title: d25A141, d25A142, mESC, Mouse

description:
Library name: d25A141_d25A142
d25


title: k2

status: Public on Jan 01 2026

type: SRA

city: Chongqing

first: Hongxiang

last: Xu

address: Tiansheng Road

country: China

institute: Southwest University

description:
Library name: k2
kuligD-KO infected with SWU1

library_source: transcriptomic

data_processing:
All analyses were performed in the R statistical environment (v4.2.2) using RStudio as the integrated development environment. For differential expression analysis of RNA-seq data, the limma package (v3.54.0) was employed, with the voom method applied for variance stabilization.
Assembly: CP000480
Supplementary files format and content: gene expression count in csv format

molecule: total RNA

organism: Mycolicibacterium smegmatis

source_name: cell

extract_protocol:
M. smegmatis and its ΔkuΔligD were cultured in 7H9 medium to an OD600 of 2.0. Bacterial cells were collected by centrifugation and resuspended in fresh 7H9 medium to an OD600 of 1.0. The cultures were then infected with SWU1 phage at an MOI of 10, followed by a 30 minutes adsorption period at 37℃. Subsequent incubation was carried out at 37°C with shaking at 200 rpm for 30 and 180 minutes. At each time point, bacteria were harvested by centrifugation, and total RNA was extracted for RNA-seq analysis.
RNA was fragmented and then used as template for first-strand cDNA synthesis with reverse transcriptase and random hexamer primers, followed by second-strand cDNA synthesis using RNase H and DNA polymerase I. The resulting double-stranded cDNA fragments underwent end repair, addition of a single “A” base, and adapter ligation. Adaptor-ligated fragments were selected using AMPure XP beads and amplified by PCR to generate the final cDNA library. Transcriptome sequencing was performed by Wuhan Feisha Gene Company using an Illumina platform.

tag: tissue

value: cell

tag: genotype

value: kuligD-KO

tag: treatment

value: Mycobacterium phage SWU1


title: k1_180

description:
Library name: k1_180
kuligD-KO infected with SWU1


title: k2_180

description:
Library name: k2_180
kuligD-KO infected with SWU1


title: Single-cell RNA-seq day1 cell65

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

library_source: transcriptomic single cell

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample

organism: Mus musculus

source_name: Mouse embryonic fibroblasts reprgramming cells

growth_protocol: Reprogramming cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were collected by trypsin digestion. Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

treatment_protocol: MEF cells were infected with OvSvK for reprogramming.

tag: cell type

value: OvSvK single-cell RNA-seq reprogramming day1


title: d25A139, d25A140, mESC, Mouse

city: Beijing

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

description:
Library name: d25A139_d25A140
d25

library_source: genomic

data_processing:
Samples with more than 50,000 remaining contacts were retained for downstream analysis. For diploid samples, the haplotype of contacts was phased according to SNP sites. Each chromosome in each sample was treated as a polymer chain, evenly divided into 20kb sections, with each section treated as a particle of the polymer chain. The contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles using the Force-Directed Graph (FDG) algorithm implemented by “hickit”. To assess the quality of the chromatin 3D structure reconstruction, we generated five replicates using different random seeds and calculated the median RMSD for each combination of three replicates. If the median RMSD of the combination with the lowest value was less than 1.5, the first replicate in that combination was used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: dip pairs file: A tab-separated file recording allele-specific contacts that conforms to 4DN Consortium standards with chromosomes
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards with chromosomes

molecule: genomic DNA

source_name: mESC

extract_protocol:
We utilized a female mouse embryonic stem cell (mESC) line derived from blastocysts at embryonic day 3.5 (E3.5) from crossbred embryos (female C57BL/6J × male CAST/EiJ). The procedures for derivation and culturing followed the methods provided by Arenas et al. (2006). Cells were cultured on flasks coated with 0.1% gelatin in an ES cell medium containing serum. The medium composition included DMEM (Gibco, 10829018), 15% ESC-grade fetal bovine serum (FBS) (VivaCell, C04002-100), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% P/S (ThermoFisher, 10378016), NEAA (Sigma, M7145), L-Glutamine (Gibco, 25030-081), nucleotides (Millipore, ES-008-D), and 1000 U/ml leukemia inhibitory factor (LIF) (PeproTech, AF-250-02-25UG). Additionally, the medium was supplemented with 2i: 3 μM Gsk3 inhibitor CT99021 (Selleck, S1263) and 1 μM MEK inhibitor PD0325901 (Selleck, S1036). Differentiation was initiated by withdrawing 2i/LIF in DMEM supplemented with 10% FBS, 1% P/S, NEAA, L-Glutamine, nucleotides, and 0.1 mM β-mercaptoethanol. The cells were plated at a density of 1.5 × 10⁴ cells/cm² on 6 well cell culture plates coated with 10 μg/ml fibronectin (GLPBIO, GP23499).
The single-cell preamplification product was diluted to 5ng/ul and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C.

value: mESC

tag: strain

value: C57BI6/J(female)x CAST/EiJ(male)


title: d25A137, d25A138, mESC, Mouse

description:
Library name: d25A137_d25A138
d25


title: d25A143, d25A144, mESC, Mouse

description:
Library name: d25A143_d25A144
d25


title: Single-cell RNA-seq day1 cell63

value: Mouse embryonic fibroblasts reprgramming cells


title: d25A145, d25A146, mESC, Mouse

description:
Library name: d25A145_d25A146
d25


title: 501M_ASO_NEG_2

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

description:
501M treated with control ASO (ASO_NEG)
GNGB11_S1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: Excel file containing raw read counts, normalized counts (by sequencing depth and median gene length) and log2(fold-change) with adjusted p-values for comparisons of interest. The file contains 3 distinct sheets for RNA-seq (501M whole extracts and fractions) and RIP-seq.

molecule: polyA RNA

organism: Homo sapiens

source_name: Skin

growth_protocol: 501mel were grown in RPMI1640 w/o HEPES medium supplemented with 10 % fetal calf serum (FCS) and gentamycin (40 µg/mL).

extract_protocol:
Total mRNA isolation was performed using Trizol (TR 118) and isopropanol precipitation. RNA was then treated with DNAseI following the TurboDNAse kit instructions (AM1907 – ThermoFisher) and 1µg of RNA was reversed transcribed using SuperScript IV (18090050 – ThermoFisher) following manufacturer instructions.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Transfections were performed using Lipofectamine RNAiMAX (Invitrogen) with 20 nmol/L of GapmeR (Qiagen).

value: Skin

tag: cell line


title: ICAM1- DPSCs-2

city: Hangzhou

first: Yi

last: Zhang

state: Zhejiang

address: 166 North Qiutao Rd

department: Department of Endodontics

institute: Zhejiang University

description:
Library name: CON-2
CON-2

data_processing:
After passing the library check, the different libraries were sequenced in Illumina after pooling them according to the effective concentration and the target sequencing output data volume, yielding 150bp paired-end reads. The basic principle of sequencing is to synthesize and sequence at the same time. Four types of fluorescently labeled dNTPs, DNA polymerase, and junction primers were added to the sequencing flow cell for amplification. When extending the complementary strand of each sequencing cluster, each fluorescently labeled dNTP added emits corresponding fluorescence, and the sequencer captures the fluorescence signals, and converts the light signals into sequencing peaks through computer software, so as to obtain the sequence information of the fragment to be tested.
1. Data Quality Control  Data quality control was performed using fastp to remove reads with adapters. Paired reads were removed under the following conditions: when the the number of N in any sequencing read exceeded 10% of the length of that read, and when any sequencing read contained low-quality bases (Q<=20) exceeding 50% of the length of that read. Subsequent analyses were based on clean reads. 2. Sequence Alignment to the Reference Genome  The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index, and clean reads were aligned to the reference genome. 3. Quantification of Gene Expression Levels  Gene expression levels were quantified using featureCounts to calculate gene alignment statistics. Subsequently, FPKM (Fragments Per Kilobase Million) values for each gene were computed based on gene length. FPKM is currently the most used method for estimating gene expression levels. 4. Differential Analysis  DESeq2 was used for differential gene expression analysis between two groups, and Benjamini & Hochberg correction was applied to P-values. Corrected P-values and log2 fold change were used as thresholds for significant differential expression. 5. Differential Gene Enrichment Analysis  Enrichment analysis was performed based on the hypergeometric test, with pathway-based hypergeometric distribution testing for KEGG and GO term-based analysis for GO. 6. Differential Splicing Analysis  rMATS was used to analyze alternative splicing events, including SE (skipped exon), RI (retained intron), MXE (mutually exclusive exons), A5SS (alternative 5' splice site), and A3SS (alternative 3' splice site). 7. SNP Analysis  GATK was used for variant site analysis, and annovar was used for variant annotation. 8. Fusion Gene Analysis STAR-Fusion was used for Gene Fusion Analysis 9. Differential Gene-Protein Interaction Analysis  Analysis of protein interactions for differentially expressed genes was based on the STRING database, which contains known and predicted protein-protein interactions. For species present in the database, a network was constructed by extracting the target gene list from the database. Otherwise, blastx was used to align target gene sequences with selected reference protein sequences, and a network was established based on known interactions in the selected reference species. 10. Gene Set Enrichment Analysis (GSEA)  Gene set enrichment analysis ( GSEA ) was conducted using the clusterProfiler R packages. 11. Weighted Gene Co-expression Network Analysis (WGCNA)  WGCNA was performed for weighted gene co-expression network analysis
reference genome: uses Ensembl database as a reference genome: Homo_sapiens.GRCh38.109.
Supplementary files format and content: All_DEG.Summary, count, fpkm

source_name: Dental Pulp Stem Cells

extract_protocol:
Plant samples were extracted by ethanol precipitation and CTAB-PBIOZOL. Animal samples were extracted by Trizol method. After successful extraction, RNA was dissolved by adding 50 µL of DEPC-treated water. Subsequently, total RNA was identified and quantified using a Qubit fluorescence quantifier and a Qsep400 high_x0002_throughput biofragment analyzer.
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection.

value: Dental Pulp Stem Cells


title: RH iAP2XI-3 +IAA 8h rep1

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

description:
Library name: RH iAP2XI-3 +IAA 8h rep1
XI81

data_processing:
To identify transcript changes in AP2XI-3 depleted strain, raw data were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then, clean data were mapped to reference genome GT1 (ToxoDB, version 68) using TopHat. The transcript per million reads (TPM) method was used to calculate the transcript levels of each gene. Differentially expressed gene (DEG) analysis was performed by Deseq2 with a p-value cutoff of 0.05 and a minimum fold change of 2.
Assembly: ToxoDB TGGT1 v68
Supplementary files format and content: RH_AP2XI-3.tpm.counts.txt

organism: Toxoplasma

source_name: Toxoplasma gondii

growth_protocol: All parasites strain used in this study were cultured in human foreskin fibroblast cells in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin, and 100 mg/mL streptomycin at 37 °C with 5% CO2.

extract_protocol:
RNA extraction was performed using TRIzol Reagent according to the manufacturer’s instructions (TransGen Biotech, China) following addition of RNase-free DNaseI to remove genomic DNA.
RNA libraries were prepared using the KCTM Stranded mRNA Library Prep Kit (Wuhan Seqhealth Co. Ltd. China) and 2 μg total RNA was used for each sample. PCR products with the sizes of 200–500 bps were enriched, quantified, and sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co. Ltd., China) with the PE150 model.

treatment_protocol: To prepare RNA samples, tachyzoites were allowed to grow in T25 flasks for 40 h and IAA or ethanol was added 24 h before sample collection. 3 × 107 tachyzoites were calculated for each sample and at least three replicates were prepared for each strain.

value: Toxoplasma gondii

value: RH iAP2XI-3-mAID-3HA

value: with IAA for 8h


title: 501M_ASO_LENT_1

description:
501M treated with LENT ASO (ASO_LENT)
GNGB16_S1


title: Single-cell RNA-seq day1 cell62


title: Single-cell RNA-seq day1 cell64


title: RH iAP2XI-3 +IAA 8h rep3

description:
Library name: RH iAP2XI-3 +IAA 8h rep3
XI83


title: 501M_ASO_LENT_2

description:
501M treated with LENT ASO (ASO_LENT)
GNGB17_S1


title: 501M_ASO_LENT_3

description:
501M treated with LENT ASO (ASO_LENT)
GNGB18_S1


title: Single-cell RNA-seq day1 cell60


title: d25A133, d25A134, mESC, Mouse

description:
Library name: d25A133_d25A134
d25


title: d25A135, d25A136, mESC, Mouse

description:
Library name: d25A135_d25A136
d25


title: Single-cell RNA-seq day1 cell66


title: 501M_ASO_NEG_3

description:
501M treated with control ASO (ASO_NEG)
GNGB12_S1


title: RH iAP2XI-3 +IAA 8h rep2

description:
Library name: RH iAP2XI-3 +IAA 8h rep2
XI82


title: Single-cell RNA-seq day1 cell61


title: Pro_seq_MCF7_WT_E2_16h

city: La Jolla

first: Amir

last: Gamliel

state: CA

address: 9500 Gilman Dr.

department: Medicine

country: USA

institute: University of California San Diego

data_processing:
Basecalling was performed using Illumina RTA (v2.7.6)
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012)  (version 2.2.6) was employed to align PRO-seq samples to hg19 genome using --very-sensitive setting. Tag directories were then generated using HOMER (version 4.10.3), keeping only unique aligned reads per genome position, but allowing up to 3 unique reads per position (-tbp 3).
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Assembly: hg19
Supplementary files format and content: BigWig
Library strategy: PRO-seq

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).

extract_protocol:
Precision Run-on sequencing (PRO-seq) experiments were performed as previously described (Mahat, D. B. et al, Nat Protoc 11, 1455-1476, 2016) with modification. Briefly, for nuclei isolation, MCF7 cells were incubated with swelling buffer (10 mM Tris-HCl pH7.5, 2 mM MgCl2, 3 mM CaCl2) for 5min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100μl of freezing buffer (50 mM Tris-Cl pH8.0, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA). For Run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 20 units of SuperaseIn, 1% sarkosyl, 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30°C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (Invitrogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (Thermo Fisher). Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the LongAmp® Taq 2X Master Mix (NEB) for deep sequencing.
Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the LongAmp® Taq 2X Master Mix (NEB) for deep sequencing.

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) dissolved in ethanol was added to a final concentration of 100 nM.  Control samples were treated with ICI 182,780, a high-affinity ERα antagonist, for 3 hours.

value: Breast cancer cells

value: 100 nM 17-beta Estradiol 16 hours


title: RH iAP2XI-3 +IAA 2h rep3

description:
Library name: RH iAP2XI-3 +IAA 2h rep3
XI23

value: with IAA for 2h


title: d25A131, d25A132, mESC, Mouse

description:
Library name: d25A131_d25A132
d25


title: RH iAP2XI-3 +IAA 0h rep3

description:
Library name: RH iAP2XI-3 +IAA 0h rep3
XI03

value: without IAA


title: d25A127, d25A128, mESC, Mouse

description:
Library name: d25A127_d25A128
d25


title: RH iAP2XI-3 +IAA 2h rep1

description:
Library name: RH iAP2XI-3 +IAA 2h rep1
XI21


title: RH iAP2XI-3 +IAA 2h rep2

description:
Library name: RH iAP2XI-3 +IAA 2h rep2
XI22


title: Pro_seq_MCF7_WT_E2_1h

value: 100 nM 17-beta Estradiol 1 hour


title: Single-cell RNA-seq day1 cell58


title: 501M_ASO_NEG_1

description:
501M treated with control ASO (ASO_NEG)
GNGB10_S1


title: Single-cell RNA-seq day1 cell56


title: Pro_seq_MCF7_WT_ICI

value: ICI 182,780 for 3 hours


title: RH iAP2XI-3 +IAA 0h rep2

description:
Library name: RH iAP2XI-3 +IAA 0h rep2
XI02


title: d25A125, d25A126, mESC, Mouse

description:
Library name: d25A125_d25A126
d25


title: Single-cell RNA-seq day1 cell55


title: d25A121, d25A122, mESC, Mouse

description:
Library name: d25A121_d25A122
d25


title: d25A129, d25A130, mESC, Mouse

description:
Library name: d25A129_d25A130
d25


title: AP2g_E2_16h

data_processing:
Basecalling was performed using Illumina RTA (v2.7.6)
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012)  (version 2.2.6) using --very-sensitive setting was employed to align ChIP-seq samples to hg19 genome. Tag directories were then generated using HOMER (version 4.10.3), keeping only unique alligned reads per genome position,  allowing 1 unique read per position (-tbp 1).
Peak finding: ChIP-seq peaks were called using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/) with the default settings (-style factor -o auto).
Generation of bedgraph files: The  HOMER scripts makeUCSCfile and makeMultiWigHub.pl were used  in order to generate bedgraph and BigWig files for visualization in the UCSC genome browser.
Assembly: hg19
Supplementary files format and content: BigWig

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
ChIP enriched DNA was purified, and 10 ng used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) dissolved in ethanol was added to a final concentration of 100 nM.  The vehicle ethanol was  added in all control vehicle samples at 0.05% .

tag: chip antibody

value: anti-AP2g (Santa Cruz, H-77)


title: d25A123, d25A124, mESC, Mouse

description:
Library name: d25A123_d25A124
d25


title: Single-cell RNA-seq day1 cell57


title: RH iAP2XI-3 +IAA 0h rep1

description:
Library name: RH iAP2XI-3 +IAA 0h rep1
XI01


title: 11h cell culture

city: Goyang-si

first: Moon-Gi

last: Hong

address: 32, Dongguk-ro, Ilsandong-gu

department: R&D Center

country: South Korea

institute: Enterobiome Inc.

description:
raw_counts.txt
Normalized_cpm.txt

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trimmomatic.
Trimmed sequence reades were mapped to EB-AMDK39 genome (GCF_010231335.1) using STAR (parameters- alignIntronMax: 1 alignMatesGapMax: 3000000 chimSegmentMin: 20).
Read count extraction was performed using Htseq-count.
Assembly: EB-AMDK39 genome (GCF_010231335.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Akkermansia muciniphila

source_name: bacterial cell

growth_protocol: A. muciniphila EB-AMDK39 was cultured in soy-peptone-based medium (20 g/L soy-peptone, 10 g/L yeast extract, 2.5 g/L K2HPO4, 2.5 g/L KH2PO4, 5 g/L N-acetyl-D-glucosamine, 5 g/L D-lactose, 2.5 g/L D-fructose, 8 g/L L-aspartic acid, 0.1 mg/L cyanocobalamin, and 0.5 g/L L-cysteine hydrochloride) in an anaerobic chamber filled with 90% N2, 5% CO2, and 5% H2 at 37°C.

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Cat. No. 74106).
RNA libraries for RNA-seq were prepared using Truseq strandard Total RNA ribo-zero Library kit following manufacturer's protocols.

value: WT

tag: time

tag: group

value: after mid-log phase with inhibition effect

value: bacterial cell


title: AP2r_E2_1h


title: 12h cell culture

description:
raw_counts.txt
Normalized_cpm.txt


title: d25A117, d25A118, mESC, Mouse

description:
Library name: d25A117_d25A118
d25

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: Single-cell RNA-seq day1 cell53

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day1


title: Single-cell RNA-seq day1 cell59


title: 8h cell culture

description:
raw_counts.txt
Normalized_cpm.txt

value: before mid-log phase without inhibition effect


title: AP2r_Veh

value: Vehicle


title: Single-cell RNA-seq day1 cell52


title: d25A119, d25A120, mESC, Mouse

description:
Library name: d25A119_d25A120
d25


title: RARa_E2_1h

value: Anti-RARa (Diagenode, C15310155)


title: Single-cell RNA-seq day1 cell54


title: Single-cell RNA-seq day1 cell51


title: d25A115, d25A116, mESC, Mouse

description:
Library name: d25A115_d25A116
d25


title: 7h cell culture

description:
raw_counts.txt
Normalized_cpm.txt


title: GATA3_E2_16h

value: Breast cancer cells

value: anti-GATA3 (Santa Cruz, HG3-31)


title: d25A113, d25A114, mESC, Mouse

description:
Library name: d25A113_d25A114
d25


title: 10h cell culture

description:
raw_counts.txt
Normalized_cpm.txt


title: Single-cell RNA-seq day1 cell50


title: d25A111, d25A112, mESC, Mouse

description:
Library name: d25A111_d25A112
d25


title: Multiome, Immune cells, Adult 1, ATAC

city: New York

first: Siddhi

last: Nargund

state: NY

address: 3960 Broadway, Lasker 203A

department: Department of Systems Biology

institute: Columbia University

description: Library name: PDC142 Spleen ATAC

library_source: genomic single cell

data_processing:
Data was processed using Cell Ranger pipeline and fastqs were made using Cell Ranger(atac) mkfastq
Assembly: hg38
Supplementary files format and content: Cellranger output files:filtered_feature_bc_matrix.h5
Supplementary files format and content: Cellranger output files:atac_fragments.tsv.gz

source_name: Spleen

extract_protocol:
Nuclei were isolated from infant and adult spleen samples following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression sample preparation workflow (10x Genomics). Tissue was dissociated, lysed, filtered, and washed according to the manufacturer’s instructions to obtain clean, intact nuclei suitable for Multiome library preparation.
Single-nucleus Multiome ATAC and gene expression libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics). Library construction followed the standard workflow, including GEM generation and barcoding, post-GEM cleanup, amplification, and construction of separate indexed ATAC and gene expression libraries for sequencing on an Illumina platform.

value: Spleen


title: GATA3_E2_1h


title: RARa_Veh


title: Multiome, T cells, Infant 3, ATAC

description: Library name: HDL163 Spleen ATAC


title: d25A109, d25A110, mESC, Mouse

description:
Library name: d25A109_d25A110
d25


title: Single-cell RNA-seq day1 cell49


title: d25A105, d25A106, mESC, Mouse

description:
Library name: d25A105_d25A106
d25


title: d25A107, d25A108, mESC, Mouse

description:
Library name: d25A107_d25A108
d25


title: GATA3_Veh


title: Single-cell RNA-seq day1 cell48


title: Single-cell RNA-seq day1 cell47


title: 6h cell culture

description:
raw_counts.txt
Normalized_cpm.txt


title: RARa_E2_16h

value: 100 nM 17-beta Estradiol 16 hours


title: Single-cell RNA-seq day1 cell46


title: d25A103, d25A104, mESC, Mouse

description:
Library name: d25A103_d25A104
d25


title: ER_E2_1h

value: anti-ER (Santa Cruz, HC-20)

value: 100 nM 17-beta Estradiol 1 hour


title: ER_E2_16h


title: Multiome, T cells, Infant 3, GEX

description: Library name: HDL163 Spleen RNA

molecule: nuclear RNA


title: Multiome, Immune cells, Adult 1, GEX

description: Library name: PDC142 Spleen RNA


title: Multiome, T cells, Infant 2, ATAC

description: Library name: LI018 Spleen ATAC


title: Single-cell RNA-seq day1 cell45


title: Multiome, T cells, Infant 2, GEX

description: Library name: LI018 Spleen RNA


title: d25B240, d25A100, mESC, Mouse

description:
Library name: d25B240_d25A100
d25


title: kidney, cholesterol crystal embolism, scRNA (SCX-CCE-14)

city: nantong

first: Zhaozhi

last: Wen

state: jiangsu

address: Seyuan Road 9

institute: Nantong University

description:
Library name: sample2_14
10x Genomics

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCm38
Supplementary files format and content: tar archives include barcodes.tsv, genes.tsv, and matrix.mtx files.

source_name: kidney

extract_protocol:
After the kidneys are excised, wash the surface blood with saline, HBSS, or PBS, and place them in a sterile culture dish. Wash three times with HBSS balanced salt solution, then transfer into a DNFU dissociation bottle. Add an appropriate amount of tissue dissociation solution and set the tissue dissociation instrument program to 180rpm-36 cycles-15 minutes. Run the program once and observe under a microscope to check if the kidney tissue is fully dissociated. If not, increase the number of cycles as needed to obtain a single-cell suspension. After digestion, filter the cell suspension using a 40μm filter, and use PBS with 0.04% BSA as the buffer solution. Centrifuge the filtered cell suspension at 350×g for 5 minutes, discard the supernatant, and resuspend the cell pellet in PBS. Then, add red blood cell lysis buffer at a 1:2 volume ratio to the cell suspension and incubate on ice for 5-8 minutes. Centrifuge at 300×g for 5 minutes, discard the supernatant, and resuspend the cell pellet in 1mL PBS. Wash again by adding PBS to bring the volume to a constant level, centrifuge at 300×g for 5 minutes, discard the supernatant, and resuspend the cell pellet in an appropriate amount of PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a HiSeq 4000 platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

value: kidney

tag: condition

value: cholesterol crystal embolism


title: kidney, cholesterol crystal embolism, scRNA (SCX-CCE-11)

description:
Library name: sample2_11
10x Genomics


title: Single-cell RNA-seq day1 cell42


title: d25A101, d25A102, mESC, Mouse

description:
Library name: d25A101_d25A102
d25


title: Single-cell RNA-seq day1 cell43


title: d25B238, d25B239, mESC, Mouse

description:
Library name: d25B238_d25B239
d25


title: ER_Veh


title: Multiome, T cells, Infant 1, GEX

description: Library name: LI004 Spleen RNA


title: Single-cell RNA-seq day1 cell44


title: Apex_WT_D55

city: Cleveland

first: Ya

last: Chen

state: OH

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description:
Library name: sample6
10x Genomics

data_processing:
Seurat pipeline
Assembly: merge and List
Supplementary files format and content: rds

source_name: Apex human iPSC

growth_protocol: All iPSC cells were cultured on a feeder layer of iMEF cells in hES medium consisting of DMEM/F12, 20% knockout serum replacement, 1% GlutaMAX, and 1% Non-essential AA . Prior to the experiment, ReleSR media was used to remove iMEF cells. Subsequently, iPSC cells were plated onto vitronectin-coated culture dishes and cultured in E8 medium until they reached approximately 60% confluence. The iPSC cells were then collected and dissociated into single cells using TrypLE.

extract_protocol:
10x used: Chromium Nest GEM single Cell 3' Reagent Kits V3.1 (Dual Index). Drop-seq used: McCarroll laboratory publised protocol (34. Macosko,E.Z., Basu,A., Satija,R., Nemesh,J., Shekhar,K., Goldman,M., Tirosh,I., Bialas,A.R., Kamitaki,N., Martersteck,E.M., et al. (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell, 161, 1202-1214)
Seurat scRNA-seq

treatment_protocol: Cells were plated at a density of 6000 cells per well of V-shaped 96-well plates in CDM medium containing DMEM/F12, 250mg/ml BSA, 15µg/ml apo-transferrin , 39nl/ml 1-thioglycerol, and 7µg/ml insulin. On the first day, half of the CDM medium was replaced with fresh medium containing 50ng/ml βFgf2 and 10µM SB431542. On day 7 of the differentiation protocol, fresh CDM medium containing 25ng/ml βFgf2 and 5µM SB431542 was added to the cells. On day 14, the organoids were transferred from the V-shaped 96-well plate to a U-shaped 96-well plate containing a new CDM medium supplemented with 100ng/ml Fgf19. On day 21, the culture medium was switched to CMM1 medium, which contained neurobasal medium, N2 supplement, and 1% Penicillin-streptomycin. On day 28, fresh CMM1 medium containing 300ng/ml recombinant human SDF-1α (CXCL12) was added. From day 35 onwards, all organoids were maintained in CMM1 medium.

value: Apex human iPSC

value: stem cells

value: ASD

value: neuronal differentiation

tag: batch


title: kidney, control, scRNA (SCX-CCE-4)

description:
Library name: sample1_4
10x Genomics

value: control


title: Apex_PTEN_KO_D55

description:
Library name: sample5
10x Genomics


title: d25B232, d25B233, mESC, Mouse

description:
Library name: d25B232_d25B233
d25

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: Single-cell RNA-seq day1 cell41

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day1


title: d25B234, d25B235, mESC, Mouse

description:
Library name: d25B234_d25B235
d25


title: Single-cell RNA-seq day1 cell40


title: d25B236, d25B237, mESC, Mouse

description:
Library name: d25B236_d25B237
d25


title: Apex_PTEN_I135L_D55

description:
Library name: sample4
10x Genomics


title: Single-cell RNA-seq day1 cell39


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 8 (batch 2)

city: Boston

first: Rosalind

middle: A

last: Segal

state: MA

address: 360 Longwood Ave, LC6301

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
Library name: XDRG-8
Column name in raw_counts_allSamples.txt: XDRG-8

data_processing:
Sequences were aligned to mouse reference genome with STAR_2.7.2b
Raw gene counts were generated from STAR output
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Lumbar Dorsal Root Ganglia

extract_protocol:
Ribosomal-associated RNAs were extracted using a TRAP protocol paired with Absolutely RNA NanoPrep Kit (Agilent). RNA concentrations were estimated as <100pg for axon samples and <1ng for soma samples.
RNA libraries were prepared using the SMART-Seq v4 Mouse Kit (Takara Bio Inc.)

value: Lumbar Dorsal Root Ganglia

value: L10a-eGFP-fl/fl (neg ctrl)


title: d25B230, d25B231, mESC, Mouse

description:
Library name: d25B230_d25B231
d25


title: kidney, control, scRNA (SCX-CCE-1)

description:
Library name: sample1_1
10x Genomics


title: kidney, control, scRNA (SCX-CCE-3)

description:
Library name: sample1_3
10x Genomics


title: Chap_PTEN_KO_D55

description:
Library name: sample3
10x Genomics

source_name: Chap human iPSC

value: Chap human iPSC

value: WT


title: Multiome, T cells, Infant 1, ATAC

description: Library name: LI004 Spleen ATAC

value: Spleen


title: Single-cell RNA-seq day1 cell37


title: kidney, cholesterol crystal embolism, scRNA (SCX-CCE-9)

description:
Library name: sample2_9
10x Genomics


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 7 (batch 2)

description:
Library name: XDRG-7
Column name in raw_counts_allSamples.txt: XDRG-7


title: Single-cell RNA-seq day1 cell38


title: d25B226, d25B227, mESC, Mouse

description:
Library name: d25B226_d25B227
d25


title: Chap_WT_D55

description:
Library name: sample1
10x Genomics


title: Chap_PTEN_I135L_D55

description:
Library name: sample2
10x Genomics


title: d25B224, d25B225, mESC, Mouse

description:
Library name: d25B224_d25B225
d25


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 6 (batch 2)

description:
Library name: XDRG-6
Column name in raw_counts_allSamples.txt: XDRG-6


title: Single-cell RNA-seq day1 cell36


title: Single-cell RNA-seq day1 cell33


title: 95-B4-Tumor

city: Philadelphia

first: Kara

last: Maxwell

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description:
Library name: Sample 73
95-B4-Tumor raw RNA Seq Counts

data_processing:
RNA-seq: Reads were aligned with STAR version 2.4.1d
RNA-seq: Reads were counted with HTSeq version 2.0.5
Assembly: GRCh38
Supplementary files format and content: RNA-seq: tab-delimited text file includes raw counts for each Sample

source_name: Breast Tumor

extract_protocol:
RNA was harvested using RNeasy mini kit (QIAGEN). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit following manufacturer's protocols.

value: Breast Tumor

value: WT TP53

value: Non LFS Samples


title: 95-D3-Normal

description:
Library name: Sample 74
95-D3-Normal raw RNA Seq Counts

source_name: Control Breast Tissue

value: Control Breast Tissue


title: d25B228, d25B229, mESC, Mouse

description:
Library name: d25B228_d25B229
d25


title: Single-cell RNA-seq day1 cell35


title: d25B222, d25B223, mESC, Mouse

description:
Library name: d25B222_d25B223
d25


title: d25B208, d25B217, mESC, Mouse

description:
Library name: d25B208_d25B217
d25


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 3 (batch 1)

description:
Library name: XDRG-3
Column name in raw_counts_allSamples.txt: XDRG-3


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 5 (batch 2)

description:
Library name: XDRG-5
Column name in raw_counts_allSamples.txt: XDRG-5


title: 9-6I-Normal

description:
Library name: Sample 72
9-6I-Normal raw RNA Seq Counts


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 4 (batch 1)

description:
Library name: XDRG-4
Column name in raw_counts_allSamples.txt: XDRG-4


title: d25B218, d25B219, mESC, Mouse

description:
Library name: d25B218_d25B219
d25


title: Single-cell RNA-seq day1 cell32


title: d25B220, d25B221, mESC, Mouse

description:
Library name: d25B220_d25B221
d25


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 2 (batch 1)

description:
Library name: XDRG-2
Column name in raw_counts_allSamples.txt: XDRG-2


title: Single-cell RNA-seq day1 cell34


title: DRG Soma, L10a-eGP-fl/fl (neg ctrl), bio rep 1 (batch 1)

description:
Library name: XDRG-1
Column name in raw_counts_allSamples.txt: XDRG-1


title: 88-D6-Tumor

description:
Library name: Sample 70
88-D6-Tumor raw RNA Seq Counts

value: Mutant TP53

value: LFS Samples


title: 88-D15-surrounding

description:
Library name: Sample 69
88-D15-surrounding raw RNA Seq Counts

source_name: Tissue Surrounding Breast Tumor

value: Tissue Surrounding Breast Tumor


title: Single-cell RNA-seq day1 cell29


title: d25B206, d25B207, mESC, Mouse

description:
Library name: d25B206_d25B207
d25


title: DRG Peripheral Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 2

description:
Library name: XPA-2
Column name in raw_counts_allSamples.txt: XPA-2

source_name: Sciatic Nerve

value: Sciatic Nerve


title: 9-6H-Tumor

description:
Library name: Sample 71
9-6H-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell30


title: DRG Peripheral Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 4

description:
Library name: XPA-4
Column name in raw_counts_allSamples.txt: XPA-4


title: 88-B6-contralateral

description:
Library name: Sample 68
88-B6-contralateral raw RNA Seq Counts

source_name: Contralateral Breast Tissue

value: Contralateral Breast Tissue


title: Single-cell RNA-seq day1 cell26


title: Single-cell RNA-seq day1 cell31


title: Single-cell RNA-seq day1 cell28


title: d25B198, d25B199, mESC, Mouse

description:
Library name: d25B198_d25B199
d25

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: d25B204, d25B205, mESC, Mouse

description:
Library name: d25B204_d25B205
d25


title: 84-A12-Tumor

description:
Library name: Sample 64
84-A12-Tumor raw RNA Seq Counts


title: DRG Central Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 4

description:
Library name: XCA-4
Column name in raw_counts_allSamples.txt: XCA-4

source_name: Lumbar Dorsal Root, Spinal Cord

value: Lumbar Dorsal Root, Spinal Cord


title: DRG Peripheral Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 1

description:
Library name: XPA-1
Column name in raw_counts_allSamples.txt: XPA-1


title: Single-cell RNA-seq day1 cell25

source_name: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day1


title: 84-C16-contralateral

description:
Library name: Sample 65
84-C16-contralateral raw RNA Seq Counts


title: DRG Central Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 1

description:
Library name: XCA-1
Column name in raw_counts_allSamples.txt: XCA-1

value: L10a-eGFP-fl/fl (neg ctrl)


title: d25B202, d25B203, mESC, Mouse

description:
Library name: d25B202_d25B203
d25

source_name: mESC


title: d25B196, d25B197, mESC, Mouse

description:
Library name: d25B196_d25B197
d25


title: DRG Central Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 3

description:
Library name: XCA-3
Column name in raw_counts_allSamples.txt: XCA-3


title: 85-1Y-Normal

description:
Library name: Sample 67
85-1Y-Normal raw RNA Seq Counts


title: d25A94, d25A95, mESC, Mouse

description:
Library name: d25A94_d25A95
d25


title: Single-cell RNA-seq day1 cell23

value: Mouse embryonic fibroblasts reprgramming cells


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 8 (batch 2)

description:
Library name: DRG-8
Column name in raw_counts_allSamples.txt: DRG-8

value: Lumbar Dorsal Root Ganglia


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 7 (batch 2)

description:
Library name: DRG-7
Column name in raw_counts_allSamples.txt: DRG-7


title: Single-cell RNA-seq day1 cell27


title: d25B200, d25B201, mESC, Mouse

description:
Library name: d25B200_d25B201
d25


title: Single-cell RNA-seq day1 cell22


title: d25A96, d25B193, mESC, Mouse

description:
Library name: d25A96_d25B193
d25


title: d25B194, d25B195, mESC, Mouse

description:
Library name: d25B194_d25B195
d25


title: 58-8E-contralateral

description:
Library name: Sample 60
58-8E-contralateral raw RNA Seq Counts


title: 75-1C-Tumor

description:
Library name: Sample 62
75-1C-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell24


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 5 (batch 2)

description:
Library name: DRG-5
Column name in raw_counts_allSamples.txt: DRG-5


title: 75-1J-Normal

description:
Library name: Sample 63
75-1J-Normal raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell20


title: d25A89, d25A9, mESC, Mouse

description:
Library name: d25A89_d25A9
d25


title: DRG Central Axon, L10a-eGP-fl/fl (neg ctrl), bio rep 2

description:
Library name: XCA-2
Column name in raw_counts_allSamples.txt: XCA-2


title: 72-A1-Tumor

description:
Library name: Sample 61
72-A1-Tumor raw RNA Seq Counts


title: 85-1E-Tumor

description:
Library name: Sample 66
85-1E-Tumor raw RNA Seq Counts


title: d25A90, d25A91, mESC, Mouse

description:
Library name: d25A90_d25A91
d25


title: d25A92, d25A93, mESC, Mouse

description:
Library name: d25A92_d25A93
d25


title: d25A87, d25A88, mESC, Mouse

description:
Library name: d25A87_d25A88
d25


title: Single-cell RNA-seq day1 cell21


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 6 (batch 2)

description:
Library name: DRG-6
Column name in raw_counts_allSamples.txt: DRG-6


title: 58-2I-surrounding

description:
Library name: Sample 59
58-2I-surrounding raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell19


title: 53-1M-Tumor

description:
Library name: Sample 56
53-1M-Tumor raw RNA Seq Counts


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 4 (batch 1)

description:
Library name: DRG-4
Column name in raw_counts_allSamples.txt: DRG-4


title: Single-cell RNA-seq day1 cell18


title: Single-cell RNA-seq day1 cell17


title: d25A85, d25A86, mESC, Mouse

description:
Library name: d25A85_d25A86
d25


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 1 (batch 1)

description:
Library name: DRG-1
Column name in raw_counts_allSamples.txt: DRG-1


title: d25A83, d25A84, mESC, Mouse

description:
Library name: d25A83_d25A84
d25


title: DRG Peripheral Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 3

description:
Library name: PA-3
Column name in raw_counts_allSamples.txt: PA-3


title: 58-2E-Tumor

description:
Library name: Sample 58
58-2E-Tumor raw RNA Seq Counts


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 2 (batch 1)

description:
Library name: DRG-2
Column name in raw_counts_allSamples.txt: DRG-2


title: 50-1I-surrounding_R

description:
Library name: Sample 53
50-1I-surrounding_R raw RNA Seq Counts


title: DRG Soma, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 3 (batch 1)

description:
Library name: DRG-3
Column name in raw_counts_allSamples.txt: DRG-3


title: d25A81, d25A82, mESC, Mouse

description:
Library name: d25A81_d25A82
d25


title: 50-2D-Tumor

description:
Library name: Sample 55
50-2D-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell16


title: d25A74, d25A75, mESC, Mouse

description:
Library name: d25A74_d25A75
d25


title: 50-1O-Tumor

description:
Library name: Sample 54
50-1O-Tumor raw RNA Seq Counts


title: d25A78, d25A79, mESC, Mouse

description:
Library name: d25A78_d25A79
d25


title: d25A8, d25A80, mESC, Mouse

description:
Library name: d25A8_d25A80
d25


title: DRG Peripheral Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 4

description:
Library name: PA-4
Column name in raw_counts_allSamples.txt: PA-4


title: 57-2E-Tumor

description:
Library name: Sample 57
57-2E-Tumor raw RNA Seq Counts


title: d25A76, d25A77, mESC, Mouse

description:
Library name: d25A76_d25A77
d25


title: DRG Peripheral Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 1

description:
Library name: PA-1
Column name in raw_counts_allSamples.txt: PA-1


title: Single-cell RNA-seq day1 cell11


title: 42-B2-Tumor

description:
Library name: Sample 50
42-B2-Tumor raw RNA Seq Counts


title: DRG Central Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 3

description:
Library name: CA-3
Column name in raw_counts_allSamples.txt: CA-3


title: 46-D3-Tumor

description:
Library name: Sample 52
46-D3-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell15


title: Single-cell RNA-seq day1 cell10


title: d25A72, d25A73, mESC, Mouse

description:
Library name: d25A72_d25A73
d25


title: Single-cell RNA-seq day1 cell14


title: Single-cell RNA-seq day1 cell13


title: DRG Peripheral Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 2

description:
Library name: PA-2
Column name in raw_counts_allSamples.txt: PA-2


title: Single-cell RNA-seq day1 cell9


title: 35-C7-surrounding_L

description:
Library name: Sample 49
35-C7-surrounding_L raw RNA Seq Counts


title: 45-2-Tumor

description:
Library name: Sample 51
45-2-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell12


title: DRG Central Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 4

description:
Library name: CA-4
Column name in raw_counts_allSamples.txt: CA-4


title: 33-C4-Tumor

description:
Library name: Sample 46
33-C4-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day1 cell7


title: DRG Central Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 2

description:
Library name: CA-2
Column name in raw_counts_allSamples.txt: CA-2


title: 33-C3-Normal

description:
Library name: Sample 45
33-C3-Normal raw RNA Seq Counts


title: 35-B4-surrounding_R

description:
Library name: Sample 48
35-B4-surrounding_R raw RNA Seq Counts


title: d25A63, d25A64, mESC, Mouse

description:
Library name: d25A63_d25A64
d25


title: d25A70, d25A71, mESC, Mouse

description:
Library name: d25A70_d25A71
d25


title: Single-cell RNA-seq day1 cell4


title: d25A61, d25A62, mESC, Mouse

description:
Library name: d25A61_d25A62
d25


title: Single-cell RNA-seq day1 cell6


title: 27-C-Tumor

description:
Library name: Sample 44
27-C-Tumor raw RNA Seq Counts


title: 35-B18-Tumor

description:
Library name: Sample 47
35-B18-Tumor raw RNA Seq Counts


title: Day7_2 no CSB

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

description: Library name: Sample_12

data_processing:
Samples were sequenced using a 2x150bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts  were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
Assembly: mm10
Supplementary files format and content: csv file contains raw gene counts

source_name: Eosinophil

growth_protocol: C57BL/6 mice were either untreated or transplanted with Balb/c lungs with costimulatory blockade. Infiltrating lung eosinophils are recipient origin in this lung transplant model. Eosinophils were isolated by flow cytometry sorting on resting, day 7 or day 30 post-transplant lungs.

extract_protocol:
Trizol Extraction
NEBNext Ultra II RNA Library Prep Kit

value: Eosinophil

value: transplant with  Day 7


title: DRG Central Axon, Nav1.8-Cre;L10a-eGP-fl/fl, bio rep 1

description:
Library name: CA-1
Column name in raw_counts_allSamples.txt: CA-1


title: d25A69, d25A7, mESC, Mouse

description:
Library name: d25A69_d25A7
d25


title: d25A67, d25A68, mESC, Mouse

description:
Library name: d25A67_d25A68
d25


title: Single-cell RNA-seq day1 cell3


title: Day 7_5 no CSB

description: Library name: Sample_15


title: Single-cell RNA-seq day1 cell8


title: Day 7_4 no CSB

description: Library name: Sample_14


title: Single-cell RNA-seq day1 cell5


title: d25A65, d25A66, mESC, Mouse

description:
Library name: d25A65_d25A66
d25


title: 3 months DiNP 100 ug/kg/day-rep 3

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

data_processing:
FASTQC (version 0.11.8) on individual samples. No trimming necessary.
The quality-scores line in fastq files use an ASCII offset of 33 known as Sanger scores
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming). Adaptor sequence in read1:AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index)
Salmon version 0.11.3 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed, then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases and --numBootstraps=30 to compute bootstrap transcript abundance estimates. Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package.
The TMM (trimmed mean of M values) normalization in the edgeR package was used to calculate a normalization factor. Dectection threshold was set at 0.5 cpm (counts per million) in at least three samples. After filtering, TMM normalization was used and normalized log2-based count per million values (logCPM) were calculated using edgeR's cmp() function with prior.count = 3.
R version 3.5.2 (2018-12-20)
reads are 100 nt in length
Genome_build: NCBI GRCm38.p6 Annotation Release 106
Supplementary_files_format_and_content: log2-transformed counts per million (logCPM)
Supplementary_files_format_and_content: ENTREZID, SYMBOL and GENENAME weree obtained by using org.Mm.eg.db package from Bioconductor release 3.8.

source_name: ovary

extract_protocol:
Ovaries were removed and flash frozen in liquid nitrogen. Total RNA (>100 ng) was extracted from the whole ovaries using the RNeasy Mini kit (Qiagen, Austin, TX, USA) according to the manufacturer's protocol, including DNase digestion.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand. The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000.

value: ovary

tag: age

value: adult

tag: agent

value: DiNP 100 ug/kg/day

tag: time after 10 day treatment

value: 3 months


title: d25A6, d25A60, mESC, Mouse

description:
Library name: d25A6_d25A60
d25


title: Single-cell RNA-seq day1 cell2


title: Day 7_3 no CSB

description: Library name: Sample_13


title: 3 months DiNP 100 ug/kg/day-rep 1


title: Day7_1 no CSB

description: Library name: Sample_11


title: d25A50, d25A51, mESC, Mouse

description:
Library name: d25A50_d25A51
d25


title: 197-2O-Normal

description:
Library name: Sample 41
197-2O-Normal raw RNA Seq Counts

value: Control Breast Tissue

value: WT TP53

value: Non LFS Samples


title: d25A54, d25A55, mESC, Mouse

description:
Library name: d25A54_d25A55
d25


title: d25A56, d25A57, mESC, Mouse

description:
Library name: d25A56_d25A57
d25


title: d25A58, d25A59, mESC, Mouse

description:
Library name: d25A58_d25A59
d25


title: 3 months DiNP 100 ug/kg/day-rep 2


title: 24-A6-contralateral

description:
Library name: Sample 42
24-A6-contralateral raw RNA Seq Counts

value: Contralateral Breast Tissue

value: Mutant TP53

value: LFS Samples


title: 193-3F-Tumor

description:
Library name: Sample 36
193-3F-Tumor raw RNA Seq Counts

value: Breast Tumor


title: 24-C8-Tumor

description:
Library name: Sample 43
24-C8-Tumor raw RNA Seq Counts


title: 196-2M-Tumor

description:
Library name: Sample 39
196-2M-Tumor raw RNA Seq Counts


title: d25A52, d25A53, mESC, Mouse

description:
Library name: d25A52_d25A53
d25

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: 196-2EE-Normal

description:
Library name: Sample 38
196-2EE-Normal raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell83

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day0


title: 187-3C-Tumor

description:
Library name: Sample 35
187-3C-Tumor raw RNA Seq Counts


title: 3 months DiNP 20 ug/kg/day-rep 3

value: DiNP 20 ug/kg/day


title: 3 months DEHP 200 ug/kg/day-rep 3

value: DEHP 200 ug/kg/day


title: 197-2B-Tumor

description:
Library name: Sample 40
197-2B-Tumor raw RNA Seq Counts


title: 3 months DiNP 20 ug/kg/day-rep 2

value: ovary


title: Single-cell RNA-seq day0 cell85


title: 3 months DEHP 200 ug/kg/day-rep 2

value: adult


title: Single-cell RNA-seq day1 cell1

value: OvSvK single-cell RNA-seq reprogramming day1


title: Single-cell RNA-seq day0 cell86


title: 186-6Z-Tumor

description:
Library name: Sample 33
186-6Z-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell81


title: d25A47, d25A48, mESC, Mouse

description:
Library name: d25A47_d25A48
d25


title: d25A49, d25A5, mESC, Mouse

description:
Library name: d25A49_d25A5
d25


title: 3 months DEHP 200 ug/kg/day-rep 1

value: 3 months


title: 193-3H-Normal

description:
Library name: Sample 37
193-3H-Normal raw RNA Seq Counts

value: Control Breast Tissue


title: Single-cell RNA-seq day0 cell80


title: d25A37, d25A38, mESC, Mouse

description:
Library name: d25A37_d25A38
d25


title: Single-cell RNA-seq day0 cell82


title: Single-cell RNA-seq day0 cell84


title: 3 months vehicle control-rep 2

value: vehicle control


title: 3 months DiNP 20 ug/kg/day-rep 1


title: Single-cell RNA-seq day0 cell79


title: d25A39, d25A4, mESC, Mouse

description:
Library name: d25A39_d25A4
d25


title: d25A35, d25A36, mESC, Mouse

description:
Library name: d25A35_d25A36
d25


title: 180-5C-Tumor

description:
Library name: Sample 30
180-5C-Tumor raw RNA Seq Counts

value: WT TP53

value: Non LFS Samples


title: d25A42, d25A43, mESC, Mouse

description:
Library name: d25A42_d25A43
d25


title: d25A45, d25A46, mESC, Mouse

description:
Library name: d25A45_d25A46
d25


title: 187-1H-Normal

description:
Library name: Sample 34
187-1H-Normal raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell75


title: 177-3H-Tumor

description:
Library name: Sample 28
177-3H-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell77


title: d25A40, d25A41, mESC, Mouse

description:
Library name: d25A40_d25A41
d25


title: 186-6C-Normal

description:
Library name: Sample 32
186-6C-Normal raw RNA Seq Counts


title: 177-3C-Tumor

description:
Library name: Sample 27
177-3C-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell78


title: 0 month DiNP 100 ug/kg/day-rep 3

value: DiNP 100 ug/kg/day

value: immediately (0 month)


title: d25A31, d25A32, mESC, Mouse

description:
Library name: d25A31_d25A32
d25


title: 3 months vehicle control-rep 3


title: 3 months vehicle control-rep 1


title: Single-cell RNA-seq day0 cell73


title: 0 month DiNP 100 ug/kg/day-rep 2


title: 3 months DEHP 20 ug/kg/day-rep 3

value: DEHP 20 ug/kg/day


title: d25A33, d25A34, mESC, Mouse

description:
Library name: d25A33_d25A34
d25

value: mESC


title: 177-3K-Normal

description:
Library name: Sample 29
177-3K-Normal raw RNA Seq Counts

value: Breast Tumor


title: 180-5J-Normal

description:
Library name: Sample 31
180-5J-Normal raw RNA Seq Counts


title: d25A3, d25A30, mESC, Mouse

description:
Library name: d25A3_d25A30
d25

value: C57BI6/J(female)x CAST/EiJ(male)


title: Single-cell RNA-seq day0 cell72

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day0


title: 0 month DiNP 20 ug/kg/day-rep 3

value: DiNP 20 ug/kg/day


title: Single-cell RNA-seq day0 cell71


title: 160-3C-Tumor

description:
Library name: Sample 23
160-3C-Tumor raw RNA Seq Counts


title: d25A20, d25A21, mESC, Mouse

description:
Library name: d25A20_d25A21
d25


title: Single-cell RNA-seq day0 cell70


title: 169-5I-Normal

description:
Library name: Sample 26
169-5I-Normal raw RNA Seq Counts


title: d25A26, d25A27, mESC, Mouse

description:
Library name: d25A26_d25A27
d25


title: d25A28, d25A29, mESC, Mouse

description:
Library name: d25A28_d25A29
d25


title: d25A22, d25A23, mESC, Mouse

description:
Library name: d25A22_d25A23
d25


title: Single-cell RNA-seq day0 cell74


title: Single-cell RNA-seq day0 cell69


title: 3 months DEHP 20 ug/kg/day-rep 2

value: ovary


title: Single-cell RNA-seq day0 cell76


title: 160-3L-Normal

description:
Library name: Sample 24
160-3L-Normal raw RNA Seq Counts


title: d25A24, d25A25, mESC, Mouse

description:
Library name: d25A24_d25A25
d25


title: 169-5H-Tumor

description:
Library name: Sample 25
169-5H-Tumor raw RNA Seq Counts


title: 157-1M-Tumor

description:
Library name: Sample 21
157-1M-Tumor raw RNA Seq Counts


title: 0 month DEHP 200 ug/kg/day-rep 3

value: adult

value: DEHP 200 ug/kg/day


title: 0 month DiNP 100 ug/kg/day-rep 1


title: d25A19, d25A2, mESC, Mouse

description:
Library name: d25A19_d25A2
d25


title: Single-cell RNA-seq day0 cell68


title: 152-NA-Normal

description:
Library name: Sample 20
152-NA-Normal raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell66


title: 3 months DEHP 20 ug/kg/day-rep 1

value: 3 months


title: 157-1V-Normal

description:
Library name: Sample 22
157-1V-Normal raw RNA Seq Counts

value: Control Breast Tissue


title: 130-1O-Normal

description:
Library name: Sample 18
130-1O-Normal raw RNA Seq Counts


title: 0 month DEHP 200 ug/kg/day-rep 2


title: 0 month DiNP 20 ug/kg/day-rep 1


title: 0 month DEHP 200 ug/kg/day-rep 1


title: d25A1, d25A10, mESC, Mouse

description:
Library name: d25A1_d25A10
d25


title: 0 month vehicle control-rep 3

value: vehicle control


title: d25A17, d25A18, mESC, Mouse

description:
Library name: d25A17_d25A18
d25


title: 128-2C-Tumor

description:
Library name: Sample 16
128-2C-Tumor raw RNA Seq Counts

value: Mutant TP53

value: LFS Samples


title: Single-cell RNA-seq day0 cell67


title: d25A15, d25A16, mESC, Mouse

description:
Library name: d25A15_d25A16
d25


title: Single-cell RNA-seq day0 cell65


title: 126-D2-contralateral

description:
Library name: Sample 14
126-D2-contralateral raw RNA Seq Counts

value: Contralateral Breast Tissue

value: Mutant TP55


title: d25A11, d25A12, mESC, Mouse

description:
Library name: d25A11_d25A12
d25


title: d25A13, d25A14, mESC, Mouse

description:
Library name: d25A13_d25A14
d25


title: 0 month DiNP 20 ug/kg/day-rep 2

value: immediately (0 month)


title: 130-1L-Tumor

description:
Library name: Sample 17
130-1L-Tumor raw RNA Seq Counts

value: WT TP53

value: Non LFS Samples


title: Single-cell RNA-seq day0 cell63


title: d05B237, d05B238, mESC, Mouse

description:
Library name: d05B237_d05B238
d05

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: 0 month DEHP 20 ug/kg/day-rep 3

value: DEHP 20 ug/kg/day


title: 0 month vehicle control- rep 2


title: 0 month vehicle control-rep 1


title: 128-2O-surrounding_R

description:
Library name: Sample 15
128-2O-surrounding_R raw RNA Seq Counts

value: Tissue Surrounding Breast Tumor


title: Single-cell RNA-seq day0 cell62

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day0


title: Single-cell RNA-seq day0 cell64


title: d05B239, d05B240, mESC, Mouse

description:
Library name: d05B239_d05B240
d05


title: Single-cell RNA-seq day0 cell61


title: 152-2F-Tumor

description:
Library name: Sample 19
152-2F-Tumor raw RNA Seq Counts

value: Breast Tumor


title: 0 month DEHP 20 ug/kg/day-rep 2

value: ovary

value: adult


title: 126-B7-Tumor

description:
Library name: Sample 13
126-B7-Tumor raw RNA Seq Counts

value: Mutant TP54


title: d05B233, d05B234, mESC, Mouse

description:
Library name: d05B233_d05B234
d05


title: Single-cell RNA-seq day0 cell59


title: d05B235, d05B236, mESC, Mouse

description:
Library name: d05B235_d05B236
d05


title: Single-cell RNA-seq day0 cell60


title: d05B229, d05B230, mESC, Mouse

description:
Library name: d05B229_d05B230
d05


title: Single-cell RNA-seq day0 cell56


title: 0 month DEHP 20 ug/kg/day-rep 1


title: 126-B4-Tumor

description:
Library name: Sample 12
126-B4-Tumor raw RNA Seq Counts

value: Mutant TP53


title: Sperm RNA Nrf2 LKO2

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

description:
Library name: 23118FL-51-01-73_S6_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Exp_E1B

data_processing:
Tesmall
Assembly: mirbase
Supplementary files format and content: Count Matrix

source_name: Sperm

extract_protocol:
Trizol
Qiaseq small RNA library prep

value: Sperm

value: Nrf2 LKO

value: Floxed Nrf2 + Albumin-Cre (Nrf2 liver KO)


title: Sperm RNA Nrf2 LKO4

description:
Library name: 23118FL-51-01-75_S8_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Exp_G3R


title: 126-B1-Normal

description:
Library name: Sample 11
126-B1-Normal raw RNA Seq Counts

value: Control Breast Tissue

value: LFS Samples


title: d05B225, d05B226, mESC, Mouse

description:
Library name: d05B225_d05B226
d05


title: 120-3S-Normal

description:
Library name: Sample 8
120-3S-Normal raw RNA Seq Counts

value: WT TP53

value: Non LFS Samples


title: Sperm RNA Nrf2 LKO3

description:
Library name: 23118FL-51-01-74_S7_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Exp_B1R


title: Single-cell RNA-seq day0 cell58


title: d05B223, d05B224, mESC, Mouse

description:
Library name: d05B223_d05B224
d05

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: 125-3O-Normal

description:
Library name: Sample 10
125-3O-Normal raw RNA Seq Counts


title: Sperm RNA flox  Control3

description:
Library name: 23118FL-51-01-70_S3_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Con_C3R

value: Nrf2 Flox

value: Floxed Nrf2 (Nrf2 control)


title: Sperm RNA flox  Control4

description:
Library name: 23118FL-51-01-71_S4_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Con_J2R


title: Single-cell RNA-seq day0 cell57

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day0


title: 125-3I-Tumor

description:
Library name: Sample 9
125-3I-Tumor raw RNA Seq Counts

value: Breast Tumor


title: Sperm RNA Nrf2 LKO1

description:
Library name: 23118FL-51-01-72_S5_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Exp_D1R


title: 120-3C-Tumor

description:
Library name: Sample 7
120-3C-Tumor raw RNA Seq Counts


title: Single-cell RNA-seq day0 cell52


title: d05B231, d05B232, mESC, Mouse

description:
Library name: d05B231_d05B232
d05


title: Single-cell RNA-seq day0 cell54


title: d05B227, d05B228, mESC, Mouse

description:
Library name: d05B227_d05B228
d05


title: 108-3T-Normal

description:
Library name: Sample 6
108-3T-Normal raw RNA Seq Counts


title: d05B219, d05B220, mESC, Mouse

description:
Library name: d05B219_d05B220
d05


title: Single-cell RNA-seq day0 cell55


title: Single-cell RNA-seq day0 cell53


title: 108-3N-Tumor

description:
Library name: Sample 5
108-3N-Tumor raw RNA Seq Counts


title: Sperm RNA flox  Control2

description:
Library name: 23118FL-51-01-69_S2_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Con_G1R


title: Single-cell RNA-seq day0 cell51


title: Sperm RNA Nrf2 -/- Ethanol4

description:
Library name: SE8749_SA226669_S56_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: D56

value: Nrf2 KO Ethanol (alcohol exposed)


title: d05B217, d05B218, mESC, Mouse

description:
Library name: d05B217_d05B218
d05


title: Sperm RNA flox  Control1

description:
Library name: 23118FL-51-01-68_S1_L006_R1_001.fastq
count_summary_LKO.txt
on count file: Con_N2R


title: d05B215, d05B216, mESC, Mouse

description:
Library name: d05B215_d05B216
d05


title: 106-3L-Normal

description:
Library name: Sample 4
106-3L-Normal raw RNA Seq Counts


title: d05B213, d05B214, mESC, Mouse

description:
Library name: d05B213_d05B214
d05


title: Single-cell RNA-seq day0 cell50


title: d05B221, d05B222, mESC, Mouse

description:
Library name: d05B221_d05B222
d05


title: Sperm RNA Nrf2 -/- Ethanol3

description:
Library name: SE8749_SA226668_S55_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S55


title: 106-3B-Tumor

description:
Library name: Sample 3
106-3B-Tumor raw RNA Seq Counts


title: 103-B36-Normal

description:
Library name: Sample 2
103-B36-Normal raw RNA Seq Counts


title: d05B209, d05B210, mESC, Mouse

description:
Library name: d05B209_d05B210
d05


title: Single-cell RNA-seq day0 cell48


title: SD014/23_BA46

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: CGND-HRA-03753

data_processing:
Demultiplex with bcl2fastq
Align to hg38 with STAR
Count using ENSEMBL v98 annotations with htseq-count
Assembly: hg38
Supplementary files format and content: BA44_BA46_COUNT_DATA.tsv.gz Raw integer count data in compressed TSV
Supplementary files format and content: BA44_BA46_TPM_DATA.tsv.gz Standardized TPM count data in compressed TSV
Supplementary files format and content: BA44_BA46_RNASEQ_PROCESSED.h5ad Combined RNAseq analysis in h5ad

extract_protocol:
Trizol
KAPA Stranded RNA-Seq Kit with RiboErase

tag: donor id

tag: Sex

value: Male

tag: als phenotype

value: ALS

tag: pmi


title: d05B207, d05B208, mESC, Mouse

description:
Library name: d05B207_d05B208
d05


title: 103-B27-Tumor

description:
Library name: Sample 1
103-B27-Tumor raw RNA Seq Counts

tag: tissue

tag: genotype


title: d05B211, d05B212, mESC, Mouse

description:
Library name: d05B211_d05B212
d05

tag: cell type


title: Sperm RNA Nrf2 -/- Ethanol2

description:
Library name: SE8749_SA226667_S54_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S54

value: Sperm

tag: treatment


title: SD019/23_BA46

description: Library name: CGND-HRA-03756

value: ALSci


title: Single-cell RNA-seq day0 cell49

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample

extract_protocol:
Cells were collected by trypsin digestion. Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).


title: Single-cell RNA-seq day0 cell46


title: SD013/23_BA46

description: Library name: CGND-HRA-03752

value: Female

value: Control


title: Single-cell RNA-seq day0 cell47


title: d05B205, d05B206, mESC, Mouse

description:
Library name: d05B205_d05B206
d05

data_processing:
Samples with more than 50,000 remaining contacts were retained for downstream analysis. For diploid samples, the haplotype of contacts was phased according to SNP sites. Each chromosome in each sample was treated as a polymer chain, evenly divided into 20kb sections, with each section treated as a particle of the polymer chain. The contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles using the Force-Directed Graph (FDG) algorithm implemented by “hickit”. To assess the quality of the chromatin 3D structure reconstruction, we generated five replicates using different random seeds and calculated the median RMSD for each combination of three replicates. If the median RMSD of the combination with the lowest value was less than 1.5, the first replicate in that combination was used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: dip pairs file: A tab-separated file recording allele-specific contacts that conforms to 4DN Consortium standards with chromosomes
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards with chromosomes

extract_protocol:
We utilized a female mouse embryonic stem cell (mESC) line derived from blastocysts at embryonic day 3.5 (E3.5) from crossbred embryos (female C57BL/6J × male CAST/EiJ). The procedures for derivation and culturing followed the methods provided by Arenas et al. (2006). Cells were cultured on flasks coated with 0.1% gelatin in an ES cell medium containing serum. The medium composition included DMEM (Gibco, 10829018), 15% ESC-grade fetal bovine serum (FBS) (VivaCell, C04002-100), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% P/S (ThermoFisher, 10378016), NEAA (Sigma, M7145), L-Glutamine (Gibco, 25030-081), nucleotides (Millipore, ES-008-D), and 1000 U/ml leukemia inhibitory factor (LIF) (PeproTech, AF-250-02-25UG). Additionally, the medium was supplemented with 2i: 3 μM Gsk3 inhibitor CT99021 (Selleck, S1263) and 1 μM MEK inhibitor PD0325901 (Selleck, S1036). Differentiation was initiated by withdrawing 2i/LIF in DMEM supplemented with 10% FBS, 1% P/S, NEAA, L-Glutamine, nucleotides, and 0.1 mM β-mercaptoethanol. The cells were plated at a density of 1.5 × 10⁴ cells/cm² on 6 well cell culture plates coated with 10 μg/ml fibronectin (GLPBIO, GP23499).
The single-cell preamplification product was diluted to 5ng/ul and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C.

tag: strain


title: Sperm RNA Nrf2 -/- Ethanol1

description:
Library name: SE8749_SA226666_S53_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S53


title: Sperm RNA Nrf2 -/- Control1

description:
Library name: SE8749_SA226662_S49_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S49

value: Nrf2 KO Control (no alcohol exposure)


title: SD002/23_BA46

description: Library name: CGND-HRA-03750


title: Sperm RNA Nrf2 -/- Control2

description:
Library name: SE8749_SA226663_S50_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S50


title: d05B201, d05B202, mESC, Mouse

description:
Library name: d05B201_d05B202
d05


title: Single-cell RNA-seq day0 cell43


title: Sperm RNA Nrf2 -/- Control4

description:
Library name: SE8749_SA226665_S52_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S52


title: SD019/19_BA46

description: Library name: CGND-HRA-03718


title: Sperm RNA Nrf2 -/- Control3

description:
Library name: SE8749_SA226664_S51_L008_R1_001.fastq
count_summary_Nrf2.txt
on count file: S51


title: Single-cell RNA-seq day0 cell42


title: Sperm RNA High2

description:
Library name: QD1065-10_S10_L003_R1_001.fastq
count_summary WT.txt
on count file: H23

value: WT

value: High (high dose of alcohol)


title: Single-cell RNA-seq day0 cell45


title: SD035/14_BA44

description: Library name: CGND-HRA-03663


title: Single-cell RNA-seq day0 cell41


title: Sperm RNA Medium2

description:
Library name: QD1065-12_S12_L003_R1_001.fastq
count_summary WT.txt
on count file: EM7

value: Medium (medium dose of alcohol)


title: SD026/19_BA44

description: Library name: CGND-HRA-03714


title: Single-cell RNA-seq day0 cell40


title: d05B199, d05B200, mESC, Mouse

description:
Library name: d05B199_d05B200
d05

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: d05B197, d05B198, mESC, Mouse

description:
Library name: d05B197_d05B198
d05


title: Sperm RNA High1

description:
Library name: QD1065-09_S9_L003_R1_001.fastq
count_summary WT.txt
on count file: H20


title: d05B195, d05B196, mESC, Mouse

description:
Library name: d05B195_d05B196
d05


title: d05B193, d05B194, mESC, Mouse

description:
Library name: d05B193_d05B194
d05


title: SD025/17_BA46

description: Library name: CGND-HRA-03662


title: Single-cell RNA-seq day0 cell44


title: Single-cell RNA-seq day0 cell39


title: Sperm RNA Medium1

description:
Library name: QD1065-11_S11_L003_R1_001.fastq
count_summary WT.txt
on count file: H25


title: SD025/17_BA44

description: Library name: CGND-HRA-03661


title: SD041/19_BA44

description: Library name: CGND-HRA-03713


title: Single-cell RNA-seq day0 cell37


title: SD028/18_BA44

description: Library name: CGND-HRA-03659


title: Single-cell RNA-seq day0 cell38


title: SD020/20_BA44

description: Library name: CGND-HRA-03653


title: d05A98, d05A99, mESC, Mouse

description:
Library name: d05A98_d05A99
d05


title: Sperm RNA Low4

description:
Library name: QD1065-08_S8_L003_R1_001.fastq
count_summary WT.txt
on count file: L214

value: Low (low dose of alcohol)


title: d05B203, d05B204, mESC, Mouse

description:
Library name: d05B203_d05B204
d05


title: Sperm RNA Low1

description:
Library name: QD1065-05_S5_L003_R1_001.fastq
count_summary WT.txt
on count file: L23


title: d05A188, d05A189, mESC, Mouse

description:
Library name: d05A188_d05A189
d05


title: Sperm RNA Low2

description:
Library name: QD1065-06_S6_L003_R1_001.fastq
count_summary WT.txt
on cout file: L25


title: Single-cell RNA-seq day0 cell35

value: Mouse embryonic fibroblasts reprgramming cells


title: Sperm RNA Control3

description:
Library name: QD1065-03_S3_L003_R1_001.fastq
count_summary WT.txt
on count file: C22

value: Control (no alcohol exposure)


title: Single-cell RNA-seq day0 cell36

value: OvSvK single-cell RNA-seq reprogramming day0


title: d05A192, d05A97, mESC, Mouse

description:
Library name: d05A192_d05A97
d05


title: d05A184, d05A185, mESC, Mouse

description:
Library name: d05A184_d05A185
d05


title: SD014/18_BA44

description: Library name: CGND-HRA-03660


title: Sperm RNA Low3

description:
Library name: QD1065-07_S7_L003_R1_001.fastq
count_summary WT.txt
on count file: L213


title: Sperm RNA Control2

description:
Library name: QD1065-02_S2_L003_R1_001.fastq
count_summary WT.txt
on count file: C21


title: SD022/21_BA46

description: Library name: CGND-HRA-03648


title: d05A190, d05A191, mESC, Mouse

description:
Library name: d05A190_d05A191
d05


title: d05A180, d05A181, mESC, Mouse

description:
Library name: d05A180_d05A181
d05


title: Single-cell RNA-seq day0 cell34


title: Single-cell RNA-seq day0 cell31


title: Sperm RNA Control4

description:
Library name: QD1065-04_S4_L003_R1_001.fastq
count_summary WT.txt
on count file: C23


title: Single-cell RNA-seq day0 cell33


title: RAW264.7 cells ATP-3

city: Hubei

first: 文

last: 李

address: Wuhan

institute: Wuhan University

description: Library name: ATP-3

data_processing:
Different libraries are assembled according to the amount of target data and sequenced on the Illumina platform. Matrix table with raw gene counts for every gene and every sample,Trimmomatic (Version: 0.36; Parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:18 MINLEN:36) was used to clean raw data, and clean data was obtained after data cleaning. HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) (version: 2.2.1) was used for clean reads alignment. After reads alignment, String Tie was used to quantify the above reads.
Assembly: Mus_musculus
Supplementary files format and content: tab-delimited text fles include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trimmomatic (Version: 0.36; Parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:18 MINLEN:36) was used to clean raw data, and clean data was obtained after data cleaning. HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) (version: 2.2.1) was used for clean reads alignment. After reads alignment, String Tie was used to quantify the above reads.

source_name: cells

extract_protocol:
mRNA was enriched from total RNA using oligomer (dT) magnetic beads. The mRNA fragments were cut into short fragments of about 300bp using a cleavage buffer. The first cDNA was synthesized by using mRNA as template and random hexamer as primer.
The purified double-stranded cDNA was subjected to terminal repair, A-tail modification and sequencing joint connection. Select fragment size using AMPure XP beads. PCR amplification was performed to obtain the final cDNA library.

value: cells

tag: cell line

value: RAW264.7 cells

value: Mouse macrophages


title: SD044/21_BA46

description: Library name: CGND-HRA-03642

value: Male


title: SD006/21_BA44

description: Library name: CGND-HRA-03649

value: ALSci


title: d05A186, d05A187, mESC, Mouse

description:
Library name: d05A186_d05A187
d05


title: d05A174, d05A175, mESC, Mouse

description:
Library name: d05A174_d05A175
d05


title: SD026/21_BA46

description: Library name: CGND-HRA-03646


title: Single-cell RNA-seq day0 cell32

first: Hui

last: Zheng

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences


title: SD044/21_BA44

description: Library name: CGND-HRA-03641


title: Single-cell RNA-seq day0 cell27


title: Single-cell RNA-seq day0 cell28


title: d05A178, d05A179, mESC, Mouse

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

description:
Library name: d05A178_d05A179
d05


title: Single-cell RNA-seq day0 cell30


title: d05A172, d05A173, mESC, Mouse

description:
Library name: d05A172_d05A173
d05


title: RAW264.7cells Blank-3

description: Library name: Blank-3


title: SD048/21_BA46

description: Library name: CGND-HRA-03638

value: Female

value: ALS


title: Sperm RNA Control1

description:
Library name: QD1065-01_S1_L003_R1_001.fastq
count_summary WT.txt
on count file: C18

value: Sperm


title: RAW264.7 cells ATP-2

description: Library name: ATP-2

value: WT


title: Single-cell RNA-seq day0 cell25


title: d05A176, d05A177, mESC, Mouse

description:
Library name: d05A176_d05A177
d05


title: d05A166, d05A167, mESC, Mouse

description:
Library name: d05A166_d05A167
d05


title: RAW264.7 cells Blank-2

description: Library name: Blank-2


title: SD031/22_BA46

description: Library name: CGND-HRA-03630


title: Single-cell RNA-seq day0 cell24


title: TMJ condyles of 1-month-old C57BL6/J mice

first: Yang

last: Xiao

address: 22  Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

description: Library name: Sample1

data_processing:
scRNA-seq data analysis was performed by NovelBio Bio-Pharm Technology Co., Ltd. with the NovelBrain cloud analytics platform. Adapter sequences were filtered using fastp with default parameters and feature barcode matrix were obtained through CellRanger v6.1.1. Cells with less than 200 expressed genes and a mitochondrial UMI rate more than 20% are filtered out by cell quality, and mitochondrial genes were removed from the expression list. Seurat software package (version: 4.1.1) were used for cell normalization and regression. The top 2000 highly variable genes were selected for PCA construction, and the top 10 principals used for tSNE and UMAP construction.
Assembly: /
Supplementary files format and content: /

source_name: TMJ condyles

extract_protocol:
scRNA sequencing was performed on condyle of 1month wild-type C57BL/6J mice (n=20). The condylar bone and cartilage was cut into 1mm3 under a microscope. They were then digested in DPBS solution with 0.25% trypsin (Hyclone, cat. No. SH30042.01), 10 ug/mL recombinant DNAse I (RNase-free) (TaKaRa, cat. No. 2270B), and 5% fetal bovine serum (Thermo Fisher Scientific, cat. No. SV30087.02) for 30 minutes at 37°C. The cell suspension was filtered through a 40-μm strainer and erythrocytes were removed using a lysis reagent (Thermo Fisher Scientific, cat. No. 00-4333-57).
Disscociated single cells were stained for viability assessment with AO/PI using a Countstar Fluorescence Cell Analyzer. Cells were loaded into Chromium Single Cell 3' V3.1 Kit (10X Genomics, Pleasanton, CA) and remaining steps followed the manufacturer's instructions.

value: TMJ condyles


title: SD031/22_BA44

description: Library name: CGND-HRA-03629


title: d05A164, d05A165, mESC, Mouse

description:
Library name: d05A164_d05A165
d05


title: Single-cell RNA-seq day0 cell29


title: d05A162, d05A163, mESC, Mouse

description:
Library name: d05A162_d05A163
d05


title: Single-cell RNA-seq day0 cell23


title: SD026/21_BA44

description: Library name: CGND-HRA-03645


title: RAW264.7 cells ATP-1

description: Library name: ATP-1


title: SD015/22_BA44

description: Library name: CGND-HRA-03621


title: SD045/21_BA44

description: Library name: CGND-HRA-03639


title: SD046/17_BA44

description: Library name: CGND-HRA-03566

value: Control


title: Single-cell RNA-seq day0 cell26


title: RAW264.7 cells Blank-1

description: Library name: Blank-1


title: d05A168, d05A169, mESC, Mouse

description:
Library name: d05A168_d05A169
d05

value: mESC


title: d05A158, d05A159, mESC, Mouse

description:
Library name: d05A158_d05A159
d05

value: C57BI6/J(female)x CAST/EiJ(male)


title: d05A182, d05A183, mESC, Mouse

description:
Library name: d05A182_d05A183
d05


title: Single-cell RNA-seq day0 cell19


title: SD014/13_BA44

description: Library name: CGND-HRA-03562


title: SD045/21_BA46

description: Library name: CGND-HRA-03640


title: d05A156, d05A157, mESC, Mouse

description:
Library name: d05A156_d05A157
d05


title: primary rat midbrain astrocytes,PT109B treatment,6h,rep2

city: Guangdong

first: Shisong

last: Wang

state: Shenzhen

address: No. 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-Sen university

description: Library name: PT6H-2

data_processing:
StringTie v2.2.1
Assembly: CT
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM for each Sample

organism: Rattus norvegicus

source_name: midbrain

growth_protocol: Primary midbrain astrocytes from newborn SD rats were maintained in DMEM supplemented with 10% fetal bovineserum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)，1.0 ug of total RNA was used for theconstruction of sequencing libraries.
RNA libraries for RNA-seg were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® followingmanufacturer's protocols.

treatment_protocol: Astrocytes were treatment by 10 μM PT109B for 0, 1.5, 3 or 6 hours.

value: midbrain

value: primary cell

value: astrocytes

value: PT109B treatment


title: Single-cell RNA-seq day0 cell22

city: Guangzhou

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day0


title: SD053/21_BA46

description: Library name: CGND-HRA-03634


title: primary rat midbrain astrocytes,PT109B treatment,1.5h,rep3

description: Library name: PT1-5H-3


title: Single-cell RNA-seq day0 cell18


title: d05A160, d05A161, mESC, Mouse

city: Beijing

description:
Library name: d05A160_d05A161
d05


title: d05A170, d05A171, mESC, Mouse

description:
Library name: d05A170_d05A171
d05


title: primary rat midbrain astrocytes,PT109B treatment,6h,rep1

description: Library name: PT6H-1


title: SD030/19_BA46

description: Library name: CGND-HRA-03002


title: d05A154, d05A155, mESC, Mouse

description:
Library name: d05A154_d05A155
d05


title: primary rat midbrain astrocytes,PT109B treatment,6h,rep3

description: Library name: PT6H-3


title: SD027/14_BA44

description: Library name: CGND-HRA-03565


title: Single-cell RNA-seq day0 cell20


title: SD030/19_BA44

description: Library name: CGND-HRA-03001


title: primary rat midbrain astrocytes,PT109B treatment,1.5h,rep2

description: Library name: PT1-5H-2


title: Single-cell RNA-seq day0 cell21


title: d05A152, d05A153, mESC, Mouse

description:
Library name: d05A152_d05A153
d05


title: primary rat midbrain astrocytes,PT109B treatment,3h,rep3

description: Library name: PT3H-3


title: d05A150, d05A151, mESC, Mouse

description:
Library name: d05A150_d05A151
d05


title: Single-cell RNA-seq day0 cell17


title: primary rat midbrain astrocytes,PT109B treatment,3h,rep1

description: Library name: PT3H-1


title: SD034/19_BA46

description: Library name: CGND-HRA-02999


title: SD024/18_BA46

description: Library name: CGND-HRA-02992


title: primary rat midbrain astrocytes,PT109B treatment,3h,rep2

description: Library name: PT3H-2


title: Single-cell RNA-seq day0 cell16


title: d05A148, d05A149, mESC, Mouse

description:
Library name: d05A148_d05A149
d05


title: SD024/18_BA44

description: Library name: CGND-HRA-02991


title: Single-cell RNA-seq day0 cell15


title: primary rat midbrain astrocytes,CT,rep2

description: Library name: CT-2

value: control


title: Single-cell RNA-seq day0 cell14


title: SD006/17_BA44

description: Library name: CGND-HRA-02987

value: Male


title: d05A144, d05A145, mESC, Mouse

description:
Library name: d05A144_d05A145
d05


title: d05A146, d05A147, mESC, Mouse

description:
Library name: d05A146_d05A147
d05


title: SD010/18_BA46

description: Library name: CGND-HRA-02988

value: ALSci


title: Single-cell RNA-seq day0 cell11


title: KO;NAC-3

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

data_processing:
trim_galore; subread
Assembly: hg38
Supplementary files format and content: featureCounts output

extract_protocol:
Extract total RNA using Trizol
DNBSEQ eukaryotic mRNA library construction

value: Melanoma cell

value: OGDH knock out

value: NAC


title: SD003/17_BA44

description: Library name: CGND-HRA-02985


title: primary rat midbrain astrocytes,CT,rep1

description: Library name: CT-1

value: WT


title: primary rat midbrain astrocytes,CT,rep3

description: Library name: CT-3


title: d05A140, d05A141, mESC, Mouse

description:
Library name: d05A140_d05A141
d05


title: Single-cell RNA-seq day0 cell12


title: SD004/16_BA46

description: Library name: CGND-HRA-02979

value: Female

value: ALS


title: Single-cell RNA-seq day0 cell10


title: Single-cell RNA-seq day0 cell13


title: primary rat midbrain astrocytes,PT109B treatment,1.5h,rep1

description: Library name: PT1-5H-1


title: SD002/16_BA44

description: Library name: CGND-HRA-02978


title: d05A142, d05A143, mESC, Mouse

description:
Library name: d05A142_d05A143
d05

value: mESC


title: KO;NAC-2


title: KO;NAC-1


title: d05A138, d05A139, mESC, Mouse

description:
Library name: d05A138_d05A139
d05

value: C57BI6/J(female)x CAST/EiJ(male)


title: Single-cell RNA-seq day0 cell9


title: d05A136, d05A137, mESC, Mouse

description:
Library name: d05A136_d05A137
d05


title: d05A132, d05A133, mESC, Mouse

description:
Library name: d05A132_d05A133
d05


title: KO;ctrl-3


title: KO;ctrl-2


title: Single-cell RNA-seq day0 cell8


title: KO;ctrl-1


title: SD002/16_BA46

description: Library name: CGND-HRA-02977


title: SD029/15_BA44

description: Library name: CGND-HRA-02972


title: Single-cell RNA-seq day0 cell7


title: d05A134, d05A135, mESC, Mouse

description:
Library name: d05A134_d05A135
d05


title: Single-cell RNA-seq day0 cell6


title: Single-cell RNA-seq day0 cell5


title: d05A128, d05A129, mESC, Mouse

description:
Library name: d05A128_d05A129
d05


title: d05A130, d05A131, mESC, Mouse

description:
Library name: d05A130_d05A131
d05


title: WT;NAC-3


title: Single-cell RNA-seq day0 cell4


title: SD014/14_BA44

description: Library name: CGND-HRA-02969


title: WT;NAC-1


title: SD027/14_BA46

description: Library name: CGND-HRA-02970


title: WT;NAC-2


title: WT;ctrl-3


title: d05A124, d05A125, mESC, Mouse

description:
Library name: d05A124_d05A125
d05


title: SD006/13_BA46

description: Library name: CGND-HRA-02959


title: d05A126, d05A127, mESC, Mouse

description:
Library name: d05A126_d05A127
d05


title: SD047/13_BA44

description: Library name: CGND-HRA-02964


title: Single-cell RNA-seq day0 cell3


title: d05A122, d05A123, mESC, Mouse

description:
Library name: d05A122_d05A123
d05


title: Single-cell RNA-seq day0 cell2


title: SD010/14_BA46

description: Library name: CGND-HRA-02966


title: SD026/12_BA46

description: Library name: CGND-HRA-02955


title: OK Bulk RNA-seq rep2

growth_protocol: Cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were lysised by Trizol and total RNAs were extracted by chloroform-isopropanol method.
Libraries for RNA-seq were prepared using VAHTS mRNA-seq V2 Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with different TF combinations.

value: Over expression OCT4 and KLF4


title: d05A120, d05A121, mESC, Mouse

description:
Library name: d05A120_d05A121
d05


title: WT;ctrl-2


title: WT;ctrl-1


title: Single-cell RNA-seq day0 cell1


title: SD032/16_BA46

description: Library name: CGND-HRA-02765

value: Control


title: SD030/18_BA46

description: Library name: CGND-HRA-02766


title: OK Bulk RNA-seq rep1


title: WT(Col-0)_BAP_Bio3

city: ghent

first: Wei

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

description: Library name: WT(Col-0)_BAP_3

data_processing:
using Galaxy Belgium platform
Trimmomatic to remove adaptors
Salmon quant to align reads
tximport to count read
Deseq2 to differentially expressed gened
Assembly: TAIR10 on Galaxy (for Arabidopsis thaliana), Genome Selaginella moellendorffii v1.0 (for Selaginella moellendorffii)
Supplementary files format and content: tab-delimited file of count read for each sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: 1/2 MS  plates 22°C constant light 4d old root of Arabidopsis thaliana, and 14d old root of Selaginella moellendorffii

extract_protocol:
ReliaPrep™ RNA Miniprep Systems
BGI RNA Library Prep Kit protocol

treatment_protocol: 0.2 cm of the root tip of the root. Rna extraction with ReliaPrep RNA Miniprep Systems kit (Z6112)

value: Root

value: 10μM BAP


title: WT(Col-0)_BAP_Bio2

description: Library name: WT(Col-0)_BAP_2


title: d05A116, d05A117, mESC, Mouse

description:
Library name: d05A116_d05A117
d05


title: d05A114, d05A115, mESC, Mouse

description:
Library name: d05A114_d05A115
d05


title: SD015/16_BA46

description: Library name: CGND-HRA-02764


title: OS Bulk RNA-seq rep2

value: Mouse embryonic fibroblasts reprgramming cells

value: Over expression OCT4 and SOX2


title: SD014/16_BA46

description: Library name: CGND-HRA-02763


title: SK Bulk RNA-seq rep1

value: Over expression SOX2 and KLF4


title: SK Bulk RNA-seq rep2


title: WT(Col-0)_NAA_Bio2

description: Library name: WT(Col-0)_NAA_2

value: 10μM NAA


title: d05A110, d05A111, mESC, Mouse

description:
Library name: d05A110_d05A111
d05


title: WT(Col-0)_BAP_Bio1

description: Library name: WT(Col-0)_BAP_1


title: OS Bulk RNA-seq rep1


title: SD006/17_BA46

description: Library name: CGND-HRA-02759

value: Male


title: d05A108, d05A109, mESC, Mouse

description:
Library name: d05A108_d05A109
d05


title: SD012/13_BA46

description: Library name: CGND-HRA-02762