title: C_GY005371

data_processing:
Data was asses used FastQC and adapter sequences were trimmed
Data was aligned using STAR and counts generated using HT-seq count
Genome_build: GRCh38
Supplementary_files_format_and_content: A text file contained gene names alonside their respective count number

source_name: Skin biopsy

extract_protocol:
2mm biopsies were extracted from soles or palms of PPP patients or healthy controls and stored in RNAlater at -80. RNA was then extracted using a miRVana kit.
Samples were sent to GENEWIZ for library construction and sequencing. Briefly, polyA RNA was selected and seuqenced in 2 x 150bp confuguration

value: Skin biopsy

tag: skin type

value: Healthy


title: PPP01

status: Public on May 31 2022

type: SRA

city: London

first: Dan

last: McCluskey

address: Guy's Hospital

country: United Kingdom

institute: King's College London

library_source: transcriptomic

data_processing:
Sequencing output files were demultiplexed and coverted to fastq files using Cell Ranger v3.0.2 (10X genomics).
Cell Ranger was used to align demultiplexed reads to the reference genome, perform filtering, barcode counting, UMI counting and estimate the number of cells.
Data analaysis was performed in R using Seurat v3.
Genome_build: Ensembl release 86 and GRCh38.p7
Supplementary_files_format_and_content: For each sample there are three associated files: tab-seperated values file containing barcdoes, tab-separated file containing annotated genes (features), matrix file containing UMI counts and indices for the barcode and gene tsv files

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from the whole blood of either PPP patients or healthy controls and then cryopreserved until sequencing
Libraries were prepared using the Chromium 10X Single Cell 3'  reagent Kits v2 according to the manufacturer's instructions

tag: tissue

value: Peripheral blood mononuclear cells

tag: disease state

value: Palmoplantar pustulosis


title: C_GY004362

value: Healthy control


title: C_GY005158


title: DA-G20 - 15µM Copper(II), rep1

city: Rapid City

first: Rajesh

middle: Kumar

last: Sani

state: SD

address: 501 E St. JOSEPH STREET

department: Chemical and Biological Engineering

country: USA

institute: South Dakota School of Mines and Technology

description: Sample 7

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (version 0.38). Illuminaclip step was used to remove adapter sequences (TruSeq3 pair ended) from the reads. The raw reads were further filtered using a sliding window filtration to truncate reads at a 4-base average Q score of 20 or lower. The sequences greater than 20bp were retained.
Reads were mapped against Desulfovibrio alaskensis G20 reference genome (accession PRJNA329) using the HISAT2 alignment program (version 2.1.0) using default parameters. Paired-end files for each sample were used for alignment. The strand information was selected as unstranded.
Reads were assigned to features of type 'gene' in the input annotation grouped by gene_id in the reference genome using featureCounts (version 1.6.4) (Liao et al., 2014). The Desulfovibrio alaskensis G20 genome annotation file was downloaded from Ensembl. Strandedness was set to ‘unstranded’ and all other parameters were set to default.
DeSeq2 (version 1.22.1) was used to generate normalized counts and log2-Fold change for pairwise comparisons between control and treated samples..
Genome_build: GCA_000012665 (https://bacteria.ensembl.org/Desulfovibrio_alaskensis_g20_gca_000012665/Info/Index)
Supplementary_files_format_and_content: tab-delimited text files containing raw counts (counts obtained from featureCounts) for each gene in every sample.

molecule: total RNA

organism: Oleidesulfovibrio alaskensis

source_name: Bacterial culture

growth_protocol: Seed culture of strain DA-G20 was prepared by inoculating 1.5 mL of a frozen stock (40% v/v glycerol solution and cells grown in lactate-C medium) into 100 mL of deoxygenated lactate-C medium. Hydrogen sulfide (H2S) initially present in active inoculum was purged out using filter-sterilized ultrapure nitrogen for 1 hour. From this sparged culture, 5% v/v active inoculum (OD = 0.18) was used for Cu(II) toxicity experiments. For Cu(II) toxicity experiments, filter sterilized stock solution of 0.05M CuCl2 was prepared  and supplemented  to serum bottles containing 125mL lactate-C media to give the desired metal concentrations (5µM and 15µM). Total RNA was extracted from 10 ml of bacterial culture from the serum bottles on 5th day from different Cu(II) concentration.

extract_protocol:
Cell pellet was collected and washed three times with anaerobic phosphate buffer saline (pH 7.2). Total RNA was extracted  using TRIzol RNA extraction method and eluted in 20 µL nuclease free water. Extracted RNA was further purified using the RNA clean and concentrator kit following manufacturer’s instructions (Zymo Research, USA), and eluted in 10 µL nuclease free water.
1µg total RNA used for library preparation. The library preparation step consisted of the following steps: i) rRNA depletion by RiboCop rRNA Depletion Kit (Lexogen, New Hampshire, USA). cDNA library was prepared using Swift Rapid RNA Library kit using the manufacturers protocol (Swift Biosciences, Michigan, USA).

treatment_protocol: Sample 4, Sample 5, and Sample 6 were treated with 5µM CuCl2 for 5 days. And Sample 7, Sample 8, and Sample 9 were treated with 15µM CuCl2 for 5 days.

tag: strain

tag: cellular respiration

value: Anaerobic

tag: treatment

value: 15µM Copper(II)


title: C_GY004360


title: DA-G20 - 15µM Copper(II), rep2

description: Sample 8


title: DA-G20 - 5µM Copper(II), rep2

description: Sample 5

value: 5µM Copper(II)


title: DA-G20 - 5µM Copper(II), rep3

description: Sample 6


title: C_GY004358


title: C_GY004359


title: DA-G20 - 5µM Copper(II), rep1

description: Sample 4


title: NL_T045033

value: Non-lesional


title: DA-G20 - Control, rep3

description: Sample 3

value: No treatment (Control)


title: DA-G20 - Control, rep1

description: Sample 1


title: DA-G20 - Control, rep2

description: Sample 2


title: NL_T039148


title: NL_GY005467


title: NL_T041038


title: MAT2A-inhibited_rep3, RNA-Seq

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

data_processing:
The sequencing reads were trimmed to remove adapter sequence, quality checked and mapped to the bovine genome (bosTau8) using Tophat 2.0.14. The mapped reads were fed to Cufflinks 2.2.1 to calculate the FPKM values as expression levels.
Assembly: bosTau8
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by Cufflinks.

organism: Bos taurus

source_name: bovine morula

growth_protocol: Bovine morulae were in vitro produced by in vitro fertilization (IVF) and further cultured in mSOF up to day 6 (IVF = day 0).

extract_protocol: RNA-seq library was generated from three single morulae cultured in the control and MAT2A-inhibited (FIDAS-5-treated) groups, respectively, by using SMART-Seq HT PLUS Kit (Takara Bio USA) according to the manufacturer’s manual.

treatment_protocol: The culture was chemically semi-defined (bovine serum albumin was added) and performed under low oxygen tension (5%). The 8-16 cell stage embryos at 72 hpi (day 3 of IVF) were allocated to control (0.1% (v/v) DMSO, a vehicle of FIDAS-5) or MAT2A-inhibited (20 µM FIDAS-5) groups and further cultured up to day6 (144 hpi).

tag: sourse

value: in vitro produced, inhibitor (FIDAS-5) treated from the 8-16 cell stage

tag: day after ivf

value: day 6


title: MAT2A-inhibited_rep2, RNA-Seq


title: NL_GY005236


title: NL_GY001826


title: DA-G20 - 15µM Copper(II), rep3

description: Sample 9


title: L_GY005466

value: Lesional


title: L_GY004086


title: Control_rep3, RNA-Seq

value: in vitro produced, vehicle treated from the 8-16 cell stage


title: Control_rep1, RNA-Seq


title: MAT2A-inhibited_rep1, RNA-Seq


title: NL_T0450072


title: Control_rep2, RNA-Seq


title: L_GY005235


title: C_CY004357


title: Polyp 3

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

data_processing:
Basecalls performed by cellrange mkfastq (bcl2fastq_2.20)
CellRanger version 3.0.2 was used to align reads to GRCh38 and to generate feature-barcode matrices.
Data were read into R version 4.0.2 and analyzed using Seurat.  Low quality cells and potential doubets were filtered from the data.  Data from individual samples were normalized using the SCT method and integrated. Preliminary clustering was used to isolate data from epithelial cells / remove data from immune cells before final integration and clustering.
Assembly: GRCh38
Supplementary files format and content: Feature, barcode and matrix output files from CellRanger are provided as gzip files.
Supplementary files format and content: RDS R data set containing a Seurat object including epithelial cells from all samples as well as cell type assignments and other meta data.

source_name: sinus epithelial brush

growth_protocol: n/a freshly obtained sample

extract_protocol:
15 min with 0.25% trypsin
10X Single Cell 3’v3

tag: group

value: polyp


title: Polyp 5


title: Polyp 1


title: scATAC_SK-HEP-1

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

library_source: genomic

data_processing:
base-calling:  PISA(V0.4)
alignment: PISA(V0.4)
filtering:  PISA(V0.4)
cellCount:  PISA(V0.4)
peak-calling: macs2
Genome_build: STAR
Supplementary_files_format_and_content: .txt

molecule: genomic DNA

source_name: liver cancer cell line

growth_protocol: Cells were cultured in high glucose Dulbecco's modified Eagle's medium (DMEM) containing with 10% fetal bovine serum (FBS), 1% Penicillin-Streptomycin. 0.25% trypsin was used to digest cells.

extract_protocol:
scATAC-seq：Nuclei extraction was separated by mechanical extraction method and cells were lysed using lysis buffer and then centrifuged.
scATAC-seq: DNBelab C Series Single-Cell ATAC Library Prep Set (BGI-research, China) was used to prepare single-nucleus ATAC-seq libraries.

value: liver cancer cell line

tag: cell line

tag: library strategy

value: scATAC-seq


title: scRNA_HepG2

extract_protocol:
CITE-seq/scRNA-seq: Single cell was encapsulated into droplets and lysed in the droplet. mRNA and antibody-derived oligos were anneal to beads. After the reverse transcription procedure and PCR, the product was separated into ADTs and cDNA using Ampure Bead.
CITE-seq/scRNA-seq: DNBelab C Series High-throughput Single-cell System (BGI-research, China) was utilized for library preparation.

value: scRNA-seq


title: Polyp 4


title: scATAC_MHCC97L


title: scATAC_MHCC97H


title: Polyp 2


title: scATAC_HepG2


title: NL_GY004085

value: Skin biopsy


title: scCite_SK-HEP-1

data_processing:
Library strategy: CITE-seq
base-calling:  PISA(V0.4)
alignment: PISA(V0.4)
filtering:  PISA(V0.4)
cellCount:  PISA(V0.4)
peak-calling: macs2
Genome_build: STAR
Supplementary_files_format_and_content: .txt

value: CITE-seq


title: scCite_MHCC97L


title: scATAC_Huh7


title: 2W, Hashtags [2W_hto]

city: Minneapolis

first: Adam

last: Herman

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Cellranger 6.0.0  Data were read into R space using the Read10X tool and Seurat. A Seurat object file was then created using min.cells = 3, min.features = 200 settings.
Seurat object data were filtered to allow for focused analysis of singlets, CD4 T cells, and particular treatment groups (Gliadin, eLm, and select naïve samples for the gliadin-fed experiment 1;  3X, 6X, CT, and naïve samples for the 2W-fed experiment 2).
Seurat object reads were normalized using the sctransform method.
Differential gene expression was determined using the Seurat Principle Components Analysis, and visualized using Uniform Manifold Approximation and Projection (UMAP) dimension reduction (seurat_clusters).
Assembly: mm10-2020-A
Supplementary files format and content: Filtered Cellranger 6.0.0 data files (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) include nCount_RNA and nFeature_RNA values for each cell, barcode assignments, and as well gene expression features with Ensembl annotations. as seurat_clusters assignment
Supplementary files format and content: Tab-separated-value metadata files (gliadin_fed.tsv, 2W_fed.tsv) describe the Seurat cell-filtering scheme as well as provide seurat_clusters assignments for analyzed cells in 2 separate experiments.

organism: Mus musculus

source_name: sorted 2W peptide specific CD4 T cells

extract_protocol: NOT PROVIDED

tag: background strain

tag: genotype

value: wild-type

value: 3x 2W peptide fed mice, 6x 2W peptide fed mice, 3x 2W peptide plus cholera toxin fed mice, mice immunized with 2W peptide in CFA, untreated mice

tag: totalseq a hashtag


title: 2W, RNA [2W_gex]


title: Gliadin Pool 2, RNA [gliadin_pool2_gex]

source_name: sorted polyclonal CD44lo-phenotype CD4 T cells

value: infected >30 d with 2W-expressing Listeria monocytogenes, infected >30 d with 2W-expressing Influenza A virus, gliadin fed mice


title: scCite_MHCC97H


title: scCite_Huh7


title: YUMMER_Ctr_MEKi_D14

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

description: 10x Genomics single cell barcoded mRNA, Sample #1

data_processing:
The reads are first mapped to Grcm38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat
The normalized count from the Seurat object after NormalizeData step are provided as processed data file
Subsequent clustering analyses are descibed in the full manuscript
Assembly: GRCm38
Supplementary files format and content: Gene level expression matrix

source_name: BRAF mutant mouse melanoma model

extract_protocol:
Single Cell 5' Gene Expression Libraries v1.1; Single Cell V(D)J Libraries v1.1
10x Genomics single cell 5' RNA-Seq and V(D)J sequencing

value: Trametinib

value: 5' gene expression sequencing

tag: molecule type

value: 5' mRNA


title: Gliadin Pool 2, Hashtags [gliadin_pool2_hto]


title: Gliadin Pool 1, Hashtags [gliadin_pool1_hto]

value: infected 7 d with 2W-expressing Listeria monocytogenes, infected 7 d with 2W-expressing Listeria monocytogenes


title: CD4SP&CD25pos&FOXP3lo&Treg&CD73pos&CD4CD8dp [GEX]

first: Rebecca

last: LaRue

department: Department of Lab medicine and Pathology

description: Gene expression data for 6 different sorted cell populations. Each cell population tagged with HTO. VDJ(TCR) clonal sequence assigned to cells as 'CDR3'.

data_processing:
The 10X Genomics Cell Ranger (v3.1.0) software was used to demultiplex samples and generate fastq files using the ‘fastq’ command, map and quantify the GEX data to the mouse genome (mm10-3.0.0) using the ‘count’ command, and map the VDJ sequence to a curated mouse VDJ reference (vdj_GRCm38_alts_ensembl-2.2.0) using the ‘vdj’ command.
Raw counts for the GEX and HTO data were processed using the R-based Seurat package (v 3.1.1). The first processing step included filtering out multiplets (GEMS with >1 cell), and the second processing step included normalization, principal components analysis, clustering of cells and differential gene expression with the filtered expression data. The VDJ data was processed using custom R scripts to filter out only the T-cell receptor alpha amino acid sequences (labeled as numbered CDR3). The TCR alpha sequence data was then merged with the final single cell gene expression data.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Supplementary_files_format_and_content: Tab-delimited text files include (1) raw and normalized read count for each HTO sample type, (2) the Cell Ranger VDJ  ‘filtered_contig_annotations’ output, (3) a matrix of cells assigned to a TCR alpha CDR3 aa sequence, and (4) 2 files that contain the metadata from the Seurat analysis – one with the CDR3 assigned clones and one without.

source_name: Thymocytes

extract_protocol:
Mechanically dissociated thymus depleted of CD8 via negative magnetic enrichment (double postive thymocytes were captured from non-enriched whole thymocytes) was sorted via flow cytometry of a BD FACSAria II to isolate each input cell population. Cells were sorted into 1xPBS + 50% FBS prior to hashtag staining then resuspension in 1xPBS + 5% FBS @ 3000 cells/uL for single cell library preparation.
The 10x Genomics Chromium Next GEM Single Cell 5’ Kit (v2) was used to generate three libraries: (1) mRNA transcript expression (RNA), (2) mouse-specific hastag oligos (HTO) and (3) sequencing of single T-cell receptor sequence (TCR) sequence (specifically enriched for TCR alpha sequence).

value: C56Bl/6- Tcli{beta} x TCR{alpha}+/- x Foxp3-GFP

tag: Sex

value: Female

value: Thymus

tag: expression

value: Live-Dead/CD8/Dump-, TCR-Vα2+, CD4+, CD73-, CD25-, FOXP3-


title: Gliadin Pool 1, RNA [gliadin_pool1_gex]


title: CD4SP&CD25pos&FOXP3lo&Treg&CD73pos&CD4CD8dp [HTO]

molecule: other


title: CD4SP&CD25pos&FOXP3lo&Treg&CD73pos&CD4CD8dp [TCR]


title: YUMMER_ITCH-sh3_MEKi_D14

description: 10x Genomics single cell barcoded mRNA, Sample #2


title: 3D-TEC

city: Pittsburgh

first: Yong

last: Fan

state: Pennsylvania

address: 320 E North Ave

department: Institute of Cellular Therapeutics

institute: Allegheny Health Network

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The 2D-TEC count files were demultiplexed and aligned using Cell Ranger-5.0.0 pipeline.
The 3D-TEC count files were demultiplexed and aligned using Cell Ranger-6.0.0 pipeline.
Assembly: GRCH38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 3D iPSC-TECs

growth_protocol: 2D TECs were cultured in 6 well plates in DMEM/F12 media supplemented with B27. 3D TECs began as single cell iPSCs that were polymerized within a spherical capsule and then placed in a thymic epithelial differentiation protocol.

extract_protocol:
Single cells were suspended in PBS supplemented with 20% FBS and sent to the Genomics Research Core at the University of Pittsburgh for QC, library preparation, and droplet sequencing on the 10X Genomics Chromium controller. Single cells (>70% viability) were washed, strained, and subjected to 10X Genomics single cell library construction using the Chromium single-cell 3’ reagent v3 kit and sequencing protocol according to the manufacturer’s recommendations.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

treatment_protocol:
No treatments were used in this study.
2D TECs were removed from wells via trypsinization. Media was removed from the wells and TrypLE Select dissociation buffer was added. Cells were then incubated for 7 minutes, after which cells were gently pipetted off the wells and any remaining aggregates were manually broken up. Cells were then placed in DMEM/F12 media supplemented with 1X B27  and Y-27632 Rock inhibitor (1:1000) and centrifuged at 250 g for 5 minutes to pellet. 3D TECs were decapsulated with 100mM EDTA and placed in a Ficoll gradient to remove both capsular debris and dead cells. The live cell layer was pipetted off the gradient to be dissociated for analysis. Live cellular aggregates were placed in DMEM/F12 media supplemented with 1X B27 and Y-27632 Rock inhibitor and allowed to settle for 10 minutes. Media was then gently removed and aggregates were placed in TrypLE Select and incubated for 17 minutes. Upon completion, cells were centrifuged at 250 g for 5 minutes to pellet. Once pelleted, cells were then checked for both viability as well as the presence of any remaining aggregates using the Countess II Automated Cell Counter.

value: 3D iPSC-TECs

tag: cell type

value: Thymic epithelial cells

value: Grown in 3D culture


title: Marmoset_y2_R3

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: marmoset_snRNA_metadata.txt: Y2, R1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0, with custom build pre-mRNA reference version ASM275486v1.93.
All replicates were first processed independently using cellranger count and then aggregated, downsampling all libraries to the same complexity per cell
the data was processed using Seurat following a similar workflow as for the mouse scRNA-seq, retaining only cells with more than 1000 genes and genes detected in more than 10 cells
we performed batch correction using CCA as implemented in the Seurat package.
Assembly: ASM275486v1.93
Supplementary files format and content: gene-cell matrix with raw counts (RDS format) and tab-delimited text file with cell metadata

organism: Callithrix jacchus

source_name: somatosensory cortex

growth_protocol: Experiments using marmoset were conducted under protocols approved by the MIT Animal Care and Use Committee and followed the guidelines set forth in the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
A cerebellum was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl of 100 mM phenylmethylsulfonyl fluoride (PMSF, Sigma-Aldrich) and 5 μl of 1 M 1,4-dithiothreitol (DTT, Sigma-Aldrich). In addition, 7.5 μl of 40 U/μl RNase inhibitor (N2611, Promega) was also added when mRNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was filtered with 40 μm nylon mesh cell strainer (22363547, Fisher Scientific) and then transferred into a 15 ml centrifugation tube. The sample was centrifuged at 1000 g for 10 min. The supernatant was removed and the cell pellet was gently resuspended in 1 ml cold nuclei extraction buffer with freshly added 10 μl protease inhibitor cocktail, 1 μl of 100 mM PMSF and 1 μl of 1 M DTT. 1.5 μl of 40 U/μl RNase inhibitor was mixed with the nuclei extraction buffer when mRNA-seq was conducted. The 1 ml sample suspension was split into two 1.5-ml micro-centrifuge tubes (500 μl in each tube). Each sample (500 μl) was gently mixed with 0.75 ml of 50% iodixanol to yield 30% iodixanol solution. 50% iodixanol was prepared by adding 0.4 ml diluent (150 mM KCl, 30 mM MgCl2, and 120 mM Tris-HCl, pH 7.8) to 2 ml of 60% iodixanol (D1556, Sigma). The samples were then centrifuged at 10,000 g for 20 min before the supernatant was removed. The nuclei in each tube were incubated on ice for 10 min in 0.5 ml Dulbecco’s phosphate-buffered saline (14190144, Life Technologies) containing 2.0% normal goat serum (50062Z, Life Technologies). The nuclei were resuspended and then pooled together (generating ~1 ml in total).
Nuclei were sequenced using the 10x Genomics Chromium Single Cell 3' kit v2 (10x Genomics) according to the manufacturer’s suggested protocol for nuclei.

treatment_protocol:
Non
Somatosensory and motor cortex from wild-type animals was dissected and flash-frozen in RNAlater (Invitrogen). Each library was made from tissue from an independent individual.

tag: tissue

value: somatosensory cortex

value: Wild type

tag: age


title: Marmoset_y2_R4

description: marmoset_snRNA_metadata.txt: Y2, R2


title: splenic_treg_pool

data_processing:
The 10X Genomics Cell Ranger (v3.0.0) software was used to demultiplex samples and generate fastq files using the ‘fastq’ command, map and quantify the GEX data to the mouse genome (mm10) using the ‘count’ command
Raw counts were processed using the R-based Seurat package (version 3.1.1). Processing of the data included normalization, principal components analysis, clustering of cells and differential gene expression.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Supplementary_files_format_and_content: Seurat global-scaling normalization method “LogNormalize”

source_name: Splenocytes

extract_protocol:
Mechanically dissociated spleen depleted of CD8, B220, and red blood cells via negative magnetic enrichment was sorted via flow cytometry of a BD FACSAria II to isolate the input cell population. Cells were sorted into 1xPBS + 50% FBS prior to hashtag staining then resuspension in 1xPBS + 5% FBS @ 3000 cells/uL for single cell library preparation.
The 10x Genomics Chromium Next GEM Single Cell 5’ Kit (v1) was used to generate library

value: female

tag: strain

value: C57Bl/6 Tcli{beta} x TCR{alpha} x Foxp3-RFP

value: Spleen

tag: cell population

value: Live-Dead/CD8/Dump-, TCR-V{alpha}2+, CD4+, Foxp3+


title: Control_rep2

data_processing:
Sequencing reads were aligned to the bovine genome (Bos_taurus_UMD_3.1.1/bosTau8, Jun. 2014) using Bowtie (version 1.1.1). The peaks were called in the ChIP samples relative to the baseline using Model-based Analysis of ChIP-Seq (MACS, version 1.4.2) with following options; --nomodel --nolambda --shiftsize=300.
Assembly: bosTau8
Supplementary files format and content: wig.gz files of called peaks

source_name: bovine morulae

extract_protocol:
Morula-stage embryos at 144 h post IVF were collected as approximately 50 embryos per biological replicate for ChIP. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The morulae were freed from the zona pellucida by using pronase before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was processed for ChIP using 3.2 µg anti-H3K27me3 antibody (C15410069, Diagenode). For the normalization of sequencing read count, Drosophila-derived chromatin (0.17 ng, Active Motif) and corresponding antibody (1 µg, Active Motif) were added as spike-in. The ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer.
Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.

value: in vitro produced, vehicle treated from the 8-16 cell stage

value: day 6

tag: chip antibody

value: Diagenode C15410069


title: Marmoset_y0_R1

description: marmoset_snRNA_metadata.txt: D0, R1


title: MAT2A-inhibited_rep1

tag: sourse

value: in vitro produced, inhibitor (FIDAS-5) treated from the 8-16 cell stage


title: Marmoset_D0_R3

description: marmoset_snRNA_metadata.txt: D0, R2


title: KOX-4 strain rep02

city: Wuhan

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

data_processing:
The raw sequencing reads were trimmed and quality controlled by SeqPrep and Sickle
Then clean reads were mapped to the reference genome ME49 (downloaded from ToxoDB) using TopHat
The transcript level for each gene was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method
Genome_build: https://toxodb.org/toxo/app/downloads/Current_Release/TgondiiME49/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Toxoplasma gondii

source_name: KOX-4 (ME49ΔAP2X-4)

growth_protocol: KO-X-4 strain and wild type ME49 are cultured in confluent HFF monolayers at 37℃ in 5% CO2, and HFF were cultured in Dulbecco's modified eagle medium supplemented with 10% fetal bovine serum, 100 unit/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Total RNA was extracted using the Trizol methods according to the manufacturer’s instructions (TransGen Biotech, Beijing, China)
RNA libraries were constructed using the TruSeqTM RNA Sample Preparation Kit (Illumina, San Diego, USA) and sequenced with the Illumina HiSeq X Ten sequencer

tag: strain/genotype

value: tachyzoites

value: AP2X-4 knock out


title: Y8.rep3.calJac3

library_source: genomic single cell

data_processing:
Mouse and marmoset libraries were first downsampled to similar overall complexity in terms of reads/cell across all conditions
Cleaned data was processed with the scasat83 pipeline using macs2 as peak caller
Only cells with at least 1,000 reads and 300 peaks from the master list overlapping with at least one read, but not more than 15,000 reads and 8,000 peaks were retained for analysis
matrix was processed using R implementing a custom processing pipeline based on the strategy outlined in Cusanovich et al. 2018 and refined by Andrew Hill, following the log-LSI workflow
Assembly: mm10, calJac3
Supplementary files format and content: gene-cell matrix with raw counts (RDS format) and tab-delimited text file with cell metadata

growth_protocol: Experiments using animal were conducted under protocols approved by the Harvard University and MIT Institutional Animal Care and Use Committee and followed the guidelines set forth in the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
To prepare nuclei, around 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
For mouse: Briefly, cells were fixed with 0.1% formaldehyde and incubated at room temperature for 5 min. The fixation was stopped by adding glycine to the final concentration of 125 mM. The sample was incubated at room temperature for 5 min and washed in PBS. The cell concentration was counted, and approximately 1600-2000 cells per well were distributed into each well of a 96-well plate. Cells were transposed with 96 uniquely barcoded Tn5 at 37°C for 30 min with shaking at 300 rpm. The reaction was stopped by adding 0.5 M EDTA and incubated at 37°C for 15 min. All the cells were then pooled and MgCl2 was added to the pooled sample to quench EDTA. The sample was re-distributed onto another 96-well plate with 20 cells in each well by FACS sorting. Reverse crosslinking buffer and barcode PCR primers were added to each sample. The plate was incubated at 55°C for 16 hours for reverse crosslinking. Tween 20 was then added to quench SDS before PCR amplification. The PCR reaction was carried out at the following conditions: 72°C for 5 min (extension), 98°C for 5 min, and then thermocycling at 98°C for 10 s, 70°C for 30 s and 72°C for 1 min for 12-15 cycles. Libraries were pooled and purified using Qiagen MinElute PCR purification column. The libraries were quantified using KAPA library quantification kit. Libraries were sequenced on the Next-seq platform (Illumina) using a 150-cycle kit (Read 1: 47 cycles, Index 1: 36 cycles, Index 2: 36 cycles, Read 2: 47 cycles). For marmoset: Somatosensory and motor cortex from wild-type animals was dissected and dissociated with the Worthington Papain Dissociation System (Worthington Biochemical Corporation), and live cells were isolated by FACS sorting as DAPI-negative, Vybrant DyeCycle Ruby (Thermo Fisher)-positive events. Libraries were prepared using the 10x Genomics Chromium Single Cell ATAC kit (10x Genomics).

treatment_protocol:
non
Cortex was dissected in cold dissociation medium (20 mm glucose, 0.8 mm kynurenic acid, 0.05 mmAPV, 50 U/ml penicillin–0.05 mg/ml streptomycin, 0.09mNa2SO4, 0.03mK2SO4, and 0.014m MgCl2). The cortex was enzymatically digested in dissociation medium containing 0.16 gm/l l-cysteine and 12 U/ml papain at 37°C for 30 min. Papain digestion was then blocked with dissociation medium containing 10 mg/ml ovomucoid (Sigma, St. Louis, MO) and 10 mg/ml bovine serum albumin (BSA) at room temperature. Neurons were mechanically dissociated to create a single cell suspension by gentle trituration in iced OptiMem (Life Technologies, Gaithersburg, MD) containing 20 mm glucose and both 0.4 mmkynurenic acid and 0.025 mm APV to protect against glutamate-induced neurotoxicity. Td-tomato labeled projection neurrons were purified from the cortical cell suspension by fluorescence-activated cell sorting (FACS) using a FACSVantage flow cytometer.


title: JaSenescence_1wk_MeJA

type: RNA

city: Qingdao

first: Hongbo

last: Zhang

state: Shandong

address: No.11 Keyuan Rd.

institute: Tobacco Research Institute, Chinese Academy of Agricultural Sciences

description: Gene expression after 1wk of MeJA treatment.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: The slides were scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Nicotiana tabacum

source_name: Leaf, 1wk, MeJA

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The tobacco plants were grown in a controlled indoor growth room at 23℃ with 14h_light/10h_dark photoperiod.

extract_protocol: The total RNA from tobacco leaves was extracted using TRIzol reagent (Invitrogen) with DNase treatment following the manufacturer's instructions.

treatment_protocol: Tobacco leaves were daily sprayed with 100μM MeJA or mock solution till the indicated time.

value: Leaf

tag: treatment

value: MeJA

tag: time point


title: JaSenescence_2wk_MeJA

description: Gene expression after 2wk of MeJA treatment.

source_name: Leaf, 2wk, MeJA


title: JaSenescence_1wk_Mock

description: Gene expression after 1wk of mock treatment.

source_name: Leaf, 1wk, Mock

value: Mock


title: 2D-TEC

description: 10X Genomics

source_name: 2D iPSC-TECs

tag: cell line

value: 2D iPSC-TECs

value: Thymic epithelial cells

value: Grown in 2D culture


title: Y8.rep1.calJac3

value: somatosensory cortex

value: Wild type


title: WT ME49 rep03

source_name: WT ME49

value: wild type


title: JaSenescence_2wk_Mock

description: Gene expression after 2wk of mock treatment.

source_name: Leaf, 2wk, Mock


title: Y7.rep2.calJac3


title: JaSenescence_0wk_Control

description: Gene expression at 0wk of mock treatment.

source_name: Leaf, 0wk, Control


title: WT ME49 rep02


title: Y8.rep2.calJac3


title: WT ME49 rep01


title: Control_rep1

tag: day after ivf


title: KOX-4 strain rep03

tag: genotype


title: HSPCs, HLA-DR(+) rep2

city: Kanazawa

first: Noriaki

last: Tsuji

address: 13-1 Takaramachi

department: Hematology

institute: Kanazawa University

description: Sample 4

data_processing:
Basecalls performed using bcl2fastq2 v2.20
Sequenced reads were mapped to GRCh38 whole genome using DRAGEN Bio-IT Platform (version 3.6.3).
Transcripts per million (TPM) were calculated using DRAGEN Bio-IT Platform (version 3.6.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values and raw counts values for each sample.
Supplementary_files_format_and_content: Matrix table with TPM values and raw gene counts for every gene and every sample

source_name: peripheral blood

extract_protocol:
HLA-DR(+) HSPCs and HLA-DR(-) HSPCs were isolated by magnetic cell separation and fluorescence-activated cell sorting. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, San Jose, CA) was used for the construction of sequencing libraries.
cDNA libraries were prepared for sequencing using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and Nextera XT Index Kit v2 set A/B/C/D (Illumina, San Diego, CA).

value: peripheral blood

value: hematopoietic stem progenitor cells

tag: phenotype

value: HLA-DR(+)


title: HSPCs, HLA-DR(-) rep3

description: Sample 5

value: HLA-DR(-)


title: KOX-4 strain rep01


title: Day0.rep5.calJac3


title: HSPCs, HLA-DR(+) rep3

description: Sample 6


title: HSPCs, HLA-DR(-) rep2

description: Sample 3


title: Day0.rep4.calJac3


title: Y7.rep1.calJac3


title: HSPCs, HLA-DR(-) rep1

description: Sample 1


title: Day0.rep2.calJac3


title: Day0.rep1.calJac3


title: Day0.rep3.calJac3


title: M2 RGX104 replicate 2

city: Bari

first: Maria Carmela

last: Vegliante

address: Viale Orazio Flacco,65

department: Hematology and Cell Therapy Unit

country: Italy

institute: IRCCS-Istituto tumori "Giovanni Paolo II"

description: gene expression

hyb_protocol: Hybridizations were performed for 16 h at 45 °C in a rotisserie oven (60 RPM). GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were analyzed with packages available from Bioconductor (http://www.bioconductor.org). Normalization and calculation of gene expression was performed with the Robust Multichip Average expression measure using the oligo package.

label: biotin

source_name: M2 in vitro generated from ThP1 cell line

label_protocol: Biotinylated cRNA was prepared using the GeneChip 3'IVT Pico Reagent Kit according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: THP-1 cell line was obtained from ATCC (Manassas, VA, USA) and grown in RPMI 1640 (Gibco, Thermo Fisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum, 1% Penicillin-Streptomycin (10,000 U/mL, 10mg respectively) (Sigma Aldrich), 2mM glutamine (Gibco) and 0.05 mM of 2-mercaptoethanol (Sigma Aldrich). To obtain polarized macrophages, 0.5 x106 THP-1 cells were seeded in 3D system using Alvetex Scaffold 12-well plate and treated with 320 nM of phorbol myristate acetate (PMA) for 6 hours. Then, the medium was supplemented with either lipopolysaccharides (LPS, 100 ng/ml) and INF-γ (20 ng/ml) for 18 h to obtain M1 or IL-4 (20 ng/ml) and IL-13 (20 ng/ml) for M2 Mo.

extract_protocol: RNAs were extracted with the RNeasy Mini Kit (Quiagen) following the manufacturer’s recommendations.

treatment_protocol: DMSO or RGX-104 (2µM) for 24h


title: MAT2A-inhibited_rep2

value: day 6

value: Diagenode C15410069


title: M2 RGX104 replicate 1

description: gene expression

value: M2 in vitro generated from ThP1 cell line


title: NAC 8000 mg/L 30 min R1

status: Public on May 30 2022

city: Siena

first: Felice

last: Valzano

state: Siena

address: Viale Mario Bracci, 16

department: Medical Biotechnologies

institute: University of Siena

data_processing:
Bioinformatic analysis was performed using the SeqMan NGen v17.3 software tool (DNASTAR Lasergene, Madison, WI, USA), with default parameters.
There are two sequencing files (fastq.gz) for the second biological replicate in order to achieve the guaranteed number of reads. For downstream analysis, we used both files and we grouped them as the same replicate for each sample.
Reads were aligned using P. aeruginosa Z154 complete genome (n=6,344 CDSs) as reference (GenBank accession number CP069177).
DESeq2 was selected as RNA-Seq normalization method.
Differentially expressed genes (DEGs) of the NAC-exposed cultures compared to control were analyzed considering false discovery rate (FDR) adjusted p-values of <0.05 from DESeq2.
Genome_build: GenBank accession number CP069177.
Supplementary_files_format_and_content: text files containing raw counts and normalized abundance measurements from DESeq2 of sequencing reads per replicate per sample.
Supplementary_files_format_and_content: text file containing all the processed results for each feature type and each sample (i.e., raw counts, linear rlog reads, p-value, adjusted p-value, log2 fold-change).

organism: Pseudomonas aeruginosa

source_name: NAC 8000 mg/L 30 min

growth_protocol: Overnight cultures in cation-adjusted Mueller-Hinton broth of P. aeruginosa Z154 were diluted 1:50 into 40 mL of the same medium (appropriately concentrated in order to avoid broth dilution when NAC solution were used), and incubated at 35°C in agitation to achieve OD600 = 1.0. 5 mL of the cells at mid-exponential phase (OD600 = 1.0) were moved into 2 wells of a multiwell plate prior to treatment.

extract_protocol:
Total RNA extraction was performed using the SV Total RNA Isolation System (Promega, Madison, WI, USA) with minor modifications. Briefly, 1 mL of each culture was transferred to sterile tubes and cells harvested by centrifugation (12,000 xg for 10 minutes) at 5°C. The cell pellet was resuspended in 100 µL of 0.4 mg/mL lysozyme in TE buffer and incubated at room temperature for 5 minutes. RNA was purified according to the manufacturer’s RNA purification by centrifugation protocol, including a second elution step performed with 50 μL of nuclease-free water. The purified RNA was then stored at –70°C prior to ribosomal RNA depletion and sequencing. Total RNA quantity and quality, ribosomal RNA (rRNA) depletion, cDNA library construction and Illumina HiSeq 4000 platform-based RNA-sequencing were performed by Eurofins Genomics Europe Sequencing (Constance, Germany).
The transcriptome libraries were strand-specific and single-end sequenced with 50-bp reads, for a total of 10 million reads per sample. At least 20 ng of rRNA-depleted RNA was used as input.

treatment_protocol: The cells were challenged with or without NAC 8000 mg/L for 30 minutes at 35°C in static conditions. All experiments were carried out in 2 biological replicates.

tag: strain type

value: mucoid strain from CF

value: planktonic cells

tag: growth phase

value: mid-exponential phase

value: treated with NAC 8000 mg/L for 30 minutes


title: Control 30 min R2

source_name: Control 30 min

value: untreated (control)


title: Control 30 min R1


title: HSPCs, HLA-DR(+) rep1

description: Sample 2


title: M2 DMSO replicate 2

description: gene expression

value: DMSO


title: sample 484

status: Public on May 27 2022

city: Vienna

first: Spyridon

last: Sideromenos

address: Schwarzspanierstrasse 17

department: Center for Physiology and Pharmacology

country: Austria

institute: Medical University of Vienna

data_processing:
reads in fastq format were aligned to the murine reference genome version mm10, with RefSeq annotations, using STAR aligner version 2.5.0a
Reads per gene were counted, and differential gene expression was calculated using edgeR version 3.22.2 with a quasi-likelihood F-test
Raw p values were adjusted using the Benjamini-Hochberg method to correct for multiple testing, with the false discovery rate (FDR) set to 5%.
Assembly: mm10
Supplementary files format and content: TSV file containing normalized counts of all processed samples

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using the Qiagen miRNA mini kit
NEBNext® Ultra™ II RNA Library Prep Kit

value: Hippocampus

value: 3-4 Months

value: KO

tag: Sex

value: MALE


title: sample 553


title: sample 547

value: WT


title: sample 530

value: FEMALE


title: sample 493


title: sample 523


title: d2-E2+MPA-3

status: Public on May 26 2022

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20.
Remove reads carrying adaptor sequences using cutadapt (v2.7).
Reads were mapped to the human genome (UCSC hg38) using Tophat
Assembly: hg38
Supplementary files format and content: RPKM was calculated for each gene in Partek Genomics Suite

source_name: uterine epithelial cells

growth_protocol: Organoids were grown in Advanced DMEM/F12 containing B27, ITS, Primocin, Glutamax,1.25 mM N-acetyl-L-cysteine, 500 nM A83-01, 50 µg/ml human HGF, 500 µg/ml human EGF, 100 µg/ml human FGF-10, 500 µg/ml human Rspondin-1, 100 µg/ml human Noggin, 10 nM Nicotinamide

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions. Donor 1 RNA was cleaned up using RNeasy Mini kit. Donor 2 RNA was cleaned up using Zymo's RNA Clean and Concentrator 5 kit
to prepare libraries, for Donor 1 samples, Illumina Gold kit was used; For donor 2 Illumina mRNA Illumina Stranded mRNA Prep kit was used

treatment_protocol: 0.1% ethanol (V) or 10 nM estradiol (E2) for 2 days, and then with V, E2 or 10 nM E2 and 1 µM medroxyprogesterone acetate (E2+MPA) for 3 more days. Organoids were collected 6 hours after a meda+treatment change on the last day for RNA isolation.

tag: donor


title: d2-E2+MPA-2


title: sample 490

tag: tissue


title: SHSY5Y KO+M2 (SH-SY5Y TRPM2 KO transfected with pCDNA3.1 V5 TRPM2) - replicate 1

city: Hershey

first: Fernanda

last: Festa

state: PA

address: 500 University Dr BMR C7846

department: Pediatrics

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78). EdgeR was used to fit the read counts to the negative binomial model along with generalized linear model (GLM) and differentially expressed genes were determined by the likelihood ratio test method implemented in the edgeR package. Significance was defined to be those with q-value < 0.05 calculated by the Benjamini-Hochberg method to control the false discovery rate (FDR). The list of differentially expressed genes was analyzed with Ingenuity Pathway Analysis (Qiagen).
Assembly: GRCh38
Supplementary files format and content: txt file containing the result of edgeR differential expression analysis and CPM (copy per million) values for each sample

growth_protocol: SHSY5Y TRPM2 KO cells were generated through the depletion of endogenous TRPM2 with CRISPR technology, using pCas9-guide TRPM2 gRNA vector (target sequence GAGGAAAGCTGGCTCGGAGC) and donor vector containing 600-bp left and right homologous arms to the TRPM2 gene with GFP and puromycin markers (OriGene Technologies Inc.; Rockville, MD). These cells were then used to test the effect of overexpression of TRPM2. Either pcDNA3.1 V5-TRPM2 or the empty vector pcDNA3.1 V5 (Invitrogen) was transfected into SH-SY5Y TRPM2 KO neuroblastoma cells using the Neon Transfection System (Invitrogen), following the manufacturer’s instructions, generating the new cell line SH-SY5Y KO+M2 or the control cell line SH-SY5Y KO+V5 (empty vector). Cells were passed up to 8 passages with G418 selection. Single-cell clones were generated and the TRPM2 levels were measured through RT-PCR and Western blot analysis.

extract_protocol: SHSY5Y KO+V5 and SHSY5Y KO+M2 cells were maintained under normal culture conditions. Each cell line was collected in duplicate, and RNA was isolated using RNeasy Mini Kit (Qiagen) before being subjected to total RNA sequencing (RNAseq)

treatment_protocol: SH-SY5Y KO+M2 and SH-SY5Y KO+V5 cells were cultured in 50% DMEM and 50% Ham’s F-12 (DMEM/F-12 50/50) media supplemented with 10% heat-inactivated FBS. Cells were plated at 70-80% confluence and incubated for 24 hours with regular media and then harvest for RNA extraction.

tag: cell type

value: neuroblastoma

tag: vector

value: pCas9-guide vector with TRPM2 gRNA + pcDNA 3.1 V5 TRPM2

tag: markers

value: GFP + puromycin + G418


title: d2-E2+MPA-1


title: sample 564

tag: strain

tag: age


title: SHSY5Y KO+V5 (SH-SY5Y TRPM2 KO transfected with pCDNA3.1 V5 (empty vector)) - replicate 2

value: pCas9-guide vector with TRPM2 gRNA + pcDNA 3.1 V5


title: SHSY5Y KO+V5 (SH-SY5Y TRPM2 KO transfected with pCDNA3.1 V5 (empty vector)) - replicate 1


title: NAC 8000 mg/L 30 min R2


title: sample 482


title: sample 488


title: M2 DMSO replicate 1

description: gene expression

value: M2 in vitro generated from ThP1 cell line


title: SHSY5Y KO+M2 (SH-SY5Y TRPM2 KO transfected with pCDNA3.1 V5 TRPM2) - replicate 2


title: d2-E2-3


title: d2-E2-2


title: input_Prolif_endo

data_processing:
50nt sequence reads were identified by the NIEHS Core (using NextSeq-High Output).
Reads were mapped to the human genome hg38 using  Bowtie with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
Assembly: hg38
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: endometrial biopsy

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

treatment_protocol: Organoids were treated with 0.1% ethanol (V) or 10 nM estradiol (E2) for 2 days, and then with 10 nM E2 and 1 µM medroxyprogesterone acetate (E2+MPA) for 3 more days. Organoids were collected 1 hours after a meda+treatment change on the last day for chromatin isolation

tag: sample source

value: proliferative

tag: sample type

value: endometrial biopsy

tag: treament

tag: antibody


title: d1-E2-3

tag: treatment


title: d2-V3

value: V


title: d2-V2


title: d2-V1


title: d1-E2-1


title: sample573

tag: genotype


title: sample 522


title: donor_2.HiC

data_processing:
The raw reads were mapped to human reference genome (GRCh38/hg38) using HiCUP version 0.7.1
Juicer version 1.8.9 was used to identify chromatin loops
Assembly: hg38
Supplementary files format and content: Chromatin loops were identified with Juicer tool

extract_protocol: none provided by the submitter

treatment_protocol: Organoids were treated with 0.1% ethanol (V) or 10 nM estradiol (E2) for 2 days, and then with 10 nM E2 and 1 µM medroxyprogesterone acetate (E2+MPA) for 3 more days. Organoids were collected 1 hours after a meda+treatment change on the last day. Ovariectomized mice were treated for 1 hour with 1 mg progesterone or oil vehicle. Uterine tissue was frozen.

value: uterine epithelial cells


title: ESR1_MS_endo

value: mid-secretory

value: ESR1 (Millipore, cat# 06-935)


title: input_d2_org

value: organoid culture


title: d1-E2+MPA-3


title: input_d1_org


title: d1-E2+MPA-1


title: input_MS_endo


title: d2-E2-1


title: ciTotiSC RRBS-seq rep1

status: Public on May 25 2022

city: Haidian

first: Pengcheng

last: Tan

address: 30 Shuangqing Rd

institute: Tsinghua University

data_processing:
Raw reads were trimmed adaptors, and were mapped to the reference genome mm10 using BS-Seeker2 (v2.1.1) (parameter: -m 0.06) in mode of bowtie
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for ciTotiSC RRBS-seq rep1
Supplementary_files_format_and_content: bigwig file for ciTotiSC RRBS-seq rep1

source_name: ciTotiSC induced from OG2 mESC

growth_protocol: ciTotiSCs were cultured in KSR basal medium composed of KO DMEM, 5% KSR (Gibco, 10828010), CDL (CD lipid concentrate, 500X, Gibco, 11905-031), 1% N2 (ThermoFisher, A1370701), 1X L-glutaMAX, 1X penicillin-streptomycin, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, 55 μM 2-mercaptoethanol and 1000 U/mL mouse leukemia inhibitory factor (mLIF), 50 ng/ml Sodium L-ascorbyl-2-phosphate (Selleck, S5115) supplemented with 2.5 μM 1-Azakenpaullone (Selleck, S7193), 0.5 μM WS6 (Selleck, S7442) and 0.2 μM TTNPB (Selleck, S4627). Cells were passaged every 2-3 days using 0.05% Trypsin-EDTA at a ratio of 1:3-1:5 on inactivated MEF feeder layers.

extract_protocol:
Genomic DNAs were extracted using DNeasy Blood and Tissue Kits (QIAGEN) and digested by MspI (NEB).
The digested DNAs were filled in and tailed. Then, bisulfate conversion was performed using MethyCode bisulfite conversion kit (Invitrogen). After amplification and purification，all libraries were constructed and subjected to 150 bp paired-ends Illumina Novaseq 6000 platform.

tag: cell line

value: ciTotiSC


title: 38

status: Public on May 18 2022

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
TopHat (v. 2.2.1)
Cufflinks (v. 2.2.1)
Assembly: GRCh38
Supplementary files format and content: Normalized counts

source_name: Breast, upper outer quadrant

extract_protocol:
Frozen and OCT Tissue: Qiagen RNAeasy plus mini kit for RNA; FFPE: Covaris Ultrasonication FFPE DNA/RNA kit
Illumina TruSeq RNA Exome (Single Library Hyb)

value: Primary Tumor

value: FFPE


title: ciTotiSC ATAC-seq rep1

data_processing:
cut adapter using python cutadapt version 1.18  parameter -q20 --quality-base=33  adapters detected using first 1million reads
reads aligned to mm10 genome using bowtie2 version 2.3.3.1  with parameters -X2000 -t -1 -N1 -L 25 --no-mixed --no-discordant --threads 16
using samtools(version 1.6) to filter out low mapping quality reads  samtools view -F 1804 -f 2 -q 30 -@ {threads} -u {input.bam} | samtools sort -@ {threads} -m 2G -n /dev/stdin -o {output.bam}
using samtools to sort reads by coordinate and fixmate   samtools fixmate -@ {threads} -r {input.bam} {output.fixmate}  samtools view -F 1804 -f 2 -@ {threads} -u {output.fixmate} |\  samtools sort -@ {threads} -m 2G /dev/stdin -o {output.bam}
using picard(version 2.20.4) and samtools to remove duplicated reads    java -Xmx10G -Djava.io.tmpdir={params.tempdir} \    -jar /applications/picard_2.20.4/picard.jar MarkDuplicates \    INPUT={input.bam} \    OUTPUT={output.marked} \    METRICS_FILE={output.metrics} \    VALIDATION_STRINGENCY=LENIENT \    ASSUME_SORTED=true \    REMOVE_DUPLICATES=false        samtools view -F 1804 -f 2 -@ 5 -b -u {output.marked} |\    samtools sort -@ 5 -m 2G /dev/stdin -o {output.nodup}         samtools index -@ 5 {output.nodup}
using bedtools(version 2.26.0) to filter out unmappable genome regions according to blacklist(https://github.com/Boyle-Lab/Blacklist/tree/master/lists/Blacklist_v1)    bedtools intersect -v -abam {input.bam} -b {params.blacklist} |\    samtools view -F 1804 -f 2 -@ {threads} -S -h -b |\    samtools sort -@ {threads} -m 2G  /dev/stdin -o  {output.bam}        samtools index -@ {threads} {output.bam}
using bedtools to shift each end of mate pair 5bp toward mate pair center, and make a bed file with the shifted end as center, and extend 125bp to each side, that marks the total 250bp region we considered accessible
convert such a bed file to bigWig file mentioned below using bedtools genomecov
using macs2 (version 2.2.7.1) to callpeak with parameters:  --bdg -g mm --nomodel --call-summits  this produced narrowPeak file mentioned below
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file of two replicates of ciTotiSC and mESC and narrowPeak file of two replicates of ciTotiSC and mESC

extract_protocol:
Briefly, after cells were collected by flow cytometry as described before, 100,000 cells were centrifuged at 500 rcf for 5 min in a 4 °C pre-chilled fixed-angle centrifuge and washed by ice-cold PBS. After centrifugation, supernatant was removed with two pipetting steps to avoid the cell pellet. Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 10 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted for six times to mix. Nuclei were then centrifuged for 10 min at 500 rcf. in a 4 °C pre-chilled fixed-angle centrifuge.
Supernatant was removed and nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Novaprotein, N248). After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. Reactions were cleaned up with 2.2x VAHTS DNA Clean Beads (Vazyme, N411). PCR was performed to amplify the library for 8 cycles by KAPA HiFi PCR Kit (Kapa Biosystems, kk2102) using the following PCR conditions: 72 °C for 5 min; 98 °C for 3mins; and thermocycling at 98 °C for 20 s, 63 °C for 30 s and 72 °C for 3 min. After the PCR reaction, libraries were purified with the 1.8x VAHTS DNA Clean Beads.


title: d1-V3


title: PGR_d2_org

value: PGR  (Santa Cruz sc-7208)


title: PGR_d1_org


title: 37


title: d1-V2


title: 36

source_name: Breast, lower inner quadrant


title: 35

source_name: Breast, upper inner quadrant

value: Unprocessed Solid Tumor


title: ESR1_d2_org


title: d1-V1


title: ESR1_Prolif_endo


title: ESR1_d1_org


title: mESC ATAC-seq rep2

source_name: OG2 mESC

value: mESC


title: 34


title: d1-E2+MPA-2


title: donor_1.HiC


title: 31


title: ciTotiSC RRBS-seq rep2


title: 28

value: Metastatic Tumor


title: d1-E2-2


title: mESC ATAC-seq rep1


title: ciTotiSC ATAC-seq rep2


title: 23

source_name: Breast, NOS


title: 33


title: 32

source_name: Breast, central portion


title: 29


title: 18


title: 30


title: 19


title: 27


title: P8 ciTotiSC RNA-seq rep2

data_processing:
TrimGalore software (with Cutadapt v1.18) was used to trim adaptor and first 10-bp of both reads
TopHat2 (v2.1.1) was used for the alignment to the mm10 reference genome with default parameters
The gene expression count matrix and FPKM value were analyzed by Cufflinks (v2.2.1) default pipline
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated-value table with FPKM values for every gene and every sample

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
mRNA-seq libraries were generated using KAPA stranded mRNA library preparation kit (KAPA Biosystems, KK8421) according to the manufacturer’s protocol.

tag: passage


title: 24


title: 22


title: 25


title: 10


title: 13


title: 9


title: 5


title: 21


title: 20


title: 17


title: 15


title: 14


title: 16


title: 12


title: 26


title: 8


title: 6


title: 7


title: NTG.9818X4

status: Public on May 09 2022

city: Birmingham

first: Arun

last: Jyothidasan

state: ALABAMA

institute: University of Alabama at Birmingham

data_processing:
Novoindex (2.8) was used to create a reference index
Reads were aligned to the transcriptome reference index as described above using Novoalign (v2.08.01), allowing up to 50 alignments for each read
USeq's SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space
The transcriptome was mapped to mm10 (GRCm38 genome assembly).
Deseq2 (Ver 1.32.0) package was used for normalization, visualization, and differential analysis of high dimensional count data.
Assembly: mm10
Supplementary files format and content: text files include Rlog values for each Sample

source_name: Non-Transgenic

extract_protocol:
Approximately 15 mg of flash frozen cardiac tissue was thawed from mNrf2-TG and controls, then mechanically tissue was homogenized with 50μl 2-Mercaptoethanol. Total RNA was isolated using RNeasy mini kit (Qiagen, 74106),
TruSeq Stranded mRNA Library Preparation Kit (Illumina, RS-122-2101, RS-122-2102). Purified libraries were qualified using a D1000 ScreenTape assay (Agilent, 5067-5582/3) with the 2200 TapeStation Instrument (Agilent Technologies). cBot and TruSeq SR Cluster Kit (Illumina, Cat. GD-401-3001) were used to apply 18pM of the sequencing library to a TruSeq v3 flowcell (Illumina) and for clonal amplification respectively

value: whole heart lysate

value: NTG

value: Male


title: NTG.9818X3


title: 4


title: NTG.9818X1


title: si-NC  rep 3

status: Public on May 06 2022

city: Chongqing

first: Cong

last: Lan

state: Chognqing

address: 10 Changjiangzhilu Road

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Rattus_norvegicus_ensemble_98
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

source_name: primary cardiomyocytes

growth_protocol: We isolated  cardiomyocytes using 1-day-old SD rats and  cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum at 37℃ in atmosphere with 5% CO2.

extract_protocol:
Cells were collected and Total RNA was extracted using Trizol reagent and mRNA was enriched and Illumina TruSeq RNA Sample Prep Kit  was for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neonatal cardiomyocytes in primary culture were transfected with siRNA against DYRK1A (si-DYRK1A) or scramble siRNA (si-NC) and cultured for 48 h to prepare sample (three biological replicates for each group)

value: Sprague-Dawley (SD) rats

value: heart

value: postnatal day 1


title: si-DYRK1A  rep 3


title: 1


title: 2


title: Patient J, PTEN lost section

status: Public on May 05 2022

city: Houston

first: Lawrence

middle: N

last: Kwong

state: TX

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description: J-

data_processing:
Raw-sequencing data from the Illumina platform were converted to fastq files and aligned to the reference genome (hg19), using the STAR algorithm in single-pass mode with default parameters.
HTSeq-count was then utilized to generate the raw counts for each gene.
Raw counts were then analyzed by DESeq2 for data processing, normalization, and differential expression analysis, according to standard procedures.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Melanoma

extract_protocol:
RNA was isolated from scraped FFPE samples using the Allprep DNA/RNA FFPE kit (Qiagen GmbH)
Libraries were prepared according to Illumina's instructions.

value: Melanoma

tag: patient id

value: J

tag: pten protein status

value: PTEN lost


title: Patient J, PTEN retained section

description: J+

value: PTEN retained


title: Patient I, PTEN lost section

description: I-

value: I


title: 11

value: Primary Tumor


title: mWT.9818X18

source_name: Cardiac specific Nrf2-Transgenic, 6 months

value: TG

tag: Sex


title: mWT.9818X19

tag: tissue


title: mWT.9818X17


title: Patient F, PTEN lost section

description: F-

value: F


title: Patient F, PTEN retained section

description: F+


title: Patient E, PTEN retained section

description: E+

value: E


title: si-DYRK1A  rep 2


title: si-DYRK1A  rep 1


title: NTG.9818X2


title: Patient I, PTEN lost section #2


title: Patient A, PTEN lost section

description: A-

value: A


title: si-NC rep 1

value: postnatal day1


title: CD3+ T cells purified from spleens in allograft C57BL/6 recipient mice T1

status: Public on May 03 2022

first: Le

last: Sheng

state: Hubei

address: JieFang Road 1277

department: Department of Cardiovascular Surgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Spleen

growth_protocol: CD3+ T cells purified from spleens in C57BL/6 recipient mice and were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Spleen

value: CD3+ T cells

tag: cell type

value: WT

value: allograft


title: CD3+ T cells purified from spleens in isograft C57BL/6 recipient mice C3

value: isografts


title: normal_OSKM_Day6-2 (CNV)

status: Public on Apr 28 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: normal_OSKM_Day6-2 (CNV)

data_processing:
Read alignment was done with BWA mem 0.7.15 to the mouse reference genome mm9 including PhiX174
Copy number analysis was performed by cnvkit 0.9.6 using control and control-gfp IPSCs as reference.
Genome_build: mm9
Supplementary_files_format_and_content: cns file

source_name: OSKM reprogrammed stem cells

extract_protocol:
The DNA extraction was done using the Dneasy Mini Blood and Tissue Kit (Qiagen) according to the manufacturer's instructions. The DNA concentration was measured using a Qubit.
Libraries for whole-genome sequencing were done using the Truseq Nano DNA low throughput library kit (Illumina). Multiplexing was done using the IDT for Illumina Truseq DNA UD Indexes. Library quality was evaluated using a Bioanalyzer.

tag: days from treatment

tag: reprogramming factors

value: OSKM

value: embryonic stem cells


title: normal_OSKM_day0B (CNV)

description: normal_OSKM_day0B (CNV)


title: CD3+ T cells purified from spleens in isograft C57BL/6 recipient mice C1


title: normal_OSKM_day0A (CNV)

description: normal_OSKM_day0A (CNV)


title: 3

value: FFPE


title: normal_OSK_day0B (CNV)

description: normal_OSK_day0B (CNV)

source_name: OSK reprogrammed stem cells

value: OSK


title: Patient I, PTEN retained section

description: I+

value: Melanoma

value: PTEN retained


title: Patient H, PTEN lost section

description: H-

value: H

value: PTEN lost


title: Patient H, PTEN retained section

description: H+


title: Patient D, PTEN lost section

description: D-

value: D


title: Patient D, PTEN retained section

description: D+


title: Patient C, PTEN lost section

description: C-

value: C


title: si-NC rep 2

tag: strain

value: Sprague-Dawley (SD) rats

value: heart

value: postnatal day 1


title: normal_Get_day6-2 (CNV)

description: normal_Get_day6-2 (CNV)

source_name: GET reprogrammed stem cells

value: GET


title: CD3+ T cells purified from spleens in allograft C57BL/6 recipient mice T3

value: Spleen

value: CD3+ T cells

value: WT


title: normal_Get_day3 (CNV)

description: normal_Get_day3 (CNV)


title: Patient C, PTEN retained section

description: C+


title: Patient A, PTEN retained section

description: A+

value: A


title: normal_Colony23_Dox0106B (CNV)

description: normal_Colony23_Dox0106B (CNV)

source_name: partialy programmed stem cells

value: embryonic stem cells


title: normal_Colony23_Dox0106A (CNV)

description: normal_Colony23_Dox0106A (CNV)


title: CD3+ T cells purified from spleens in allograft C57BL/6 recipient mice T2

value: allograft


title: cell-line-17_IPSC (CNV)

description: cell-line-17_IPSC (CNV)

source_name: induced pluripotent stem cells


title: control_IPSC (CNV)

description: control_IPSC (CNV)


title: normal_OSKM_Day3 (CNV)

description: normal_OSKM_Day3 (CNV)

value: OSKM


title: normal_OSK_Day3B (CNV)

description: normal_OSK_Day3B (CNV)

value: OSK


title: normal_OSK_Day6-2 (CNV)

description: normal_OSK_Day6-2 (CNV)


title: normal_Colony20_pellet (CNV)

description: normal_Colony20_pellet (CNV)


title: normal_OSK_Day3A (CNV)

description: normal_OSK_Day3A (CNV)


title: normal_OSK_day0A (CNV)

description: normal_OSK_day0A (CNV)


title: normal_GetM_day6-2 (CNV)

description: normal_GetM_day6-2 (CNV)

source_name: GETM reprogrammed stem cells

value: GETM


title: cell-line-10_IPSC (CNV)

description: cell-line-10_IPSC (CNV)


title: normal_GetM_day3 (CNV)

description: normal_GetM_day3 (CNV)


title: CD3+ T cells purified from spleens in isograft C57BL/6 recipient mice C2

value: isografts


title: cell-line-07_IPSC (CNV)

description: cell-line-07_IPSC (CNV)


title: cell-line-04_IPSC (CNV)

description: cell-line-04_IPSC (CNV)


title: cell-line-03_IPSC (CNV)

description: cell-line-03_IPSC (CNV)


title: cell-line-01_IPSC (CNV)

description: cell-line-01_IPSC (CNV)


title: cell-line-06_IPSC (CNV)

description: cell-line-06_IPSC (CNV)


title: cell-line-02_IPSC (CNV)

description: cell-line-02_IPSC (CNV)


title: control-gfp_IPSC (CNV)

description: control-gfp_IPSC (CNV)


title: cell-line-13_IPSC (CNV)

description: cell-line-13_IPSC (CNV)


title: S36_SINGLE_COLONY-A5 (RNA-seq)

description: S36_SINGLE_COLONY-A5 (RNA-seq)

data_processing:
Low quality bases and sequencing adaptors of 36 raw fastq files RNA-seq containing single 61bp-long reads were trimmed using Trim Galore (V 0.6.0, https://github.com/FelixKrueger/TrimGalore)
Reads were mapped to the mm9 reference genome using HISAT2 (V 2.1.0) with default parameters
Read counting was performed using featureCounts (V 1.6.2) with (Mus_musculus.NCBI37.gtf annotation)
Differential gene expression analysis was performed using DESeq2_1.26.0 package
Unsupervised hierarchical clustering was performed for 10,000 most variable genes among ESCs, bdTSCs, fibroblasts and cells during reprogramming
Genome_build: mm9
Supplementary_files_format_and_content: FPKM bed file for each sample

source_name: embryonic stem cells

extract_protocol:
pooled libraries were sequenced on an Illumina NextSeq 500 platform to generate 75-bp single reads
RNA was isolated using the Qiagen RNeasy kit. mRNA libraries were prepared using the SENSE mRNA-seq library prep kit V2 (Lexogen)


title: S38_TSC_B (RNA-seq)

description: S38_TSC_B (RNA-seq)

source_name: blastocyst-derived  trophoblast stem cells

value: trophoblast stem cells


title: d6_S1 (scRNA-seq)

description: d6_S1 (RNA-seq)

data_processing:
SC-RNA-seq libraries were generated from each time point using the 10X Genomics. The cellranger-3.0.2, https://github.com/10XGenomics/cellranger was used for mapping of the 10x single cell RNA-seq data. Read1 data of pooled cells were split into single-cell data using the barcode sequences contained in the first 16 bps. The next 10 bps were recorded as unique molecular identifiers (UMIs). Read2 with 75 bp were aligned to the mm9 reference genome
We used Seurat (V 3.1.4) to pre-processing the data and perform clustering. The function 'FindAllMarkers' to identify the marker genes for each of the clusters in the UMAP representation
Genome_build: mm9
Supplementary_files_format_and_content: feature, matrix and barcode tables

source_name: GETM and OSKM reprogrammed stem cells

extract_protocol:
Single cell RNA libraries were prepared using Chromium Single Cell 3' Library Kit v2 (10X genomics, 120234) and the generated libraries were sequenced using Illumina NextSeq 500 platform.
Reprogrammable cells at day 6 or 12 were prepared as instructed in the 10X Genomics cell preparation guidelines. Briefly, cells were trypsinized and centrifuged at 1000 RPM for 3 minutes, then were washed twice with PBSx1 containing 0.04% BSA and cleaned from cell debris and large clumps by filtering throw mesh paper. Next, resuspended cells were subjected to dead cell removal kit (MACS, 130-090-101) to remove any non-viable cells. Cell viability were estimated using trypan blue staining. Cells were then resuspended in PBSx1 with 0.04% BSA at the concentration 1000 cells/µl and 4000 cells from each condition were subjected to 10x Genomics.

value: OSKM and GETM


title: S30_GETM_D18_B (RNA-seq)

description: S30_GETM_D18_B (RNA-seq)


title: S34_GETM_D31_B (RNA-seq)

description: S34_GETM_D31_B (RNA-seq)


title: cell-line-12_IPSC (CNV)

description: cell-line-12_IPSC (CNV)


title: cell-line-11_IPSC (CNV)

description: cell-line-11_IPSC (CNV)


title: cell-line-09_IPSC (CNV)

description: cell-line-09_IPSC (CNV)


title: cell-line-08_IPSC (CNV)

description: cell-line-08_IPSC (CNV)


title: cell-line-05_IPSC (CNV)

description: cell-line-05_IPSC (CNV)


title: d12_S1 (scRNA-seq)

description: d12_S1 (RNA-seq)


title: S27_GETM_D15_A (RNA-seq)

description: S27_GETM_D15_A (RNA-seq)


title: S26_GETM_D12_B (RNA-seq)

description: S26_GETM_D12_B (RNA-seq)


title: S37_TSC_A (RNA-seq)

description: S37_TSC_A (RNA-seq)


title: S35_SINGLE_COLONY-AB (RNA-seq)

description: S35_SINGLE_COLONY-AB (RNA-seq)


title: S33_GETM_D31_A (RNA-seq)

description: S33_GETM_D31_A (RNA-seq)


title: S23_GETM_D09_A (RNA-seq)

description: S23_GETM_D09_A (RNA-seq)


title: S25_GETM_D12_A (RNA-seq)

description: S25_GETM_D12_A (RNA-seq)


title: S22_GETM_D06_B (RNA-seq)

description: S22_GETM_D06_B (RNA-seq)


title: S32_GETM_D21_B (RNA-seq)

description: S32_GETM_D21_B (RNA-seq)


title: S29_GETM_D18_A (RNA-seq)

description: S29_GETM_D18_A (RNA-seq)


title: S28_GETM_D15_B (RNA-seq)

description: S28_GETM_D15_B (RNA-seq)


title: S16_ESC_B (RNA-seq)

description: S16_ESC_B (RNA-seq)


title: S19_GETM_D03_A (RNA-seq)

description: S19_GETM_D03_A (RNA-seq)


title: S31_GETM_D21_A (RNA-seq)

description: S31_GETM_D21_A (RNA-seq)


title: S13_OSKM_D20_A (RNA-seq)

description: S13_OSKM_D20_A (RNA-seq)


title: S14_OSKM_D20_B (RNA-seq)

description: S14_OSKM_D20_B (RNA-seq)


title: S12_OSKM_D15_B (RNA-seq)

description: S12_OSKM_D15_B (RNA-seq)


title: S24_GETM_D09_B (RNA-seq)

description: S24_GETM_D09_B (RNA-seq)


title: S09_OSKM_D12_A (RNA-seq)

description: S09_OSKM_D12_A (RNA-seq)


title: S20_GETM_D03_B (RNA-seq)

description: S20_GETM_D03_B (RNA-seq)


title: S06_OSKM_D06_B (RNA-seq)

description: S06_OSKM_D06_B (RNA-seq)


title: S04_OSKM_D03_B (RNA-seq)

description: S04_OSKM_D03_B (RNA-seq)


title: S21_GETM_D06_A (RNA-seq)

description: S21_GETM_D06_A (RNA-seq)


title: S05_OSKM_D06_A (RNA-seq)

description: S05_OSKM_D06_A (RNA-seq)


title: S18_MEFs_D (RNA-seq)

description: S18_MEFs_D (RNA-seq)

source_name: mouse embryonic fibroblasts

value: embryonic fibroblasts


title: S15_ESC_A (RNA-seq)

description: S15_ESC_A (RNA-seq)


title: TSC_Oct4_A_R3_R2 (RRBS)

description: TSC_Oct4_A_R3_R2 (RRBS)

data_processing:
Low quality bases and sequencing adaptors of 45 raw fastq files were trimmed using Trim galore (V 0.6.0)
Reads were mapped to the mm9 reference genome using Bsmap (V 2.90) with flags -S 10 -R -p 8 -D C-CGG
Bam files belonging to same reprogramming system and day were merged to ensure maximum overlap between all samples.
Methylation beta values were extracted from the BAM files using wgbs_tools (https://github.com/nloyfer/wgbs_tools)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig with beta values for each sample
Supplementary_files_format_and_content: beta file for each sample. This is a binary table storing the number of methylated and unmethylated observations for each CpG. See https://github.com/nloyfer/wgbs_tools

extract_protocol:
The RRBS libraries were sequenced by Illumina HiSeq 2000 platform.
RRBS assay was performed as previously described (Boyle et al., 2012), briefly, 20ng of genomic DNA were digested with Msp1 restriction enzyme (NEB, R0106L), DNA fragments were end-repaired and A-Tailed using Klenow fragment (3'-5- exo-) (NEB, M0212L), the DNA fragments were then size selected using AMPure XP beads (Beckman Coulter Genomics, A63881) and ligated to illumina adaptors (Illumina, PE-940-2001) using T4 ligase (NEB, M0202M). The samples were then subjected to two consecutive bisulfite conversions using EpiTect Bisulfite Kit (QIAGEN, 59104) and PCR using PfuTurbo Cx hotstart DNA polymerase (Agilent Technologies, 600412).


title: S17_MEFs_C (RNA-seq)

description: S17_MEFs_C (RNA-seq)


title: S11_OSKM_D15_A (RNA-seq)

description: S11_OSKM_D15_A (RNA-seq)


title: S10_OSKM_D12_B (RNA-seq)

description: S10_OSKM_D12_B (RNA-seq)


title: S08_OSKM_D09_B (RNA-seq)

description: S08_OSKM_D09_B (RNA-seq)


title: OSKM_D6A_R2_R2 (RRBS)

description: OSKM_D6A_R2_R2 (RRBS)


title: S07_OSKM_D09_A (RNA-seq)

description: S07_OSKM_D09_A (RNA-seq)


title: OSKM_D20A_R3_R2 (RRBS)

description: OSKM_D20A_R3_R2 (RRBS)


title: OSKM_D20A2_R4_R2 (RRBS)

description: OSKM_D20A2_R4_R2 (RRBS)


title: OSKM_D15A_R3_R2 (RRBS)

description: OSKM_D15A_R3_R2 (RRBS)


title: S02_MEFs_B (RNA-seq)

description: S02_MEFs_B (RNA-seq)


title: S01_MEFs_A (RNA-seq)

description: S01_MEFs_A (RNA-seq)


title: TSC_Oct4_B_R3_R2 (RRBS)

description: TSC_Oct4_B_R3_R2 (RRBS)


title: OSKM_D0B2_R3_R2 (RRBS)

description: OSKM_D0B2_R3_R2 (RRBS)


title: OSKM_D12B1_R3_R2 (RRBS)

description: OSKM_D12B1_R3_R2 (RRBS)


title: TSC_OCT4_A3_R4_R2 (RRBS)

description: TSC_OCT4_A3_R4_R2 (RRBS)


title: ITSC_SC_A3_R4_R2 (RRBS)

description: ITSC_SC_A3_R4_R2 (RRBS)

source_name: induced trophoblast stem cells


title: OSKM_D0A_R2_R2 (RRBS)

description: OSKM_D0A_R2_R2 (RRBS)


title: OSKM_D9_R1_R2 (RRBS)

description: OSKM_D9_R1_R2 (RRBS)


title: ITSC_R1_R2 (RRBS)

description: ITSC_R1_R2 (RRBS)


title: OSKM_D9B2_R4_R2 (RRBS)

description: OSKM_D9B2_R4_R2 (RRBS)


title: GETM_D9_R1_R2 (RRBS)

description: GETM_D9_R1_R2 (RRBS)


title: OSKM_D9A_R2_R2 (RRBS)

description: OSKM_D9A_R2_R2 (RRBS)


title: OSKM_D6_R1_R2 (RRBS)

description: OSKM_D6_R1_R2 (RRBS)


title: OSKM_D6A3_R4_R2 (RRBS)

description: OSKM_D6A3_R4_R2 (RRBS)


title: GETM_D6_R1_R2 (RRBS)

description: GETM_D6_R1_R2 (RRBS)


title: GETM_D9A_R2_R2 (RRBS)

description: GETM_D9A_R2_R2 (RRBS)


title: OSKM_D15_R1_R2 (RRBS)

description: OSKM_D15_R1_R2 (RRBS)


title: GETM_D6A2_R4_R2 (RRBS)

description: GETM_D6A2_R4_R2 (RRBS)


title: OSKM_D15B1_R_R2 (RRBS)

description: OSKM_D15B1_R_R2 (RRBS)


title: S03_OSKM_D03_A (RNA-seq)

description: S03_OSKM_D03_A (RNA-seq)


title: OSKM_D12_R1_R2 (RRBS)

description: OSKM_D12_R1_R2 (RRBS)


title: GETM_D18B_R2_R2 (RRBS)

description: GETM_D18B_R2_R2 (RRBS)


title: OSKM_D0_R1_R2 (RRBS)

description: OSKM_D0_R1_R2 (RRBS)


title: OSKM_D12A_R3_R2 (RRBS)

description: OSKM_D12A_R3_R2 (RRBS)


title: GETM_D18A_R2_R2 (RRBS)

description: GETM_D18A_R2_R2 (RRBS)


title: GETM_D12_R1_R2 (RRBS)

description: GETM_D12_R1_R2 (RRBS)


title: ITSC_2Aplus2B_R2_R2 (RRBS)

description: ITSC_2Aplus2B_R2_R2 (RRBS)

value: pluripotent stem cells


title: IPSC_R1_R2 (RRBS)

description: IPSC_R1_R2 (RRBS)


title: GETM_D9B_R2_R2 (RRBS)

description: GETM_D9B_R2_R2 (RRBS)


title: Patient E, PTEN lost section

description: E-

value: Melanoma

value: E

value: PTEN lost


title: GETM_D9B2_R4_R2 (RRBS)

description: GETM_D9B2_R4_R2 (RRBS)


title: GETM_D6A_R2_R2 (RRBS)

description: GETM_D6A_R2_R2 (RRBS)


title: OSKM_Utf1_D03_b1 (ATAC-seq)

description: OSKM_Utf1_D03_b1 (ATAC-seq)

data_processing:
Fastq files were mapped to the mm9 reference using bwa [version 0.7.17-r1188].
The mapped reads were converted to BAM format and filtered by mapping quality (MAPQ) of >=10, retaining only properly aligned pairs (samtools -F 1796 flag)
Bigwig coverage tracks were generated using deepTools bamCoverage [version 3.4.1] with the following flags: --normalizeUsing RPGC -bs 50 -e 500 --effectiveGenomeSize 2150570000.
Coverage peaks were called using MACS [version 2.1.2] with flags -g mm --slocal=2000 --llocal=20000 --nomodel --extsize=300 -f BAMPE.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig generated using deepTools
Supplementary_files_format_and_content: bed genereted using MACS2

extract_protocol:
The samples were purified using Qiagen MiniElute kit (QIAGEN, 28204), Transposed fragments were directly PCR amplified and sequenced on an Illumina NextSeq 500 platform to generate 2 × 36-bp paired-end reads.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2013). Briefly, cells were trypsinized and 50,000 cells were counted and incubated in lysis buffer to isolate nuclei. Nuclei were then resuspended in transposase reaction mix for 30 min at 37 °C (Illumina, Fc-121-1030).

tag: pluripotent reporter


title: OSKM_Utf1_D09_b1 (ATAC-seq)

description: OSKM_Utf1_D09_b1 (ATAC-seq)


title: OSKM_Nanog_D09_b1 (ATAC-seq)

description: OSKM_Nanog_D09_b1 (ATAC-seq)

value: Nanog


title: OSKM_Esrrb_D06_b1 (ATAC-seq)

description: OSKM_Esrrb_D06_b1 (ATAC-seq)

value: Esrrb


title: GETM_D12A_R2_R2 (RRBS)

description: GETM_D12A_R2_R2 (RRBS)


title: GETM_D21A_R2_R2 (RRBS)

description: GETM_D21A_R2_R2 (RRBS)


title: OSKM_All_D09_b1 (ATAC-seq)

description: OSKM_All_D09_b1 (ATAC-seq)

value: All


title: OSKM_All_D09_b2 (ATAC-seq)

description: OSKM_All_D09_b2 (ATAC-seq)


title: GETM_D18A3_R4_R2 (RRBS)

description: GETM_D18A3_R4_R2 (RRBS)


title: GETM_D18_R1_R2 (RRBS)

description: GETM_D18_R1_R2 (RRBS)


title: GETM_D21A3_R4_R2 (RRBS)

description: GETM_D21A3_R4_R2 (RRBS)


title: OSKM_All_D03_b1 (ATAC-seq)

description: OSKM_All_D03_b1 (ATAC-seq)


title: GETM_D12A2_R4_R2 (RRBS)

description: GETM_D12A2_R4_R2 (RRBS)


title: GETM_Utf1_D06_b1 (ATAC-seq)

description: GETM_Utf1_D06_b1 (ATAC-seq)


title: GETM_Utf1_D03_b1 (ATAC-seq)

description: GETM_Utf1_D03_b1 (ATAC-seq)


title: GETM_D0A_R2_R2 (RRBS)

description: GETM_D0A_R2_R2 (RRBS)


title: GETM_D0A2_R3_R2 (RRBS)

description: GETM_D0A2_R3_R2 (RRBS)


title: OSKM_All_D06_b2 (ATAC-seq)

description: OSKM_All_D06_b2 (ATAC-seq)


title: BYKE4_B_R3_R2 (RRBS)

description: BYKE4_B_R3_R2 (RRBS)


title: BYKE4_A_R3_R2 (RRBS)

description: BYKE4_A_R3_R2 (RRBS)


title: GETM_D21_R1_R2 (RRBS)

description: GETM_D21_R1_R2 (RRBS)


title: OSKM_Utf1_D06_b1 (ATAC-seq)

description: OSKM_Utf1_D06_b1 (ATAC-seq)


title: OSKM_Nanog_D06_b1 (ATAC-seq)

description: OSKM_Nanog_D06_b1 (ATAC-seq)


title: GETM_All_D03_b2 (ATAC-seq)

description: GETM_All_D03_b2 (ATAC-seq)


title: H3K4me2_OSKM_D09_B_S7 (ChIP-seq)

description: H3K4me2_OSKM_D09_B_S7 (ChIP-seq)

extract_protocol:
DNA was extracted using AMPure XP beads (Beckman Coulter Genomics, A63881). Chip sample libraries were prepared according to Illumina Genomic DNA protocol as described (Mikkelsen et al., 2007).
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Mendenhall et al., 2013). Briefly, cells were fixed for 10 min at RT with a final concentration of 0.8% formaldehyde. Formaldehyde was quenched with glycine for a final concentration of 125mM. The cells were then lysate with lysis buffer (100mM Tris-HCl, 300mM NaCl, 2% Triton® X-100, 0.2%v sodium deoxycholate, 10mM Cacl2) supplemented with EDTA free protease inhibitor Roche- 11873580001 for 20 min at Ice and the chromatin was digested by MNase (micrococcal nuclease)- Thermo Scientific™- 88216 for 20 min at 37OC. MNase was inactivated by 20mM EGTA. The fragmented chromatin was incubated with pre-bounded Dynabeads (A and G mix) - Invitrogen 10004D/ 10002D using H3K27ac antibody (Abcam, ab4729) and H3K4me2 antibody (Millipore, 07-030).  Samples were then washed twice with RIPA buffer, twice with RIPA high salt buffer (NaCl 360mM), twice with LiCl wash buffer (10mM Tris-Hcl, 250mM LiCl, 0.5% DOC, 1mM EDTA, 0.5% IGEPAL), twice with 10mM Tris-HCl pH=8. DNA was purified by incubating the samples with RNAse A (Thermo Scientific™ EN0531) for 30 min at 37OC followed by a 2 hours incubation with Proteinase K (Invitrogen™ 25530049). DNA was eluted by adding 2X concentrated elution buffer (10mM Tris-HCl, 300mM NaCl, 1% SDS, 2mM EDTA) and then reverse crosslinked overnight at 65OC.

tag: chip-seq antibody


title: OSKM_Esrrb_D09_b1 (ATAC-seq)

description: OSKM_Esrrb_D09_b1 (ATAC-seq)


title: OSKM_Nanog_D03_b1 (ATAC-seq)

description: OSKM_Nanog_D03_b1 (ATAC-seq)


title: OSKM_Esrrb_D03_b1 (ATAC-seq)

description: OSKM_Esrrb_D03_b1 (ATAC-seq)


title: H3K4me2_OSKM_D09_A_S4 (ChIP-seq)

description: H3K4me2_OSKM_D09_A_S4 (ChIP-seq)


title: GETM_Utf1_D09_b1 (ATAC-seq)

description: GETM_Utf1_D09_b1 (ATAC-seq)


title: OSKM_All_D03_b2 (ATAC-seq)

description: OSKM_All_D03_b2 (ATAC-seq)


title: OSKM_All_D06_b1 (ATAC-seq)

description: OSKM_All_D06_b1 (ATAC-seq)


title: H3K4me2_MEF_BYKE_B_S3 (ChIP-seq)

description: H3K4me2_MEF_BYKE_B_S3 (ChIP-seq)


title: H3K4me2_OSKM_D03_A_S7 (ChIP-seq)

description: H3K4me2_OSKM_D03_A_S7 (ChIP-seq)


title: GETM_Esrrb_D06_b1 (ATAC-seq)

description: GETM_Esrrb_D06_b1 (ATAC-seq)


title: GETM_Utf1_D03_b2 (ATAC-seq)

description: GETM_Utf1_D03_b2 (ATAC-seq)


title: H3K4me2_GETM_D06_B_S13 (ChIP-seq)

description: H3K4me2_GETM_D06_B_S13 (ChIP-seq)


title: GETM_Utf1_D06_b2 (ATAC-seq)

description: GETM_Utf1_D06_b2 (ATAC-seq)


title: GETM_Esrrb_D09_b1 (ATAC-seq)

description: GETM_Esrrb_D09_b1 (ATAC-seq)


title: GETM_Esrrb_D03_b1 (ATAC-seq)

description: GETM_Esrrb_D03_b1 (ATAC-seq)


title: H3K4me2_GETM_D03_A_S9 (ChIP-seq)

description: H3K4me2_GETM_D03_A_S9 (ChIP-seq)


title: H3K4me2_ESC_BYKE_B_S13 (ChIP-seq)

description: H3K4me2_ESC_BYKE_B_S13 (ChIP-seq)


title: H3K4me2_ESC_BYKE_A_S11 (ChIP-seq)

description: H3K4me2_ESC_BYKE_A_S11 (ChIP-seq)


title: GETM_All_D09_b2 (ATAC-seq)

description: GETM_All_D09_b2 (ATAC-seq)


title: GETM_All_D09_b1 (ATAC-seq)

description: GETM_All_D09_b1 (ATAC-seq)


title: GETM_All_D06_b2 (ATAC-seq)

description: GETM_All_D06_b2 (ATAC-seq)


title: GETM_All_D06_b1 (ATAC-seq)

description: GETM_All_D06_b1 (ATAC-seq)


title: H3K4me2_TSC_B_S17 (ChIP-seq)

description: H3K4me2_TSC_B_S17 (ChIP-seq)


title: GETM_All_D03_b1 (ATAC-seq)

description: GETM_All_D03_b1 (ATAC-seq)


title: H3K4me2_TSC_A_S15 (ChIP-seq)

description: H3K4me2_TSC_A_S15 (ChIP-seq)


title: H3K27ac_OSKM_D06_B_S6 (ChIP-seq)

description: H3K27ac_OSKM_D06_B_S6 (ChIP-seq)


title: H3K27ac_OSKM_D06_A_S18 (ChIP-seq)

description: H3K27ac_OSKM_D06_A_S18 (ChIP-seq)


title: H3K4me2_OSKM_D06_B_S5 (ChIP-seq)

description: H3K4me2_OSKM_D06_B_S5 (ChIP-seq)


title: H3K4me2_OSKM_D06_A_S17 (ChIP-seq)

description: H3K4me2_OSKM_D06_A_S17 (ChIP-seq)


title: H3K4me2_GETM_D09_B_S15 (ChIP-seq)

description: H3K4me2_GETM_D09_B_S15 (ChIP-seq)


title: H3K27ac_MEFs_B_S10 (ChIP-seq)

description: H3K27ac_MEFs_B_S10 (ChIP-seq)


title: H3K27ac_GETM_D09_B_S16 (ChIP-seq)

description: H3K27ac_GETM_D09_B_S16 (ChIP-seq)


title: H3K27ac_GETM_D06_B_S14 (ChIP-seq)

description: H3K27ac_GETM_D06_B_S14 (ChIP-seq)


title: H3K4me2_GETM_D06_A_S7 (ChIP-seq)

description: H3K4me2_GETM_D06_A_S7 (ChIP-seq)


title: H3K4me2_GETM_D03_B_S11 (ChIP-seq)

description: H3K4me2_GETM_D03_B_S11 (ChIP-seq)


title: H3K4me2_OSKM_D03_B_S9 (ChIP-seq)

description: H3K4me2_OSKM_D03_B_S9 (ChIP-seq)


title: H3K4me2_MEF_BYKE_A_S1 (ChIP-seq)

description: H3K4me2_MEF_BYKE_A_S1 (ChIP-seq)


title: H3K27ac_TSC_B_S18 (ChIP-seq)

description: H3K27ac_TSC_B_S18 (ChIP-seq)


title: H3K4me2_GETM_D09_A_S10 (ChIP-seq)

description: H3K4me2_GETM_D09_A_S10 (ChIP-seq)


title: H3K27ac_TSC_A_S16 (ChIP-seq)

description: H3K27ac_TSC_A_S16 (ChIP-seq)


title: H3K27ac_OSKM_D09_B_S8 (ChIP-seq)

description: H3K27ac_OSKM_D09_B_S8 (ChIP-seq)


title: T20496

status: Public on Apr 24 2022

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg19, using STAR in two-pass mode with GENCODE v19 annotation
Gene expression levels were quantified using RSEM.
Assembly: Hg19

source_name: lung tumor

extract_protocol:
Total RNA was extracted from frozen lung tissues using TRIzol (Invitrogen) according to the manufacturer’s protocol. Only RNA samples with RNA sufficient RNA were included for analysis.
Libraries suitable for paired-ended sequencing were generated using Illumina’s TruSeq Stranded Total RNA Library Prep Kit.

tag: batch

value: S

tag: histology

value: Squamous Cell Carcinoma


title: s_treat_group

status: Public on Apr 25 2022

city: Changchun

first: Xiaodan

last: Lu

address: 1183 Gongnong Road, Chaoyang District, Changchun City, Jilin Province

institute: Jilin Provincial General Hospital

data_processing:
pipline_version: RNA_RNAref_2018a
GraphPad Prism 9.0 (GraphPad Software Inc.) was used to create all of the images.
report_version: MRNA_v0.1
seq_platform: BGISEQ-500
SPSS 22.0 (SPSS Inc., IL, USA) was used for statistical analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary Granulosa Cell

growth_protocol: Collect the follicle flushing fluid(FFF) in a sterile container and promptly transport it to the laboratory. GCs were removed from the liquid using the standard stratified separation procedure. Centrifuge at FFF 2500g for 10 minutes, discard the supernatant, resuspend in PBS, add an equal volume of 0.25% trypsin, digest for 15 minutes at room temperature, stop the digestion with DMEM/F12 medium containing 10% FBS,then suspend and count again. centrifuge at 1000g for 10 minutes, discard the supernatant, resuspend in PBS, then transfer the suspension to the surface of an equal amount of lymphocyte separation solution slowly and carefully. Centrifuge for 10 min at 1500g. It is possible to lengthen the time until the distinction is visible. Wash once with DMEM/F12 medium containing 10% FBS, then suspend and count again.

extract_protocol:
The TransZol reagent (TransGen Biotech, Beijing, China) was used to extract total RNA from the cells. An iScript RT-PCR Kit (Bio-Rad, CA, USA) was used for reverse-transcribe 1 μg pure RNA. The real-time qPCR analysis was carried out on 7500fast Real-time PCR System (Applied Biosystems) with SYBR Green PCR Master Mix (Bio-Rad, California, USA). Denaturation (98℃, 5 mins), 40 cycles (98℃ for 30 s, 72℃ for 1 min) were used for real-time PCR. The 2-△△Ct technique was used to calculate the expression of target genes, which was then normalized to 18S.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Primary ovarian GCs were obtained and cultivated two days prior to the start of the experiment. Cell densities of 0.1×104 cells/well and 1×105 cells/well were used to seed GCs in 96-well and 6-well plates, respectively. Human ovarian GCs are treated with various doses of zinc sulfate and zinc high affinity chelating agent TPEN.

value: human ovarian granulosa cells

value: XX

value: Zinc treatment (50mM)

tag: time

value: Day 1


title: T18603


title: T15883

value: B


title: H3K27ac_OSKM_D03_B_S10 (ChIP-seq)

description: H3K27ac_OSKM_D03_B_S10 (ChIP-seq)

value: OSKM

value: embryonic stem cells


title: T12952


title: T14366


title: H3K27ac_GETM_D03_A_S10 (ChIP-seq)

description: H3K27ac_GETM_D03_A_S10 (ChIP-seq)

value: GETM


title: H3K27ac_ESC_BYKE_B_S14 (ChIP-seq)

description: H3K27ac_ESC_BYKE_B_S14 (ChIP-seq)


title: H3K27ac_ESC_BYKE_A_S12 (ChIP-seq)

description: H3K27ac_ESC_BYKE_A_S12 (ChIP-seq)


title: T17404


title: H3K27ac_OSKM_D09_A_S5 (ChIP-seq)

description: H3K27ac_OSKM_D09_A_S5 (ChIP-seq)


title: s_control_group

tag: treatment

value: Control group, normal cells are not treated


title: T12696


title: H3K27ac_MEFs_A_S48 (ChIP-seq)

description: H3K27ac_MEFs_A_S48 (ChIP-seq)

value: embryonic fibroblasts


title: T15226

value: Adenocarcinoma


title: H3K27ac_GETM_D06_A_S19 (ChIP-seq)

description: H3K27ac_GETM_D06_A_S19 (ChIP-seq)


title: T20172


title: T20080


title: H3K27ac_GETM_D03_B_S12 (ChIP-seq)

description: H3K27ac_GETM_D03_B_S12 (ChIP-seq)


title: T12869

value: Non Small Cell Lung Cancer


title: T18100


title: T21469


title: T15618

value: H


title: T13965


title: T18544


title: T13761


title: T12650


title: T13473


title: T13054


title: T13388


title: T13372


title: T12664


title: T12860


title: T14352


title: T17126


title: T17624


title: T13539


title: 30795T

value: Lung Cancer


title: 1507300070T


title: 1507400923T


title: 1507300434T


title: 1507209471T


title: 30382T


title: 1507206893T


title: 1507207285T


title: 1507204497T


title: 21207T


title: 1507400090T


title: 1507401220T


title: T20155


title: 1507300598T


title: 1507208809T


title: 1507208696T


title: 1507208197T


title: 1507208573T


title: 1507208979T


title: 13077T


title: 1507207694T


title: 1507207238T


title: 1507203348T


title: 11134T


title: 1507202838T


title: 13809T


title: 1318401896T


title: 12952T


title: 13054T


title: 12900T


title: 12696T S3


title: 12839T


title: 12860T


title: 14468T


title: 15053T


title: 15883T


title: 12664T


title: 10419T


title: 14352T


title: 24916T


title: 23709T


title: 22020T


title: 23255T


title: 20997T


title: 18193T


title: 138401831T


title: 19032T


title: 17548T


title: H3K27ac_GETM_D09_A_S11 (ChIP-seq)

description: H3K27ac_GETM_D09_A_S11 (ChIP-seq)


title: HSC from injured liver (4xCCl4) RS016

status: Public on Apr 07 2022

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

institute: Columbia University

description:
HSC from injured liver (4xCCl4)
scRNA-seq (10x) on FACS-sorted-HSC

data_processing:
10x genomics' cellranger software version 2.0.0 was used to process the data.
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
raw counts in the following formats: h5 and barcodes.tsv, genes.tsv, matrix.mtx
Genome_build: mm10

source_name: liver

extract_protocol:
For single cell RNA-seq of the whole liver, hepatic cell populations were obtained by perfusing and digesting the liver and enriched in non-parenchymal.
HSC were obtained perfusing and digesting the liver, followed by gradient centrifucation (Mederacke et al, Nat Protocol 2015) and FACS sorting for LratCre-induced TdTom.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina HiSeq and NovaSeq 6000 sequencing system instrument at the JP Sulzberger Columbia Genome Center.

treatment_protocol: Before HSC or whole liver cells isolation, mice were treated with one or multiple injection of CCl4  or were fed with a Fructose, Palmitate, Cholesterol and Trans-Fat (FPC) for 2 months after hydrodynamic tail vein injection of pT3-EF1α-TAZS89A plasmid in combination with sleeping beauty transposase SB13 or fed with a a L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline (CDAA-diet)

value: LratCre+, TdTom+ in C57BL/6J

tag: liver damage

value: CCl4 (4 times)

value: Hepatic Stellate Cells


title: HSC from injured liver (1xCCl4) RS015

description:
HSC from injured liver (1xCCl4)
scRNA-seq (10x) on FACS-sorted-HSC

value: CCl4  (1 time)


title: 14366T


title: Pou2af1 -/- CD8+ , 4

status: Public on Mar 24 2022

city: Montreal

first: Sylvie

last: Lesage

address: 2900 Bd Édouard-Montpetit

country: Canada

institute: Universite de Montreal

description:
Activated cells
CD8_KO_4

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the GRCm38 reference genome (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
Raw reads extracted from STAR were normalized using DESeq2 v1.26.0
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized counts
Supplementary_files_format_and_content: raw counts

source_name: Sorted CD8+ T cells

growth_protocol: Sorted T cells were activated in vitro for 2 days using anti-CD3 and anti-CD28 antibodies

extract_protocol:
Trizol
KAPA RNA HyperPrep PolyA (Roche)

value: Spleen

tag: age

value: 12 weeks

tag: genotype/variation


title: 13761T


title: 13911T


title: Pou2af1 -/- CD8+ , 3

description:
Activated cells
CD8_KO_3


title: Pt2_1

status: Public on Mar 31 2022

city: New York

first: Daylon

last: James

address: 515 East 71st

institute: Weill Cornell Medicine

data_processing:
fastq files were processed using CellRangr count and individual libraries were aggregated using CellRangr aggr
Resultant features/barcodes file was imported into R Studio and used to generate a Seurat Object in Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature matrix and barcodes

source_name: human antral follicle derived cells

growth_protocol: cells were isolated from primary patient derived ovarian follicles

extract_protocol:
cells were enzymatically separated and sorted by fluorescence activated cell sorting
RNA libraries were prepared for sequencing using version 3 10x Chromium library preparation kits

value: stromal cells

tag: source

value: ovarian antral follicle

tag: follicle size

value: 2 mm


title: 13320T

value: B


title: Don1_4

value: granulosa and stroma cells

value: 1 mm


title: 20080T


title: Pou2af1 -/- CD8+ , 2

description:
Activated cells
CD8_KO_2


title: Pou2af1+/- CD8+ , 4

description:
Activated cells
CD8_Het_4


title: Pou2af1 -/- CD8+ , 1

description:
Activated cells
CD8_KO_1


title: injured liver (8xCCl4) RS025

description:
injured liver (8xCCl4)
scRNA-seq (10x) on fresh isolated liver cells

value: CCl4 (8 times)

value: all cell types


title: Pou2af1+/- CD8+ , 3

description:
Activated cells
CD8_Het_3