title: IL4_1h_R1

description: Chromatin Associated RNA


title: ATAC_control_IL4_2h_R1

status: Public on Apr 16 2024

type: SRA

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description:
ATACseq
ATAC_reference_peaks.bed
ATAC_reference_peaks_extended.bed
ATAC_reference_summits.bed

library_source: genomic

data_processing:
Reads were quality filtered according to the illumina pipeline
Following adapter trimming, single end reads were trimmed with trimmomatic (Bolger et al. 2014) (version 0.39 flags: EADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:38).
Resulting reads were mapped with ShortStack (Axtell 2013).
Resulting bam files were then filtered using SAMtools (version 1.9) in order to remove unmapped reads, failing quality or mapping to mitochondrial chromosome.
Reads were then shifted of 4nt on the positive strand and -5nt on the negative strand using basic awk operations (Buenrostro et al. 2013).
Peak calling was performed using MACS2 (version 2.2.6; options --nomodel --extsize 146 --nolambda --keep-dup 'all' --call-summits). A reference set of peaks was created by selecting peaks called in each samples/replicate with qvalue ≤ 0.01 and being consistent between replicates (overlapping area of at least 50% between replicates).
The resulting set of peaks was used to count reads in each sample using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013).
Sample normalization was achieved by selecting invariant ATAC peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Assembly: mm10
Supplementary files format and content: .bw are BigWig normalised files

molecule: genomic DNA

organism: Mus musculus

source_name: mouse bone marrow derived macrophages

extract_protocol:
genomic DNA
5 × 104 BMDM cells were pelleted by centrifugation and resuspended in 50 µl of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM MgCl2, 0.1% Igepal CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation for 10 min at 500g at 4 °C and resuspended in 25 µl of reaction buffer containing 1 µl of Tn5 transposase made in-house using a described protocol (Picelli et al. 2014a), 5 µl of 5x transposase buffer (50 mM Tris-HCl, (pH 8.4) and 25 mM MgCl2), and 19 µl of milliQ water. The tagmentation mix was incubated at 37 °C for 60 min gently shaking, in order to avoid precipitation of nuclei. The reaction was stopped by the addition of 5 µl of cleanup buffer (900 mM NaCl, 30 mM EDTA), 2 µl of 5% SDS and 2 µl of Proteinase K (20 µg /µl) (Merck cod. P2308) and incubation for 30 min at 40 °C. Tagmented DNA was isolated using 2× Agencourt Ampure Xp beads (Beckman cod.A63881) and amplified by PCR with the HotStart Kapa HiFi enzyme (Roche cod. 07958889001). Fragments smaller than 600 bp were isolated by negative size selection (using 0.65× Agencourt Ampure Xp beads) and then purified with 1.8× Agencourt Ampure Xp beads. Libraries were single-end sequenced (76 bp) on an Illumina NextSeq500 platform.

treatment_protocol: LPS (10 ng/ml) treatment for 30min, 1h, 2h or 4h, IL4 (10 ng/ml) for 30min, 1h, 2h or 4h

tag: cell type

value: BMDM

tag: treatment

value: 1h DMSO followed by 2h IL4 10ng/mL

tag: genotype

value: wild type


title: ATAC_control_LPS_2h_R2

value: 1h DMSO followed by 2h LPS 10ng/mL


title: MCF7_U150.1_R4

city: London

first: Heena

last: Dhiman

address: 72 Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
Raw reads were trimmed for adapters and quality with trim_galore followed by alignment to hg38 human genome reference with bwa mem.
After removal of PCR duplicates, post-processing and variant identification were performed using the Genome Analysis Toolkit best practices. Joint variant calling was performed using Platypus and variant annotation was done using VEP.
Assembly: hg38

organism: Homo sapiens

source_name: MCF7 cell line

growth_protocol: For MCF7, differentially barcoded cells were expanded for 13 days from 1x105 cells to reach a POT population of ~90x106 cells and plated based on the following scheme: 1) 34 hyperflasks were seeded (1.2x106 and 2.8x106 cells for -E2 and TAM conditions respectively) 2) 2x10^6 cells were kept in culture as untreated arm (UT, 3 replicates), 3) 8x10^6 were expanded to 90x10^6 and harvested as triplicate POT samples. Harvesting of each HYPERflask was performed at the indicated time points. Following awakening, TAMɑ-𝝵 and AIɑ-ε samples were further cultured for 1 month in T150 flasks (Corning) with cell passaging giving rise to Terminal End Points (TEPs). For T47D, differentially barcoded cells were expanded for 12 days to reach a POT population of ~20x106 cells and plated based on the following scheme: 1) 8 HYPERflasks were seeded (1.1x106 cells) for -E2, 1.1x106 cells were kept in culture as untreated arm (UT, 3 replicates), 3) 3.5x106 were expanded to 20x106 and harvested as triplicate POT samples (5x106 cells each) with rest of the barcoded population frozen 4) 4.4x106 cells were used for plating of four T0 samples (1.1x106 )and collected after 48 hours. Oestrogen deprivation of the 8 HYPERflask carbon copies (-E2) started 48 hours after seeding.Harvesting of each HYPERflask was performed at the indicated time points (shared timepoints for 2 replicates of 1 month and diverging time points for individual awakenings). Following awakening, AI A-F samples were further cultured for 1 month in T150 flasks (Corning) with cell passaging giving rise to Terminal End Points (TEPs).

extract_protocol:
At time of collection, cells were snap-frozen in multiple pellets for subsequent DNA extraction using DNeasy Blood and Tissue DNA extraction kit (Qiagen) according to manufacturer’s recommendations. Qubit (Life Technologies) was used for quantification.
Quality control and library preparation (all samples exluding a29 and a30 were prepared using PCR-free library protocol) were performed by Novogene (Cambridge, UK) where 150 bp paired-end sequencing (30X coverage) was performed on the Illumina NovaSeq6000 platform.
MCF7: Whole Genome Sequencing, T47D: Targeted genome sequencing (targeted panel available on request)

treatment_protocol: Cell treatment of the 34 aliases, with either E2 or TAM, started 48 hours after seeding.

value: Untreated

tag: Stage

value: Untreated equivalent for awakening

tag: rep


title: ATAC_control_LPS_1h_R2

value: 1h DMSO followed by 1h LPS 10ng/mL


title: EXOSC2 AID ESCs, H3K4me3, 0 hr-1, rep2 (ctrl for 4 hr)

city: Beijing

first: Xue

last: Han

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

data_processing:
Raw reads of ChIP-seq were mapped to mouse genome mm10 by Bowtie2 (version 2.2.6). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count

source_name: AID-FBEXOSC2 ESCs

growth_protocol: AID-FBEXOSC2 ESCs were maintained in a complete ESC culture medium that consisted of DMEM (Corning) supplemented with 15% heat-inactivated fetal bovine serum (FBS), GlutaMAX (100× stock, Gibco), Penicillin-Streptomycin Solution (100× stock, Corning), MEM nonessential amino acids (100× stock, Gibco), nucleoside mix (100× stock, Millipore), 0.1 mM 2-mercaptoethanol (Gibco), and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, Millipore). The mESCs were seeded onto 0.1% gelatin-coated dishes. All cultured cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and subjected to immunoprecipitation. After elution and reverse-crosslinking, the DNA was purified using DNA Clean-up Kit (CWBIO).
ChIP-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

treatment_protocol: EXOSC2 degradation was induced by treatment of IAA (0.5 mM, Sigma, Cat#: I5148) for indicated hours to adherent ESCs.

tag: cell line

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

tag: time

value: 0 hour

tag: chip antibody


title: ATAC_control_LPS_1h_R1


title: MCF7_U150.2_R3


title: EXOSC2 AID ESCs, nascent RNA, EU, 2 hr, rep2

library_source: transcriptomic

data_processing:
Adapters and low-quality reads were removed and polyC tracts were cut from the reads by Trim_galore. Reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11). We additionally mapped the raw reads to drosophila genome dm6, which is the RNA spike-in.
RPKM was calculated for each genebody from Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count
Supplementary files format and content: tab-delimited text file includes RPKM values for RNA-seq samples

molecule: total RNA

extract_protocol:
ESCs were labeled with 1 mM 5-EU for 10 minutes and harvested by TRIzol with the addition of RNA spike-ins (5-EU labeled S2 cells) for cell number control. Apply purified RNA to DNase I treatment, fragmentation, ethanol precipitation, and biotinylation. Purify biotinylated RNA by phenol-chloroform, followed by two rounds of biotin-affinity purification using M-280 Streptavidin Dynabeads.
Eluted RNA was applied for cDNA synthesis and strand-specific library construction by ssDNA-seq Lib Prep Kit (Abclonal, Cat#: RK20222) following manufacturer’s protocols.

value: IAA

value: 2 hour


title: MCF7_U150.1_R2


title: ATAC_control_IL4_4h_R1

value: 1h DMSO followed by 4h IL4 10ng/mL


title: EXOSC2 AID ESCs, H3K4me3, 0 hr-1, rep1 (ctrl for 4 hr)


title: ATAC_control_IL4_30_R2

value: 1h DMSO followed by 30min IL4 10ng/mL


title: CT26, tumor, Glutaminase 2 [T2LP]

city: Houston

first: Navin

last: Varadarajan

state: TX

address: 4726 Calhoun Rd

department: William A Brookshire Chemical and Biomolecular Engineering Department

country: USA

institute: University of Houston

data_processing:
Fastqc quality check and no trimming was required
Reads were aligned to BALBc reference genome (Ensembl v1.108) using STAR in paired end mode
Gene abundances were quantified using featureCounts
Raw counts were normalized for library size by DeSeq2
Assembly: BALB_cJ_v1
Supplementary files format and content: Comma seperated values file includes DeSEQ normalized raw counts for each sample

source_name: Tumor

extract_protocol:
Tissue lyzed in RLT buffer (Qiagen) using Tissuelyzer. Total RNA extracted using RNAeasy kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: 50 IU/kg Glutaminase or vehicle was injected intraperitoneally every three days in tumor bearing mice

tag: tissue

value: Tumor

tag: host strain

value: BALB/c

value: WT

value: Glutmainase


title: CT26, tumor, Vehicle 3 [C2LP]

value: Vehicle


title: MCF7_U150.2_R1


title: ATAC_control_IL4_30_R1

value: BMDM

value: wild type


title: CT26, tumor, Vehicle 2 [C1LP]


title: ATAC_control_IL4_2h_R2

value: 1h DMSO followed by 2h IL4 10ng/mL


title: EXOSC2 AID ESCs, nascent RNA, EU, 4 hr, rep2

value: 4 hour


title: MCF7_U150.2_R2

value: Untreated

value: Untreated equivalent for awakening


title: MCF7_POT.3_R2

value: Oestrogen deprivation

value: Awakening


title: 2042GFPPOS

city: San Francisco

first: Jinyoung

last: Lee

address: 513 Parnassus Avenue

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: mm10
Supplementary files format and content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: Lung

extract_protocol:
Dissected mouse lung was tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) after perfusion with PBS and removed from the chest. The lung was incubated in digestion cocktail for 45 mins at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM). The mixture was passed through a 70 μm cell strainer and resuspended in red blood cell (RBC) lysis buffer, then passed through a 40 μm cell strainer. Cell suspensions were incubated with the appropriate conjugated antibodies in sorting buffer for 30 min at 4C and washed with FACS buffer. Doublets and dead cells were excluded based on forward and side scatter and SYTOX Blue (Invitrogen, S34857), respectively.  The following antibodies were used for staining: CD45-BV421 (BD, 563890), CD31-BV421 (Invitrogen, 48-0311-82), EpCAM-BV421 (BD, 563214). Immune (CD45-biotin, Biolgened, Cat#103104), epithelial (CD326-biotin, Biolegend, Cat#118204) and endothelial (CD31-Biotin, Biolegend, Cat#102404) cells are removed with EasySep mouse streptavidin RapidShperes (StemCell, 19860A). FACS was performed on a BD FACS Aria using FACSDiva Software. CD45- CD31- EpCAM- cells were sorted for mesenchymal cells, the GFP+ fibroblasts were further separated and were sorted into FACS buffer.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.

value: Lung

value: Fibroblasts


title: EXOSC2 AID ESCs, nascent RNA, EU, 4 hr, rep1

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: IAA


title: ATAC_control_IL4_1h_R2

value: 1h DMSO followed by 1h IL4 10ng/mL


title: CT26, tumor, Glutaminase 3 [T3LP]

value: Tumor

value: BALB/c

value: WT


title: MCF7_U150.1_R3


title: EXOSC2 AID ESCs, nascent RNA, EU, 2 hr, rep1

value: 2 hour


title: CT26, tumor, Glutaminase 1 [T1LP]

value: Glutmainase


title: MCF7_U150.1_R1


title: MCF7_POT.2_R4

value: Treatment naïve

value: POT


title: EXOSC2 AID ESCs, nascent RNA, EU, 1 hr, rep1

value: 1 hour


title: CT26, tumor, Vehicle 1 [C0LP]

value: Vehicle


title: Linc-ADAIN KD_LPS_3

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Kallisto (version 0.44.0) was used to quantify gene expression using pseudoalignment. Differential gene expression analysis was performed using DESeq2 version 1.32.0.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with estimated gene counts for each sample computed from tximport R package.

molecule: polyA RNA

source_name: ASC52telo hTERT

growth_protocol: ASC52telo, hTERT immortalized adipose derived mesenchymal stem cells were purchased from ATCC (SCRC-4000). To induce adipocyte differentiation, confluent ASCs or hTERT ASCs were incubated in differentiation media containing insulin (1.7µM), dexamethasone (1µM), isobutylmethylxanthine (500 μM), Rosiglitazone (2 μM), panthothenate (17µM) and biotin (33µM). After 7 days, cells were incubated with maintenance media containing insulin (1.7µM), dexamethasone (1µM), panthothenate (17µM) and biotin (33µM) for an additional 7 days (a total of 14 days culture).

extract_protocol:
RNA samples were extracted using Trizol and Direct-zol RNA miniprep kit (Zymo Research R2052) from ASC-adipocytes. Following DNase treatment, RNA samples were assessed using Agilent Bioanalyzer (Agilent, Santa Clara, CA) and all samples had an RNA Integrity Number (RIN) larger than 9 with a minimum of 200ng input RNA.
Libraries were prepared by Columbia Genome center using Illumina Stranded mRNA prep kit (Illumina, San Diego, CA).

treatment_protocol: ShRNA sequences were cloned into pLVX-shRNA2 vector containing ZsGreen (Clonetech). The pLVX-shRNA2 vector was transfected into LentiX-293T cells (Clonetech) with packaging vectors psPAX2 (Addgene plasmid 12260) and pMD2.G (Addgene plasmid 12259) using Lipofectamine 3000 (Life technologies). Forty-eight hours after transfection, virus supernatants were collected and centrifuged at 1000g for 5 min to remove cell debris. Confluent ASCs were treated with lentiviral supernatant and 5 μg/mL polybrene. Cells were expanded and flow activated cell sorted (FACS) for ZsGreen-positive cells.

value: ASC52telo hTERT

value: Adipose stromal cell adipocyte

value: Linc-ADAIN knockdown

value: Linc-ADAIN shRNA, LPS


title: Linc-ADAIN KD_LPS_1


title: MCF7_POT.2_R3


title: MCF7_POT.2_R2


title: ATAC_control_IL4_1h_R1

value: BMDM

value: wild type


title: EXOSC2 AID ESCs, nascent RNA, EU, 0 hr, rep2

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: 0 hour


title: MIN6N8 cells +IL-22_2

city: Brisbane

first: haressh

last: sajiir

state: QLD

address: 37 Kent Street

country: Australia

institute: Mater Research Institute - The University of Queensland

description: IL-22_2 CPM

data_processing:
After processing samples were pooled with equal molarity, (as determined using sizing and qPCR) and  sequenced on the Illumina Hiseq4000 machine using a 75 bp paired end sequencing configuration.
Assembly: mm10
Supplementary files format and content: .csv file includes raw counts, CPM and FDR per sample

growth_protocol: MIN6N8 cells were maintained in DMEM media containing high glucose ( 4.5 g/L or 22 mM), 10% Fetal Bovine Serum,  1% Penicillin/Streptomycin, 1% L-Glutamine + 2.5 ul/500 ml β-mercapto ethanol

extract_protocol:
RNA was harvested using the Bioline Isolate II RNA Mini Kit following the Manufacturer's protocol
Libraries were processed using the Illumina Truseq stranded mRNA library kit.  Samples were normalised and 1 ug of RNA was used per sample for processing.

treatment_protocol: Media was changed to DMEM media containing low glucose (5.5mM), and cells were treated with either PBS or 100ng/mL IL-22 for 4 hours

value: Pancreatic beta cells


title: MIN6N8 cells +IL-22_5

description: IL-22_5 CPM


title: Linc-ADAIN KD_3

value: Linc-ADAIN shRNA


title: MCF7_POT.3_R1

value: Oestrogen deprivation

value: Awakening


title: EXOSC2 AID ESCs, nascent RNA, EU, 0 hr, rep1


title: MCF7_POT.1_R3

value: Treatment naïve


title: MIN6N8 cells +IL-22_4

description: IL-22_4 CPM


title: Linc-ADAIN KD_2


title: EXOSC2 AID ESCs, nascent RNA, EU, 1 hr, rep2

value: IAA


title: LlincADAIN KD_1


title: Linc-ADAIN KD_LPS_2


title: EXOSC2 AID ESCs, RNA, RNPmesh, rep2, 12 hr

data_processing:
Raw reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11). We additionally mapped the raw reads to drosophila genome dm6, which is the RNA spike-in.
FPKM was calculated by Cufflinks (version 2.0.2) using Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count
Supplementary files format and content: tab-delimited text file includes FPKM values for RNA-seq samples

extract_protocol:
ESC nuclei were subjected to DNase I treatment followed by sequential washes using detergents (1 M urea and 1% NP40) and high-salt (2 M NaCl). The resulting pellet, representing the ‘insoluble’ RNP mesh, was used for RNA-seq. Add the RNA spike-in (drosophila S2 cells) directly to samples according to number of cells. Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to poly(A) purification by VAHTS mRNA Capture Beads (Vazyme) according to manufacturer's instruction.
RNA-seq libraries were constructed by NEBNext Ultra II directional RNA library prep kits (NEB) following manufacturer’s protocols.

value: 12 hour


title: EXOSC2 AID ESCs, RNA, RNPmesh, rep1, 12 hr


title: EXOSC2 AID ESCs, RNA, RNPmesh, rep2, 0 hr


title: MIN6N8 cells + PBS_4

description: PBS_4 CPM

value: Control (PBS)


title: EXOSC2 AID ESCs, RNA, RNPmesh, rep2, 4 hr

value: 4 hour


title: MIN6N8 cells +IL-22_1

description: IL-22_1 CPM


title: Scramble_LPS_3

value: ASC52telo hTERT

value: Adipose stromal cell adipocyte

value: WT

value: Scramble shRNA, LPS


title: MCF7_POT.2_R1

value: POT


title: EXOSC2 AID ESCs, RNA, RNPmesh, rep1, 0 hr

value: AID-FBEXOSC2 ESCs


title: MCF7_POT.1_R1


title: MIN6N8 cells + PBS_2

description: PBS_2 CPM


title: AI.epsilonTEP

data_processing:
Raw reads for all the RNA-Seq samples were trimmed for adapters and quality (Phred quality >= 30) with trim_galore.
The trimmed reads were pseudo-aligned to reference transcriptome (GRCh38.96) with Kallisto (v-0.46.2) and estimated transcript abundance values were reported by ‘kallisto quant’.
Assembly: GRCh38

growth_protocol: Differentially barcoded cells were expanded for 13 days from 1x105 cells to reach a POT population of ~90x106 cells and plated based on the following scheme: 1) 34 hyperflasks were seeded (1.2x106 and 2.8x106 cells for -E2 and TAM conditions respectively) 2) 2x106 cells were kept in culture as untreated arm (UT, 3 replicates), 3) 8x106 were expanded to 90x106 and harvested as triplicate POT samples. Harvesting of each HYPERflask was performed at the indicated time points. Following awakening, TAMɑ-𝝵 and AIɑ-ε samples were further cultured for 1 month in T150 flasks (Corning) with cell passaging giving rise to Terminal End Points (TEPs).

extract_protocol:
At time of collection, cells were snap-frozen in multiple pellets for subsequent total RNA was extracted using QIAzol (Qiagen) and RNeasy Mini Kit (Qiagen)
Quality control, mRNA library preparation (polyA enrichment) and sequencing were done at Novogene (Cambridge, UK) using NovaSeq6000 platform (paired-end 150 bp).

value: Tamoxifen

value: TEP

value: epsilon


title: EXOSC2 AID ESCs, RNA, RNPmesh, rep1, 4 hr

value: mouse embryonic stem cell


title: MIN6N8 cells + PBS_1

description: PBS_1 CPM

value: Pancreatic beta cells


title: Scramble_LPS_1


title: EXOSC2 AID ESCs, RNA, 20 hr, RAD1, rep1

data_processing:
Raw reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11).
FPKM was calculated by Cufflinks (version 2.0.2) using Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count
Supplementary files format and content: tab-delimited text file includes FPKM values for RNA-seq samples

growth_protocol: AID-FBEXOSC2 ESCs were maintained in a complete ESC culture medium that consisted of DMEM (Corning) supplemented with 15% heat-inactivated fetal bovine serum (FBS), GlutaMAX (100× stock, Gibco), Penicillin-Streptomycin Solution (100× stock, Corning), MEM nonessential amino acids (100× stock, Gibco), nucleoside mix (100× stock, Millipore), 0.1 mM 2-mercaptoethanol (Gibco), and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, Millipore). The mESCs were seeded onto 0.1% gelatin-coated dishes. To induce ESC differentiation, the cells were differentiated by withdrawal of LIF and addition of 2 μM retinoic acid (Sigma, R2625) in the ESC culture medium with FBS for 24 hours. All cultured cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to poly(A) purification by VAHTS mRNA Capture Beads (Vazyme) according to manufacturer's instruction.
RNA-seq libraries were constructed by NEBNext Ultra II directional RNA library prep kits (NEB) following manufacturer’s protocols.

value: 20 hour


title: MIN6N8 cells +IL-22_3

description: IL-22_3 CPM


title: T.zetaTEP

value: zeta


title: MCF7_POT.1_R2

value: Treatment naïve


title: MIN6N8 cells + PBS_5

description: PBS_5 CPM


title: MIN6N8 cells + PBS_3

description: PBS_3 CPM


title: EXOSC2 AID ESCs, RNA, 20 hr, RAD1, rep2

value: IAA


title: T.epsilonTEP


title: EXOSC2 AID ESCs, RNA, 4 hr, RAD1, rep2


title: Scramble_LPS_2


title: Scramble_3

value: Scramble shRNA


title: WT_7d_Mg_R2

city: San Francisco, CA

first: Katerina

last: akassoglou

state: CA

address: 1650 Owens st

institute: Gladstone Institutes

data_processing:
Paired-end fastq files were processed using the open-access Nextflow RNA-seq pipeline with nextflow v20.12.0-edge in Singularity with default nf-core/rnaseq v3.0 parameters and packages.
Fastq files were mapped to GRCm38.mm10 genome. Gene analyses was performed in R v4.2.0 using DeSeq2 v1.36.0 on the salmon.merged.gene_counts_scaled file. Reads with fewer than 3 counts per gene across replicates were filtered out.
For differential gene analysis the results function in DeSeq2 was used with contrast to test between two genotypes and timepoints of interest. The data were then filtered for significance using abs(log2FC) > 1 and adjusted P value < 0.05 unless otherwise stated. Unbiased KEGG analysis was performed using clusterProfiler and enrichplot with default parameters and pvalueCutoff set to 0.1.
Assembly: mm10
Supplementary files format and content: txt file containing salmon processed data

source_name: brain

extract_protocol:
Following TBI experiments, animals were perfused with 4C DPBS and a 1 mm tissue block spanning the lesion sites of each mouse was isolated. To increase cell yield for RNA-seq analysis, two mouse brain tissue samples per genotype and timepoint were randomly pooled together for each biological replicate. Single cell suspensions were prepared using the adult brain dissociation kit (Miltenyi Biotec). Samples were then treated with Fc-block in DPBS supplemented with 0.2% BSA (Thermo Fischer Scientific) for 5 min at 4C, then incubated with primary antibodies for 30 min at 4C. The following primary antibodies were used at 1:200 dilution and purchased from Biolegend: CD11b (M1/70) conjugated to APC-Cy7 and CD45 (30-F11) conjugated to 488. Samples were incubated with Sytox blue live/dead stain for 10 min prior to sorting. FACS of 40,000 live microglia with CD45lowCD11b+ expression or 25,000 live infiltrating myeloid cells with CD45hiCD11b+ expression were sorted directly into tubes containing RLT plus lysis buffer (Qiagen) supplemented with 1% 2-mercaptoethanol and 0.25% reagent DX (Qiagen) using FACSAria II with BD FACSDiva v8 software.
cDNA libraries were generated using the Ovation RNA-seq System V2 low input kit following manufacturer’s instructions (NuGEN). Libraries were QC checked by KAPA qPCR (Roche) and Bioanalyzer DNA chip analysis (Agilent). All 21 libraries were equimolar pooled and sequenced on Hiseq4000 with paired-end 100 base pairs (Illumnia). The median sequencing depth was ~63 million reads per sample.

value: brain

tag: celltype

value: Microglia (Mg)

value: wildtype

value: 7 days post TBI


title: Scramble_2

value: ASC52telo hTERT

value: Adipose stromal cell adipocyte

value: WT


title: WT_7d_Mg_R3


title: EXOSC2 AID ESCs, RNA, 4 hr, RAD1, rep1

value: AID-FBEXOSC2 ESCs

value: 4 hour


title: Scramble_1


title: WT_1d_Mp_R3

value: Macrophage (Mp)

value: 1 day post TBI


title: Treg + IL12, rep5

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: In vitro. Live CD4+CD45RO-CD25HiCD127Lo/-CXCR5- cells

data_processing:
fastqs were aligned to GRCh38 with STAR with the parameters “--outFilterMultimapNmax 20 --outFilterMismatchNmax 6 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --genomeSAindexNbases 14”
duplicates were marked using Picard MarkDuplicates and ignored for the counting of reads to exons
reads mapping to exons of RefSeq were counted using an in-house R script utilizing the GenomicRanges package.
Assembly: GRCh38.p14
Supplementary files format and content: raw count table of reads mapping to exons of RefSeq ( GCF_000001405.40-RS_2023_10) genes

source_name: Cord blood

growth_protocol: Freshly isolated naive Treg cells (7.5 × 10˄4 cells per well) from cord blood were cultured at 37 ºC in serum-free AIM-V with 2 µL Dynabeads Human T-Activator CD3/CD28 in the presence of 5 ng/mL IL-2. After two days, cells were split into two wells and cultured with fresh AIM-V medium without further cytokine addition. Cells were harvested at 2.5 days for RNA isolation.

extract_protocol:
Total RNA was extracted with RNeasy plus micro kit (Qiagen) following manufacturer’s instructions and eluted in 14 µL of RNase free water
1-10 ng purified total RNA was converted into cDNA and amplified (9-12 cycles) using the SMART-Seq HT kit (Takara Bio) or the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio), for Tfr analyzed ex vivo or after the in vitro differentiation, respectively. 10 ng of cDNA were used to prepare DNA libraries using Nextera XT DNA Library Preparation Kit (96 samples, Illumina) and Nextera XT Index Kit (96 Indexes, Set A, Illumina). Next, Barcoded samples were pooled, diluted at 1.8 pM and loaded onto a NextSeq 500/550 High Output Kit v2.5 flow cell (75 Cycles, 120-300 million of reads, Illumina). Single-end sequencing was performed on a NextSeq 550 (Illumina).

treatment_protocol: Absence or presence of 5 ng/mL recombinant human IL-12

value: Cord blood

value: Naive Treg CXCR5-

tag: Sex

value: Female

value: Anti-CD3 + anti-CD28, IL-2, IL12


title: EXOSC2 AID ESCs, RNA, 0 hr, RAD1, rep2

value: mouse embryonic stem cell

value: 0 hour


title: AI.gammaTEP

value: Oestrogen deprived

value: TEP

value: gamma


title: EXOSC2 AID ESCs, RNA, 0 hr, RAD1, rep1


title: WT_7d_Mg_R1

value: brain

value: Microglia (Mg)

value: wildtype

value: 7 days post TBI


title: EXOSC2 AID ESCs, RNA, 20 hr, RAD0, rep2

value: AID-FBEXOSC2 ESCs

value: IAA

value: 20 hour


title: Treg -IL12, rep5

value: Anti-CD3 + anti-CD28, IL-2, no IL-12


title: WT_1d_Mp_R2

value: Macrophage (Mp)

value: 1 day post TBI


title: AI.alphaTEP

value: alpha


title: EXOSC2 AID ESCs, RNA, 20 hr, RAD0, rep1


title: Treg + IL12, rep4

value: Cord blood

value: Naive Treg CXCR5-

value: Female

value: Anti-CD3 + anti-CD28, IL-2, IL12


title: T.alpha TEP

value: Tamoxifen

value: TEP


title: WT_1d_Mp_R1

value: brain


title: EXOSC2 AID ESCs, RNA, 4 hr, RAD0, rep2

value: mouse embryonic stem cell

value: 4 hour


title: WT_1d_Mg_R3

value: Microglia (Mg)

value: wildtype


title: Treg -IL12, rep4


title: T.deltaTEP

value: delta


title: Treg + IL12, rep3


title: EXOSC2 AID ESCs, RNA, 4 hr, RAD0, rep1

value: AID-FBEXOSC2 ESCs

value: IAA


title: WT_1d_Mg_R2


title: AI.betaTEP

value: Oestrogen deprived

value: beta


title: T.gammaTEP

value: gamma


title: Treg -IL12, rep3

value: Cord blood

value: Anti-CD3 + anti-CD28, IL-2, no IL-12


title: U170.3

value: Untreated


title: EXOSC2 AID ESCs, RNA, 0 hr, RAD0, rep2

value: 0 hour


title: WT_1d_Mg_R1

value: 1 day post TBI


title: T.beta TEP

value: Tamoxifen

value: TEP


title: Treg -IL12, rep2

value: Naive Treg CXCR5-

value: Female


title: U170.2


title: Sham_Mg_R2

value: brain

value: Microglia (Mg)

value: Sham control


title: EXOSC2 AID ESCs, RNA, wcl, rep2, 4 hr

data_processing:
Raw reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11). We additionally mapped the raw reads to an in-house reference containing spike-in sequence (GFP, mCherry, lacZ and Luciferase).
FPKM was calculated by Cufflinks (version 2.0.2) using Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count
Supplementary files format and content: tab-delimited text file includes FPKM values for RNA-seq samples

extract_protocol: Cells were fractionated by sequential lysis and centrifugation. We first isolated the cytosolic fraction (‘cyto’) by 0.15% NP-40, and then used salt and detergents (0.15 M NaCl, 0.5 M urea and 0.5% NP40) to partition nuclear constituents. The soluble nucleoplasmic fraction (‘np’) with greater biochemical extraction captured the highly dynamic RNP mesh components, whereas the insoluble fraction contained chromatin and less extractable RNP mesh components, designated as the ‘chr/RNPmesh’. Add the RNA spike-in (a combination of GFP, mCherry, lacZ, and Luciferase transcripts) directly to the samples of each subcellular fraction according to number of cells for normalization. Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to ribosomal RNA depletion by Ribo-Zero rRNA removal kits (Illumina) according to manufacturer's instruction.

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: 4 hour


title: EXOSC2 AID ESCs, RNA, 0 hr, RAD0, rep1


title: Sham_Mg_R1

value: wildtype


title: Sham_Mg_R3


title: Treg + IL12, rep1

value: Anti-CD3 + anti-CD28, IL-2, IL12


title: U170.1


title: Treg -IL12, rep1

value: Cord blood


title: AI.epsilon

value: Oestrogen deprived

value: Awakening

value: epsilon


title: EXOSC2 AID ESCs, RNA, cyto, rep2, 4 hr

value: IAA


title: Fgg_7d_Mg_R3

value: 7 days post TBI


title: EXOSC2 AID ESCs, RNA, wcl, rep1, 4 hr


title: Fgg_7d_Mg_R2


title: Cord blood, rep3

description: Ex vivo. Live CD4+CD45RO-CD25HiCD127Lo/-CXCR5- cells

value: No treatment


title: AI.beta

value: beta


title: Fgg_7d_Mg_R1


title: AI.gamma

value: gamma


title: AI.alpha

value: alpha


title: Cord blood, rep2

value: Naive Treg CXCR5-

value: Female


title: EXOSC2 AID ESCs, RNA, cyto, rep1, 4 hr

value: AID-FBEXOSC2 ESCs


title: EXOSC2 AID ESCs, RNA, np, rep2, 4 hr

value: mouse embryonic stem cell


title: Treg + IL12, rep2


title: Fgg_1d_Mp_R3

value: brain

value: Macrophage (Mp)

value: 1 day post TBI


title: Cord blood, rep1

value: Cord blood


title: T.beta

value: Tamoxifen


title: EXOSC2 AID ESCs, RNA, chrRNP, rep2, 4 hr

value: 4 hour


title: Fgg_1d_Mp_R2


title: T.alpha

value: Awakening


title: EXOSC2 AID ESCs, RNA, chrRNP, rep1, 4 hr

value: IAA


title: Fgg_1d_Mp_R1


title: Cord blood, rep4


title: Tonsil / Tfr, rep1

description: Ex vivo. Live CD20-CD4+CD45RO+CD69+ICOS+CD127-/Lo CD25HiCXCR5+ cells. The purity of the sorted cells was confirmed by FOXP3 staining (> 97% FOXP3+ cells for naive Treg and >92% FOXP3+ cells for Tfr cells)

source_name: Tonsil

value: Tonsil

value: Tfr


title: T.delta

value: delta


title: T.gamma

value: gamma


title: Fgg_1d_Mg_R3

value: Microglia (Mg)


title: EXOSC2 AID ESCs, RNA, wcl, rep2, 0 hr

value: 0 hour


title: EXOSC2 AID ESCs, RNA, wcl, rep1, 0 hr


title: RNA M395 R n=3

city: Liège

first: Najla

last: El-Hachem

address: 1 avenue de l'hopital

department: Stem Cells

country: Belgium

institute: GIGA Institute

data_processing:
Step - Tool - Parameters - Version
Sequencing quality control and filter - FastQC - no Parameters - v0.11.7
Reads trimming - Cutadapt - 5' and 3' -adaptor bases removed. Reads filtered (18nt ⩽ length ⩽ 40 nt) - 1.14
Alignment to cytoplasmic mature-tRNA sequences from GtRNAdb and mitochondrial tRNA sequences from mitotRNAdb - BWA - Max mismatches : 2 - 0.7.12-r1039
Assembly: cytoplasmic mature-tRNA sequences from GtRNAdb and mitochondrial tRNA sequences from mitotRNAdb
Supplementary files format and content: Expression_Count.xlsx represents cytoplasmic mature-tRNA sequences and mitochondrial tRNA sequences

source_name: M395 RES

extract_protocol:
Total RNA was harvested using the TriPure isolation method (ref. 11667157001, Roche).
RNA libraries were prepared using the Agilent DNA 1000 chip kit (Agilent, part# 5067-1504) according to the manufacturer's protocols.
tRNA-seq

value: M395 RES

value: Primary melanoma culture

value: No treatment


title: EXOSC2 AID ESCs, RNA, cyto, rep2, 0 hr

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell


title: Fgg_1d_Mg_R2

value: brain

value: 1 day post TBI


title: AI.delta

value: Oestrogen deprived


title: EXOSC2 AID ESCs, RNA, np, rep1, 4 hr

value: 4 hour


title: EXOSC2 AID ESCs, RNA, cyto, rep1, 0 hr


title: RNA M395 R n=1


title: RNA M395 S n=3

source_name: M395 SENS

value: M395 SENS


title: T.zeta

value: Tamoxifen

value: Awakening

value: zeta


title: pash-1(ram33), 25C, rep 4

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

data_processing:
Data processing was done using the default configuration in the tinyRNA pipeline (https://github.com/MontgomeryLab/tinyRNA)
Assembly: WS279
Supplementary files format and content: wt_pash-1_20C_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in wild type and pahsh-1 mutants grown at 20˚C.
Supplementary files format and content: wt_pash-1_25C_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in wild type and pahsh-1 mutants grown at 25˚C.

organism: Caenorhabditis elegans

source_name: gravid hermaphroditic adult whole animals

growth_protocol: Worms were grown from synchronized L1 larvae for 72 hours at 20˚C or 54 hours at 25˚C on NGM containing E. coli (OP50).

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. RNA was isolated using trizol/chloroform and isopropanol precipitation.
Libraries were then prepared from total RNA according to the NEBNext® Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels.
small RNA-seq

value: TAM93[pash-1(ram33) I]

tag: temperature


title: EXOSC2 AID ESCs, RNA, np, rep2, 0 hr


title: T.epsilon

value: epsilon


title: pash-1(ram33), 25C, rep 3

value: gravid hermaphroditic adult whole animals


title: UT120.2

value: Untreated


title: pash-1(ram33), 25C, rep 2


title: EXOSC2 AID ESCs, RNA, np, rep1, 0 hr

value: 0 hour


title: UT120.1


title: EXOSC2 AID ESCs, RNA, chrRNP, rep2, 0 hr


title: pash-1(ram33), 25C, rep 1


title: AI90.2


title: RNA M395 R n=2

value: M395 RES

value: Primary melanoma culture


title: RPF M395 RES shVARS-1_3

description:
RPF_OHMX_cleaned_counts.tsv
shVARS-3_R1

data_processing:
Step - Tool - Parameters - Version
Quality check - FastQC - no Parameters - 0.11.9
Trimming (For RNA-seq) - SeqPurge - 3’ adaptor and 5’ trimming - 2.0.1
Trimming (For RPFs) - Trimmomatic - Adaptor (‘TGGAATTCTCGGGTGCCAAGG’)  clipping and 3' and 5' trimming based on quality. Reads filtered by length (<20nt discarded) and quality (<28 discarded) - 0.39
Contaminants removal RPFs (PhiX, rRNA, snRNA, sn-o-RNA and tRNA) - Bowtie2 - no Parameters - no Version
Contaminants removal RNA (rRNA) - Bowtie2 - no Parameters -
Alignment - STAR - no Parameters - 2.7.2b
Assembly: Human reference genome (Ensembl version 104).
Supplementary files format and content: counts
Library strategy: Ribo-seq

extract_protocol:
Frozen lysate of patient derived melanoma cells has been delivered to the OHMX facility. Total RNA from 2 µg of the lysate was purified with the RNA Clean and Concentrator-5 kit (Zymo Research). 10 µg of lysate was digested with RNase I (Thermofisher) at 21°C for 45 min. The reaction was stopped with the addition of Superase In RNase Inhibitor (Thermofisher). The digested lysate was purified on a MicroSpin S-400 HR Sephacryl column (GE Healthcare). The flow through was collected and purified with the RNA Clean and Concentrator-5 (ZymoResearch). The footprints were visualized on the Agilent Bioanalyzer with the RNA 6000 Nano kit (Agilent). Ribosome-protected fragments (RPFs) of 28-30 nt were selected by loading the footprints on a Novex TBE-Urea gel (15%) (Thermofisher) and performing gel electrophoresis
RPFs were 3’ dephosphorylated with T4 PNK (New England Biolabs)  and were subsequently purified using the Oligo Clean and Concentrator kit (ZymoResearch). The 3’ adapter was ligated to the RPFs and the ligated fragments were purified following the protocol of the Small RNA Library prep kit (Lexogen). After the 5’ phosphorylation of the RPFs and their purification with the Oligo Clean and Concentrator kit, 5’ adapter ligation took place based on the Small RNA Library prep kit. First strand cDNA synthesis was performed according to the Small RNA Library prep kit manual. Ribosomal RNA (rRNA) was depleted with the addition of LNA probes from the QIAseq FastSelect rRNA HMR kit (Qiagen) during the cDNA synthesis reaction. During PCR, a unique index primer (Lexogen) was added to one end of the fragment.The PCR amplification protocol from the Small RNA Library prep kit was followed.

value: shVARS


title: wild type, 25C, rep 4

value: wild type (N2)


title: AI90.1


title: Fgg_1d_Mg_R1

value: brain

value: Microglia (Mg)


title: EXOSC2 AID ESCs, RNA, chrRNP, rep1, 0 hr

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell


title: RPF M395 RES shVARS-1_2

description:
RPF_OHMX_cleaned_counts.tsv
shVARS-2_R1


title: EXOSC2 AID ESCs, HiC, 20 hr, rep2

data_processing:
Paired end raw reads of Hi-C libraries were aligned, processed and iteratively corrected using HiC-Pro (version 2.7.1b). To eliminate the possible effects on data analyses of variable sequencing depths, we combined valid_interaction_rmdup from replicates and randomly sampled equal numbers of valid_interaction_rmdup read pairs (n = 70 million) from each time point of IAA treatment for downstream analyses.
Assembly: mm9
Supplementary files format and content: hic, binary format for storing contact matrices and annotations of chromatin structural features

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was subjected to MboI digestion, biotin end repairing and ligation, then reverse-crosslinking and DNA purification. The purified DNA was then sonicated and subjected to biotin pull down by C1 Streptavidin beads. Library construction procedures including end repairing, dATP tailing and adaptor ligation were proceeded on beads. Finally, the DNA was eluted and subjected to PCR and size selection for sequencing.
HiC libraries were constructed following TruSeq DNA preparation procedures including end repairing, dATP tailing, adaptor ligation and PCR amplification.

value: IAA

value: 20 hour


title: wild type, 25C, rep 3


title: T.eta

value: Tamoxifen

value: Awakening

value: eta


title: T.theta

value: theta


title: wild type, 25C, rep 2

value: gravid hermaphroditic adult whole animals


title: EXOSC2 AID ESCs, HiC, 20 hr, rep1


title: RPF M395 RES shCTRL_3

description:
RPF_OHMX_cleaned_counts.tsv
WT-3_R1

value: shCTRL


title: EXOSC2 AID ESCs, HiC, 4 hr, rep2

value: 4 hour


title: AI60.2

value: Oestrogen deprived


title: wild type, 25C, rep 1


title: RPF M395 RES shCTRL_2

description:
RPF_OHMX_cleaned_counts.tsv
WT-2_R1

value: M395 RES

value: Primary melanoma culture


title: pash-1(ram33), 20C, rep 3

value: TAM93[pash-1(ram33) I]


title: RNA M395 S n=2

value: M395 SENS

value: No treatment


title: EXOSC2 AID ESCs, HiC, 4 hr, rep1

value: AID-FBEXOSC2 ESCs


title: RNA M395 S n=1


title: RPF M395 RES shCTRL_1

description:
RPF_OHMX_cleaned_counts.tsv
WT-1_R1


title: EXOSC2 AID ESCs, HiC, 0 hr, rep2

value: mouse embryonic stem cell

value: 0 hour


title: AI60.1


title: pash-1(ram33), 20C, rep 2


title: Input M395 RES shVARS-1_3

description:
RNA_OHMX_cleaned_counts.tsv
shVARS-RNA-3_R1

value: shVARS


title: pash-1(ram33), 20C, rep 1


title: EXOSC2 AID ESCs, HiC, 0 hr, rep1


title: RPF M395 RES shVARS-1_1

description:
RPF_OHMX_cleaned_counts.tsv
shVARS-1_R1


title: wild type, 20C, rep 3

value: wild type (N2)


title: Input M395 RES shVARS-1_2

description:
RNA_OHMX_cleaned_counts.tsv
shVARS-RNA-2_R1


title: EXOSC2 AID ESCs, RNA, sucrose F8, 12 hr

data_processing:
Raw reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11). We additionally mapped the raw reads to an in-house ERCC reference (4 transcripts spike-in).
FPKM was calculated by Cufflinks (version 2.0.2) using Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count
Supplementary files format and content: tab-delimited text file includes FPKM values for RNA-seq samples

extract_protocol:
Native nuclear lysates were fractioned by sucrose gradient centrifugation (6%-40% w/v). Add an equal amount of RNA spike-in (4 ERCC transcripts) to each fraction for normalization to cell number. Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to ribosomal RNA depletion by Ribo-Zero rRNA removal kits (Illumina) according to manufacturer's instruction.
RNA-seq libraries were constructed by NEBNext Ultra II directional RNA library prep kits (NEB) following manufacturer’s protocols.

value: IAA

value: 12 hour


title: wild type, 20C, rep 2


title: EXOSC2 AID ESCs, RNA, sucrose F9, 12 hr


title: T60.2

value: Tamoxifen


title: AI30.2


title: Input M395 RES shVARS-1_1

description:
RNA_OHMX_cleaned_counts.tsv
shVARS-RNA-1_R1


title: AI30.1


title: EXOSC2 AID ESCs, RNA, sucrose F7, 12 hr


title: Input M395 RES shCTRL_2

description:
RNA_OHMX_cleaned_counts.tsv
WT-RNA-2_R1


title: T30.2


title: Input M395 RES shCTRL_3

description:
RNA_OHMX_cleaned_counts.tsv
WT-RNA-3_R1


title: EXOSC2 AID ESCs, RNA, sucrose F6, 12 hr


title: #11 iAM-1 D9, P10, Sbk2 shRNA #2, n=3

city: Leiden

first: Pim

last: van Gorp

state: Zuid-Holland

address: Albinusdreef 2

department: Experimental Cardiology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Read counting was performed in the DESeq2 software package (version 2-1.14) and in parallel normalized using depth normalization (counts per million, CPM) as well as length normalization (transcript per million, TPM).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for the pooled samples of every gene

organism: Rattus norvegicus

source_name: iAM-1 cells

growth_protocol: iAM-1 cells were cultured in Advanced DMEM/F-12 (Thermo Fisher Scientific, cat# 12634010) supplemented with 2% FBS and 1⨯ GlutaMAX Supplement (Thermo Fisher Scientific).

extract_protocol:
Total RNA was collected using the RNeasy Mini Kit. The quality of the RNA samples designated for RNA-Seq was confirmed using the Advanced Analytical Fragment Analyzer.
cDNA was generated from total RNA samples with RNA integrity numbers of 10 using the NEBNext Ultra Directional RNA library preparation method including polyA enrichment (New England Biolabs, cat# E7760S/L). Sequencing was performed on a NovaSeq 6000 system (Illumina, San Diego, CA). For each sample at least 40 million 150-bp paired-end reads were obtained.

treatment_protocol: During the differentiation phase no doxycyclin was added to the culture medium. Lentiviral vectors containing the shRNA constructs were added shortly after the the initiation of differentiation

tag: strain

value: wistar

tag: transduction

value: Sbk2 shRNA #2


title: T30.1


title: EXOSC2 AID ESCs, RNA, sucrose F5, 12 hr


title: Input M395 RES shCTRL_1

description:
RNA_OHMX_cleaned_counts.tsv
WT-RNA-1_R1

value: shCTRL


title: UT30.2

value: Untreated


title: #11 iAM-1 D9, P10, Sbk2 shRNA #2, n=2


title: EXOSC2 AID ESCs, RNA, sucrose F4, 12 hr


title: T60.1


title: #11 iAM-1 D9, P10, Sbk2 shRNA #1, n=3

value: Sbk2 shRNA #1


title: #11 iAM-1 D9, P10, Sbk2 shRNA #2, n=1


title: UT30.1


title: EXOSC2 AID ESCs, RNA, sucrose F3, 12 hr


title: wild type, 20C, rep 1

value: gravid hermaphroditic adult whole animals


title: #11 iAM-1 D9, P10, Sbk2 shRNA #1, n=2


title: AI14.1

value: Oestrogen deprived


title: EXOSC2 AID ESCs, RNA, sucrose F9, 0 hr


title: T14.2


title: EXOSC2 AID ESCs, RNA, sucrose F8, 0 hr


title: HUVEC_ATAC_16hr_PS_3

city: Riverside

first: Brendan

last: Gongol

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Data was processed using the systemPipeR R package.
ChIP-seq reads were aligned to the GRCh38 genome assembly using hisat2 version 2.0.1 with the following configurations: -k 1 --min-intronlen 30 --max-intronlen 3000
MACS2 version 2.1.2 with a q-value threshold of 0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated using GenomicAlignments and rtracklayer R packages.

source_name: Human Unbilical Vein Endothelial Cells

growth_protocol: HUVECS were cultured in M199 medium (Gibco) supplemented with 15% fetal bovine serum (FBS) , 1 ng/ml recombinant human fibroblast growth factor, 90 μg/ml heparin, 20 mM HEPES (pH 7.4), and 100 U/ml penicillin-streptomycin.

extract_protocol:
Qiagen MinElute PCR purification kit
Nextera DNA Library Preparation Kit; Illumina

treatment_protocol: HUVECs were exposed to pulsatile shear stress (PS, i.e., 12 ± 5 dyn/cm2) or oscillatory shear stress (OS, i.e., 0.5 ± 5 dyn/cm2) for 0 (static control), 2, 8, 12, 16 hours.

value: HUVEC

value: Pulsatile Shear Stress

tag: treatment time

value: 16 hr


title: HUVEC_ATAC_16hr_OS_2

value: Oscillatory Shear Stress


title: HUVEC_ATAC_16hr_OS_3


title: HUVEC_ATAC_16hr_PS_2


title: HUVEC_ATAC_16hr_PS_1


title: T14.1


title: HUVEC_ATAC_16hr_OS_1


title: #7 iAM-1 D9, P10, ppluc shRNA, n=2

value: ppluc shRNA


title: EXOSC2 AID ESCs, RNA, sucrose F7, 0 hr

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: 0 hour


title: HUVEC_ATAC_8hr_PS_3

value: 8 hr


title: EXOSC2 AID ESCs, RNA, sucrose F6, 0 hr


title: #6 iAM-1 D9, P10, ppluc shRNA, n=1


title: AI7.1


title: HUVEC_ATAC_8hr_PS_2


title: AI14.2


title: #5 iAM-1 D9, P10, untransduced, n=3

value: untransduced


title: EXOSC2 AID ESCs, RNA, sucrose F2, 12 hr

value: IAA

value: 12 hour


title: HUVEC_ATAC_8hr_PS_1


title: EXOSC2 AID ESCs, RNA, sucrose F5, 0 hr


title: #11 iAM-1 D9, P10, Sbk2 shRNA #1, n=1

value: wistar


title: EXOSC2 AID ESCs, RNA, sucrose F4, 0 hr


title: #3 iAM-1 D9, P10, untransduced, n=2


title: T7.1

value: Tamoxifen


title: HUVEC_ATAC_8hr_OS_3


title: #10 iAM-1 D9, P10, ppluc shRNA, n=3


title: EXOSC2 AID ESCs, RNA, sucrose F3, 0 hr


title: #2 iAM-1 D9, P10, untransduced, n=1


title: POT.3

value: POT


title: AI7.2


title: POT.2


title: EXOSC2 AID ESCs, RNA, sucrose F2, 0 hr


title: HUVEC_ATAC_8hr_OS_1


title: SFPQKO_sg2_3

city: Boston

first: Benjamin

last: Gewurz

state: MA

address: 181 Longwood Avenue, Channing Laboratory, 8th Floor

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly and Akata EBV transcriptome
Salmon (v1.0.0) was used to quantify the transcripts, and DESeq v1.14.1 was used to determine differentially expressed genes. Genes that had a log2(fold change) of at least 1 and an adjusted p-value of < 0.05 were considered significant. Heatmaps were generated using Morpheus, and Enrichr was used to conduct gene ontology enrichment analysis.
Assembly: GRCh37.83 (hg19), Akata EBV
Supplementary files format and content: Excel sheets of the log2FC data are provided.

source_name: P3HR1 cell line

growth_protocol: Human P3HR1 cells were cultured in RPMI (Life Technologies) with 10% FBS and 1% penicillan/streptomycin at 37 degrees C and 5% CO2.

extract_protocol:
Total RNA was isolated using a Qiagen RNeasy extraction kit. An on-column DNA digestion was performed to remove any genomic DNA contamination.
For library preparation, 1 µg of RNA was used for each sample, rRNA-depletion using the NEBNext rRNA Depletion Kit v2 (#E7400, New England Biolabs) was performed, and library construction was completed using NEBNext Ultra RNA Library Prep Kit for Illumina (#E7760L, New England Biolabs) as per the manufacturer’s instructions.

treatment_protocol: Human P3HR1 cells expressing Cas9 were transduced with lentivirus for sgControl, sgSFPQ #1 or sgSFPQ #2 and samples were collected post selection with puromycin.

value: P3HR1 cell line

value: B cells

value: SFPQ KO sg2


title: SFPQKO_sg2_2B


title: HUVEC_ATAC_8hr_OS_2

value: HUVEC


title: EXOSC2 AID ESCs, H3K27ac, 20 hr, rep1

data_processing:
Raw reads of ChIP-seq were mapped to mouse genome mm10 by Bowtie2 (version 2.2.6). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
Peaks were called using MACS2 with the parameters -broad -nomodel –nolambda. Weak peaks were removed.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count
Supplementary files format and content: tab-delimited text files include peaks for ChIP-seq samples

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and subjected to immunoprecipitation. After elution and reverse-crosslinking, the DNA was purified using DNA Clean-up Kit (CWBIO).
ChIP-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

value: 20 hour

value: H3K27ac (Active Motif, #39133)


title: HUVEC_ATAC_2hr_PS_3

value: Pulsatile Shear Stress

value: 2 hr


title: SFPQKO_sg2_2A


title: T7.2


title: HUVEC_ATAC_2hr_PS_2


title: EXOSC2 AID ESCs, H3K27ac, 0 hr-2, rep2 (ctrl for 20 hr)

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell


title: SFPQKO_sg2_1


title: HEK293T-REPAIRv1-EZH2-REP1

city: Chicago

first: Hao

last: Yan

state: Illinois

address: 929 E 57th St, GCIS E535

institute: University of Chicago

data_processing:
R1 reads were trimmed to 97 nt by Cutadapt
Aligned to the hg19 (GRCh37) reference genome using STAR 2.6.1b
A-to-G RNA editing call with REDItools2.0
Assembly: hg19 (GRCh37)
Supplementary files format and content: tab-delimited text files include A-to-G RNA editing rate for each Sample

source_name: Embryonic Kidney

growth_protocol: HEK293T cell lines were cultured in Dulbecco’s Modified Eagle Medium with high glucose, sodium pyruvate, and L-Glutamine (Corning) supplemented with 10% fetal bovine serum (Corning). Cells were maintained in 5% CO2 and passaged regularly at a confluency of 80%.

extract_protocol:
Total RNA extraction with TRIzol (Invitrogen), mRNA was enriched by a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs)
Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs)

value: Embryonic Kidney

value: epithelial

tag: rna editor


title: SFPQKO_sg1_3

tag: cell type

value: SFPQ KO sg1


title: EXOSC2 AID ESCs, H3K27ac, 0 hr-2, rep1 (ctrl for 20 hr)

tag: treatment

value: 0 hour


title: HUVEC_ATAC_2hr_PS_1


title: HEK293T-REPAIRv1-NT-REP1


title: EXOSC2 AID ESCs, H3K27ac, 4 hr, rep2

value: IAA

value: 4 hour


title: HUVEC_ATAC_2hr_OS_3

value: Oscillatory Shear Stress


title: POT.1

value: POT


title: EXOSC2 AID ESCs, H3K27ac, 20 hr, rep2


title: EXOSC2 AID ESCs, H3K27ac, 4 hr, rep1


title: HEK293T-hfDECOR-V106G-EZH2-REP2


title: sgControl_3

value: P3HR1 cell line

value: B cells

value: control


title: HUVEC_ATAC_0hr_3

value: HUVEC

value: untreated

value: 0 hr


title: EXOSC2 AID ESCs, H3K27ac, 0 hr-1, rep1 (ctrl for 4 hr)

value: H3K27ac (Active Motif, #39133)


title: EXOSC2 AID ESCs, H3K27ac, 0 hr-1, rep2 (ctrl for 4 hr)

value: AID-FBEXOSC2 ESCs


title: HEK293T-REPAIRv1-EZH2-REP2


title: HUVEC_ATAC_2hr_OS_1

value: 2 hr


title: sgControl_2


title: EXOSC2 AID ESCs, RNA, 20 hr, rep2

extract_protocol:
Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to ribosomal RNA depletion by Ribo-Zero rRNA removal kits (Illumina) according to manufacturer's instruction.
RNA-seq libraries were constructed by NEBNext Ultra II directional RNA library prep kits (NEB) following manufacturer’s protocols.

value: mouse embryonic stem cell

value: 20 hour


title: sgControl_1


title: HEK293T-hfDECOR-V106G-NT-REP1

value: Embryonic Kidney

value: epithelial


title: HUVEC_ATAC_0hr_2


title: HEK293T-hfDECOR-V106G-NT-REP2


title: EXOSC2 AID ESCs, RNA, 20 hr, rep1

value: IAA


title: Blood monocytes CD115+ intact 3

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
nf-core/rnaseq pipeline with STAR aligner
Assembly: GRCm39
Supplementary files format and content: comma delimeted text files include RPKM values for each Sample

source_name: Blood

extract_protocol:
The mouse mononuclear cell fraction was obtained from peripheral blood and spleen by gradient centrifugation. After that, the cells were subjected to immunomagnetic sorting on a manual MidiMACS™ Separator using LS Columns (Miltenyi Biotec, Bergisch Gladbach,Germany) and using Anti-CD115 MicroBeads magnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) in accordance with the manufacturer's recommendations. For each sample, monocytes were obtained from 5 mice.
DNBSEQ Eukaryotic Strand-specific mRNA library

treatment_protocol: In this work, the effect of splenectomy on liver regeneration was studied. For this purpose in the animals were reproduced splenectomy, and after 7 days 70% liver resection was performed. Animals in which the spleen was intact and only 70% liver resection was performed served as a comparison group. Also, the control group included in whom only the spleen was removed. Peripheral blood and spleen monocytes from intact animals (spleen and liver intact) and from animals in which the liver was resected (spleen intact) were isolated for transcriptome analysis.

value: Blood

value: monocytes CD115+

value: spleen and liver intact


title: SFPQKO_sg1_2

value: P3HR1 cell line

value: SFPQ KO sg1


title: HUVEC_ATAC_2hr_OS_2

value: Oscillatory Shear Stress


title: HEK293T-hfDECOR-F148A-EZH2-REP2


title: n-w3

city: Austin

first: Anna

last: Battenhouse

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description:
AID-knockout B6 mouse TBLV-WT derived tumor
snp_counts_miseq.csv

data_processing:
*library strategy: DNA amplicon
Aligned against provided reference using BWA mem
Duplicates marked using Picard MarkDuplicates
Marked duplicates filtered out using samtools
Mapped read counts quantified by position using bam-readcount (https://github.com/genome/bam-readcount)
Resulting positional counts analyzed using custom Python and R scripts
Alternative base frequencies were dichotomized using a cutoff of 3%.For each pair (reference base to alternate base), the dichotomized alternate calls were modeled as a function of sample group (TBLV-SD versus TBLV-WT in wild-type, AID-knockout, or mA3/AID double-knockout B6 mice).A mixed-effects logistic regression approach was used, incorporating a random effect that accounted for sample variation within the group.
Assembly: Custom TBLV (T-cell tropic MMTV) sequence
Supplementary files format and content: csv file containing readcount results

source_name: lymphoma

extract_protocol:
For MiSeq sequencing, genomic DNA extracted from tumors induced by TBLV-WT and TBLV-SD at the higher dose (3 tumors each) in wild-type and Aicda-/- B6 mice was used for PCR with primers env7254(+) (5’-ATC GCC TTT AAG AAG GAC GCC TTC T-3’) and LTR9604(-) (5’-GGA AAC CAC TTG TCT CAC ATC-3’), resulting in ~2 kb amplicon of the envelope-LTR junction region. Reactions were performed with JumpStart RED Accutaq LA polymerase (Sigma-Aldrich) in the supplied buffer, 1 µg of tumor DNA, 50 pmol of each primer, and 0.5 mM deoxynucleoside triphosphates in 20 µl.  PCR parameters were: 94oC for 1 min, then 10 cycles at 94oC for 10 sec, 53oC for 30 sec, and 68oC for 2 min followed by 25 cycles of 95oC for 15 sec, 50oC for 30 sec, and 68oC for 2 min with a final incubation at 68oC for 7 min. Sixteen independent reactions for each tumor sample were pooled, and DNA was sheared to a size of approximately 400 bp using a Covaris ultrasonicator at the UT Austin Genomic Sequencing and Analysis Facility (GSAF). For Nanopore sequencing, genomic DNA extracted from tumors from B6, B6 AID (Aicda)-knockout, or B6 mA3-AID double-knockout mice induced by TBLV-WT or TBLV-SD was used for PCR with primers env7254(+) (5’-ATC GCC TTT AAG AAG GAC GCC TTC T-3’) and LTR9604(-) (5’-GGA AAC CAC TTG TCT CAC ATC-3’) for the region spanning the envelope-LTR junction. PCRs were performed in 25 µl with JumpStart RED Accutaq LA polymerase (Sigma-Aldrich, cat# D8045) in the supplied buffer, 500 ng of tumor DNA, 25 to 50 pmol of each primer, and 0.5 mM deoxynucleoside triphosphates.  PCR parameters were: 94oC for 1 min, 10 cycles at 94oC for 10 sec, 53oC for 30 sec, 68oC for 2 min followed by 25 cycles of 95oC for 15 sec, 50oC for 30 sec, and 68oC for 2 min with a final incubation at 68oC for 7 min. The fragment size for the env-LTR junction was ~2kb.
For MiSeq sequencing, fragmented DNA was end repaired and used for dA-tailing and ligation with Illumina adapters (unique to each tumor sample). Adapter-ligated DNA was amplified using these PCR parameters: 98oC for 30 sec, 6 cycles at 98oC for 10 sec, 65oC for 30 sec, and 72oC for 30 sec with a final incubation at 72oC for 5 min. Library preparations were submitted for sequencing on the MiSeq platform at the UT Austin Genome Sequencing and Analysis Facility (GSAF). Nanopore sequencing was employed for high-throughput sequence analysis of TBLV proviruses from the tumors induced by low-dose infection. The extracted PCR fragment used for Sanger sequencing was purified using a Zymoclean Gel DNA Recovery Kit (Zymo Research, cat# D4002). DNA (~1 µg) was prepared for Nanopore long amplicon sequencing by the University of Wisconsin Biotechnology Center.

treatment_protocol: For each strain of mice, age-matched weanlings 4-to-6 weeks of age were injected intraperitoneally with either 1 x 106 (low dose) or 2 x 107 (high dose) stably transfected Jurkat T cells. Infectious clones were used for transfection of Jurkat cells and selected for three weeks in hygromycin  and then screened for production of equivalent amounts of TBLV-WT or TBLV-SD (Rem-null) as judged by Western blotting with antibodies to MuLV capsid protein. Mice were monitored for the development of thymic and/or splenic tumors for a period of 9-12 months

value: lymphoma

tag: genotype

value: AID-knockout B6

value: TBLV-WT


title: n-w2


title: Blood monocytes CD115+ intact 2


title: HEK293T-hfDECOR-V106G-EZH2-REP1


title: SFPQKO_sg1_1

value: B cells


title: EXOSC2 AID ESCs, RNA, 4 hr, rep2

value: AID-FBEXOSC2 ESCs

value: 4 hour


title: HEK293T-hfDECOR-F148A-EZH2-REP1


title: EXOSC2 AID ESCs, RNA, 4 hr, rep1

value: mouse embryonic stem cell


title: Blood monocytes CD115+ intact 1


title: HEK293T-hfDECOR-F148A-NT-REP2


title: EXOSC2 AID ESCs, RNA, 0 hr, rep2

value: 0 hour


title: HEK293T-hfDECOR-F148A-NT-REP1

value: Embryonic Kidney


title: Blood monocytes CD115+ PH70% 24 h 2

value: spleen intact, 70% liver resection


title: n-s3

description:
AID-knockout B6 mouse TBLV-SD derived tumor
snp_counts_miseq.csv

value: TBLV-SD


title: EXOSC2 AID ESCs, RNA, 0 hr, rep1


title: n-w1


title: Blood monocytes CD115+ PH70% 24 h 3

value: Blood


title: n-s2


title: HEK293T-DECOR-EZH2-REP2

value: epithelial


title: Blood monocytes CD115+ PH70% 24 h 1

value: monocytes CD115+


title: (2) Combo [TCR]

city: Chuncheon

first: Hawon

last: Song

address: Gangwon Daehak-gil 1

country: South Korea

institute: Kangwon National University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The 10x Genomics Cell Ranger, version (1) 4.0.0 or (2) 6.1.2 was used to align reads and count the single-cell sequencing data using the GRCm38 as the reference genome: ‘cell ranger count’ and ‘cell ranger vdj’ pipelines were applied to process scRNA-seq and TCR-seq, respectively, that led to generating feature, barcode, and matrices for (1) treatment with either buffer or rhIL-7-hyFc or (2) treatment with either rhIL-7-hyFc or a combination of rhIL-7-hyFc and TCE.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger outs are compressed with gzip

extract_protocol:
Mice were euthanized at indicated time points and tumor tissues were harvested. Tumor tissues were mechanically dissected and then digested with collagenase D (400 units/mL; Roche) and DNase I (200 ug/mL; Roche) in washing buffer (2% NCS plus Antibiotic-Antimycotic in RPMI-1640) for 30 min in a shaking incubator at 37 °C. The enzyme-digested tumor meshed over a 70-um cell strainer. Red blood cells (RBC) were lysed with RBC lysing buffer (Sigma-Aldrich). For the enrichment of CD8 T cells, cells were isolated by positive selection methods with IMag according to the manufacturer’s protocol (condition 1) or sorted by FACS (GhostDyeCD45+TCRb+CD8a+) (condition 2) after single-cell preparation. The purified CD8 T cells were analyzed by scRNA-seq paired with scTCR-seq.
Chromium Next GEM Single Cell 5p RNA library v2 for gene expression and Chromium Next GEM Single Cell VDJ library v2 for TCR seq

treatment_protocol: (Condition 1) C57BL/6 mice bearing palpable MC38 tumors were treated s.c. with rhIL-7-hyFc (10 mg kg-1). Tumors were collected 7 days after the rhIL-7-hyFc treatment for scRNA-seq/scTCR-seq analyses of TILs. (Condition 2) C57BL/6 mice bearing palpable MC38 tumors given rhIL-7-hyFc (1.25 mg kg-1) were treated i.v. with anti-mPD-L1  anti-CD3ε TCE 3 times daily 3 days after rhIL-7-hyFc treatment. Tumors were collected 24 hours after the last treatment for scRNA-seq analyses of TILs

value: Tumor

value: CD8 T cell

value: Wild type

value: rhIL-7-hyFc (1.25mpk, s.c.) + TCE (i.v.)


title: HEK293T-DECOR-EZH2-REP1


title: HUVEC_ATAC_0hr_1

value: HUVEC

value: untreated

value: 0 hr


title: n-s1

value: lymphoma

value: AID-knockout B6


title: (2) rhIL-7-hyFc [TCR]

description: 10X Genomics

value: rhIL-7-hyFc (1.25mpk, s.c.)


title: Spleen monocytes CD115+ PH70% 24 h 3

source_name: Spleen

value: Spleen


title: c-w3

description:
C57BL/6 (B6) mouse TBLV-WT derived tumor
snp_counts_miseq.csv

value: TBLV-WT


title: HEK293T-DECOR-NT-REP2

value: Embryonic Kidney

value: DECOR-NT


title: c-w2


title: Spleen monocytes CD115+ PH70% 24 h 2

value: spleen intact, 70% liver resection


title: Spleen monocytes CD115+ PH70% 24 h 1


title: (1) rhIL-7-hyFc [TCR]

description: 10X Genomics

value: rhIL-7-hyFc (10mpk, s.c.)


title: (1) Buffer [TCR]

description: 10X Genomics

value: Buffer


title: HEK293T-NON-TREATED-REP2

value: epithelial

value: non-treated


title: HEK293T-DECOR-NT-REP1


title: c-w1


title: Spleen monocytes CD115+ intact 3

value: monocytes CD115+

value: spleen and liver intact


title: c-s3

description:
C57BL/6 (B6) mouse TBLV-SD derived tumor
snp_counts_miseq.csv

value: TBLV-SD


title: (2) rhIL-7-hyFc [Gene Expression]

description: 10X Genomics

value: Tumor

value: CD8 T cell

value: Wild type


title: Spleen monocytes CD115+ intact 2


title: (2) Combo [Gene Expression]

description: 10X Genomics

value: rhIL-7-hyFc (1.25mpk, s.c.) + TCE (i.v.)


title: (1) rhIL-7-hyFc [Gene Expression]

description: 10X Genomics


title: c-s2

value: lymphoma


title: Spleen monocytes CD115+ intact 1

value: Spleen


title: (1) Buffer [Gene Expression]

description: 10X Genomics


title: female zebra finch embryonic gonad

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

description: 10X genomics

data_processing:
Sequenced reads were mapped to lab maintained ant genome assembly using cellranger version 6.0.1
Assembly: GCF_003957565.2
Assembly: GCF_000002315.6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Taeniopygia guttata

source_name: early embryonic gonad (HH28)

extract_protocol:
single cell extraction protocol
10X Genomics 3' v3 kit

value: Female

value: early embryonic gonad (HH28)


title: S3Yan-2, 140mM, Root, Rep 2

status: Public on Apr 15 2024

city: Islamabad

first: Muhammad Ramzan

last: Khan

address: Park Rd

department: National Institute Of Genomics And Advanced Bio-Technology (NIGAB)

country: Pakistan

institute: National Agricultural Research Centre

data_processing:
Raw reads were subjected to FastQC for quality assessment.
Low quality bases and adaptor sequences were removed using Trimmomatic.
Clean reads were aligned to reference genome assembly using Hisat2.
Gene-level quantification was performed with featureCounts.
Differentially expressed genes were identified using DESeq2 in R.
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Oryza sativa

source_name: Root

growth_protocol: Seeds of two genotypes were grown in normal conditions for 30 days. Half of the seedlings were transferred to culture solution supplemented with 140 mM NaCl for 12 days. The remaining seedlings were remained in normal conditions for 12 further days and used as control plants.

extract_protocol:
Total RNA was extracted from roots of each sample in control and stress condition using phenol/chloroform method.
cDNA libraries were constructed using Illumina's standard protocol.

treatment_protocol: Under normal and salt stress.

tag: developmental stage

value: 42 days

value: Root

value: Salt Susceptible

value: Salinity

value: 12 day


title: S3Yan-3, 140mM, Root, Rep 3


title: S3Yan-1, 140mM, Root, Rep 1


title: c-s1


title: S3-1, 0mM, Root, Rep 1

value: Control


title: S13Yan-3, 140mM, Root, Rep 3

value: Salt Tolerant


title: S13Yan-2, 140mM, Root, Rep 2


title: S3-2, 0mM, Root, Rep 2


title: AS15, brain, Delta-variant infected 1 month

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

data_processing:
STAR v. 2.7.10a
sequencing reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Assembly: GRCm39
Supplementary files format and content: raw counts in text file format

source_name: mouse brain

extract_protocol:
Trizol
RNA libraries were prepared using NEBNext polyA mRNA Magnetic Isolation Module and NEB Ultra II RNA library preparation kit for illumina following manufacturer's protocol

value: mouse brain

tag: infection

value: Delta-variant infected 1 month


title: S13Yan-1, 140mM, Root, Rep 1


title: AS16, brain, Delta-variant infected 1 month


title: S13-2, 0mM, Root, Rep 2


title: HEK293T-NON-TREATED-REP1

value: Embryonic Kidney

tag: cell line

value: epithelial

value: non-treated


title: AS13, brain, Delta-variant infected 1 month


title: S13-1, 0mM, Root, Rep 1

tag: time


title: AS6, brain, Delta-variant infected 4 month

value: Delta-variant infected 4 month


title: AS7, brain, Delta-variant infected 4 month


title: male zebra finch embryonic gonad

description: 10X genomics

value: Male


title: AS5, brain, Delta-variant infected 4 month


title: AS4, brain, Mock-infected

value: Mock-infected 4 month


title: AS3, brain, Mock-infected


title: AS1, brain, Mock-infected


title: AS2, brain, Mock-infected


title: paracancerous6

city: Nanchong

first: kang

last: liu

state: State...

address: 55 Dongshun Road, Gaoping District, Nanchong city, Sichuan Province

institute: north sichuan medical college

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8)
Quality control was checked on the raw sequence data using FastQC
Raw data were pre-processed using Cutadapt to remove adaptor sequences
Trimmed reads are mapped to the corresponding reference genome using HISAT2 and StringTie was used to reconstruct the transcriptome
Ballgown software was applied to calculate the fragments per kilobase of exon per million fragments mapped (FPKM)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: paracancerous tissues

extract_protocol:
Total RNA was extracted from the tissue using Trizol reagent (Invitrogen, Carlsbad) according to the manufacturer’s protocol.1-2 ug of total RNA was used for the construction of sequencing libraries.
The cDNA library was constructed using KAPA Stranded RNA-Seq Library Preparation Kit (Illumina) following the manufacturer’s protocol

value: paracancerous tissues


title: TC-32 siFLI1, H3K27ac, rep 1a

city: Bethesda

first: Natasha

middle: J

last: Caplen

state: Maryland

address: 37 Convent Drive, Bldg. 37, Rm 6128

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
ChIP-seq analysis were carried out using center for cancer research bioinformatics resource (CCBR) pipeline (https://github.com/CCBR/Pipeliner/wiki/Pipeline-Documentation - chip-seq).
Sequence reads were trimmed for adaptor sequence using cutadapt v4.4.
Trimmed reads were aligned to GRCh38/hg38 human genes and Drosophila melanogaster dm6 genes using BWA mem v.0.7.17.
PCR duplicates were removed with the Picard v.2.17.11 SamToFasq (for blacklist read removal) and MarkDuplicates (to remove PCR duplicates).
Peak calling was performed against input control using model-based MACS2 v2.1.1, with the cut-off q-value < 0.02.
Assembly: GRCh38/hg38
Supplementary files format and content: narrowPeak (except for Input sample)

growth_protocol: Cells were cultured in RPM1 1640 supplemented with 10% FBS and Plasmocin Prophylactic (Invivogen, San Diego, CA), and grown at 37°C, 5% CO2. We confirmed the identity of cell lines using short tandem repeat (STR) analysis (ATCC) at intervals throughout experimentation, and we monitored for mycoplasma contamination using the MycoAlert Plus system (Lonza, Walkersville, MD).

extract_protocol:
ChIP assays were performed using SimpleChIP plus Enzymatic Chromatin IP kit (9005S; Cell Signaling Technology, Danvers, MA). Briefly, cells were crosslinked with final concentration of 1% formaldehyde for 10 minutes. After quenching, cell lysis and enyzmatically digested, chromatin was sonicated using Branson SFX250 Digital Sonifier (Branson Ultrasonics) to obtain a fragment size of 200 - 900 bp. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Thermo Fisher Scientific).
ChIP-seq libraries were using SMARTer ThruPlex TAKARA Library Prep kit following manufacturer's instructions. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 8 cycles on the thermocycler.

treatment_protocol: RNAi-based studies, cells were reverse transfected with 20 nM siRNA complexed with Lipofectamine RNAi-Max (Invitrogen). siNeg (SI03650318, Qiagen) and siFLI1 (s5266, Thermo Fisher Scientific).

value: Ewing sarcoma

tag: chip antibody

tag: sirna


title: paracancerous5

tag: tissue


title: paracancerous2


title: paracancerous3


title: TC-32 siNEG, H3K27ac, rep 1a

value: siNeg


title: paracancerous4


title: paracancerous1


title: LT-HSCs_Ikba_WT_2 [RNA-seq]

city: Barcelona

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020).
Trimmed reads were aligned to reference genome (GRCm38 release 102 from Ensembl) with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for the number of allowed mismatches which was set to 1
Uniquely mapped reads were considered for further analysis. Raw gene expression was directly quantified in STAR with --quantMode GeneCounts option.
Raw counts matrix was imported into R Statistical software (v4.2.1). Prior to statistical analysis, those genes with less than 10 raw counts across the 8 samples per timepoint were discarded
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.38.3)
Assembly: mm10
Supplementary files format and content: Tab-separated value file: RNAseq_All_samples_Raw_counts.txt: RNAseq Raw expression levels for each gene (55,487 rows) in each individual sample as obtained from STAR. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_Norm_counts_Gender_corrected.txt. Normalized expression levels including the expression of 20,610 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.38.3)

source_name: fetal liver

growth_protocol: Primary LT-HSCs from foetal liver were obstained by disection follwed by FACS sorting directly into RTLplus Buffer.

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004]
Samples were processed to obtain cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified byimmobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation andDouble last bead purification was performed to remove fragments below 200 bp.Next, samples wereused to generate an Illumina sequencing library byNEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer andtotal cDNA was sequenced using an Illumina HiSeq 2000 sequencer.
RNA-seq single-end 50bp

tag: developmental time

value: fetal liver

value: 500 LT-HSCs

tag: condition

value: WT


title: LT-HSCs_Ikba_WT_1 [RNA-seq]

tag: Sex


title: TC32, pLOC ETS1-High, Rep 3

data_processing:
RNA-seq analysis were carried out using center for cancer research bioinfoirmatics resource (CCBR) pipeline (https://github.com/CCBR/Pipeliner/wiki/Pipeline-Documentation - rna-seq)
Sequence reads were triimmed for adaptor sequence using cutadapt v4.4
Trimmed reads were mapped to the GRCh38/hg38 human genome using STAR v.2.7.3 with standard parameters.
FeatureCounts in the Subread v.2.0.3 package (Liao et al., 2013) was used to summarize gene level reads by counting reads that overlapped the GRCh38/hg38 annotated gene exons.
Gene counts were normalized and used to quantify differential gene expression between control and experimental conditions using limma v.3.38.3.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each samples
Supplementary files format and content: Tab-delimited text file includes FPKM

source_name: Cell line

growth_protocol: TC-32 cells were  cultured in RPM1 1640 supplemented with 10% FBS and Plasmocin Prophylactic (Invivogen, San Diego, CA), and grown at 37°C, 5% CO2. We confirmed the identity of cell line using short tandem repeat (STR) analysis (ATCC) at intervals throughout experimentation, and we monitored for mycoplasma contamination using the MycoAlert Plus system (Lonza, Walkersville, MD)

extract_protocol:
Total RNA was extracted using Maxwell 16 LEV simply RNA kits (Promega)
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep Ligation kit following manufacturer's protocols.

treatment_protocol: To generate the ETS1-pLOC construct, we used a synthetic human ETS1 cDNA (NM_001143820) with custom flanking restriction enzyme sites (GENEWIZ, South Plainfield, NJ) cloned into the pLOC vector (OHS5832; Dharmacon/Horizon Discovery, Cambridge, UK). Lentivirus was produced in HEK-293T cells using either the Trans-Lentiviral ORF Packaging Kit (Dharmacon/Horizon Discovery). Viral supernatants were collected 72 hrs post-transfection and concentrated (PEG Virus Precipitation Kit, Abcam, Waltham, Boston). Concentrated virus was added dropwise to cells in the presence of media supplemented with 8 µg/ml polybrene and transduced cells selected using puromycin (2 µg/ml) and subjected to single cell sorting.

value: Cell line

value: pLOC ETS1


title: AS14, brain, Delta-variant infected 1 month


title: LT-HSCs_Ikba_Het_1 [RNA-seq]

value: HET


title: TC32, pLOC ETS1-High, Rep 2


title: ESCC6

source_name: esophageal squamous cell carcinoma

value: esophageal squamous cell carcinoma


title: CD4, CD8 double negative thymocytes in Rag2 deficient background. Mouse 95 [R2b_DN_95]

city: Vienna

first: Tobias

last: Suske

state: Vienna

address: Veterinärplatz 1

department: Functional Cancer Genomics

country: Austria

institute: University of Veterinary Medicine

data_processing:
Quality control was performed using FastQC (version 0.11.8, Andrews S., 2010). Removal of low-quality bases and adapter trimming was achieved with trimmomatic (version 0.35, Bolger AM et al. 2014) followed by mapping using STAR aligner (version 2.7, Dobin A et al. 2013) with the GRCm38 genome (ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/GRCm38.primary_assembly.genome.fa.gz) and ensembl gene annotation release 93 (ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz, used in several SFBF61 projects). The genome for mapping with STAR was generated with the command:  STAR --runMode genomeGenerate --genomeDir STAR93 –genomeFastaFiles GRCm38.primary_assembly.genome.fa –sjdbGTFfile Mus_musculus.GRCm38.93.gtf.  For further analysis, only uniquely mapped reads were considered by using bamtools (Derek W et al.2011, Version 2.4.1) command: bamtools filter -tag NH:1 <mapped.bam> <filtered.bam>.
Counting features was achieved using GenomicAlignments package (Lawrence M et al. 2013)  on the GRCm38.93.gtf annotation: reads mapping to exons with the tag “basic” were summarized using the GenomicAlignments::summarizeOverlaps() method.  For RPKM calculations, the length of a gene was determined by summing up the width of the exons of a gene using the methods sum() and width(). Differential expression analysis contrasting each pair of conditions was performed using DESeq2 (Love MI et al. 2014, version 1.18.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: Differential expression (DE) results using DESeq2 with single contrasts from RPKM-normalized values from the respective GeneCounts2cols.tsv files
Supplementary files format and content: all_DIFF_N642H_DE_result_tables.xlsx: focussed on contrasts along T cell differentiation and on STAT5BN642H
Supplementary files format and content: all_DIFF_S710F_DE_result_tables.xlsx: focussed on contrasts along T cell differentiation and on Stat5aS710F
Supplementary files format and content: all_GT_N642H_DE_result_tables.xlsx: focussed on contrasts across genotypes and on STAT5BN642H
Supplementary files format and content: all_GT_S710F_DE_result_tables.xlsx: focussed on contrasts across genotypes and on Stat5aS710F

source_name: thymocytes

extract_protocol:
DN, DP and SP8 T-cells were harvested from thymi by generating single-cell suspensions and FACS-sorting for viable Thy1.2-positive cells with respective CD4/CD8 expression patterns (Supplementary table). RNA was isolated from snap-frozen cell pellets using the DNA/RNA Allprep Kit (QIAGEN).
Library preparation and sequencing were performed at the Center for Molecular Medicine (CeMM), Vienna, Austria. Libraries were prepared using the NEBNext ®UltraTMRNA Library Prep Kit. Next, the samples were multiplexed and sequenced on an Ilumina Hisat2000 sequencer.

tag: strain background

tag: name stage_replicate

tag: replicate id

value: DN

value: thymocytes


title: TC32, pLOC ETS1-High, Rep 1


title: ESCC5


title: CD4, CD8 double negative thymocytes in Rag2 and STAT5BN642H double deficient background. Mouse 94 [R2S5b_DN_94]

value: STAT5BN642H Rag2-/-


title: CD4, CD8 double positive thymocytes in Rag2 and STAT5BN642H double deficient background. Mouse 94 [R2S5b_DP_94]

value: DP


title: ESCC4


title: CD4, CD8 double negative thymocytes in Rag2 and STAT5BN642H double deficient background. Mouse 93 [R2S5b_DN_93]


title: CD4 negative, CD8 positive thymocytes in Rag2 and STAT5BN642H double deficient background. Mouse 94 [R2S5b_CD8_94]


title: TC32, pLOC ETS1-Low, Rep 3


title: ESCC3


title: TC32, pLOC ETS1-Low, Rep 2


title: CD4, CD8 double positive thymocytes in STAT5BN642H deficient background. Mouse 67 [S5b_DP_67]


title: TC32, pLOC ETS1-Low, Rep 1


title: ESCC2


title: TC32, pLOC RFP, Rep 3

value: pLOC RFP


title: plasmid pool

first: Christos

last: Miliotis

address: 330 Brookline Ave

department: Cancer Center

institute: BIDMC

library_source: other

data_processing:
Barcode counts were calculated from raw reads and then normalized per sample based on sequencing depth. For each sample, a barcode RNA to DNA ratio was calculated by dividing the barcode counts in each replicate to that in the plasmid pool library.
The RNA to DNA ratios were then log-transformed and quantile normalized across samples. A two-sided Wilcoxon test was performed to compare barcode count ratios between reference and alternative allele oligos in each replicate. To combine replicate p-values, the Stouffer’s method was used, and false discovery rate (FDR) correction was applied. Each oligo was represented by 10 barcodes, so to obtain a per-oligo activity in each sample, the median activity was calculated. Fold-change was defined as the ratio of the alternative to the reference allele median activity.
Assembly: hg38
Supplementary files format and content: Barcode counts for each sample.
Library strategy: Amplicon sequencing from cDNA

molecule: other

source_name: Plasmid

extract_protocol:
SNU719 and AGS cells were seeded in 15 cm plates to achieve 80% confluence the next day. Cells were transfected with 10 μg of the MPRA plasmid library using TransIT-X2 reagent (Mirus Bio, MIR 6004) as per the manufacturer’s protocol, aiming for a transfection efficiency of 50-80%. Total RNA was collected 48 hr post-transfection using the miRNeasy mini kit (Qiagen, #217004). Genomic DNA was removed using the Turbo DNA-free kit (ThermoFisher Scientific, AM1907) following the manufacturer’s “Rigorous DNase treatment” protocol. Per replicate, 15 μg total RNA was reverse transcribed with SuperScript IV Reverse Transcriptase (ThermoFisher Scientific, #18090010) using oligo-dT primers.
Amplicon sequencing libraries from cDNA or plasmid pool DNA were constructed through two PCR reactions. In the first PCR round, 1:10 diluted cDNA was amplified using 0.2 μM of the DT_barcodePE_Fv2 and 0.2 μM of an isomolar mix of the DT_barcodePE_Rv2 primers (0 to 6 random Ns, Table S2). The PCR reaction was performed with the NEB Next High-Fidelity 2x PCR Master Mix (NEB, M0541L) and the following conditions: 98C for 30 sec, 10 cycles (98C for 10 sec, 63C for 10 sec, 72C for 15 sec), 72C for 2 min. Enough PCR reactions were run to ensure that all the cDNA from each replicate was amplified. In the second PCR reaction, 1:10 diluted PCR round 1 product was amplified using 0.5 μM of a unique pair of multiplexing Illumina primers (PE_i5 and PE_index in Table S2). The following PCR conditions were used: 98C for 30 sec, 10 cycles (98C for 10 sec, 62C for 10 sec, 72C for 15 sec), 72C for 2 min. For each replicate, the second round PCR product was purified through gel extraction using the Monarch Gel Extraction kit (NEB, T1020S). The quality of each library was assessed by an Agilent Tapestation D1000 assay (Agilent). An equimolar mix of all libraries was sent for single-end 150 bp sequencing on an Illumina sequencer, with 20% PhiX spike-in to increase library complexity.

value: Plasmid


title: CD4, CD8 double positive thymocytes in STAT5BN642H deficient background. Mouse 132 [S5b_DP_132]


title: CD4, CD8 double negative thymocytes in STAT5BN642H deficient background. Mouse 132 [S5b_DN_132]


title: CD4, CD8 double negative thymocytes in STAT5BN642H deficient background. Mouse 65 [S5b_DN_65]


title: TC32, pLOC RFP, Rep 2


title: TC32, pLOC RFP, Rep 1


title: SNU719, rep3


title: CD4 negative, CD8 positive thymocytes in STAT5BN642H deficient background. Mouse 132 [S5b_CD8_132]


title: CD4, CD8 double negative thymocytes in Rag2 deficient background. Mouse 90 [R2b_DN_90]


title: BMSC,dex1,day4

city: Wuhan, Hubei, China

first: yongle

last: yu

state: 湖北

address: Wuhan, Hubei, China

institute: 武汉大学第二临床学院

description: dex 4d

data_processing:
GLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes read counts for each sample

organism: Rattus

source_name: bone

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: bone

value: BMSC

value: Mesenchymal stem cells

value: DEX


title: BMSC,dex2,day4

description: dex 4d


title: CD4, CD8 double positive thymocytes in STAT5BN642H deficient background. Mouse 131 [S5b_DP_131]


title: BMSC,nc3,day4

description: control


title: SNU719, rep2


title: BMSC,dex3,day4

description: dex 4d


title: SNU719, rep1


title: TC-32 WT, B, H3K27me3, rep 2

data_processing:
CUT&RUN analysis were carried out using center for cancer research bioinfoirmatics resource (CCBR) pipeline (https://github.com/CCBR/CARLISLE)
Sequence reads were triimmed for adaptor sequence using cutadapt v4.4
trimmed reads were aligned to GRCh38/hg38 human genes and S. cerevisiae genes using Bowtie2
PCR duplicates were removed with the Picard v.2.17.11 SamToFasq (for blacklist read removal) and MarkDuplicates (to remove PCR duplicates)
Peak calling was performed against input control using model-based MACS2 v2.1.1, with the cut-off q-value < 0.02.
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak.bed (except for Input sample)

growth_protocol: Cells were cultured in RPM1 1640  supplemented with 10% FBS and Plasmocin Prophylactic (Invivogen, San Diego, CA), and grown at 37°C, 5% CO2. We confirmed the identity of cell lines using short tandem repeat (STR) analysis (ATCC) at intervals throughout experimentation, and we monitored for mycoplasma contamination using the MycoAlert Plus system (Lonza, Walkersville, MD)

extract_protocol:
CUT&RUN (14-1048, EpiCypher) was carried following manufacture's instructions with slight modifications. In brief, 5 x 105 cell/condition were harvested, washed, and bound to activated Concanavalin A (ConA) conjugated paramagnetic beads. The ConA beads–cell complex was resuspended in antibody buffer, and incubated with the appropriate antibody overnight at 4°C. Following incubation, pAG-MNase  was added to each CUT&RUN reaction to allow binding to the antibody-labelled chromatin. Targeted chromatin was digested and released by addition of CaCl2 (supplemented with S. cerevisiae spike-in, 29987L; Cell Signal Technology). Fragmented chromatin was purified using CUTANA Purification kit. Purified DNAs were quantified using Qubit fluorometer.
The CUTANA CUT&RUN Library Prep kit (14-1001, EpiCypher) was used for library preparation following manufacturer’s instructions

value: Ewing sarcoma


title: ESCC1


title: CD4, CD8 double negative thymocytes in STAT5BN642H deficient background. Mouse 131 [S5b_DN_131]


title: BMSC,nc2,day4

description: control


title: BMSC,nc1,day4

description: control


title: TC-32 WT, B, H3K27me3, rep 1


title: CD4 negative, CD8 positive thymocytes in STAT5BN642H deficient background. Mouse 131 [S5b_CD8_131]


title: CD4 negative, CD8 positive thymocytes in STAT5BN642H deficient background. Mouse 67 [S5b_CD8_67]


title: TC-32 WT, B, H3K9me3, rep 2

value: H3K9me3 (Abcam, #ab8898)


title: CD4, CD8 double positive thymocytes in Rag2 and STAT5BN642H double deficient background. Mouse 129 [R2S5b_DP_129]


title: LPMC2

city: Beijing

first: Liu

last: Yang

address: Qinghuayuan street

institute: Tsinghua University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, to obtain clean reads.
HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited txt file includes fpkm, tpm, and read counts

source_name: intestine

extract_protocol:
The RNA from the sorted mast cells was extracted using kits from BGI genomics
The libraries were prepared using kits from BGI genomics according to manufacturer instructions

value: intestine

value: H. polygyrus infected


title: AGS, rep1

source_name: AGS

value: AGS


title: TC-32 WT, B, H3K9me3, rep 1

value: Cell line


title: AGS, rep2


title: LPMC4


title: CD4 negative, CD8 positive thymocytes in Rag2 and STAT5BN642H double deficient background. Mouse 129 [R2S5b_CD8_129]


title: PWH P8 CSF scTCRseq

city: New Haven

first: Meng

state: CT

address: 300 George St

institute: Yale University

data_processing:
Cell Ranger 7.0.0 count subcommand was used to generate the count matrices, barcode assignments, and feature calls for gene expression data.
Cell Ranger 7.0.0 vdj subcommand was used to assemble TCR and BCR sequences.
Cell Ranger 7.0.0 aggr subcommand was used to aggregate samples into a single data matrix
Seurat v4 was used to filter out low quality cells and Azimuth was used to perform cell type annotations.
Assembly: GCRhg38
Supplementary files format and content: cell ranger count matrix in h5 file format, cell ranger vdj clonotype files, seurat object in RDS format
Library strategy: scTCRseq

source_name: CSF

extract_protocol:
Fresh CSF and blood were processed within one hour of collection. CSF was centrifuged at 300g for 10 minutes at room temperature (25°C). The supernatant was aspirated to 40 µl and the pelleted cells were used for single-cell RNA sequencing. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood via Ficoll gradient with Sepmate tubes and resuspended in .04% PBS-BSA for single-cell RNA sequencing.
For blood, approximately 8000 single cells per sample were processed using the Chromium 5′ single-cell expression system (10x Genomics). For CSF, the entire cell pellet was processed for 10X. Samples were sequenced on Illumina HiSeq 4000 or Illumina HiSeq2500 at an average depth of 30-50,000 reads per cell.

tag: donor

value: CSF

value: T cell

tag: disease status

value: chronic HIV

tag: study id


title: CD4, CD8 double negative thymocytes in Rag2 deficient background. Mouse 106 [R2b_DN_106]

tag: genotype

value: DN

tag: cell type

value: thymocytes


title: IEMC4

tag: treatment


title: TC-32 WT, B, FLI1, rep 1

tag: cell line

value: FLI1 (Abcam, #ab15289)


title: PWH P8 CSF scRNAseq

data_processing:
Cell Ranger 7.0.0 count subcommand was used to generate the count matrices, barcode assignments, and feature calls for gene expression data.
Cell Ranger 7.0.0 vdj subcommand was used to assemble TCR and BCR sequences.
Cell Ranger 7.0.0 aggr subcommand was used to aggregate samples into a single data matrix
Seurat v4 was used to filter out low quality cells and Azimuth was used to perform cell type annotations.
Assembly: GCRhg38
Supplementary files format and content: cell ranger count matrix in h5 file format, cell ranger vdj clonotype files, seurat object in RDS format

value: CSF cells


title: TC-32 WT, B, IgG, rep 2


title: IEMC2


title: CD4 negative, CD8 positive thymocytes in Stat5AS710F background. Mouse 104 [R2S5b_DP_104]

value: STAT5BN642H Rag2-/-

value: DP


title: AGS, rep3


title: CD4 negative, CD8 positive thymocytes in Stat5AS710F and Rag2 deficient backbackground. Mouse 104 [R2S5b_DN_104]


title: PWH P8 Blood scTCRseq

source_name: PBMC

value: PBMC


title: TC-32 WT, B, IgG, rep 1


title: PWH P8 Blood scRNAseq


title: Hepatic _10wpi

city: Ultimo

first: Dayna

last: Sais

state: New South Wales

address: 15 Broadway

institute: University of Technology Sydney

description:
fhe_miRNA_rawcount_matrix.txt
ova_miRNA_rawcount_matrix.txt

data_processing:
The quality of the raw FASTq files was assessed using FastQC, and consequently the adaptor sequences were excised, and low-quality sequences were removed (< 20 phred score, and short read length < 18 nt) using the bioinformatic tool CutAdapt (v3.4). The cleaned sheep sera sequence reads were then aligned against known sheep mature miRNAs from miRBase: Ovis aries (Oar_V4.0) using Bowtie (v1), allowing zero mismatches. The miRNA sequence reads that did not align against the sheep miRNAs were then aligned against F. hepatica mature miRNA sequences from miRBase (Fhepatica_v1) and other published sources, allowing zero mismatches. The counts for the sheep and F. hepatica miRNAs were extracted from the resultant Sam files using SamTools.
Assembly: Oar_V4.0 from miRbase
Supplementary files format and content: tab-deliminated text files include the raw counts for ova miRNAs for each samples
Supplementary files format and content: tab-deliminated text files include the raw counts for fhe miRNAs for each samples

organism: Ovis aries

source_name: serum

extract_protocol:
Total RNA was harvested from 6 replicates for each timpoint using TriReagent RT LS (Molecular Research Centre) according to the manufactureres instructions. A total of 800uL of starting serum was used for Total RNA extraction. Total RNA for each timepoint was pooled for small RNA sequneincg (representing 6 animals per timepoint). For construction of sequencing libraries 1ug of total RNA was used for small RNA seq.
RNA libraries for small RNA seq were prepared using TruSeq Small RNA library prep kit.

value: serum

value: Infected


title: Hepatic_14wpi


title: CD4 negative, CD8 positive thymocytes in Stat5AS710F background. Mouse 104 [R2S5b_CD8_104]


title: PWH P7 Blood scTCRseq (biol rep 2)


title: TC-32 WT, B, FLI1, rep 2

value: Ewing sarcoma