title: 4121 GSC Input


title: Non-COV18 [GC1003234]

status: Public on Aug 28 2022

type: SRA

city: Vienna

first: Laura

middle: de

last: Rooij

address: Lazarettgasse 14

country: Austria

institute: CeMM

description:
GC1003234
bulk RNA-seq

library_source: transcriptomic

data_processing:
Bulk RNA-seq: Single-end reads of 50 bp length were produced with aminimum of 1 million reads per sample. Quality control of raw reads was performed with FastQC v0.11.7, available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc . Adapters were filtered with ea-utils fastq-mcf v1.05 (https://github.com/ExpressionAnalysis/ea-utils). Splice-aware alignment was performed with HiSAT2 against the human reference genome hg38. Reads mapping to multiple loci in the referencegenome were discarded. Resulting BAM files were handled with Samtoolsv1.5. Quantification of reads per genewas performed with htseq-count v2.7.14.
Genome_build: human reference genome GRCh38
Supplementary_files_format_and_content: raw counts (.csv) and accompanying metadata/cell annotations (.csv).

molecule: total RNA

organism: Homo sapiens

source_name: lung

extract_protocol: Bulk RNA-seq: For RNA preparation from formalin fixed paraffin embedded (FFPE) material, up to 5 10-um tissue sections were pooled, deparaffinized with Deparaffinization Solution (Qiagen) and RNA was isolated using the miRNEASY FFPE kit (Qiagen) according to the manufacturer’s instructions. Sequencing libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq library prep kit according to the manufacturer’s instructions. Samples were indexed to allow for multiplexing. Library quality and size range was assessed using a Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA). Libraries were diluted to a final concentration of 2nM and subsequently sequenced on an Illumina HiSeq4000 instrument.

tag: condition

tag: tissue

value: lung

tag: sample type

value: autopsy


title: Control_3_S3

city: Chicago

first: Md Zahid

last: Akhter

state: IL

address: 835 S Wolcott Ave

department: Pharmacology & Regenerative Medicine

country: USA

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to reference genome mm10 using STAR (Dobin et al., 2013). Ensembl gene expression was quantified using featureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: Control_vs_KO_Differential_Expression.xlsx

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

growth_protocol: FAK floxe and EC-FAK knockout mice were maintained following Institute Animal Care and Use guidelines.

extract_protocol:
Lungs harvested from FAK flox and EC-FAK knockout mice  were subjected to single cell suspension and stained with anti-CD31 and CD45 antibodies. Endothelial cells (CD31+CD45-) were flow sorted and RNA isolation was performed using Trizol. Quality check was done by Bioanalyzer. RNA-seq was performed on samples with RIN 7-10.
Oligo-dT library

value: Lung

tag: cell type

value: Flow sorted endothelial cells (CD31+CD45-) from mice lung

tag: genotype

value: FAK Flox


title: Non-COV19 [GC1003233]

description:
GC1003233
bulk RNA-seq


title: Non-COV5 [GC1003232]

description:
GC1003232
bulk RNA-seq


title: ATAC_387 NSTC

city: Beijing

first: Jiayi

last: Chen

address: Taiping Road 27, Haidian district

country: China

institute: National Center of Biomedical Analysis, Beijing

library_source: genomic

data_processing:
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v 2.4.2) and generated SAM files were converted to BAM files using Samtools (v 1.11) using the view function.
Samblaster (v 0.1.26) was used to further sort, index and remove potential PCR duplicates (rmdup) from BAM files which were converted to BigWig files using Deeptools (v 3.5.3; bamCoverage —ignoreDuplicates —skipNonCoveredRegions —normalizeUsing RPKM -p 16 —extendReads —binSize 50).
BigWig files were visualized using the Integrative Genomics Viewer (IGV; Broad Institute).
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: 387 NSTC

growth_protocol: GSCs and NPC were maintained in the Neurobasal™ Medium supplemented with B-27™ Supplement, sodium pyruvate, L-glutamine, penicillin-streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF) and 10 ng/ml epidermal growth factor (EGF). GSCs were cultured in DMEM with 10% FBS for 7 days to differentiate into paried NSTCs.

extract_protocol:
5×104 cells were harvest and following the manufacturer’s protocol of the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD501).
Libraries were prepared according to Illumina's standard protocol.

tag: cell line

value: 387 NSTC

value: Non-stem tumor cell


title: ATAC_4121 NSTC

source_name: 4121 NSTC

value: 4121 NSTC


title: H2_H

city: Cambridge

first: Thomas

middle: James

last: LaSalle

state: MA

address: 415 Main Street

institute: Broad Institute

description:
Neutrophil_RNAseq_Count_Matrix.txt.gz
Neutrophil_RNAseq_TPM_Matrix.txt.gz

data_processing:
A custom FASTA was generated from the Homo sapiens (human) genome assembly GRCh38 (hg38) following exclusion of ALT, HLA, and Decoy contigs according to documentation in the Broad Institute GTEx-TOPMed RNA-seq pipeline (https://github.com/broadinstitute/gtex-pipeline/), with an appended SARS-CoV2 genome. GENCODE v35 with the appended SARS-CoV2 GTF was used for annotation. Raw FASTQ files were aligned to the custom genome FASTA in the Terra platform with the Broad Institute GTEx pipeline using STAR v2.5.3a, and expression quantification based on a collapsed annotation was performed using RSEM v1.3.0.
RNA-SeQC 2 (https://github.com/getzlab/rnaseqc) was used to calculate quality control metrics for each sample.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) following exclusion of ALT, HLA, and Decoy contigs with an appended SARS-CoV2 genome
Supplementary files format and content: Neutrophil_RNAseq_Count_Matrix.txt.gz: RNA-seq count matrix provided as a gzipped .txt file
Supplementary files format and content: Neutrophil_RNAseq_TPM_Matrix.txt.gz: RNA-seq TPM matrix provided as a gzipped .txt file

source_name: Enriched neutrophils from whole blood

extract_protocol:
Blood samples were collected in EDTA vacutainer tubes and transported to the laboratory. Neutrophils were isolated from whole blood via negative selection using the EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL Technologies, Cat# 19666). All described procedures in this section were done at room temperature unless otherwise noted. Between 0.25-0.5 mL whole blood was lysed with ACK Lysis Buffer (ThermoFisher Scientific, Cat# A1049201) in a 15 mL conical tube and white blood cells were pelleted at 300 xg for 5 min. Following aspiration of the lysed red blood cells and resuspension of the pellet in 250 µL 1 mM EDTA in PBS, 50 µL each of the RapidSpheres and Isolation Cocktail were added to the cell suspension. Following a 5 min incubation, sample volumes were completed to 4 mL with 1 mM EDTA in PBS, mixed gently, and placed on an EasyEights™ EasySep™ Magnet (STEMCELL Technologies, Cat# 18103) for 5 min. Next, supernatants were transferred to new 15 mL conical tubes, 25 µL RapidSpheres were added, and the samples were gently mixed and incubated for 5 min. Samples were then placed on the magnet, and after 5 min incubation supernatants were transferred to new tubes, and were placed immediately on the magnet for a second incubation before the supernatants containing the enriched neutrophil populations were collected, pelleted, and resuspended in 1 mM EDTA in PBS. Cells were counted on a TC20™ Automated Cell Counter (Bio-Rad Laboratories, Inc., Cat# 1450102) with trypan blue staining for dead cell exclusion. Neutrophils were then lysed in TCL Buffer (QIAGEN, Cat# 1031576) with 1% 2-Mercaptoethanol at a concentration of 1000 cells/µL, flash-frozen on dry ice, and then stored at -80 °C until use. cDNA was prepared from bulk populations of 2x104 neutrophils per sample via the Smart-Seq2 protocol with some modifications to the reverse transcription step. 20 µL (at a concentration of 1000 cells/µL) of neutrophil lysates were thawed on ice and plated into 96-well plates prior to centrifugation at 1500 rpm for 30 s. RNA was purified with Agencourt RNAClean XP SPRI beads (Beckman Coulter, Cat# A63987) and then the samples were resuspended in 4 µL of Mix-1 [Per 1 sample: 1 µl (10 µM) RT primer (DNA oligo) 5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′; 1 µl (10 µM) dNTPs; 1µl (10%, 4 U/µl) recombinant RNase inhibitor; 1 µl nuclease-free water], denatured at 72 °C for 3 min and placed immediately on ice for 1 min before 7 µL of Mix-2 [Per 1 sample: 0.75 µl nuclease-free water; 2 µl 5X RT buffer (Thermo Fisher Scientific, Cat# EP0753); 2 µl (5 M) betaine; 0.9 µl (100 mM) MgCl2; 1 µl (10 µM) TSO primer (RNA oligo with LNA) 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′; 0.25 µl (40 U/µl) recombinant RNase inhibitor; 0.1 µl (200 U/µl) Maxima H Minus Reverse Transcriptase] was added. Reverse transcription reactions were performed at 50 °C for 90 min, followed by 5 min incubation at 85 °C. Then, 14 µL of Mix-3 [Per 1 sample: 1 µl nuclease-free water; 0.5 µl (10 µM) ISPCR primer (DNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGT-3′; 12.5 µl 2X KAPA HiFi HotStart ReadyMix] was added to each well and the whole-transcriptome amplification step was performed at 98 °C for 3 min, followed by 16 cycles of [98 °C for 15 s, 67 °C for 20 s, and 72°C for 6 min], and final extension at 72C for 5 min. cDNA was purified using AgencourtAMPureXP SPRI beads (Beckman Coulter, Cat# A63881) as described97, to remove all primer residue. Quality control was performed on samples prior library construction and included: (1) concentration measurements via the Qubit dsDNA high sensitivity assay kit (Invitrogen, Cat# Q32854) on the Cytation 5 Microplate Reader (BioTek); (2) cDNA size distribution using the High-Sensitivity DNA Bioanalyzer Kit (Agilent, Cat# 5067-4626).
Libraries were generated using the Nextera XT Library Prep kit (Illumina, Cat# FC-131-1024) with custom indexing adapters in a 384-well PCR plate, followed by a cleanup step to remove residual primer dimers.

value: Enriched neutrophils from whole blood

tag: time point

value: H

tag: patient category

value: healthy

tag: covid-19 status


title: H1_H


title: 4121 NSTC Input

growth_protocol: 4121GSC were maintained in the Neurobasal™ Medium supplemented with B-27™ Supplement, sodium pyruvate, L-glutamine, penicillin-streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF) and 10 ng/ml epidermal growth factor (EGF). 4121GSC were cultured in DMEM with 10% FBS for 7 days to differentiate into 4121NSTC.

extract_protocol:
1×106 cells were harvest and following the manufacturer’s protocol of the SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology, Cat# 9003S).
Libraries were prepared according to Illumina's standard protocol.


title: 368_D7

value: COVID+


title: 362_D7


title: 355_DE

value: DE


title: 4121 GSC H3K27ac

value: glioblstoma stem cell

tag: chip antibody

value: H3K27ac (Millipore, #17-683)


title: ATAC_4121 GSC


title: ATAC_456 NSTC

source_name: 456 NSTC

value: 456 NSTC


title: Non-COV20 [GC1003230]

description:
GC1003230
bulk RNA-seq


title: ATAC_NPC

source_name: NPC

value: NPC

value: neural progenitor cell


title: ATAC_387 GSC

source_name: 387 GSC

value: 387 GSC


title: 4121 GSC H3K4me3

value: H3K4me3 (Millipore, #07-473)


title: Non-COV21 [GC1003229]

description:
GC1003229
bulk RNA-seq

value: lung

value: autopsy


title: ST3

city: Hangzhou

first: junli

last: liu

state: zhejiang

address: 866 Yuhangtang

institute: Zhejiang university

description: control

data_processing:
Poly-N, adapter and low-quality were removed by in-house perl scripts ，Quality control analysis was performed by ng_qc.
Clean reads were aligned to the Sus scrofa ensembl 76 using Tophat v2.0.9 with the following configurations two passMode Basic --hhlibraryhtypecfrhfirststrand.
LncRNAs were identified using four predicted tools including predictor of lncRNAs and mRNAs based on CNCI (Coding-Non-Coding-Index) (v2) , CPC (Coding Potential Calculator) (0.9-r2)  and Pfam Scan (v1.3) ，PhyloCSF (phylogenetic codon substitution frequency) (v20121028)
Cuffdiff v2.1.1 was used to calculate the FPKMs of both lncRNAs and mRNAs in each sample
Sus scrofa ensembl 76
Genome_build: tab-delimited excel files include  normalized  values for each Sample

organism: Sus scrofa

source_name: ST cells

extract_protocol:
Total RNA was isolated from infected cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: ST cells were infected with PDCoV at a multiplicity of infection (MOI) of 10 and harvested at 11 hour post infection or without, respectively.

value: swine testicular cells

tag: treatment

value: uninfected


title: endometrium_middle secretory phase of RIF_rep1

type: RNA

city: Lanzhou

first: Lin

last: Liu

address: 1547 Duanjiatan Road, Chengguan District

institute: Reproductive Center of the First Hospital of Lanzhou University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

source_name: endometrium,middle secretory phase of RIF,replicate 1

label_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated from snap-frozen endometrial biopsies of the different groups using the Trizol reagent (Invitrogen, Carlsbad, USA) following the manufacturer’s instructions. The quantity and quality of the RNA samples were determined using NanoDrop ND-1000 instrument (Thermo, Wilmington, DE).

value: middle secretory phase endometrium

tag: gender

value: female


title: endometrium_middle secretory phase of RIF_rep2

source_name: endometrium,middle secretory phase of RIF,replicate 2


title: 355_D7

value: Enriched neutrophils from whole blood


title: Non-COV2 [GC1003227]

description:
GC1003227
bulk RNA-seq


title: ATAC-seq_iMK-D7-rep2

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

data_processing:
Raw sequencing data were converted to fastq files using Illumina bcl2fastq (version 2.20; San Diego, CA, USA) and aligned to the human genome reference (Homo sapiens UCSC.hg19 x). The CellRanger analysis pipeline was used to generate a digital gene expression matrix from these data. The raw digital gene expression matrix data were further filtered as follows: cells with a very small library size (<2,500) and a very high (>0.15) mitochondrial genome transcript ratio were removed. After filtering, the data were processed using the standard workflow implemented in Monocle3.
After removal of the adaptor sequences, the reads were aligned to the hg38 human reference genome using the BWA-MEM software. The model-based analysis of ChIPseq (MACS2 v2.1.2) was applied to call the ATAC-seq peak regions of each sample by using a bam file of uniquely mapped reads as the input, and the q-value cutoff for peak calling was 0.05. Peak annotation was performed by HOMER v4.9.1 function annotatePeaks.pl, which picks putative target genes that are located within ATAC-seq called peaks or contain the transcription start sites (TSSs) nearest to these peaks. Motif analysis on peak regions was performed by HOMER v4.9.1 function findMotifsGenome.pl. Distribution of uniquely mapped reads resulting from ATAC-seq in a bigwig file across either peaks or gene body was analyzed using deeptools v3.2.1. To identify differential peaks between different stages of development, the ATAC-seq peaks of each sample were merged to generate a consensus set of unique peaks, among which the number of peaks was further counted for each sample using bedtools v2.25.0, and differential peaks were identified by DESeq2 (v1.16.0), with the thresholds of | log2FC| > 1 and P < 0.05.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cell type: Intermediate cells on day 7 during chemical reprogramming of EBs

extract_protocol: For scRNA-seq, freshly sorted EBs (day 0) and viable cells from the iMK induction culture on days 3, 5, and 7 were collected and analyzed using the Chromium system (10x Genomics) according to the manufacturer’s instructions for an expected capture rate of approximately 8,000 single cells per sample. For ATAC-seq, cells were dissociated from each pooled sample to obtain single-cell suspensions. Then, cells were suspended in nuclear isolation buffer and washed repeatedly using nuclear wash buffer following a standard nuclear isolation protocol. A total of 40,000 nuclei were pelleted and re-suspended with transposase for 30 min at 37℃. The transposed DNA was purified with a MinElute Kit (Qiagen Inc., Valencia, CA, USA) and was used to generate the library via PCR amplification.

value: Cell type:Intermediate cells on day 7 during chemical reprogramming of EBs


title: endometrium_middle secretory phase of control_rep2

source_name: endometrium,middle secretory phase of control,replicate 2


title: endometrium_middle secretory phase of control_rep1

source_name: endometrium,middle secretory phase of control,replicate 1


title: endometrium_middle secretory phase of RIF_rep3

source_name: endometrium,middle secretory phase of RIF,replicate 3


title: endometrium_middle secretory phase of control_rep3

source_name: endometrium,middle secretory phase of control,replicate 3


title: H3_H

value: H

value: healthy


title: Non-COV3 [GC1003228]

description:
GC1003228
bulk RNA-seq


title: Non-COV6 [GC1003231]

description:
GC1003231
bulk RNA-seq


title: ST2

description: control


title: Non-COV22 [GC1003226]

description:
GC1003226
bulk RNA-seq


title: ATAC_456 GSC

source_name: 456 GSC

value: 456 GSC

value: glioblstoma stem cell


title: ATAC-seq_iMK-D7-rep1


title: Non-COV1 [GC1003224]

description:
GC1003224
bulk RNA-seq

source_name: lung


title: ATAC-seq_iMK-D5-rep1

source_name: Cell type: Intermediate cells on day 5 during chemical reprogramming of EBs

value: Cell type:Intermediate cells on day 5 during chemical reprogramming of EBs


title: Non-COV23 [GC1003225]

description:
GC1003225
bulk RNA-seq


title: ATAC-seq_iMK-D5-rep2


title: ATAC-seq_iMK-D3-rep2

source_name: Cell type: Intermediate cells on day 3 during chemical reprogramming of EBs

value: Cell type:Intermediate cells on day 3 during chemical reprogramming of EBs


title: 352_DE

value: DE

value: COVID+


title: Non-COV7 [GC1003223]

description:
GC1003223
bulk RNA-seq


title: 158_DE


title: PS1

description: infected at MOI=10 and harvested at 11 hour post infection

value: infected by PDCoV (PDCoV-CH-HA3-2017(MK040455))


title: 196_DE


title: 311_DE


title: 15_DE


title: 352_D7


title: ST1

description: control


title: Non-COV4 [GC1003222]

description:
GC1003222
bulk RNA-seq

value: lung


title: PS3


title: ATAC-seq_EB-rep1

source_name: Cell type:purified CD34-CD123-CD41a-CD42b-CD110-CD235a+ erythroblasts


title: ATAC-seq_iMK-D3-rep1


title: 175_D7

source_name: Enriched neutrophils from whole blood


title: 182_D7


title: scRNA-seq_iMK-D7


title: A549 WT [batch 1, bio rep 1]

city: Hong Kong

first: Zezhuo

last: Su

address: No. 21 Sasson Rd, Pokfulam

institute: The University of Hong Kong

description:
A549-WT-1-1
batch 1, bio rep 1

data_processing:
Raw reads were first checked for quality with FastQC (Babraham Bioinformatics) followed by trimming of the adapters (12 bp) with Cutadapt. After that, we aligned reads to the human Genome Reference Consortium Human Build 38 (GRCh38) with STAR. Then transcript abundances were summarized to gene level with featureCounts to generate an expression matrix.
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt: Space-delimited text file includes raw counts.

growth_protocol: A549 and H1299 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using RNAiso Plus (TAKARA). 1.3 μg 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.

treatment_protocol: FLAG-tagged empty vector, WT, K3R, or K3Q SIRT6 were stably overexpressed in A549 and H1299 cells via lentivirus transduction.

value: non-small cell lung carcinoma cell line

value: WT


title: A549 K3Q [batch 1, bio rep 1]

description:
A549-K3Q-1-1
batch 1, bio rep 1


title: ATAC-seq_EB-rep2

value: Cell type:purified CD34-CD123-CD41a-CD42b-CD110-CD235a+ erythroblasts


title: 15_D7


title: scRNA-seq_iMK-D5


title: PS2

value: swine testicular cells


title: CEACAM6-positive monocytes

city: Fukuoka

first: Kana

last: Yokoyama

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-Ku

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University Hospital

description: Gene expression of CEACAM1-negative and CEACAM6-negative classical monocytes

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software..

label: biotin

source_name: peripheral blood, monocyte, CEACAM1 negative, CEACAM6, positive

label_protocol: The cRNA was amplified, labeled using GeneChip WT pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from sorted cells and purified using RNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Peripheral Blood samples was acquired from a dcSSc patient. Peripheral blood mononuclear cells were separated by Lymphoprep (STEMCELL Technologies). To isolate CEACAM1+CEACAM6- and CEACAM1-CEACAM6+ monocytes, CD14+monocytes purified with CD14 MicroBeads (Miltenyi) were stained with antibodies, then the aimed cell populations were sorted by flow cytometry.

value: monocyte

tag: disease state

value: dcSSc


title: Non-COV24 [GC1003221]

description:
GC1003221
bulk RNA-seq

value: autopsy


title: UPN23/29 SC_m, scRNAseq [HTO_R306-309]

city: MARSEILLE

first: MADACI

last: LAMIA

address: Parc Scientifique de Luminy case 928 163, avenue de Luminy

country: France

institute: INSERM/TAGC

description: 10x Genomics

library_source: other

data_processing:
The preparation of libraries for sequencing is performed using the NextSeq 500/550 high Output v2 kit protocol (75 cycles, Illumina) . Libraries are denatured in NaOH and mixed in the HT1 buffer (Illumina) to be loaded on the flow cell at 1.8 pM. The libraries are sequenced on a NextSeq 500 with the following parameters: 28 cycles for Read 1, 8 cycles for Index i7 and 55 cycles for Read 2.
Data processing, alignment, gene quantification and QA/QC: The sequencing data was analyzed using the Cell Ranger Pipeline (version 6.0.2) to perform quality control, the mkfastq to sample demultiplexing, barcode processing, alignment and single cell 3’ gene counting was performed using the cellranger count. Samples were demultiplexed with bcl2fastq based on the 8-bq sample index, 10-bp UMI tags, and the 16-bp GemCode barcode. The 55-bp-long read 2 containing cDNA sequence was aligned using cell Ranger version 3.0.0 and 3.1.0.
Normalization and correlation of gene expression levels : Each sample was normalized separately using "log-normalization" of the Seurat object. To analyze the correlation between the different samples, a first Seurat filter was applied to keep the genes detected in at least 3 cells and to keep the cells that have at least 200 UMI
PCA and tSNE analysis for cell clustering and classification, and data visualization:  The Cell Ranger count and aggr pipelines were used to run secondary analysis. Before clustering the cells, Principal Component Analysis (PCA) was run on the normalized, log-transformed, centered, and scaled gene-barcodes matrix to reduce the number of feature (gene) dimensions. After running PCA, t-distributed Stochastic Neighbor Embedding (t-SNE) was run to visualize cells in 2-D space. Clustering is then run to group cells together that have similar expression profiles, based on their projection into PCA space. Two clustering methods were performed: graph-based and k-means.  For multiplexed samples, HTO data are processed using the “cite-seq count, v1.4.3” tool ( https://hoohm.github.io/CITE-seq-Count/ & https://zenodo.org/record/2590196). The results are read using the Seurat "Read10X" tool (https://satijalab.org/seurat/articles/hashing_vignette.html ). Only common cell barcodes from the HTO (from cite-seq count) and mRNA (from cellranger) data are retained. These barcodes represent the cells detected by cellranger and for which an HTO was assigned. Finally, the HTO arrays are normalized using the Log-Ratio Centered (CLR) method.
Assembly: GRCh38-2020-A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: 10x Genomics normalized tables: *normalized_table.tsv,

molecule: other

source_name: peripheral blood

extract_protocol:
Human Peripheral Blood Mononuclear Cells (PBMCs) used in this study are obtained after consent from AML patients. PBMCs were isolated from peripheral blood after centrifugation to separate them from plasma and other peripheral blood components using ficoll-Hystopaque density gradient centrifugation. After the separation of PBMCs from whole blood, the cells were preserved using Cryopreservation that consists of freezing the cells at -80°C or in liquid nitrogen at -195.79°C for a long period. For this purpose, PBMCs were stored in a freezing medium (90% FBS and 10% DMSO). Cryopreserved cells in liquid nitrogen were thawed at 37°C. Cells were rinsed with RPMI 1640 medium to remove the DMSO-containing freezing medium. To enrich the samples with live cells, dead cells were removed using the Dead Cell Removal Kit. Before starting cell labeling, a 50-μL aliquot containing 1,000,000 cells suspended in a Cell Staining Buffer (CSB) with >95% viability was prepared for each sample. The antibodies used for labeling were TotalSeq -A0251(HTO1) and -A0252 (HTO2) antibody-oligo (Biolegend). Next, we proceeded to the labeling step. For this, 1μg HTO is added to each cell suspension. The two labeled samples are then incubated for 30 minutes at 4°C. The cells then undergo 3 successive washes with 3.5 mL of CSB and centrifugation at 400 g for 5 minutes at 5°C. Finally, the cells are resuspended at a concentration of 1.106 cells/mL in PBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, PBMCs labeled with/without HTOs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Peripheral Blood Mononuclear Cells

value: peripheral blood

tag: Sex

value: female

tag: age

tag: library type

value: HTO

tag: antibodies/tags

value: B2M/TotalSeq A0251-A0252


title: UPN23/29 SC_m, scRNAseq [mRNA_R306-309]

description: 10x Genomics

library_source: transcriptomic single cell

value: mRNA


title: scRNA-seq_iMK-D3

value: Cell type:Intermediate cells on day 3 during chemical reprogramming of EBs


title: Susd2-/- naive CD8 T cellss, Day0, replicate 4, Bulk RNAseq

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

data_processing:
The bulk RNA-seq profiling was performed on eight samples (four B6 and four KO). Each sample was sequenced in two lanes for replication. B6-2-D3_L002 was missing due to machine errors, resulting in 15 lanes. B6-1-D3_L001, B6-3-D0-L001, KO-3-D0-L001, and KO-4-D0-L001 were sequenced twice to ensure sufficient read depth (with following labels as L001_1 and L001_2). Quality control and data trimming of the raw sequences were performed via fastp (v0.23.2), and reads alignment was performed using HISAT2 (v2.1.0) to map sequence to the mouse reference (Mus_musculus.GRCm38.99). Samtools (v1.10) was used to convert and sort bam files, and subread (v2.0.1) was used to quantify reads to generate gene expression count matrix. Default parameters were applied for all tools used above. Read counts in L001_1 and L001_2 of four lanes (B6-1-D3_L001, B6-3-D0-L001, KO-3-D0-L001, and KO-4-D0-L001) were added together to generate the final raw read count matrix (15 columns).
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: CSV format, gene-sample raw count matrix and metadata

source_name: Spleen

extract_protocol:
CD8+ T cells were isolated by the EasySep Mouse CD8+ T Cell Isolation Kit (STEMCELL Technologies) from total splenocytes of either WT or Susd2-/- OT-I mice left untreated or stimulated with OVA257-264 for 3 days. RNA was extracted using TRIzol Reagent (Invitrogen) and were further quantified using Qubit Fluorometer, and those with RIN values > 7 were used for RNA isolation using NEBNext Poly mRNA Magnetic Isolation Module (#E7490L, New England Biolabs, NY).
purified mRNAs were fragmented for 10 minutes. cDNAs were synthesized and amplified for 12 PCR cycles using NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (E7760L; NEB) with NEBNext Multiplex Oligos Index kit (6442L; NEB). Distributions of the template length and adapter-dimer contamination were assessed using an Agilent 2100 Bioanalyzer and High Sensitivity DNA kit (Agilent Technologies). The concentration of cDNA libraries was determined using Invitrogen Qubit dsDNA HS reagents and read on a Qubit Fluorometer (Thermo Fisher Scientific), and cDNA libraries were paired-end 150bp format sequenced on a NovaSeq 6,000 SP system (Illumina).

value: Spleen

value: CD8 T cells

value: immune cells

tag: strain

value: 8-10 weeks old


title: A549 K3R [batch 1, bio rep 1]

description:
A549-K3R-1-1
batch 1, bio rep 1

value: non-small cell lung carcinoma cell line


title: Susd2-/- naive CD8 T cellss, Day0, replicate 3, Bulk RNAseq

tag: tissue


title: Susd2-/- naive CD8 T cellss, Day0, replicate 2, Bulk RNAseq


title: scRNA-seq_EB

value: Cell type:purified CD34-CD123-CD41a-CD42b-CD110-CD235a+ erythroblasts


title: H1299 WT [batch 2, bio rep 2]

description:
H1299-WT-2-2
batch 2, bio rep 2

value: WT


title: A549 Ctr [batch 2, bio rep 2]

description:
A549-Ctr-2-2
batch 2, bio rep 2

value: Ctr


title: UPN23 SC, scRNAseq [FLT3_R252]

description: 10x Genomics


title: COV-4 [LUNG29_COVID-19]

description:
LUNG29_COVID-19
snRNA-seq

data_processing:
snRNA-seq: Demultiplexing according to the sample barcodes, and subsequent read alignment were done using Cell Ranger (v3.1.0). A human reference genome (GRCh38) was used, including intron sequences for mapping of reads obtained from snRNA-seq data. After generation of the gene expression matrices, raw data was processed further in R. The following quality control steps were performed: (i) genes expressed by less than 10 nuclei were removed; (ii) nuclei that expressed fewer than 250 genes (low quality), and with a detected number of genes > 2 standard deviations above the mean (potential doublets) were excluded from further analysis; (iii) nuclei with a detected fraction of mitochondrial genes >20% were removed.
Genome_build: human reference genome GRCh38
Supplementary_files_format_and_content: raw counts (.csv) and accompanying metadata/cell annotations (.csv).

extract_protocol: snRNA-seq: For isolation of nuclei, frozen tissue samples were transferred to an Eppendorf tube containing 0.5 mL TST-buffer (comprised of 0.25 mL 2X ST-based buffer (nuclease-free water, supplemented with 192 mM NaCl, 20 mM Tris-HCl (pH 7.5), 2 mM CaCl2. 42 mM MgCl2 and 0.2 units/µL RNasin-Plus), 15 µL Tween-20, 2.5 µL BSA, 1.25 µL RNasin-Plus and 231.25 µL nuclease-free water). The samples were chopped for 5 min on ice (using scissors), after which the suspension was transferred to a Dounce homogenizer. Another 0.5 mL of TST-buffer was used to rinse the Eppendorf tube, which was also transferred to the Dounce homogenizer. Homogenization was performed for 5 min on ice (the loose pestle was used during the first 2.5 min, the tight pestle was used during the second 2.5 min). The homogenized solution was then filtered through a 40 µm strainer and transferred to a 50 mL Falcon tube. Three additional washes, using 0.5 mL of 1X ST-buffer each (1:1 of 2X ST-based buffer, in nuclease-free water), were performed to wash the Dounce homogenizer and filter. The homogenized solution was then subsequently filtered through 20 μm, 10 μm and 5 μm cell strainers placed in 50 mL Falcon tubes, washing after each filtration with 0.5 mL of 1X ST buffer, ensuring gentle pipetting to avoid formation of air bubbles. The sample was then transferred to a 15 mL Falcon tube and centrifuged at 4 °C for 5 min at 500g, followed by resuspension of the pellet in 300 μL 0.04% UltraPure BSA. Nuclei were counted using an automated cell counter (Luna, Logos Biosystems), and converted to barcoded Drop-seq libraries by using the Chromium Single 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics; Pleasanton, California, USA), aiming for an estimated number of 10,000 nuclei per library. Libraries were sequenced on an Illumina NovaSeq 6000.

tag: condition

value: lung

tag: sample type


title: CEACAM1-positive monocytes

description: Gene expression of CEACAM1-positive and CEACAM6-negative classical monocytes

source_name: peripheral blood, monocyte, CEACAM1 positive, CEACAM6, negative

value: monocyte

value: dcSSc


title: COV-5 [LUNG31_COVID-19]

description:
LUNG31_COVID-19
snRNA-seq

value: autopsy


title: A549 K3R [batch 2, bio rep 2]

description:
A549-K3R-2-2
batch 2, bio rep 2

tag: cell type

tag: genotype


title: CEACAM-positive monocytes

description: Gene expression of CEACAM-positive classical monocytes

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

source_name: peripheral blood, monocyte, CEACAM positive

treatment_protocol: Peripheral Blood samples was acquired from a dcSSc patient. Peripheral blood mononuclear cells were separated by Lymphoprep (STEMCELL Technologies). To isolate CEACAM+ and CEACAM- monocytes, CD14+monocytes purified with CD14 MicroBeads (Miltenyi) were stained with antibodies, then the aimed cell populations were sorted by flow cytometry.


title: Susd2-/- naive CD8 T cellss, Day0, replicate 1, Bulk RNAseq


title: H1299 K3R [batch 2, bio rep 2]

description:
H1299-K3R-2-2
batch 2, bio rep 2

tag: cell line


title: BMDMs induced by PgLPS and CS-PA/CNP biol rep1

city: Shanghai

first: Shuo

last: Xu

address: Zhizaoju Road

institute: Shanghai ninth people's hospital

data_processing:
Quality control: Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis .
Reads mapping: The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5
Differential expression analysis: we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.

source_name: marrow

extract_protocol: To select cDNA fragments of the preferred 400 500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina).

value: marrow

value: primary

value: bone marrow-derived macrophages

value: wt

value: induced by PgLPS and CS-PA/CNP


title: Susd2-/- activated CD8 T cellss, Day3, replicate 3, Bulk RNAseq

value: Spleen


title: COV-7 [LUNG28_COVID-19]

description:
LUNG28_COVID-19
snRNA-seq


title: Susd2-/- activated CD8 T cellss, Day3, replicate 2, Bulk RNAseq

value: CD8 T cells


title: BMDMs induced by PgLPS and CS-PA/CNP


title: H1299 K3Q [batch 2, bio rep 1]

description:
H1299-K3Q-1-2
batch 2, bio rep 1


title: A549 WT [batch 2, bio rep 1]

description:
A549-WT-1-2
batch 2, bio rep 1


title: Susd2-/- activated CD8 T cellss, Day3, replicate 4, Bulk RNAseq

value: immune cells


title: BMDMs induced by PgLPS biol rep2

value: induced by PgLPS


title: COV-3 [LUNG20_COVID-19]

description:
LUNG20_COVID-19
snRNA-seq


title: COV-2 [LUNG21_COVID-19]

description:
LUNG21_COVID-19
snRNA-seq


title: BMDMs induced by PgLPS biol rep1


title: H1299 K3R [batch 2, bio rep 1]

description:
H1299-K3R-1-2
batch 2, bio rep 1

value: non-small cell lung carcinoma cell line


title: BMDMs induced by PgLPS and CS-PA/CNP biol rep2


title: A549 K3Q [batch 2, bio rep 2]

description:
A549-K3Q-2-2
batch 2, bio rep 2


title: 17_D3

value: Enriched neutrophils from whole blood

tag: time point

tag: patient category

value: COVID+


title: BMDMs induced by PgLPS


title: CEACAM-negative monocytes

description: Gene expression of CEACAM-negative classical monocytes

source_name: peripheral blood, monocyte, CEACAM negative


title: COV-1 [LUNG19_COVID-19]

description:
LUNG19_COVID-19
snRNA-seq


title: BMDMs induced by CS-PA/CNP biol rep2

value: induced by CS-PA/CNP


title: Non-COV5 [LUNG18_HC]

description:
LUNG18_HC
snRNA-seq

value: lung


title: COV-6 [LUNG27_COVID-19]

description:
LUNG27_COVID-19
snRNA-seq


title: WT naive CD8 T cellss, Day0, replicate 3, Bulk RNAseq

value: WT

value: 8-10 weeks old


title: A549 Ctr [batch 1, bio rep 1]

description:
A549-Ctr-1-1
batch 1, bio rep 1

value: Ctr


title: WT naive CD8 T cellss, Day0, replicate 2, Bulk RNAseq


title: A549 Ctr [batch 2, bio rep 1]

description:
A549-Ctr-1-2
batch 2, bio rep 1


title: BMDMs induced by CS-PA/CNP biol rep1

value: marrow


title: Non-COV12 [LUNG17_HC]

description:
LUNG17_HC
snRNA-seq

value: autopsy


title: BMDMs induced by CS-PA/CNP

value: primary

value: bone marrow-derived macrophages


title: WT activated CD8 T cellss, Day3, replicate 3, Bulk RNAseq


title: Susd2-/- activated CD8 T cellss, Day3, replicate 1, Bulk RNAseq


title: Non-COV11 [LUNG16_HC]

description:
LUNG16_HC
snRNA-seq


title: WT naive CD8 T cellss, Day0, replicate 1, Bulk RNAseq


title: H1299 Ctr [batch 2, bio rep 1]

description:
H1299-Ctr-1-2
batch 2, bio rep 1


title: H1299 WT [batch 2, bio rep 1]

description:
H1299-WT-1-2
batch 2, bio rep 1


title: Non-COV9 [LUNG14_HC]

description:
LUNG14_HC
snRNA-seq


title: Non-COV10 [LUNG15_HC]

description:
LUNG15_HC
snRNA-seq


title: BMDMs biol rep2

value: wt

value: control


title: WT activated CD8 T cellss, Day3, replicate 2, Bulk RNAseq

value: Spleen

value: CD8 T cells


title: WT activated CD8 T cellss, Day3, replicate 1, Bulk RNAseq

value: immune cells


title: A549 K3Q [batch 2, bio rep 1]

description:
A549-K3Q-1-2
batch 2, bio rep 1

value: non-small cell lung carcinoma cell line


title: BMDMs biol rep1


title: BMDMs


title: IPF6 [LUNG13_IPF]

description:
LUNG13_IPF
snRNA-seq

value: IPF

value: explant


title: H1299 Ctr [batch 2, bio rep 2]

description:
H1299-Ctr-2-2
batch 2, bio rep 2


title: Non-COV6 [LUNG12_HC]

description:
LUNG12_HC
snRNA-seq


title: A549 WT [batch 2, bio rep 2]

description:
A549-WT-2-2
batch 2, bio rep 2


title: H1299 K3Q [batch 2, bio rep 2]

description:
H1299-K3Q-2-2
batch 2, bio rep 2


title: H1299 WT [batch 1, bio rep 1]

description:
H1299-WT-1-1
batch 1, bio rep 1


title: Non-COV3 [LUNG11_HC]

description:
LUNG11_HC
snRNA-seq


title: Non-COV8 [LUNG10_HC]

description:
LUNG10_HC
snRNA-seq


title: Non-COV7 [LUNG09_HC]

description:
LUNG09_HC
snRNA-seq


title: RNA-Seq of Mus musculus: EBs-shcircKat6b-e2-Rep1

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts(2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs (E14) were grown in culture dishes coated with 0.1% gelatin in DMEM supplemented with 15% FBS, 100 nM NEAA, 200 mM L-Glutamate, 1% Penicillin-streptomycin, 50 μM β-mercaptoethanol, 10 ng/mL LIF, 1 μM PD0325901 and 3 μM CHIR99021. The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.
RNA-seq Library. Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: RNA-seq was performed using undifferentiated and EB-differentiated (6d) WT and KD ESCs.

value: embryo, blastocyst embryo, blastocyst

value: KD


title: RNA-Seq of Mus musculus: EBs-shcircKat6b-e2-Rep2


title: RNA-Seq of Mus musculus: EBs-WT-Rep3

value: WT


title: RNA-Seq of Mus musculus: EBs-shcircKat6b-e2-Rep3


title: IPF4 [LUNG08_IPF]

description:
LUNG08_IPF
snRNA-seq

value: lung


title: H1299 Ctr [batch 1, bio rep 1]

description:
H1299-Ctr-1-1
batch 1, bio rep 1

value: Ctr


title: RNA-Seq of Mus musculus: EBs-WT-Rep2


title: RNA-Seq of Mus musculus: EBs-WT-Rep1


title: H1299 K3Q [batch 1, bio rep 1]

description:
H1299-K3Q-1-1
batch 1, bio rep 1


title: IPF3 [LUNG07_IPF]

description:
LUNG07_IPF
snRNA-seq


title: HRH1 KD ECs with histamine treatment bio rep 3

data_processing:
Clean data were obtained by Trimmomatic.
Bowtie2 and eXpress were used to calculate the FPKMs (Fragments Per kb Per Million Reads) of known genes.
Differentially expressed genes were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Assembly: mm10
Supplementary files format and content: tab-delimited matrix table text file include RPKM values for all samples

source_name: primary endothelial cells

growth_protocol: Endothelial cells were cultured in the EGMTM-MV Microvascular Endothelial Cell Growth Medium BulletKitTM (LONZA, CC-3125).

extract_protocol:
The total RNA was extracted with TRIzol (Thermo Fisher Scientific)
Libraries were prepared according to Illumina's standard protocol.

treatment_protocol: Serum-starved ECs expressing shNT or shHRH1 were stimulated with 10 μM histamine for 1 hour and then were collected.

value: primary endothelial cells

value: histamine stimulate (10 uM, 1h)


title: RNA-Seq of Mus musculus: mESC-shcircKat6b-e2-Rep3


title: Non-COV4 [LUNG06_HC]

description:
LUNG06_HC
snRNA-seq

value: autopsy


title: RNA-Seq of Mus musculus: mESC-shcircKat6b-e2-Rep2


title: Non-COV2 [LUNG05_HC]

description:
LUNG05_HC
snRNA-seq


title: RNA-Seq of Mus musculus: mESC-WT-Rep3


title: RNA-Seq of Mus musculus: mESC-shcircKat6b-e2-Rep1


title: H1299 K3R [batch 1, bio rep 1]

description:
H1299-K3R-1-1
batch 1, bio rep 1


title: IPF1 [LUNG04_IPF]

description:
LUNG04_IPF
snRNA-seq


title: RNA-Seq of Mus musculus: mESC-WT-Rep2


title: NT ECs with histamine treatment bio rep 3

value: shNT


title: IPF5 [LUNG02_IPF]

description:
LUNG02_IPF
snRNA-seq


title: NT ECs with histamine treatment bio rep 2


title: A549 K3R [batch 2, bio rep 1]

description:
A549-K3R-1-2
batch 2, bio rep 1


title: mimic, NC, Group2

status: Public on Aug 27 2022

city: Zhengzhou

first: Shijie

last: Lyu

address: Huayuan Road 116

institute: Henan Academy of Agricultural Sciences

description: sample N2

data_processing:
The adaptor sequences and low-quality reads were removed using Trimmomatic
Clean reads were mapped to the bovine genome (ARS-UCD 1.2) using HISAT2
Htseq package was used to get gene counts
Assembly: ARS-UCD 1.2
Supplementary files format and content: Excel file includes RPKM values for each Sample

organism: Bos taurus

source_name: BEND

growth_protocol: BEND were maintained in DMEM 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)
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions

treatment_protocol: After 70%-80% cell fusion, the cells were transfected with bta-miR-200b mimic and mimic NC

value: BEND

value: Bovine endometrial epithelial cells

tag: transfection

value: mimic NC

value: Cell apoptosis


title: mimic, NC, Group1

description: sample N1

value: control

tag: treatment


title: RNA-Seq of Mus musculus: mESC-WT-Rep1


title: HRH1 KD ECs with histamine treatment bio rep 2


title: bta-miR-200b, mimic, Group2

description: sample M2

value: bta-miR-200b mimic

value: bta-miR-200b overexpression


title: mimic, NC, Group3

description: sample N3


title: Non-COV1 [LUNG01_HC]

description:
LUNG01_HC
snRNA-seq


title: bta-miR-200b, mimic, Group3

description: sample M3


title: bta-miR-200b, mimic, Group1

description: sample M1


title: RF-Pc-prim-trig-biol rep3, tech rep2

city: Salamanca

first: Ivan

last: Fernandez Lopez

address: Cordel de Merinas 40

country: Spain

institute: IRNASA

description: SAMPLE 96

data_processing:
For the normalization it uses the housekeeping gene: 18S ribosomal RNA gene.
Relative quantification of specific mRNA levels was performed using the comparative method of Livak and Schmittgen (2001).
Matrix non-normalized worksheet reports raw Ct values for target genes.
Matrix normalized worksheet reports normalized signal (against housekeeping gene).
Fold Change worksheet reports test/control ratios.

label: EvaGreen

organism: Quercus robur

source_name: Leaf plant cell

label_protocol: First-strand cDNA was synthesized from 1 μg of purified total RNA using the ImProm-II Reverse Transcription System (Promega, Madison, WI, USA) according to the manufacturer’s instructions. First-strand cDNA was pre-amplified using MyTaq™ DNA Polymerase (Bioline, according to the manufacturer’s instructions) and specific primers (same primers that will be used later for gene expression analysis by qRT-PCR). For every reaction were added 2µl of the 5x MyTaq Reaction Buffer, 0.6µl of MgCl2 (25mM), 0.2µl of dNTPs (10mM), 0.2µl of MyTaq DNA Polymerase, 4µl of water (ddH2O) and 2µl of 5x pooled specific primers solution (250nM). Pre-amplification conditions were 5 min at 95°C followed by 18 cycles at 95°C for 10 s, 60°C for 1 min and 72°C for 15 s. The pre-amplified cDNA was treated with Exonuclease I (New England BioLabs) according to the manufacturer’s instructions, and their quality was checked by Real-time qRT-PCR using iQ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA, USA) and the iQ 5 real-time PCR detection system (Bio-Rad Laboratories). The expression level of the oak 18S ribosomal RNA gene was analyzed to check the quality of the pre-amplified cDNA. The qRT-PCR conditions were 10 min at 95°C followed by 40 cycles at 95°C for 15 s and 60°C for 1 min. The specificity of each PCR amplification procedure was verified by melt-curve analysis of the PCR product with a heat dissociation protocol (from 60 to 95°C). The qPCR products were diluted at 1/160 with TE buffer. The gene expression was analyzed by qRT-PCR using SsoFast™ EvaGreen® Supermix (Bio-Rad) and the 96.96 Dynamic Array™ IFC chip for Gene Expression (Fluidigm, San Francisco, CA, USA) and the BioMark™ Systems for Genetic Analysis (Fluidigm). For each assay, a mix composed of 2.5µl of 25µM of each forward and reverse primer and 2.5µl of the 2x Loading reagent was loaded into the assay inlets of the array. Into the sample inlets, 5µl of the solution containing 2µl of pre-amplified cDNA and 3µl of a mix composed of 1x SsoFast EvaGreen® Supermix (Bio-rad), 1x loading reagent and 1x ROX were loaded. The cycling program consisted of 10 min at 95°C followed by 40 cycles at 95°C for 15 s and 60°C for 1 min.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol, from 100 mg of leaf material. The total RNA was treated with RNase-free DNase set (Qiagen). The quality and quantity of RNA were checked using a Nanodrop spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA) and a Nano Chip and Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, United States).

tag: group

value: Test

tag: developmental stage

value: Root flush

tag: fungus inoculation

value: Piloderma croceum

tag: leaf herbivory

value: Lymantria dispar as both priming and triggering stimulus


title: RF-Pc-prim-trig-biol rep2, tech rep1

description: SAMPLE 93


title: RF-Pc-prim-trig-biol rep1, tech rep1

description: SAMPLE 91


title: RF-Pc-prim-trig-biol rep1, tech rep2

description: SAMPLE 92


title: IPF2 [LUNG03_IPF]

description:
LUNG03_IPF
snRNA-seq

value: IPF

value: lung

value: explant


title: RF-Pc-prim-biol rep3, tech rep2

description: SAMPLE 90

value: Lymantria dispar as priming stimulus


title: UPN29 SC, scRNAseq [CBF_R252-255]

description: 10x Genomics

value: Peripheral Blood Mononuclear Cells

value: peripheral blood

tag: Sex

value: male

tag: age

tag: library type

value: mRNA


title: RF-Pc-prim-biol rep2, tech rep2

description: SAMPLE 88


title: RF-Pc-prim-biol rep1, tech rep2

description: SAMPLE 86


title: RF-Pc-prim-biol rep2, tech rep1

description: SAMPLE 87


title: RF-Pc-prim-biol rep1, tech rep1

description: SAMPLE 85


title: RF-Pc-prim-biol rep3, tech rep1

description: SAMPLE 89


title: NT ECs with histamine treatment bio rep 1

value: primary endothelial cells

value: shNT

value: histamine stimulate (10 uM, 1h)


title: RF-Pc-trig-biol rep3, tech rep1

description: SAMPLE 83

value: Lymantria dispar as triggering stimulus


title: RF-Pc-trig-biol rep3, tech rep2

description: SAMPLE 84


title: RF-Pc-trig-biol rep2, tech rep2

description: SAMPLE 82


title: RF-Pc-trig-biol rep2, tech rep1

description: SAMPLE 81


title: RF-Pc-trig-biol rep1, tech rep2

description: SAMPLE 80


title: RF-Pc-trig-biol rep1, tech rep1

description: SAMPLE 79


title: RF-Pc-prim-trig-biol rep3, tech rep1

description: SAMPLE 95


title: RF-Pc-no-Ld-biol rep3, tech rep2

description: SAMPLE 78

value: No apply


title: RF-Pc-no-Ld-biol rep2, tech rep2

description: SAMPLE 76

value: Test


title: RF-Pc-no-Ld-biol rep3, tech rep1

description: SAMPLE 77

value: Root flush


title: RF-Pc-no-Ld-biol rep1, tech rep2

description: SAMPLE 74

value: Piloderma croceum


title: RF-Pc-no-Ld-biol rep1, tech rep1

description: SAMPLE 73


title: HRH1 KD ECs with histamine treatment bio rep 1


title: RF-Co-prim-trig-biol rep3, tech rep1

description: SAMPLE 71

value: Lymantria dispar as both priming and triggering stimulus


title: RF-Co-prim-trig-biol rep2, tech rep2

description: SAMPLE 70


title: RF-Co-prim-trig-biol rep2, tech rep1

description: SAMPLE 69


title: RF-Co-prim-trig-biol rep1, tech rep1

description: SAMPLE 67


title: RF-Co-prim-trig-biol rep1, tech rep2

description: SAMPLE 68


title: RF-Co-prim-biol rep3, tech rep1

description: SAMPLE 65


title: RF-Co-prim-biol rep3, tech rep2

description: SAMPLE 66


title: RF-Co-prim-biol rep1, tech rep2

description: SAMPLE 62


title: RF-Co-prim-biol rep2, tech rep2

description: SAMPLE 64


title: RF-Co-prim-biol rep1, tech rep1

description: SAMPLE 61


title: RF-Co-prim-trig-biol rep3, tech rep2

description: SAMPLE 72


title: RF-Pc-no-Ld-biol rep2, tech rep1

description: SAMPLE 75


title: RF-Co-trig-biol rep2, tech rep2

description: SAMPLE 58


title: RF-Co-trig-biol rep1, tech rep2

description: SAMPLE 56


title: RF-Co-trig-biol rep3, tech rep1

description: SAMPLE 59


title: RF-Co-trig-biol rep1, tech rep1

description: SAMPLE 55


title: SF-Pc-prim-trig-biol rep3, tech rep2

description: SAMPLE 48

value: Shoot flush


title: SF-Pc-prim-trig-biol rep3, tech rep1

description: SAMPLE 47


title: RF-Co-no-Ld-biol rep2, tech rep1

description: SAMPLE 51

value: Control


title: RF-Co-no-Ld-biol rep1, tech rep1

description: SAMPLE 49


title: SF-Pc-prim-trig-biol rep1, tech rep2

description: SAMPLE 44


title: RF-Co-no-Ld-biol rep2, tech rep2

description: SAMPLE 52


title: RF-Co-no-Ld-biol rep1, tech rep2

description: SAMPLE 50


title: RF-Co-no-Ld-biol rep3, tech rep2

description: SAMPLE 54


title: SF-Pc-prim-biol rep3, tech rep1

description: SAMPLE 41


title: SF-Pc-prim-biol rep3, tech rep2

description: SAMPLE 42


title: RF-Co-no-Ld-biol rep3, tech rep1

description: SAMPLE 53


title: SF-Pc-prim-trig-biol rep1, tech rep1

description: SAMPLE 43


title: SF-Pc-prim-trig-biol rep2, tech rep2

description: SAMPLE 46


title: SF-Pc-prim-trig-biol rep2, tech rep1

description: SAMPLE 45


title: RF-Co-trig-biol rep3, tech rep2

description: SAMPLE 60


title: RF-Co-trig-biol rep2, tech rep1

description: SAMPLE 57


title: SF-Pc-prim-biol rep2, tech rep1

description: SAMPLE 39


title: SF-Pc-prim-biol rep2, tech rep2

description: SAMPLE 40


title: SF-Pc-prim-biol rep1, tech rep1

description: SAMPLE 37


title: SF-Pc-prim-biol rep1, tech rep2

description: SAMPLE 38


title: SF-Pc-trig-biol rep3, tech rep2

description: SAMPLE 36


title: RF-Pc-prim-trig-biol rep2, tech rep2

description: SAMPLE 94


title: SF-Pc-trig-biol rep2, tech rep2

description: SAMPLE 34


title: SF-Pc-trig-biol rep3, tech rep1

description: SAMPLE 35


title: SF-Pc-trig-biol rep2, tech rep1

description: SAMPLE 33


title: SF-Pc-no-Ld-biol rep2, tech rep1

description: SAMPLE 27


title: SF-Pc-no-Ld-biol rep2, tech rep2

description: SAMPLE 28


title: SF-Pc-no-Ld-biol rep3, tech rep2

description: SAMPLE 30


title: SF-Pc-trig-biol rep1, tech rep1

description: SAMPLE 31


title: SF-Pc-trig-biol rep1, tech rep2

description: SAMPLE 32


title: SF-Co-prim-trig-biol rep1, tech rep1

description: SAMPLE 19


title: SF-Co-prim-trig-biol rep1, tech rep2

description: SAMPLE 20


title: SF-Co-prim-trig-biol rep2, tech rep2

description: SAMPLE 22


title: SF-Pc-no-Ld-biol rep1, tech rep1

description: SAMPLE 25


title: SF-Co-prim-trig-biol rep3, tech rep2

description: SAMPLE 24


title: SF-Pc-no-Ld-biol rep1, tech rep2

description: SAMPLE 26


title: SF-Co-prim-trig-biol rep3, tech rep1

description: SAMPLE 23


title: WT naive CD8 T cellss, Day0, replicate 4, Bulk RNAseq

tag: tissue

value: Spleen

value: CD8 T cells

value: immune cells

value: WT

tag: strain

value: 8-10 weeks old


title: SF-Pc-no-Ld-biol rep3, tech rep1

description: SAMPLE 29


title: SF-Co-prim-biol rep2, tech rep2

description: SAMPLE 16

value: Lymantria dispar as priming stimulus


title: SF-Co-prim-biol rep3, tech rep2

description: SAMPLE 18


title: SF-Co-prim-biol rep1, tech rep1

description: SAMPLE 13


title: SF-Co-prim-biol rep2, tech rep1

description: SAMPLE 15


title: SF-Co-prim-biol rep3, tech rep1

description: SAMPLE 17


title: SF-Co-prim-trig-biol rep2, tech rep1

description: SAMPLE 21


title: SF-Co-trig-biol rep3, tech rep1

description: SAMPLE 11


title: SF-Co-trig-biol rep2, tech rep1

description: SAMPLE 9


title: SF-Co-trig-biol rep1, tech rep2

description: SAMPLE 8


title: SF-Co-trig-biol rep1, tech rep1

description: SAMPLE 7


title: SF-Co-no-Ld-biol rep3, tech rep1

description: SAMPLE 5


title: SF-Co-no-Ld-biol rep2, tech rep2

description: SAMPLE 4


title: RF-Co-prim-biol rep2, tech rep1

description: SAMPLE 63


title: SF-Co-no-Ld-biol rep1, tech rep2

description: SAMPLE 2


title: SF-Co-trig-biol rep2, tech rep2

description: SAMPLE 10


title: SF-Co-no-Ld-biol rep2, tech rep1

description: SAMPLE 3


title: SF-Co-no-Ld-biol rep1, tech rep1

description: SAMPLE 1


title: Naive KLF5

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

data_processing:
For sequence trimming, first 10bp and last 90bp were discarded by cutadapt v1.18 (Martin, 2011), based on quality control tool fastqc v0.11.8 (Andrews, 2010).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38. The reads was allowed to map to maximum of 1,000 loci and the best hit was kept (--outFilterMultimapNmax 1000 –outSAMmultNmax 1). Mapping reads over splice junction was not allowed by building STAR index without general feature format file and disallowing intron length (--alignIntronMax 1).
PCR duplicates were removed by Samtools v1.2 (Li et al., 2009) rmdup function.
Deeptools v3.2.1 (Ramírez et al., 2014) was used to generate bigwig tracks.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) with 4 fold change.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format; peak tracks for each sample

source_name: Naive H1 human embryonic stem cells

growth_protocol: Human naïve ESCs were grown in FINE culture condition after research 50% confluency

extract_protocol:
Cell pellets were lyzed and chromatin was pulled down by the respective antibodies
library was prepared according to illumina DNA sequencing Library Prep Kit

treatment_protocol: Naïve ESCs were fixed with 1% formaldehyde and quenched with glycine

tag: culture condition

value: FINE

tag: genotye

value: wild type

tag: passage number

tag: antibody


title: Naive H3K27ac


title: Naive input rep2


title: SF-Co-trig-biol rep3, tech rep2

description: SAMPLE 12


title: SF-Co-no-Ld-biol rep3, tech rep2

description: SAMPLE 6


title: PrL sample from mouse 46, resequenced [S46_PrL_2]

city: Portland

first: Justin

last: Anderson

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Behavorial Neuroscience

institute: Oregon Health & Science University

data_processing:
Sequences raw files were imported into PARC's Prime‐Seq, LabKey Server‐based system (Nelson EK, Piehler B, Eckels J, et al. LabKey server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics. 2011;12(1):71.)
Quality control of the sequences was verified through FastQC (Andrews, 2010). The mean counts per sample in sequencing tray 3 was found to be low.  Trays 3 and 2 (as a common reference) were resequenced.  Original tray 3 and rerun tray 2 were excluded from further analysis.
Illumina adapters were removed and 3' read ends were trimmed using Trimmomatic (Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114‐2120)
Reads were aligned to the Mus Musculus reference genome (Ensemble_Mouse_GRCm39_GCA_000001635.9) using the STAR aligner (v. 2.7.3a) allowing for maximum of 3 mismatches and only unique alignments.
Per‐sample gene count tables were generated by STAR using Ensembl gene annotations (Mus_musculus.GRCm39.105) and were merged to form a single gene count matrix.
Genes with either: (1) less than 1 count-per-million across samples, or (2) above 50,000 counts in a single sample were removed from further analysis.
One sample (S1_NAcc) with an inter-array correlation greater than 3 standard deviations from the mean was excluded from futher analysis as outliers.
Trimmed mean of M-values and voom normalization was performed using the edgeR (v. 3.38.1)  Bioconductor package.
Differential expression (DE) between all possible 28 pairwise combiantions of the eight HS-CC founder strains was determined using the limma+voom pipeline (v. 3.52.2). Log fold change and other statistics was computed using topTable or topTreat as appropriate.  Top level comparison was done using decideTests using the "global" method.  The Benjamini-Hochberg method was used to determine the false discovery rate.
Assembly: Mmul10
Supplementary files format and content: HSCC_Founders_STAR_Counts.txt, STAR alignment counts for all 240 samples (columns) for all 55414 genes (rows).
Supplementary files format and content: HSCC_Founders_Normalized_Counts.txt, Normalized(TMM+voom) counts for all 143 samples (columns) and 14785 genes (rows) used in differential expression analysis.

source_name: Brain

extract_protocol:
RNA were extracted from each brain region using the QIASymphony robot and standard Qiagen kits/reagents (Qiagen Sciences Inc, Germantown, MD) following the manufacturer’s recommendations. Brain tissue were obtained from 1-mm coronal slices by hand under RNAse-free conditions. (Gene Profiling Shared Resource, Oregon Health & Science University)
RNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA, USA).
RNA-Seq: The libraries were sequenced on a Illumina NovaSeq 6000 (Massively Parallel Sequencing Shared Resource, Oregon Health & Science University) using a paried-end read.

value: Brain

tag: region

value: PrL

tag: genotype

value: female

value: naïve

tag: sequencing tray

tag: animal id


title: PrL sample from mouse 46 [S46_PrL]

description:
HSCC_Founders_STAR_Counts.txt
HSCC_Founders_Normalized_Counts.txt

tag: treatment


title: NAcc sample from mouse 48 [S48_NAcc]

value: NAcc

value: PWK


title: PrL sample from mouse 48 [S48_PrL]


title: PrL sample from mouse 47 [S47_PrL]

value: NOD


title: CeA sample from mouse 47 [S47_CeA]

value: CeA


title: CeA sample from mouse 48 [S48_CeA]


title: NAcc sample from mouse 47, resequenced [S47_NAcc_2]


title: CeA sample from mouse 46 [S46_CeA]


title: NAcc sample from mouse 48, resequenced [S48_NAcc_2]


title: NAcc sample from mouse 47 [S47_NAcc]


title: NAcc sample from mouse 46 [S46_NAcc]


title: PrL sample from mouse 48, resequenced [S48_PrL_2]


title: Naive NANOG

value: NANOG


title: PrL sample from mouse 45, resequenced [S45_PrL_2]

value: AJ


title: PrL sample from mouse 47, resequenced [S47_PrL_2]


title: NAcc sample from mouse 46, resequenced [S46_NAcc_2]


title: NAcc sample from mouse 44 [S44_NAcc]

value: CAST


title: PrL sample from mouse 44 [S44_PrL]


title: SF-Co-prim-biol rep1, tech rep2

description: SAMPLE 14

tag: group

value: Test

tag: developmental stage

value: Shoot flush

value: No apply


title: CeA sample from mouse 44 [S44_CeA]


title: PrL sample from mouse 44, resequenced [S44_PrL_2]


title: NAcc sample from mouse 45 [S45_NAcc]


title: Naive input rep1


title: NAcc sample from mouse 44, resequenced [S44_NAcc_2]


title: CeA sample from mouse 45 [S45_CeA]


title: PrL sample from mouse 43, resequenced [S43_PrL_2]

value: WSB


title: NAcc sample from mouse 43, resequenced [S43_NAcc_2]


title: NAcc sample from mouse 45, resequenced [S45_NAcc_2]


title: PrL sample from mouse 42, resequenced [S42_PrL_2]

value: NZO


title: NAcc sample from mouse 42, resequenced [S42_NAcc_2]


title: PrL sample from mouse 42 [S42_PrL]


title: PrL sample from mouse 43 [S43_PrL]


title: NAcc sample from mouse 43 [S43_NAcc]


title: NAcc sample from mouse 42 [S42_NAcc]


title: CeA sample from mouse 43 [S43_CeA]


title: CeA sample from mouse 42 [S42_CeA]


title: PrL sample from mouse 45 [S45_PrL]


title: NAcc sample from mouse 41, resequenced [S41_NAcc_2]


title: CeA sample from mouse 41, resequenced [S41_CeA_2]


title: CeA sample from mouse 40, resequenced [S40_CeA_2]

value: male


title: NAcc sample from mouse 40, resequenced [S40_NAcc_2]

value: Brain


title: PrL sample from mouse 41 [S41_PrL]

value: PrL


title: PrL sample from mouse 40 [S40_PrL]


title: CeA sample from mouse 40 [S40_CeA]


title: NAcc sample from mouse 40 [S40_NAcc]


title: NAcc sample from mouse 39 [S39_NAcc]


title: CeA sample from mouse 38, resequenced [S38_CeA_2]


title: NAcc sample from mouse 39, resequenced [S39_NAcc_2]


title: NAcc sample from mouse 38, resequenced [S38_NAcc_2]


title: CeA sample from mouse 38 [S38_CeA]


title: CeA sample from mouse 41 [S41_CeA]

value: female


title: NAcc sample from mouse 38 [S38_NAcc]

value: naïve


title: PrL sample from mouse 38 [S38_PrL]


title: CeA sample from mouse 37, resequenced [S37_CeA_2]


title: NAcc sample from mouse 41 [S41_NAcc]

value: NAcc


title: NAcc sample from mouse 37, resequenced [S37_NAcc_2]


title: CeA sample from mouse 36, resequenced [S36_CeA_2]


title: CeA sample from mouse 37 [S37_CeA]


title: NAcc sample from mouse 36, resequenced [S36_NAcc_2]


title: NAcc sample from mouse 37 [S37_NAcc]


title: CeA sample from mouse 36 [S36_CeA]


title: PrL sample from mouse 36 [S36_PrL]


title: CeA sample from mouse 35, resequenced [S35_CeA_2]


title: CeA sample from mouse 35 [S35_CeA]


title: NAcc sample from mouse 36 [S36_NAcc]


title: NAcc sample from mouse 35, resequenced [S35_NAcc_2]


title: PrL sample from mouse 39 [S39_PrL]


title: PrL sample from mouse 35 [S35_PrL]


title: CeA sample from mouse 39, resequenced [S39_CeA_2]


title: PrL sample from mouse 34, resequenced [S34_PrL_2]


title: NAcc sample from mouse 34 [S34_NAcc]


title: CeA sample from mouse 39 [S39_CeA]


title: PrL sample from mouse 34 [S34_PrL]


title: NAcc sample from mouse 34, resequenced [S34_NAcc_2]


title: NAcc sample from mouse 33, resequenced [S33_NAcc_2]


title: PrL sample from mouse 33 [S33_PrL]


title: NAcc sample from mouse 33 [S33_NAcc]


title: NAcc sample from mouse 32, resequenced [S32_NAcc_2]

value: PWK


title: CeA sample from mouse 33 [S33_CeA]


title: PrL sample from mouse 37 [S37_PrL]


title: CeA sample from mouse 32, resequenced [S32_CeA_2]


title: CeA sample from mouse 32 [S32_CeA]


title: NAcc sample from mouse 35 [S35_NAcc]


title: PrL sample from mouse 32 [S32_PrL]


title: CeA sample from mouse 31, resequenced [S31_CeA_2]

value: NOD


title: CeA sample from mouse 31 [S31_CeA]

value: CeA


title: NAcc sample from mouse 31, resequenced [S31_NAcc_2]


title: NAcc sample from mouse 31 [S31_NAcc]


title: NAcc sample from mouse 30 [S30_NAcc]


title: PrL sample from mouse 31 [S31_PrL]


title: CeA sample from mouse 30 [S30_CeA]


title: CeA sample from mouse 30, resequenced [S30_CeA_2]


title: PrL sample from mouse 33, resequenced [S33_PrL_2]


title: PrL sample from mouse 30 [S30_PrL]


title: CeA sample from mouse 29, resequenced [S29_CeA_2]


title: CeA sample from mouse 34 [S34_CeA]


title: NAcc sample from mouse 29, resequenced [S29_NAcc_2]


title: NAcc sample from mouse 29 [S29_NAcc]


title: PrL sample from mouse 29 [S29_PrL]


title: CeA sample from mouse 29 [S29_CeA]


title: NAcc sample from mouse 28, resequenced [S28_NAcc_2]


title: CeA sample from mouse 28, resequenced [S28_CeA_2]


title: CeA sample from mouse 28 [S28_CeA]


title: NAcc sample from mouse 28 [S28_NAcc]


title: CeA sample from mouse 27, resequenced [S27_CeA_2]


title: PrL sample from mouse 28 [S28_PrL]


title: NAcc sample from mouse 30, resequenced [S30_NAcc_2]


title: CeA sample from mouse 27 [S27_CeA]


title: dCas13b+control.3

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
Sequencing reads were mapped to hg38 reference by HISAT2
transcriptome assembly and quantitation with StringTie
Differentially expressed genes were statistically assessed by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw reads count for each Sample

source_name: bladder cancer

growth_protocol: RPMI1640 medium (Gibco)

extract_protocol: RNAiso Plus (Takara)

value: bladder cancer

tag: cell line

tag: cell type

value: cell line


title: dCas13b+gRNA.1


title: dCas13b+control.1


title: PrL sample from mouse 27 [S27_PrL]

tag: Sex


title: dCas13b+gRNA.2


title: NAcc sample from mouse 27, resequenced [S27_NAcc_2]


title: NAcc sample from mouse 32 [S32_NAcc]


title: dCas13b+gRNA.3


title: CeA sample from mouse 26, resequenced [S26_CeA_2]


title: NAcc sample from mouse 27 [S27_NAcc]


title: CeA sample from mouse 26 [S26_CeA]


title: PrL sample from mouse 25, resequenced [S25_PrL_2]


title: NAcc sample from mouse 26 [S26_NAcc]


title: PrL sample from mouse 26 [S26_PrL]


title: NAcc sample from mouse 26, resequenced [S26_NAcc_2]


title: NAcc sample from mouse 25 [S25_NAcc]


title: PrL sample from mouse 24 [S24_PrL]


title: CeA sample from mouse 25, resequenced [S25_CeA_2]


title: PrL sample from mouse 24, resequenced [S24_PrL_2]


title: PrL sample from mouse 25 [S25_PrL]


title: CeA sample from mouse 25 [S25_CeA]


title: CeA sample from mouse 24, resequenced [S24_CeA_2]


title: NAcc sample from mouse 24 [S24_NAcc]


title: CeA sample from mouse 24 [S24_CeA]


title: dCas13b+control.2


title: PrL sample from mouse 23, resequenced [S23_PrL_2]


title: PrL sample from mouse 23 [S23_PrL]


title: CeA sample from mouse 23, resequenced [S23_CeA_2]


title: CeA sample from mouse 23 [S23_CeA]


title: NAcc sample from mouse 23 [S23_NAcc]


title: CeA sample from mouse 22, resequenced [S22_CeA_2]


title: PrL sample from mouse 22, resequenced [S22_PrL_2]


title: CeA sample from mouse 21, resequenced [S21_CeA_2]

value: AJ


title: NAcc sample from mouse 22 [S22_NAcc]


title: PrL sample from mouse 21, resequenced [S21_PrL_2]


title: CeA sample from mouse 19, resequenced [S19_CeA_2]


title: CeA sample from mouse 20 [S20_CeA]

value: CAST


title: NAcc sample from mouse 20 [S20_NAcc]


title: CeA sample from mouse 20, resequenced [S20_CeA_2]


title: PrL sample from mouse 20 [S20_PrL]


title: CeA sample from mouse 21 [S21_CeA]


title: PrL sample from mouse 19 [S19_PrL]


title: CeA sample from mouse 19 [S19_CeA]


title: CeA sample from mouse 18, resequenced [S18_CeA_2]


title: NAcc sample from mouse 21 [S21_NAcc]


title: PrL sample from mouse 18, resequenced [S18_PrL_2]


title: CeA sample from mouse 18 [S18_CeA]


title: PrL sample from mouse 19, resequenced [S19_PrL_2]


title: PrL sample from mouse 21 [S21_PrL]


title: NAcc sample from mouse 19 [S19_NAcc]


title: PrL sample from mouse 18 [S18_PrL]


title: PrL sample from mouse 17, resequenced [S17_PrL_2]


title: CeA sample from mouse 17, resequenced [S17_CeA_2]


title: NAcc sample from mouse 18 [S18_NAcc]


title: CeA sample from mouse 22 [S22_CeA]


title: PrL sample from mouse 22 [S22_PrL]


title: CeA sample from mouse 17 [S17_CeA]


title: PrL sample from mouse 17 [S17_PrL]


title: NAcc sample from mouse 17 [S17_NAcc]


title: CeA sample from mouse 16 [S16_CeA]


title: CeA sample from mouse 16, resequenced [S16_CeA_2]


title: NAcc sample from mouse 16 [S16_NAcc]


title: PrL sample from mouse 20, resequenced [S20_PrL_2]


title: PrL sample from mouse 16 [S16_PrL]


title: PrL sample from mouse 16, resequenced [S16_PrL_2]


title: CeA sample from mouse 15, resequenced [S15_CeA_2]


title: NAcc sample from mouse 15 [S15_NAcc]


title: CeA sample from mouse 14, resequenced [S14_CeA_2]


title: PrL sample from mouse 14, resequenced [S14_PrL_2]


title: PrL sample from mouse 14 [S14_PrL]


title: NAcc sample from mouse 14 [S14_NAcc]


title: CeA sample from mouse 15 [S15_CeA]


title: PrL sample from mouse 15 [S15_PrL]


title: CeA sample from mouse 12 [S12_CeA]


title: CeA sample from mouse 13, resequenced [S13_CeA_2]


title: CeA sample from mouse 13 [S13_CeA]


title: NAcc sample from mouse 12 [S12_NAcc]


title: PrL sample from mouse 13, resequenced [S13_PrL_2]


title: CeA sample from mouse 14 [S14_CeA]


title: PrL sample from mouse 13 [S13_PrL]


title: PrL sample from mouse 12, resequenced [S12_PrL_2]


title: PrL sample from mouse 12 [S12_PrL]


title: NAcc sample from mouse 13 [S13_NAcc]


title: PrL sample from mouse 11, resequenced [S11_PrL_2]


title: CeA sample from mouse 11, resequenced [S11_CeA_2]


title: NAcc sample from mouse 11 [S11_NAcc]


title: Naïve WT NANOG

data_processing:
Library strategy: CUT&Tag
Quality control was performed by FastQC v0.11.8 (Andrews, 2010). For sequence trimming, Tn5 adapter (AGATGTGTATAAGAGACAG) was trimmed by cutadapt v1.18 (Martin, 2011).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38.97. Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (--outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1). By creating STAR index without general feature format file and not allowing intron length (--alignIntronMax 1), the splice junction was neglected.
PCR duplicates were removed by Samtools v1.2 (Li et al., 2009) rmdup function.
Deeptools v3.4.3 (Ramírez et al., 2014) was used to generate bigwig tracks by normalizing to RPKM using binsize of 10bp.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format; peak tracks for each sample

source_name: Naïve H1 human embryonic stem cells

treatment_protocol: CRISPR-Cas9-mediated knockout of KLF4KLF5 in naïve hESCs

value: FINE

value: WT


title: CeA sample from mouse 11 [S11_CeA]

value: WSB


title: Naïve scRNA

data_processing:
The reads were aligned and quantified by Cell Ranger v3.1.0 (Zheng et al., 2017) from 10x Genomics to both gene and TE reference genome (GRCh38.97 from Ensembl; GRCh38 from repeatmasker) with default parameters.
The cell-by-gene/TE unique molecular identifier (UMI) count matrix was processed in R package Seurat v4.0.5 (Hao et al., 2021) for downstream data visualization. We aggregated reads from individual TE copies to subfamilies due to the limited coverage in scRNA-seq data.
We retained cells that expressed over 200 gene features and 100 TE features with fewer than 30% mitochondrial genes. The UMI count matrices for both gene and TE were then Log normalized and scaled (scale. factor = 10000 for genes, scale. factor = 1000 for TEs).
The scaled data with the top 2000 variable genes were used to perform principal component analysis (PCA).
UMAPs were calculated by RunUMAP function using top 20 principal components.
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
The cultured cells were digested by TrypLE with collagenase I. Single cell suspensions were loaded onto the 10×Genomics to generate single-cell GEMs.
Single cell RNA-seq libraries were were prepared using Chromium Single Cell 3’GEM library and Gel Bead Kit V3 (10XGenomics).

value: embryonic stem cell

value: wild type


title: PrL sample from mouse 15, resequenced [S15_PrL_2]

value: Brain


title: CeA sample from mouse 10, resequenced [S10_CeA_2]

value: NZO


title: CeA sample from mouse 12, resequenced [S12_CeA_2]

value: female


title: Naïve KLF4KLF5DKO NANOG


title: PrL sample from mouse 10, resequenced [S10_PrL_2]

value: PrL

value: naïve


title: PrL sample from mouse 10 [S10_PrL]


title: Primed KLF5OE H3K27ac

data_processing:
Quality control was performed by FastQC v0.11.8 (Andrews, 2010). For PE150 reads, first 10bp and last 90bp were discarded by cutadapt v1.18 (Martin, 2011). For SE50 reads, trimming was not applied.
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38.97. Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (--outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1). By creating STAR index without general feature format file and not allowing intron length (--alignIntronMax 1), the splice junction was neglected.
PCR duplicates were removed by Samtools v1.2 (Li et al., 2009) rmdup function.
Deeptools v3.4.3 (Ramírez et al., 2014) was used to generate bigwig tracks by normalizing to RPKM using binsize of 10bp.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format; peak tracks for each sample

source_name: Primed H1 human embryonic stem cells

treatment_protocol: Primed ESCs were transduced with virus controling empty pLVTH or pLVTH-KLF5 for four days before collcted for ChIP-seq

value: mTeSR

value: KLF5 OE

tag: chip antibody


title: Primed WT input


title: Primed WT NANOG

value: NANOG


title: Primed CRISPRaLTR7Y  rep2

data_processing:
Quality control was performed by FastQC v0.11.8 (Andrews, 2010). For sequence trimming, first 10bp were discarded by cutadapt v1.18 (Martin, 2011).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38.97. Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (--outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1). TE annotation file GRCh38 from repeatmasker (http://repeatmasker.org/) and gene annotation file GRCh38.97 from Ensembl (Howe et al., 2021) was applied to all genomics analysis.
Quantification for both gene and TE were calculated by FeatureCounts v2.0.0  (Liao et al., 2014). For gene quantification, only unique mapped reads were included (-p -B -P -C), while for TE quantification, multiple mapped reads were also included (-p -B -P -C -M).
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by R package DESeq2 v1.26.0 (Love et al., 2014). Only features with mean RPKM greater than 1 in either control or treatment group were retained. Differentially expressed features were obtained from two-fold change and 0.05 FDR filtering criteria.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; count file for each sample

growth_protocol: Primed ESCs were grown in mTeSR till reaching 60-70% confluency, and naïve ESCs were grown in FINE culture condition after research 50% confluency

extract_protocol:
RNA was harvested using Trizol reagent and purified.
library was prepared according to illumina RNAseq non-stranded Library Prep Kit

treatment_protocol: Primed ESCs were transfected with CRISPRa-LTR7Y or pLVTH-KLF5 plasmid for three days before collcted for RNA-seq

value: Primed H1 human embryonic stem cells

value: CRISPRa LTR7Y


title: PrL sample from mouse 11 [S11_PrL]

tag: tissue


title: NAcc sample from mouse 9, resequenced [S9_NAcc_2]

value: NAcc

value: male


title: CeA sample from mouse 10 [S10_CeA]

value: CeA


title: NAcc sample from mouse 10 [S10_NAcc]


title: Primed CRISPRaLTR7Yctrl  rep2

value: CRISPRa LTR7Y control


title: Primed CRISPRaLTR7Y  rep1


title: NAcc sample from mouse 9 [S9_NAcc]


title: NAcc sample from mouse 8, resequenced [S8_NAcc_2]

value: PWK


title: PrL sample from mouse 9 [S9_PrL]


title: Primed KLF5OE NANOG


title: Primed KLF5OE rep3


title: NAcc sample from mouse 8 [S8_NAcc]


title: Primed WT H3K27ac


title: CeA sample from mouse 9 [S9_CeA]


title: Primed KLF5OE rep2


title: CeA sample from mouse 8 [S8_CeA]


title: PrL sample from mouse 8 [S8_PrL]


title: Primed KLF5OEctrl rep3

value: KLF5 OE control


title: Primed KLF5OEctrl rep2


title: Primed KLF5OEctrl rep1


title: NAcc sample from mouse 7, resequenced [S7_NAcc_2]

value: NOD


title: PrL sample from mouse 9, resequenced [S9_PrL_2]

value: Brain


title: Naive KLF5 KO rep3

data_processing:
For sequence trimming, first 10bp and last 90bp were discarded by cutadapt v1.18 (Martin, 2011), based on quality control tool fastqc v0.11.8 (Andrews, 2010).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38. The reads was allowed to map to maximum of 1,000 loci and the best hit was kept (--outFilterMultimapNmax 1000 –outSAMmultNmax 1). Annotation for genes were from Ensembl (Yates et al., 2020) by using GRCh38.97. Annotation for transposable elements (TE) were based on repeatmasker (http://repeatmasker.org/) by using GRCh38.
Counts for both gene and transposable elements were calculated (parameters for gene “-p -B -P -C”, parameters for TE “-p -B -P -C -M”) by FeatureCounts v2.0.0 (Liao et al., 2014).
Differentially expressed genes (DEG) and transposable elements (DETE) were generated by R package DESeq2 v1.26.0 (Love et al., 2014) with 2 fold change and 0.05 FDR.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; count file for each sample

treatment_protocol: KLF4 and/or KLF5 were knocked out by CRISPR-CAS9, and knockout lines or wild type lines were adapated in FINE naïve culture condition.

value: FINE


title: Naive KLF5 KO rep2


title: Primed KLF5OE rep1


title: Naive KLF4 KO rep2


title: Naive KLF4 KO rep1


title: Naive WT rep3

value: wild type


title: Naive KLF5 KO rep1


title: Naive WT rep2


title: Naive KLF4 KLF5 DKO rep3


title: CeA sample from mouse 7 [S7_CeA]


title: PrL sample from mouse 7 [S7_PrL]

value: PrL


title: PrL sample from mouse 6, resequenced [S6_PrL_2]

value: naïve


title: NAcc sample from mouse 5 [S5_NAcc]

value: AJ


title: PrL sample from mouse 6 [S6_PrL]


title: NAcc sample from mouse 5, resequenced [S5_NAcc_2]


title: NAcc sample from mouse 7 [S7_NAcc]


title: NAcc sample from mouse 6 [S6_NAcc]


title: CeA sample from mouse 6 [S6_CeA]


title: PrL sample from mouse 5, resequenced [S5_PrL_2]


title: Naive KLF4 KO rep3


title: Naive KLF4 KLF5 DKO rep2


title: CeA sample from mouse 5 [S5_CeA]


title: Naive KLF4 KLF5 DKO rep1


title: PrL sample from mouse 7, resequenced [S7_PrL_2]


title: PrL sample from mouse 5 [S5_PrL]


title: Naive WT rep1


title: Primed rep3

value: mTeSR


title: NAcc sample from mouse 6, resequenced [S6_NAcc_2]


title: Primed rep2


title: Primed KLF5OE

data_processing:
Adaptor sequence (CTGTCTCTTATACACATCT, AGATGTGTATAAGAGACAG) was removed and reads shorter than 30bp was discarded by cutadapt v1.18 (Martin, 2011), then quality control was performed by fastqc v0.11.8.
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38. The reads was allowed to map to maximum of 1,000 loci and the best hit was kept (--outFilterMultimapNmax 1000 –outSAMmultNmax 1). Mapping reads over splice junction is not allowed by building STAR index without general feature format file and disallowing intron length (--alignIntronMax 1).
Only the open chromatin paired-reads with distance less than 100bp were kept.
PCR duplicates were removed by Samtools v1.2 (Li et al., 2009) rmdup function.
Deeptools v3.2.1 (Ramírez et al., 2014) was used to generate bigwig tracks.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) with 4 fold change.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format; peak tracks for each sample

growth_protocol: Primed ESCs were seeded in mTeSR at 0.15 million cells per ml; naïve ESCs were seeded in FINE medium at 0.15 milliom per ml.

extract_protocol:
hESC pellet was lyzed; nuclei were isolated and treated with Tn5
libraries were prepared according to MagicSeq 619 Tn5 DNA Library Prep Kit for Illumina

treatment_protocol: Primed ESCs were transduced with virus controling empty pLVTH or pLVTH-KLF5 for four days before collcted for ATAC-seq

value: KLF5 over expression


title: PrL sample from mouse 8, resequenced [S8_PrL_2]


title: Primed rep1


title: Primed


title: CeA sample from mouse 4 [S4_CeA]

value: CAST


title: NAcc sample from mouse 4, resequenced [S4_NAcc_2]


title: NAcc sample from mouse 3, resequenced [S3_NAcc_2]

value: WSB


title: Fibroid-55_12843

city: San Francisco

first: Jyoti

last: Goad

state: California

address: 513 Parnassus

institute: University of California, San Francisco

description: This sample was run on two lanes.  Each lane of data was analyzed separately, which resulted in two sets of processed data.

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.0.
GRCh38
mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; features.tsv: gene ids per sample
Genome_build: GRCh38
Supplementary_files_format_and_content: tar archive with: barcodes.tsv.gz  genes.tsv.gz   matrix.mtx.gz

source_name: Leiomyoma

extract_protocol:
Enzymatic and mechanical dissociation; 10X Genomics Single cell 5' gene expression V2
library constructiuon was carried out using Chromium Single cell 5' library and gel bead kit as per the manufacturer's instructions.

value: Myometrium

tag: disease state

value: Fibroid tumor

value: MED12 positive


title: Fibroid55-12906


title: Fibroid-55_12382


title: Naïve

tag: culture condition


title: PrL sample from mouse 3 [S3_PrL]

value: male


title: NAcc sample from mouse 3 [S3_NAcc]

value: NAcc


title: Fibroid-55_12640


title: Myometrium-55_12745

source_name: Myometrium

value: Healthy

value: wild type/ normal


title: PrL sample from mouse 3, resequenced [S3_PrL_2]

value: Brain


title: NAcc sample from mouse 4 [S4_NAcc]


title: PrL sample from mouse 4, resequenced [S4_PrL_2]


title: PrL sample from mouse 4 [S4_PrL]


title: CeA sample from mouse 2, resequenced [S2_CeA_2]

value: CeA

value: NZO


title: CeA sample from mouse 3 [S3_CeA]


title: 147_R1 WT BLM

city: Rochester

first: Marc

last: Nuzzo

state: NY

address: 601 Elmwood Ave Box 695

department: AIR

institute: University of Rochester

data_processing:
MultiQC v1.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using MultiQC
Trimmed sequence reads were mapped to GrCM38.p6
Read count extraction and normalization were performed using MultiQC
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using manufacturer's protocols.

value: skin

tag: strain

value: wild type

value: bleomycin


title: 160_R1 WT PBS

value: PBS


title: 159_R1 WT PBS


title: 146_R1 WT BLM


title: 161_R1 WT PBS


title: 061919Myometrium

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.0.
GRCh38
mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; features.tsv: gene ids per sample
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv.gz  genes.tsv.gz   matrix.mtx.gz


title: 145_R1 WT BLM


title: NAcc sample from mouse 2, resequenced [S2_NAcc_2]

value: naïve


title: 144_R1 Thy-1 KO BLM


title: CeA sample from mouse 2 [S2_CeA]


title: Myometrium-55_11564


title: 141_R1 Thy-1 KO BLM


title: 143_R1 Thy-1 KO BLM


title: Myometrim-55_12640


title: sperm_control

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

institute: Huazhong Agricultural University

description: sperms of 10-12 adult zebrafish for each group

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with BatMeth2
The methylation level were calculated by BatMeth2
Genome_build: Download the genome from http://ftp.ensembl.org/pub/release-85/fasta/danio_rerio/dna/
Supplementary_files_format_and_content: Show the echo site methylation level with detected

organism: Danio rerio

source_name: sperm, control

growth_protocol: embryos (F1) cultured in normal water environment

extract_protocol:
Genomic DNA extraction using the ammonium acetate method
Genomic DNA (>100 ng) from each sample were used to construct the DNA library

treatment_protocol: 50-60 embryos (F1) from each group/sperms of 10-12 adult zebrafish  (F0) for each group

value: sperm of the adult fish were exposed to normal water environment (F0 fish)

value: wild-type zebrafish (AB) at 3 months (F0 fish)


title: CeA sample from mouse 1, resequenced [S1_CeA_2]

value: female


title: PrL sample from mouse 2 [S2_PrL]

value: PrL


title: 137_R1 Thy-1 KO PBS


title: 139_R1 Thy-1 KO PBS


title: NAcc sample from mouse 2 [S2_NAcc]


title: sperm_0.156uM_Cu

source_name: sperm, 0.156uM Cu

value: sperms of 10-12 adult zebrafish for each group

value: sperm of the adult fish were exposed to 0.156μM Cu (F0 fish)


title: NAcc sample from mouse 1, resequenced [S1_NAcc_2]

value: NAcc


title: Ginseng, hairy roots, Ro stress, rep2 (mRNA-seq)

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

data_processing:
Firstly, fastp and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was also verified using fastp. including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'.
The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene). All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.kegg.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND[3] with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM.
Assembly: NA
Supplementary files format and content: genes_expression
Supplementary files format and content: Trinity.gene.fasta

organism: Panax ginseng

source_name: hairy roots

growth_protocol:
This study took ginseng hairy roots as the research object, exogenously added ginsenoside Ro to regulate the growth of hairy roots, and measured the changes in its physiological and saponin content.
Place the germination paper with the seeds into a 2-gallon plastic container (a plastic bucket works fine). Fill bucket with tap water so it reaches up to 1/4 of the paper height. Incubate in a growth chamber for 6 days with a light-dark cycle of 16 hr light at 27°C and 8 hr dark at 24°C, and ~50% humidity

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA-seq:We performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: It was found that ginseng hairy roots grew significantly under Ro-0.5 mg/L stress.

value: hairy roots

value: tissue

tag: stress

value: Ro

tag: dose

value: Ro-0.5 mg/L


title: sperm_0.078uM_Cu

source_name: sperm, 0.078uM Cu

value: sperm of the adult fish were exposed to 0.078μM Cu (F0 fish)


title: Myometrium-55.11911

value: Myometrium

value: Healthy

value: wild type/ normal


title: Ginseng, hairy roots, Ro stress, rep1 (mRNA-seq)


title: 136_R1 Thy-1 KO PBS

value: skin

value: PBS


title: Ginseng, hairy roots, rep3 (mRNA-seq)

value: control


title: NAcc sample from mouse 1 [S1_NAcc]

value: Brain

tag: region

value: naïve


title: CeA sample from mouse 1 [S1_CeA]

value: CeA

tag: genotype

value: female


title: PDL1-positive-1

city: Minato City, Tokyo

first: Teh-Wei

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

data_processing:
The sequencing data were aligned to human genome (hg19) using STAR aligner (v2.5.2a)
HTSeq (v0.11.2) was used to obtain the raw gene counts from the read alignments.
Differential expression analysis was performed using DESeq2 (v1.22.2).
The genes whose FPKM positively correlated with PD-L1 (R^2>0.95) were inputted into iRegulon (v1.3) on Cytoscape platform (v3.8.2).
20kb centered around TSS were considered as promoter region of each gene and normalized enrichment score (NES) was cut-off at 3 as a threshold.
Assembly: hg19
Supplementary files format and content: xlsx files include FPKM values for all samples.
Supplementary files format and content: xlsx files include iRegulon predicted candidates of transcription factor binding site which were enriced in promoter regions of PD-L1 correlated genes.

source_name: human foreskin fibroblast cellline HCA2

growth_protocol: Cultured in DMEM with 10% FBS and 1X antibiotics

extract_protocol:
Total RNA was extracted using ISOGEN (Nippon Gene) according to the manufacturer's instructions. PolyA-tailed mRNA was selected with beads using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA) according to the manufacturer's instructions.

treatment_protocol: Cellular senescence was induced by 24 hours 100 nM doxorubicin and further maintained under 100 nM BI-2536 to exclude proliferative cells for total 12 days

tag: cell cycle state

value: Doxorubicin-induced senescent

tag: pd-l1 expression

value: positive

value: human foreskin fibroblast cell line HCA2


title: Ginseng, hairy roots, Ro stress, rep3 (mRNA-seq)

value: hairy roots

value: tissue


title: PDL1-positive-3


title: embryo_control

description: embryos at 96hpf (hours post  fertilization)

source_name: embryo, control

tag: treatment

value: embryos whose parents were exposed to normal water environment (F0 fish)

value: wild-type zebrafish (AB) at 3 months (F0 fish)


title: PDL1-negative-3

value: negative


title: PDL1-positive-2


title: Ginseng, hairy roots, rep1 (mRNA-seq)


title: PrL sample from mouse 1 [S1_PrL]

value: PrL

tag: sequencing tray

tag: animal id


title: embryo_0.156uM_Cu

source_name: embryo, 0.156uM Cu

value: embryos at 96hpf (hours post  fertilization)

value: embryos whose parents were exposed to 0.156μM Cu (F0 fish)