title: NCI-H929 cells, KO14, biol rep 2

city: Berlin

first: Uta

middle: Margareta

last: Demel

address: Hindenburgdamm 30

department: Hematology and Oncology

country: Germany

institute: Charité - CBF

description: Library name: AS-1071434-LR-69585

data_processing:
Raw BCL files were converted to fastq files using bcl-converter (4.1.5). The resulting fastq files were trimmed using fastp (Chen et al., 2018) and mapped to the human reference genome (GRCh38.p13 v39) using salmon (1.10.3) (Patro et al., 2017). Transcript level abundance estimates from salmon were imported using the tximport package (1.34) with the countsFromAbundance = "lengthScaledTPM" setting to account for transcript length and sequencing depth.
Subsequent differential gene expression analysis was carried out using DESeq2 (1.46) (Love et al., 2014) and GSEA was performed using the fgsea (1.32.4) package with the hallmark gene set from msigdbr (10.0.2) implemented in R (4.4.1).
Assembly: GRCh38.p13 v39
Supplementary files format and content: tab-delimited text file includes raw counts estimates using tximport for each sample

source_name: cell line

growth_protocol: OPM-2 was cultured in RPMI-1640 supplemented with 10% FBS. NCI-H929 was cultured in RPMI-1640 supplemented with 20% FBS, 0.05mM beta-mercaptoethanol + 2mM L-glutamine + 1mM sodium pyruvate.

extract_protocol:
RNA was extracted from cell pellets using the RNeasy Kit (Qiagen). RNA concentration was determined with a Nanodrop spectrophotometer.
Library preparation was performed using the TruSeq Stranded RNA kit (Illumina) as per manufactures instruction followed by paired-end sequencing on a NovaSeq 6000 (Illumina) at the German Cancer Research Center (DKFZ).

value: multiple myeloma


title: Cyto_HCT_WT_SG_seq_rep1

status: Public on Dec 08 2025

type: SRA

city: Boston

first: Jarrett

last: Smith

state: MA

address: 455 Main st, Room 627

country: USA

institute: Whitehead Institute

description:
RNA seq of total cytoplasmic RNA
cts_SGseq.csv

library_source: transcriptomic

data_processing:
DESeq2
Assembly: hg38
Supplementary files format and content: Comma-delimited files containing read counts for all samples.
Supplementary files format and content: Supplemental Excel tables that summarize the sequencing data.

molecule: total RNA

organism: Homo sapiens

growth_protocol: All cells were cultured at 37°C with 5% CO2 using McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine

extract_protocol:
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.

treatment_protocol: Cells were either treated with 500 μM IAA (depletion), 500 μM sodium arsenite for 1 hr (oxidative stress), or 45°C incubation for 25 min (heatshock)

tag: cell type

tag: treatment

value: oxidative stress; wt


title: CL30.7 Rep4 Dox (7d), Aux (9d)

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

description: Library name: CL307dDox9dAuxR4

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). For the E6, CL30.7/CL30.7.7 and CL31/CL31.16, the mm10 genome was used  (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

organism: Mus

growth_protocol: NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
RNA was extracted from > 1M NPCs using the RNeasy kit and on-column DNAse digestion (Qiagen). RNA integrity was measured using the Bioanalyzer Nano Kit.
Only high-quality RNA was used for subsequent library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; and the pools were loaded on the Illumina sequencer NextSeq 500 or NextSeq 2000 and sequenced bi-directionally, generating ~500 million paired-end reads, each 75 bases long.

treatment_protocol: Xist expression in TX1072 was induced by addition of doxycycline (1 µg/mL) to the NPC media. Culture media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media. Auxin-mediated depletion of SPEN was achieved by supplementing the culture media with Auxin (Sigma) at the concentration of 500 µM, as previously described [Dossin et al. 2020]. Auxin-containing media was renewed every 24h.

tag: strain

value: C57BL6/J x CAST/EiJ

tag: cell line

value: neural progenitor cell

tag: genotype

value: Xptet / R26rtTA / SPEN-AID

value: Dox (7d), Aux (9d)

tag: experiment


title: CL31.16 Rep4 Dox (7d), Aux (9d)

description: Library name: CL317dDox9dAuxR4


title: NCI-H929 cells, KO14, biol rep 3

description: Library name: AS-1071435-LR-69585


title: RPF_HCT_WT_heatshock_rep2

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: heatshock; wt


title: hippocampus CD51+ astrocyte rep3

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Library name: UKHPG3

data_processing:
Raw RNA-seq reads from hippocampal and cortical CD51⁺ and CD51⁻ astrocyte samples were aligned to the mouse reference genome (mm10) using STAR (PMID: 23104886). Raw read count matrices were generated from the aligned reads. Normalization and differential expression analyses were conducted using DESeq2 (v1.40.2) (PMID: 25516281). Variance-stabilized transformation (VST) was applied to normalized counts for visualization and downstream analyses. Principal component analysis (PCA) was used to assess sample-level clustering by CD51 status and brain region.  Differential expression analyses for CD51⁺ or CD51⁻ astrocyte samples were performed separately for cortex and hippocampus. Genes with an adjusted p-value < 0.05 and an absolute log₂ fold change greater than 1 were considered significantly differentially expressed. Volcano plots were generated with ggplot2 to visualize differential expression results.
Assembly: mm10
Supplementary files format and content: Excel file containing baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj for various DeSeq2 comparisons between astrocyte subpopulations and regions.

organism: Mus musculus

source_name: brain

extract_protocol:
FACS isolated astrocytes
RNA was extracted from sorted cells using RNeasyMicro Kit (Cat.No. 4004, QIAGEN). cDNA synthesis and sequencing libraries with 8-bp single indices were constructed from 10 ng RNA using the Revelo RNA-seq High Sensitivity kit (Cat.No. 30184149, TECAN). The resulting libraries were validated using a Standard Sensitivity NGS Fragment Analysis Kit (DNF-473-0500,) on a 12-Capillary Fragment Analyzer and quantified using a Quant-it dsDNA assay kit (Cat. Q33120). Equal concentrations (2 nM) of libraries were pooled and processed for paired-end sequencing (150 reads each direction), targeting ≥40 million reads per sample on an Illumina NovaSeq X Plus following the manufacturer’s instructions.

tag: tissue

value: brain

value: astrocyte


title: hippocampus CD51- astrocyte rep2

description: Library name: UKHPGT2


title: CL30.7 Rep2 Dox (7d) - washout (7d)

description: Library name: CL307dDox7dWOR2

value: Dox (7d) - washout (7d)


title: CL30.7 Rep4 Dox (3d)

description: Library name: CL303dDoxR4

value: Dox (3d)


title: hippocampus CD51+ astrocyte rep2

description: Library name: UKHPG2


title: hippocampus CD51+ astrocyte rep1

description: Library name: UKHPG1


title: hippocampus CD51- astrocyte rep3

description: Library name: UKHPGT3


title: hippocampus CD51- astrocyte rep1

description: Library name: UKHPGT1


title: NCI-H929 cells, WT, biol rep 3

description: Library name: AS-1071432-LR-69585

value: WT


title: RPF_HCT_depleted_Unstressed_rep4

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: unstressed; depleted


title: CL30.7 Rep4 Dox (3d), Aux (5d)

description: Library name: CL303dDox5dAuxR4

value: Dox (3d), Aux (5d)


title: RPF_HCT_WT_Unstressed_rep4

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: unstressed; wt


title: cortex CD51- astrocyte rep3

description: Library name: UKCTXGT3


title: NCI-H929 cells, WT, biol rep 2

description: Library name: AS-1071431-LR-69585


title: RPF_HCT_depleted_heatshock_rep2

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: heatshock; depleted


title: NCI-H929 cells, KO14, biol rep 1

description: Library name: AS-1071433-LR-69585


title: cortex CD51- astrocyte rep2

description: Library name: UKCTXGT2


title: CL30.7 Rep4 Aux (2d)

description: Library name: CL3002dAuxR4

value: Aux (2d)


title: RPF_HCT_WT_heatshock_rep1

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: OPM-2 cells, KO17, biol rep 3

description: Library name: AS-1071429-LR-69585

value: multiple myeloma


title: NCI-H929 cells, WT, biol rep 1

description: Library name: AS-1071430-LR-69585


title: RPF_HCT_depleted_Unstressed_rep3

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: cortex CD51- astrocyte rep1

description: Library name: UKCTXGT1


title: OPM-2 cells, KO17, biol rep 2

description: Library name: AS-1071428-LR-69585


title: CL30.7 October2023 Dox (21d) Aux (23d)

description: Library name: CL30.7_21dDaA_sorted.bam

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). For the E6, CL30/CL30.7 and CL31/CL31.16, the mm10 genome was used  (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

value: Aux (9d)

tag: batch


title: RPF_HCT_WT_Unstressed_rep3

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: cortex CD51+ astrocyte rep3

description: Library name: UKCTXG3


title: Astrocytes Rep2_dox_d7

description: Library name: lane1H1R2doxd7

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). The mm10 genome was used  (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

growth_protocol: Astrocytes were cultured in N2B27 medium supplemented with 20 ng/mL bone morphogenetic protein 4 (BMP4) (R&D system).

extract_protocol:
RNA was extracted using the RNeasy kit and on-column DNAse digestion (Qiagen). RNA integrity was measured using the Tapestation High Sensitivity RNA kit.
Only high-quality RNA was used for subsequent library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; and the pools were loaded on the Illumina sequencer NextSeq 500 or NextSeq 2000 and sequenced bi-directionally each 75 bases long.

treatment_protocol: Xist expression in TX1072 Astrocytes was induced by addition of doxycycline (1 µg/mL) to the culture media.  Media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media.

value: C57BL6/J x CAST/EiJ

value: Astrocytes

value: Xptet / R26rtTA

value: Dox (7d)


title: Astrocytes Rep2_no_dox_d7_washout_d4

description: Library name: lane1G2R2nodoxnowod7

value: Control of Dox (11d)


title: OPM-2 cells, KO17, biol rep 1

description: Library name: AS-1071427-LR-69585


title: OPM-2 cells, KO4, biol rep 3

description: Library name: AS-1071426-LR-69585


title: RPF_HCT_WT_oxidative_rep4

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: oxidative stress; wt


title: RPF_HCT_depleted_oxidative_rep4

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: oxidative stress; depleted


title: OPM-2 cells, KO4, biol rep 2

description: Library name: AS-1071425-LR-69585


title: Astrocytes Rep1_dox_d7

description: Library name: lane1F1R1doxd7


title: cortex CD51+ astrocyte rep2

description: Library name: UKCTXG2

value: brain

value: astrocyte


title: OPM-2 cells, KO4, biol rep 1

description: Library name: AS-1071424-LR-69585


title: RPF_HCT_depleted_heatshock_rep1

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: RPF_HCT_WT_oxidative_rep3

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: CL30.7 Rep4 Control

description: Library name: CL3000R4

value: neural progenitor cell

value: Xptet / R26rtTA / SPEN-AID

value: Control


title: ChIPseq_PKL_jaw-5D_rep2

city: Beijing

first: Mengfei

last: Song

state: Beijing

address: 北京市海淀区颐和园路5号

country: China

institute: Peking university

description:
Library name: WDR5A-HA_pkl-input-2
WDR5A-HA_pkl-input-2

library_source: genomic

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using bowtie2 (version 2.3.3) with default parameters.
Peak calling was performed using MACS2 (version 2.2.5) with the following parameters: --keep-dup 1 --gsize 1.2e8 --qvalue 0.05.
The alignments were converted to bigWig files using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Assembly: TAIR10
Supplementary files format and content: Bigwig files were generated using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Supplementary files format and content: peak text files

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: total seedlings

extract_protocol:
2 g of 9-day-old seedlings grown on MS medium were collected and cross-linked with 1% formaldehyde for 20 min under vacuum and then ground into a fine powder in liquid nitrogen. Chromatin was isolated and sheared into fragments (200–500 bp) by sonication. The sonicated chromatin was incubated with antibody-bound Sera-Mag SpeedBeads Protein A/G Magnetic Particles (17152104010150, GE Healthcare) overnight at 4℃. Precipitated DNA was then reverse-crosslinked and digested with RNase A and Proteinase K, after which it was purified with the ChIP DNA Clean & Concentrator kit (D5205, Zymo research) according to the manufacturer’s instructions.
All ChIP-seq libraries were generated with the NEBNext® Ultra II DNA Library Prep Kit for Illumina® (E7645S, NEB) according to the manufacturer’s instructions.

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light

tag: chip antibody

value: anti-Ha endogenous antibody


title: Astrocytes Rep1_no_dox_d7_washout_d4

description: Library name: lane1E2R1nodoxnowod7


title: RPF_HCT_depleted_Unstressed_rep2

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: unstressed; depleted


title: Astrocytes  Rep1_no_dox_d7

description: Library name: lane1E1R1nodoxd7

value: Control of Dox (7d)


title: OPM-2 cells, WT, biol rep 2

description: Library name: AS-1071422-LR-69585

value: multiple myeloma

value: WT


title: ChIPseq_PKL_jaw-5D_rep3

address: 北京市海淀区颐和园路5号

description:
Library name: WDR5A-HA_pkl-input-3
WDR5A-HA_pkl-input-3


title: ChIPseq_PKL_WT_rep3

address: 北京市海淀区颐和园路5号

description:
Library name: WDR5A-HA_pkl-IP-3
WDR5A-HA_pkl-IP-3


title: Astrocytes Rep2_dox_d3

description: Library name: lane1D1R2doxd3

value: C57BL6/J x CAST/EiJ

value: Astrocytes

value: Xptet / R26rtTA

value: Dox (3d)


title: cortex CD51+ astrocyte rep1

description: Library name: UKCTXG1


title: OPM-2 cells, WT, biol rep 1

description: Library name: AS-1071421-LR-69585


title: ChIPseq_PKL_WT_rep2

address: 北京市海淀区颐和园路5号

description:
Library name: WDR5A-HA_pkl-IP-2
WDR5A-HA_pkl-IP-2


title: Astrocytes Rep2_no_dox_d3_washout_d4

description: Library name: lane1C2R2nodoxnowod3

value: Control of Dox (3d) - washout (4d)


title: RPF_HCT_depleted_oxidative_rep2

description: ribo-seq (RPFs)

value: oxidative stress; depleted


title: Mock 2Hr + 4Hr (suppoprting cells,R14)

city: Chicago

first: Jeffrey

last: Savas

state: Illinois

address: 303 E. Chicago Avenue, Ward 12-013

department: Neurology

institute: Northwestern University

description:
Library name: Control 30
Fresh-frozen spatial transcriptomic sequencing

data_processing:
Tissue sections were processed using the GeoMx Mouse Whole Transcriptome Atlas (cat# GeoMx NGS RNA WTA Mm, NanoString, Bruker Spatial Biology) according to the manufacturer’s instructions, with the exception that 0.0001% Proteinase K was used during the slide preparation step. Regions of interest (ROIs) were selected within the designated “tissue area name.” Cells were collected sequentially as (1) β-Tubulin–positive (BTub⁺) and (2) Myosin-positive (Myosin⁺) populations, with a target of at least 50 events per ROI. Segmentation parameters were as follows: 0 Erode, 2 µm N-Dilate, 100 µm² Hole Size, and 5 µm² Particle Size. Following library construction and quality control (Qubit and Bioanalyzer), single-end 50-nucleotide sequencing was performed on an Illumina HiSeq 4000 System generating approximately 100 million reads. Sequencing data were processed using the NanoString GeoMx Digital Spatial Profiler (DSP) and the DRAGEN pipeline to convert Illumina FASTQ files into GeoMx-readable digital count files for downstream analysis in the DSP Data Analysis Suite. Data comparisons represent total cells pooled from “X” ROIs.
Assembly: mm10 (GRCm38, 2011)
Supplementary files format and content: PNG images for all the captured regions (neurons and supporting cells)
Supplementary files format and content: Text file with raw sequencing results from each captured region
Library strategy: Spatial Transcriptomics

source_name: cochlea

growth_protocol: CBA/CaJ mice, male at 16 weeks of age were used in these experiments.

extract_protocol:
Fresh-frozen cochlear sections (6 µm) were obtained from sham and treated mice and embedded in OCT.
For library construction, 1 µg of total RNA per sample was used as input. Libraries were prepared with the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s instructions, with unique index codes added to each sample.

treatment_protocol: Noise exposures were delivered to unanesthetized animals placed in small wire cages within a custom-built sound-attenuated chamber designed by Charles Liberman (Mass. Eye and Ear).

value: cochlea

value: CBA/CaJ

tag: age

tag: Sex

value: male

value: mock


title: RPF_HCT_depleted_oxidative_rep3

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: ChIPseq_PKL_WT_rep1

address: 北京市海淀区颐和园路5号

description:
Library name: WDR5A-HA_pkl-IP-1
WDR5A-HA_pkl-IP-1

value: total seedlings


title: RPF_HCT_depleted_oxidative_rep1

description: ribo-seq (RPFs)


title: RPF_HCT_WT_oxidative_rep2

description: ribo-seq (RPFs)

value: oxidative stress; wt


title: Astrocytes Rep2_no_dox_d3

description: Library name: lane1C1R2nodoxd3

value: Control of Dox (3d)


title: Astrocytes Rep1_dox_d3

description: Library name: lane1B1R1doxd3


title: Mock 2Hr + 4Hr (neurons,R15)

description:
Library name: Control 28
Fresh-frozen spatial transcriptomic sequencing


title: Mock 2Hr + 4Hr (neurons,R16)

description:
Library name: Control 29
Fresh-frozen spatial transcriptomic sequencing


title: Astrocytes Rep1_no_dox_d3_washout_d4

description: Library name: lane1A2R1nodoxnowod3


title: RPF_HCT_WT_oxidative_rep1

description: ribo-seq (RPFs)


title: ChIP-Seq_mES_S2_deadCTDP1-12h_rep2

first: Dexun

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

description: Library name: Sample 34

data_processing:
ChIP-seq reads with spike-in were trimmed by Cutadapt (v3.4) and aligned to the mm10 and hg19 genomes using Bowtie2 (v2.3.5.1) in end-to-end mode. Downstream analyses utilized uniquely mapped reads.
RNA-seq reads were trimmed by Cutadapt (v3.4) and aligned to the mm10-dm6 merged genome by STAR (v2.7.10a). Downstream analyses included gene counting by featureCounts (v2.0.1) with spike-in normalization.
Assembly: mm10, hg19, dm6
Supplementary files format and content: Processed bigWig files for each sample in ChIP-seq
Supplementary files format and content: spike-in normalized counts for each sample in RNA-seq

source_name: cell culture

growth_protocol: The cell were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, D5796) with 15 % fetal bovine serum (FBS) (GeminiBio, 900-108), also supplemented with 1 mM L-glutamine (Gibco, 25030081), 1× nucleosides (Millipore, ES-008-D), 1× nonessential amino acids (Gibco, 11140050), 1× penicillin/ streptomycin (Gibco, 15140122), 1 mM Sodium Pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107). All the cells were cultured in 0.2 % gelatin-coated plates at 37°C and 5% CO2 under humid environment.

extract_protocol: ChIP–seq and RNA-seq were performed as previously described (PMID: 40038320) with two biological replicates per sample.

treatment_protocol: For RPB1 degradation, cells were treated with 2 μg/mL Dox for 13 hours, followed by 1 μM dTAG-13 for the final indicated minutes. For CTDP1-mCherry expression, cells were treated with 2 μg/mL Dox for 12 hours.

value: cell culture

value: mESC

value: Teton-MT CTDP1-mCherry


title: ChIP-Seq_mES_S2_CTDP1-12h_rep2

description: Library name: Sample 32

value: Teton-WT CTDP1-mCherry


title: ChIP-Seq_mES_S2_deadCTDP1-12h_rep1

description: Library name: Sample 33


title: Mock 2Hr + 4Hr (neurons,R14)

description:
Library name: Control 27
Fresh-frozen spatial transcriptomic sequencing


title: RPF_HCT_depleted_Unstressed_rep1

description: ribo-seq (RPFs)

value: unstressed; depleted


title: Astrocytes Rep1_no_dox_d3

description: Library name: lane1A1R1nodoxd3

value: C57BL6/J x CAST/EiJ

value: Astrocytes


title: Mock 2Hr + 4Hr (suppoprting cells,R13)

description:
Library name: Control 26
Fresh-frozen spatial transcriptomic sequencing


title: RPF_HCT_WT_Unstressed_rep2

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: unstressed; wt


title: ChIP-Seq_mES_S2_CTDP1-12h_rep1

description: Library name: Sample 31


title: RPF_HCT_WT_Unstressed_rep1

description: ribo-seq (RPFs)


title: ChIPseq_PKL_jaw-5D_rep1

address: 北京市海淀区颐和园路5号

description:
Library name: WDR5A-HA_pkl-input-1
WDR5A-HA_pkl-input-1

value: 9-day-old seedlings grown under continuous white light

value: anti-Ha endogenous antibody


title: Mock 2Hr + 4Hr (suppoprting cells,R12)

description:
Library name: Control 25
Fresh-frozen spatial transcriptomic sequencing

value: cochlea


title: Mock 2Hr + 4Hr (suppoprting cells,R11)

description:
Library name: Control 24
Fresh-frozen spatial transcriptomic sequencing

value: CBA/CaJ


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-12h_rep1

description: Library name: Sample 21


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-12h_rep2

description: Library name: Sample 22


title: RNA_HCT_depleted_heatshock_rep2

description: matched RNA seq

value: heatshock; depleted


title: RNA_HCT_WT_heatshock_rep2

description: matched RNA seq

value: heatshock; wt


title: Normoxia-2

city: Austin

first: Qi

last: Tan

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: Univesity of Minnesota

description:
Library name: Normoxia-2
UMN

data_processing:
Completed Illumina libraries were then converted for AVITI sequencing using the AVITI Library Conversion Kit and subjected to quality control, with no polishing step included. Libraries were sequenced on the AVITI platform using a 2 × 75 bp paired-end configuration on a Cloudbreak Medium Run, producing approximately 450 million reads.
Assembly: GRCh38
Supplementary files format and content: Tab-seprated vallues files and matrix files

source_name: iAT2 cells

growth_protocol: iAT2 cells were maintained in 3D Matrigel domes and cultured in defined AT2 medium following the established protocol described by Jacob et al., Nature (2019).

extract_protocol:
Total RNA was isolated from samples using Monarch Total RNA Miniprep Kit (NEB #T2110).
Libraries were generated using the Illumina Stranded Total RNA Prep with RiboZero Plus kit according to the manufacturer’s protocol.

value: iAT2 cells

value: Lung


title: ChIP-Seq_mES_RPB1NTD_CTDP1-12h_rep2

description: Library name: Sample 20


title: Hypoxia-3

description:
Library name: Hypoxia-3
UMN


title: RNA_HCT_WT_Unstressed_rep4

description: matched RNA seq


title: RNA_HCT_depleted_Unstressed_rep4

description: matched RNA seq


title: ChIP-Seq_mES_RPB1NTD_CTDP1-12h_rep1

description: Library name: Sample 19


title: Normoxia-1

description:
Library name: Normoxia-1
UMN


title: Normoxia-3

description:
Library name: Normoxia-3
UMN


title: Mock 2Hr + 4Hr (neurons,R13)

description:
Library name: Control 23
Fresh-frozen spatial transcriptomic sequencing

value: male

value: mock


title: RNA_HCT_depleted_heatshock_rep1

description: matched RNA seq


title: Mock 2Hr + 4Hr (neurons,R11)

description:
Library name: Control 21
Fresh-frozen spatial transcriptomic sequencing


title: Hypoxia-2

description:
Library name: Hypoxia-2
UMN


title: Hypoxia-1

description:
Library name: Hypoxia-1
UMN


title: RNA-Seq_mES_deadCTDP1-48h_rep1

description: Library name: Sample 43

molecule: polyA RNA

value: cell culture

value: mESC


title: RNA-Seq_mES_deadCTDP1-48h_rep2

description: Library name: Sample 44

value: Teton-MT CTDP1-mCherry


title: Mock 2Hr + 4Hr (suppoprting cells,R10)

description:
Library name: Control 20
Fresh-frozen spatial transcriptomic sequencing


title: 2D3D-3

description:
Library name: 2D3D-3
UMN


title: Mock 2Hr + 4Hr (suppoprting cells,R9)

description:
Library name: Control 19
Fresh-frozen spatial transcriptomic sequencing


title: RNA-Seq_mES_deadCTDP1-36h_rep2

description: Library name: Sample 42


title: RNA_HCT_depleted_Unstressed_rep3

description: matched RNA seq

value: unstressed; depleted


title: 2D3D-2

description:
Library name: 2D3D-2
UMN


title: RNA-Seq_mES_deadCTDP1-36h_rep1

description: Library name: Sample 41


title: RNA_HCT_WT_Unstressed_rep3

description: matched RNA seq


title: Mock 2Hr + 4Hr (suppoprting cells,R8)

description:
Library name: Control 18
Fresh-frozen spatial transcriptomic sequencing


title: Mock 2Hr + 4Hr (neurons,R12)

description:
Library name: Control 22
Fresh-frozen spatial transcriptomic sequencing


title: OPM-2 cells, WT, biol rep 3

description: Library name: AS-1071423-LR-69585

value: multiple myeloma

value: WT


title: 2D3D-1

description:
Library name: 2D3D-1
UMN


title: RNA_HCT_depleted_oxidative_rep3

description:
matched RNA seq
cts_riboseq.csv

value: oxidative stress; depleted


title: RNA-Seq_mES_deadCTDP1-24h_rep1

description: Library name: Sample 39


title: Mock 2Hr + 4Hr (neurons,R10)

description:
Library name: Control 17
Fresh-frozen spatial transcriptomic sequencing


title: 2D-2

description:
Library name: 2D-2
UMN


title: RNA_HCT_WT_oxidative_rep4

description:
matched RNA seq
cts_riboseq.csv

value: oxidative stress; wt


title: Mock 2Hr + 4Hr (neurons,R9)

description:
Library name: Control 16
Fresh-frozen spatial transcriptomic sequencing


title: RNA-Seq_mES_deadCTDP1-12h_rep2

description: Library name: Sample 38


title: RNA_HCT_depleted_oxidative_rep4

description:
matched RNA seq
cts_riboseq.csv


title: Mock 2Hr + 4Hr (neurons,R8)

description:
Library name: Control 15
Fresh-frozen spatial transcriptomic sequencing


title: RNA_HCT_WT_heatshock_rep1

description: matched RNA seq


title: RNA_HCT_WT_oxidative_rep3

description:
matched RNA seq
cts_riboseq.csv


title: Mock 2Hr + 4Hr (suppoprting cells,R6)

description:
Library name: Control 13
Fresh-frozen spatial transcriptomic sequencing


title: RNA_HCT_depleted_Unstressed_rep2

description:
matched RNA seq
cts_riboseq.csv


title: Mock 2Hr + 4Hr (suppoprting cells,R7)

description:
Library name: Control 14
Fresh-frozen spatial transcriptomic sequencing


title: S100A2-3

description:
Library name: S100A2-3
UMN


title: S100A2-2

description:
Library name: S100A2-2
UMN


title: RNA-Seq_mES_deadCTDP1-0h_rep2

description: Library name: Sample 36


title: Mock 2Hr + 4Hr (suppoprting cells,R5)

description:
Library name: Control 12
Fresh-frozen spatial transcriptomic sequencing


title: RNA-Seq_mES_deadCTDP1-0h_rep1

description: Library name: Sample 35


title: Astrocytes  Rep2_no_dox_d7

description: Library name: lane1G1R2nodoxd7

value: C57BL6/J x CAST/EiJ

value: Astrocytes

value: Xptet / R26rtTA

value: Control of Dox (7d)


title: RNA-Seq_mES_deadCTDP1-24h_rep2

description: Library name: Sample 40


title: Mock 2Hr + 4Hr (neurons,R7)

description:
Library name: Control 11
Fresh-frozen spatial transcriptomic sequencing

value: cochlea

value: CBA/CaJ


title: 2D-3

description:
Library name: 2D-3
UMN

value: iAT2 cells

value: Lung


title: RNA_HCT_depleted_oxidative_rep2

description:
matched RNA seq
cts_riboseq.csv


title: AT2-3

description:
Library name: AT2-3
UMN


title: 2D-1

description:
Library name: 2D-1
UMN


title: RNA-Seq_mES_deadCTDP1-12h_rep1

description: Library name: Sample 37


title: NG2-DsRed cells

city: Portland

first: Xiaorui

last: Shi

address: 3250 SW Sam Jackson Park Rd

department: OHRC

institute: Oregon Health & Sciences Univers

description:
Library name: PC
10X Genomics

library_source: transcriptomic single cell

data_processing:
Bcl conversion and demultiplexing was performed using bcl2fastq version 2.20.0.422.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Stria Vascularis

extract_protocol:
Temporal bones were harvested from 1–3 month-old Tie2-GFP or NG2-DsRed reporter mice (n = 10 per batch; 20 cochleae) immediately after euthanasia and placed in ice-cold Leibovitz’s L-15 medium (Gibco, Cat# 11415064). Under a dissecting microscope, the cochlear lateral wall was opened from apex to base, and the stria vascularis (SV) was carefully microdissected from each cochlea. For each mouse line, SV tissue from both ears was pooled in 1.5 mL microcentrifuge tubes containing L-15 on ice. Pooled SV tissue was transferred to 1 mL of L-15 supplemented with collagenase IV (Gibco, Cat# 17104019) and DNase I (Roche, Cat# 10104159001), minced with sterile fine scissors, and digested at 37°C for 30 minutes with gentle shaking (~100 rpm). After collagenase digestion, the enzyme solution was removed and replaced with an EBSS-based papain solution (Gibco, Cat# 14170161) containing papain (20 U/mL; Worthington Biomedical, Cat# LS003118), 1 mM L-cysteine (Sigma Aldrich, Cat# C7352), 0.5 mM EDTA (Invitrogen, Cat# 15575020), 15 mM HEPES (Gibco, Cat# 15630080), and DNase I. Samples were incubated for an additional 30 minutes at 37°C, and the tissue was gently triturated every 10 minutes using a 1000 μL pipette tip to generate a single-cell suspension while minimizing mechanical stress. Papain activity was quenched by adding an equal volume of Leibovitz’s medium containing 20% ovomucoid protease inhibitor (Worthington, Cat# LS003085). The suspension was passed through a 20–70 μm cell strainer to remove undigested fragments, and flow-through cells were collected and centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was washed twice with PBS containing 0.04% BSA and resuspended in 0.04% BSA/PBS. An aliquot of each suspension was mixed with trypan blue (Gibco, Cat# 15250061) and counted using an automated cell counter; only preparations with >80–85% viable cells were used. For enrichment of vascular populations, alive cells were sorted by FACS according to Tie2-GFP or NG2-DsRed fluorescence, using C57BL/6 tissue as a negative control and forward/side scatter to exclude debris and doublets. Purified cells were collected into tubes containing 0.04% BSA in PBS on ice, counted, and resuspended in 0.04% BSA/PBS at the appropriate concentration for loading onto the 10x Genomics Chromium system.
Libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics), following the manufacturer’s protocol. Briefly, cells were resuspended in the master mix and loaded onto a Chromium chip along with gel beads and partitioning oil to generate gel bead-in-emulsions (GEMs).  Within each GEM, cells were lysed and poly-A RNA transcripts were reverse transcribed into cDNA. Each cDNA molecule incorporated an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and a 10x barcode during this step. Barcoded cDNA was then pooled, purified using Silane DynaBeads, and amplified by PCR. Size selection of the amplified products was performed using SPRIselect reagent. Approximately 50 ng of cDNA was obtained after 14 cycles of amplification, and 29 ng was used for library construction. During this process, the Illumina R2 primer sequence, paired-end adapters (P5 and P7), and a sample index were added.

value: Stria Vascularis

value: Pericytres


title: AT2-2

description:
Library name: AT2-2
UMN


title: RNA_HCT_WT_Unstressed_rep2

description:
matched RNA seq
cts_riboseq.csv

value: unstressed; wt


title: AT2-1

description:
Library name: AT2-1
UMN


title: Mock 2Hr + 4Hr (neurons,R5)

description:
Library name: Control 9
Fresh-frozen spatial transcriptomic sequencing

value: male

value: mock


title: Tie2-GFP cells

description:
Library name: EC
10X Genomics

value: Endothelial cell


title: RNA_HCT_WT_oxidative_rep2

description:
matched RNA seq
cts_riboseq.csv


title: Mock 2Hr + 4Hr (neurons,R6)

description:
Library name: Control 10
Fresh-frozen spatial transcriptomic sequencing


title: RNA_HCT_WT_oxidative_rep1

description:
matched RNA seq
cts_riboseq.csv


title: Tada2b_2_Input

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

description: Library name: Tada2b_2_Input

data_processing:
Raw reads were assessed for quality using FASTQC and adapters were trimmed with Trimmomatic. Reads were mapped to the mm10 genome using Bowtie2, and SAM files were converted to BAM format with Samtools. The BAM files were sorted and indexed using Samtools, and mapping statistics were generated. PCR duplicates were removed with Samtools, and BED files were created using bedtools bamtobed. Reads mapping to chrM and regions in the ENCODE mm10 blacklist were removed from the BED files. Genome coverage was calculated using bedtools genomecov to produce bedGraph files. A scale factor was calculated by dividing 5,000,000 by the number of regions in each BED file, and applied to the bedGraph files. BigWig files were generated using bedGraphToBigWig. Peaks were called with MACS2 in both broad and narrow modes. Differential peak analysis was performed using DiffBind, and differential peaks were annotated and analyzed for motif enrichment using HOMER.
Assembly: mm10
Supplementary files format and content: .broadPeak

source_name: Bone marrow

extract_protocol:
CD201+CD150+KSL cells were fixed with 1% formaldehyde (10 minutes incubation at room temperature with rotation), then washed in PBS. Cell pellets were then resuspended in 120 µl of lysis buffer (50mM Tris pH8, 10mM EDTA, 0.5% SDS, 1.2 ul PIC per every 120 µl in ddH2O), and sonicated in Covaris AFA fiber microtubes (Covaris, cat. 520045) aiming for 200 bp fragments. SDS was neutralized with 1% Triton (25 µl of 10% Triton X100 for every 225 µl of sample), and samples were incubated at room temperature for 10 minutes with rotation.
5ul of fresh Protein A dynabeads (ThermoFisher, cat. 10001D, washed with PBS to remove the residual storage buffer), were added per reaction, followed by incubation at 4°C for 30 min with rotation. Samples were then placed on a magnet and cleared chromatin was collected, 5% of each reaction was allocated to a new DNA LoBind tube and stored at -20°C as input control.  Protein A dynabeads (ThermoFisher 10001D, 10 µl per antibody per sample) were washed twice with the wash buffer (200 µL PBS with 0.5% BSA + 1ul PIC per antibody per sample), and resuspended in 200 µl wash buffer per reaction. Beads were then transferred to fresh DNA LoBind tubes and 1 µl of antibody was added to each reaction. The beads were then incubated for 3-4 hours at 4°C with rotation. The beads were then washed twice in a new wash buffer (500 µl PBS + 0.5% FCS +1 µl Tween, 250 µl for each wash), 250ul of cleared chromatin was added to each antibody-bead tube followed by an overnight incubation at 4°C with rotation. The following day each reaction was washed three times with 150 µl of RIPA buffer (50 mM HEPES pH 7.6, 50 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na Deoxycholate in ddH2O), once with 150 µl of TE buffer, and once with 150 µl of 10mM Tris pH 8. The beads were then re-suspended in 25 µl of tagmentation buffer (prepare 5X stock of 50mM Tris pH8, 25mM MgCl2 and 50% dimethylformamide in ddH20, and dilute to 1X with ddH20) pre-warmed to 37°C, followed by addition of 5 µl of diluted Tn5 transposase (Illumina, cat. 20034197, 1ul of Tn5 per 4 µl of tagmentation buffer) and incubation at 37°C for 5 min with rigorous mixing. The beads were then immediately washed once with the RIPA buffer, once with 10mM Tris pH8 (150 µl per tube) and resuspended in ddH2O (22.5 µl per tube). For input controls, 2.5 µl 50 mM MgCl2  was added to 12.5 µl of input chromatin sample, followed by the addition of 6 µl of 5x tagmentation buffer, 1 µl of Tn5 and 8 µl of ddH2O; samples were then incubated at 37°C for 10 min (mixed after 5 min), placed on ice and 20 µl were taken for library preparation step.  For library preparation, the beads were supplemented with 25 µl of 2X NEBNext Ultra II Q5 Mastermix (New England Biolabs, cat. M0544S), 1.25 µl of universal adapter primer and 1.25 µl of index adapter primer and subjected to the following PCR programme: 72°C 5 min, 95°C 5 min, 12 cycles of (98°C 10 sec, 63°C 30 sec, 72°C 3 min), 72°C 5 min, 12°C indefinite hold. Upon library preparation PCR, the tubes were transferred to the magnet and supernatant was put in fresh DNA LoBind tubes. 50 µl of the AMPure XP beads (Beckman Coulter, cat. A63881) were added to each tube, and the samples were incubated at room temperature for 2 minutes. The beads were then washed twice with 150 µl of freshly prepared 80% ethanol, incubated at room temperature for 2 min, ethanol was removed and the beads were air-dried, resuspended in 11 µl ddH2O and incubated at room temperature for 2 min again. The tubes were put on the magnet and 10 µl were collected from each tube. QC and quantification of the samples were performed using D1000 high sensitivity ScreenTape (Agilent, cat. 5067-5584) and KAPA Library Quantification Kit (Roche, cat. KK4824). Library amplification was performed using KAPA HiFi HotStart Library Amp Kit (Roche, cat. KK2612) according to manufacturer’s recommendations.

value: Bone marrow

value: HSPC

value: Tada2b KO


title: Tada2b_2_H3K9Ac

description: Library name: Tada2b_2_H3K9Ac


title: Mock 2Hr + 4Hr (suppoprting cells,R4)

description:
Library name: Control 8
Fresh-frozen spatial transcriptomic sequencing


title: Patient3, FR/SDNS

city: Bergen

first: Øystein

last: Eikrem

state: Vestland

address: Jonas Lies vei 91B

department: Department of Clinical Medicine

country: Norway

institute: University of Bergen

description: Library name: 7-A1-Patient3-FRSDNS

data_processing:
Raw sequencing data were processed using Space Ranger from 10x Genomics to generate fastq files
Sequences were aligned to the Visium Human Transcriptome Probe Set v2.0 (GRCh38) using default Space Ranger settings.
Gene expression levels were quantified using default Space Ranger settings.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz; list of spatial barcodes
Supplementary files format and content: features.tsv.gz; list of Gene Ids
Supplementary files format and content: matrix.tsv.gz; UMI count matrix
Supplementary files format and content: aligned_fiducials.jpg; aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg; image of tissue and spots
Supplementary files format and content: detected_tissue_image.jpg; image of the detected tissue
Supplementary files format and content: tissue_hires_image.png; high resolution image of the tissue
Supplementary files format and content: tissue_hlowes_image.png; low resolution image of the tissue
Supplementary files format and content: cytassist_image.tiff; cytassist image of the tissue
Supplementary files format and content: scalefactors_json.json; scalefactors in json format
Supplementary files format and content: image.tif; high resolution input image of the tissue. Used for StarDist segmentation
Supplementary files format and content: tissue_positions.parquet; list of spatial barcodes and their tissue coordinates
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
FFPE kidney biopsies were processed following the protocols decribed in the Visium HD FFPE tissue preparation handbook from 10x Genomics
Library construction was performed following the protocols described in the Visium HD spatial gene expression reagents kits from 10x Genomics

value: Kidney

tag: type

value: FR/SDNS

tag: subject status

value: patient with idiopathic nephrotic syndrome


title: Tada2b_2_H2BUb

description: Library name: Tada2b_2_H2BUb


title: RNA_HCT_depleted_Unstressed_rep1

description:
matched RNA seq
cts_riboseq.csv

value: unstressed; depleted


title: Patient2, FSGS

description: Library name: 6-D1-Patient2-FSGS

value: FSGS


title: Mock 2Hr + 4Hr (suppoprting cells,R2)

description:
Library name: Control 6
Fresh-frozen spatial transcriptomic sequencing

value: cochlea

value: CBA/CaJ


title: RNA_HCT_WT_Unstressed_rep1

description:
matched RNA seq
cts_riboseq.csv


title: S100A2-1

description:
Library name: S100A2-1
UMN

value: iAT2 cells

value: Lung


title: Tada2b_1_Input

description: Library name: Tada2b_1_Input


title: Mock 2Hr + 4Hr (suppoprting cells,R1)

description:
Library name: Control 5
Fresh-frozen spatial transcriptomic sequencing


title: Patient1, SSNS

description: Library name: 5-A1-Patient1-SSNS

value: SSNS


title: Tada2b_1_H3K9Ac

description: Library name: Tada2b_1_H3K9Ac


title: AD 10

city: Brussels

first: Siranjeevi

last: Nagaraj

address: Route de Lennik 808 B-1070 Bruxelles

country: Belgium

institute: Université Libre de Bruxelles, Brussels, Belgium

description: Library name: miRNA-SN36

data_processing:
Reads lacking a detectable spacer and UMI were discarded using UMI-tools (v1.1.2). The remaining reads were assessed for quality and length using FastQC (v0.12.1) and screened for potential contaminants against a panel of common laboratory organism genomes using FastQ Screen (v0.15.3). PCR duplicates, defined as reads with identical UMI and sequence, were collapsed to retain only one representative per group. Known miRNA identification, novel miRNA prediction, and expression quantification were performed using the mirPRo pipeline (v1.1.4) with the latest miRBase (v22.1) annotations and the human genome (GRCh38, ENSEMBL release 111). The miRBase database contains 2656 mature human miRNA sequences. For novel miRNA prediction, reference data from all mammalian species in miRBase were used. Differential gene expression analysis was done in R (v4.3.3) using the edgeR (4.0.16) package. Briefly, feature counts were TMM-normalized and dispersions were estimated. For pairwise comparison of gene expressions between conditions, we used the quasi-likelihood model and F-test for a more reliable error rate. Correction of the p values for repeated testing was done with the Benjamini-Hochberg method.
Assembly: the human genome (GRCh38, ENSEMBL release 111)
Supplementary files format and content: counts_all_mature.tsv: raw expression count table in tab separated format, with miRNA IDs as rows and samples as columns

source_name: temporal superior T1 isocortex

extract_protocol:
Total RNA was extracted from approximately 100 mg of the temporal superior T1 isocortex brain regions using mirVana PARIS RNA and Native Protein Purification Kit (Thermo Fisher Scientific)
Sequencing library was constructed with 200 ng input RNA using the QIAseq miRNA Library Kit (Qiagen). This kit appends a 19 nt spacer and 12 nt unique molecular identifier (UMI) at the 3'-end of the original small RNA in the forward read (read 1), enabling PCR duplicate identification and amplification bias correction. Libraries were amplified using 15 PCR cycles, size-selected on an 8% native PAGE gel (Invitrogen) and purified. Library quality was assessed with the DNF-474 HS NGS Fragment (1-6000 bp) Kit on a Fragment Analyzer (Agilent Technologies) and quantified using the ‘Sequencing Library qPCR Quantification Guide’ from Illumina. Equimolar-pooled libraries were spiked with 15% PhiX as an internal control and sequenced as single-read 76 on a NextSeq 500 platform (Illumina).

value: temporal superior T1 isocortex

value: Mixed brain cells

value: F

tag: sample group

value: Alzheimer's diseases patient


title: Mock 2Hr + 4Hr (neurons,R4)

description:
Library name: Control 4
Fresh-frozen spatial transcriptomic sequencing

value: male

value: mock


title: AD 9

description: Library name: miRNA-SN30


title: Trial2_E2_GFP_High

city: Salt Lake City

first: Alexandra

last: Richey

state: UT

address: 2000 Cir of Hope Dr

department: Biomedical Engineering

institute: University of Utah

description: Library name: Sample 10

data_processing:
Sequencing reads (read 1 only) were aligned to sgRNA library using  the Human Epigenetic Knockout library file provided with the plasmid library using MAGeCK count
Read counts were normalized by MAGeCK count and then analyzed for enrichment by MAGeCK test
Assembly: Human Epigenetic Knockout Library
Supplementary files format and content: Gene counts (raw) in text file
Library strategy: CRISPR Screen

source_name: Ishikawa

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 4 days prior to 17beta-estradiol (E2) treatments, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
gDNA was extracted from cells using the Quick-DNA Miniprep Kit (Zymo)
Libraries were constructed for sequencing the CRISPR sgRNA region using a two-step pcr process.  Genomic DNA (100 to 5000 ng) was PCR amplified for 14 cycles using custom CRISPR PCR primers with NEBNext Ultra II Q5 Master Mix (NEB, M0544) (Forward Primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTGTGGAAAGGACGA AACACCG; Reverse Primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCAATTCCCACTCC TTTCAAGACCT). This was performed as 8 replicate reactions with the amplicons being pooled before the next step. Dual unique indexing adapters (Illumina, 20027213) (Read 1 Adapter: CTGTCTCTTATACACATCT; Read 2 Adapter: CTGTCTCTTATACACATCT) were added to the CRISPR amplicons during a second PCR with 6 cycles and performed as 3 replicate reactions. Libraries were pooled and sequenced on an Illumina NovaSeq X instrument as 150 x 150 cycle paired-end sequence runs.

treatment_protocol: Cells were treated with 10 nM 17beta-estradiol (E2) for 72 hours, and sorted based on GFP levels into Neg GFP, Low GFP, Med GFP, and High GFP.

value: Ishikawa

value: endometrioid adenocarcinoma

value: 72 hr 10nm E2

value: Trial 2


title: Trial2_E2_GFP_Med

description: Library name: Sample 9


title: RNA_HCT_depleted_oxidative_rep1

description:
matched RNA seq
cts_riboseq.csv

value: oxidative stress; depleted


title: Mock 2Hr + 4Hr (neurons,R3)

description:
Library name: Control 3
Fresh-frozen spatial transcriptomic sequencing


title: Tada2b_1_H2BUb

description: Library name: Tada2b_1_H2BUb

value: Bone marrow

value: HSPC

value: Tada2b KO


title: Mock 2Hr + 4Hr (suppoprting cells,R3)

description:
Library name: Control 7
Fresh-frozen spatial transcriptomic sequencing

value: cochlea

value: CBA/CaJ


title: Trial2_E2_GFP_Low

description: Library name: Sample 8


title: Mock 2Hr + 4Hr (neurons,R2)

description:
Library name: Control 2
Fresh-frozen spatial transcriptomic sequencing


title: WT_2_H3K9Ac

description: Library name: WT_2_H3K9Ac

value: WT


title: AD 7

description: Library name: miRNA-SN27

value: temporal superior T1 isocortex

value: M


title: Trial2_E2_GFP_Neg

description: Library name: Sample 7


title: Mock 2Hr + 4Hr (neurons,R1)

description:
Library name: Control 1
Fresh-frozen spatial transcriptomic sequencing


title: WT_2_Input

description: Library name: WT_2_Input


title: AD 6

description: Library name: miRNA-SN26

value: Mixed brain cells


title: WT_1_Input

description: Library name: WT_1_Input


title: 100 DB SPL 2Hr + 4Hr (neurons,R13)

description:
Library name: Noise 21
Fresh-frozen spatial transcriptomic sequencing

value: 100 dB SPL, 2 hr + 4hr


title: AD 5

description: Library name: miRNA-SN24

value: F

value: Alzheimer's diseases patient


title: Trial1_E2_GFP_High

description: Library name: Sample 5

value: Ishikawa

value: Trial 1


title: WT_2_H2BUb

description: Library name: WT_2_H2BUb


title: AD 4

description: Library name: miRNA-SN23


title: WT_1_H3K9Ac

description: Library name: WT_1_H3K9Ac


title: 100 DB SPL 2Hr + 4Hr (neurons,R12)

description:
Library name: Noise 20
Fresh-frozen spatial transcriptomic sequencing

value: male


title: Trial1_E2_GFP_Med

description: Library name: Sample 4

value: endometrioid adenocarcinoma

value: 72 hr 10nm E2


title: 100 DB SPL 2Hr + 4Hr (neurons,R11)

description:
Library name: Noise 19
Fresh-frozen spatial transcriptomic sequencing


title: WT_1_H2BUb

description: Library name: WT_1_H2BUb

value: Bone marrow


title: Trial1_E2_GFP_Low

description: Library name: Sample 3


title: AD 8

description: Library name: miRNA-SN28


title: AD 2

description: Library name: miRNA-SN19


title: 100 DB SPL 2Hr + 4Hr (neurons,R10)

description:
Library name: Noise 18
Fresh-frozen spatial transcriptomic sequencing


title: Trial1_E2_GFP_Neg

description: Library name: Sample 2


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R8)

description:
Library name: Noise 17
Fresh-frozen spatial transcriptomic sequencing


title: AD 1

description: Library name: miRNA-SN15


title: AD 3

description: Library name: miRNA-SN21


title: mRNA_HFD6w_3

city: Guiyang

first: Li

last: Li

address: No. 50, East Shicheng Road

institute: Guizhou University of Traditional Chinese Medicine

description:
Library name: sample6
10× Genomics

data_processing:
Using the official 10x Genomics analysis software Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome), the raw data underwent filtering, genome alignment, transcript quantification, and cell identification, ultimately yielding gene expression matrices for each cell type. Subsequent steps employed Seurat (https://satijalab.org/seurat/) for further cell filtering, standardisation of cell expression quantification, classification of cell subpopulations, analysis of differentially expressed genes across subpopulations, and marker gene selection. V(D)J data: Statistical analysis and graphical representation were performed using the R programming language. Integrated analysis of mRNA and immunoflorescence data.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
ApoE knockout mice subjected to either high-fat diet alone or high-fat diet combined with chronic restraint stress for 6 weeks underwent spleen homogenisation to obtain a single-cell suspension. Single-cell suspension of spleen was obtained and analyzed using scRNA-seq. Cell Quality Control: Adjust the cell concentration to the desired level, typically 700–1200 cells/μL.
Digest cDNA into fragments of approximately 200–300 bp, incorporate sequencing adapters and primers, and perform conventional second-generation sequencing library preparation. Finally, conduct PCR amplification to obtain the DNA library. Immune repertoire library construction: TCR/BCR constant regions are enriched via nested PCR using nested primers. Fragmentation is then performed with controlled cleavage lengths to generate sequences covering the entire V(D)J fragment cDNA. Through end-repair, A-adding, and adapter ligation with Read2 sequencing primers, a V(D)J library containing P5 and P7 adapters is constructed.

value: spleen

value: primary cells

value: splenic cell

value: ApoE

value: fed a high-fat diet alone for 6 weeks


title: mRNA_HFD6w_2

description:
Library name: sample5
10× Genomics


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R7)

description:
Library name: Noise 16
Fresh-frozen spatial transcriptomic sequencing

value: cochlea

value: CBA/CaJ


title: mRNA_HFD6w_1

description:
Library name: sample4
10× Genomics


title: 100 DB SPL 2Hr + 4Hr (neurons,R9)

description:
Library name: Noise 15
Fresh-frozen spatial transcriptomic sequencing


title: Control 9

description: Library name: miRNA-SN13

value: temporal superior T1 isocortex

value: Mixed brain cells

value: M

value: control


title: Control 8

description: Library name: miRNA-SN12


title: D11

city: Santa Cruz

first: Vikas

last: Peddu

email: vpeddu@ucsc.edu, dkim142@ucsc.edu

state: CA

address: 1156 High Street

department: Biomolecular engineering

institute: University of California Santa Cruz

data_processing:
We assembled a transcriptome of ~5.5 million transcripts, annotated with the corresponding ENSEMBL transcript IDs, UCSC genome browser repeat instance names, and novel gene IDs from IsoQuant. Transcript counts were aggregated to the gene level for GENCODE genes, and to the repeat ‘family’ level for repeat elements as previously described
Assembly: HG38
Supplementary files format and content: Counts matrix

source_name: Plasma

extract_protocol:
Norgen Biotek Plasma/Serum Circulating and Exosomal RNA purification slurry format kit(20)
Illumina libraries were prepared using full-length cDNA generated from the isolated plasma RNA of healthy, Barrett’s esophagus, and esophageal cancer samples using the SMART-Seq HT kit from Takara Bio USA. Final libraries were prepared with the Nextera XT Prep Kit from Illumina and sequenced on an Illumina Novaseq using a 2x151 sequencing chemistry.

value: Plasma

value: cell-free RNA


title: 100 DB SPL 2Hr + 4Hr (neurons,R8)

description:
Library name: Noise 14
Fresh-frozen spatial transcriptomic sequencing

value: male

value: 100 dB SPL, 2 hr + 4hr


title: mRNA_CS6w_3

description:
Library name: sample3
10× Genomics

value: subjected to chronic restraint stress combined with high-fat feeding for 6 weeks


title: Trial2_PreTreatment_Ctrl

description: Library name: Sample 6

value: Ishikawa

value: endometrioid adenocarcinoma

value: Trial 2


title: Control 7

description: Library name: miRNA-SN11

value: F


title: Control 6

description: Library name: miRNA-SN10


title: D10


title: mRNA_CS6w_2

description:
Library name: sample2
10× Genomics

value: spleen

value: primary cells

value: splenic cell

value: ApoE


title: 100 DB SPL 2Hr + 4Hr (neurons,R7)

description:
Library name: Noise 13
Fresh-frozen spatial transcriptomic sequencing

value: cochlea

value: CBA/CaJ


title: mRNA_CS6w_1

description:
Library name: sample1
10× Genomics


title: D09


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R6)

description:
Library name: Noise 12
Fresh-frozen spatial transcriptomic sequencing


title: Control 5

description: Library name: miRNA-SN06

value: temporal superior T1 isocortex

value: Mixed brain cells

value: M


title: D08

value: Plasma

value: cell-free RNA

value: Barrett's Esophagus (BE)


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R5)

description:
Library name: Noise 11
Fresh-frozen spatial transcriptomic sequencing

value: male

value: 100 dB SPL, 2 hr + 4hr


title: LNIO-Contra3

city: Suzhou

first: kaici

last: Tang

address: Renailu 199

institute: Soochow University

description: Library name: LNIO-Contra3

data_processing:
The qualities of the paired-end sequencing data were controlled via Fastp (version 0.24.0), and the data were aligned to the reference genome via HISAT2 (version 2.2.1). The reference genome and annotation files were obtained from GRCm39.RNA-seq data were analyzed with R (version 4.4.2) for bioinformatics processing.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing raw read counts and fpkm for each gene (rows) and sample (columns). The file includes gene identifiers (Gene Symbol) and expression values.

extract_protocol:
The injured and contralateral tissues were isolated from the corpus callosum at 4 days after LPC-induced repair injury or L-NIO-induced WMS. The corpus callosum tissue collected from the sham-operated mice served as a control.
total RNA was extracted via TRIzol reagent and quantified, after which ribosomal RNA depletion and poly(A) purification were performed. The cDNA library was subsequently prepared via the RNA Library Prep Kit. Libraries were quantified and pooled for paired-end sequencing on an Illumina NovaSeq 6000 platform.

value: brain

value: the corpus callosum

value: contra site of L-NIO injection


title: Trial1_PreTreatment_Ctrl

description: Library name: Sample 1

value: Ishikawa

value: endometrioid adenocarcinoma

value: Trial 1


title: LNIO-Contra2

description: Library name: LNIO-Contra2


title: LNIO-Contra1

description: Library name: LNIO-Contra1


title: D12

value: control


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R4)

description:
Library name: Noise 10
Fresh-frozen spatial transcriptomic sequencing

value: cochlea


title: Control 3

description: Library name: miRNA-SN04


title: Control 4

description: Library name: miRNA-SN05


title: LNIO-Ipsil3

description: Library name: LNIO-Ipsil3

value: L-NIO injection site


title: Control 2

description: Library name: miRNA-SN03

value: temporal superior T1 isocortex


title: 100 DB SPL 2Hr + 4Hr (neurons,R6)

description:
Library name: Noise 9
Fresh-frozen spatial transcriptomic sequencing

value: CBA/CaJ


title: D05

value: adenocarcinoma


title: 100 DB SPL 2Hr + 4Hr (neurons,R5)

description:
Library name: Noise 8
Fresh-frozen spatial transcriptomic sequencing


title: D06

value: Plasma


title: Control 1

description: Library name: miRNA-SN01

value: Mixed brain cells

value: M


title: D04

value: cell-free RNA


title: LNIO-Ipsil1

description: Library name: LNIO-Ipsil1


title: 100 DB SPL 2Hr + 4Hr (neurons,R4)

description:
Library name: Noise 7
Fresh-frozen spatial transcriptomic sequencing

value: male

value: 100 dB SPL, 2 hr + 4hr


city: New York

first: Marko

last: Jovanovic

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day17
Riboseq_Rep2_Day17

library_source: other

data_processing:
Reads were pre-processed using cutadapt (v1.17) to remove the first three nucleotides and the poly-A tail (--cut 3 -a "A{15}" -j 8 --nextseq-trim=20 --minimum-length 17). Bowtie (v1.2.2) was used to align reads to the human 45S pre-rRNA (NR_146144.1, downloaded from GenBank) using the -v 0 and --un flags to remove rRNA reads from the analysis. Reads were aligned to the genome using STAR (--runMode alignReads --outSAMtype BAM SortedByCoordinate –alignSJoverhangMin 400 –outFilterMismatchNmax 0 --outFilterMatchNmin 15 --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM). Post-processing was performed using tools from the plastid package. The plastid P-site program was used to estimate the location of ribosomal P-sites for each read length in each library (--min_counts 50 --require_upstream --min_length 17 --max_length 35). P offsets were generally in the range of 6-13, and some manual corrections were necessary in cases where the P-site program identified an incorrect peak. All manual corrections were done blinded to library identity. A default of 13 was used in cases where the P-site could not be clearly determined. For all subsequent analyses, reads were reduced to single counts offset from the 5’ end of the read by the value computed by the P-site program.
Read counting was performed using genomic alignments and a custom Python script built using tools from the plastid package. Briefly, for each gene, all associated transcripts were combined to create a single “meta-transcript”. Any genomic position mapping to the CDS of any annotated transcript was assigned to the CDS of the meta-transcript. Conversely, the 5’- and 3’UTRs of the meta-transcript were comprised of genomic positions assigned to the 5’/3’UTR of at least one transcript but never to a CDS. Ribo-seq reads (reduced to a single count with a 5’ offset as defined above) in each defined meta region (5’UTR, CDS, 3’UTR) were counted. Count matrices were read into R and CDS counts were propagated forward into DESeq2 using the DESeqDataSetFromMatrix function
CDS counts from genome-aligned libraries were normalized using DESeq2’s median of ratios method.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample
Library strategy: Ribo-Seq

molecule: other

growth_protocol: RUES2 human embryonic stem cells were maintained and expanded in MEF plates with hES medium

extract_protocol:
Homogenates were clarified by centrifugation at 13,000 x g for 10 min at 4°C. Clarified cell lysates were treated with E. coli RNase I (Ambion) and incubated for 30 min at room temperature. Ribosome-protected fragments were pelleted in 50% sucrose solution using an Ultracentrifuge (Beckman, with TLA-100.3 rotor) at 70,000 rpm for 3.5 hours at 4°C and isolated by Trizol extraction.
Ribosome-protected fragments in ~28-34 nucleotide length were size-selected by gel electrophoresis and later dephosphorylated by T4 Polynucleotide kinase (NEB). Ligation-free ribosome profiling libraries were generated from dephosphorylated footprints using the SMARTer small RNA-Seq Library Preparation Kit (Clontech) according to the manufacturer’s instructions. rRNA depletion was performed by using the oligo pool annealing to rRNAs. The rRNA-depleted libraries were amplified by PCR. The libraries were quantified using a Qubit dsDNA HS kit (Thermo Fisher Scientific), and the library quality was assessed by a Bioanalyzer (Agilent).

treatment_protocol: Cells were grown confluent (80-90%) before starting the differentiation. On Day 0 (start of differentiation), the medium was changed to the differentiation medium composed of RPMI containing glutamine (1%), CHIR 99021 (2 mM), Activin A (100 ng/ml), and diluted MTG (3 ml/ml). The 6-well plates were incubated in a humidified incubator at 37°C in 5% CO2, 5% O2, and 90% N2. On Day 1 and Day 2, the medium was changed to the differentiation medium composed of RPMI containing glutamine (1%), Activin A (100 ng/ml), diluted MTG (3 ml/ml), bFGF (5 ng/ml), and ascorbic acid (AA) (50 mg/ml). On Day 3, Day 4, and Day 5, the medium was changed to the differentiation medium composed of RPMI containing glutamine (1%), diluted MTG (3 ml/ml), dorsomorphin (0.75 mM), FGF10 (50 ng/ml), and B27 (1%). On Day 6, Day 7, and Day 8, the medium was changed to the differentiation medium composed of DMEM high glucose (HG) containing glutamine (1%), AA (50 mg/ml), FGF10 (50 ng/ml), B27 (1%), SANT-1 (0.25 mM), Retinoic Acid (RA) (2 mM), and NOGGIN (50 ng/ml). On Day 9 and Day 11, the medium was changed to the differentiation medium composed of DMEM high glucose (HG) containing glutamine (1%), AA (50 mg/ml), B27 (1%), NOGGIN (50 ng/ml), and SB 431542 (6 mM). On Day 13, the medium was changed to the differentiation medium composed of SFD medium containing glutamine (1%), AA (50 mg/ml), NOGGIN (50 ng/ml), SB 431542 (6 mM), L-658548 (1 mM), and D-Glucose (20 mM). After Day 13, the medium was changed to the Day 13 medium every 3 days.

value: human embryonic stem cells

value: WT

value: Polyhormonal cell differentiation


title: D03


title: D02


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day13
Riboseq_Rep2_Day13


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R3)

description:
Library name: Noise 6
Fresh-frozen spatial transcriptomic sequencing


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R2)

description:
Library name: Noise 5
Fresh-frozen spatial transcriptomic sequencing


title: LPC-Contra2

description: Library name: LPC-Contra2

value: brain

value: the corpus callosum

value: contra site of LPC injection


title: D07

value: Barrett's Esophagus (BE)


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day10
Riboseq_Rep2_Day10


title: D01


title: 100 DB SPL 2Hr + 4Hr (suppoprting cells,R1)

description:
Library name: Noise 4
Fresh-frozen spatial transcriptomic sequencing

value: cochlea


title: LPC-Contra1

description: Library name: LPC-Contra1


title: 100 DB SPL 2Hr + 4Hr (neurons,R3)

description:
Library name: Noise 3
Fresh-frozen spatial transcriptomic sequencing


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day5
Riboseq_Rep2_Day5


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day6
Riboseq_Rep2_Day6


title: 100 DB SPL 2Hr + 4Hr (neurons,R2)

description:
Library name: Noise 2
Fresh-frozen spatial transcriptomic sequencing


title: LNIO-Ipsil2

description: Library name: LNIO-Ipsil2

value: L-NIO injection site


title: LPC-Ipsil2

description: Library name: LPC-Ipsil2

value: LPC injection site


title: LPC-Ipsil3

description: Library name: LPC-Ipsil3


title: C10

value: control


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day4
Riboseq_Rep2_Day4


title: LPC-Ipsil1

description: Library name: LPC-Ipsil1


title: LPC-Contra3

description: Library name: LPC-Contra3


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day3
Riboseq_Rep2_Day3


title: Sham-Ipsil3

description: Library name: Sham-Ipsil3

value: saline injection site


title: C12

value: Plasma


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, input

city: Novosibirsk

first: Natalya

last: Bondar

address: 10, Ac. Lavrentieva ave.

country: Russia

institute: Institute of Cytology and Genetics SB RAS

description: Library name: input

data_processing:
Adapter trimming was performed using Trimmomatic. Reads were aligned to the mouse reference genome (GRCm38/mm10) using bowtie2.
Library quality metrics were evaluated using Phantompeakqualtools.
Peak calling was performed with MACS2 using nucleosome-optimized parameters (–shift 37, –extsize 73). Peaks overlapping DAC blacklist regions were removed.
Read counts per peak region were obtained from aligned BAM files using only uniquely mapped reads with MAPQ ≥ 10.
Between-sample normalization of peak counts was performed using scaling factors derived from library size and composition (size-factor–based normalization). Statistical testing for differential enrichment was conducted using a generalized linear modeling framework with default parameters.
Assembly: Mouse genome assembly GRCm38 (mm10), GENCODE release M13 (GRCm38.p5) used for read alignment, peak annotation, and assignment to nearest transcription start sites.
Supplementary files format and content: CSV table of normalized H3K4me3 peak counts per sample, with peak_loc (coordinates), peak_score, and library-size–adjusted counts (DEseq2).

source_name: prefrontal cortex

growth_protocol: Adult male C57BL/6J mice (10–12 weeks old) were maintained under standard housing conditions (12:12 h light/dark cycle; lights on at 08:00), with food and water available ad libitum.

extract_protocol:
Prefrontal cortex tissue was homogenized in douncing buffer, followed by micrococcal nuclease digestion to generate mononucleosome-sized fragments. Chromatin was lysed, precleared with protein G magnetic beads, and subjected to immunoprecipitation using an anti-H3K4me3 antibody (Abcam, ab8580). After extensive washes, DNA was eluted, treated with RNase A and proteinase K, and purified by phenol-chloroform extraction. Input DNA (10%) was collected prior to immunoprecipitation.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Fragment size selection was performed using AMPure XP beads. Libraries were PCR-amplified (6–8 cycles), quality-checked using an Agilent Bioanalyzer 2100, and sequenced (1×100 bp, single-end) on an Illumina HiSeq 4000 platform.

treatment_protocol: Chronic social defeat stress (SDS) was induced using a modified sensory contact model. Experimental C57BL/6J mice were exposed daily to a brief aggressive encounter with an unfamiliar CD1 mouse for 10 days (S10 group) or 30 days (S30 group). Between sessions, animals were housed adjacent to an aggressive CD1 mouse separated by a perforated barrier. Control animals were housed in divided cages without exposure to an aggressor. Behavioral testing was performed on days 8–9 (S10) and 28–29 (S30). Mice were euthanized 24 hours after the last SDS session, and the prefrontal cortex was dissected.

value: prefrontal cortex

value: control, standard housing conditions


title: C11

value: cell-free RNA


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day2
Riboseq_Rep2_Day2


title: C08


title: Sham-Ipsil2

description: Library name: Sham-Ipsil2


title: C07

value: adenocarcinoma


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS30, rep5

description: Library name: CSDS30_5

value: 30 days of chronic social defeat stress


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day0
Riboseq_Rep2_Day0

value: human embryonic stem cells

value: WT


title: Sham-Ipsil1

description: Library name: Sham-Ipsil1

value: brain


title: C06


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS30, rep3

description: Library name: CSDS30_3


title: LPD,concogene

city: New Brunswick

first: Xinlu

last: Han

address: 164 Frelinghuysen Road Piscataway

institute: Rutgers university

description: Library name: M80

data_processing:
We used CellRanger to align sequencing reads to a custom genome constructed by adding the human c-Met and ꞵ-Catenin genes to the mm10 genome. We then analyzed the data using Seurat (v5) and prepared the data using the standard Seurat pre-processing workflow. We removed cells with fewer than 200 genes, greater than 7000 genes, or greater than 21%  of reads mapping to mitochondrial genes. We then performed data normalization and scaling using Seurat’s built-in functions NormalizeData and ScaleData to adjust for sequencing depth and standardize genes. We also selected the top 5,000 variable genes for downstream analyses using the FindVariableFeatures function.
Assembly: mm10 genome
Supplementary files format and content: Tab-separate value files and matrix files

molecule: nuclear RNA

source_name: liver

extract_protocol:
Frozen liver tissue was isolated for single nucleus RNA sequencing using the Chromium Nuclei, Isolation Kit (PN-1000494,10x Genomics) according to manufacturer’s protocol.
10,000 cells were used to prepare snRNA-seq libraries. Chromium Single cell 3’ Library and Gel Bead Kit V3.1 (10×Genomics, PN1000268) was used to generate single cell gel beads in emulsion (GEM). The captured cells were lysed, and the released RNA was reverse-transcribed with primers containing poly-T, barcode, unique molecular identifiers (UMIs) and read 1 primer sequence in GEMs. Barcoded cDNA was purified and amplified by PCR. The adapter ligation reaction was performed to add sample index and read 2 primer sequence. After quality control, the libraries were sequenced on Illumina Novaseq 6000 platform in 150 bp pair-ended manner (Berry Genomics Corporation, Beijing, China).

value: liver

value: liver cell


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day17
Riboseq_Rep1_Day17

value: Polyhormonal cell differentiation


title: C04


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day13
Riboseq_Rep1_Day13


title: C03


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS30, rep2

description: Library name: CSDS30_2


title: LPD,control

description: Library name: M79


title: 100 DB SPL 2Hr + 4Hr (neurons,R1)

description:
Library name: Noise 1
Fresh-frozen spatial transcriptomic sequencing

value: cochlea

value: CBA/CaJ

value: male

value: 100 dB SPL, 2 hr + 4hr


title: C09

value: control


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS30, rep1

description: Library name: CSDS30_1


title: C02

value: Plasma


title: CD,concogene

description: Library name: M015


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS10, rep5

description: Library name: CSDS10_5

value: prefrontal cortex

value: 10 days of chronic social defeat stress


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep2_Day1
Riboseq_Rep2_Day1


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS10, rep4

description: Library name: CSDS10_4


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day5
Riboseq_Rep1_Day5


title: C01

value: cell-free RNA


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day6
Riboseq_Rep1_Day6


title: B12


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS30, rep4

description: Library name: CSDS30_4


title: BMDMs Irf9 KO, 3 hrs, Ethanol-Treated, Rep1

city: Memphis

first: Thirumala-Devi

last: Kanneganti

state: Tennessee

address: 262 Danny Thomas Pl

department: Immunology

institute: St. Jude Children's Research Hospital

description:
Library name: Irf9_KO_BMDMs_Ethanol-Treated1
Column name in RSEM_genes_raw_counts.txt: 2618564_QQ011

data_processing:
TrimGalore v0.6.3 was used for filtering low quality reads and trimming adaptor sequences from the FASTQs.
Proccessed FASTQs were then aligned to mm10 mouse genome (Gencode M22) using STAR aligner.
Gene and isoform level quantifications were computed using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone Marrow-Derived Macrophages

growth_protocol: Primary mouse bone marrow–derived macrophages (BMDMs) were generated from the bone marrow of wild-type and mutant mice. Cells were cultured for 5–6 days in IMDM (Thermo Fisher Scientific, 12440-053) supplemented with 1% non-essential amino acids (Thermo Fisher Scientific, 11140-050), 10% heat-inactivated fetal bovine serum (Biowest, S1620), 30% L929-conditioned medium, and 1% penicillin–streptomycin (Thermo Fisher Scientific, 15070-063). Differentiated BMDMs were then seeded into antibiotic-free medium at 1×10^6 cells/well in 12-well plates or 5×10^5 cells/well in 24-well plates and incubated overnight before downstream experiments.

extract_protocol:
RNA was extracted from WT and Irf9 KO  BMDMs using the RNeasy Mini Kit (QIAGEN, 74014) according to the manufacturer's instructions.
Libraries were prepared using TruSeq stranded mRNA library prep kit from Illumina (product #20020595) according to the manufacturer's instructions.

treatment_protocol: 5% ethanol (vol/vol; Fisher, 04-355-451) for 3 hrs

value: Bone Marrow-Derived Macrophages

value: Irf9 KO

value: Ethanol


title: BMDMs Irf9 KO, 3 hrs, Ethanol-Treated, Rep2

description:
Library name: Irf9_KO_BMDMs_Ethanol-Treated2
Column name in RSEM_genes_raw_counts.txt: 2618565_QQ012


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS10, rep3

description: Library name: CSDS10_3


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS10, rep2

description: Library name: CSDS10_2


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day4
Riboseq_Rep1_Day4

value: human embryonic stem cells

value: WT


title: B11


title: BMDMs WT, 3 hrs, Ethanol-Treated, Rep2

description:
Library name: WT_BMDMs_Ethanol-Treated2
Column name in RSEM_genes_raw_counts.txt: 2618561_QQ008


title: B10


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, CSDS10, rep1

description: Library name: CSDS10_1


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day10
Riboseq_Rep1_Day10


title: BMDMs Irf9 KO, 0 hrs, Control, Rep2

description:
Library name: Irf9_KO_BMDMs_Control2
Column name in RSEM_genes_raw_counts.txt: 2618559_QQ006

value: Control


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day2
Riboseq_Rep1_Day2


title: B09


title: BMDMs WT, 3 hrs, Ethanol-Treated, Rep1

description:
Library name: WT_BMDMs_Ethanol-Treated1
Column name in RSEM_genes_raw_counts.txt: 2618560_QQ007


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, control, rep3

description: Library name: cntrl_3

value: control, standard housing conditions


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, control, rep2

description: Library name: cntrl_2


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day1
Riboseq_Rep1_Day1

value: Polyhormonal cell differentiation


title: B08

value: Barrett's Esophagus (BE)


title: BMDMs Irf9 KO, 0 hrs, Control, Rep1

description:
Library name: Irf9_KO_BMDMs_Control1
Column name in RSEM_genes_raw_counts.txt: 2618558_QQ005


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day0
Riboseq_Rep1_Day0


title: B07


title: CD,control

description: Library name: M013

value: liver

value: liver cell


title: H3K4me3 ChIP-seq of mus musculus: adult male PFC, control, rep1

description: Library name: cntrl_1


title: BMDMs WT, 0 hrs, Control, Rep2

description:
Library name: WT_BMDMs_Control2
Column name in RSEM_genes_raw_counts.txt: 2618555_QQ002


title: B06


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day17

data_processing:
RNA-seq reads were aligned to the genome using STAR. Unprocessed reads were fed to STAR using the --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterType BySJout –outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif and --outFilterMultimapNmax 10 flags.
Read counting was performed using genomic alignments and a custom Python script built using tools from the plastid package. Briefly, for each gene, all associated transcripts were combined to create a single “meta-transcript”. Any genomic position mapping to the CDS of any annotated transcript was assigned to the CDS of the meta-transcript. Conversely, the 5’- and 3’UTRs of the meta-transcript were comprised of genomic positions assigned to the 5’/3’UTR of at least one transcript but never to a CDS. RNA-seq reads (reduced to a single count at the 5’ end) were counted in the meta-CDS and for the full meta-transcript. Count matrices were read into R and CDS counts were propagated forward into DESeq2 using the DESeqDataSetFromMatrix function.
CDS counts from genome-aligned libraries were normalized using DESeq2’s median of ratios method.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

extract_protocol:
Homogenates were cleared by centrifugation at 13,000 x g for 10 min at 4°C. Total RNA was isolated from the collected supernatant by a QIAGEN RNeasy kit, and the quality of total RNA was checked by a Bioanalyzer (Agilent).
Ribosomal RNA was depleted by the NEBNext rRNA depletion kit (Human/Mouse/Rat) according to the manufacturer’s instructions. Strand-specific sequencing libraries were generated from rRNA-depleted total RNA samples by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The libraries were quantified using a Qubit dsDNA HS kit (Thermo Fisher Scientific), and the library quality was assessed by a Bioanalyzer (Agilent)


title: D1tamx2333ko

city: Los Angeles

first: Zhenqi

last: Zhou

address: 650 Charles E Young Dr. S

department: Medicine

institute: University of California Los Angeles

description: Library name: Sample_F

data_processing:
Raw reads were checked for quality using FastQC, aligned to the Mus musculus GRCm38, and then counted using Mus musculus GRCm38 version 97. Alignment and counting occurred used Rsubread v 2.4.2. Raw counts were then analyzed for differential gene expression using the DESeq2 v1.30.0
Assembly: Grcm38
Supplementary files format and content: Excel. Differentail expressed genes

source_name: quadriceps muscle

extract_protocol:
A homogenous portion of frozen skeletal muscle samples were homogenized using a tissue homogenizer in Trizol. RNA was isolated using the Qiagen RNeasy Mini QIAcube Kit following the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit and RiboZero Gold following the manufacturer’s instructions.

value: quadriceps muscle

value: normal chow diet


title: BMDMs WT, 0 hrs, Control, Rep1

description:
Library name: WT_BMDMs_Control1
Column name in RSEM_genes_raw_counts.txt: 2618554_QQ001


description:
Library name: AK_Riboseq_hESCtoPHcellDifferentiation_Rep1_Day3
Riboseq_Rep1_Day3


title: B05

value: Plasma


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day13


title: Low protein diet, WT-3

description:
Library name: LPW656
Column name in Counts_allSamples.txt : Ctrl_LPD3

data_processing:
The RNA-seq reads were mapped to the mouse genome reference (Mus musculus genome (UCSC mm10)) using HISAT2, Gene-level quantification was counted using FEATURE COUNTS, differentially expressed gene analysis was conducted using DEseq, heatmap was generated using iDEP online tool https://bioinformatics.sdstate.edu/idep/. Functional enrichment analysis was performed using the Metascape online tool https://metascape.org/gp/index.html#/main/step1.
Assembly: UCSC mouse genome build mm10
Supplementary files format and content: The processed data files are in txt format.  The first column contains the geneID and the other columns contain read counts of the gene.

source_name: Liver

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues using a TRIzol™ (Invitrogen #15596026) and PureLink RNA Mini Kit (Invitrogen, #12183018A) combined method.
Approximately 500 ng total RNA was used for RNA-seq library preparation by following kapa rRNA depletion Total RNA-se sample preparation kit.

value: Liver

value: Hepatocyte


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day10


title: D1tamx2332ko

description: Library name: Sample_E


title: B04

value: cell-free RNA

value: adenocarcinoma


title: D1tamx2300c

description: Library name: Sample_D

value: Control f/f


title: Low protein diet, WT-2

description:
Library name: LPW650
Column name in Counts_allSamples.txt : Ctrl_LPD2


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day6


title: B03


title: D1tamx2299c

description: Library name: Sample_C


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day5


title: D1tamx2271c

description: Library name: Sample_B


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day4


title: Low protein diet, cMet & β-catenin-3

description:
Library name: LPO665
Column name in Counts_allSamples.txt : Onco_LPD3


title: Low protein diet, WT-1

description:
Library name: LPW649
Column name in Counts_allSamples.txt : Ctrl_LPD1


title: B01


title: Low protein diet, cMet & β-catenin-2

description:
Library name: LPO664
Column name in Counts_allSamples.txt : Onco_LPD2


title: D1tamx2263ko

description: Library name: Sample_A


title: A12

value: control


title: Low protein diet, cMet & β-catenin-1

description:
Library name: LPO654
Column name in Counts_allSamples.txt : Onco_LPD1


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day2

value: human embryonic stem cells


title: P23 SSp Ht Eml1 cKO

city: Geneva

first: Sergi

last: ROIG-PUIGGROS

state: Geneva

address: 1 Rue Michel Servet

department: Fundamental Neuroscience

country: Switzerland

institute: University of Geneva

data_processing:
Pre processing using cellranger
Assembly: mm10
Supplementary files format and content: Seurat object (.RDS) with Ctl and cKO (Cx and Ht) samples merged.

source_name: P23 SSp cells

extract_protocol:
10x Genomics Chromium Single Cell 3ʹ GEM kit v3
10x Genomics Chromium Single Cell 3ʹ library kit v3

value: P23 SSp cells

value: Emx1Cre; Eml1lox/lox


title: A11


title: Chow diet, WT-3

description:
Library name: HPW735
Column name in Counts_allSamples.txt : Ctrl_HPD3


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day1

value: WT


title: A10


title: A09


title: Chow diet, WT-2

description:
Library name: HPW662
Column name in Counts_allSamples.txt : Ctrl_HPD2


title: ChIP-Seq_mES_S5_deadCTDP1-12h_rep2

city: Beijing

description: Library name: Sample 30

data_processing:
ChIP-seq reads with spike-in were trimmed by Cutadapt (v3.4) and aligned to the mm10 and hg19 genomes using Bowtie2 (v2.3.5.1) in end-to-end mode. Downstream analyses utilized uniquely mapped reads.
RNA-seq reads were trimmed by Cutadapt (v3.4) and aligned to the mm10-dm6 merged genome by STAR (v2.7.10a). Downstream analyses included gene counting by featureCounts (v2.0.1) with spike-in normalization.
Assembly: mm10, hg19, dm6
Supplementary files format and content: Processed bigWig files for each sample in ChIP-seq
Supplementary files format and content: spike-in normalized counts for each sample in RNA-seq

extract_protocol: ChIP–seq and RNA-seq were performed as previously described (PMID: 40038320) with two biological replicates per sample.

value: cell culture

value: mESC

value: Teton-MT CTDP1-mCherry


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day0

value: Polyhormonal cell differentiation


title: P23 SSp Eml1lox/lox


title: Chow diet, WT-1

description:
Library name: HPW647
Column name in Counts_allSamples.txt : Ctrl_HPD1


title: B02


title: ChIP-Seq_mES_S5_deadCTDP1-12h_rep1

description: Library name: Sample 29


title: Chow diet, cMet & β-catenin-3

description:
Library name: HPO669
Column name in Counts_allSamples.txt : Onco_HPD3


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day17


title: A07

value: Barrett's Esophagus (BE)


title: A08


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day13


title: ChIP-Seq_mES_S5_CTDP1-12h_rep2

description: Library name: Sample 28

value: Teton-WT CTDP1-mCherry


title: Chow diet, cMet & β-catenin-2

description:
Library name: HPO634
Column name in Counts_allSamples.txt : Onco_HPD2


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep2_Day3


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day6


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day10


title: Chow diet, cMet & β-catenin-1

description:
Library name: hPO585
Column name in Counts_allSamples.txt : Onco_HPD1


title: P23 SSp Cx Eml1 cKO


title: ChIP-Seq_mES_S5_CTDP1-12h_rep1

description: Library name: Sample 27


title: ChIP-Seq_mES_Y1_deadCTDP1-12h_rep2

description: Library name: Sample 26


title: A05

value: Plasma


title: A04


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day5


title: ChIP-Seq_mES_Y1_deadCTDP1-12h_rep1

description: Library name: Sample 25


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day4


title: A03


title: si-NS+AngII

city: Shijiazhuang

first: siming

last: Bu

state: CHINA

address: Zhongshan East Road

institute: Hebei Medical university

description: Library name: si-NS + AngII

data_processing:
Libraries were quantified with Bioptic Qsep100 Analyzer（Bioptic lnc.）and paired-end sequenced with read lengths of 150. FastQC was used to analyze the quality of sequencing data, and the distribution of sequencing quality, base content distribution, and proportion of repeated sequencing fragments were obtained.
Assembly: mm10

source_name: aortic tissues

extract_protocol:
Add 1M DNase, mix thoroughly, and incubate at 37℃ for 30 minutes. Then, add 1 ml of pre-cooled EPITM ATAC Lysis Buffer and mix again.
DNA were resuspended in 25 µL of 2×HiFi PCR mix, 1 µL of each Nextera i5 primer（N5xx） and Nextera i7 primer（N7xx）.The following PCR program was performed: 72 °C for 5 min, 98 °C for 1 min, 14 cycles at 98 °C for 15 s, 60 °C for 30 s, and 72 °C for 1 min.

value: aortic tissues


title: ChIP-Seq_mES_Y1_CTDP1-12h_rep2

first: Dexun

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

description: Library name: Sample 24


title: Old, d7, rep7, collagenase-treated hematoma, GEX

city: Berlin

first: Anne

last: Noom

address: Augustenburger Pl. 1

institute: Charité - Universitätsmedizin

description:
Library name: Od7_7c_GEX
10x Genomics
Od7_7c_output_filtered.h5

data_processing:
Sequencing data were processed using the CellRanger pipeline (v7.1.0)
Assembly: mm10
Supplementary files format and content: CellRanger output files: output_filtered_cellblender_0_01.h5

source_name: Femur

extract_protocol:
The bone marrow was flushed from murine femora using a syringe with PBS containing 2% FCS and passed through a 70um cell strainer. Red blood cells were lysed using ACK lysis buffer for 1 min at RT, followed by washing with PBS + 2% FCS. Cortical bone fragments were subjected to digestion buffer (HBSS with 2 mg/mL collagenase IV and 1 mg/mL DNase II) at 37C for 30 min with gentle shaking. Following digestion, cells were passed through a 70um strainer, washed and resuspended in PBS + 0.04% BSA. Viable single cells were counted using trypan blue and used for downstream single-cell libraries.
Single-cell suspensions from bone marrow and cortical bone were processed using 10x Genomics Chromium Single Cell 3' v3 chemistry (10x Genomics) according to the manufacturer's protocol. Cells were first labeled with TotalSeq-B hashtag oligonucleotide (HTO) antibodies (BioLegend) for multiplexing. After washing to remove unbound antibodies, labeled cells were loaded into the Chromium Controller for droplet encapsulation. Libraries for both gene expression (GEX) and HTO were generated from the same Gel Bead-in Emulsion (GEM) reaction. Following reverse transcription, GEMs were broken and cDNA was purified. Separate amplification and indexing steps were performed for GEX and HTO libraries, which were then pooled and sequenced according to the 10x Genomics recommendations.

value: Femur

value: Female

tag: injured?

value: Yes

tag: library type

value: mRNA


title: ChIP-Seq_mES_Y1_CTDP1-12h_rep1

description: Library name: Sample 23

source_name: cell culture

tag: cell type


title: A02

value: cell-free RNA

value: adenocarcinoma


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day3

value: human embryonic stem cells

tag: treatment


title: Old, d7, rep7, collagenase-treated hematoma, HTO

description:
Library name: Od7_7c_CSP
10x Genomics
Od7_7c_output_filtered.h5

molecule: protein

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day2

tag: cell line

value: WT


title: ChIP-Seq_mES_MED4_deadCTDP1-12h_rep2

description: Library name: Sample 18

value: cell culture

value: mESC


title: A06

tag: genotype


title: Old, d7, rep7, GEX

description:
Library name: Od7_7_GEX
10x Genomics
7Od7_output_filtered.h5


title: chicken hindlimb ID3, 7days11hours, 06

city: Yokohama

first: Satomi

last: Ono

state: Kanagawa

address: B-17, 4259, Nagatsuta-cho, Midori-ku

country: Japan

institute: Institute of Science Tokyo

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to the chicken reference sequences of GCF_000002315.6_rna.fna, using BWA mem (version 0.7.17-r1188)  with the default parameters.
The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0).
Assembly: GCF_000002315.6_rna.fna
Supplementary files format and content: CSV

organism: Gallus gallus

source_name: Interdigital region 3 of chicken hindlimb

extract_protocol:
RNA was extracted using TRIzol-LS Reagent (Molecular Research Center) in combination with an AcroPrep Advance 96-well Long Tip Filter Plate for Nucleic Acid Binding (Pall) as previously described (Ujibe, K., Nishimura, K., Kashima, M., and Hirata, H. (2021). Direct-TRI: High-throughput RNA-extracting Method for all Stages of Zebrafish Development. Bio-protocol 11(17): e4136. DOI: 10.21769/BioProtoc.4136.). 180 ng of total RNA were used for the construction of libraries.
RNA-Seq library preparation were conducted according to the Lasy-Seq ver. 1.1 protocol.

treatment_protocol: Chicken embryos from HH30 to HH31 incubated for 7 days +4 hours, +6 hours, +8 hours, and +11 hours (each 6 samples) were dissected and immersed in RNAlater (Sigma-Aldrich), then interdigital region 3 (ID3) were dissected.

value: Incubation for 7days and 11hours


title: chicken hindlimb ID3, 7days11hours, 05

value: Interdigital region 3 of chicken hindlimb


title: Old, d7, rep6, collagenase-treated hematoma, GEX

description:
Library name: Od7_6c_GEX
10x Genomics
Od7_6c_output_filtered.h5


title: si-Ythdc1+AngII

description: Library name: si-Ythdc1+AngII


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day1

value: Polyhormonal cell differentiation


description: Library name: AK_RNAseq_hESCtoPHcellDifferentiation_Rep1_Day0


title: ChIP-Seq_mES_MED4_deadCTDP1-12h_rep1

description: Library name: Sample 17

value: Teton-MT CTDP1-mCherry