 6 day 10 HA 4KO Donor 1


title: IL_C3_M


title: 6 day 10 HA NT Donor 1


title: LC_D4_F


title: 6 day 10 HA GLY Donor 1


title: TLT_8_2

description: removed from analysis


title: 8h post-infection_biol rep1 [8hpi2_S13]

description:
rawcounts_8hpi.txt
normcounts.txt


title: 1 day 10 HA NT Donor 2


title: RC_D4_F


title: 6 day 10 HA AAVS1 Donor 2


title: 1 day 10 HA NT Donor 1


title: LC_C1_M


title: 1 day 10 HA LT Donor 2


title: TLT_8_1

description: removed from analysis


title: IL_D4_F


title: 1 day 10 HA LT Donor 1


title: TLT_4_3


title: LC_D3_F

value: Control


title: 1 day 10 HA T Donor 2


title: 1 day 10 HA L Donor 1


title: IL_D3_F


title: Old_OA_Female_A

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
MAP-RSeqversion 3.1.4 and theSTARv2.6.1c tool were usedto align the raw RNA seq reads to the reference human genome build hg38
QC was performed by FastQC pre- and post-read trimming
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featureCounts
edgeR v3.40.2 for defining differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-separated tsv file containing raw counts

source_name: knee articular cartilage

growth_protocol: Chondrocytes were grown in DMEM/F-12 media supplemented with 10% fetal bovine serum and 1 % Penicillin/streptomycin.

extract_protocol:
RNA isolation: Two step RNA isolation protocols were followed for total RNA extraction: Organic phase isolation was performed with TriReagent®/ bromo–3–chloropropane (BCP) (Thermo Fisher Scientific/Molecular Research Center, Inc., Cincinnati, OH, USA) on the samples and then used for total RNA isolation using a RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions. RNA concentration was measured using a nanophotometer® (Implen, Inc., Westlake Village, CA, USA). RNA purity was A260/280 and A260/230 ˃ 2.0.
Illumina Stranded mRNA library prep with Illlumina NextSeq2000 Sequencing: RNA libraries were prepared using 200 ng of total RNA in 20 µl according to the manufacturer’s instructions for the Illumina Stranded mRNA Ligation Sample Prep Kit (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries were determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced using Illumina’s standard protocol for the NovaSeq 6000. The NovaSeq SP PE100 flow cell was sequenced as 100 X 2 paired end reads using NovaSeq Control Software v1.8.0. Base-calling is performed using Illumina’s RTA version 3.4.4.

treatment_protocol: Chonndrocytes that were passage 1-3 designated as young cells. Chondrocytes later were subjected to serial passaging until they reached to passage 15-18. Late passages were designated as old cells.

value: knee articular cartilage


title: 1 day 10 HA T Donor 1


title: TLT_4_1

value: lung embryonic fibroblast


title: TLT_0_2

value: TLT


title: Old_OA_Male_B


title: Old_Healthy_Male_A


title: RC_D3_F


title: RC_D2_F


title: TLT_0_3


title: Old_OA_Male_A


title: TLT_4_2


title: Young_Healthy_Male_B


title: Old_Healthy_Male_B


title: Young_Healthy_Male_A


title: IL_D2_F


title: Old_OA_Female_B


title: Young_OA_Female_B


title: Young_OA_Female_A


title: LC_D1_F


title: GFP_4_2


title: 1 day 10 HA L Donor 2


title: Young_OA_Male_B


title: LC_D2_F


title: ST_48_3

value: ST


title: RC_D1_F


title: ST_48_2


title: IL_D1_F