title: Liver,Napabucasin 20mg/kg/d,7d,bio rep 5

city: Guangzhou

first: Li

last: Lin

address: No.1838, Guangzhou Avenue North

institute: Southern Medical University

data_processing:
Quality control The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm38 (mm10)
Supplementary files format and content: gene_count.xls This file contains the raw read counts for each gene in each sample. The file is in Excel format with the following columns: - gene_id: Ensembl gene identifier - Ctrl_1, Ctrl_2, Ctrl_3, Ctrl_4, Ctrl_5: Read counts for the 5 1% NaCMC treated replicates - BBI608_1, BBI608_2, BBI608_3, BBI608_4, BBI608_5: Read counts for the 5 BBI608 treated replicates - gene_name: Gene symbol - gene_chr: Chromosome name - gene_start: Gene start position - gene_end: Gene end position - gene_strand: Strand that the gene is located on - gene_length: Length of the gene in base pairs - gene_biotype: Category of the gene (e.g., protein_coding, lincRNA, etc.) - gene_description: Detailed description for the gene - tf_family: Transcription factor family that the gene belongs to (if applicable)
Supplementary files format and content: gene_fpkm_group.xls  This file contains the normalized expression values in FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene in each sample group. The file is in Excel format with the following columns: - gene_id: Ensembl gene identifier - vehicle: Average FPKM value for the vehicle control group - BBI608: Average FPKM value for the BBI608 treated group - Ctrl_1, Ctrl_2, Ctrl_3, Ctrl_4, Ctrl_5: Read counts for the 5 1% NaCMC treated replicates - BBI608_1, BBI608_2, BBI608_3, BBI608_4, BBI608_5: Read counts for the 5 BBI608 treated replicates - gene_name: Gene symbol - gene_chr: Chromosome name - gene_start: Gene start position - gene_end: Gene end position - gene_strand: Strand that the gene is located on - gene_length: Length of the gene in base pairs - gene_biotype: Category of the gene (e.g., protein_coding, lincRNA, etc.) - gene_description: Detailed description for the gene - tf_family: Transcription factor family that the gene belongs to (if applicable)

source_name: Liver

growth_protocol: Mice were housed under standard conditions with free access to food and water.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Control group: 1% NaCMC by daily oral gavage for 7 days. Treatment group: Napabucasin (20mg/kg body weight) by daily oral gavage for 7 days.

value: Liver

value: 7 days

value: Napabucasin 20mg/kg/d gavage


title: 38B_DH_6NJ_Cue

status: Public on Jul 01 2026

type: SRA

city: Boston

first: Lisa

last: Goldberg

state: Massachusetts

address: 72 E Concord St, R604

country: USA

institute: Boston University School of Medicine

description: Library name: 38B_DH

library_source: transcriptomic

data_processing:
FastQC reports were generated and inspected to check the quality of the dataset
Samples were mapped to the mouse reference genome using Hisat2
Gene-level raw read counts were obtained with featureCounts
Transcript-level read counts were obtained with Kallisto
Normalization and differential expression were done using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file with gene-level raw read counts for each sample
Supplementary files format and content: Tab delimited text file with transcript-level read counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Dorsal Hippocapus

extract_protocol:
RNA was extracted using Trizol (Qiagen, Valencia, CA, USA) and RNAeasy extraction kit (Qiagen, Valencia, CA, USA), as previously described(Yazdani, Shen et al. 2016, Goldberg, Zeid et al. 2021). RNA concentration and quality were evaluated using NanoDrop2000 (NanoDrop, Wilmington, DE, USA) and Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA)
Libraries were prepared by the Huck Institutes of the Life Sciences Genomics Core Facility (Penn State University) for 75 bp single-end reads using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: To investigate baseline and learning-induced changes in hippocampal transcriptome that may underlie the observed behavioral differences between B6J and B6NJ, dorsal (DH) and ventral hippocampi (VH) were dissected for RNAsequencing (n=6 per group). To determine the impact of learning on hippocampal transcriptome, three groups were utilized: home cage, fear conditioned, and cue alone.

tag: tissue

value: Dorsal Hippocapus

tag: genotype

tag: treatment

value: Cue

tag: Sex

value: Male


title: Caco-2.batch1.COL.rep1.D10

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: Caco2_Batch1_COL_1_D10

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

organism: Homo sapiens

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: colon

tag: cell line

tag: cell type

value: epithelial

value: cell line


title: 38A_VH_6NJ_Cue

description: Library name: 38A_VH

source_name: Ventral Hippocampus

value: Ventral Hippocampus


title: Liver,Napabucasin 20mg/kg/d,7d,bio rep 4

country: China

tag: time


title: 38A_DH_6NJ_Cue

description: Library name: 38A_DH


title: Caco-2.batch1.COL.rep1.C10

description: Library name: Caco2_Batch1_COL_1_C10


title: Liver,Napabucasin 20mg/kg/d,7d,bio rep 3


title: 37C_DH_6NJ_Shock_Cue

description: Library name: 37C_DH


title: 37C_VH_6NJ_Shock_Cue

description: Library name: 37C_VH


title: Caco-2.batch1.COL.rep1.B10

description: Library name: Caco2_Batch1_COL_1_B10


title: 37B_VH_6NJ_Shock_Cue

description: Library name: 37B_VH


title: Liver,Napabucasin 20mg/kg/d,7d,bio rep 2


title: 37B_DH_6NJ_Shock_Cue

description: Library name: 37B_DH


title: Caco-2.batch1.COL.rep1.A10

description: Library name: Caco2_Batch1_COL_1_A10


title: 37A_VH_6NJ_Shock_Cue

description: Library name: 37A_VH


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 3

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

institute: Washington University, St Louis

description:
Library name: Sample70
all.gene_moderated_log2cpm_BAL.tsv
BAL_5471_RNA

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation, and read distribution over known gene models with RSeQC version 2.3
Gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for sample differences in library size.
The TMM size factors and the matrix of counts were imported into R/Bioconductor package Limma, and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were then calculated for all samples with the Voom function
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample.

source_name: BAL

growth_protocol: Mice were maintained and propagated in shoebox-sized cages in a 12-hour light-dark cycle with food available ad lib. To shift the circadian phases of mice, they were acclimated in custom light-tight enclosures (Gorilla Grow Tenet) for two weeks with the light cycle controlled by a programmable timer

extract_protocol:
To obtain BALs, mice were euthanized and their tracheas were cannulated with a 20G flexible catheter, 1-2 mm distal to the larynx.   The lungs were then slowly lavaged in 2 passes with a total of 1 ml sterile phosphate buffered saline (PBS).
Whole lungs were manually excised and immersed in RNAlater solution
Total RNA was isolated from lung homogenates using RNeasy Mini Kits (Qiagen)
RNA from whole lung homogenates or BAL cell pellets were converted to cDNA libraries for sequencing using the the SMARTer kit following manufacturer protocols

treatment_protocol: Mice were anesthetized with 3% isoflurane and then intranasally treated with 30ul of virus diluted in PBS. After viral infection, mice were housed in constant dark conditions until the end of the experiment.

value: BAL

tag: tissue type

value: BAL cell pellet

value: Wild type

value: MHV1 infection, collected post-infection day 4, ZT6


title: Caco-2.batch2.CAR.rep1.G04

description: Library name: Caco2_Batch2_CAR_1_G04


title: Liver,Napabucasin 20mg/kg/d,7d,bio rep 1


title: 39A_VH_6NJ_Shock_Cue

description: Library name: 39A_VH


title: 37A_DH_6NJ_Shock_Cue

description: Library name: 37A_DH


title: 2 Gy Irradiated, organoids, 11 days, mouse 2

city: Groningen

first: Rufina

last: Maturi

address: Antonius Deusinglaan 1

department: Radiotherapy

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: 2 Gy Irradiated, 11 days 2
Smart3SEQ

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. STAR aligner software was used to align the results of the sequencing. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file including the raw counts from all replicates and conditions is provided.

molecule: polyA RNA

source_name: Thyroid gland

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, Y27632 10 µM, B27 0.5%. All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
80 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Smart3SEQ protocol, adhering to the manufacturer`s instructions.

treatment_protocol: E

value: Thyroid gland

value: Thyroid gland cells derived from organoids

tag: age

value: 8-12 weeks old

tag: strain

value: Irradiated, 2 Gy


title: 2 Gy Irradiated, organoids, 11 days, mouse 3

description:
Library name: 2 Gy Irradiated, 11 days 3
Smart3SEQ


title: 36C_VH_6J_HomeCage

description: Library name: 36C_VH

value: HomeCage


title: Caco-2.batch1.CLP.rep3.H12

description: Library name: Caco2_Batch1_CLP_3_H12


title: Liver,1% NaCMC,7d,bio rep 5

value: Liver

value: 7 days

value: 1% NaCMC


title: Control, organoids, 11 days, mouse 2

description:
Library name: Control 11 days 2
Smart3SEQ

value: Non-irradiated


title: Caco-2.batch1.COL.rep1.F10

description: Library name: Caco2_Batch1_COL_1_F10

value: colon


title: Caco-2.batch1.CLP.rep3.G12

description: Library name: Caco2_Batch1_CLP_3_G12

value: epithelial


title: 36C_DH_6J_HomeCage

description: Library name: 36C_DH

value: Dorsal Hippocapus

value: Male


title: 36B_VH_6J_HomeCage

description: Library name: 36B_VH

value: Ventral Hippocampus


title: 38C_DH_6NJ_Cue

description: Library name: 38C_DH

value: Cue


title: Liver,1% NaCMC,7d,bio rep 4


title: 4 Gy Irradiated, organoids, 7 days, mouse 2

description:
Library name: 4 Gy Irradiated, 7 days 2
Smart3SEQ

value: Irradiated, 4 Gy


title: 36B_DH_6J_HomeCage

description: Library name: 36B_DH


title: Liver,1% NaCMC,7d,bio rep 3


title: 36A_VH_6J_HomeCage

description: Library name: 36A_VH


title: 36A_DH_6J_HomeCage

description: Library name: 36A_DH


title: Caco-2.batch1.CLP.rep3.F12

description: Library name: Caco2_Batch1_CLP_3_F12

value: cell line


title: 35C_VH_6J_HomeCage

description: Library name: 35C_VH


title: Liver,1% NaCMC,7d,bio rep 2


title: 35C_DH_6J_HomeCage

description: Library name: 35C_DH


title: Caco-2.batch1.CLP.rep3.D12

description: Library name: Caco2_Batch1_CLP_3_D12


title: Liver,1% NaCMC,7d,bio rep 1


title: 35B_DH_6J_HomeCage

description: Library name: 35B_DH


title: 35B_VH_6J_HomeCage

description: Library name: 35B_VH


title: Caco-2.batch1.CLP.rep3.C12

description: Library name: Caco2_Batch1_CLP_3_C12


title: RFP55

city: Shanghai

first: Qing

last: Li

state: Shanghai

address: Xuhui Yueyang road 320, ShangHai, China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file include numble of different reads for each sample. For RNA-seq, tab-delimited text file include RPKM values for each sample

source_name: Blastocyst

extract_protocol:
For deep-seq, The genomic DNA of various tissues (brain, heart, liver, testis, and tail) from wild-type mice and Gjb235delG/35delG mice derived from diploid compensation, was isolated using the TIANamp Genomic DNA Kit (TIANGEN). This was followed by PCR amplification for Sanger sequencing. Target sites were amplified from the extracted genomic DNA using Phanta® Max Super-Fidelity DNA Polymerase (Vazyme)For RNA-seq, single cells were picked using a Piezo-drill micromanipulator and transferred into a 200 µl tube containing 1.2 µl of lysis buffer. The lysate underwent cDNA amplification with the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712)
For deep-seq,  the PCR products were then ligated with different barcodes and pooled together. Libraries were generated from adapter-modified PCR products. For RNA-seq, the RNA-seq library was prepared using the TruePrep DNA Library Prep Kit V2 (Vazyme, Cat#TD503) for Illumina sequencing
Libraries of deep-seq and RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: Blastocyst

tag: genetic modification

value: Actin-RFP transgene


title: 35A_DH_6J_HomeCage

description: Library name: 35A_DH


title: Caco-2.batch1.CLP.rep3.B12

description: Library name: Caco2_Batch1_CLP_3_B12


title: 34C_VH_6J_Cue

description: Library name: 34C_VH


title: 35A_VH_6J_HomeCage

description: Library name: 35A_VH


title: RFP54


title: Caco-2.batch1.CLP.rep3.A12

description: Library name: Caco2_Batch1_CLP_3_A12


title: 34C_DH_6J_Cue

description: Library name: 34C_DH


title: 34B_DH_6J_Cue

description: Library name: 34B_DH


title: Caco-2.batch1.CLP.rep2.H12

description: Library name: Caco2_Batch1_CLP_2_H12


title: RFP53


title: 34A_VH_6J_Cue

description: Library name: 34A_VH


title: 34A_DH_6J_Cue

description: Library name: 34A_DH


title: RFP52


title: RFP51


title: Caco-2.batch1.CLP.rep2.G12

description: Library name: Caco2_Batch1_CLP_2_G12


title: 33C_VH_6J_Shock_Cue

description: Library name: 33C_VH


title: Caco-2.batch1.CLP.rep2.F12

description: Library name: Caco2_Batch1_CLP_2_F12


title: 33B_VH_6J_Shock_Cue

description: Library name: 33B_VH


title: 33B_DH_6J_Shock_Cue

description: Library name: 33B_DH


title: RFP50


title: Caco-2.batch1.CLP.rep2.E12

description: Library name: Caco2_Batch1_CLP_2_E12


title: RFP49


title: 33A_DH_6J_Shock_Cue

description: Library name: 33A_DH


title: 32C_VH_6J_Cue

description: Library name: 32C_VH


title: Caco-2.batch1.CLP.rep2.D12

description: Library name: Caco2_Batch1_CLP_2_D12


title: 32C_DH_6J_Cue

description: Library name: 32C_DH


title: 32B_VH_6J_Cue

description: Library name: 32B_VH


title: Caco-2.batch1.CLP.rep2.C12

description: Library name: Caco2_Batch1_CLP_2_C12


title: RFP47


title: Caco-2.batch1.CLP.rep2.B12

description: Library name: Caco2_Batch1_CLP_2_B12


title: RFP46


title: 32A_VH_6J_Cue

description: Library name: 32A_VH


title: 32A_DH_6J_Cue

description: Library name: 32A_DH


title: RFP45


title: Caco-2.batch1.CLP.rep2.A12

description: Library name: Caco2_Batch1_CLP_2_A12


title: 31C_VH_6J_Shock_Cue

description: Library name: 31C_VH


title: 31C_DH_6J_Shock_Cue

description: Library name: 31C_DH


title: 31B_VH_6J_Shock_Cue

description: Library name: 31B_VH


title: RFP44


title: 31B_DH_6J_Shock_Cue

description: Library name: 31B_DH


title: Caco-2.batch1.CLP.rep1.G12

description: Library name: Caco2_Batch1_CLP_1_G12


title: 31A_VH_6J_Shock_Cue

description: Library name: 31A_VH


title: RFP43


title: Caco-2.batch1.CLP.rep1.F12

description: Library name: Caco2_Batch1_CLP_1_F12


title: Drop_CC_KTrp53_AC_2

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

data_processing:
Raw counts were obtained with kallisto
Assembly: mm10
Supplementary files format and content: Raw counts in a tab delineated matrix.

source_name: Pancreas

extract_protocol:
RNA was extracted using RNeasy Kits (QIAGEN) and RNA quality was assessed using the Agilent 2100 BioAnalyzer. RNA with a RNA integrity value >8 was further analyzed.
Libraries were prepared using the standard protocol for Illumina Stranded mRNA Prep (Illumina).

value: Pancreas

value: Yes

value: PDAC

value: Ptf1aCreER; LSL-KrasG12D; Trp53f/f; R26RYFP

value: Dropout Media


title: RFP42


title: Drop_CC_KTrp53_AC_1


title: RFP41


title: Drop_CC_KTrp53_DU_1

value: Sox9CreER; LSL-KrasG12D; Trp53f/f; R26RYFP


title: Drop_CC_KTrp53_DU_2


title: Drop_CC_KPten_AC_3

value: Ptf1aCreER; LSL-KrasG12D; Ptenf/f; R26RYFP


title: Caco-2.batch1.CLP.rep1.C12

description: Library name: Caco2_Batch1_CLP_1_C12

value: colon


title: RFP40


title: Drop_CC_KPten_AC_2


title: Drop_CC_KPten_AC_1


title: RFP39


title: Caco-2.batch1.CLP.rep1.B12

description: Library name: Caco2_Batch1_CLP_1_B12

value: epithelial


title: Drop_CC_KPten_DU_1

value: Sox9CreER; LSL-KrasG12D; Ptenf/f; R26RYFP


title: Caco-2.batch1.CLP.rep1.A12

description: Library name: Caco2_Batch1_CLP_1_A12


title: Comp_CC_KPten_AC_2

value: Ptf1aCreER; LSL-KrasG12D; Ptenf/+; R26RYFP

value: Complete Media


title: RFP37


title: Comp_CC_KPten_AC_1


title: Drop_CC_KPten_DU_2

value: Sox9CreER; LSL-KrasG12D; Ptenf/+; R26RYFP


title: Caco-2.batch1.CLN.rep3.H02

description: Library name: Caco2_Batch1_CLN_3_H02


title: Comp_CC_KPten_AC_3


title: RFP38


title: Caco-2.batch1.CLP.rep3.E12

description: Library name: Caco2_Batch1_CLP_3_E12


title: Comp_CC_KPten_DU_3


title: RFP36


title: RFP35


title: Comp_CC_KPten_DU_1


title: Comp_CC_KPten_DU_2


title: 34B_VH_6J_Cue

description: Library name: 34B_VH

value: Ventral Hippocampus

value: Cue

value: Male


title: Caco-2.batch1.CLN.rep3.G02

description: Library name: Caco2_Batch1_CLN_3_G02

value: cell line


title: Comp_CC_KTrp53_AC_20

value: Pancreas


title: 33C_DH_6J_Shock_Cue

description: Library name: 33C_DH

value: Dorsal Hippocapus


title: RFP34

value: Blastocyst

value: Actin-RFP transgene


title: Caco-2.batch1.CLN.rep3.F02

description: Library name: Caco2_Batch1_CLN_3_F02


title: Comp_CC_KTrp53_AC_19

value: Yes

value: PDAC

value: Ptf1aCreER; LSL-KrasG12D; Trp53f/f; R26RYFP


title: Caco-2.batch1.CLN.rep3.E02

description: Library name: Caco2_Batch1_CLN_3_E02

value: colon


title: Comp_CC_KTrp53_AC_18


title: 33A_VH_6J_Shock_Cue

description: Library name: 33A_VH


title: Comp_CC_KTrp53_AC_17


title: RFP48


title: RFP33


title: Comp_CC_KTrp53_AC_16


title: Caco-2.batch1.CLN.rep3.D02

description: Library name: Caco2_Batch1_CLN_3_D02

value: epithelial


title: Comp_CC_KTrp53_AC_15


title: 32B_DH_6J_Cue

description: Library name: 32B_DH


title: RFP32


title: Comp_CC_KTrp53_AC_14


title: Comp_CC_KTrp53_AC_13


title: Caco-2.batch1.CLN.rep3.C02

description: Library name: Caco2_Batch1_CLN_3_C02


title: Comp_CC_KTrp53_AC_11


title: Comp_CC_KTrp53_AC_12


title: RFP31


title: RFP30


title: Caco-2.batch1.CLN.rep3.B02

description: Library name: Caco2_Batch1_CLN_3_B02


title: Comp_CC_KTrp53_AC_10


title: Caco-2.batch1.CLN.rep3.A02

description: Library name: Caco2_Batch1_CLN_3_A02


title: Caco-2.batch1.CLP.rep1.H12

description: Library name: Caco2_Batch1_CLP_1_H12


title: Comp_CC_KTrp53_AC_9


title: Comp_CC_KTrp53_AC_8

value: Ptf1aCreER; LSL-KrasG12D; Trp53f/+; R26RYFP


title: RFP29


title: Caco-2.batch1.CLN.rep2.H03

description: Library name: Caco2_Batch1_CLN_2_H03


title: Comp_CC_KTrp53_AC_6


title: Caco-2.batch1.CLN.rep2.G03

description: Library name: Caco2_Batch1_CLN_2_G03


title: Comp_CC_KTrp53_AC_5


title: Comp_CC_KTrp53_AC_7


title: RFP28


title: RFP27


title: 31A_DH_6J_Shock_Cue

description: Library name: 31A_DH


title: Single-cell RNAseq of iMGLs exposed to Interferon-Beta or PBS_IFN_1

city: Dublin

first: Michael John

last: Dolan

state: Dublin 2

address: Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin

country: Ireland

institute: Trinity College Dublin

description: Library name: sample2

data_processing:
iAstrocyte: FastQC (v.0.12.1) and MultiQC (v.1.23) were to generate initial quality control (QC) reports. STAR (v.2.7.10b) was used to build the reference index (based on GRCh38) and align reads, then the quality of the generated BAM files was assessed with Samtools (v.1.6) quickcheck (all samples had greater than 94% alignment). The count matrix was generated using featureCounts (v.2.0.6). R (v.4.3.1) was used for subsequent analyses.  iMGL scRNAseq: Cellranger (version 6, 10X Genomics) was used for demultiplexing, barcode preprocessing, generation of fastq files, alignment and the counting of unique molecular identifiers (UMI). We applied Cellranger’s aggr function to all samples to merge and normalize by sequencing depth. We then applied CellBender to remove ambient RNA and technical artifacts due to barcode swapping (Fleming et al. 2023).
Assembly: GRCh38
Supplementary files format and content: Seurat object of iMGL scRNAseq data

source_name: cell line

growth_protocol: iMGL Differentiation: Human H1 embryonic stem cells were cultured in Essential 8 media on Matrigel, dissociated with Accutase, and aggregated in low-adherence plates with ROCK inhibitor. Cells were differentiated through sequential exposure to hematopoietic cytokines (FGF2, BMP4, VEGF, TPO, SCF, IL6, IL3) in HPC medium under hypoxic and then normoxic conditions. By day 10, cells were cryopreserved and later thawed for microglia maturation in iMG media containing M-CSF, IL-34, and TGF-β1. Final maturation occurred between days 30–45 with additional supplementation of CD200 and CX3CL1.  iAstro Differentiation: H1 hESCs were genetically engineered to express doxycycline-inducible NFIB and SOX9 from the AAVS1 locus. After transfection, cells were selected with geneticin and expanded. iAstrocyte induction was initiated with doxycycline in E8 medium, followed by sequential exposure to expansion, FGF, and maturation media containing BMP4, CNTF, and dbcAMP. Cells were dissociated on day 7, replated, and matured in MM medium until day 20 before use.

extract_protocol:
RNA was extracted either with Qiagen RNeasy Mini extraction kit (iAstrocytes) or subjected to single-cell RNA sequencing (iMGLs)
iAstrocye RNA underwent library preparation based on PolyA sequencing. iMGL underwent single-cell library preparation according to 10X Genomics protocol

treatment_protocol: Cells were treated with PBS or 25ng/ml Interferon Beta

value: stemcell microglia


title: Comp_CC_KTrp53_AC_4

value: Complete Media


title: Comp_CC_KTrp53_AC_3


title: Caco-2.batch1.CLN.rep2.F03

description: Library name: Caco2_Batch1_CLN_2_F03


title: RFPpos-7

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file includes number of different reads for each sample. For RNA-seq, tab-delimited text file includes RPKM values for each sample. For WGBS, bed file includes the average methylation sites per 200bp in the genome. For scRNA-seq of E7.5 embryos, cellfocus file includes the representation matrix of different cells.

value: Actin-GFP transgene


title: RFP26


title: Caco-2.batch1.CLN.rep2.E03

description: Library name: Caco2_Batch1_CLN_2_E03


title: Comp_CC_KTrp53_AC_2


title: Comp_CC_KTrp53_AC_1


title: RFP25


title: Caco-2.batch1.CLN.rep2.D03

description: Library name: Caco2_Batch1_CLN_2_D03


title: RFP24


title: Caco-2.batch1.CLP.rep1.E12

description: Library name: Caco2_Batch1_CLP_1_E12


title: Comp_CC_KTrp53_DU_15

value: Sox9CreER; LSL-KrasG12D; Trp53f/f; R26RYFP


title: Comp_CC_KTrp53_DU_14


title: Caco-2.batch1.CLN.rep2.C03

description: Library name: Caco2_Batch1_CLN_2_C03


title: Comp_CC_KTrp53_DU_13


title: 41C_DH_6NJ_HomeCage

description: Library name: 41C_DH

value: HomeCage


title: Comp_CC_KTrp53_DU_11


title: Comp_CC_KTrp53_DU_12


title: RFP23


title: Caco-2.batch1.CLN.rep2.B03

description: Library name: Caco2_Batch1_CLN_2_B03


title: Comp_CC_KTrp53_DU_10


title: RFP22


title: Caco-2.batch1.CLN.rep2.A03

description: Library name: Caco2_Batch1_CLN_2_A03


title: Comp_CC_KTrp53_DU_9


title: RFP21


title: Comp_CC_KTrp53_DU_8


title: Caco-2.batch1.CLN.rep1.H03

description: Library name: Caco2_Batch1_CLN_1_H03


title: Comp_CC_KTrp53_DU_6


title: RFP20


title: RFPpos-3


title: Comp_CC_KTrp53_DU_5


title: Comp_CC_KTrp53_DU_3


title: Comp_CC_KTrp53_DU_4


title: RFP19


title: Caco-2.batch1.CLN.rep1.G03

description: Library name: Caco2_Batch1_CLN_1_G03


title: Caco-2.batch1.CLN.rep1.F03

description: Library name: Caco2_Batch1_CLN_1_F03


title: RFP18


title: Comp_CC_KTrp53_DU_2


title: Comp_CC_KTrp53_DU_7


title: Caco-2.batch1.CLN.rep1.E03

description: Library name: Caco2_Batch1_CLN_1_E03


title: RFP17


title: Bulk_KTrp53_AC_4

value: No


title: Comp_CC_KTrp53_DU_1


title: Caco-2.batch1.CLP.rep1.D12

description: Library name: Caco2_Batch1_CLP_1_D12

value: cell line


title: Bulk_KTrp53_AC_3

value: Pancreas


title: Caco-2.batch1.CLN.rep1.D03

description: Library name: Caco2_Batch1_CLN_1_D03


title: Bulk_KTrp53_AC_2


title: Caco-2.batch1.CLN.rep1.C03

description: Library name: Caco2_Batch1_CLN_1_C03


title: Bulk_KTrp53_AC_1


title: Bulk_KTrp53_DU_5


title: RFP16


title: Bulk_KTrp53_DU_4


title: Caco-2.batch1.CLN.rep1.B03

description: Library name: Caco2_Batch1_CLN_1_B03


title: RFP15


title: RFP14


title: Bulk_KTrp53_DU_3


title: Caco-2.batch1.CLN.rep1.A03

description: Library name: Caco2_Batch1_CLN_1_A03


title: RFP13


title: Bulk_KTrp53_DU_1


title: RCA-RiboTag_5

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.7.3a  with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Duplicate reads were removed with Picard 2.21.7 (https://github.com/broadinstitute/picard).
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
A combined raw count matrix was produced and used for differential expression analysis using DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 08.03.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

source_name: right carotid artery

growth_protocol: Endothelial cell-specific RiboTag mice (EC-RiboTag) were generated by crossing endothelial cell-specific Cre-driver mice (Cdh5-CreERT2) with Ribo-Tag (Rpl22HA/HA) mice. The offspring were backcrossed with C57BL/6J mice (Charles River) for at least 8-10 generations. Both male and female mice were included in all studies. Animals were housed under a 12 hour light-dark cycle with free access to water and a normal chow diet. One group of animals was sacrificed after deep anesthetization with 180 mg/kg ketamine and 16 mg/kg xylazine 10 days after the last tamoxifen injection. Thereafter, thorax was opened and intracardiac perfusion (through the left and right ventricles) was performed with 10 mL 100 μg/mL cycloheximide (Sigma-Aldrich) in phosphate buffered saline (PBS). After perfusion, vessels and organs were harvested, snap frozen in liquid nitrogen and stored at -80°C until processed further. All animal experiments were performed in accordance with the Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes and approved by the Federal Authority for Animal Research at the Regierungspräsidium Darmstadt (Hessen, Germany) under study protocols B2/1102 and B2/1187.

extract_protocol:
Murine tissues were homogenized in lysis buffer (2-3% w/v) containing: Tris/HCl pH 7.5 (50 mmol/L), NaCl (150 mmol/L), MgCl2 (12 mmol/L), NP-40 (1%), DTT (1 mmol/L), EDTA-free protease inhibitor mix (AppliChem GmbH, Darmstadt, Germany), SUPERase In RNase Inhibitor (200U/mL, Thermo Fisher Scientific), murine RNase inhibitor (1000 U/mL for lung tissue, 500 U/mL for all other tissues; New England Biolabs, Frankfurt am Main, Germany), heparin (10 mg/mL), cycloheximide (100 µg/mL) and TURBO DNaseI (25U/mL, Thermo Fisher Scientific) in UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific). Lysates were centrifuged (16,000g, 10 minutes, 4°C) and the supernatants were passed through 70 µm pre-separation filters (Miltenyi Biotec, Bergisch Gladbach, Germany). Ten % of the total lysate volume was mixed with 9 volumes of QIAZOL and frozen at -80°C. The remaining lysates were incubated with anti-HA antibody-conjugated magnetic beads (50 µl/sample, washed and resuspended in lysis buffer, Biozol, Eching, Germany) before being incubated overnight on end-over-end rocker at 4°C. HA immunoprecipitates were washed three times with a freshly prepared high salt buffer containing: Tris/HCl pH 7.5 (50 mmol/L), NaCl (300 mmol/L), MgCl2 (12 mmol/L), NP-40 (0.5%), DTT (1 mmol/L), SUPERase In RNase Inhibitor (200 U/mL, Thermo Fisher Scientific), murine RNase inhibitor (1000 U/mL for lung tissue, 500 U/mL for all other tissues; New England Biolabs) and cycloheximide (100 µg/mL). After the final wash, HA immunoprecipitates were resuspended in 700 µL QIAZOL and immediately processed for RNA purification. The total input RNA (from the total lysates) as well as the ribosome-associated RNA (from the RiboTag immunoprecipitates) were purified using the miRNeasy Micro kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions.
10 ng of total RNA was used for SMART-Seq stranded Kit (Takara) following the manufacturer’s instructions with standard RNA fragmentation (6 minutes, +85°C) and no further size selection. Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in 8-62M reads per library (average 25M) with 1x75 nt single-end setup.

treatment_protocol: Cre-mediated recombination was induced in 8-9 weeks old mice by intraperitoneal injections of tamoxifen (50 mg/kg/day dissolved in 50 µL Miglyol; Merck, Darmstadt, Germany) for 5 consecutive days. Three to five days after the last tamoxifen injection, EC-RiboTag mice (9-10 weeks of age) were injected once with AAV-PCSK9 (1011 VG) via the tail vein. Thereafter, mice were fed a cholesterol rich diet (metabolizable energy 35 kJ% fat, containing 12.5 mg/kg cholesterol, EF PAIGEN, Ssniff, Soest, Germany). One week after AAV-PCSK9 injection and initiation of the cholesterol rich diet, partial ligation of the left carotid artery was performed as described (Siragusa, M. et al. Nitric oxide maintains endothelial redox homeostasis through PKM2 inhibition. EMBO J 38, e100938; 10.15252/embj.2018100938 (2019)). Seven days after ligation, animals were sacrificed and vessels and organs were harvested, snap frozen in liquid nitrogen and stored at -80°C until processed further.

value: right carotid artery

tag: protocol

value: RiboTag

value: EC-RiboTag mice (Cdh5-CreERT2 x Rpl22HA/HA), C57BL/6J


title: RCA-RiboTag_4


title: RFP12

value: Blastocyst

value: Actin-RFP transgene


title: RCA-RiboTag_3


title: Caco-2.batch1.CAT.rep3.H09

description: Library name: Caco2_Batch1_CAT_3_H09


title: Bulk_KTrp53_DU_2

value: PDAC


title: Caco-2.batch1.CAT.rep3.G09

description: Library name: Caco2_Batch1_CAT_3_G09

value: colon


title: RCA-RiboTag_1


title: Caco-2.batch1.CAT.rep3.F09

description: Library name: Caco2_Batch1_CAT_3_F09

value: epithelial


title: RCA-RiboTag_2


title: RFP11


title: RCA-Input_5

value: RNA-Seq


title: RFP10


title: Caco-2.batch1.CAT.rep3.E09

description: Library name: Caco2_Batch1_CAT_3_E09


title: RCA-Input_2


title: RCA-Input_3


title: Caco-2.batch1.CAT.rep3.D09

description: Library name: Caco2_Batch1_CAT_3_D09


title: LCA-RiboTag_4

source_name: left carotid artery

value: left carotid artery


title: LCA-RiboTag_5


title: Caco-2.batch1.CAT.rep3.C09

description: Library name: Caco2_Batch1_CAT_3_C09


title: RFP7


title: LCA-RiboTag_3


title: Caco-2.batch1.CAT.rep3.B09

description: Library name: Caco2_Batch1_CAT_3_B09


title: RFP6


title: LCA-RiboTag_2


title: LCA-RiboTag_1


title: LCA-Input_5


title: Caco-2.batch1.CAT.rep3.A09

description: Library name: Caco2_Batch1_CAT_3_A09


title: RFP5


title: LCA-Input_4


title: LCA-Input_3


title: RFP4


title: Caco-2.batch1.CAT.rep2.H09

description: Library name: Caco2_Batch1_CAT_2_H09


title: LCA-Input_1


title: LCA-Input_2


title: RFP3


title: Caco-2.batch1.CAT.rep2.G09

description: Library name: Caco2_Batch1_CAT_2_G09


title: Lung-RiboTag_5

source_name: Lung

extract_protocol:
Murine tissues were homogenized in lysis buffer (2-3% w/v) containing: Tris/HCl pH 7.5 (50 mmol/L), NaCl (150 mmol/L), MgCl2 (12 mmol/L), NP-40 (1%), DTT (1 mmol/L), EDTA-free protease inhibitor mix (AppliChem GmbH, Darmstadt, Germany), SUPERase In RNase Inhibitor (200U/mL, Thermo Fisher Scientific), murine RNase inhibitor (1000 U/mL for lung tissue, 500 U/mL for all other tissues; New England Biolabs, Frankfurt am Main, Germany), heparin (10 mg/mL), cycloheximide (100 µg/mL) and TURBO DNaseI (25U/mL, Thermo Fisher Scientific) in UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific). Lysates were centrifuged (16,000g, 10 minutes, 4°C) and the supernatants were passed through 70 µm pre-separation filters (Miltenyi Biotec, Bergisch Gladbach, Germany). Ten % of the total lysate volume was mixed with 9 volumes of QIAZOL and frozen at -80°C. The remaining lysates were incubated with anti-HA antibody-conjugated magnetic beads (50 µl/sample, washed and resuspended in lysis buffer, Biozol, Eching, Germany) before being incubated overnight on end-over-end rocker at 4°C. HA immunoprecipitates were washed three times with a freshly prepared high salt buffer containing: Tris/HCl pH 7.5 (50 mmol/L), NaCl (300 mmol/L), MgCl2 (12 mmol/L), NP-40 (0.5%), DTT (1 mmol/L), SUPERase In RNase Inhibitor (200 U/mL, Thermo Fisher Scientific), murine RNase inhibitor (1000 U/mL for lung tissue, 500 U/mL for all other tissues; New England Biolabs) and cycloheximide (100 µg/mL). After the final wash, HA immunoprecipitates were resuspended in 700 µL QIAZOL and immediately processed for RNA purification. The total input RNA (from the total lysates) as well as the ribosome-associated RNA (from the RiboTag immunoprecipitates) were purified using the miRNeasy Micro kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions.
One hundred ng - 1 µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina, Sand Diego, USA) without fragmentation (5 minutes 65°C for RT annealing). Finished libraries were size selected by Pippin device (Sage science, Beverly, USA) for insert sizes < 300nt. Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in 8-62M reads per library (average 25M) with 1x75 nt single-end setup.

treatment_protocol: Cre-mediated recombination was induced in 8-9 weeks old mice by intraperitoneal injections of tamoxifen (50 mg/kg/day dissolved in 50 µL Miglyol; Merck, Darmstadt, Germany) for 5 consecutive days.

value: Lung


title: Caco-2.batch1.CAT.rep2.F09

description: Library name: Caco2_Batch1_CAT_2_F09


title: RFP2


title: Lung-RiboTag_3


title: Caco-2.batch1.CAT.rep2.E09

description: Library name: Caco2_Batch1_CAT_2_E09


title: RFP1


title: Lung-RiboTag_1


title: Caco-2.batch1.CAT.rep2.D09

description: Library name: Caco2_Batch1_CAT_2_D09


title: GFP39

value: Actin-GFP transgene


title: Lung-Input_3


title: Caco-2.batch1.CAT.rep2.C09

description: Library name: Caco2_Batch1_CAT_2_C09


title: Lung-Input_5


title: Lung-Input_2


title: GFP38


title: Caco-2.batch1.CAT.rep2.A09

description: Library name: Caco2_Batch1_CAT_2_A09


title: Lung-Input_1


title: Heart-RiboTag_6

source_name: Whole heart

value: Heart


title: GFP37


title: Caco-2.batch1.CAT.rep1.H09

description: Library name: Caco2_Batch1_CAT_1_H09


title: Heart-RiboTag_5


title: Heart-RiboTag_4


title: Heart-RiboTag_3


title: Heart-RiboTag_2


title: Caco-2.batch1.CAT.rep1.G09

description: Library name: Caco2_Batch1_CAT_1_G09


title: GFP36


title: Heart-RiboTag_1


title: Caco-2.batch1.CAT.rep1.F09

description: Library name: Caco2_Batch1_CAT_1_F09


title: RCA-Input_4


title: Heart-Input_5


title: GFP35


title: Heart-Input_6


title: GFP34


title: RFP9


title: RFP8


title: Heart-Input_4


title: Caco-2.batch1.CAT.rep1.E09

description: Library name: Caco2_Batch1_CAT_1_E09


title: Heart-Input_3


title: RCA-Input_1


title: GFP33


title: Heart-Input_2


title: Heart-Input_1


title: GFP32


title: Arch-RiboTag_6

source_name: Aortic arch

value: Arch


title: Arch-RiboTag_5


title: Caco-2.batch1.CAT.rep1.D09

description: Library name: Caco2_Batch1_CAT_1_D09


title: Arch-RiboTag_3


title: Caco-2.batch1.CAT.rep1.B09

description: Library name: Caco2_Batch1_CAT_1_B09


title: GFP31


title: Lung-RiboTag_4


title: Arch-RiboTag_1


title: Caco-2.batch1.CAT.rep1.C09

description: Library name: Caco2_Batch1_CAT_1_C09


title: Arch-RiboTag_4


title: GFP29


title: Arch-Input_5


title: Arch-RiboTag_2


title: Caco-2.batch1.CAT.rep1.A09

description: Library name: Caco2_Batch1_CAT_1_A09


title: GFP30


title: GFP28


title: Caco-2.batch1.ATA.rep3.H01

description: Library name: Caco2_Batch1_ATA_3_H01


title: Arch-Input_4


title: Arch-Input_3


title: Lung-Input_4


title: GFP40


title: Aorta-RiboTag_6

source_name: Thoracic aorta

value: Aorta


title: Caco-2.batch1.ATA.rep3.G01

description: Library name: Caco2_Batch1_ATA_3_G01

value: cell line


title: Arch-Input_2


title: Arch-Input_1


title: GFP26


title: GFP27


title: Caco-2.batch1.ATA.rep3.E01

description: Library name: Caco2_Batch1_ATA_3_E01


title: Caco-2.batch1.ATA.rep3.F01

description: Library name: Caco2_Batch1_ATA_3_F01


title: Aorta-RiboTag_5


title: Aorta-RiboTag_4


title: GFP25


title: Caco-2.batch1.CAT.rep2.B09

description: Library name: Caco2_Batch1_CAT_2_B09


title: Aorta-RiboTag_3


title: Caco-2.batch1.ATA.rep3.D01

description: Library name: Caco2_Batch1_ATA_3_D01


title: GFP24


title: Aorta-RiboTag_2


title: Aorta-RiboTag_1


title: Caco-2.batch1.ATA.rep3.C01

description: Library name: Caco2_Batch1_ATA_3_C01


title: GFP23


title: Aorta-Input_6


title: Aorta-Input_4


title: Caco-2.batch1.ATA.rep3.B01

description: Library name: Caco2_Batch1_ATA_3_B01


title: GFP22


title: Caco-2.batch1.ATA.rep3.A01

description: Library name: Caco2_Batch1_ATA_3_A01


title: Aorta-Input_3


title: Aorta-Input_5


title: GFP21


title: Aorta-Input_1


title: Caco-2.batch1.ATA.rep2.H01

description: Library name: Caco2_Batch1_ATA_2_H01


title: Aorta-Input_2


title: GFP20


title: NHEK-siTEDAR#3

type: RNA

city: Uppsala

first: Andor

last: Pivarcsi

address: BMC B11:3

department: Department of Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala Univesrity

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions for the Affymetrix GeneChip Human Transcriptome Array 2.0 (HTA-2_0).

scan_protocol: Arrays were scanned according to the manufacturer’s instructions.

data_processing: aw CEL files were processed using Affymetrix Expression Console software (med-polish, gc-correction, RMA background correction, quantile normalization, log2 transformation), with annotation to genome build hg19/GRCh37, NetAffx build 36. Differential expression and multiple testing correction were performed in R.

label: biotin

source_name: siTEDAR

label_protocol: Biotin-labeled sense-strand cDNA was generated from total RNA using the Affymetrix GeneChip WT PLUS Reagent Kit according to the manufacturer’s instructions.

growth_protocol: Primary adult human keratinocytes were nucleofected with siPool (siRNA pool) targeting TEDAR or non-targeting control siPool and allowed to recover for 24 hours in complete medium.

extract_protocol: Total RNA from keratinocytes growing in monolayer was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Total RNA from organotypic skin cultures was isolated using the RNeasy Plus mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: After recovery, keratinocytes were trypsinized, counted, and resuspended in keratinocyte growth medium (66% DMEM, 22% Ham’s F-12, 1% Pen-Strep, 1% Antibiotic-antimycotic, 10% FBS, 0.2% Hydrocortisone, 0.2% Adenine, 0.1% Cholera toxin, 0.1% Insulin, 0.1% EGF, 0.1% T/T3). Cells (500,000 per tissue) were seeded onto the basement membrane side of devitalized dermis and raised to the air–liquid interface to initiate stratification and differentiation. Medium for differentiation was changed every other day. Organotypic tissues were harvested on day 4 of differentiation.

value: siTEDAR


title: Caco-2.batch1.ATA.rep2.G01

description: Library name: Caco2_Batch1_ATA_2_G01


title: GFP19


title: Caco-2.batch1.ATA.rep2.F01

description: Library name: Caco2_Batch1_ATA_2_F01


title: Caco-2.batch1.ATA.rep2.E01

description: Library name: Caco2_Batch1_ATA_2_E01


title: NHEK-siTEDAR#1


title: GFP18


title: Caco-2.batch1.ATA.rep2.D01

description: Library name: Caco2_Batch1_ATA_2_D01


title: GFP17


title: GFP16


title: GFP15


title: NHEK-siCtrl#3

source_name: siCTRL

value: siCTRL


title: Caco-2.batch1.ATA.rep2.C01

description: Library name: Caco2_Batch1_ATA_2_C01


title: NHEK-siCtrl#2


title: Human_lung_P77 HTA 99

city: Columbus

first: Daniel

middle: Yui

last: Weng

state: OH

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

institute: The Ohio State University

description:
Human_lung_P77
Gene expression data

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix). Heat 65C for 5 minutes, 99C for 5 minutes, 45C for 5 minutes centrifuge top speed for 5 minutes. Hybridize 16 hours at 45°C at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were analyzed with Partek Genomics Suite using GC-RMA as normalization method and applied batch remove.

source_name: Bronchial epithelial cells

label_protocol: 5.5 ug of single stranded cDNA were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted using the TriplePure High Impact Zirconium beads and AllPrep DNA/RNA Mini Kit according to the manufacturer's instructions.

tag: race

value: White

value: Male

tag: smoking status

value: E-cig


title: NHEK-siCtrl#1


title: Human_lung_P62 HTA 98

description:
Human_lung_P62
Gene expression data

value: Smoker


title: Human_lung_P45 HTA 96

description:
Human_lung_P45
Gene expression data

value: Other

value: Never


title: Human_lung_P29 HTA 97

description:
Human_lung_P29
Gene expression data


title: Caco-2.batch1.ATA.rep2.B01

description: Library name: Caco2_Batch1_ATA_2_B01

value: colon

value: epithelial


title: GFP14

value: Blastocyst


title: Caco-2.batch1.ATA.rep2.A01

description: Library name: Caco2_Batch1_ATA_2_A01


title: Human_lung_P98 HTA 95

description:
Human_lung_P98
Gene expression data

value: Female


title: NHEK-siTEDAR#2


title: GFP13

value: Actin-GFP transgene


title: Human_lung_P63 HTA 94

description:
Human_lung_P63
Gene expression data


title: Human_lung_P41 HTA 92

description:
Human_lung_P41
Gene expression data


title: GFP12


title: Caco-2.batch1.ATA.rep1.G02

description: Library name: Caco2_Batch1_ATA_1_G02


title: Caco-2.batch1.ATA.rep1.H02

description: Library name: Caco2_Batch1_ATA_1_H02


title: Human_lung_P46 HTA 91

description:
Human_lung_P46
Gene expression data


title: GFP11


title: Human_lung_P81 HTA 9

description:
Human_lung_P81
Gene expression data


title: Caco-2.batch1.ATA.rep1.F02

description: Library name: Caco2_Batch1_ATA_1_F02


title: Human_lung_P88 HTA 89

description:
Human_lung_P88
Gene expression data

value: AA


title: Human_lung_P8 HTA 85

description:
Human_lung_P8
Gene expression data


title: Human_lung_P99 HTA 86

description:
Human_lung_P99
Gene expression data


title: Human_lung_P55 HTA 87

description:
Human_lung_P55
Gene expression data


title: Human_lung_P6 HTA 88

description:
Human_lung_P6
Gene expression data


title: Caco-2.batch1.ATA.rep1.E02

description: Library name: Caco2_Batch1_ATA_1_E02


title: GFP10


title: GFP9


title: Caco-2.batch1.ATA.rep1.D02

description: Library name: Caco2_Batch1_ATA_1_D02


title: GFP8


title: Human_lung_P43 HTA 83

description:
Human_lung_P43
Gene expression data


title: Human_lung_P60 HTA 82

description:
Human_lung_P60
Gene expression data


title: Human_lung_P2 HTA 8

description:
Human_lung_P2
Gene expression data


title: Lung-RiboTag_2

value: Lung

value: RiboTag

value: EC-RiboTag mice (Cdh5-CreERT2 x Rpl22HA/HA), C57BL/6J


title: Caco-2.batch1.ATA.rep1.C02

description: Library name: Caco2_Batch1_ATA_1_C02

value: cell line


title: Human_lung_P59 HTA 78

description:
Human_lung_P59
Gene expression data


title: GFP7


title: Caco-2.batch1.ATA.rep1.B02

description: Library name: Caco2_Batch1_ATA_1_B02


title: GFP6


title: Human_lung_P53 HTA 79

description:
Human_lung_P53
Gene expression data


title: Caco-2.batch1.ATA.rep1.A02

description: Library name: Caco2_Batch1_ATA_1_A02


title: Human_lung_P5 HTA 73

description:
Human_lung_P5
Gene expression data


title: GFP5


title: Human_lung_P90 HTA 74

description:
Human_lung_P90
Gene expression data


title: Human_lung_P21 HTA 71

description:
Human_lung_P21
Gene expression data


title: Human_lung_P32 HTA 72

description:
Human_lung_P32
Gene expression data


title: Human_lung_P33 HTA 76

description:
Human_lung_P33
Gene expression data


title: MOLT4,SP11 treated

city: Bengaluru

first: Bibha

last: Choudhary

state: Karnataka

address: Biotech Park, GN Ramachandran Rd, Electronics City Phase 1, Electronic City,

country: India

institute: Institute of Bioinformatics and Applied Biotechnology

description: Library name: sclib_MOLT4_SP11

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline, which included demultiplexing, alignment, barcode processing, and gene counting. Reads were mapped to the human reference genome (hg38), and gene expression matrices were generated for downstream analysis.
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cell line

extract_protocol:
The MOLT-4 cell line was cultured under standard conditions in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO₂. The cell suspension was collected and centrifuged at 300 × g for 5 minutes at 4 °C. The supernatant was discarded, and the cell pellet was washed twice with sterile PBS containing 0.04% BSA to remove residual media and serum components.
Following washing, cells were resuspended gently to obtain a single-cell suspension. Cell clumps were removed by passing the suspension through a 40–70 µm cell strainer. Cell viability and concentration were determined using Trypan Blue staining, ensuring viability >85%. Finally, the cells were resuspended in PBS containing 0.04% BSA at a concentration of 700–1200 cells/µL and kept on ice prior to loading onto the 10x Genomics platform for downstream single-cell RNA sequencing.

treatment_protocol: IC50 concentratin for 48h

value: Cell line

value: Leukemia

value: SP11 treated


title: MOLT4,Untreated

description: Library name: sclib_MOLT4_CONTROL

value: untreated


title: GFP4


title: GFP3


title: Human_lung_P79 HTA 70

description:
Human_lung_P79
Gene expression data

value: White

value: Male

value: E-cig


title: 28_rgal

city: Saint Louis

first: Stephen

last: Oh

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

description: Library name: Sample 10

data_processing:
Basecalling and demultiplexing were performed via Illumina bcl2fastq allowing a maximum of one mismatch. Paired-end 150bp reads were aligned to the Ensembl release 101 primary assembly using STAR v2.7.9a1. Gene counts were derived from uniquely aligned unambiguous reads using Subread:featureCounts v2.0.32, and isoform expression was quantified using Salmon v1.5.23. Quality control metrics, including ribosomal fraction, junction saturation, and read distribution, were quantified with RSeQC v4.04.
Assembly: GRCh38.101
Supplementary files format and content: gene-count.csv

source_name: CD14+ MPN monocyte

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany) with DNase treatment following the manufacturer's protocol. RNA integrity was verified using an Agilent Bioanalyzer or 4200 TapeStation.
Libraries were generated from 1-50ng of total RNA. ds-cDNA was synthesized using the SeqPlex RNA Amplification Kit (Sigma-Aldrich). cDNA was fragmented using a Covaris E220 sonicator (peak incident power 18, duty factor 20%, 50 cycles/burst, 120s), followed by blunt-ending, 3' A-tailing, and Illumina adapter ligation. Ligated fragments were PCR-amplified for 12-15 cycles using unique index primers.

treatment_protocol: Magnetic bead-enriched CD14+ human monocytes from MPN patients were incubated with vehicle (PBS) or recombinant Galectin-1 (5 μg/mL) for 7 hours

value: CD14+ MPN monocyte


title: Human_lung_P89 HTA 68

description:
Human_lung_P89
Gene expression data

value: Never


title: Human_lung_P34 HTA 66

description:
Human_lung_P34
Gene expression data


title: Human_lung_P72 HTA 62

description:
Human_lung_P72
Gene expression data

value: Other


title: Human_lung_P86 HTA 64

description:
Human_lung_P86
Gene expression data

value: Female


title: Human_lung_P82 HTA 69

description:
Human_lung_P82
Gene expression data


title: 28_nc

description: Library name: Sample 9

value: PBS


title: GFP1

value: Blastocyst

value: Actin-GFP transgene


title: GFP2


title: 23_rgal

description: Library name: Sample 8


title: 35G-deep6

library_source: genomic

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file include numble of different reads for each sample. For RNA-seq, tab-delimited text file include RPKM values for each sample
Library strategy: deep-seq

molecule: genomic DNA

source_name: testis

value: testis

value: Gjb2 35delG


title: Human_lung_P7 HTA 57

description:
Human_lung_P7
Gene expression data


title: 23_nc

description: Library name: Sample 7


title: Human_lung_P97 HTA 58

description:
Human_lung_P97
Gene expression data

value: Smoker


title: Human_lung_P70 HTA 6

description:
Human_lung_P70
Gene expression data


title: Human_lung_P27 HTA 54

description:
Human_lung_P27
Gene expression data


title: Human_lung_P31 HTA 60

description:
Human_lung_P31
Gene expression data


title: Human_lung_P38 HTA 56

description:
Human_lung_P38
Gene expression data


title: 20_nc

description: Library name: Sample 5


title: Human_lung_P68 HTA 52

description:
Human_lung_P68
Gene expression data


title: 35G-deep5


title: 20_rgal

description: Library name: Sample 6


title: 35G-deep3

source_name: heart

value: heart


title: 35G-deep4

source_name: tail

value: tail


title: 17_rgal

description: Library name: Sample 4


title: Human_lung_P64 HTA 47

description:
Human_lung_P64
Gene expression data


title: Human_lung_P3 HTA 51

description:
Human_lung_P3
Gene expression data


title: Human_lung_P74 HTA 5

description:
Human_lung_P74
Gene expression data


title: Human_lung_P100 HTA 46

description:
Human_lung_P100
Gene expression data


title: Human_lung_P87 HTA 45

description:
Human_lung_P87
Gene expression data


title: Human_lung_P42 HTA 49

description:
Human_lung_P42
Gene expression data


title: 35G-deep2

source_name: liver

value: liver


title: 17_nc

description: Library name: Sample 3


title: 14_rgal

description: Library name: Sample 2


title: 35G-deep1

source_name: brain

value: brain


title: mouse_post-estropause_acylic_ovary5

city: New York

first: Jiping

last: Yang

state: NY

department: OBGYN

institute: Columbia University

description: 10x Genomics 3' V3

data_processing:
Processed data were generated by cellranger v7.2
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Ovary

extract_protocol:
Ovary samples were collected separately from each individual at different days. Estrous cycle stages of mice were measured before noon and mice at diestrus stage were anesthetized and perfused with PBS. Two ovaries were isolated and immersed in chilled M2 medium (Sigma, M7167). Surrounding fat and connective tissue were trimmed and removed. Two intact ovaries were minced in 1.5 ml Eppendorf tube and treated by enzymatic digestion in dissociation buffer (M2 medium supplemented with 30 ug/ml Liberase DH (Roche, LIBDH-RO) and 1000U/mL DNase (Thermo Fisher)) at 37°C for 15 min with shaking on thermomixer (1000 rpm). The tube was briefly spun at 1000 rpm and the supernatant was collected in a 15 ml centrifuge tube. Next, the remaining tissues were cut and incubated in a dissociation buffer for 10 min with shaking. The cell suspension was pooled with the supernatant in a 15 mL tube and neutralized with M2 medium with 1% BSA. The pooled cell suspension was filtered with a 70-um cell strainer (Miltenyi Biotec) and was centrifuged. Cell pellets were incubated with RBC Lysis Buffer (Thermo Fisher) to remove red blood cells and subsequently washed with 1%BSA in PBS and 10% FBS in EMEM. Pelleted cells were resuspended in 10% FBS in EMEM and further submitted to Columbia Genomic Core for scRNA-seq library construction.
The cell suspension was loaded onto Chromium Single Cell Chip from 10x Genomics Chromium Single Cell 3’ Reagent Kits v3, aiming for a target output of 5000 cells per sample. Followed by reverse transcription, cDNA amplification, indexed adaptor ligation, and library amplification were performed according to the manufacturer’s protocol. The final libraries were sequenced on Illumina NovaSeq 6000 at Columbia Genome Center.
10x Genomics 3' V3

value: Ovary

tag: estrous cycle

value: acyclic


title: Human_lung_P54 HTA 44

description:
Human_lung_P54
Gene expression data

value: White

value: Male


title: mouse_post-estropause_acylic_ovary4

description: 10x Genomics 3' V3


title: Human_lung_P28 HTA 42

description:
Human_lung_P28
Gene expression data


title: Human_lung_P58 HTA 41

description:
Human_lung_P58
Gene expression data

value: E-cig


title: 14_nc

description: Library name: Sample 1

value: CD14+ MPN monocyte


title: Human_lung_P56 HTA 38

description:
Human_lung_P56
Gene expression data

value: Female

value: Never


title: Human_lung_P44 HTA 40

description:
Human_lung_P44
Gene expression data

value: Other


title: mouse_post-estropause_acylic_ovary3

description: 10x Genomics 3' V3


title: H2

description:
Library name: Sample 4
10x Genomics

data_processing:
FASTQ file generation, read alignment, barcode assignment, and UMI counting were performed utilizing 10x Genomics Cell Ranger v6.1.1. Reads were aligned to the reference transcriptome, with intronic reads explicitly included in the gene expression quantification.
Assembly: GRCh38-2020-A
Supplementary files format and content: barcodes, features, and matrix files

source_name: BMMC

extract_protocol:
CD34+ and CD14+ cells were sequentially isolated using Miltenyi magnetic beads via positive selection, counted, and mixed into a single-cell suspension. The cells were then loaded onto a 10x Genomics Chromium Controller for GEM (Gel Bead-in-Emulsion) generation.
GEM generation, cell barcoding, and cDNA library preparation were performed using the Chromium Next GEM Single Cell 3′ Reagent v3.1 (Dual Index) kit (10x Genomics) following the manufacturer’s protocol.

value: BMMC

tag: cell subtype

value: CD34+ and CD14+ cells enriched


title: H1

description:
Library name: Sample 3
10x Genomics


title: Human_lung_P11 HTA 36

description:
Human_lung_P11
Gene expression data

value: AA


title: Human_lung_P13 HTA 37

description:
Human_lung_P13
Gene expression data

value: Smoker


title: Human_lung_P48 HTA 34

description:
Human_lung_P48
Gene expression data


title: Human_lung_P78 HTA 30

description:
Human_lung_P78
Gene expression data


title: mouse_post-estropause_acylic_ovary2

description: 10x Genomics 3' V3


title: Human_lung_P75 HTA 32

description:
Human_lung_P75
Gene expression data


title: ET3

description:
Library name: Sample 2
10x Genomics


title: ET1

description:
Library name: Sample 1
10x Genomics


title: mouse_peri-estropause_irregular_ovary4

description: 10x Genomics 3' V3

value: irregular


title: mouse_peri-estropause_irregular_ovary3

description: 10x Genomics 3' V3


title: SiRNA_6

city: Fuzhou

first: dan

middle: li

last: he

address: College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian  Medical University, Fuzhou 350122, Fujian, China

institute: Fujian  Medical University

description:
Library name: USP22_KD_6
FPKM.SiRNA_6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: csv files include FPKMvalues for each Sample

source_name: placenta

growth_protocol: HTR-8/SVneo cells (CL-0765, Procell) were cultured in DMEM complete medium (KGM12800S, Kaiji Bio) containing 10% FBS and 1% penicillin-streptomycin at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: To establish the hypoxia model, HTR-8/SVneo cells were cultured under hypoxic conditions (1% O2, 5% CO2, 94% N2) for 48 hours.To investigate the role of USP22, cells were transfected with USP22 knockdown vector and USP22 overexpression vector (ZvastBio) using Lipofectamine 3000.

value: placenta

value: trophoblast

value: USP27 knockdown


title: mouse_post-estropause_acylic_ovary1

description: 10x Genomics 3' V3

value: Ovary


title: Human_lung_P96 HTA 3

description:
Human_lung_P96
Gene expression data


title: SiRNA_5

description:
Library name: USP22_KD_5
FPKM.SiRNA_5

value: USP26 knockdown


title: Human_lung_P18 HTA 28

description:
Human_lung_P18
Gene expression data

value: White


title: mouse_peri-estropause_irregular_ovary2

description: 10x Genomics 3' V3


title: Human_lung_P15 HTA 29

description:
Human_lung_P15
Gene expression data


title: Human_lung_P25 HTA 27

description:
Human_lung_P25
Gene expression data


title: Human_lung_P52 HTA 25

description:
Human_lung_P52
Gene expression data


title: Human_lung_P67 HTA 22

description:
Human_lung_P67
Gene expression data

value: Male


title: SiRNA_4

description:
Library name: USP22_KD_4
FPKM.SiRNA_4

value: USP25 knockdown


title: Human_lung_P9 HTA 23

description:
Human_lung_P9
Gene expression data


title: mouse_peri-estropause_irregular_ovary1

description: 10x Genomics 3' V3


title: SiRNA_3

description:
Library name: USP22_KD_3
FPKM.SiRNA_3

value: USP24 knockdown


title: mouse_peri-estropause_regular_ovary3

description: 10x Genomics 3' V3

value: regular


title: SiRNA_2

description:
Library name: USP22_KD_2
FPKM.SiRNA_2

value: USP23 knockdown


title: Human_lung_P49 HTA 20

description:
Human_lung_P49
Gene expression data

value: Other

value: Female

value: Never


title: Human_lung_P1 HTA 2

description:
Human_lung_P1
Gene expression data


title: Human_lung_P51 HTA 17

description:
Human_lung_P51
Gene expression data


title: Human_lung_P83 HTA 19

description:
Human_lung_P83
Gene expression data

value: AA


title: mouse_peri-estropause_regular_ovary2

description: 10x Genomics 3' V3


title: Human_lung_P66 HTA 15

description:
Human_lung_P66
Gene expression data

value: E-cig


title: mouse_peri-estropause_regular_ovary1

description: 10x Genomics 3' V3


title: Human_lung_P76 HTA 14

description:
Human_lung_P76
Gene expression data


title: SiRNA_1

description:
Library name: USP22_KD_1
FPKM.SiRNA_1

value: USP22 knockdown


title: Multiome, central amygdala, RT00282N, AUD, human, GEX

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

description: Library name: RT00282N_GEX

data_processing:
Multiome files were demultiplexed using Cellranger-arc mkfastq
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5,  atac_fragments.tsv.gz

source_name: Central Amygdala

extract_protocol:
Nuclei were isolated from fresh-frozen human central amygdala tissue and purified to generate single-nucleus suspensions for simultaneous chromatin accessibility and gene-expression profiling.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, which constructs matched ATAC-seq (genomic DNA accessibility) and gene-expression (polyA nuclear RNA) libraries from the same nucleus.

value: Central Amygdala

value: alcohol use disorder

tag: batch


title: mouse_young_regular_ovary5

description: 10x Genomics 3' V3

tag: tissue


title: Human_lung_P16 HTA 12

description:
Human_lung_P16
Gene expression data


title: NC_6

description:
Library name: Control_6
FPKM.NC_6

value: placenta

value: trophoblast

tag: genotype

value: control vector


title: Human_lung_P73 HTA 101

description:
Human_lung_P73
Gene expression data

value: White


title: Human_lung_P102 HTA 100

description:
Human_lung_P102
Gene expression data

value: Smoker


title: NC_5

description:
Library name: Control_5
FPKM.NC_5

tag: treatment


title: mouse_young_regular_ovary4

description: 10x Genomics 3' V3

value: Ovary


title: Sort-purified (CD8+/Ly5.1-/CD44+) CD8 T cells isolated from spleens Input Control

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: CD8_500k_input_naive_1

data_processing:
Sequence reads were aligned to the mouse reference genome (GRCm38.p6) using the nf-core/cutandrun pipeline v3.2.2 with default parameters. In brief, reads were quality-checked with FastQC v0.12.1, trimmed with TrimGalore v0.6.6. and aligned with Bowtie2 v2.4.4. Alignments were de-duplicated using Picard MarkDuplicates v3.1.0. Peaks were called using MACS3 v3.0.3 in paired-end mode with input control, using a q-value threshold of 0.01. Signal tracks (bigWig) were generated using deepTools bamCoverage v3.5.1 with BPM normalization and 50 bp bin size.
Assembly: GRCm38
Supplementary files format and content: BigWig files for each sample
Supplementary files format and content: MACS3 peak calls for each sample (except input)
Library strategy: CUT&RUN

source_name: spleen

extract_protocol:
After flow sorting, samples were fixed with PFA, quenched with Glycine and transferred to a BSA-coated 96 well plate. Cells were washed and resuspended in buffer (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine, + 2uM EDTA in H2O) containing anti-LEF1, anti-TCF1, anti-H3K4me3 (positive control) or no antibody (negative input control) overnight. The following day, cells were resuspended in buffer (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in H2O)  containing pAG-MNase (CELL SIGNALING) for 1 hour before wash and incubation in calcium-containing buffer (0.05% w/v Saponin, 1X Roche Complete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS + CaCl2 2uM) for 30 minutes. After incubation, STOP buffer (0.05% w/v Saponin, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS+ 20uM EDTA + 4uM EGTA) was added to the samples, supernatant was collected, and DNA was isolated with the MiniElute Kit. DNA fragments were digested with Proteinase K (Thermo Fisher, cat. EO0491) under addition of 0.1% SDS for 4h at 65°C.
Library prep was conducted on the product using a KAPA HyperPrep Kit (Kapa Biosystems, cat. KK8504). The final product was cleaned by AMPure XP beads (Beckman Coulter catalog no. A63882).

value: spleen

value: CD8 T cells

value: WT

tag: t cells

value: TCRP14 transgenic CD8 T cells


title: Human_lung_P35 HTA 10

description:
Human_lung_P35
Gene expression data

tag: Sex

value: Female


title: TCF1  C&R, Sort-purified (CD8+/Ly5.1+/CD44-/CD62L+) TCR-P14 CD8 T cells isolated from spleens replicate #2

description: Library name: CD8_500k_TCF7_naive_R5

tag: cell type


title: NC_4

description:
Library name: Control_4
FPKM.NC_4

tag: cell line


title: TCF1  C&R, Sort-purified (CD8+/Ly5.1+/CD44-/CD62L+) TCR-P14 CD8 T cells isolated from spleens replicate #3

description: Library name: CD8_500k_TCF7_naive_R6


title: mouse_young_regular_ovary3

description: 10x Genomics 3' V3

value: regular


title: TCF1  C&R, Sort-purified (CD8+/Ly5.1+/CD44-/CD62L+) TCR-P14 CD8 T cells isolated from spleens replicate #1

description: Library name: CD8_500k_TCF7_naive_R4


title: Human_lung_P22 HTA 24

description:
Human_lung_P22
Gene expression data

value: Male


title: Human_lung_P84 HTA 1

description:
Human_lung_P84
Gene expression data


title: LEF1  C&R, Sort-purified (CD8+/Ly5.1+/CD44-/CD62L+) TCR-P14 CD8 T cells isolated from spleens replicate #3

description: Library name: CD8_500k_Lef1_naive_R4


title: mouse_young_regular_ovary2

description: 10x Genomics 3' V3


title: NC_3

description:
Library name: Control_3
FPKM.NC_3


title: LEF1  C&R, Sort-purified (CD8+/Ly5.1+/CD44-/CD62L+) TCR-P14 CD8 T cells isolated from spleens replicate #2

description: Library name: CD8_500k_Lef1_naive_R3


title: LEF1 C&R, Sort-purified (CD8+/Ly5.1+/CD44-/CD62L+) TCR-P14 CD8 T cells isolated from spleens replicate #1

description: Library name: CD8_500k_Lef1_naive_R2


title: mouse_young_regular_ovary1

description: 10x Genomics 3' V3


title: NC_1

description:
Library name: Control_1
FPKM.NC_1


title: DW_S3

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

country: France

institute: Université Claude Bernard Lyon 1

description:
Library name: D2wt
Single cell transcriptome

data_processing:
For spatial transcriptomics, data demultiplexed in fastq format was checked with fastqc and fastq_screen to control quality sequencing. Sequencing reads were processed with SpaceRanger (v.2.1.1) to align and count data for each sample. Genome and transcriptome used is refdata-gex-mm10-2020-A from 10x Genomics. For single cell transcriptomics, data demultiplexed in fastq format was checked with fastqc and fastq_screen to control quality sequencing. Sequencing reads were processed with STAR (v.2.7.11b) to align and count data for each sample with conservation of rRNA during process. Genome and transcriptome used is GRCm39.111 from Ensembl Database. We counts pre-mRNA overlap gene loci included both exonic and intronic reads where priority is purely exonic alignment (GeneFull_ExonOverIntron option) and spiced, unspliced and ambiguous counts per cell similar to the velocyto.py (Velocyto option).
Assembly: GRCm39.111
Supplementary files format and content: barcodes.tsv : list of single cell transcriptomic barcodes
Supplementary files format and content: features.tsv : list of single cell transcriptomic features Ids
Supplementary files format and content: matrix.tsv : list of genes expression count data in Matrix Market Exchange Format for single cell transcriptomic
Supplementary files format and content: barcodes.tsv.gz : list of spatial transcriptomic barcodes
Supplementary files format and content: features.tsv : list of spatial transcriptomic features Ids
Supplementary files format and content: matrix.tsv : list of genes expression count data in Matrix Market Exchange Format for spatial transcriptomic
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg : image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scalefactor in json format
Supplementary files format and content: tissue_hires_image.png : high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png : low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv : list of spatial barcodes and the coordinates specifying spots

source_name: Skeletal Muscle

extract_protocol:
For spatial transcriptomics, gastrocnemius muscles were either isolated, embedded in OCT and flash-frozen in liquid nitrogen-cooled isopentane. Embedded muscle was transversely sectioned at 10µm thickness with cryostat and processed with 10X Visium Spatial Gene Expression. For single-cell RNA-sequencing, gastrocnemius muscles were digested in a collagenase/dispase solution and mononucleated cells were isolated by Fluorescence-activated cell sorting (FACS) using Hoeschst and Propidium iodide staining and captured using the 10X Genomics Chromium Platform.
Spatial transcriptome sequencing libraries were prepared following the manufacturer's instructions from 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit. Single cell libraries were generated according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Skeletal Muscle


title: NC_2

description:
Library name: Control_2
FPKM.NC_2


title: DM_S4

description:
Library name: D2mdx
Single cell transcriptome


title: SHIF23

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Supplementary files format and content: tab-delimited text files fpkm gene counts

source_name: Cerebral artery

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol: Mice underwent ad libitum eating or intermittant fasting for 3 months. After 3 months, chronic cerebral hypoperfusion was induced by the bilateral carotid arterys stenosis (BCAS) surgery. Control mice underwent sham surgery. Mice were culled at days 1, 14, 21 and 30 days post-surgery and cerebral arteries were collected.

value: Cerebral artery

tag: disease state

value: Control


title: BCAL9

value: Chronic cerebral hypoperfusion


title: NFIL3_KO_Tm_H3K27ac_HiChIP_SET3_rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: NFIL3_KO_Tm_H3K27ac_HiChIP_SET3_rep2

data_processing:
Paired-end Hi-C sequencing reads were processed using HiC-Pro (v2.11.4).
Chromatin loops from HiChIP data were identified using FitHiChIP (v8.0). Loop calling was performed in peak-to-all mode (IntType=3) using paired ChIP-seq peaks as input. The bin size was set to 5kb (default), with interaction distance range defined as 10kb to 2Mb. Bias correction was enabled using coverage normalization, and peak-to-all background was used for contact probability estimation (UseP2PBackgrnd = 0). Loops were identified at a threshold of Q-value < 0.00001 for H3K27Ac HiChIP data, Q-value < 0.01 for ATF4 HiChIP data.
Assembly: hg19
Supplementary files format and content: hic contaning validpairs
Library strategy: HiChIP

growth_protocol: The human colorectal cancer cell line HCT116 was cultured in RPMI-1640 medium (Welgene) supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% penicillin–streptomycin (Welgene) at 37 ℃ in a humidified incubator containing 5% CO2. Cells were subcultured every 48–72 h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, cross-linked chromatin was digested with the DpnII restriction enzyme, with enzyme amounts adjusted in proportion to the number of cells, followed by fill-in with biotin-14-dATP (Jena Bioscience) and proximity ligation. The resulting ligation products were sheared by sonication using a Qsonica sonicator (30 s ON/30 s OFF, 10 cycles) and incubated overnight at 4 ℃ with either an H3K27ac antibody (Abcam, ab4729) or an ATF4 antibody (Cell Signaling Technology, 11815). After sequential washes with standard ChIP wash buffers, chromatin–antibody complexes were reverse cross-linked overnight. De-cross-linked DNA was purified and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and 5 ng of DNA was subjected to biotin pull-down using a streptavidin C-1 magnetic beads.
Tagmentation was directly performed on bead-bound DNA with Tn5 transposase with enzyme amounts adjusted according to the DNA input, followed by washing with appropriate buffers. Tagmented DNA was released from the beads by a simplified PCR procedure and further amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.5x–0.75x).

treatment_protocol: Cells were treated with tunicamycin (Sigma-Aldrich) at a final concentration of 0.5 µg ml-1 for 6 h. Cells treated with 0.1% DMSO for the same duration served as vehicle controls.

tag: chip antibody

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer

value: 0.5 μg/ml tunicamycin

tag: time


title: BM_S2

description:
Library name: B6mdx
Single cell transcriptome


title: BW_S1

description:
Library name: B6wt
Single cell transcriptome


title: NFIL3_KO_Tm_H3K27ac_HiChIP_SET3_rep1

description: Library name: NFIL3_KO_Tm_H3K27ac_HiChIP_SET3_rep1


title: C-GA-D2-mdx_S1

description:
Library name: D2mdx_rep2
Flash-frozen muscle transcriptome

data_processing:
For spatial transcriptomics, data demultiplexed in fastq format was checked with fastqc and fastq_screen to control quality sequencing. Sequencing reads were processed with SpaceRanger (v.2.1.1) to align and count data for each sample. Genome and transcriptome used is refdata-gex-mm10-2020-A from 10x Genomics. For single cell transcriptomics, data demultiplexed in fastq format was checked with fastqc and fastq_screen to control quality sequencing. Sequencing reads were processed with STAR (v.2.7.11b) to align and count data for each sample with conservation of rRNA during process. Genome and transcriptome used is GRCm39.111 from Ensembl Database. We counts pre-mRNA overlap gene loci included both exonic and intronic reads where priority is purely exonic alignment (GeneFull_ExonOverIntron option) and spiced, unspliced and ambiguous counts per cell similar to the velocyto.py (Velocyto option).
Assembly: GRCm39.111
Supplementary files format and content: barcodes.tsv : list of single cell transcriptomic barcodes
Supplementary files format and content: features.tsv : list of single cell transcriptomic features Ids
Supplementary files format and content: matrix.tsv : list of genes expression count data in Matrix Market Exchange Format for single cell transcriptomic
Supplementary files format and content: barcodes.tsv.gz : list of spatial transcriptomic barcodes
Supplementary files format and content: features.tsv : list of spatial transcriptomic features Ids
Supplementary files format and content: matrix.tsv : list of genes expression count data in Matrix Market Exchange Format for spatial transcriptomic
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg : image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scalefactor in json format
Supplementary files format and content: tissue_hires_image.png : high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png : low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv : list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics


title: D_S4

description:
Library name: D2mdx_rep1
Flash-frozen muscle transcriptome


title: BCIF46

tag: strain


title: NFIL3_KO_Con_H3K27ac_HiChIP_SET3_rep2

description: Library name: NFIL3_KO_Con_H3K27ac_HiChIP_SET3_rep2

value: 0.1% DMSO


title: C_S3

description:
Library name: B6mdx_rep1
Flash-frozen muscle transcriptome


title: D-GA-B6mdx_S3

description:
Library name: B6mdx_rep2
Flash-frozen muscle transcriptome


title: normal-3

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

description: Library name: S18

data_processing:
Raw data of fastq format were firstly processed to clean data by removing reads containing adapter.
HISAT2 tools software was used to map clean reads to GRCm38 genome.
The gene counts were calculated with gene annotation from DisGenet database.
Assembly: GRCm38
Supplementary files format and content: txt count

source_name: lung

extract_protocol:
After excision of the lung tissues of each mouse (3 mice per group), a tissue homogenizer was used to homogenize the tissue samples. Subsequentially, TRIzolTM reagent (Thermo Scientific, 15596026) was used to extract total RNA from each sample according to the manufacturer’s instruction.
After passing the detection of total RNA samples, purification is carried out based on the characteristics of mRNA from different sources. The end of eukaryotic mRNA3 has a polyA tail structure, and magnetic beads with Oligo (dT) were selected for enrichment and purification; Prokaryotic mRNA does not possess this characteristic, so a reagent kit was used to remove rRNA to obtain more effective information. Add Fragmentation Buffer to the purified mRNA to make its fragments short. Using the fragmented RNA as a template, reverse transcription was performed using random primers to synthesize the first strand of cDNA, and the second strand of cDNA was synthesized by adding the 2nd Strand Marking Buffer and 2nd Strand/End Repair Enzyme Mix. After end repair, addition of base A, sequencing adapter, magnetic bead screening to recover the target fragment, and PCR amplification, the entire library preparation work was completed.

value: lung


title: NFIL3_KO_Con_H3K27ac_HiChIP_SET3_rep1

description: Library name: NFIL3_KO_Con_H3K27ac_HiChIP_SET3_rep1


title: normal-1

description: Library name: S16


title: BCIF80


title: CEBPB_KO_Tm_H3K27ac_HiChIP_SET3_rep2

description: Library name: CEBPB_KO_Tm_H3K27ac_HiChIP_SET3_rep2


title: normal-2

description: Library name: S17


title: BCIF31


title: pulmonary fibrosis model-3

description: Library name: S15


title: SHIF55


title: SHIF54


title: pulmonary fibrosis model-1

description: Library name: S13


title: PepNzymeSOD-CAT-3

description: Library name: S8


title: CEBPB_KO_Con_H3K27ac_HiChIP_SET3_rep2

description: Library name: CEBPB_KO_Con_H3K27ac_HiChIP_SET3_rep2


title: PepNzymeSOD-CAT-2

description: Library name: S5


title: CEBPB_KO_Tm_H3K27ac_HiChIP_SET3_rep1

description: Library name: CEBPB_KO_Tm_H3K27ac_HiChIP_SET3_rep1


title: pulmonary fibrosis model-2

description: Library name: S14


title: PepNzymeSOD-CAT-1

description: Library name: S2


title: BCIF77


title: CEBPB_KO_Con_H3K27ac_HiChIP_SET3_rep1

description: Library name: CEBPB_KO_Con_H3K27ac_HiChIP_SET3_rep1


title: W3

city: Shenzhen

first: Wen

middle: Ting

address: No,1120,LianHua Road,FuTian District

institute: Shenzhen PKU-HKUST Medical Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: gene_counts.txt
Supplementary files format and content: gene_fpkm.txt

source_name: epidermis

growth_protocol: Not applicable.

extract_protocol:
Total RNA was extracted from Control/Paxbp1 KO epidermal tissues using TRIzol reagent. Purified RNA was quantified using a NanoDrop 2000 (Thermo Scientific) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Mouse epidermal tissues were isolated as previously described (Li et al., 2017). Firstly, we euthanized the newborn mice and removed their heads, tails as well as limbs in a sterile environment. Next, the subcutaneous adipose tissues and dermis layer were removed from the skin specimens of Control/Paxbp1 KO mice. Then, the epidermal tissues were cut into 1 cm × 1 cm sections and allowed to incubate in Dispase II at 4 °C overnight. To collect RNA samples for RNA sequencing, we peeled off the dermis from the epidermis, gently washed the epidermis in PBS for 3 times and stored them in liquid nitrogen.

value: epidermis

value: Wildtype


title: BCAL28


title: W2


title: CHOP_KO_Tm_H3K27ac_HiChIP_SET3_rep2

description: Library name: CHOP_KO_Tm_H3K27ac_HiChIP_SET3_rep2


title: W1


title: K3

value: Paxbp1 knockout


title: BCIF15

value: WT


title: K2


title: CHOP_KO_Tm_H3K27ac_HiChIP_SET3_rep1

description: Library name: CHOP_KO_Tm_H3K27ac_HiChIP_SET3_rep1


title: SHAL50


title: K1


title: CHOP_KO_Con_H3K27ac_HiChIP_SET3_rep2

description: Library name: CHOP_KO_Con_H3K27ac_HiChIP_SET3_rep2


title: BCIF64


title: Ovarian granulosa  cells, CPC3

city: Chongqing

first: Xin

last: Yin

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

data_processing:
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts (fragments per thousand nucleotides per million mapped reads).
Assembly: hg19_ucsc
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: SKOV3 epithelial cells were maintained in Mc5a supplemented with 10% fetal bovine serum (FBS) and antibody in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: SKOV3 epithelial cells were tansfection with vector and GATA4 using PEI for 48 hours, respectively

value: Ovarian granulosa  cells

value: Cetylpyridinium chloride


title: CHOP_KO_Con_H3K27ac_HiChIP_SET3_rep1

description: Library name: CHOP_KO_Con_H3K27ac_HiChIP_SET3_rep1


title: Ovarian granulosa  cells,  Con3

value: PBS


title: Ovarian granulosa  cells, CPC2


title: Ovarian granulosa  cells, CPC1


title: BCAL12

value: Male


title: SHAL51


title: Ovarian granulosa  cells,  Con2


title: Ovarian granulosa  cells, Con1


title: WT_Tm_H3K27ac_HiChIP_SET3_rep1

description: Library name: WT_Tm_H3K27ac_HiChIP_SET3_rep1


title: Fibrosis

city: Philadelphia

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

institute: University of Pennsylvania

data_processing:
Cellranger 3.1.0
Cellranger mkfastq
Assembly: mm10
Supplementary files format and content: h5 files from the ouput of cellranger, containing matrix, barcodes, and features

extract_protocol:
Healthy and fibrotic murine liver were perfused with 1X PBS, cut into small pieces and digested in collagenase II (5mg/mL, Worthington Biochemical Corporation) at 37 oC for 2h with shaking. Digested cells were filtered through 40 μm nylon mesh and lysed with ACK lysis buffer (Quality Biological) for 10 min. After spinning, the cells were resuspended into 1X PBS. Hepatocytes were removed by spinning at 50xg for 10 min. The supernatant was further spined at 650xg for 3 min to get the nonparenchymal cells, which was further stained with CD45+ (BV785, Cat#103149, Biolegend) and F4/80+ (BV421, Cat#123132, Biolegend) for 30 min. Cells were further suspended in 1X PBS with 0.1% Draq7 live/dead staining. CD45+/F4/80+ macrophage was further sorted with BD FACSAria Fusion Sorter (BD Biosciences).
Chromium Single Cell 3ʹ Feature Barcode Library Kit

value: liver

value: Sorted primary cells

value: liver macrophages

value: BALB/c WT


title: BCIF13

value: Cerebral artery

value: Chronic cerebral hypoperfusion


title: Control

value: Vehicle control


title: WT_Con_H3K27ac_HiChIP_SET3_rep2

description: Library name: WT_Con_H3K27ac_HiChIP_SET3_rep2

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer

value: 0.1% DMSO