title: CD4 positive, CD8 positive thymocytes in Stat5AS710F background. Mouse 6 [S5a_DP_6]


title: Hepatic_3wpi

status: Public on Apr 15 2024

type: SRA

city: Ultimo

first: Dayna

last: Sais

state: New South Wales

address: 15 Broadway

country: Australia

institute: University of Technology Sydney

description:
fhe_miRNA_rawcount_matrix.txt
ova_miRNA_rawcount_matrix.txt

library_source: transcriptomic

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

molecule: total RNA

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.

tag: tissue

value: serum

tag: treatment

value: Infected


title: TC-32 WT, A, H3K27ac, rep 1

city: Bethesda

first: Natasha

middle: J

last: Caplen

state: Maryland

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

department: National Cancer Institute

country: USA

institute: National Institutes of Health

library_source: genomic

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)

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line

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: Cell line

tag: cell line

tag: cell type

value: Ewing sarcoma

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: PWH P7 Blood scRNAseq (biol rep 2)

city: New Haven

first: Meng

last: Wang

state: CT

address: 300 George St

institute: Yale University

library_source: transcriptomic single cell

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

source_name: PBMC

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: PBMC

tag: disease status

value: chronic HIV

tag: study id


title: CD4 positive, CD8 positive thymocytes in Stat5AS710F background. Mouse 3 [S5a_DP_3]

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

organism: Mus musculus

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: genotype

tag: strain background

tag: name stage_replicate

tag: replicate id

tag: condition

value: DP

value: thymocytes


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

value: FLI1 (Abcam, #ab15289)


title: HEK293T-REPAIRv1-NT-REP2

status: Public on Apr 16 2024

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

molecule: polyA RNA

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: Non-infected_14wpi

value: Uninfected


title: PWH P7 CSF scTCRseq

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

value: CSF

value: T cell


title: CD4 positive, CD8 positive thymocytes in Stat5AS710F background. Mouse 1 [S5a_DP_1]


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


title: CD4 negative, CD8 positive thymocytes in Stat5AS710F background. Mouse 3 [S5a_CD8_3]


title: TC-32 WT, A, H3K27ac, rep 2


title: Pre-hepatic _9dpi


title: 16_108-008_7

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

library_source: other

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination
Library strategy: CITE-seq

molecule: other

source_name: blood

growth_protocol: PBMCs from three high-dose group subjects were stained with the commercially available TotalSeq-C human universal cocktail V1.0 reagent (Bioloegend Cat. #39905). For each experiment we processed thawed PBMCs from one patient including three different time points (baseline, early timepoint (1 or 2 weeks and an late timepoints (4 or 13 weeks)). PBMCs (1x106/well) were distributed in a 96-well plate and incubated with human TruStain FcX block (BioLegend Cat. #422301) for 10min at 4C

extract_protocol:
After two washes approximately 100,000 PBMCs per sample were processed according to the 10X Genomics protocol. A single cell suspension was prepared and loaded onto the 10x Chromium Controller (10X Genomics) according to the manufacturer’s protocol, with a target capture of 5,000 cells per channel.
Sequencing libraries were generated using the NextGEM Single Cell 5' v1.1 kit (10x Genomics).

treatment_protocol: Then they samples were incubated with Total-Seq C (1:6 dilution) for 30min at 4C.

value: blood

value: Treg

tag: library type

value: GEX, ADT

tag: trex id

tag: day

value: Day 7


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

tag: tissue

value: Cell line


title: PWH P7 Blood scTCRseq (biol rep 1)


title: Pre-hepatic_2dpi

value: serum

tag: treatment

value: Infected


title: CD4 negative, CD8 positive thymocytes in Stat5AS710F background. Mouse 1 [S5a_CD8_1]


title: PWH P7 CSF scRNAseq

value: CSF cells


title: Pre-hepatic_14dpi


title: PWH P7 Blood scTCRseq

value: PBMC

value: T cell (CD4 enriched)

value: chronic HIV


title: Hepatic_7wpi


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

tag: cell line

value: Ewing sarcoma


title: PWH P7 Blood scRNAseq

tag: cell type

value: PBMC (CD4 enriched)


title: 15_108-008_6

value: Day 28


title: CD4, CD8 double positive in Rag deficient and Stat5aS710F background. Mouse 6 [R2S5a_DP_6]

value: Stat5aS710F Rag2-/-

value: DP

value: thymocytes


title: 14_108-008_3

value: blood

value: Day 0


title: PWH P7 Blood scRNAseq (biol rep 1)


title: TAN, PM8, scRNA-seq

city: New York

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 (GRCm38)
Supplementary files format and content: Digital gene expression matrices (genes x cells) in sparse matrix format. Compressed, flat text files with tab delimiters. File format is compatible with the R package Seurat. Requires the corresponding features (genes) and barcodes (cell names) files.

source_name: iWAT

extract_protocol:
The fourth inguinal white adipose tissue (iWAT) depot from Ad-Lib or TAN mice were dissected and placed on a sterile 6-well tissue culture plate with ice-cold 1X DPBS. Excess liquid was removed from fat pads by blotting. Each tissue was cut and minced with scissors and then placed in 15 ml conical tubes containing digestion buffer (2 ml DPBS and Collagenase II at 3 mg/ml; Worthington Biochemical, Lakewood, NJ, USA) for 40 min of incubation at 37°C with gentle shaking at 100 rpm. Following tissue digestion, enzyme activity was stopped with 8 ml of resuspension media (DMEM/F12 with glutamax supplemented with 15%FBS and 1% pen/strep; Thermo Scientific, CA). The digestion mixture was passed through 100 μm cell strainer and centrifuged at 150 x g for 8 min at room temperature. To remove red blood cells, the pellet was resuspended and incubated in RBC lysis buffer (Thermo Scientific, CA) for 3 min at room temperature, followed by centrifugation at 150 x g for 8 min. The pellet was then resuspended in resuspension media and again spun down at 150 x g for 8 min. The cell pellet was resuspended in 1 ml of 0.01% BSA (in DPBS) and passed through a 40 μm cell strainer (Fisher Scientific, Hampton, NH, USA) to discard debris. Cell number was counted for 10X Genomics single cell application.
To yield an expected recovery of 4000-7000 single cells, an estimated 10,000 single cells per channel were loaded onto Single Cell 3’ Chip (10X Genomics, CA). The Single Cell 3’ Chip was placed on a 10X Genomics instrument to generate single cell gel beads in emulsion (GEMs). Chromium Single Cell 3’ v3 Library and Cell Bead Kits were used according to the manufacturer’s instructions to prepare single cell RNA-Seq libraries.

value: SVF

value: iWAT

tag: strain

tag: age

value: 8 weeks old

value: TAN


title: PWH P6 Blood scTCRseq (biol rep 2)

tag: donor

value: T cell

tag: disease status


title: 13_TG02-17-045_Infusion

value: Treg

value: GEX, ADT

value: Infusion


title: Pre-hepatic _18dpi

value: serum

value: Infected


title: CD4, CD8 double positive in Rag deficient and Stat5aS710F background. Mouse 3 [R2S5a_DP_3]

tag: genotype


title: CD4 negative, CD8 positive thymocytes in Stat5AS710F background. Mouse 6 [S5a_CD8_6]

tag: strain background


title: Ad-Lib, PM7, scRNA-seq

description: 10x Genomics

value: Ad-Lib


title: PWH P6 Blood scRNAseq (biol rep 2)

value: PBMC

value: chronic HIV

tag: study id


title: 8_106-003_8

value: Day 91


title: PWH P6 CSF scRNAseq

value: CSF

value: CSF cells


title: CD4, CD8 double negative in Rag deficient and Stat5aS710F background. Mouse 3 [R2S5a_DN_3]

value: Stat5aS710F Rag2-/-

tag: name stage_replicate

tag: replicate id

value: DN

value: thymocytes


title: 6_106-003_3

value: blood

value: Day 0


title: PWH P6 CSF scTCRseq

value: T cell


title: TAN, PM6, scRNA-seq

description: 10x Genomics

value: SVF

value: iWAT

value: 8 weeks old

value: TAN


title: Ad-Lib, PM5, scRNA-seq

description: 10x Genomics


title: CD4, CD8 double negative in Rag deficient and Stat5aS710F background. Mouse 6 [R2S5a_DN_6]

tag: condition


title: 5_TG02-17-063_Infusion

value: Treg

tag: library type

value: GEX, ADT

value: Infusion


title: 7_106-003_5

value: PBMC

tag: trex id

value: Day 14


title: CD8 positive thymocytes in Rag deficient and Stat5aS710F background. Mouse 6 [R2S5a_CD8_6]


title: CD4, CD8 double positive in Rag deficient and Stat5aS710F background. Mouse 4 [R2S5a_DP_4]

value: DP


title: CD4, CD8 double negative in Rag deficient and Stat5aS710F background. Mouse 4 [R2S5a_DN_4]


title: PWH P6 Blood scTCRseq

value: T cell (CD4 enriched)

value: chronic HIV


title: PWH P6 Blood scTCRseq (biol rep 1)


title: Non-infected_0dpi

value: serum

value: Uninfected


title: CD8 positive thymocytes in Rag deficient and Stat5aS710F background. Mouse 2 [R2S5a_CD8_2]

value: Stat5aS710F Rag2-/-

value: thymocytes


title: TAN, PM2, scRNA-seq

description: 10x Genomics


title: PWH P6 Blood scRNAseq

value: PBMC (CD4 enriched)


title: Ad-Lib, PM3, scRNA-seq

description: 10x Genomics

value: SVF

value: Ad-Lib


title: CD8 positive thymocytes in Rag deficient and Stat5aS710F background. Mouse 1 [R2S5a_CD8_1]


title: 3_102-017_5

value: blood

tag: day


title: PWH P6 Blood scRNAseq (biol rep 1)

tag: tissue


title: Ad-Lib, PM1, scRNA-seq

description: 10x Genomics

value: iWAT

value: 8 weeks old

tag: treatment


title: 2_102-017_3

value: Treg

value: GEX, ADT

value: Day 0


title: CD4, CD8 double positive thymocytes in wildtype background. Mouse 5 [WT_DP_5]

value: wild type


title: AidKO_RemSD_b48b_4

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
AIDKOSD-48B-4

data_processing:
TagSeq (5' mRNA-seq) preprocessing was performed in order to collapse duplicates based on defined TagSeq molecular indices (swMWWM, swGC, swTG, swMW) plus the adjacent 24 bases. Reads with no matching TagSeq tag were discarded. Adapter sequences (AGATCGGAAG) and PolyA tails (AAAAAAAA+) were removed. Resulting sequences shorter than 20 bases were discarded, as were sequences with more than 10% of the remaining bases having base qualities less than 10.
Single-end pseudo alignment was performed using kallisto (ver. 0.45.0, options --single-overhang --bias --fragment-length 200) against the mouse transcriptome (GENCODE M26 transcript sequences).
Downstream analysis of kallisto estimated counts was performed in R (ver. 4.0.3).
The tximport package (v1.18.0) was used to roll up transcript-level counts into gene-level counts provided to the DESeq2 package (ver. 1.30.0).
Before DESeq2 analysis, count data matrices were filtered to remove genes with fewer than 1 read across all included samples.
The DGE models analyzed included Rem SD vs Rem WT in both AID WT and AID KO tumors
Assembly: GENCODE M26 transcriptome (transcript sequences and main gene annotation set)
Supplementary files format and content: Tab-delimited kallisto_counts.tsv text files provide kallisto per-transcript estimated counts and transcripts per million values for each sample. Full DESeq2 DGE analysis details can be found in the Supplementary zip file.

source_name: lymphoma

extract_protocol:
Library preparation and sequencing for TagSeq, a form of 3' RNA sequencing were performed by the Genomic Sequencing and Analysis Facility (GSAF) at The University of Texas at Austin. Total RNA was isolated from each sample (0.375 mL) by addition of Trizol (1.125 mL; Thermo Fisher) and the sample (1.4 mL) was transferred to a Phasemaker tube (Thermo Fisher). Total RNA was extracted following the protocol supplied by the manufacturer and further cleaned up using a RNeasy MinElute Cleanup Kit (QIAGEN).
RNA integrity number (RIN) was measured using an Agilent Bioanalyzer and 100 ng of RNA was used for the Tag-Seq protocol. The fragmentation/RT mix was prepared then added to each RNA sample and then heated to 95 degrees for 2.5 minutes on a Thermocyler then immediately put on ice for 2 minutes. After cooling and addition of the template switching oligo and SmartScribe RT the fragmented RNA reaction was incubated 42°C for 1hr, 65°C for 15 min. Next an AmPure bead clean-up was completed for the cDNA before it was amplified for 18 cycles, also incorporating the Illumina sequencing primer site, followed by another cleanup. The remaining portions of the Illumina adapater (the i5 and i7 indices) were then incorporated through an additional 4 cycles of PCR. Final libraries were quantified with PicoGreen then pooled equally for size selection using the Blue Pippin from 355-550 bp.

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

value: Aicda-/-

value: infected with a mutant MMTV strain defective in Rem and its cleavage product Rem-CT


title: CD4, CD8 double positive thymocytes in wildtype background. Mouse 2 [WT_DP_2]

value: DP


title: 1_TG02-17-012_Infusion

value: PBMC

value: Infusion


title: TAN, PM4, scRNA-seq

description: 10x Genomics

value: TAN


title: PWH P5 Blood scRNAseq (biol rep 2)

value: chronic HIV


title: PWH P5 Blood scTCRseq (biol rep 2)

value: T cell


title: AidKO_RemSD_b48b_3

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
AIDKOSD-48B-3


title: A673 siFLI1, 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

growth_protocol: Cells were cultured in RPM1 1640 (TC-32, TC71, ES-5838) or DMEM media (A673) (Thermo Fisher Scientific, Waltham, MA) 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:
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: RNAi-based studies, cells were reverse transfected with 20 nM siRNA complexed with Lipofectamine RNAi-Max (Invitrogen). siNeg (SI03650318, Qiagen), siFLI1 (s5266, Thermo Fisher Scientific) and siERG (s4812, Thermo Fisher Scientific)

tag: cell line

value: Ewing sarcoma

tag: sirna


title: A673 siFLI1, rep 2

tag: cell type


title: AidKO_RemSD_b48a_1

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
AIDKOSD-48A-1

tag: strain


title: AidKO_RemSD_b35_6

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
AIDKOSD-35-6


title: CD4, CD8 double negative thymocytes in wildtype background. Mouse 5 [WT_DN_5]

value: DN

value: thymocytes


title: 4_102-017_8

value: blood

value: Day 91


title: CD4, CD8 double positive thymocytes in wildtype background. Mouse 1 [WT_DP_1]


title: PWH P5 CSF scRNAseq

tag: donor

value: CSF

value: CSF cells


title: PWH P5 CSF scTCRseq

tag: disease status


title: AidKO_RemSD_b35_1

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
AIDKOSD-35-1

tag: genotype


title: A673 siFLI1, rep 1


title: PWH P5 Blood scTCRseq

value: T cell (CD4 enriched)


title: CD4, CD8 double negative thymocytes in wildtype background. Mouse 2 [WT_DN_2]

value: wild type

tag: strain background


title: CD4, CD8 double negative thymocytes in wildtype background. Mouse 1 [WT_DN_1]


title: PWH P5 Blood scTCRseq (biol rep 1)

tag: study id


title: AidKO_RemWT_b47b_2

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
AIDKOWT-47B-2

value: lymphoma

value: Aicda-/-

value: infected with superantigen-independent lymphomagenic MMTV strain


title: A673 siNEG, rep 2

value: siNeg


title: CD8 positive thymocytes in wildtype background. Mouse 5 [WT_CD8_5]

tag: name stage_replicate


title: AidKO_RemWT_b47a_1

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
AIDKOWT-47A-1


title: PWH P5 Blood scRNAseq

value: PBMC

value: PBMC (CD4 enriched)


title: A673 siNEG, rep 1


title: AidKO_RemWT_b32_2

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
AIDKOWT-32-2


title: CD8 positive thymocytes in wildtype background. Mouse 1 [WT_CD8_1]

tag: replicate id


title: CD8 positive thymocytes in wildtype background. Mouse 2 [WT_CD8_2]

tag: condition


title: TC-71 siFLI1, rep 3


title: AidKO_RemWT_b32_1

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
AIDKOWT-32-1


title: PWH P5 Blood scRNAseq (biol rep 1)

value: chronic HIV


title: TC-71 siFLI1, rep 2


title: CD4, CD8 double negative thymocytes in Stat5AS710F background. Mouse 3 [S5a_DN_3]


title: A673 siNEG, rep 3


title: PWH P4 Blood scRNAseq (biol rep 2)


title: AidWT_RemSD_b46b_2

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
B6SD-46B-2

value: Aicda+/+

value: infected with a mutant MMTV strain defective in Rem and its cleavage product Rem-CT


title: AidWT_RemSD_b34_8

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
B6SD-34-8


title: TC-71 siNEG, rep 3

value: Ewing sarcoma


title: AidKO_RemWT_b31_2

description:
5' mRNA
AID/Aicda knockout C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
AIDKOWT-31-2


title: CD4, CD8 double negative thymocytes in Stat5AS710F background. Mouse 1 [S5a_DN_1]

value: DN

value: thymocytes


title: TC-71 siFLI1, rep 1


title: PWH P4 CSF scRNAseq


title: AidWT_RemSD_b34_1

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
B6SD-34-1


title: PWH P4 Blood scTCRseq


title: TC-71 siNEG, rep 1


title: TC-71 siNEG, rep 2


title: CD4, CD8 double negative thymocytes in Rag2 deficient background. Mouse 4 [R2a_DN_4]


title: AidWT_RemSD_b33_6

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by Rem/TBLV defective MMTV
B6SD-33-6


title: PWH P4 Blood scTCRseq (biol rep 1)

value: T cell


title: CD4, CD8 double negative thymocytes in Rag2 deficient background. Mouse 3 [R2a_DN_3]


title: PWH P4 Blood scTCRseq (biol rep 2)


title: CD4, CD8 double negative thymocytes in Stat5AS710F background. Mouse 6 [S5a_DN_6]


title: AidWT_RemWT_b45b_2

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
B6WT-45B-2


title: TC-32 siFLI1, rep 2


title: PWH P4 Blood scRNAseq


title: PWH P4 CSF scTCRseq

value: CSF


title: LT-HSCs_Ikba_KO_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: E14.5 foetal 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 by immobilization 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 and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

tag: developmental time

value: foetal liver

value: 500 LT-HSCs

tag: Sex

value: Female

value: KO


title: LT-HSCs_Ikba_KO_1 [RNA-seq]


title: CD4, CD8 double negative thymocytes in Rag2 deficient background. Mouse 5 [R2a_DN_5]


title: PWH P4 Blood scRNAseq (biol rep 1)


title: AidWT_RemWT_b45a_1

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
B6WT-45A-1

value: lymphoma


title: TC-32 siNEG, rep 3


title: AidWT_RemWT_b30_1

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
B6WT-30-1

value: infected with superantigen-independent lymphomagenic MMTV strain


title: TC-32 siFLI1, rep 1


title: LT-HSCs_Ikba_Het_2 [RNA-seq]

value: HET


title: TC-32 siNEG, rep 2

value: siNeg


title: PWH P3 Blood scTCRseq (biol rep 2)

value: PBMC


title: LT-HSCs_Ikba_Het_3 [RNA-seq]


title: LT-HSCs_Ikba_WT_3 [RNA-seq]

value: WT


title: CD11bmidLy6Cmid cells from bone marrow (BM) cells cocultured with human mesenchymal stem/stromal cells (MSCs)

city: Seoul

first: Joo Youn

last: Oh

state: Korea, Republic of

address: 103 Daehakro, Jongrogu, Yeongondong

department: Ophthalmology

country: South Korea

institute: Seoul National University College of Medicine

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing and UMI counting were carried out using the official 10x Genomics pipeline Cell Ranger (https://support.10xgenomics.com). Briefly, raw base cell files generated by Illumina sequencers were demultiplexed into FASTQ format reads using the Illumina bcl2fastq software (https://github.com/brwnj/bcl2fastq). The raw reads were trimmed from the 3’ end to obtain the recommended number of cycles for read pairs (Read1: 28 bp; Read2: 90 bp). Each library’s reads were individually processed using the Cell Ranger pipeline to generate a gene-barcode matrix. During this step, the reads were aligned to a reference genome, and cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering.
Assembly: mm10, mm11
Supplementary files format and content: tap-separated values files, matrix files

source_name: Bone marrow

growth_protocol: BM was obtained by flushing the femurs of mice using a 30G needle and a plastic syringe. BM cells were isolated by filtering the BM through a 70-μm cell strainer (Corning Inc., Corning, NY) and centrifugation at 630 g for 3 minutes. To remove red blood cells (RBCs), the BM cells were subjected to RBC lysis in ACK Lysing Buffer (Gibco/Thermo Fisher Scientific, Waltham, MA) for 2 minutes. The BM cells were then cultured in RPMI1640 media (Welgene, Daegu, Korea) with 10% (vol/vol) heat-inactivated fetal bovine serum (FBS; Gibco/Thermo Fisher Scientific) and 1% penicillin-streptomycin (Lonza, Walkersville, MD) at 37°C in a 5% CO2 incubator.

extract_protocol:
CD11bmidLy6Cmid cells were isolated from GM-CSF-stimulated BM cells in the presence of MSCs, as were CD11bhiLy6Chi cells from GM-CSF-stimulated BM cells in the absence of MSCs, by staining with anti-CD11b and anti-Ly6C Abs (all from Invitrogen/Thermo Fisher Scientific) in FACS buffer (Invitrogen/Thermo Fisher Scientific) and sorting using a flow cytometer (BD FACSAria™ III Cell Sorter, BD Biosciences, San Jose, CA). eBioscience™eFluor™ 780 dye (Invitrogen/Thermo Fisher Scientific) was added to stained cells for viability assessment. FACS-sorted CD11bmidLy6Cmid and CD11bhiLy6Chi cells were validated for > 70% viability using a Countess 2 Automated Cell Counter (Thermo Fisher Scientific). The cells along with the reverse transcription master mix were loaded onto the 10x Genomics Chromium platform to capture and barcode the cells, generating single-cell Gel Beads-in-Emulsion (GEMs) according to the manufacturer’s instructions.
Following reverse transcription, cDNAs with both barcodes were amplified, and a library was constructed using the Single Cell 3’ Reagent Kit (v2 chemistry) for each sample. These libraries were then sequenced on an Illumina NovaSeq 6000 System (Illumina, San Diego, CA) in the 2 × 150 bp paired-end mode.

treatment_protocol: BM cells were treated with GM-CSF (40 ng/mL, GenScript, Piscataway, NJ) for 5 days in order to induce differentiation. In coculture experiments, human MSCs were seeded in 0.4 μM Millicell® Cell Culture Inserts (Merck Millipore, Darmstadt, Germany) at a ratio of 1:5 (MSCs to BM cells) and incubated in CCM for 24 hours. Then, MSCs in transwell inserts were cocultured with BM cells in DMEM media (Welgene) that included 10% heat-inactivated FBS (Gibco/Thermo Fisher Scientific) and 1% penicillin-streptomycin (Lonza).

value: Bone marrow

value: Bone marrow cell

value: C57BL/6NCrljOri, H-2b

value: GM-CSF, MSC coculture


title: PWH P3 CSF scRNAseq

value: CSF cells

value: chronic HIV


title: TC-32 siFLI1, rep 3

value: Ewing sarcoma


title: AidWT_RemWT_b45a_2

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
B6WT-45A-2

value: Aicda+/+


title: CD11bhiLy6Chi cells from bone marrow (BM) cells without human mesenchymal stem/stromal cells (MSC) coculture

description: 10x Genomics

value: GM-CSF


title: AOB_#5_Septum_rep6

city: Giessen

first: Axel

last: Weber

state: Hesse

address: Schubertstrasse 81

department: Rudolf Buchheim Institute of Pharmakology

country: Germany

institute: Justus-Liebig-University Giessen

description:
col_names:"raw_reads.AOB_comp_#5_Spt", "normalized_reads.AOB_comp_#5_Spt", "fpkm.AOB_comp_#5_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1179

data_processing:
Nexflow nf/core rna_seq v1.5 dev
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore integrated into nf-core/rnaseq (parameter- Quality limit: 20)
Trimmed reads were mapped to rnor6 usinf STAR integrated into nf-core/rnaseq (default parameters)
Readcount extraction was perfomed using FeatureCounts integrated into nf-core/rnaseq
Normalization and differential expression analysis was performed using DEseq2 for Galaxy (using DEseq2's internal median based normalization)
Assembly: rnor6
Supplementary files format and content: bigwig files
Supplementary files format and content: unnormalized read count, DEseq2-normalized read count and FPKM count tables in single CSV file
Supplementary files format and content: DEseq2 Output in two Excel files

organism: Rattus norvegicus

source_name: interventricular septum

extract_protocol:
RNA was extracted using TRIzol, cleaned using Macherey & Nagel Nucleospin RNA kit
Libraries were prepared using NEBnext Ultra II RNA Library kit with poly-A Enrichment module according to manual;  0.67ng of RNA were used for library preparation

treatment_protocol: 6 month old weanling rats were clipped nonconstrictively at the pulmonary artery or aorta respectively. Compensatory hypertrophy of left or right ventricle developed 7 weeks after banding, after which the samples for tehe compensatory phase were harvested. Heart failure developed 21 (right ventricle) or 25 (left ventricle) weeks, after which decompensatory samples were harvested

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: interventricular septum

value: male

tag: animal id

tag: age

value: 11 weeks

value: aortic banding

tag: disease progression

value: compensatory

tag: treatment time

value: 7 weeks


title: PAB_#2_Septum_rep6

description:
col_names:"raw_reads.PAB_comp_#2_Spt", "normalized_reads.PAB_comp_#2_Spt", "fpkm.PAB_comp_#2_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1178

tag: tissue

tag: treatment

value: pulmonary artery banding


title: sham_#1_Septum_rep6

description:
col_names:"raw_reads.sham_comp_#1_Spt", "normalized_reads.sham_comp_#1_Spt", "fpkm.sham_comp_#1_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1177

value: sham


title: PWH P3 Blood scTCRseq

value: PBMC

tag: cell type

value: T cell (CD4 enriched)


title: TC-32 siFLI1, H3K27ac, rep 2

data_processing:
ChIP-seq analysis were carried out using center for cancer research bioinfoirmatics resource (CCBR) pipeline (https://github.com/CCBR/Pipeliner/wiki/Pipeline-Documentation - chip-seq)
Sequence reads were triimmed 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)

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 miunites. 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 amplited 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)

tag: cell line

tag: chip antibody

value: H3K27ac (Active Motif, #39133)

tag: sirna


title: TC-32 siFLI1, H3K27ac, rep 1


title: PWH P3 Blood scRNAseq (biol rep 1)

tag: donor

tag: disease status

value: chronic HIV


title: sham_#14_Septum_rep2

description:
col_names:"raw_reads.sham_comp_#14_Spt", "normalized_reads.sham_comp_#14_Spt", "fpkm.sham_comp_#14_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1175

tag: strain background


title: AidWT_RemWT_b29_1

description:
5' mRNA
C57BL/6 mouse lymphoma cells induced by MMTV with enhanced Rem/TBLV
B6WT-29-1

value: lymphoma

tag: strain

tag: genotype

value: infected with superantigen-independent lymphomagenic MMTV strain


title: sham_#17_Septum_rep4

description:
col_names:"raw_reads.sham_comp_#17_Spt", "normalized_reads.sham_comp_#17_Spt", "fpkm.sham_comp_#17_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1176


title: WJL4343_RLF_N036_JoinT

city: Stanford

first: Jinglong

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. Indicated inhibitors were added to some of the samples the same day as STI-571.

value: vAbl-ProB

value: pro-B cells

tag: total reads


title: PWH P3 Blood scRNAseq

value: PBMC (CD4 enriched)

tag: study id


title: PWH P3 Blood scTCRseq (biol rep 1)

value: T cell


title: WJL4341_RLF_N036_JoinT


title: TC-32 siFLI1, H3K4me3, rep 1

value: Ewing sarcoma


title: WJL4344_RLF_N036_JoinT


title: TC-32 siFLI1, Input, rep 2_II


title: WJL4342_RLF_N036_JoinT


title: TC-32 siFLI1, Input, rep 1_I


title: PWH P3 CSF scTCRseq

value: CSF


title: WJL4340_RLF_N036_JoinT


title: PWH P3 Blood scRNAseq (biol rep 2)


title: TC-32 siFLI1, H3K4me3, rep 2


title: TC-32 siNEG, rep 1

value: siNeg


title: PWH P2 CSF scRNAseq

value: CSF cells


title: sham_#4_Septum_rep3

description:
col_names:"raw_reads.sham_comp_#4_Spt", "normalized_reads.sham_comp_#4_Spt", "fpkm.sham_comp_#4_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1173

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: interventricular septum

tag: Sex

value: male

tag: animal id

value: 11 weeks

value: compensatory

value: 7 weeks


title: TC-32 siNEG, H3K4me3, rep 2


title: PWH P2 Blood scTCRseq

value: PBMC

value: chronic HIV


title: WJL4339_RLF_N036_JoinT

value: vAbl-ProB


title: TC-32 siNEG, H3K4me3, rep 1


title: AOB_#7_Septum_rep7

description:
col_names:"raw_reads.AOB_comp_#7_Spt", "normalized_reads.AOB_comp_#7_Spt", "fpkm.AOB_comp_#7_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1172

tag: age

value: aortic banding

tag: disease progression


title: WJL4338_RLF_N036_JoinT

value: pro-B cells

value: STI-571 + DMSO


title: PWH P2 CSF scTCRseq

tag: tissue

value: T cell


title: WJL4337_RLF_N036_JoinT

tag: treatment


title: sham_#8_Septum_rep7

description:
col_names:"raw_reads.sham_comp_#8_Spt", "normalized_reads.sham_comp_#8_Spt", "fpkm.sham_comp_#8_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1174

value: sham

tag: treatment time


title: AOB_#9_Septum_rep3

description:
col_names:"raw_reads.AOB_comp_#9_Spt", "normalized_reads.AOB_comp_#9_Spt", "fpkm.AOB_comp_#9_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1171


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

tag: cell line

tag: cell type

value: Ewing sarcoma

value: H3K27ac (Active Motif, #39133)

value: siNeg


title: PWH P2 Blood scRNAseq


title: PWH P1 Visit 4 CSF scTCRseq

value: CSF


title: AOB_#16_Septum_rep2

description:
col_names:"raw_reads.AOB_comp_#16_Spt", "normalized_reads.AOB_comp_#16_Spt", "fpkm.AOB_comp_#16_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1170

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: interventricular septum


title: PWH P1 Visit 4 CSF scRNAseq

value: CSF cells


title: WJL4336_RLF_N036_JoinT


title: TC-32 siNEG, H3K27ac, rep 2_II

tag: chip antibody

tag: sirna


title: WJL4335_RLF_N036_JoinT

value: Cycling


title: TC-32 siNEG, Input, rep 1_I


title: PWH P1 Visit 4 Blood scTCRseq

tag: donor

value: PBMC

tag: disease status


title: AOB_#20_Septum_rep4

description:
col_names:"raw_reads.AOB_comp_#20_Spt", "normalized_reads.AOB_comp_#20_Spt", "fpkm.AOB_comp_#20_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1169

tag: strain background

value: male

value: 11 weeks

value: compensatory

value: 7 weeks


title: PAB_#22_Septum_rep2

description:
col_names:"raw_reads.PAB_comp_#22_Spt", "normalized_reads.PAB_comp_#22_Spt", "fpkm.PAB_comp_#22_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1168

value: pulmonary artery banding


title: PWH P1 Visit 4 Blood scRNAseq

value: chronic HIV


title: WJL4334_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells

tag: genotype


title: TC-32 siNEG, Input, rep 2_II

value: Ewing sarcoma


title: PAB_#19_Septum_rep4

description:
col_names:"raw_reads.PAB_comp_#19_Spt", "normalized_reads.PAB_comp_#19_Spt", "fpkm.PAB_comp_#19_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1167


title: TC-32 siFLI1, ETS1, rep 2


title: WJL4333_RLF_N036_JoinT

tag: total reads


title: PWH P1 Visit 3 CSF scTCRseq

value: T cell

tag: study id


title: PAB_#11_Septum_rep7

description:
col_names:"raw_reads.PAB_comp_#11_Spt", "normalized_reads.PAB_comp_#11_Spt", "fpkm.PAB_comp_#11_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1166

tag: Sex


title: TC-32 siFLI1, ETS1, rep 1


title: WJL4332_RLF_N036_JoinT

value: WT


title: PWH P1 Visit 3 CSF scRNAseq

value: CSF


title: TC-32 siFLI1, Input, rep 2


title: WJL4331_RLF_N036_JoinT


title: PWH P1 Visit 3 Blood scRNAseq


title: WJL4329_RLF_N036_JoinT


title: TC-32 siNEG, ETS1, rep 2

value: siNeg


title: sham_AOB_decomp_#26_Septum_rep2

description:
col_names:"raw_reads.sham_AOB_decomp_#26_Spt", "normalized_reads.sham_AOB_decomp_#26_Spt", "fpkm.sham_AOB_decomp_#26_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1163

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: interventricular septum

tag: animal id

value: 30 weeks

value: sham

value: decompensatory

value: 24 weeks


title: TC-32 siFLI1, Input, rep 1


title: sham_AOB_decomp_#24_Septum_rep1

description:
col_names:"raw_reads.sham_AOB_decomp_#24_Spt", "normalized_reads.sham_AOB_decomp_#24_Spt", "fpkm.sham_AOB_decomp_#24_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1162

value: male

tag: age


title: PWH P1 Visit 3 Blood scTCRseq

value: PBMC


title: sham_AOB_decomp_#33_Septum_rep3

description:
col_names:"raw_reads.sham_AOB_decomp_#33_Spt", "normalized_reads.sham_AOB_decomp_#33_Spt", "fpkm.sham_AOB_decomp_#33_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1164

tag: disease progression


title: WJL4330_RLF_N036_JoinT


title: WJL4327_RLF_N036_JoinT


title: TC-32 siNEG, Input, rep 1


title: AOB_decomp_#29_Septum_rep3

description:
col_names:"raw_reads.AOB_decomp_#29_Spt", "normalized_reads.AOB_decomp_#29_Spt", "fpkm.AOB_decomp_#29_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1160

tag: tissue

value: aortic banding


title: PWH P1 Visit 2 Blood scTCRseq

value: chronic HIV


title: PWH P1 Visit 2 CSF scTCRseq


title: AOB_decomp_#35_Septum_rep4

description:
col_names:"raw_reads.AOB_decomp_#35_Spt", "normalized_reads.AOB_decomp_#35_Spt", "fpkm.AOB_decomp_#35_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1161

tag: treatment


title: WJL4328_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells


title: TC-32 siNEG, ETS1, rep 1

value: Ewing sarcoma


title: PWH P1 Visit 2 Blood scRNAseq


title: WJL4326_RLF_N036_JoinT

value: WT

value: STI-571 + DMSO


title: AOB_decomp_#27_Septum_rep2

description:
col_names:"raw_reads.AOB_decomp_#27_Spt", "normalized_reads.AOB_decomp_#27_Spt", "fpkm.AOB_decomp_#27_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1159

tag: treatment time


title: O2, WT, SODKO, D10, rep3

city: HOUSTON

first: Margaret

last: Goodell

address: 1 Baylor Plz, Rm N1030

institute: Baylor College of Medicine

data_processing:
Fastq files quality were controlled using fastqc/multiqc
Duplicate reads were removed and unique sequence reads were trimmed for adaptor sequence/low-quality sequence
Paired-end bulk RNA-sequencing reads were mapped to the STAR mouse reference genome index (mm39) using STAR
Quantification of mapped reads for RNA-sequencing was performed using Subread package (featureCount) to obtain count files
Assembly: hg19
Supplementary files format and content: tab-delimited text files including feature counts for each Sample

growth_protocol: OCI-AML2 cells were cultured in RPMI supplemented with 10% FBS + 1% Pen/strep.

extract_protocol:
RNA was harvested from 300,000 sorted OCI-AML2 cells and isolated using Allprep DNA/RNA Micro Kit (Qiagen) of each independent Sample for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using True-Seq Stranded mRNA library preparation kit (Illumina, 20020594) based on manufacturer’s protocol.

treatment_protocol:
WT or PPM1D-mutant Cas9-OCI-AML2 cells were transduced with lentivirus (pKLV2-U6gRNA5-PGKpuro2ABFP, Addgene #67991) with either empty vector backbone or with SOD1-gRNA.
Cells were cultured for 10 days and sorted for BFP expression.

tag: cell line

value: Human AML cell line

tag: transfection

tag: time

value: 10 Days


title: WJL4325_RLF_N036_JoinT

tag: cell type


title: PAB_#6_Septum_rep3

description:
col_names:"raw_reads.PAB_comp_#6_Spt", "normalized_reads.PAB_comp_#6_Spt", "fpkm.PAB_comp_#6_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1165

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: 11 weeks

value: pulmonary artery banding

value: compensatory

value: 7 weeks


title: O2, WT, SODKO, D10, rep2


title: AOB_decomp_#25_Septum_rep1

description:
col_names:"raw_reads.AOB_decomp_#25_Spt", "normalized_reads.AOB_decomp_#25_Spt", "fpkm.AOB_decomp_#25_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1158

value: interventricular septum

value: male

value: 30 weeks

value: decompensatory

value: 24 weeks


title: PWH P1 Visit 2 CSF scRNAseq

tag: donor

value: CSF

value: CSF cells

value: chronic HIV


title: WJL4324_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells

value: WT

value: STI-571 + DMSO


title: PWH P1 Visit 1 CSF scRNAseq

tag: disease status


title: WJL4323_RLF_N036_JoinT

value: Cycling


title: PWH P1 Visit 1 Blood scTCRseq

value: PBMC

value: T cell


title: sham_PAB_decomp_#31_Septum_rep2

description:
col_names:"raw_reads.sham_PAB_decomp_#31_Spt", "normalized_reads.sham_PAB_decomp_#31_Spt", "fpkm.sham_PAB_decomp_#31_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1157

tag: strain background

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: 27 weeks

value: sham

value: 21 weeks


title: O2, WT, SODKO, D10, rep1

value: Human AML cell line

tag: genotype

value: 10 Days


title: sham_PAB_decomp_#30_Septum_rep1

description:
col_names:"raw_reads.sham_PAB_decomp_#30_Spt", "normalized_reads.sham_PAB_decomp_#30_Spt", "fpkm.sham_PAB_decomp_#30_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1156

value: interventricular septum

value: male

value: decompensatory


title: WJL4322_RLF_N036_JoinT

value: vAbl-ProB

tag: total reads


title: PWH P1 Visit 1 Blood scRNAseq

value: chronic HIV

tag: study id


title: PAB_decomp_#32_Septum_rep2

description:
col_names:"raw_reads.PAB_decomp_#32_Spt", "normalized_reads.PAB_decomp_#32_Spt", "fpkm.PAB_decomp_#32_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1154

tag: Sex

value: pulmonary artery banding


title: O2, WT, EV, D10, rep3

value: WT

value: pKLV2-U6(BbsI)-PGKpuro2ABFP (Empty Vector, EV)


title: O2, WT, EV, D10, rep2


title: PAB_decomp_#36_Septum_rep3

description:
col_names:"raw_reads.PAB_decomp_#36_Spt", "normalized_reads.PAB_decomp_#36_Spt", "fpkm.PAB_decomp_#36_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1155

tag: animal id


title: O2, WT, EV, D10, rep1


title: WJL4321_RLF_N036_JoinT

value: pro-B cells

value: Cycling


title: Control C6 Blood scTCRseq (biol rep 2)

value: PBMC

value: T cell

value: uninfected control


title: Control C6 Blood scRNAseq (biol rep 2)


title: WJL4308_RLF_N036_JoinT


title: PAB_decomp_#28_Septum_rep1

description:
col_names:"raw_reads.PAB_decomp_#28_Spt", "normalized_reads.PAB_decomp_#28_Spt", "fpkm.PAB_decomp_#28_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1153

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

tag: age

value: 27 weeks


title: PWH P1 Visit 1 CSF scTCRseq

value: CSF


title: O2, PPM1D-mutant, SODKO, D10, rep3

value: Human AML cell line

value: 10 Days


title: WJL4307_RLF_N036_JoinT


title: Control C6 CSF scTCRseq


title: AOB_#7_RV_rep7

description:
col_names:"raw_reads.AOB_comp_#7_RV", "normalized_reads.AOB_comp_#7_RV", "fpkm.AOB_comp_#7_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1152

source_name: right ventricle

value: whole heart; left ventricle

value: male

value: 11 weeks

value: aortic banding

tag: disease progression

value: compensatory

value: 7 weeks


title: O2, PPM1D-mutant, SODKO, D10, rep2


title: Control C6 CSF scRNAseq

tag: tissue

value: CSF cells


title: AOB_#7_LV_rep7

description:
col_names:"raw_reads.AOB_comp_#7_LV", "normalized_reads.AOB_comp_#7_LV", "fpkm.AOB_comp_#7_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1151

source_name: left ventricle

value: left ventricle

tag: treatment


title: O2, PPM1D-mutant, SODKO, D10, rep1


title: WJL4305_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells


title: AOB_#5_RV_rep6

description:
col_names:"raw_reads.AOB_comp_#5_RV", "normalized_reads.AOB_comp_#5_RV", "fpkm.AOB_comp_#5_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1150

tag: treatment time


title: Control C6 Blood scTCRseq (biol rep 1)

value: PBMC

value: T cell

value: uninfected control


title: Control C6 Blood scRNAseq (biol rep 1)


title: O2, PPM1D-mutant, EV, D10, rep3

tag: cell line

value: pKLV2-U6(BbsI)-PGKpuro2ABFP (Empty Vector, EV)


title: WJL4303_RLF_N036_JoinT


title: AOB_#5_LV_rep6

description:
col_names:"raw_reads.AOB_comp_#5_LV", "normalized_reads.AOB_comp_#5_LV", "fpkm.AOB_comp_#5_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1149

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart


title: Control C5 Blood scTCRseq (biol rep 2)


title: WJL4304_RLF_N036_JoinT


title: O2, PPM1D-mutant, EV, D10, rep1

value: Human AML cell line

tag: transfection

value: 10 Days


title: O2, PPM1D-mutant, EV, D10, rep2

tag: time


title: PAB_#11_RV_rep7

description:
col_names:"raw_reads.PAB_comp_#11_RV", "normalized_reads.PAB_comp_#11_RV", "fpkm.PAB_comp_#11_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1148

value: whole heart; left ventricle

value: male

value: pulmonary artery banding


title: PAB_#11_LV_rep7

description:
col_names:"raw_reads.PAB_comp_#11_LV", "normalized_reads.PAB_comp_#11_LV", "fpkm.PAB_comp_#11_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1147

value: 11 weeks

value: compensatory


title: WJL4301_RLF_N036_JoinT

tag: cell type

value: STI-571 + DMSO


title: Control C5 Blood scRNAseq (biol rep 2)

tag: donor


title: Control C5 CSF scTCRseq

value: CSF

tag: disease status


title: WJL4302_RLF_N036_JoinT

value: vAbl-ProB


title: PAB_#2_RV_rep6

description:
col_names:"raw_reads.PAB_comp_#2_RV", "normalized_reads.PAB_comp_#2_RV", "fpkm.PAB_comp_#2_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1146

tag: strain background

value: 7 weeks


title: 3D_Day 1_4

city: Aveiro

first: Pedro

last: Lavrador

address: Campus Universitário de Santiago, Universidade de Aveiro

department: CICECO - Aveiro Institute of Materials

country: Portugal

institute: University of Aveiro

description:
D1.4B_S16_R1_001.fastq.gz.bam
2Dvs3D_normalizedcounts.csv
D1.4B_S16
Library IDs in SRA: 3D_Day 1_4

data_processing:
Sequence information was extracted in FASTQ format using DRAGEN FASTQ Generation v3.8.4 software (Illumina) and aligned to the GRCh38.p13 reference genome obtained from Ensembl using HISAT2 v2.2.0.
Feature count was performed with Subread v2.03, based on Ensembl annotation GRCh38.106. Raw counts tables were loaded into R Studio (v2023.03.0) and pre-filtered based on counts per million (CPM) > 0.5 in at least 3 different samples to account for library size differences.
Gene lists meeting this threshold were then processed and analyzed for differential expression using the DESeq2 R package standard workflow. Processed counts tables are obtained from the counts(dds, normalized = TRUE) function.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include processed counts values for each sample obtained from the counts(dds, normalized = TRUE) function in DESeq2.

source_name: Adipose tissue

growth_protocol: hASCs were maintained in alpha-MEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Qiagen RNeasy micro kit, performed according to manufacturer's instructions. Specifically, 2D conditions were carried out following Total RNA Isolation from Animal Cells procedure in the handbook. 3D conditions were carried out following Total RNA Isolation from Fibrous Tissues procedure in the handbook.
Full-length cDNAs were generated from total RNA following the SMART-Seq2 protocol. After quality control using Fragment Analyzer HS RNA Kit (Agilent Technologies), library preparation including cDNA tagmentation, PCR-mediated adaptor addition and amplification of the adapted libraries were prepared using Nextera transposase-based protocol (Illumina). Libraries were then quantified using HS NGS Fragment Kit for the Fragment Analyzer and then sequenced (NextSeq2000, Illumina) to reach ~25 Million of 100 bp Single End reads
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: azide-functionalized hASCs assembled into a 3D construct via bioorthogonal click chemistry with an interfacial glycosaminoglycan

value: Adipose tissue

value: female

value: Adipose tissue-derived mesenchymal stromal cells

tag: isolate

tag: biomaterial provider

value: João Belo, Hospital da Luz Aveiro

tag: sample type

value: cell culture

value: 3D_Day 1


title: WJL4300_RLF_N036_JoinT

value: pro-B cells

tag: genotype

tag: total reads


title: WJL4306_RLF_N036_JoinT


title: PAB_#2_LV_rep6

description:
col_names:"raw_reads.PAB_comp_#2_LV", "normalized_reads.PAB_comp_#2_LV", "fpkm.PAB_comp_#2_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1145

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: left ventricle

tag: Sex

tag: animal id

tag: age


title: TC-32 siNEG, Input, rep 2

value: Ewing sarcoma

tag: chip antibody

tag: sirna

value: siNeg


title: WJL4299_RLF_N036_JoinT

tag: cell line

tag: treatment

value: Cycling


title: 3D_Day 1_3

description:
D1.3B_S15_R1_001.fastq.gz.bam
2Dvs3D_normalizedcounts.csv
D1.3B_S15
Library IDs in SRA: 3D_Day 1_3

tag: tissue


title: 3D_Day 1_2

description:
D1.2A_S14_R1_001.fastq.gz.bam
2Dvs3D_normalizedcounts.csv
D1.2A_S14
Library IDs in SRA: 3D_Day 1_2

tag: cell type


title: sham_#8_RV_rep7

description:
col_names:"raw_reads.sham_comp_#8_RV", "normalized_reads.sham_comp_#8_RV", "fpkm.sham_comp_#8_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1144

value: whole heart; left ventricle

value: male

value: 11 weeks

value: sham

tag: disease progression

value: compensatory

tag: treatment time


title: Control C5 Blood scTCRseq (biol rep 1)

tag: donor

value: PBMC

value: T cell

tag: disease status

value: uninfected control

tag: study id


title: Control C5 CSF scRNAseq

value: CSF

value: CSF cells


title: WJL4297_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells


title: Control C4 Blood scTCRseq (biol rep 2)


title: 3D_Day 1_5

description:
D1.5B_S17_R1_001.fastq.gz.bam
2Dvs3D_normalizedcounts.csv
D1.5B_S17
Library IDs in SRA: 3D_Day 1_5

value: Adipose tissue

value: female

value: Adipose tissue-derived mesenchymal stromal cells

tag: isolate

tag: biomaterial provider

value: João Belo, Hospital da Luz Aveiro

tag: sample type

value: cell culture

value: 3D_Day 1


title: sham_#1_RV_rep6

description:
col_names:"raw_reads.sham_comp_#1_RV", "normalized_reads.sham_comp_#1_RV", "fpkm.sham_comp_#1_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1142

tag: strain background

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

tag: Sex

value: male

value: 7 weeks


title: Control C5 Blood scRNAseq (biol rep 1)

value: PBMC


title: Control C4 Blood scRNAseq (biol rep 2)


title: WJL4296_RLF_N036_JoinT

tag: genotype

value: WT

tag: total reads


title: sham_#8_LV_rep7

description:
col_names:"raw_reads.sham_comp_#8_LV", "normalized_reads.sham_comp_#8_LV", "fpkm.sham_comp_#8_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1143

value: whole heart

value: left ventricle

tag: animal id

tag: age

value: 11 weeks

value: sham

value: compensatory


title: sham_#1_LV_rep6

description:
col_names:"raw_reads.sham_comp_#1_LV", "normalized_reads.sham_comp_#1_LV", "fpkm.sham_comp_#1_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1141

tag: treatment


title: WJL4298_RLF_N036_JoinT

tag: cell line

value: vAbl-ProB

value: pro-B cells

value: Cycling


title: 2D_Glycoengineered_4

description:
G4VGaspar_S33_R1_001.fastq.bam
2D_normalizedcounts.csv
2Dvs3D_normalizedcounts.csv
G4VGaspar_S33
Library IDs in SRA: 2D_Glycoengineered_4

treatment_protocol: hASCs grown on tissue cultured-treated plates treated with N-azidoacetylmannosamine-tetraacylated (100 µM in culture media with 0.1 % v/v DMSO)

tag: tissue

value: Adipose tissue

value: female

tag: cell type

value: Adipose tissue-derived mesenchymal stromal cells

value: João Belo, Hospital da Luz Aveiro


title: WJL4295_RLF_N036_JoinT


title: AOB_#12_Septum_rep1

description:
col_names:"raw_reads.AOB_comp_#12_Spt", "normalized_reads.AOB_comp_#12_Spt", "fpkm.AOB_comp_#12_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1063

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: interventricular septum

value: aortic banding

tag: disease progression

tag: treatment time


title: Control C4 CSF scTCRseq

tag: donor

value: CSF

value: T cell

tag: disease status

value: uninfected control


title: 3D_Day 1_1

description:
D1.1A_S13_R1_001.fastq.gz.bam
2Dvs3D_normalizedcounts.csv
D1.1A_S13
Library IDs in SRA: 3D_Day 1_1

tag: isolate

value: cell culture

value: 3D_Day 1


title: 2D_Glycoengineered_5

description:
G5VGaspar_S35_R1_001.fastq.bam
2D_normalizedcounts.csv
2Dvs3D_normalizedcounts.csv
G5VGaspar_S35
Library IDs in SRA: 2D_Glycoengineered_5

tag: biomaterial provider


title: Control C4 CSF scRNAseq

value: CSF cells

tag: study id


title: 2D_Glycoengineered_2

description:
G2VGaspar_S25_R1_001.fastq.bam
2D_normalizedcounts.csv
2Dvs3D_normalizedcounts.csv
G2VGaspar_S25
Library IDs in SRA: 2D_Glycoengineered_2

tag: sample type


title: WJL4293_RLF_N036_JoinT

value: WT


title: PAB_#3_Septum_rep1

description:
col_names:"raw_reads.PAB_comp_#3_Spt", "normalized_reads.PAB_comp_#3_Spt", "fpkm.PAB_comp_#3_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1062

tag: strain background

value: whole heart

tag: Sex

value: male

value: 11 weeks

value: pulmonary artery banding

value: compensatory

value: 7 weeks


title: sham_#13_Septum_rep1

description:
col_names:"raw_reads.sham_comp_#13_Spt", "normalized_reads.sham_comp_#13_Spt", "fpkm.sham_comp_#13_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1061

value: sham


title: 2D_Glycoengineered_1

description:
G1VGaspar_S24_R1_001.fastq.bam
2D_normalizedcounts.csv
2Dvs3D_normalizedcounts.csv
G1VGaspar_S24
Library IDs in SRA: 2D_Glycoengineered_1

value: Adipose tissue

value: female

value: Adipose tissue-derived mesenchymal stromal cells

value: João Belo, Hospital da Luz Aveiro


title: WJL4294_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells

tag: genotype

tag: total reads


title: WJL4292_RLF_N036_JoinT


title: Control C4 Blood scRNAseq (biol rep 1)

value: PBMC

value: uninfected control


title: AOB_#10_Septum_rep5

description:
col_names:"raw_reads.AOB_comp_#10_Spt", "normalized_reads.AOB_comp_#10_Spt", "fpkm.AOB_comp_#10_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1060

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: interventricular septum

tag: animal id

tag: age

value: aortic banding


title: 2D_Native_5

description:
C5VGaspar_S27_R1_001.fastq.bam
2D_normalizedcounts.csv
C5VGaspar_S27
Library IDs in SRA: 2D_Native_5

treatment_protocol: hASCs grown on tissue cultured-treated plates treated with vehicle (culture media with 0.1 % v/v DMSO)

value: cell culture

tag: treatment


title: WJL4290_RLF_N036_JoinT

tag: cell line

value: WT

value: STI-571 + DMSO


title: PAB_#15_Septum_rep5

description:
col_names:"raw_reads.PAB_comp_#15_Spt", "normalized_reads.PAB_comp_#15_Spt", "fpkm.PAB_comp_#15_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1059

tag: tissue

value: whole heart

value: male

value: 11 weeks

value: pulmonary artery banding

value: compensatory


title: 2D_Native_4

description:
C4VGaspar_S25_R1_001.fastq.bam
2D_normalizedcounts.csv
C4VGaspar_S25
Library IDs in SRA: 2D_Native_4

value: Adipose tissue

value: female

tag: cell type

value: Adipose tissue-derived mesenchymal stromal cells


title: 2D_Glycoengineered_3

description:
G3VGaspar_S31_R1_001.fastq.bam
2D_normalizedcounts.csv
2Dvs3D_normalizedcounts.csv
G3VGaspar_S31
Library IDs in SRA: 2D_Glycoengineered_3

value: João Belo, Hospital da Luz Aveiro


title: WJL4291_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells


title: sham_#21_Septum_rep5

description:
col_names:"raw_reads.sham_comp_#21_Spt", "normalized_reads.sham_comp_#21_Spt", "fpkm.sham_comp_#21_Spt"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1058

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: sham

tag: disease progression

tag: treatment time

value: 7 weeks


title: Control C4 Blood scTCRseq (biol rep 1)

tag: donor

value: PBMC

value: T cell

tag: disease status

value: uninfected control


title: 2D_Native_2

description:
C2VGaspar_S20_R1_001.fastq.bam
2D_normalizedcounts.csv
C2VGaspar_S20
Library IDs in SRA: 2D_Native_2

tag: isolate

tag: biomaterial provider

value: cell culture


title: R80_PAB-F_f_RV_#89_rep5

description:
col_names:"raw.reads.PAB_decompensatory_female_#89_RV", "normalized.reads.PAB_decompensatory_female_#89_RV", "fpkm.PAB_decompensatory_female_#89_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

data_processing:
Nexflow nf/core rna_seq v3.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore integrated into nf-core/rnaseq (parameter- Quality limit: 20)
Trimmed reads were mapped to rnor6 usinf STAR integrated into nf-core/rnaseq (default parameters)
Readcount extraction was perfomed using FeatureCounts (Rsubreads v2.2.6), disallowing multiple overlap
Normalization and differential expression analysis was performed using DEseq2 1.28.1, using the independed filtering option and beta_prior LFC-shrinkage
Assembly: rnor6
Supplementary files format and content: bigwig files
Supplementary files format and content: unnormalized read count, DEseq2-normalized read count and FPKM count tables in single csv-file
Supplementary files format and content: DEseq2 Output in Excel file

extract_protocol:
After extraction and perfusion for cleanup, fre hearts were digested using collagenase II in a Langendorff aparatus for 25 minutes. Afterwards the ventricles were seperated, cut into small pieces and digested again with collagenase II for 5min. Afterwards the suspension was filtered using a nylon filter (200µm), and cardiac myocytes seperated from other cell types via a series of centrifugation steps.
RNA was extracted  using Macherey & Nagel Nucleospin RNA kit
Libraries were prepared by Novagene using a rRNA depletion strategy

treatment_protocol: 6 month old weanling rats were clipped nonconstrictively at the pulmonary artery or aorta respectively. Compensatory hypertrophy of left or right ventricle developed 7 weeks after banding, after which the samples for the compensatory phase were harvested. Heart failure developed 22 (right ventricle) or 26 (left ventricle) weeks, after which decompensatory samples were harvested

value: cardiac myocytes

value: right ventricle

value: 28 weeks

value: decompensatory

value: 22 weeks


title: 2D_Native_1

description:
C1VGaspar_S19_R1_001.fastq.bam
2D_normalizedcounts.csv
C1VGaspar_S19
Library IDs in SRA: 2D_Native_1

value: Adipose tissue

value: female

tag: sample type


title: WJL4288_RLF_N036_JoinT

value: WT

value: STI-571 + DMSO


title: R79_PAB-F_f_LV_#89_rep5

description:
col_names:"raw.reads.PAB_decompensatory_female_#89_LV", "normalized.reads.PAB_decompensatory_female_#89_LV", "fpkm.PAB_decompensatory_female_#89_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

tag: strain background

value: left ventricle

value: pulmonary artery banding


title: 2D_Native_3

description:
C3VGaspar_S21_R1_001.fastq.bam
2D_normalizedcounts.csv
C3VGaspar_S21
Library IDs in SRA: 2D_Native_3

tag: Sex

value: Adipose tissue-derived mesenchymal stromal cells

value: João Belo, Hospital da Luz Aveiro


title: WJL4289_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells

tag: genotype


title: WJL4286_RLF_N036_JoinT

value: Cycling

tag: total reads


title: R77_PAB-F_m_LV_#107_rep4

description:
col_names:"raw.reads.PAB_decompensatory_male_#107_LV", "normalized.reads.PAB_decompensatory_male_#107_LV", "fpkm.PAB_decompensatory_male_#107_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: male

tag: animal id


title: PAB_#15_RV_rep5

description:
col_names:"raw_reads.PAB_comp_#15_RV", "normalized_reads.PAB_comp_#15_RV", "fpkm.PAB_comp_#15_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1055

value: whole heart; left ventricle

tag: age

value: 11 weeks

value: compensatory

value: 7 weeks


title: WJL4287_RLF_N036_JoinT

tag: treatment


title: R78_PAB-F_m_RV_#107_rep4

description:
col_names:"raw.reads.PAB_decompensatory_male_#107_RV", "normalized.reads.PAB_decompensatory_male_#107_RV", "fpkm.PAB_decompensatory_male_#107_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: 28 weeks

value: decompensatory

value: 22 weeks


title: PAB_#15_LV_rep5

description:
col_names:"raw_reads.PAB_comp_#15_LV", "normalized_reads.PAB_comp_#15_LV", "fpkm.PAB_comp_#15_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1054

value: whole heart

value: left ventricle

value: pulmonary artery banding


title: NL4.3 dNef CEMM7 20dpi IFN

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

description:
410_8
Counts dNef vs WT.xlsx

data_processing:
SeqPrep to merge paired ends into one file (Using Galaxy)
FastQC for quality control (Using Galaxy)
MAGeCK count using the gRNA_list_by_gene.tab (in supplementary file) to attribute each read to a unique gRNA and a gene (Using Galaxy)
MAGeCK test comparing either one time point to input virus or dNef to WT for the same time point using the normalized counts file from the MAGeCK count (Using Galaxy)
Assembly: gRNA list are indicated in gRNA_list_by_gene.tab (in supplementary file)
Supplementary files format and content: "Counts" file are the output of the MAGeCK count showing normalized counts of the gRNA listed by genes taregtted
Supplementary files format and content: "Test" file are the genes output of the MAGeCK Test showing enrichement of the targetted genes in the condition compared to a refence condition
Supplementary files format and content: "Test sgRNA" file are the sgRNA output of the MAGeCK Test showing enrichement of the targetted genes in the condition compared to a refence condition

organism: Human immunodeficiency virus 1

source_name: Virus-containing supernatant

growth_protocol: Supernatants are collected from HIV-1 infected cell lines at various time points and after passaging of the cells. The virus in the supernantant is concentrated and lysed

extract_protocol:
Total RNA was isolated using the Viral RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
cDNA reactions were performed according to the manufacturer’s instructions of the PrimeScript™ RT Reagent Kit (Takara) using primers specifically targeting the U6 and scaffold region (forward primer 5´-CCGACTCGGTGCCACTTTTT-3´, reverse primer 5´-CGTGACGTAGAAAGTAATAATTT-CTTGGG-3´). cDNA reactions were purified using the Monarch PCR Purification Kit (NEB) and eluted in 10µl elution buffer. The gRNA cassette was amplified using the NEBNext® High-Fidelity 2X PCR Master Mix and primers including Illumina adaptors and 8nt barcodes to allow Next Generation Sequencing (NGS) analysis. PCR reactions were purified using the Monarch PCR Purification Kit (NEB) and eluted in 10µl elution buffer.

treatment_protocol: For samples indicated, cells were treated with 1000U/mL of IFN-β for CEMM7 Cas9 cells and repleanished every 3 days or with 100U/mL of IFN-β for SupT1 CCR5 Cas9 cells

value: Virus-containing supernatant

tag: cell line

value: CEM-M7 Cas9

value: Cell line

value: IFN-β


title: WJL4285_RLF_N036_JoinT

value: vAbl-ProB

value: pro-B cells

value: WT

value: Cycling


title: R76_PAB-F_m_RV_#104_rep3

description:
col_names:"raw.reads.PAB_decompensatory_male_#104_RV", "normalized.reads.PAB_decompensatory_male_#104_RV", "fpkm.PAB_decompensatory_male_#104_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

tag: tissue

value: male


title: sham_#21_RV_rep5

description:
col_names:"raw_reads.sham_comp_#21_RV", "normalized_reads.sham_comp_#21_RV", "fpkm.sham_comp_#21_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1053

value: whole heart; left ventricle

value: 11 weeks

value: sham

value: compensatory

value: 7 weeks


title: R81_PAB-F_f_LV_#102_rep6

description:
col_names:"raw.reads.PAB_decompensatory_female_#102_LV", "normalized.reads.PAB_decompensatory_female_#102_LV", "fpkm.PAB_decompensatory_female_#102_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

tag: cell type

value: cardiac myocytes

value: left ventricle

value: female

value: 28 weeks

value: decompensatory

value: 22 weeks


title: sham_#21_LV_rep5

description:
col_names:"raw_reads.sham_comp_#21_LV", "normalized_reads.sham_comp_#21_LV", "fpkm.sham_comp_#21_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1052

value: whole heart

tag: disease progression


title: R75_PAB-F_m_LV_#104_rep3

description:
col_names:"raw.reads.PAB_decompensatory_male_#104_LV", "normalized.reads.PAB_decompensatory_male_#104_LV", "fpkm.PAB_decompensatory_male_#104_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: pulmonary artery banding

tag: treatment time


title: NL4.3 dNef CEMM7 15dpi

description:
410_5
Counts dNef vs WT.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line


title: Tonsil / Tfr, rep2

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

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)

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: Tonsil

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: Tonsil

value: Tfr

value: Male

value: No treatment


title: AOB_#10_RV_rep5

description:
col_names:"raw_reads.AOB_comp_#10_RV", "normalized_reads.AOB_comp_#10_RV", "fpkm.AOB_comp_#10_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1057

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: male

value: 11 weeks

value: aortic banding

value: compensatory


title: R74_PAB-F_m_RV_#97_rep2

description:
col_names:"raw.reads.PAB_decompensatory_male_#97_RV", "normalized.reads.PAB_decompensatory_male_#97_RV", "fpkm.PAB_decompensatory_male_#97_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: 28 weeks

value: decompensatory


title: AOB_#10_LV_rep5

description:
col_names:"raw_reads.AOB_comp_#10_LV", "normalized_reads.AOB_comp_#10_LV", "fpkm.AOB_comp_#10_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1056

value: whole heart

value: left ventricle

value: 7 weeks


title: AOB_decomp_#35_RV_rep4

description:
col_names:"raw_reads.AOB_decomp_#35_RV", "normalized_reads.AOB_decomp_#35_RV", "fpkm.AOB_decomp_#35_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1051

value: 30 weeks

value: 24 weeks


title: NL4.3 dNef CEMM7 10dpi IFN

description:
410_4
Counts dNef vs WT.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line

value: IFN-β


title: B cells, LPS, disulfiram, exp2

city: Bunkyo-ku

first: Etsuko

last: Toda

state: Tokyo

country: Japan

institute: Nippon Medical School

description:
LPS_DSF
gene_count_2
gene_fpkm_2

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using Fastp (remove reads containing N>10% ; remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50% of the read)
Trimmed sequence reads were mapped to mm10 using HISAT2 v2.0.5 (parameter: Default)
Read count extraction and normalization were performed using featureCounts v1.5.0-p3
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 FPKM values for each sample

source_name: Spleen

growth_protocol: B cells were isolated and seeded at 4 × 100000 cells/well in 48-well plates and culture for 3 hours in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted from the cell samples using the RNeasy Mini kit (Qiagen) and frozen at -80 °C for next-generation RNA sequencing (Novogene, Beijing, China).
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 using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: B cells without stimulation and without inhibitor (NS_DMSO), stimulated with LPS without inhibitor (LPS_DMSO), stimulated with IL-4 + anti-CD40 without inhibitor (IL4CD40_DMSO), stimulated with LPS and treated with 1 uM DSF (LPS_DSF) or ibrutinib (LPS_IBRU), and stimulated with IL-4 + anti-CD40 and treated with 1 uM DSF (IL4CD40_DSF)or ibrutinib (IL4CD40_IBRU).

value: Spleen

tag: strain

value: B cell

value: WT

value: LPS+disulfiram


title: B cells, IL-4+anti-CD40, ibrutinib, exp2

description:
IL4CD40_IBRU
gene_count_2
gene_fpkm_2


title: B cells, LPS, ibrutinib, exp2

description:
LPS_IBRU
gene_count_2
gene_fpkm_2

value: LPS+ibrutinib


title: R73_PAB-F_m_LV_#97_rep2

description:
col_names:"raw.reads.PAB_decompensatory_male_#97_LV", "normalized.reads.PAB_decompensatory_male_#97_LV", "fpkm.PAB_decompensatory_male_#97_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: male

value: pulmonary artery banding

value: 22 weeks


title: NL4.3 dNef CEMM7 10dpi

description:
410_3
Counts dNef vs WT.xlsx


title: B cells, IL-4+anti-CD40, disulfiram, exp2

description:
IL4CD40_DSF
gene_count_2
gene_fpkm_2


title: R72_PAB-F_m_RV_#84_rep1

description:
col_names:"raw.reads.PAB_decompensatory_male_#84_RV", "normalized.reads.PAB_decompensatory_male_#84_RV", "fpkm.PAB_decompensatory_male_#84_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle

value: 28 weeks

value: decompensatory


title: B cells, LPS, vehicle, exp2

description:
LPS_DMSO
gene_count_2
gene_fpkm_2

value: LPS


title: R71_PAB-F_m_LV_#84_rep1

description:
col_names:"raw.reads.PAB_decompensatory_male_#84_LV", "normalized.reads.PAB_decompensatory_male_#84_LV", "fpkm.PAB_decompensatory_male_#84_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle


title: AOB_decomp_#29_RV_rep3

description:
col_names:"raw_reads.AOB_decomp_#29_RV", "normalized_reads.AOB_decomp_#29_RV", "fpkm.AOB_decomp_#29_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1049

value: whole heart; left ventricle

value: 30 weeks

value: aortic banding

value: 24 weeks


title: R82_PAB-F_f_RV_#102_rep6

description:
col_names:"raw.reads.PAB_decompensatory_female_#102_RV", "normalized.reads.PAB_decompensatory_female_#102_RV", "fpkm.PAB_decompensatory_female_#102_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: female


title: NL4.3 dNef CEMM7 input

description:
410_1
Counts dNef vs WT.xlsx

source_name: Virus stock

value: Virus stock


title: B cells, IL-4+anti-CD40, vehicle, exp2

description:
IL4CD40_DMSO
gene_count_2
gene_fpkm_2

value: Spleen

value: B cell

value: WT


title: AOB_decomp_#29_LV_rep3

description:
col_names:"raw_reads.AOB_decomp_#29_LV", "normalized_reads.AOB_decomp_#29_LV", "fpkm.AOB_decomp_#29_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1048

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: male


title: R70_AOB-F_f_RV_#100_rep7

description:
col_names:"raw.reads.AOB_decompensatory_female_#100_RV", "normalized.reads.AOB_decompensatory_female_#100_RV", "fpkm.AOB_decompensatory_female_#100_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: 31 weeks

value: 26 weeks


title: sham_aob_decomp_#33_RV_rep3

description:
col_names:"raw_reads.sham_AOB_decomp_#33_RV", "normalized_reads.sham_AOB_decomp_#33_RV", "fpkm.sham_AOB_decomp_#33_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1047

value: sham

value: decompensatory


title: NL4.3 dNef CEMM7 15dpi IFN

description:
410_6
Counts dNef vs WT.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line

value: IFN-β


title: NL4.3 SupT1 20dpi

description:
378_6
Counts NL4.3 in SupT1.xlsx


title: R69_AOB-F_f_LV_#100_rep7

description:
col_names:"raw.reads.AOB_decompensatory_female_#100_LV", "normalized.reads.AOB_decompensatory_female_#100_LV", "fpkm.AOB_decompensatory_female_#100_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: female

value: aortic banding


title: B cells, IL-4+anti-CD40, disulfiram, replicate 4, exp1

description:
IL4CD40DSF_4
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT


title: sham_aob_decomp_#33_LV_rep3

description:
col_names:"raw_reads.sham_AOB_decomp_#33_LV", "normalized_reads.sham_AOB_decomp_#33_LV", "fpkm.sham_AOB_decomp_#33_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1046

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: male

value: 30 weeks

value: 24 weeks


title: B cells, unstimulated, exp2

description:
NS_DMSO
gene_count_2
gene_fpkm_2

value: No stimuli


title: AOB_decomp_#27_RV_rep2

description:
col_names:"raw_reads.AOB_decomp_#27_RV", "normalized_reads.AOB_decomp_#27_RV", "fpkm.AOB_decomp_#27_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1045

value: whole heart; left ventricle

value: decompensatory


title: AOB_decomp_#35_LV_rep4

description:
col_names:"raw_reads.AOB_decomp_#35_LV", "normalized_reads.AOB_decomp_#35_LV", "fpkm.AOB_decomp_#35_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1050


title: B cells, IL-4+anti-CD40, disulfiram, replicate 3, exp1

description:
IL4CD40DSF_3
gene_count_1
gene_fpkm_1


title: NL4.3 SupT1 14dpi

description:
378_5
Counts NL4.3 in SupT1.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: R68_AOB-F_f_RV_#99_rep6

description:
col_names:"raw.reads.AOB_decompensatory_female_#99_RV", "normalized.reads.AOB_decompensatory_female_#99_RV", "fpkm.AOB_decompensatory_female_#99_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: 31 weeks

value: 26 weeks


title: AOB_decomp_#27_LV_rep2

description:
col_names:"raw_reads.AOB_decomp_#27_LV", "normalized_reads.AOB_decomp_#27_LV", "fpkm.AOB_decomp_#27_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1044

value: left ventricle

value: aortic banding


title: NL4.3 SupT1 11dpi IFN

description:
378_4
Counts NL4.3 in SupT1.xlsx

value: Cell line

value: IFN-β


title: R67_AOB-F_f_LV_#99_rep6

description:
col_names:"raw.reads.AOB_decompensatory_female_#99_LV", "normalized.reads.AOB_decompensatory_female_#99_LV", "fpkm.AOB_decompensatory_female_#99_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: female


title: AOB_decomp_#25_RV_rep1

description:
col_names:"raw_reads.AOB_decomp_#25_RV", "normalized_reads.AOB_decomp_#25_RV", "fpkm.AOB_decomp_#25_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1043

value: male

value: 30 weeks


title: NL4.3 SupT1 11dpi

description:
378_3
Counts NL4.3 in SupT1.xlsx


title: B cells, IL-4+anti-CD40, disulfiram, replicate 2, exp1

description:
IL4CD40DSF_2
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT


title: NL4.3 dNef CEMM7 5dpi

description:
410_2
Counts dNef vs WT.xlsx

value: Virus-containing supernatant


title: NL4.3 SupT1 5dpi IFN

description:
378_2
Counts NL4.3 in SupT1.xlsx

value: CEM-M7 Cas9


title: AOB_decomp_#25_LV_rep1

description:
col_names:"raw_reads.AOB_decomp_#25_LV", "normalized_reads.AOB_decomp_#25_LV", "fpkm.AOB_decomp_#25_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1042

value: whole heart

value: decompensatory

value: 24 weeks


title: R65_AOB-F_f_LV_#86_rep5

description:
col_names:"raw.reads.AOB_decompensatory_female_#86_LV", "normalized.reads.AOB_decompensatory_female_#86_LV", "fpkm.AOB_decompensatory_female_#86_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: 31 weeks

value: 26 weeks


title: B cells, IL-4+anti-CD40, disulfiram, replicate 1, exp1

description:
IL4CD40DSF_1
gene_count_1
gene_fpkm_1


title: NL4.3 SupT1 5dpi

description:
378_1
Counts NL4.3 in SupT1.xlsx

value: Cell line


title: B cells, IL-4+anti-CD40, vehicle, replicate 4, exp1

description:
IL4CD40_4
gene_count_1
gene_fpkm_1


title: R64_AOB-F_m_RV_#136_rep4

description:
col_names:"raw.reads.AOB_decompensatory_male_#136_RV", "normalized.reads.AOB_decompensatory_male_#136_RV", "fpkm.AOB_decompensatory_male_#136_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle

value: aortic banding


title: sham_aob_decomp_#26_RV_rep2

description:
col_names:"raw_reads.sham_AOB_decomp_#26_RV", "normalized_reads.sham_AOB_decomp_#26_RV", "fpkm.sham_AOB_decomp_#26_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1041

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: sham


title: CH077 CEMM7 31dpi IFN

description:
379_9
Counts CH077 in CEMM7.xlsx

value: IFN-β


title: B cells, IL-4+anti-CD40, vehicle, replicate 3, exp1

description:
IL4CD40_3
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell


title: R63_AOB-F_m_LV_#136_rep4

description:
col_names:"raw.reads.AOB_decompensatory_male_#136_LV", "normalized.reads.AOB_decompensatory_male_#136_LV", "fpkm.AOB_decompensatory_male_#136_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: male


title: sham_aob_decomp_#26_LV_rep2

description:
col_names:"raw_reads.sham_AOB_decomp_#26_LV", "normalized_reads.sham_AOB_decomp_#26_LV", "fpkm.sham_AOB_decomp_#26_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1040

value: whole heart

value: 30 weeks