title: Skin_Spleen_Pool, CD4cre_and_WT_cMaf_CD4cre_KO_002 [LaneC_GEX_HTO]

description: dual index

source_name: Naïve (HT1), CD4-cre WT Skin (HT2), cMaf CD4-cre KO Skin (HT3), CD4cre WT Spleen (HT4), cMaf CD4cre KO Spleen (HT5)


title: Skin_Spleen_Pool, B6_WT_and_Hobit_KO_002 [LaneD_GEX_HTO]

status: Public on Oct 24 2023

type: SRA

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

description: dual index

library_source: transcriptomic

data_processing:
library strategy: CITE-seq
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the multi subcommand to align samples from two batches to the transcriptome, CITE-seq, and TCR references
The hashtag anitbodies are treated as CITE-seq antibodies as well and demultiplexed using HTODemux command in Seurat
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: CSV file for CITE-seq antibodies and hashtag sequences for demultiplexing
Supplementary files format and content: Tar files of VDJ-seq contains CSV files from the cellranger multi command
Supplementary files format and content: Tar files of filtered feature barcode matrices from the cellranger multi command.

molecule: total RNA

organism: Mus musculus

source_name: Naïve (HT1), B6 WT Skin (HT2), Hobit KO Skin (HT3), B6 WT Spleen (HT4), Hobit KO Spleen (HT5)

extract_protocol:
10x Genomics Chromium Next GEM Single Cell 5' Gene Expression Kit with Feature Barcoding technology for Cell Surface Protein and Immune Receptor Mapping (v2 Chemistry Dual Index)
Chromium Single Cell Mouse TCR Amplification Kit. Libraries were sequenced across two separate flow cells (Batch 1 and Batch 2 in the raw files correspond to these runs).

tag: tissue

tag: time

tag: cell type

value: CD8+ T cell


title: Microdissection_WT_Internal_4

city: Rennes

first: Luc

last: Paillard

state: Brittany

address: 2 Ave Leon Bernard

department: IGDR (UMR6290)

country: France

institute: Univ Rennes

description:
Internal
DEA_tab_Microdissection_3D_WT_Internal_vs_External.csv

data_processing:
Only sens reads are use for this analysis since the library correspond to 3’end RNA-seq
reads were trimmed following lexogene suggestion, the adaptator and the polyA tail, only read with a length superior to 20 nt were kept
Trimmed reads were map to the mouse genome (GRCm38.p6) with STAR software (2.7.8a)
Uniquely mapped reads were count by featureCount (v1.6.0)
Supplementary files format and content: GRCm38.p6
Supplementary files format and content: Differential expression analysis by edgr, with cpm (count per millions) normaliezd for each sample and statistical Gene Expression difference for each genes.

source_name: Lens epithelial cells

extract_protocol:
RNA from 2D and 3D sample have been extracted with the Nucleospin kit (Macherey-Nagel) and the RNA from the microdissection (internal and external part) were extracted with a specific kit, the Arcturus PicoPure (ThermoFisher)
3’ end seq library were prepared using the QuantSeq 3’ mRNA-Seq library Kit (Lexogen)

value: Lens epithelial cells

tag: cell line

tag: protocol

value: Internal


title: Microdissection_WT_Internal_3


title: Microdissection_WT_Internal_1


title: WT_3D_4

description:
3D
DEA_tab_WT_2D_vs_3D.csv


title: WT_3D_2

description:
3D
DEA_tab_WT_2D_vs_3D.csv


title: WT_3D_1

description:
3D
DEA_tab_WT_2D_vs_3D.csv


title: Microdissection_WT_Internal_2


title: control_cKIT_K27me3_2

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

country: USA

institute: Yale University

description: 150bp PE CUT&Tag

library_source: genomic

data_processing:
Quality filtering was performed using FASTX-Toolkit. The adapter sequences (CTGTCTCTTATACACATCT) were trimmed for each filtered file using cutadapt and Seqkit was then used to match paired reads. Reads were then aligned to the mm10 mouse genome assembly using Bowtie2 with –end-to-end –very-sensitive settings enabled. The sequencing depth was equalized across all samples and the resultant .sam file was converted to bam files. After sorting and indexing using SAMtools the bam files were converted to bigwig format using bamCoverage. We generated metagene plots from the bigwig files using deepTools. Peak calling was performed using SEACR.
see data processing associated with each sample
Assembly: mm10
Supplementary files format and content: .bed files of peaks

molecule: genomic DNA

source_name: testis

extract_protocol:
Dissociated germ cells were incubated in the dark for 30 mins with PE conjugated anti-cKIT at 1:800 (Thermo, 12-1171-82). Stained cells were then washed twice, resuspended to 10 million cells/ml and sorted on a two-laser (466 nm and 561 nm) cell sorter (Bio-Rad S3) as previously described (Vasiliauskaitė et al., 2018). 50,000 cells were pelleted for library prep.
CUT&Tag libraries were prepared using the Active Motif anti-Rabbit assay kit (Active Motif, 53160) with minor amendments to the manufacturer’s protocol. Briefly, cKIT+ cells were sorted from dissociated testis and centrifuged at 1,000 xg for 3 mins at room temperature before washing the cell pellet in the buffer provided. For each reaction, 50 µl of cell suspension (50,000 cKIT+ cells) was incubated with 6 µl of concanavalin A beads in a 0.5ml tube. After 10 minutes, the beads were captured using a magnetic stand and resuspended in 50 µl of antibody buffer containing PIC ,digitonin, and 1 µg of primary antibody. After overnight incubation at 4°C, the liquid was removed, and the beads were incubated at room temperature for 60 minutes with 50 µl of secondary antibody diluted in Dig-wash buffer. The beads were then washed once with 500 µl Dig-wash buffer before incubating with 50 µl of diluted transposomes for 60 minutes. After a single wash with 500 µl of Dig-300 buffer the beads were incubated with 125 µl of Tagmentation buffer for 60 minutes in a thermomixer set at 400rpm 37°C. The DNA was then extracted and PCR amplified according to the manufacturer’s instructions. Finally, SPRI bead clean-up was performed before eluting purified DNA into 16 µl elution buffer. An Agilent 2100 Bioanalyzer using a high sensitivity DNA assay kit was used to assess the quality of prepared libraries, which were then paired-end sequenced to achieve ~30 million reads.

value: testis

value: cKIT+ spermatogonia

tag: genotype

value: Kdm6a fl/y; Cre- (control)

tag: antibody

value: CST9733 anti-H3K27me3


title: WT_2D_3

description:
2D
DEA_tab_WT_2D_vs_3D.csv


title: WT_2D_2

description:
2D
DEA_tab_WT_2D_vs_3D.csv


title: WT_2D_1

description:
2D
DEA_tab_WT_2D_vs_3D.csv


title: Skin_Spleen_Pool, CD4cre_and_WT_cMaf_CD4cre_KO_001 [LaneB_GEX_HTO]

description: dual index

source_name: Naïve (HT1), CD4-cre WT Skin (HT2), cMaf CD4cre KO Skin (HT3), CD4cre WT Spleen (HT4), cMaf CD4-cre KO Spleen (HT5)


title: scWAT, YT-AKO_2

city: Beijing

first: Xun

last: Huang

address: Zhongguancun Street

country: China

institute: Peking University

data_processing:
Linux system
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke software (parameter: –lowQual=20，–nRate=0.005，–qualRate=0.5).
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2.
Read summarization were performed using featureCounts.
Differential gene expression (DGE) was analyzed  using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: scWAT

extract_protocol:
Total RNA was isolated from cells or tissues using TRIzol (Sigma) and 2 ug total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following manufacturer's protocols

value: scWAT

tag: Sex

value: male

tag: age

value: 8 weeks old

value: Yapfl/fl/Tazfl/fl;AdipoqCre


title: scWAT, YT-AKO_3


title: scWAT, WT_3

value: WT


title: scWAT, WT_2


title: scWAT, WT_1


title: kdm6a_cKO_cKIT_ATAC_3

description: 100bp PE ATAC-seq

data_processing:
Adapter trimming was performed using Cutadapt (Martin, 2011). Trimmed reads were aligned to the mouse genome (mm10) using Bowtie2 in very sensitive mode (Langmead and Salzberg, 2012). Peak calling was performed using MACS2 with default parameters. Subsequent processing was performed according to the workflow previously described by Reske et al. (2020).
Assembly: mm10
Supplementary files format and content: ATAC-seq: .bed files of peaks
Supplementary files format and content: bulk RNA-seq: .tsv files of read counts by gene
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files

extract_protocol:
Dissociated germ cells were incubated in the dark for 30 mins with PE conjugated anti-cKIT at 1:800 (Thermo, 12-1171-82). Stained cells were then washed twice, resuspended to 10 million cells/ml and sorted on a two-laser (466 nm and 561 nm) cell sorter (Bio-Rad S3) as previously described (Vasiliauskaitė et al., 2018). 100,000 cells were pelleted for library prep.
Libraries were prepared using the Active Motif ATAC-Seq kit (53150) according to the manufacturer’s instructions except 11 PCR cycles were used instead of the recommended 10 cycles.

value: Kdm6a fl/y; Ddx4-Cre+ (cKO)


title: kdm6a_cKO_cKIT_ATAC_2

description: 100bp PE ATAC-seq


title: scWAT, YT-AKO_1


title: shScr-GC1_ATAC_2

description: 100bp PE ATAC-seq

extract_protocol:
100,000 cells were counted and pelleted before proceeding with library prep.
Libraries were prepared using the Active Motif ATAC-Seq kit (53150) according to the manufacturer’s instructions except 11 PCR cycles were used instead of the recommended 10 cycles.

value: shScr


title: shScr-GC1_ATAC_1

description: 100bp PE ATAC-seq


title: WT_3D_3

description:
3D
DEA_tab_WT_2D_vs_3D.csv


title: kdm6a_f2_testis_3

description: 100bp PE polyA RNA-seq

data_processing:
Raw sequence files were filtered and their quality was assessed using FASTX-toolkit and FastQC. Filtered paired-end reads were matched to yield a file of common reads which were then pseudoaligned to the mouse (mm39) transcriptome from Ensembl release 107 (Cunningham et al., 2022) and quantified using Kallisto v0.45.0 (Bray et al., 2016).
Assembly: mm10
Supplementary files format and content: ATAC-seq: .bed files of peaks
Supplementary files format and content: bulk RNA-seq: .tsv files of read counts by gene
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files

molecule: polyA RNA

source_name: whole testis

extract_protocol:
Decapsulated testes were incubated in DMEM containing 0.75 mg/ml collagenase type IV (Gibco, 17104-019) for 10 mins at 37°C with occasional inversion. Equal volume of DMEM was added to the suspension of dissociated tubules before centrifuging at 400 xg for 5 mins at 4 °C. After removing the supernatant, the cell pellet was washed in DMEM and resuspended in 0.05% trypsin-EDTA (Gibco, 25200-056) for 10 mins incubation at room temperature. An equal volume of ice-cold DMEM+10%FBS was then added to the cell suspension before washing the pellet twice with media. The cell pellet was resuspended in DPBS (Sigma, D8537) containing 0.04% bovine serum albumin (sigma, A9647) and filtered through a 100 µm filter (Falcon, 22363549) then a 40 µm filter (Falcon, 352340) to generate a single cell suspension. Total RNA was extracted from dissociated testis cells by homogenizing in 1 ml of TRIzol reagent (Invitrogen, 15596026). After 5 mins of incubation, the lysate was mixed with 200µl of chloroform and centrifuged at 12,000 xg for 15 mins at 4°C. The aqueous phase was mixed with an equal volume of 100% ethanol and transferred to an RNeasy MinElute spin column (Qiagen, 74104) for purification according to the manufacturer's instructions. The quality of the eluted RNA was assessed by 28S/18S ribosomal ratios and RNA integrity number (RIN) using an Agilent Bioanalyzer.
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche # 08098123702) according to the manufacturer’s instructions

value: whole testis

value: Kdm6a fl/y; Cre- (F2 of cKO)


title: ST6004

city: New York

first: Alejandra

last: Borjabad

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine

data_processing: Data processing was performed by Novogene Co.

source_name: Brain / striatum

extract_protocol:
RNA was extracted using Rneasy Kit from Qiagen.
Libraries were prepared by Novogene Co.

value: Brain / striatum


title: control_cKIT_ATAC_2

description: 100bp PE ATAC-seq


title: control_cKIT_ATAC_1

description: 100bp PE ATAC-seq


title: kdm6a_f2_testis_4

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_ATAC_2

description: 100bp PE ATAC-seq


title: shKdm6a-GC1_ATAC_1

description: 100bp PE ATAC-seq


title: kdm6a_f2_testis_1

description: 100bp PE polyA RNA-seq


title: kdm6a_f1_testis_3

description: 100bp PE polyA RNA-seq

value: Kdm6a fl/y; Cre- (F1 of cKO)


title: WT_2D_4

description:
2D
DEA_tab_WT_2D_vs_3D.csv

value: Lens epithelial cells


title: kdm6a_f2_testis_2

description: 100bp PE polyA RNA-seq


title: kdm6a_f1_testis_1

description: 100bp PE polyA RNA-seq


title: kdm6a_cKO_testis_2

description: 100bp PE polyA RNA-seq


title: kdm6a_cKO_testis_3

description: 100bp PE polyA RNA-seq


title: kdm6a_cKO_cKIT_ATAC_1

description: 100bp PE ATAC-seq


title: kdm6a_f1_testis_2

description: 100bp PE polyA RNA-seq


title: kdm6a_cKO_testis_1

description: 100bp PE polyA RNA-seq


title: control_testis_5

description: 100bp PE polyA RNA-seq


title: control_testis_4

description: 100bp PE polyA RNA-seq


title: control_testis_6

description: 100bp PE polyA RNA-seq


title: control_testis_3

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_RNA_B3

description: 100bp PE polyA RNA-seq

extract_protocol:
Total RNA was extracted from pelleted cells by homogenizing in 1 ml of TRIzol reagent (Invitrogen, 15596026). After 5 mins of incubation, the lysate was mixed with 200µl of chloroform and centrifuged at 12,000 xg for 15 mins at 4°C. The aqueous phase was mixed with an equal volume of 100% ethanol and transferred to an RNeasy MinElute spin column (Qiagen, 74104) for purification according to the manufacturer's instructions. The quality of the eluted RNA was assessed by 28S/18S ribosomal ratios and RNA integrity number (RIN) using an Agilent Bioanalyzer.
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche # 08098123702) according to the manufacturer’s instructions

value: spermatogonia-derived


title: control_testis_7

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_RNA_B2

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_RNA_A3

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_RNA_A1

description: 100bp PE polyA RNA-seq


title: shScr-GC1_RNA_3

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_RNA_A2

description: 100bp PE polyA RNA-seq


title: shKdm6a-GC1_RNA_B1

description: 100bp PE polyA RNA-seq


title: kdm6a_scRNAseq

description: 150bp PE scRNA-seq from Utx cKO testes

library_source: transcriptomic single cell

data_processing:
Raw count matrices were generated using CellRanger (10X Genomics) and imported to Seurat 4.1.0 (Hao et al., 2021) and combined into one Seurat object. Reads were filtered to exclude doublets (nCount_RNA < mean + one standard deviation), dead or dying cells (nFeature_RNA > mean – one standard deviation) or high mitochondrial content (present.mt < mean + standard deviation). This filtered subset was log normalized and scaled. A linear dimensional reduction was performed using principal component analysis (PCA), and it was determined that 20 dimensions was optimum. Clusters were identified at a resolution of 0.5, and the “RunUMAP()” function was used to further investigate the dataset. Three of the initial clusters had a low number of detected molecules per cell, indicating dead or dying cells, and did not have any top genes associated with the transition from spermatogonia to elongating spermatid. Therefore, these three clusters were removed, and the data was normalized, scaled, and regressed again using the same parameters as described.
Assembly: mm10
Supplementary files format and content: ATAC-seq: .bed files of peaks
Supplementary files format and content: bulk RNA-seq: .tsv files of read counts by gene
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files

extract_protocol:
Decapsulated testes were incubated in DMEM containing 0.75 mg/ml collagenase type IV (Gibco, 17104-019) for 10 mins at 37°C with occasional inversion. Equal volume of DMEM was added to the suspension of dissociated tubules before centrifuging at 400 xg for 5 mins at 4 °C. After removing the supernatant, the cell pellet was washed in DMEM and resuspended in 0.05% trypsin-EDTA (Gibco, 25200-056) for 10 mins incubation at room temperature. An equal volume of ice-cold DMEM+10%FBS was then added to the cell suspension before washing the pellet twice with media. The cell pellet was resuspended in DPBS (Sigma, D8537) containing 0.04% bovine serum albumin (sigma, A9647) and filtered through a 100 µm filter (Falcon, 22363549) then a 40 µm filter (Falcon, 352340) to generate a single cell suspension.
Single cell RNA-seq libraries were constructed from whole dissociated testis samples using the Chromium Next GEM Single Cell 3’ GEM kit v3.1 (10x Genomics PN-1000121) according to the manufacturer’s instructions.

value: Kdm6a fl/y; Ddx4-Cre+ (Utx cKO)


title: shScr-GC1_RNA_1

description: 100bp PE polyA RNA-seq


title: shScr-GC1_RNA_2

description: 100bp PE polyA RNA-seq


title: MD4-2D-S3

first: Rohit

last: Chandwani

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the mouse reference genome (mm9) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M1) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Differentially expressed genes (DEG) were determined with limma-voom.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: Pancreas

extract_protocol:
tdTomato+ acinar cells were FACS sorted into 1.5 mL Eppendorf tubes containing Trizol. Total RNA was purified using a standard phenol-chloroform extraction method.
Sequencing libraries were constructed using Illumina TruSeq Library Prep Kit (Non-Stranded and Poly-A selection) and sequenced on either Illumina HiSeq 2500 or NovaSeq 6000 (2x50 cycles paired-end run)

tag: strain

tag: biological context

value: Inflammation-naive

tag: recovery duration

value: 2 days


title: MD4-2D-S2


title: MD4-2D-S1


title: MD4-2D-C1

value: Pancreatitis

tag: agent

value: Caerulein


title: MD4-12W-S4

value: 12 weeks


title: MD4-2D-C2


title: MD4-12W-S3


title: control_testis_2

description: 100bp PE polyA RNA-seq

value: Kdm6a fl/y; Cre- (control)


title: MD4-12W-S1


title: MD4-12W-S2


title: MD4-12W-C4


title: MD4-2D-C3


title: MD4-12W-C3


title: MD4-12W-C2


title: INV3-2D-mtS-1729


title: control_testis_1

description: 100bp PE polyA RNA-seq


title: ST6005


title: INV3-2D-mtC-1726


title: control_scRNAseq

description: 150bp PE scRNA-seq from control testes


title: INV3-2d-mtS-1663


title: INV3-2D-mktS-1732


title: INV3-2D-mktS-1731


title: INV3-2D-mktC-1751


title: INV3-2D-mktS-1669


title: INV3-2d-mtC-1667


title: INV3-2D-mktC-1780


title: INV3-2D-mtC-1777


title: INV3-2d-mtS-1662


title: INV3-2D-mktC-1737


title: CP_wt_C2D_555


title: MD4-12W-C1


title: C2D_1

data_processing:
The quality of the sequenced reads was assessed with Cell Ranger v3.0.2, FastQC, and FastX toolkit.
The alignment, deemultiplexing, and postprocessing were performed using Cell Ranger v3.0.2 as suggested by 10X Genomics.
Assembly: mm10
Supplementary files format and content: Filtered feature-barcode matrices in TSV and MTX format from Cell Ranger

extract_protocol:
Single cell suspensions were prepared from pancreata and stained with DAPI. DAPI-negative cells were sorted and collected via FACS.
10X Genomics Chromium was employed to add barcoded primer gel beads to each single cell. The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following the standard 10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays protocol. Libraries were sequenced on Illumina NovaSeq6000 at the Epigenomics Core Facility at Weill Cornell Medicine.


title: PBS 2

type: protein

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: 2 positive controls (anti-IgG and IgG control) were also imprinted on the arrays as positive controls.

hyb_protocol: not provided

scan_protocol: not provided

data_processing: NFI were normalized by robust linear model using build-in Ig control with various dilutions

molecule: protein

organism: Homo sapiens

source_name: Serum

label_protocol: Human serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-human IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

extract_protocol: Serum samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. Sera of all subjects were aliquoted and stored at -80ºC.

tag: file

tag: slide

tag: block

tag: condition

value: Negative control


title: 30_IgG


title: S6W_1

value: WT

value: Inflammation-naïve

value: 6 weeks


title: mtS_2546_12WRec

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2).
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v6.0.2) in two steps. In the first step, cellranger mkfastq demultiplexed samples and generated fastq files; and in the second step, cellranger count aligned fastq files to the reference genome and extracted gene expression UMI counts matrix.
In order to measure both mouse and marker gene expression, we built a custom reference genome by integrating the tdTomato-WPRE marker gene into the 10X pre-built mouse reference (refdata-gex-mm10-2020-A) using cellranger mkref.
Assembly: mm10

extract_protocol:
Single cell suspensions were prepared from pancreata and stained with DAPI. ~300k DAPI(-) cells were sorted and collected via FACS. ~300k DAPI(-) tdTomato(+) cells were sorted and collected via FACS. ~300k DAPI(-) & ~300k DAPI(-) tdTomato(+) were combined into a single tube.
10X Genomics Chromium was employed to add barcoded primer gel beads to each single cell. The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following the standard 10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays protocol. Libraries were sequenced on Illumina NovaSeq6000 at the Epigenomics Core Facility at Weill Cornell Medicine.

tag: recovery duration 1

tag: recovery duration 2


title: mktS_2544_12WRec_2DRas


title: mktC_2524_12WRec_2DRas


title: 29_IgG


title: S2D_1


title: 28_IgG


title: C6W_1


title: 27_IgG


title: 24_IgG


title: 25_IgG


title: 20_IgG


title: 22_IgG


title: 21_IgG


title: 18_IgG


title: 23_IgG


title: 19_IgG


title: 26_IgG


title: PBS 1


title: CP_wt_C2D_558


title: 14_IgG


title: 15_IgG


title: 16_IgG


title: 13_IgG


title: 10_IgG


title: 9_IgG


title: mtC_2547_12WRec


title: 4_IgG


title: 2_IgG


title: 5_IgG


title: 8_IgG


title: 1_IgG


title: 11_IgG


title: 6_IgG


title: 17_IgG


title: 3_IgG


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 3, tech rep2

city: Knoxville

first: Brynn

last: Voy

state: Tennessee

address: 2506 River Drive

department: Animal Science

institute: The University of Tennessee

data_processing:
CLC Genomics Workbench v 23.0.1
Reads were aligned to the reference genome and read counts obtained using CLC Genomics Workbench
Assembly: galGal6
Supplementary files format and content: raw counts for each sample

organism: Gallus gallus

source_name: Pectoralis major

growth_protocol: After isolation, primary broiler satellite cells were cultured in Ham's F10 containing 20% fetal bovine serum (FBS), 10% non-heat activated horse serum (HS), 1% chicken embryo extract (CEE), 2.5 ng/mL basic fibroblast growth factor, and 100 IU/mL penicillin-streptomycin (PS).

extract_protocol:
Cells were harvested immediately before differentiation induction (0 h) and after differentiation (12 h, 24 h, 36 h, and 48 h) for RNA isolation. Total RNA was isolated using Direct-zol RNA Miniprep kit according to the manufacturer’s instructions (Zymo Research).
Total RNA (500 ng) was reverse transcribed into cDNA using iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions. Primers were designed based on the chicken refseq genome (Gallus_gallus-6.0/galGal6) using NCBI Primer Blast (https://www.ncbi.nlm.nih.gov/tools/primer-blast) to represent the consensus transcript for each gene and to yield products that spanned exon boundaries.
Targeted RNAseq

treatment_protocol: The next day, media was replaced with DMEM/F12 containing 10% HS, 2% CEE, and 100 IU/ml PS to induce myogenic differentiation. Then, cells were  transferred to a hypoxic chamber (1% O2 / 5% CO2 / 94% N2) and cultured for 48 h.

tag: tissue

value: Pectoralis major

value: Primary cells

tag: cell type

value: Satellite cells

tag: treatment

value: Hypoxia


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 3, tech rep1

tag: cell line

tag: genotype


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 6, tech rep2


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 5, tech rep1


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 6, tech rep1

value: Normoxia


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 1, tech rep1


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 6, tech rep1


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 2, tech rep1


title: trNK, 6h, IL-21 1

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

description: bulk RNA-Seq

data_processing:
For bulk RNA-Seq, sequence reads were mapped to the mouse (mm10) genome with hisat2 (2.1.0) with default settings and we kept one hit if multiple reads were mapped to the same position for each RNA-Seq library.For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
For single-cell RNA-Seq, the sequencing data were aligned and quantified using the BD Rhapsody WTA Local bioinformatics pipeline (version 1.9.1, BD) against the mouse mm10 reference genome
For ATAC-Seq, raw sequencing reads were trimmed with Trimmomatic. Trimmed reads were aligned to mm10 assembly of mouse genome using Bowtie2. Then, the aligned reads were sorted using samtools, and duplicates were removed using PICARD. Peak-calling for ATAC-Seq was performed with MACS on bam files, with a q-value threshold of 0.01. Consensus peaks from all NK samples were merged to create a raw peak universe. Peak annotation and motif analysis were performed with HOMER. ATAC-Seq tracks were visualized using Integrative Genomics Viewer.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample
Supplementary files format and content: bigWig

source_name: uterus

growth_protocol: Wild-typre males co-habited with virgin females overnight and the detection time of a copulation plug was thought as gestation day(gd) 0.5. Then the males and females were separated into different cages. Uterine trNK or cNK were isolated at gd6.5. For the experiments in vitro, trNK were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Single Cell Full Length mRNA-Amplification Kit (Vazyme) following manufacturer's protocols. 5ng total RNA was used for the construction of sequencing libraries. DNA was harvested using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)  following manufacturer's protocols.
RNA libraries for RNA-seq or DNA libraries for ATAC-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)  following manufacturer's protocols.

treatment_protocol: 15ng/ml IL-15 with or without 20ng/mL IL-21 were added into the medium where sorted trNK were cultured in vitro.

value: uterus

value: trNK


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 5, tech rep1


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 6, tech rep2


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 4, tech rep1


title: 7_IgG


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 2, tech rep1


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 6, tech rep1


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 1, tech rep1


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 6, tech rep2


title: Primary broiler satellite cells, hypoxia, 48 h, biol rep 4, tech rep1


title: 12_IgG


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 5, tech rep1


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 4, tech rep1


title: Primary broiler satellite cells, normoxia, 48 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 6, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 1, tech rep1


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 6, tech rep1


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 5, tech rep1


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 4, tech rep1


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 2, tech rep1


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 1, tech rep1


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 6, tech rep2


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 5, tech rep1


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 6, tech rep1


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 4, tech rep1


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 2, tech rep1


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, hypoxia, 24 h, biol rep 1, tech rep1


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 6, tech rep1


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 6, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 4, tech rep1


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, normoxia, 36 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 1, tech rep1


title: HEK-293T cells, mock transfected,  26h, replicate 2

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

data_processing:
MGI DNBSEQ G400 sequencer built-in software was used for basecalling
Sequenced reads were trimmed for adaptor sequences, and filtered for low-complexity or low-quality sequence using Trimmomatic v0.36.
Trimmed reads were mapped to Ensembl GRCh38.104 whole genome using HISAT2 v.2.2.1 with default parameters.
Raw read counts were generated with featureCounts v1.6.2 with default settings using the Ensembl Build GRCh38.104 annotation gtf file. Read counts were normalized using the median-of-ratios method introduced with the DESeq2 v4.0.3 R package.
Assembly: GRCh38.104.primary assembly
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table including normalized gene counts for every sample and every gene, generated using the median-of-ratios method

source_name: embrionic kidney

growth_protocol: HEK293T cells (Invitrogen, CA, USA) were maintained in DMEM media supplemented with 10% FBS, 1% L-Glutamine and 1% penicilin/streptomicin. Day before transduction, cells were plated into 6-well plate with 5*10^5 cell/ well in 1500 µl of DMEM.

extract_protocol:
Cells were collected at eight, 12 and 26 hours after transduction, media was discarded and cells were washed with 500 µl PBS, and then suspended into 500 µl TRIzol Reagent (Thermo Fisher Scientific, MA, USA). RNA isolation was carried out according to the manufacturer's instructions.
RNA quality was determined by Agilent RNA 6000 Nano kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Thereafter,  sequencing was performed on the DNBSEQ G400 sequencer using MGIEasy RNA Library Prep Set.

treatment_protocol: Medium was discarded and the cells were transduced with 5 ng RT-equivalent of HIV-1 / HIV-2, or mock pseudovirions in 1500 µl serum- and antibiotic-free media, complemented with 8 µg/ml polybrene.

value: embrionic kidney

value: epithelial cells

value: treated with VSV.G-mock for 26 hours

tag: time


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 2, tech rep1


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 6, tech rep2


title: HEK-293T cells, mock transfected,  12h, replicate 1

value: treated with VSV.G-mock for 12 hours


title: HEK-293T cells, mock transfected,  26h, replicate 1


title: HEK-293T cells, mock transfected,  12h, replicate 2


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 6, tech rep1


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 5, tech rep2


title: Primary broiler satellite cells, hypoxia, 36 h, biol rep 2, tech rep1


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 5, tech rep1


title: HEK-293T cells, mock transfected,  8h, replicate 2

value: treated with VSV.G-mock for 8 hours


title: HEK-293T cells, HIV-2 transfected,  26h, replicate 1

value: treated with HIV-2 for 26 hours


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 4, tech rep1


title: HEK-293T cells, mock transfected,  8h, replicate 1


title: Primary broiler satellite cells, normoxia, 24 h, biol rep 5, tech rep1


title: HEK-293T cells, HIV-2 transfected,  26h, replicate 2


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 3, tech rep2


title: HEK-293T cells, HIV-2 transfected,  8h, replicate 2

value: treated with HIV-2 for 8 hours


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 3, tech rep1

value: WT


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 2, tech rep1


title: HEK-293T cells, HIV-2 transfected,  12h, replicate 1

value: treated with HIV-2 for 12 hours


title: HEK-293T cells, HIV-2 transfected,  8h, replicate 1


title: HEK-293T cells, HIV-2 transfected,  12h, replicate 2


title: HEK-293T cells, HIV-1 transfected,  26h, replicate 3

value: treated with HIV-1 for 26 hours


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 1, tech rep2

value: Pectoralis major


title: HEK-293T cells, HIV-1 transfected,  26h, replicate 2


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 6, tech rep2

value: Primary cells


title: HEK-293T cells, HIV-1 transfected,  26h, replicate 1


title: HEK-293T cells, HIV-1 transfected,  12h, replicate 3

value: treated with HIV-1 for 12 hours


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 5, tech rep1

value: Satellite cells


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 6, tech rep1

value: Normoxia


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 5, tech rep2


title: HEK-293T cells, HIV-1 transfected,  12h, replicate 1


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 4, tech rep2


title: HEK-293T cells, HIV-1 transfected,  8h, replicate 3

value: treated with HIV-1 for 8 hours


title: HEK-293T cells, HIV-1 transfected,  12h, replicate 2


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 4, tech rep1


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 1, tech rep1

value: Hypoxia


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, hypoxia, 12 h, biol rep 2, tech rep2


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 2, tech rep1


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 1, tech rep1


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 1, tech rep2


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 4, tech rep2


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 5, tech rep1


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 4, tech rep1


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 3, tech rep1


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 2, tech rep2


title: Ikzf2-/- Tregs rep 3

type: RNA

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

institute: IGBMC

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7µm.

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

source_name: sorted cells from mouse spleen

label_protocol: Biotinylated double strand cDNA targets were prepared from 15ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro  kit

value: CD4+CD25+ (Treg)


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 2, tech rep1


title: HEK-293T cells, HIV-1 transfected,  8h, replicate 1

value: embrionic kidney

value: epithelial cells


title: Primary broiler satellite cells, normoxia, 12 h, biol rep 3, tech rep2


title: Primary broiler satellite cells, normoxia, 0 h, biol rep1, tech rep1


title: Primary broiler satellite cells, normoxia, 0 h, biol rep 5, tech rep2


title: dKO Tregs rep 3

value: dKO


title: WT Tregs rep 5


title: Ikzf2-/- Tregs rep 1


title: WT Tregs rep 4


title: Primary broiler satellite cells, normoxia, 0 h, biol rep1, tech rep2


title: Corolla 7PM replicate 3

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

data_processing:
Adapters were trimmed using Cutadapt and the reads were aligned to the P. axillaris genome using TopHat2.C
Counts were assigned to gene features using HTSeq.
Assembly: Petunia axillaris draft genome sequence v1.6.2
Supplementary files format and content: a tab-delimited file containing alignment counts for each sample at annotated P. axillaris gene loci

organism: Petunia x hybrida

source_name: corolla

growth_protocol: Petunia were grown under normal greenhouse conditions, with a 14h light and 10h dark cycle. Light period was from 6AM to 8PM.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plant Mini kit. DNA was removed using Ambion TURBO DNA-free kit.
PolyA library prep and sequencing was performed by the Purdue Genomics Core Facility at Purdue University.

value: corolla

tag: cultivar

value: Mitchell


title: HEK-293T cells, HIV-1 transfected,  8h, replicate 2


title: dKO Tregs rep 2


title: Ikzf4-/- Tregs rep 2


title: Ikzf4-/- Tregs rep 1


title: WT Tregs rep 6


title: Ikzf4-/- Tregs rep 3


title: Ikzf2-/- Tregs rep 2


title: dKO Tregs rep 1


title: Corolla 7PM replicate 2


title: Corolla 7AM replicate 3


title: WT Tregs rep 2


title: WT Tregs rep 3


title: Corolla 7AM replicate 2


title: Corolla 7AM replicate 1


title: RIM101 CO2 3

city: Iowa City

first: Damian

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

description:
RIM101 CO2 3
Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx
gene_count_matrix_H99_RIM101.xlsx

data_processing:
Paired-end Illumina sequence read files were evaluated for quality and the absence of adaptor sequence using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read files were mapped to C. neoformans reference genome H99 v48 (FungiDB).
Gene transcript expression was quantified using HISAT2 and Stringtie.
Differential expression fold change, Wald test p values, and Benjamini-Hochberg adjustment for multiple comparisons were determined using DESeq2.
Principle component analysis was performed on regularized log transformed gene counts to confirm the absence of batch effects.
Assembly: FungiDB-48_CneoformansH99
Supplementary files format and content: Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx; abundance measurements relative to ambient conditions for each time point
Supplementary files format and content: Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx; abundance measurements for RIM101 relative to H99

organism: Cryptococcus neoformans

growth_protocol: Overnight cultures of indicated strains were washed and diluted to 7.5x105 cells/mL, 3 mL cultured per condition in a 6-well plate in RPMI 1640 medium with 165 mM MOPS, pH 7 for 4, 8, or 24 hours at 37°C in ambient air or 5% CO2.

extract_protocol:
Cells were collected via centrifugation from growth medium, lyophilized overnight and RNA harvested according to manufacturer protocol for Invitrogen PureLink RNA Mini Kit.
Total RNA (>2 ug per sample) was submitted to Azenta Life Sciences for standard RNA-Seq next-generation sequencing. The RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher) and RNA integrity was checked using TapeStation (Agilent Technologies). The RNA sequencing libraries were prepared using the NEB Next Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 min at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher) as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.


title: H99 CO2 3

description:
H99 CO2 3
Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx
gene_count_matrix_H99_RIM101.xlsx

value: wild-type


title: H99 CO2 2

description:
H99 CO2 2
Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx
gene_count_matrix_H99_RIM101.xlsx


title: RIM101 CO2 1

description:
RIM101 CO2 1
Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx
gene_count_matrix_H99_RIM101.xlsx


title: RIM101 CO2 2

description:
RIM101 CO2 2
Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx
gene_count_matrix_H99_RIM101.xlsx


title: Corolla 7PM replicate 1


title: WT Tregs rep 1

value: WT


title: CO2 24h 2

description:
24 hour C02 2
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: H99 CO2 1

description:
H99 CO2 1
Supplemental Table 5 - RIM101 CO2 vs H99 CO2 RNA-Seq.xlsx
gene_count_matrix_H99_RIM101.xlsx


title: CO2 24h 3

description:
24 hour C02 3
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: Amb 24h 3

description:
24 hour Amb 3
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx

value: Ambient air


title: CO2 24h 1

description:
24 hour C02 1
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 12-m-o Vav2Onc EpSC rep2

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from epidermal stem cells

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.3.1).

source_name: Epidermal stem cells from Vav2Onc 12-m-o mice

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

extract_protocol: RNeasy Micro Kit (QIAGEN, Catalog No. 74004) was used according to the manufacturer's instructions.

treatment_protocol: No treatment was applied to the animals

tag: strain

tag: age

value: 12 months

value: Stem cells from the epidermis


title: 6-m-o Vav2Onc EpSC rep1

source_name: Epidermal stem cells from Vav2Onc 6-m-o mice

value: 6 months


title: Amb 24h 2

description:
24 hour Amb 2
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 2.5-m-o Vav2Onc EpSC rep3

source_name: Epidermal stem cells from Vav2Onc 2.5-m-o mice

value: 2.5 months


title: 6-m-o Vav2Onc EpSC rep3


title: 12-m-o Vav2Onc EpSC rep3


title: 6-m-o Vav2Onc EpSC rep2


title: 12-m-o Vav2Onc EpSC rep1


title: 4-m-o Vav2Onc EpSC rep3

source_name: Epidermal stem cells from Vav2Onc 4-m-o mice

value: 4 months


title: 4-m-o Vav2Onc EpSC rep1


title: 1-m-o Vav2Onc EpSC rep2

source_name: Epidermal stem cells from Vav2Onc 1-m-o mice

value: 1 month


title: 2.5-m-o Vav2Onc EpSC rep1


title: 1-m-o Vav2Onc EpSC rep3


title: Amb 24h 1

description:
24 hour Amb 1
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: CO2 8h 2

description:
8 hour C02 2
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 4-m-o Vav2Onc EpSC rep2


title: CO2 8h 3

description:
8 hour C02 3
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 2.5-m-o Vav2Onc EpSC rep2


title: 0.6-m-o Vav2Onc EpSC rep2

source_name: Epidermal stem cells from Vav2Onc 0.6-m-o mice

value: 18 days


title: Amb 8h 3

description:
8 hour Amb 3
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: Amb 8h 2

description:
8 hour Amb 2
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: CO2 8h 1

description:
8 hour C02 1
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 1-m-o Vav2Onc EpSC rep1


title: CO2 4h 2

description:
4 hour C02 2
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: CO2 4h 3

description:
4 hour C02 3
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 0.6-m-o Vav2Onc EpSC rep1


title: somatic cells from procine antral follicle 1

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger Single-Cell Software Suite (v6.0.2, 10X Genomics)
Assembly: Sscrofa 11.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: ovary

growth_protocol: a 210-day-old pubertal Landrace  Yorkshire pig that was grown up in natural envrionment

extract_protocol:
the ovaries were carefully extracted from the gilts at a local slaughterhouse and promptly transferred to the laboratory within 2 hours, maintaining a temperature-controlled environment using iced 0.1% DEPC PBS. Healthy antral follicles with a diameter exceeding 7 mm were subjected to a 1% Penicillin-Streptomycin PBS wash. Subsequently, the follicles were punctured, and the follicular fluid was flushed into a 60 mm petri dish. Cumulus-oocyte complexes (COCs) were mechanically isolated through aspiration using 29 G needles, followed by gentle pipetting in 0.1% hyaluronidase enzyme and subsequent washing with DPBS.  The isolated granulosa cells suspended in the resulting fluid were centrifuged at 2000 rpm for 5 min, and the supernatant was discarded. The pellet was then resuspended in 100 μL DPBS. Single-cell suspensions were processed into barcoded scRNA libraries using the 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1, following standardized protocols.
library construction was carried out according to the manufacturer's instructions (10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1).

value: ovary

value: somatic cells


title: 12-m-o WT EpSC rep3

source_name: Epidermal stem cells from WT 12-m-o mice


title: Amb 4h 3

description:
4 hour Amb 3
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: CO2 4h 1

description:
4 hour C02 1
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: Amb 8h 1

description:
8 hour Amb 1
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: stD1

city: Yaan

first: Yongliang

last: Fan

address: 36 Xinkang Road

institute: Sichuan Agricultural University

data_processing:
Raw FASTQ files and histology images were processed by sample with the Space Ranger (version spaceranger-1.2.0, 10X Genomics) software with default parameters. The filtered gene-spots matrix and the fiducial-aligned low-resolution image was used for down-streaming data analyses (Seurat v4.3.0).
Assembly: Sscrofa11.1 reference genome
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx
Library strategy: Spatial Transcriptomics

source_name: stRNA data of PI2

extract_protocol: Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics)

value: mammary gland

value: 2 days post natural involution


title: 0.6-m-o Vav2Onc EpSC rep3


title: 12-m-o WT EpSC rep2


title: 235H5_DPP4_POS

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description: PI- CD31- CD45- Sca1+ DPPIV+

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Assembly: mm10
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: Tibialis Anterior

extract_protocol:
Mice were initially anesthetized via intraperitoneal injection of 2,2,2-tribromoethyl alcohol (Aldrich T4840-2). Following removing the fascia, skeletal muscle from both hindlimbs of the mice were then carefully dissected. A mixture of Collagenase D (Roche; 1.5 U ml-1; # 11088882001) and Dispase II (Roche; 2.4 U ml-1; # 04942078001), and 10mM CaCl2 was added to the samples and was incubated at 37°C for 60 minutes. During the incubation period, the muscle mixtures were vortexed initially and then once every 20 minutes, for a total of four times. Preparations were passed through a 40μm cell strainer (Falcon™, # 352340) and washed with PBS. This filtration created a single suspension of cells which was then centrifuged for 7 minutes at 550g. Following antibody staining, sorting was performed using Influx cell sorter (Becton Dickinson). RNeasy Micro Kit (Qiagen, # 74004) was used to isolate RNA from sorted cells. 10 μ of 2β-mercaptoethanol was added to 1mL of the buffer RLT (lysis buffer) before use.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Paired-end sequencing was performed on the Illumina NextSeq 2000 using the P2 100 cycle Kit (Illumina).

value: CSF1R inh/wd D3

value: DPPIV+ FAPs

value: Wild-type mice subjected to 3 weeks of CSF1R inhibition followed by 3 days of a regular diet


title: stA1

source_name: stRNA data of G90

value: day 90 gestation


title: 6-m-o WT EpSC rep3

source_name: Epidermal stem cells from WT 6-m-o mice

value: WT


title: 235H5_DPP4_NEG

description: PI- CD31- CD45- Sca1+ DPPIV-

treatment_protocol: 3 weeks of CSF1R inhibition followed by 3 days of a regular diet

value: DPPIV- FAPs


title: somatic cells from porcine antral follicle 2

description: 10x Genomics


title: 12-m-o WT EpSC rep1

value: 12 months


title: 6-m-o WT EpSC rep2

value: Stem cells from the epidermis


title: Amb 4h 2

description:
4 hour Amb 2
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx

value: wild-type

value: Ambient air


title: 231H6_DPP4_NEG

description: PI- CD31- CD45- Sca1+ DPPIV-


title: K562.LTR2.etoposide.B3

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection and subjected for 1 round of etoposide treatment and recovery bioreplica 3

data_processing:
Only paired-end raw reads with the read 2 starting with LTR tag “GCCTTGTGTGTGGTAGATCCACAGATCAAGGATATCTTGTCTTCGTTGGGAGTGAATTAGCCCTTCCA” and each base of each read having Phred quality score > 20 were selected.
Such reads were aligned to the GRCh37/hg19 using BWA-MEM (v0.7.12) with default settings.
Only read-pairs where both read 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
The insertion position was defined as the first base upstream of the LTR tag in the read 2.
Read count of each insertion position was calculated and normalized to total number of uniquely aligned reads of each sample.
Assembly: GRCh37/hg19
Supplementary files format and content: Processed data are in BED files containing coordinates of lentivirus insertion sites. The 5th column shows the normalized count of each insertion position.

growth_protocol: Human liver hepatocellular carcinoma cell line HepG2 and human chronic myeloid leukemia cell line K562 were maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (ExCell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco) at 37℃ in 5% CO2.

extract_protocol:
DNA was isolated with TIANamp Genomic DNA Kit (Tiangen)
1 μg of genomic DNA was used as the template for a linear PCR in a 50 μl reaction system containing 1x Taq Buffer, 2.5 U Taq DNA polymerase (Tiangen), 4 μl of 2.5 mM dNTP mix (Takara), and 0.3 μM biotinated primer 3-LTR_prime (5’-biotin-GCTCAACTGGTACTAGCTTGTAGCACCATCC-3’), which anneals to the 3’ LTR region of the lentivirus vector. 50 cycles of linear PCR were performed with 2.5 U Taq DNA polymerase (Tiangen) added at the beginning and immediately after 25 cycles of the reaction. PCR conditions were as follows: 94℃ for 5 min; 50 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 5 min. After the linear amplification, the PCR products were mixed with 10 μl of BeaverBeadsTM Streptavidin (Beaver) and incubated for 2 h at room temperature with shaking (400 rpm) in a metal bath. Beads were then collected with a magnetic stand and washed with 300 μl Binding/Wash buffer (10 mM Tris-HCl (pH 7.5), 1 M NaCl, 1 mM EDTA, 0.1% Tween-20) for 6 times, and with 65°C H2O for twice. For the second strand synthesis, beads were resuspended in a 24 μl reaction volume containing 1x Klenow Fragment Buffer (NEB), 2 μl of 2.5 mM dNTP mix (Takara), 6.25 μM P5_N6 primer (5’-CTACACGACGCTCTTCCGATCTNNNNNN-3’) and pre-incubated at 15℃ for 20 min. Then, 2 U of Klenow polymerase (NEB) were added and the mixtures were incubated at the following conditions: slow ramp at 0.5℃ per minute from 15℃ to 25℃ followed by 30 min incubation; then slow ramp at 0.5℃ per minute to 37℃ followed by 1 h incubation. Beads were captured with a magnetic stand and washed gently with 300 μl of 4℃ water. To construct the library for NGS, nested PCR was performed. First, beads were resuspended in a 25 μl PCR reaction volume containing 1x Taq Buffer, 1.25 U Taq DNA polymerase (Tiangen), 2 μl of 2.5 mM dNTP mix (Takara), 0.5 μM of primer P5 (5’-CTACACGACGCTCTTCCGATCT-3’) and 0.5 μM of primer 3-LTR_Nest (5’-CCTGGTGTGTAGTTCTGCCAATCAG-3’). PCR conditions were as follows: 94℃ for 3 min; 20 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 7 min. Second, 5 μl of the PCR products from the previous step were used for the next round of PCR in 50 μl volume containing 1x Taq Buffer, 2.5 U Taq DNA polymerase (Tiangen), 4 μl of 2.5mM dNTP mix (Takara), 0.4 μM of primer Illumina_P5 (5’-AATGATACGGCGACCACCGAGAtctACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 μM of primer Illumina_P7-3LTR (5’- CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCTTGTGTGTGGTAGATCCACAG-3’). PCR conditions were as follows: 94℃ for 3 min; 15 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 7 min. PCR products were purified with 1.2x volumes of VAHTS DNA Clean Beads (Vazyme) to a final volume of 21 μl. The concentration of PCR products was measured by Qubit 3.0 fluorometer using Equalbit dsDNA HS Assay Kit (Vazyme). To achieve a better coverage, five libraries were prepared in parallel from 1 μg of genomic DNA and pooled together.

value: human chronic myeloid leukemia cell

tag: transfection

value: lentiviral insertional mutagenesis library


title: 6-m-o WT EpSC rep1

value: 6 months


title: Amb 4h 1

description:
4 hour Amb 1
Supplemental Table 3 - H99 CO2-Amb RNA-Seq time course.xlsx
gene_count_matrix_time_course.xlsx


title: 4-m-o WT EpSC rep2

source_name: Epidermal stem cells from WT 4-m-o mice

value: 4 months


title: MZM_0403_male6_d287_skin

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4.
The RNA sequencing reads were aligned to the N. furzeri genome assembly (assembly version Nfu_20150522, gene annotation version 150922)  using STAR 2.5.1b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique) (PMID: 23104886).
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 under default settings (PMID: 24227677).
Assembly: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de) (PMID: 26638077)
Supplementary files format and content: csv file containing raw read counts per gene over all samples

organism: Nothobranchius furzeri

source_name: skin

extract_protocol:
Brain and skin tissue samples were prepared from each specimen and RNA was extracted using the RNeasy Mini Kit (Quiagen).
Library preparation was done using Illumina’s TruSeq RNA v2 kit following the manufacturer’s instruction.

value: skin

tag: Sex

value: male

tag: age in_days


title: MZM_0403_male6_d287_brain

source_name: brain

value: brain


title: K562.LTR2.etoposide.B1

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection and subjected for 1 round of etoposide treatment and recovery bioreplica 1


title: MZM_0403_male5_d287_skin


title: K562.LTR2.imatinib.B3

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection and subjected for 5 rounds of imatinib treatment and recovery bioreplica 3


title: K562.LTR2.imatinib.B2

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection and subjected for 5 rounds of imatinib treatment and recovery bioreplica 2


title: K562.LTR2.imatinib.B1

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection and subjected for 5 rounds of imatinib treatment and recovery bioreplica 1


title: 2.5-m-o WT EpSC rep3

description: Gene expression data from epidermal stem cells

source_name: Epidermal stem cells from WT 2.5-m-o mice

value: 2.5 months


title: K562.LTR2.etoposide.B2

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection and subjected for 1 round of etoposide treatment and recovery bioreplica 2


title: 4-m-o WT EpSC rep3


title: 4-m-o WT EpSC rep1


title: K562.LTR2.control.B3

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection bioreplica 3


title: 231H6_DPP4_POS

description: PI- CD31- CD45- Sca1+ DPPIV+

value: CSF1R inh/wd D3

value: DPPIV+ FAPs


title: MZM_0403_male5_d287_brain


title: brain, RNAi, prp19, r6

city: Philadelphia

first: Dong

last: Li

state: PA

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

data_processing:
aligned onto the BDGP6 fly reference genome
features were counted by featureCounts
DESeq2 was then used to detected differentially expressed genes
Assembly: BDGP6 fly reference genome
Supplementary files format and content: tabl-delimited text file includes raw coutns for each sample

organism: Drosophila melanogaster

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen)
RNA libararies were prepared using Illumina TruSeq Library Prep Kit folloiwing manufacturer's protocols

value: prp19 RNAi


title: MZM_0403_male4_d287_skin


title: brain, RNAi, prp19, r5


title: 2.5-m-o WT EpSC rep2

value: WT


title: K562.LTR2.control.B1

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection bioreplica 1


title: brain, RNAi, prp19, r4


title: brain, RNAi, prp19, r3


title: MZM_0403_male4_d287_brain


title: 1-m-o WT EpSC rep3

source_name: Epidermal stem cells from WT 1-m-o mice

value: 1 month


title: 1-m-o WT EpSC rep2


title: 1-m-o WT EpSC rep1


title: K562.LTR2.control.B2

description: K562 insertional mutagenesis cell library grown for 3 months after lentivirus transfection bioreplica 2


title: brain, RNAi, prp19, r2


title: 2.5-m-o WT EpSC rep1


title: 0.6-m-o WT EpSC rep3

source_name: Epidermal stem cells from WT 0.6-m-o mice

value: 18 days


title: brain, RNAi, u2af50, r6

value: u2af50 RNAi


title: brain, RNAi, prp19, r1


title: MZM_0403_male3_d287_skin


title: brain, RNAi, u2af50, r5


title: AcinarCer18w_rep2

data_processing:
Read Trimming Fastq files containing ATAC-seq paired-end reads were trimmed for both base quality (q <=15) and Illumina adaptor sequences using TrimGalore v0.4.4
Alignment Trimmed reads were mapped to the mm9 mouse genome and BAMs were generated using Bowtie2 v2.3.4.1
Sorting and indexing BAMs were sorted and indexed using Samtools v1.8
Remove duplicates PCR Duplicates were removed using Picard MarkDuplicates v2.16
Peak-calling Peak calling was performed using MACS2 v2.1.2
Peak aggregation The peaks from all samples were then were merged within a 500 bp window to create a full peak atlas using in house bash and python scripts
Counting reads Raw read counts were tabulated over this peak atlas using FeatureCounts v1.6.3
Generation of normalized abundance measurements The raw read counts were normalized using the median of ratios normalization method in DESeq2 v1.22.2
Assembly: mm9
Supplementary files format and content: bigwig files

source_name: Pancreas

extract_protocol:
tdTomato+ acinar cells were FACS sorted. Standard ATAC-seq protocol was followed (Buenrostro et al. 2013).
Illumina Nextera kit

tag: biological context

value: Pancreatitis

tag: recovery duration

value: 18 weeks


title: MZM_0403_male2_d287_skin


title: brain, RNAi, u2af50, r3


title: MZM_0403_male2_d287_brain


title: AcinarCer18w_rep1


title: brain, RNAi, u2af50, r4


title: brain, RNAi, u2af50, r2


title: brain, RNAi control 3

value: wild type


title: MZM_0403_male1_d287_skin


title: brain, RNAi control 1


title: brain, RNAi control 2


title: brain, RNAi, u2af50, r1


title: 0.6-m-o WT EpSC rep2

value: Stem cells from the epidermis


title: right ventricular tissue, MCT3

city: Changsha

first: Yusi

last: Chen

state: Hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

data_processing:
Trimmed reads (trimmed 5', 3'-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis.
If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated.
Principal Component Analysis (PCA), Correlation Analysis, Pieplots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics.
Assembly: mm10
Supplementary files format and content: FASTA

organism: Rattus norvegicus

source_name: right ventricular tissue

extract_protocol:
Six right ventricular tissue samples from PAH and normal rats were used to obtain total RNA using the manufacturer's instructions and TRIzol (Invitrogen). Then, using a NanoDrop ND-1000 spectrophotometer, the amount of RNA was determined, and the integrity of the RNA was evaluated using denaturing agarose gel electrophoresis. The RNA samples were processed using the rtStar tsRNA Pretreatment kit (Cat# AS-FS-005, Arraystar) to eliminate changes like acetylation and methylation that might interfere with the construction of tiny RNA microarray libraries. To create a 3-OH end, whole RNA (100 ng) was first dephosphorylated. Following the manufacturer's recommendations, the labelled sample mixes were hybridized on an array using the Arraystar Small RNA Microarray.
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and PCR finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer. amplified fragments were extracted and purified from the PAGE gel. And amplification primers. Subsequently, ~134-160 bp

value: right ventricular tissue

tag: disease state

value: pulomonary arterial hypertension

value: monocrotaline


title: right ventricular tissue, MCT2


title: 0.6-m-o WT EpSC rep1


title: AcinarCer18w_rep3


title: right ventricular tissue, MCT1


title: MZM_0403_male1_d287_brain

value: male


title: MZM_0403_male3_d287_brain

value: brain


title: MZCS_0403_male2_d287_skin

value: skin


title: MZCS_0403_male2_d287_brain


title: MZCS_0403_male1_d287_skin


title: right ventricular tissue, control2

value: healthy control

value: saline


title: AcinarCer3w_rep5

value: 3 weeks


title: S8PB.EBV

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description: viral RNA

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) pipeline (v1.12.1).
Downstream analyses were mainly conducted with Seurat R package (v4.1.1).
Assembly: human: hg38; EBV: GCF_002402265.1
Supplementary files format and content: barcodes.tsv:
Supplementary files format and content: genes.tsv
Supplementary files format and content: matrix.mtx

organism: human gammaherpesvirus 4

source_name: peripheral blood

extract_protocol:
Individual cells were isolated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare) and washed with Ca/Mg-free PBS. After removal of red blood cells, the remaining were isolated by centrifuged at 400g for 10 min at 4°C. The supernatant was discarded and the cells were resuspended by phosphate buffered saline to obtain single-cell suspension, which were then loaded onto microwell chip using the Singleron Matrix®Single Cell Processing System.
The scRNA-seq libraries were constructed according to the protocol of the FocuSCOPE® Single Cell mRNA x EBV Library Kit (Singleron).

value: peripheral blood

tag: cell type_enrichment

tag: disease

tag: subject

value: subject 8


title: AcinarCer3w_rep2

first: Rohit

last: Chandwani

address: 413 East 69th St, BRB 1360G

value: WT


title: right ventricular tissue, control3

tag: tissue


title: AcinarCer3w_rep3


title: AcinarCer2d_rep1

value: 2 days


title: MZCS_0403_female7_d287_skin

value: female


title: AcinarCer3w_rep4

value: Pancreatitis


title: right ventricular tissue, control1

tag: treatment


title: S8BM.EBV

description: viral RNA

source_name: bone marrow

value: bone marrow


title: MZCS_0403_male1_d287_brain


title: Acinar_rep5

value: Inflammation-naive


title: Acinar_rep4


title: Acinar_rep3


title: MZCS_0403_female6_d287_skin


title: Acinar_rep2


title: S7BM.EBV

description: viral RNA

value: subject 7


title: Acinar_rep1


title: HCC without metastasis sample 3

city: 成都

first: xiangnan

last: teng

address: 四川大学华西医院

institute: 四川大学华西医院

description:
HCC tissues didn't exhibited pathological features of metastasis.
Y3_(HTA-2_0).1.sst-rma-gene-full

hyb_protocol: Ssample was hybridized to the Affymetrix Human Gene 1.0ST Array for 16-18 h at 45°C.

scan_protocol: The microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450. Microarrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner  3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek® Genomics Suite 6.6. Values presented are log2 RMA signal intensity. Normalized data were further analyzed using one-way ANOVA to screen out the differential expression gene.

label: Biotin

source_name: HCC without metastasis sample

label_protocol: A total of 500 ng RNA was used for a double-round of cDNA synthesis. After fragmentation of 2nd-cycle single-stranded cDNA (ss-cDNA), sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT).

extract_protocol: Total RNA was extracted by Trizol/Chloroform, and then purified with magnetic beads of Agencourt Ampure (APN 000132, Beckman Coulter).

value: HCC

tag: tissue type

value: HCC without metastasis


title: HCC without metastasis sample 1

description:
HCC tissues didn't exhibited pathological features of metastasis.
Y1_(HTA-2_0).1.sst-rma-gene-full


title: HCC with metastasis sample 3

description:
HCC tissues exhibited pathological features of metastasis included microvascular invasion, vascular thrombosis, portal vein tumor thrombosis, intra-hepatic metastasis, lymphatic metastasis and extra-hepatic infringement.
W3_(HTA-2_0).1.sst-rma-gene-full

source_name: HCC with metastasis sample

value: HCC with metastasis


title: AcinarCer2d_rep2

city: New York

institute: Weill Cornell Medicine

tag: genotype


title: HCC with metastasis sample 1

description:
HCC tissues exhibited pathological features of metastasis included microvascular invasion, vascular thrombosis, portal vein tumor thrombosis, intra-hepatic metastasis, lymphatic metastasis and extra-hepatic infringement.
W1_(HTA-2_0).1.sst-rma-gene-full


title: HCC with metastasis sample 2

description:
HCC tissues exhibited pathological features of metastasis included microvascular invasion, vascular thrombosis, portal vein tumor thrombosis, intra-hepatic metastasis, lymphatic metastasis and extra-hepatic infringement.
W2_(HTA-2_0).1.sst-rma-gene-full


title: HCC without metastasis sample 2

description:
HCC tissues didn't exhibited pathological features of metastasis.
Y2_(HTA-2_0).1.sst-rma-gene-full


title: MZCS_0403_female6_d287_brain

value: brain


title: CP_wt_C3W_4

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the mouse reference genome (mm9) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M1) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Differentially expressed genes (DEG) were determined with limma-voom.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

extract_protocol:
tdTomato+ acinar cells were FACS sorted into 1.5 mL Eppendorf tubes containing Trizol. Total RNA was purified using a standard phenol-chloroform extraction method.
Sequencing libraries were constructed using Illumina TruSeq Library Prep Kit (Non-Stranded and Poly-A selection) and sequenced on either Illumina HiSeq 2500 or NovaSeq 6000 (2x50 cycles paired-end run)

tag: agent

value: Caerulein


title: MZCS_0403_female7_d287_brain


title: S6BM.EBV

description: viral RNA

value: EBV-HLH

value: subject 6


title: CP_wt_C3W_3

value: 3 weeks


title: S6PB.EBV

description: viral RNA

value: peripheral blood


title: scC1

data_processing:
Sequencing data were processed using the CeleScope v1.1.7 pipeline (Singleron).
Assembly: Sscrofa11.1 reference genome
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx

source_name: scRNA data of L20

extract_protocol: GEXSCOPETM Single-Cell RNA Library Kit

value: mammary gland

tag: time

value: day 20 lactation


title: Ewing sarcoma ES-049

city: Utrecht

first: Lindy

middle: L.

last: Visser

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Paediatric Oncology

data_processing:
Cell barcodes and UMI were extracted from read 1 using the Sharq pipeline Version 1.0
Mapping was performed using STAR version 2.6.1
Count tables were generated using the Sharq pipeline Version 1.0
Assembly: Genome Reference Consortium GRCh38
Supplementary files format and content: Raw count matrix for all genes and all cells of each plate.

source_name: Ewing sarcoma primary tissue

extract_protocol:
The primary EwS material was minced using scalpels and mechanically disrupted by pipetting up and down. Single cells were taken off and kept apart on ice. Left over tissue clumps were digested at 37C using digestion buffer, containing basal medium supplemented with 1 mg/mL Collagenase1A and 100 U/mL DNAse I for three 10 min rounds; after each round, single cells were collected and kept on ice and fresh digestion buffer was added to the left-over clumps. After digestion, Red Blood Cell lysis buffer was applied for 5 min to lyse the red blood cells. The single cells were washed with FACS buffer, containing PBS supplemented with 2% FCS, 2 mM EDTA and 100 U/mL DNAse I. The cells were stained for 30 min with Human CD45 PE-conjugated Antibody in FACS buffer. Prior to sorting, single cell suspensions were stained in 5μM DRAQ5 and 1 µM DAPI. Viable single cells (and/or CD45-/+ cells) were sorted into 384-well plates  containing 10 µL of mineral oil and 50 nL of RT primers.
Libraries were prepared using the CEL-Seq2 method.

value: Ewing sarcoma primary tissue


title: CP_wt_S

tag: strain

value: WT


title: CP_wt_S_2


title: S7PB.EBV

description: viral RNA

value: healthy control


title: Ewing sarcoma ES-048


title: MZCS_0403_female5_d287_skin

value: skin

value: female


title: CP_wt_C3W_2

value: Pancreatitis


title: MZCS_0403_female5_d287_brain


title: S5BM.EBV

description: viral RNA

value: bone marrow

value: CAEBV

value: subject 5


title: S5PB.EBV

description: viral RNA


title: scA1

source_name: scRNA data of L0

value: day 0 lactation


title: S4TPB.EBV

description: viral RNA

value: hematopoietic stem cell transplantation

value: subject 4


title: MZCS_0403_female4_d287_brain

value: brain


title: MZCS_0403_female4_d287_skin


title: MZCS_0403_female3_d287_skin


title: S4TBM.EBV

description: viral RNA


title: Ewing sarcoma ES-162


title: snE1

molecule: nuclear RNA

source_name: snRNA data of PI7

extract_protocol: GEXSCOPE® Single NucleusRNA-seq Kit

value: 7 days post natural involution


title: snE2


title: MZCS_0403_female3_d287_brain


title: S4PB.EBV

description: viral RNA

value: peripheral blood


title: Ewing sarcoma ES-039 plate 2 + Ewing sarcoma ES-030 cryo


title: snD2

source_name: snRNA data of PI2

value: mammary gland

value: 2 days post natural involution


title: MZCS_0403_female5_d217_skin


title: Ewing sarcoma ES-046

value: Ewing sarcoma primary tissue


title: snD1


title: S4BM.EBV

description: viral RNA


title: S3PB.EBV

description: viral RNA

value: subject 3


title: snC2

source_name: snRNA data of L20

value: day 20 lactation


title: MZCS_0403_female5_d217_brain


title: S4HC.EBV

description: viral RNA


title: snB2

source_name: snRNA data of L0


title: MZCS_0403_female4_d217_brain

source_name: brain


title: snB1


title: S3HC.EBV

description: viral RNA


title: Ewing sarcoma ES-042-L1 plate 2


title: Ewing sarcoma ES-042-L2 plate 2


title: S3BM.EBV

description: viral RNA


title: snC1


title: Ewing sarcoma ES-042-L1 plate 1


title: Ewing sarcoma ES-042-L2 plate 1


title: MZCS_0403_female3_d217_brain


title: MZCS_0403_female2_d217_skin

source_name: skin

value: skin


title: snA1

source_name: snRNA data of G90

value: day 90 gestation


title: Ewing sarcoma ES-039 plate 1


title: Ewing sarcoma ES-006-L2


title: MZCS_0403_female2_d217_brain

value: female


title: snA2


title: MZCS_0403_female4_d217_skin


title: Ewing sarcoma ES-036


title: MZCS_0403_female1_d217_skin


title: MZCS_0403_female3_d217_skin


title: MZCS_0403_female1_d217_brain


title: Ewing sarcoma ES-034


title: Ewing sarcoma ES-030 fresh plate 3


title: Ewing sacoma ES-006-L1


title: Ewing sarcoma ES-030 fresh plate 2


title: MZM_0403_female5_d147_brain


title: MZM_0403_female5_d147_skin


title: MZM_0403_female4_d147_skin


title: iT - BCMA CAR + hnCD16 replicate 2

city: San Diego

first: Eigen

last: Peralta

state: CA

address: 12278 Scripps Summit Drive

institute: Fate Therapeutics Inc. (FHQ1)

hyb_protocol: 100 ng of total RNA were hybridized with the Reporter CodeSet and Capture ProbeSet of the Human Immunology V2 Panel (NanoString Technologies): in a C1000 Touch Thermal Cycler (Bio-Rad) all samples were incubated with 5 μL Hybridization Buffer, 3 μL Reporter Codeset, and 2 μL Capture ProbeSet at 65 °C for 16 hours

scan_protocol: Data collection was performed using the nCounter Digital Analyzer at maximum resolution

data_processing: The nSolver Analysis Software 4.0 (NanoString Technologies) was used for data QC and normalization (background substraction, standard normalization to positive controls)

label: biotin/fluorescence

source_name: TiPSC-derived iT cells

label_protocol: not provided

extract_protocol: Total RNA was isolated from 5e+6 cells using the RNeasy Micro Kit (QIAgen)

treatment_protocol: cell cryo vials of indicated samples were thawed in Optimizer Media, spun down at 500xg for 5 min at 4°C and resuspended in RLT buffer

tag: cell type

value: TiPSC-derived iT cells

tag: source

value: Fate Therapeutics

tag: cryo vial

value: cryo vial

tag: engineering design

value: BCMA CAR + hnCD16


title: iT - BCMA CAR + hnCD16 + NYESO TCR replicate 1

value: BCMA CAR + hnCD16 + NYESO TCR


title: iT - BCMA CAR + hnCD16 + MR1 TCR replicate 1

value: BCMA CAR + hnCD16 + MR1 TCR


title: iT - BCMA CAR + hnCD16 + NYESO TCR replicate 2


title: Brain, CS, rep1

city: Bangalore

first: Jsmine

last: Kaur

state: Karnatka

address: GKVK Campus

department: Biological Sciences

country: India

institute: NCBS

data_processing:
Raw files (FASTQ files) were run for quality check using FASTQC.
Bowtie2 to convert fastq to SAM file. Then samtools were used to convert SAM file to BAM file
PCR duplicates and mitochondrial reads were removed
bamCoverage was used to convert bam file to bigwig file
BigWig files are a compressed, indexed, binary format for genome-wide signal data(Pohl et al., 2014)
Assembly: UCSC dm6
Supplementary files format and content: bigwig file

source_name: Brain

growth_protocol: Drosophila strains were reared on standard cornflour agar media consisting of 80 g corn flour, 20 g glucose, 40 g sugar, 15 g yeast extract, 4 ml propionic acid, 5 ml p-hydroxybenzoic acid methyl ester in ethanol, 5 ml ortho butyric acid in 1l at 25°C under a 12:12 hr light: dark cycle.

extract_protocol:
Following brain dissections and spin down. Tissue samples were lysed to isolate nuclei. Nucle integrity examined and proceeded for transposition reaction before amplification and generation of libraries.
Purification of DNA fragments after transposition, PCR amplification using Nextera DNA CD indexes

treatment_protocol: Brain dissections from adult 2-5 days old CS. Nuclei isolated from dissected brain

value: Brain

tag: age

value: 2-5 days old adult

value: CS


title: iT - BCMA CAR + hnCD16 replicate 1


title: TiPSC

source_name: TiPSC

value: TiPSC


title: Brain, CS, rep2


title: Ewing sarcoma ES-030 fresh plate 1


title: MZM_0403_female4_d147_brain

value: brain

tag: Sex

tag: age in_days


title: Ewing sarcoma ES-027 plate 2

value: Ewing sarcoma primary tissue


title: TMZ320EA35

city: Bonn

first: Anastasiia

last: Shcherbakova

state: NRW

address: Sigmund-Freud-Straße, 25

institute: University Clinic Centre Bonn, Medical Clinic III

description: HiSeq2500 V4 in High Input Mode

data_processing:
trimming with cuting bases off the start and the end of a read, if below of threshold quality
Alignment with the HISAT2
Quantification with the htseq-count
Assembly: hg38
Supplementary files format and content: matrix of non-normalized counts

growth_protocol: U-87 cells were grown in Minimum Essential Medium with L-glutamine (MEM) supplemented with 10% Fetal Bovine Serum (FBS), penicillin (100 IU/ml) / streptomycin (100µg/ml), 1mM sodium pyruvate, and 0.1 mM non-essential amino acids

extract_protocol:
RNA was extracted using the RNeasy MiniPlus kit (QIAGEN) according to the manufacturer’s instruction. The amount and purity of RNA was measured by nanodrop as described earlier (37,42). The ratio of absorbance of RNA at 260 nm to the one of RNA at 280 nm was used as indicator of RNA purity. All samples were between 1.99 and 2.05 which accepted as pure. 100 ng/µl were used for the RNA-sequencing.
The enrichment was performed by QuantSeq 3´-mRNA Library Prep/ Lexogen

treatment_protocol: Cells (106 cells/well) were seeded in 6-wellplates and stimulated for 24 h with the following treatments: 1) EA (30 µM); 2) EA (45 µM); 3) TMZ (600 µM); 4) EA (20 µM) + TMZ (380 µM); 5) EA (20 µM) + TMZ (580 µM); 6) EA (35 µM) + TMZ (320 µM)

tag: cell line

value: glioblastoma

value: evernic acid at 35 uM + temozolomide at 320 uM


title: TMZ380EA20

description: HiSeq2500 V4 in High Input Mode

value: evernic acid at 20 uM + temozolomide at 380 uM


title: TMZ600

description: HiSeq2500 V4 in High Input Mode

value: temozolomide at 600 uM


title: EA45

description: HiSeq2500 V4 in High Input Mode

value: evernic acid at 45 uM


title: MZM_0403_female3_d147_skin

value: skin

value: female


title: CD8+ T

source_name: CD8+ T

value: CD8+ T

value: commercially available

value: cryo vial, StemCell Technologies, Cat.no. 200-0164


title: EA30

description: HiSeq2500 V4 in High Input Mode

value: evernic acid at 30 uM


title: Ewing sarcoma ES-027 plate 1


title: TMZ580EA20

description: HiSeq2500 V4 in High Input Mode

value: evernic acid at 20 uM + temozolomide at 580 uM


title: Macrophage

source_name: Macrophage

value: Macrophage

value: cryo vial, StemCell Technologies, Cat.no. 70042


title: Control3

description: HiSeq2500 V4 in High Input Mode

value: no


title: Control2

description: HiSeq2500 V4 in High Input Mode


title: Monocyte

source_name: Monocyte

value: Monocyte

value: cryo vial, StemCell Technologies, Cat.no. 70035.1


title: CD56+ NK

source_name: CD56+ NK

value: CD56+ NK

value: cryo vial, StemCell Technologies, Cat.no. 70037


title: Control1

description: HiSeq2500 V4 in High Input Mode

value: glioblastoma


title: MZM_0403_female2_d147_brain

value: brain


title: iT - BCMA CAR + hnCD16 + MR1 TCR replicate 2

value: TiPSC-derived iT cells

value: Fate Therapeutics

value: cryo vial

value: BCMA CAR + hnCD16 + MR1 TCR


title: Ewing sarcoma ES-025 plate 2

value: Ewing sarcoma primary tissue


title: U2AF2 R150C knockin, c4

data_processing:
aligned onto the human reference genome
features were counted by featureCounts
DESeq2 was then used to detected differentially expressed genes
Assembly: GRCh37
Supplementary files format and content: tabl-delimited text file includes raw coutns for each sample

source_name: H9 human pluripotent stem cells

value: H9 human pluripotent stem cells

value: het U2AF2 R150C


title: Ewing sarcoma ES-016-biopsy

source_name: Ewing sarcoma primary tissue


title: MZM_0403_female1_d147_skin

value: skin

value: female


title: Ewing sarcoma ES-025 plate 1


title: MZM_0403_female1_d147_brain


title: U2AF2 R150C knockin, c3


title: Ewing sarcoma ES-026 plate 2


title: Neutrophil

source_name: Neutrophil

value: Neutrophil

value: commercially available

value: cryo vial, StemCell Technologies, Cat.no. 200-0384


title: U2AF2 R150C knockin, c2


title: HepG2 cells, 3D 8 days, Rep 3

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
Base-calling was generated using Illumina Real-Time Analysis (RTA) 1.18.54
The raw data in FASTQ format was processed using Salmon (https://doi.org/10.1038/nmeth.4197) with default settings and human transcriptome Homo_sapiens.GRCh38.cdna.all.fa.gz of ensembl release 98 to obtain transcript abundance.
Transcript abundance was summarized into read count per gene using tximport (doi:10.12688/f1000research.7563.1).
Assembly: Human GRCh38
Supplementary files format and content: tab-delimited text files include raw counts of reads per gene for each sample

source_name: Liver

growth_protocol: 2D growth: Commercially available HepG2 (human hepatocellular carcinoma cells) cells (ECACC, Porton Down, UK) were grown in minimal essential media (MEM) containing non-essential amino acids (ThermoFisher Scientific, Loughborough, UK), and supplemented with 2 mM glutamine (ThermoFisher Scientific) and 10 % Foetal Bovine Serum (FBS, ThermoFisher Scientific). Cultures were maintained in culture flasks (Greiner Bio-One, Kremsmünster, Austria) at 37 °C, 5% CO2 in a humidified environment. 3D growth: 5 mL of growth medium was added into the well of a 6 well culture plate to reach the bottom of the Alvetex® insert and 500 μL of growth medium was then added to the top of the membrane. Cells were seeded at a density of 1x10^6 cells per 6 well insert. Culture medium was changed every 2 days and after 8 days in culture, 3D cultures were either harvested for analysis or cells liberated for downstream analysis.

extract_protocol:
HepG2 cells were liberated from culture surfaces through trypsinisation and collected for extraction. Both cells and homogenised tissue was lysed using a commercially available kit: Qiagen RNeasy® mini plus (Qiagen, Hilden, Germany), and by following manufacturer’s instructions. RNA was quantified using a Nanodrop Spectrophotometer ND-100™.
NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional Library Prep Kit for Illumina (New England Biolabs, Massachusetts, USA) were used to create the libraries.

treatment_protocol: 2D growth was compared to 3D growth (protocol described above)

value: Liver

value: Hepatocyte (Hepatocellular Carcinoma)

value: WT

value: 3D cultured


title: HepG2 cells, 3D 8 days, Rep 4


title: HepG2 cells, 3D 8 days, Rep 2


title: Ewing sarcoma ES-026 plate 1


title: U2AF2 R150C knockin, c1


title: MZM_0403_female3_d147_brain

value: brain


title: MZCS_0403_male4_d147_brain

value: male


title: Ewing sarcoma ES-016-meta


title: Ewing sarcoma ES-024 plate 2


title: HepG2 cells, 3D 8 days, Rep 1


title: U2AF2 R149W knockin, c10

value: het U2AF2 R149W


title: MZCS_0403_male4_d147_skin


title: MZCS_0403_male3_d147_skin


title: MZM_0403_female2_d147_skin


title: U2AF2 R149W knockin, c9


title: Ewing sarcoma ES-024 plate 1


title: MZCS_0403_male3_d147_brain


title: HepG2 cells, 2D 8 days, Rep 4

value: 2D cultured


title: MZCS_0403_male1_d147_skin


title: HepG2 cells, 2D 8 days, Rep 3


title: HepG2 cells, 2D 8 days, Rep 2


title: U2AF2 R149W knockin, c7


title: ChIP_SMARCA4_IMR32_DMSO_rep1

city: Houston

first: H. Courtney

last: Hodges

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: SMARCA4 ChIP-seq in IMR32 cells treated with DMSO

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis.
All bigWig files are unscaled counts and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

growth_protocol: Cells were cultured in 10% FBS DMEM medium using standard approaches.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with either 1% formaldehyde and 2 mM disuccinimidyl glutarate (double cross-linking) for ASCL1, or 1% formaldehyde alone (single cross-linking) for all other targets. Protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either either DMSO or 1 uM BRM014 for 1 h

tag: chip antibody

value: Anti-SMARCA4, Proteintech #21634-1-AD, Lot 000928

value: DMSO


title: MZCS_0403_male1_d147_brain


title: U2AF2 R149W knockin, c6

value: H9 human pluripotent stem cells


title: ChIP_RARA_IMR32_DMSO_rep2

description: RARA ChIP-seq in IMR32 cells treated with DMSO

value: Anti-RARA, Abcam #ab41934 , LotGR329


title: ChIP_RARA_IMR32_BRM014_rep2

description: RARA ChIP-seq in IMR32 cells treated with BRM014


title: U2AF2 R149W knockin, c3


title: MZCS_0403_female5_d147_skin

value: skin


title: MZCS_0403_female5_d147_brain

value: female


title: U2AF2 R149W knockin, c4


title: GRZ_D_male6_d147_brain

value: GRZ-D


title: GRZ_D_male5_d147_skin


title: U2AF2 R149W knockin, c5


title: U2AF2 R149W knockin, c1


title: U2AF2 R149W knockin, c2


title: OXA-2

city: Gunagzhou

first: Zhaoliang

last: Yu

address: No. 26, Yuancun Erheng Road

institute: The sixth Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed  following STAR  instruction.
RSEM were used for counting
IGV and R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: colorectal adenocarcinoma cell lines

growth_protocol: DLD1 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: DLD1 cells were plated into 6-well plate 20 h before treated with oxaliplatin and volasertib.

value: OXA


title: ChIP_RARA_IMR32_BRM014_rep1


title: OXA+Vola-2

value: OXA+Vola


title: Vola-1

value: Vola


title: ChIP_RARA_IMR32_DMSO_rep1


title: ChIP_PHOX2B_IMR32_DMSO_rep2

description: PHOX2B ChIP-seq in IMR32 cells treated with DMSO

value: Anti-PHOX2B, Santa Cruz #sc376997, Lot Jo622


title: OXA+Vola-1


title: GRZ_D_male5_d147_brain


title: ChIP_PHOX2B_IMR32_BRM014_rep2

description: PHOX2B ChIP-seq in IMR32 cells treated with BRM014

value: WT


title: GRZ_D_male4_d147_skin


title: ChIP_PHOX2B_IMR32_DMSO_rep1


title: Vola-2


title: ChIP_SMARCA4_IMR32_DMSO_rep2


title: U2AF2 R149W knockin, c8


title: knockin, control 9

value: wild type


title: DMSO-2


title: knockin, control 10


title: OXA-1


title: DMSO-1


title: GRZ_D_male6_d147_skin


title: knockin, control 7


title: GRZ_D_male3_d147_brain

value: brain


title: ChIP_MYCN_IMR32_DMSO_rep1

description: MYCN ChIP-seq in IMR32 cells treated with DMSO

value: Anti-MYCN, Active Motif #61185, Lot 31511001


title: ChIP_MYCN_IMR32_BRM014_rep2

description: MYCN ChIP-seq in IMR32 cells treated with BRM014


title: GRZ_D_male3_d147_skin

value: male


title: ChIP_MYCN_IMR32_DMSO_rep2


title: ChIP_PHOX2B_IMR32_BRM014_rep1


title: HepG2 cells, 2D 8 days, Rep 1

value: Liver

value: Hepatocyte (Hepatocellular Carcinoma)

value: 2D cultured


title: GRZ_D_male4_d147_brain


title: knockin, control 8

value: H9 human pluripotent stem cells


title: GRZ_D_male2_d147_brain


title: ChIP_MYCN_IMR32_BRM014_rep1


title: knockin, control 5


title: knockin, control 6


title: ChIP_ISL1_IMR32_DMSO_rep1

description: ISL1 ChIP-seq in IMR32 cells treated with DMSO

value: Anti-ISL1, DSHB mix of #40.2D6 Lot 1, #39.4D5 Lot 1, #39.3F7 Lot 1, and #40.3A4 Lot 1

value: DMSO


title: GRZ_D_male1_d147_skin

value: skin


title: knockin, control 3


title: AcinarCer6w_rep2

source_name: Pancreas

tag: biological context

value: Pancreatitis

tag: recovery duration

value: 6 weeks


title: ChIP_ISL1_IMR32_DMSO_rep2

tag: treatment


title: GRZ_D_male1_d147_brain

value: GRZ-D

tag: tissue