title: ESC, differentiation day 10, rep2

city: Jerusalem

first: Alana

last: Amelan

address: 9 Wolfson Boulevard

country: Israel

institute: The Hebrew University of Jerusalem

description:
Library name: Sample 6
Column name in CRISPR screen RNA-seq combined gene counts.csv: D10_2

data_processing:
Sequences were processesed and aligned using STAR (version 2.7) to the full genome sequences of Mus musculus (GRCm39).
Assembly: GRCm39
Supplementary files format and content: Files that end in "CPM" contain the combined counts per million, the relevant column for each sample is indicated.

growth_protocol: Cells were cultured at 37 °C and with 5% CO2 on gelatin-coated plates in 2I medium (knockout Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% ES cell qualified Fetal bovine serum, 0.1 mM non-essential amino acids, 100 μM βmercaptoethanol, 50 µg ml−1 penicillin, 50 µg ml−1 streptomycin, 100 units ml−1 Leukemia inhibitory factor, 2 mM L-glutamine, 3uM CHIR99021 and 1 uM PD0325901).

extract_protocol:
Total mRNA was extracted from samples using the Nuclespin® RNA Plus kit (Macherey-Nagel)
Libraries were constructed using KAPA Stranded mRNA-Seq Kit.

treatment_protocol: For neuronal differentiation, cells were transferred to new gelatin-coated plates at a plating density of ~ 8,334 cells per cm2 and grown in NDiff 227

value: ESC

value: CRISPR screen

value: Neural differentiation day 10


title: ESC, differentiation day 10, rep1

status: Public on Oct 19 2025

type: SRA

department: Genetics

description:
Library name: Sample 5
Column name in CRISPR screen RNA-seq combined gene counts.csv: D10_1

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Mo_1

city: Fushan

first: Jianhua

last: Xu

state: Guangdong

address: No. 12, Jinsha Avenue, Shunde District, Foshan, Guangdong, P.R. China

country: China

institute: Department of Laboratory Medicine Shunde Hospital of Guangzhou University of Chinese Medicine

data_processing:
The original data obtained from high-throughput sequencing were converted to raw sequence reads by base calling, and the results were stored in FASTQ format.
Low-quality reads and reads without primers were discarded. PCR and sequencing errors were corrected by unique molecular identifiers (UMIs).
The reads with same UMI were one clone. Only duplicate reads with different UMIs will be kept in downstream processing. A clonotype was defined by the CDR3 amino acid sequence for further analysis.
TCRβ V, D, J gene and clonotype defined according to IMGT59 and Igblast; TCRβ VDJ combination defined by MIXCR. We performed mRNA-Seq profiling on 70 samples.Reads mapped to the IPD-IMGT/HLA database and HLA -HD determining HLA alleles using mRNA-seq results
Categorical variables were described as count (%), and two group comparison was performed using Fisher’s exact test. Continuous variables were expressed as median and interquartile range (IQR) values and compared by Mann–Whitney U test between groups. Spearman correlation coefficient was calculated to assess the association between two vectors of quantitative variables. The significance of monotonic trend across multiple groups was assessed by Cuzick's test . The significance of overlap between tow gene sets was assessed by hypergeometric test (the “dhyper” function of R software). All statistical analyses were performed using R software (version 4.0.2). A two-sided P-value lower than 0.05 was considered as statistically significant. Given the exploratory nature of the present study, unadjusted p-values not accounting for multiple testing were used to screen COVID-19 associated TCR variables.

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
PBMC, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Symptomatic


title: 100 μg BKC treated heart control group 2

city: Busan

first: Tae Hwan

last: Shin

address: Nakdong-daero 550 beon-gil

department: Health Sciences

country: South Korea

institute: Dong-A University

description: Library name: B100-2_H

data_processing:
Trimmomatics (ver. 0.38) was used for a program that performs trimming depending on various parameters on illumina paired-end or single-end.
HISAT2 (ver. 2.1.0) was used for a fast and sensitive alignment program for mapping next-generation sequencing reads to genomes. Its first implementation based on an extension of BWT for graphs, designed a graph FM index (GFM). In addition to using one global GFM index, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).
StringTie (ver. 2.1.3b) was used for a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
edgeR (ver. 3.40.2) is used for differential expression analysis of RNA-seq expression profiles with biological replication.
Assembly: The Rattus norvegicus reference genome (GRCr8) and its corresponding annotation files were obtained from NCBI.
Supplementary files format and content: FPKM

organism: Rattus norvegicus

source_name: heart

growth_protocol: Six-week-old male Sprague-Dawley (SD) rats (Doo Yeol Biotech, Seoul, Korea) were acclimatized for 1 week before the experiment. Rats were housed in an individually ventilated cage system with controlled temperature and humidity (i.e., 20–25°C, 50 ± 10% humidity, and a 12-h light/dark cycle). The water and feed were supplied ad libitum. All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of the Korea Institute of Radiology and Medical Science (approval number: KIRAMS 2024-0014).

extract_protocol:
Quantitative RNA sequencing was performed with adrenal glands, heart, and pancreas at 24 h after the 10th intratracheal instillation. Collected organs were added 1 mL of TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) per 50 mg of organ tissues. The paired adrenal glands per animal were pooled, and the heart was dissected in the left ventricular area. Samples weighed approximately 50 mg and were stored in TRIzol at -80℃ in a deep freezer until RNA purification.
Total RNA was isolated using a RNeasy Mini kit (Qiagen, Valencia, CA, USA), and the RNA integrity was analyzed using a Bioanalyzer (Agilent, Santa Clara, CA, USA). RNA samples with RNA integrity values greater than 9 were selected to prepare the mRNA sequencing library. The library was prepared using a TruSeq Stranded mRNA library kit (Illumina, San Diego, CA, USA).

treatment_protocol: Single-dose instillation of benzalkonium Chloride (BKC) induced approximately 40% polymorphonuclear leukocytes (PMNs) at a dose of 200 μg/rat, whereas less than 10% PMNs were observed at 100 μg/rat. Therefore, the doses for repeated exposure were selected as 50 and 100 μg/rat. Repeated instillations (total 10 times) were conducted every 3 days, starting from 7 weeks of age. Rats were euthanized on day 31 (24 h after the final administration).

tag: tissue

value: heart

value: wildtype

value: 100 μg BKC


title: ESC, differentiation day 4, rep2

description:
Library name: Sample 4
Column name in CRISPR screen RNA-seq combined gene counts.csv: D4_2

value: Neural differentiation day 4


title: ethanol1, RNA

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

institute: Peking University

description: Library name: ethanol1

data_processing:
ChIP-seq data was processed as in Ho et al. (61). Fastq files were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using trim_galore (version 0.6.4), then ChIP-seq trimmed fastq reads were aligned to C. elegans genome version WBcel235 using bowtie2 (version 2.3.5.1) with default parameters. Bam files were then sorted and indexed using samtools (version 1.10). ChIP enrichment was normalized by dividing to input using DeepTools bamCompare (v3.3.0) with the following parameters: RPKM, bin-size of 10bp, ignore duplicates, extend reads to 200bp and remove ENCODE blacklisted regions (https://github.com/Boyle-Lab/Blacklist/). C. elegans enhancers were obtained from Jänes et al. (62). Genome-wide data was visualized using the Integrative Genomics Viewer (v2.6.1, Robinson et al., 2011(63).
For RNA-seq, the raw fastq files (stranded SE75) were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using trim_galore (version 0.6.4), then mapped to WBcel235 whole genome using HISAT 2.2.1 with default parameters. The number of reads mapped to genes was determined with featureCounts (Version 1.6.4). FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads at gene level. The resulting read count data were processed by DESeq2 (v1.35.0) to identify differentially expressed transcripts among experimental groups. Genes with log2 fold change > ± 1 and Padj <0,01 were considered to have significant expression change.
Assembly: WBcel235
Supplementary files format and content: bigWig

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C.elegans strains were grown at 20°C on NGM (Nematode Growth Medium) plates seeded with E.Coli OP50 bacteria, following standard procedures (Brenner, 1974), unless otherwise stated. Double mutants were generated by standard genetic crosses.

extract_protocol: Young adult animals were selected for these analyses as they can be highly synchronised. Chromatin extraction from large animal’s population was performed as described in Zaghet et al. 2021. Briefly, animals (at young adult stage) were collected and fixed for 10 minutes with a solution of 1% formaldehyde.

value: whole organism

value: ethanol


title: Mi_2


title: 100 μg BKC treated heart control group 1

description: Library name: B100-1_H


title: ESC, differentiation day 4, rep1

description:
Library name: Sample 3
Column name in CRISPR screen RNA-seq combined gene counts.csv: D4_1


title: ESC, differentiation day 0, rep2

description:
Library name: Sample 2
Column name in CRISPR screen RNA-seq combined gene counts.csv: D0_2

value: Neural differentiation day 0


title: As_8

value: Asymptomatic


title: As_9


title: 50 μg BKC treated heart control group 2

description: Library name: B50-1_H

value: 50 μg BKC


title: 50 μg BKC treated heart control group 1

description: Library name: B-2_H


title: Peds1 knockout, clone 2, differentiation day 4, rep3

description:
Library name: Sample 18
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: Peds1_c2_D4_3

value: Peds1 knockout clone 2


title: As_6


title: Vehicle treated heart control group 2

description: Library name: VEH-1_H

value: Vehicle


title: ESC, differentiation day 0, rep1

description:
Library name: Sample 1
Column name in CRISPR screen RNA-seq combined gene counts.csv: D0_1


title: Mo_2


title: PEC cells, HB-EGF+Eplerenone, S3

city: Paris

first: Sheerazed

last: BOULKROUN

address: 56 rue Leblanc

country: France

institute: Inserm

data_processing:
STAR (v2.7.6a), RSEM (v1.3.1), R 4.2.2, DESeq2_1.38.1
STAR --genomeDir /path/to/STAR/reference/directory --sjdbGTFfile /path/to/gtf --runThreadN 20 --readFilesIn /path/to/fastq/R1 /path/to/fastq/R2 --outFileNamePrefix $echantillon --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output /path/to/AlignedToTranscriptome/file /path/to/rsem-prepare-reference/files [sample-rsem-suffix]
Deseq2 Design : ~ Clone + Condition
Assembly: Ensembl release 101, GRCm38
Supplementary files format and content: Raw counts from rsem in tabulated format, filename ending by .resultsRSEM.genes.results
Supplementary files format and content: Normalized matrix in tabulated format : NGS22-060_ensemblGRCh38r101_deseq2_NormalizedMatrix.tsv

source_name: PEC

growth_protocol: Parietal Epithelial Cells (PEC) were maintained in endothelial cell growth medium containing endothelial cell basal medium supplement mix growth medium kit with 1% penicillin/streptomycin and 20% charcoal-stripped fetal bovine serum

extract_protocol:
RNA was extracted using Trizol (Thermo Fischer Scientific). 250 ng of total RNA was used for the construction of sequecing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA Prep kit (Illumina).

treatment_protocol: 24 hours after seeding, the supplement mix was removed from the medium. After additional 24 hours, cells were treated for 24 hours with vehicle (DMSO), HB-EGF (20mg/ml), eplerenone (10-5M) or HG-EGF (20mg/ml) + eplerenone (10-5M)

value: PEC

value: Parietal Epithelial Cells

value: WT

value: Growth factor and Mineralocorticoid receptor antagonis


title: As_5


title: Peds1 knockout, clone 2, differentiation day 4, rep2

description:
Library name: Sample 17
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: Peds1_c2_D4_2

value: ESC


title: Vehicle treated heart control group 1

description: Library name: V-2_H


title: PEC cells, HB-EGF+Eplerenone, S2


title: As_4


title: 100 μg BKC treated adrenal glands control group 2

description: Library name: B100-2_AG

source_name: adrenal glands

value: adrenal glands


title: As_11


title: Peds1 knockout, clone 2, differentiation day 4, rep1

description:
Library name: Sample 16
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: Peds1_c2_D4_1


title: PEC cells, HB-EGF+Eplerenone, S1


title: PEC cells, Eplerenone, S3

value: Mineralocorticoid receptor antagonist


title: Mi_1

value: Symptomatic


title: 100 μg BKC treated adrenal glands control group 1

description: Library name: B100-1_AG

value: wildtype

value: 100 μg BKC


title: 50 μg BKC treated adrenal glands control group 2

description: Library name: B-4_A


title: Peds1 knockout, clone 1, differentiation day 4, rep2

description:
Library name: Sample 14
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: Peds1_c1_D4_2

value: Peds1 knockout clone 1

value: Neural differentiation day 4


title: PEC cells, Eplerenone, S2


title: As_2


title: As_3


title: 50 μg BKC treated adrenal glands control group 1

description: Library name: B-3_A


title: As_1


title: PEC cells, Eplerenone, S1


title: A549 cells, 0.2% PGM, rep 3

city: Jyvaskyla

first: Daniel

middle: de Oliveira

last: Patricio

address: Survontie 9C

department: Department of Biological and Environmental Science and Nanoscience Center

country: Finland

institute: University of Jyvaskyla

description:
Library name: PGM_3
A549 cells; Treatment: Mucin; Replicate: 3

data_processing:
Chipster v4.16.2 platform was used for initial data processing
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC
Trimmed sequence reads were aligned to Homo_sapiens.GRCh38 genome using STAR v2.7.10a (parameters- max aligments per read: 10; max mismatches per read pair: 10)
Read count extraction and normalization were performed using HTSeq-count (parameters- organism: GRCh38; mode: union; min mapping quality: 10)
Differential expression analysis was performed using DESseq2 and edgeR, then a venn diagram was generated from both method results (log2 fild-change threshold: ±0.5; adjusted P < 0.05)
Supplementary files format and content: TSV file includes raw counts for each processed Sample individually

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized doublestranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

treatment_protocol: A549 cells were exposed to 0.2% type III porcine gastric mucin (PGM, Sigma) for 18 hours.

value: Lung epithelial cells

tag: batch

value: rep 3


title: WT, clone 2, differentiation day 4, rep3

description:
Library name: Sample 12
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: WT_c2_D4_3

value: Wildtype clone 2


title: PEC cells, HB-EGF, S3

value: Growth factor


title: Vehicle treated adrenal glands control group 1

description: Library name: V-3_A

value: Vehicle


title: A549 cells, 0.2% PGM, rep 2

description:
Library name: PGM_2
A549 cells; Treatment: Mucin; Replicate: 2

value: rep 2


title: As_10

value: Asymptomatic


title: PEC cells, HB-EGF, S2

value: PEC

value: Parietal Epithelial Cells

value: WT

value: Growth facto


title: A549 cells, 0.2% PGM, rep 1

description:
Library name: PGM_1
A549 cells; Treatment: Mucin; Replicate: 1

value: rep 1


title: WT, clone 2, differentiation day 4, rep2

description:
Library name: Sample 11
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: WT_c2_D4_2

value: ESC


title: 847_2

city: Patras

first: Adamantia

last: Kouvela

address: Asklipiou 1

country: Greece

institute: Department of Biochemistry, School of Medicine, University of Patras

description: Library name: Sample4

data_processing:
RNA-seq
Basecalling, de-multiplexing and filtering of low quality reads was performed within the Torrent Suite 5.12.3
The resulting fastq files were uploaded to the Galaxy web platform through the usegalaxy.eu public server
The differential gene expression was calculated with limma-voom (v3.50.1)
Assembly: Staphylococcus aureus RN4220
Supplementary files format and content: limma-voom ouput in xlsx format

organism: Staphylococcus aureus

source_name: Staphylococcus aureus RN4220

growth_protocol: All bacterial cultures were grown in minimal growth conditions (AAM) in the presence (847) or absence (cntrl) of T-box-i.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s protocol after sonication with the LABSONIC M sonicator (Sartorius, Göttingen, Germany). The samples were treated with DNase I and the quality of the RNA was visualized using agarose gel electrophoresis. Ribosomal RNA (rRNA) was depleted using the RiboMinusTM Bacteria 2.0 Transcriptome Isolation Kit (Thermo Fisher Scientific).
cDNA libraries were prepared from 100 ng rRNA-depleted RNA using the Ion Total RNA-Seq v2 Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Briefly, RNAs were digested with RNase III to produce 200 nt RNA fragments, which were successively treated for adapter ligation, reverse transcription, and 14 cycles of PCR amplification using the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific). The quantity of the libraries was measured with the Qubit 1x dsDNA HS Assay Kit (Thermo Fisher Scientific) and the size distribution was assessed using the Agilent High Sensitivity DNA Kit on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Template preparation and the Ion chip 540™ loading were performed on the Ion Chef system using the Ion 540™ Chef kit. The single-end sequencing was carried out on an Ion GeneStudio S5 sequencer. RNA sequencing analysis was performed in biological duplicates. For the sequencing of small RNAs, total RNA was run onto a 12% UREA-PAGE and the <150 nt RNA fraction was gel extracted . The library preparation procedure was the same as in the case of the total transcriptome analysis, except for the steps of ribosomal RNA depletion and RNase III treatment.

value: Staphylococcus aureus RN4220

value: grown in presence of T-box-i


title: PEC cells, HB-EGF, S1

value: Gorwth factor


title: 847_1

description: Library name: Sample3


title: PEC cells, DMSO, S3

value: Solvent


title: A549 cells, control, rep 2

description:
Library name: Control_2
A549 cells; Treatment: Control; Replicate: 2

value: Lung epithelial cells

value: Control


title: WT, clone 1, differentiation day 4, rep2

description:
Library name: Sample 8
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: WT_c1_D4_2

value: Wildtype clone 1

value: Neural differentiation day 4


title: WT, clone 1, differentiation day 4, rep1

description:
Library name: Sample 7
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: WT_c1_D4_1


title: PEC cells, DMSO, S1


title: Vehicle treated adrenal glands control group 2

description: Library name: V-4_A

value: adrenal glands

value: wildtype

value: Vehicle


title: As_7

value: Asymptomatic


title: Peds1 knockout, clone 1, differentiation day 4, rep3

description:
Library name: Sample 15
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: Peds1_c1_D4_3

value: Peds1 knockout clone 1


title: Peds1 knockout, clone 1, differentiation day 4, rep1

description:
Library name: Sample 13
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: Peds1_c1_D4_1


title: PEC cells, DMSO, S2

value: PEC

value: Parietal Epithelial Cells

value: WT


title: A549 cells, control, rep 3

description:
Library name: Control_3
A549 cells; Treatment: Control; Replicate: 3

value: rep 3


title: WT, clone 2, differentiation day 4, rep1

description:
Library name: Sample 10
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: WT_c2_D4_1

value: ESC

value: Wildtype clone 2


title: WT, clone 1, differentiation day 4, rep3

description:
Library name: Sample 9
Column name in RNA-seq Peds1 mut day 4 combined gene counts.csv: WT_c1_D4_3


title: MDA-MB 231 siDEPDC1_4

status: Public on Oct 18 2025

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: MDA-MB-231 cell line treated with DEPDC1 siRNA

data_processing:
RNA-seq quality control performed with FastQC
Transcripts were aligned using the STAR package (v2.7.9a) and quantified using the “quantMode GeneCounts” function with ENSEMBL annotation and the human genome version GRCh38 as a reference.
Read counts generated by STAR were analyzed using the DESeq2 R package to detect differentially expressed genes (DEGs) with an adjusted P value (Adj.P) less than 0.05.
Assembly: human genome version GRCh38 with ENSEMBL annotation v102 GTF
Supplementary files format and content: tab delimited file with gene raw count for each sample

source_name: Human breast cancer

growth_protocol: MDA-MB 231 BC cells were mantained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics, in humified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested using Rneasy mini kit (Qiagen). 1 ug was used for sequencing.
Libraries were constructed with the Illumina TruSeq RNA kits. 100 base pair reads (pair ends).

treatment_protocol: MDA-MB 231 BC cells were transfected with 300 µl of Opti-MEM (Life-Technologies), 5 μl of 20 μM control or DEPDC1 siRNA, 5 µl of Lipofectamine RNAiMAX reagent in DMEM 10% FBAS. After 8 h, the media was replenished with DMEM 10%FBS and 1% antibiotics. Two days after transfection, cells were harvested and RNA extracted.

value: Human breast cancer

value: MDA-MB 231

value: TNBC

value: DEPDC1 KD

value: 300 µl of Opti-MEM (Life-Technologies), 5 μl of 20 μM DEPDC1 siRNA, 5 µl of Lipofectamine RNAiMAX reagent


title: MDA-MB 231 siDEPDC1_3


title: A549 cells, control, rep 1

description:
Library name: Control_1
A549 cells; Treatment: Control; Replicate: 1

value: Lung epithelial cells

value: Control

value: rep 1


title: cntrl1

description: Library name: Sample1

value: Staphylococcus aureus RN4220

value: control


title: MDA-MB 231 siDEPDC1_2


title: cntrl2

description: Library name: Sample2


title: MDA-MB 231 siDEPDC1_1


title: MDA-MB 231 siCTL_2

description: MDA-MB-231 cell line treated with control siRNA

value: DEPDC1 WT

value: 300 µl of Opti-MEM (Life-Technologies), 5 μl of 20 μM control siRNA, 5 µl of Lipofectamine RNAiMAX reagent


title: Col-0_-N_2

type: RNA

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

country: Japan

institute: The University of Tokyo

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: whole seedlings from 10 day-old wild-type and dof1.7-KO seedlings grown under nitrogen-sufficient and nitrogen-defficient conditions

value: deficient nitrogen


title: dof1.7_-N_3


title: MDA-MB 231 siCTL_1


title: Col-0_+N_2

value: sufficient nitrogen


title: Col-0_+N_3


title: nTE_TFAP2C-ko_rep1

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

description: dox-inducible

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed RNA-Seq reads were mapped to hg38 genome using STAR (v2.5.2b). Refseq genes were quantified to FPKM using Stringtie.
Assembly: hg38
Supplementary files format and content: tab files of FPKM values

source_name: naïve trophectoderm

extract_protocol:
total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions.
mRNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: male

value: pluripotent stem cells

value: +dox


title: Col-0_+N_1


title: nTE_ctr_rep2

description: dox-inducible

value: -dox


title: nTE_TFAP2C-ko_rep2

description: dox-inducible


title: dof1.7_-N_2


title: nTE_ctr_rep1

description: dox-inducible


title: IRI_2

city: Nanjing

first: Xinghua

last: Gao

state: Jiangsu

address: #639 Longmian Dadao

institute: China Pharmaceutical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.
The gene alignment and FPKM were calculated using featureCounts v1.6.2 / StringTie v1.3.4d.
DESeq2 v1.22.1 / edgeR v3.24.3 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Total RNA was extracted using Trizol (Takara, Japan) and checked for a RIN number to inspect RNA integrity by an Bioanalyzer 2100 (Agilent technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 tumor cells were treated with Irinotecan (CPT-11) at a concentration of 10 μM for 48 hours.

value: tumor cell

value: WT

value: CPT-11 treatment


title: IRI_3


title: Col-0_-N_3


title: dof1.7_+N_3


title: Col-0_-N_1


title: dof1.7_-N_1


title: dof1.7_+N_2


title: dof1.7_+N_1


title: Con_3

value: DMSO treatment


title: IRI_1


title: Con_2


title: Con_1


title: MDA-MB 231 siCTL_3

value: Human breast cancer

value: MDA-MB 231

value: TNBC


title: KO-CF-P3-R2

city: HONG KONG

first: JITIAN

last: ZHANG

address: Tat Chee Avenue

institute: CITY UNIVERSITY OF HONG KONG

data_processing:
Raw reads were processed for obtaining clean reads through fastp (v0.20.0).
reads were mapped to human reference genome (UCSC hg38) using HISTA2 (v2.0.5).
The number of reads was counted using RSEM (rsem-1.2.4).
Differential expression analysis of two groups were performed using DESeq2 R package. The adjusted p-value were processed to control the false discovery rate (FDR) using the Benjamini and Hochberg’s approach. Genes with p-value < 0.05 found by DESeq2 were considered as significant difference.
KEGG pathway analysis was enriched using clusterProfiler R package (v4.2.0).
Assembly: GRCh38/hg38
Supplementary files format and content: count

source_name: blastocyst

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blastocyst

value: NPC

value: STAMBP-KO+CFLAR


title: B16F10 cells, Bub1KO,  radiation, replicate 3

city: Durham

first: Mengjie

last: Hu

state: North Carolina

address: 1228 Northcreek Dr

country: USA

institute: Duke University

description:
B16_KOIR_3
VC-IR_vs_KO-IR.txt

data_processing:
RNA-seq data was processed using the TrimGalore tool kit which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads
Reads were mapped to the GRCm38.p6 of the mouse genome and transcriptome using the STAR RNA-seq alignment tool
Reads were kept for subsequent analysis if they mapped to a single genomic location using the SAMtools
Gene counts were compiled using the HTSeq tool
Normalization and differential expression were carried out using the DESeq27 Bioconductor package with the R statistical programming environment. Differentially expressed genes (DEGs) were displayed in heatmaps and volcano plot using R program (version 3.6.0).
Assembly: mm10
Supplementary files format and content: tap-delimited text fils induce genes and RPKM values for each samples

source_name: melanoma

growth_protocol: B16F10 melanoma cells were cultriled in DMEM with 10% Fetal bovine serum (FBS) and antibiotics incubator with 5% CO2 at 37C

extract_protocol:
ToTal RNA was extrated by TRIzol
RNA libraries for RNA-seq were prepared usingllumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit following manufacturer's protocol

treatment_protocol: Vector control and Bub1KO B16F10 cells were treated 8-Gy radiation

value: melanoma

value: melanoma cancer cell line

value: Bub1 KO

value: radiation


title: KO-CF-P3-R1


title: KO-ST-P3-R2

value: STAMBP-KO+STAMBP


title: KO2_P3-R2

value: STAMBP-KO


title: KO-ST-P3-R1


title: B16F10 cells, vector control, radiation, replicate 2

description:
B16_VCIR_2
VC-IR_vs_KO-IR.txt

value: vector control


title: KO2_P3-R1


title: B16F10 cells, Bub1KO,  radiation

description:
B16_KOIR_1
VC-IR_vs_KO-IR.txt


title: B16F10 cells, vector control, radiation

description:
B16_VCIR_1
VC-IR_vs_KO-IR.txt


title: KO1_P3-R2


title: B16F10 cells, Bub1KO, no treatment, replicate 3

description:
B16_KO_3
VC-NoIR_vs_KO-NoIR.txt

value: no treatment


title: KO1_P3-R1


title: B16F10 cells, Bub1KO, no treatment

description:
B16_KO_1
VC-NoIR_vs_KO-NoIR.txt


title: WT_P3-R2

value: WT


title: WT_P3-R1


title: B16F10 cells, vector control, no treatment, replicate 3

description:
B16_VC_3
VC-NoIR_vs_KO-NoIR.txt


title: B16F10 cells, Bub1KO, no treatment, replicate 2

description:
B16_KO_2
VC-NoIR_vs_KO-NoIR.txt


title: shTRIM15_3

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

data_processing:
NOT PROVIDED; REQUESTED
Assembly: mm10
Supplementary files format and content: fpkm_expression

source_name: liver

growth_protocol: Huh7 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement

value: liver

value: liver cancer cells

value: kncokdown of TRIM15


title: VCD Rattus 4 ,m6A_IP RNA

city: Guangzhou

first: yang

middle: li

last: Li

state: guangdong

address: No. 111, Dade Road, Guangzhou City, Guangdong Province

institute: The Second Clinical College, Guangzhou University of Chinese Medicine

description: Library name: VCD4_IP_

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: eg GRCH38
Supplementary files format and content: VCD_inputVSCON_input_Gene_differential_expression.xlsx
Supplementary files format and content: VCD_IPVSVCD_input_peak.xlsx
Supplementary files format and content: VCDVSCON_all_diffPeak_Gene_differential_expression.xlsx
Supplementary files format and content: VCDVSCON_diffPeak_result.xlsx
Supplementary files format and content: CON_IPVSCON_input_peak.xlsx
Library strategy: MeRIP-Seq

source_name: ovary

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: ovary

value: VCD


title: VCD Rattus 3,m6A_IP RNA

description: Library name: VCD3_IP_


title: B16F10 cells, vector control, no treatment, replicate 2

description:
B16_VC_2
VC-NoIR_vs_KO-NoIR.txt


title: B16F10 cells, Bub1KO,  radiation, replicate 2

description:
B16_KOIR_2
VC-IR_vs_KO-IR.txt


title: B16F10 cells, vector control, no treatment

description:
B16_VC_1
VC-NoIR_vs_KO-NoIR.txt


title: shTRIM15_2


title: VCD Rattus 4 ,m6A_input RNA

description: Library name: VCD4_input_


title: VCD Rattus 3,m6A_input RNA

description: Library name: VCD3_input_


title: VCD Rattus 2  ,m6A_IP RNA

description: Library name: VCD2_IP_


title: MLL4SET_HSA-Cre, HFD biological rep2

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

description:
D4
Gastrocnemius muscle total RNA from MLL4SET muscle specific knock-out mouse

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks version 2.2.1 and Cuffdiff version 2.2.1.
Assembly: mm10
Supplementary files format and content: FPKM values and gene expression ratio.

source_name: Gastrocnemius muscle from  MLL4SETf/fHSA-Cre mouse

extract_protocol:
Gastrocnemius muscle  were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Gastrocnemius muscle

tag: age

value: 20 weeks of age

value: Muscle specific MLL4SET knock-out

value: High fat diet


title: VCD Rattus 1,m6A_input RNA

description: Library name: VCD1_input_


title: shTRIM15_1


title: MLL4SET_HSA-Cre, HFD biological rep1


title: shcontrol_3

value: control


title: shcontrol_2


title: Rattus 4 ,m6A_input RNA

description: Library name: CON4_input_

value: CON


title: B16F10 cells, vector control, radiation, replicate 3

description:
B16_VCIR_3
VC-IR_vs_KO-IR.txt

value: melanoma

value: melanoma cancer cell line

value: radiation


title: MLL4SET_HSA-Cre, CD biological rep2

description:
B2
Gastrocnemius muscle total RNA from MLL4SET muscle specific knock-out mouse

value: Chow diet


title: Rattus 3 ,m6A_IP RNA

description: Library name: CON3_IP_


title: shcontrol_1


title: Rattus 3 ,m6A_input RNA

description: Library name: CON3_input_


title: MLL4SET_HSA-Cre, CD biological rep1


title: Rattus 2,m6A_input RNA

description: Library name: CON2_input_


title: HCT116 cells, BUB1KO, radiaiton, rep2

description:
KOIR_rep2
VCIR_vs_KO-IR.txt

data_processing:
RNA-seq data was processed using the TrimGalore tool kit which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads
Reads were mapped to the human genome and transcriptome using the STAR RNA-seq alignment tool
Reads were kept for subsequent analysis if they mapped to a single genomic location using the SAMtools
Gene counts were compiled using the HTSeq tool
Normalization and differential expression were carried out using the DESeq27 Bioconductor package with the R statistical programming environment. Differentially expressed genes (DEGs) were displayed in heatmaps and volcano plot using R program (version 3.6.0).
Assembly: hg38
Supplementary files format and content: VC_vs_KO.txt
Supplementary files format and content: VCIR_vs_KO-IR.txt

molecule: cytoplasmic RNA

organism: Homo

source_name: colon

growth_protocol: HCT116 colon cancer cells were cultriled in DMEM with 10% Fetal bovine serum (FBS) and antibiotics incubator with 5% CO2 at 37C

extract_protocol:
Fractionated cells and cytoplasmic RNA was extrated by TRIzol
RNA libraries for RNA-seq were prepared usingllumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit following manufacturer's protocol

treatment_protocol: Vector control and BUB1KO HCT116 cells were treated with 8-Gy radiation

value: colon

value: colon cancer cell


title: Rattus 2 ,m6A_IP RNA

description: Library name: CON2_IP_


title: HCT116 cells, vector control, radiation rep2

description:
VCIR_rep2
VCIR_vs_KO-IR.txt

value: vector control


title: WT, CD biological rep2

description:
A1
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for muscle specific MLL4SET knock-out

source_name: Gastrocnemius muscle from wild-type mouse

value: Wild-type


title: SH2

first: Weixiang

last: Zhan

address: 广东省广州市天河区员村二横路东璟花园

institute: Sun Yat-sen university

description: Library name: Sample 5

library_source: transcriptomic single cell

data_processing:
For quality control, Fastp and Seurat were employed with the following thresholds: ≥3 cells per gene and ≥200 genes per cell. Data integration was achieved using Canonical Correlation Analysis (CCA) for batch correction, followed by dimensionality reduction via t-SNE and UMAP. Differential expression analysis was conducted using the edgeR package, and tissue-specific markers were identified.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
CT26 tumors were enzymatically dissociated into single-cell suspensions, and the cell concentration was adjusted to 600–1200 cells/μL. Library preparation was performed using the DNBelab C4 scRNA-seq kit (MGI) with droplet-based mRNA capture. The workflow included cDNA synthesis, amplification via PCR and Fragmentase treatment, end repair, A-tailing, and adapter ligation.
Subsequently, the libraries were loaded onto DNB nanoarrays and sequenced using Combinatorial Probe-Anchor Synthesis (cPAS) on the DNBSEQ-T7 platform.

value: Tumor

value: CT26 and immune cell

value: BALB/c mice

value: CTSD knockdown


title: Rattus1 ,m6A_IP RNA

description: Library name: CON1_IP_

value: ovary


title: WT, HFD biological rep2

description:
C3
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for muscle specific MLL4SET knock-out

value: Gastrocnemius muscle

value: 20 weeks of age


title: Rattus 4 ,m6A_IP RNA

description: Library name: CON4_IP_


title: VCD Rattus 2 ,m6A_input RNA

description: Library name: VCD2_input_

value: VCD


title: Rattus 1,m6A_input RNA

description: Library name: CON1_input_

value: CON


title: WT, CD biological rep1


title: NC2

address: 广东省广州市天河区员村二横路东璟花园

description: Library name: Sample 2

value: NC


title: WT, HFD biological rep1

value: High fat diet


title: MLL4SET_HSA-Cre, Liver biological rep2

description: Liver total RNA from MLL4SET muscle specific knock-out mouse

source_name: Liver from MLL4SETf/fHSA-Cre mouse

extract_protocol:
Liver  were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: Muscle specific MLL4SET knock-out


title: nup50c-3

city: Weifang

first: Yu

last: Tang

state: Shandong

address: No. 699, Binhu Road, Xiashan Ecological Economic Development Zone

institute: Peking University Institute of Advanced Agricultural Sciences

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: whole seedlings

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 9-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: whole seedlings

value: nup50c mutant


title: SH3

address: 广东省广州市天河区员村二横路东璟花园

description: Library name: Sample 6


title: MLL4SET_HSA-Cre, Liver biological rep1


title: HCT116 cells, vector control, no treatment rep2

description:
VC_rep2
VC_vs_KO.txt

value: colon

value: colon cancer cell

value: vector control

value: no treatment


title: WT, Liver biological rep2

description: Liver total RNA from wild-type mouse - control mouse for muscle specific MLL4SET knock-out

source_name: Liver from wild-type mouse

value: Wild-type


title: SH1

address: 广东省广州市天河区员村二横路东璟花园

description: Library name: Sample 4

value: Tumor

value: CT26 and immune cell

value: BALB/c mice

value: CTSD knockdown


title: VCD Rattus 1 ,m6A_IP RNA

description: Library name: VCD1_IP_

value: ovary

value: VCD


title: HCT116 cells, BUB1KO, no treatment rep1

description:
KO_rep1
VC_vs_KO.txt


title: nup50c-2


title: NC3

address: 广东省广州市天河区员村二横路东璟花园

description: Library name: Sample 3

value: NC


title: Col-0_1

value: wild type


title: WT, Liver biological rep1

value: liver

value: 20 weeks of age

value: High fat diet


title: HCT116 cells, BUB1KO, no treatment rep2

description:
KO_rep2
VC_vs_KO.txt


title: HCT116 cells, BUB1KO, radiaiton, rep1

description:
KOIR_rep1
VCIR_vs_KO-IR.txt

value: radiation


title: nup50c-1

value: whole seedlings

value: nup50c mutant


title: sgNLN_3

status: Public on Oct 17 2025

city: Dallas

first: Ping

last: Mu

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Cente

data_processing:
The alignment of the reads to the human reference genome (GRCh38) was executed using STAR (v2.7.2b)72, while FeatureCounts (v1.6.4)73 was employed for gene counts, biotype counts, and rRNA estimation. The differential expression analysis was conducted using the R package DEseq2 (v1.26)74, with selected cutoff values of an absolute fold change greater than 2 and a false discovery rate of less than 0.1. The differentially expressed genes were then identified, and GSEA was performed using the R package fgsea (v1.14.0) in conjunction with the 'Hallmark' libraries from MsigDB.
Assembly: GRCh38
Supplementary files format and content: DESeq normalized reads are stored in xlsx file and contains gene counts normalized by DESeq2

source_name: Prostate

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 4 days.

extract_protocol:
RNA was extracted from LNCaP/AR cells using Trizol (Ambion, 15596018).
RNA-seq libraries were then prepared using the stranded Illumina TruSeq mRNA kit. The preparation began with 500 ng of total RNA and included 10 cycles of PCR amplification
These barcoded RNA-seq libraries were run as paired-end, 50-nucleotide reads on an Illumina HiSeq 2500 and were selectively filtered by poly(A).

treatment_protocol: For RNAseq samples: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% Full serum.

value: Prostate

value: LNCaP/AR

value: prostate cancer cells

value: sgNLN


title: Col-0_3


title: sgNT_2

value: sgNT


title: sgNT_1


title: HCT116 cells, vector control, no treatment rep1

description:
VC_rep1
VC_vs_KO.txt

value: colon

value: colon cancer cell

value: vector control

value: no treatment


title: Col-0_2


title: HCT116 cells, vector control, radiation rep1

description:
VCIR_rep1
VCIR_vs_KO-IR.txt


title: sgNLN_2


title: sgNLN_1


title: sgNT_3


title: GNE-495 + PTX, biol rep 3, tech rep 2

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Library name: Sample34
GNE-495 + PTX, biol rep 3, tech rep 2

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with Homo Sapiens genome (hg38) as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCh38 (hg38)
Supplementary files format and content: counts

source_name: Lonza GR1.1

growth_protocol: iPSC-derived sensory neurons were grown in DMEM/F12 media supplemented with N2, B27 (without vitamin A), 25ng/mL BDNF, 25ng/mL GDNF, 25ng/mL NT-3 and 25ng/mL β-NGF, 1 µM PD0332991 and 1x penicillin/streptomycin. Cells were grown in 37C at 5% CO2.

extract_protocol:
RNA isolation was performed using RNAeasy Plus Micro kit (Qiagen). 1 µg of total RNA was used for construction of sequencing libraries.
Library was prepared using TruSeq Stranded RNA, and RNA samples were barded into cDNA libraries and sequencing was carried out as paired end

treatment_protocol: 28DIV sensory neurons were treated with either 0.1% DMSO, 0.3 µM paclitaxel (EMD Millipore), 3 µM JNK-IN-8 (MedChem Express), 3 µM GNE-495 (MedChem Express), 3 µM JNK-IN-8 + paclitaxel or 3 µM GNE-495 + paclitaxel. Treatment was done for 24 hours.

value: Lonza GR1.1

value: sensory neurons

value: GNE-495 + PTX

value: Batch 3


title: JNK-IN-8 + PTX, biol rep 3, tech rep 1

description:
Library name: Sample30
JNK-IN-8 + PTX, biol rep 3, tech rep 1

value: JNK-IN-8 + PTX


title: JNK-IN-8 + DMSO, biol rep 3, tech rep 2

description:
Library name: Sample35
JNK-IN-8 + DMSO, biol rep 3, tech rep 2

value: JNK-IN-8 + DMSO


title: NC1

address: 广东省广州市天河区员村二横路东璟花园

description: Library name: Sample 1

value: Tumor

value: CT26 and immune cell

value: BALB/c mice

value: NC


title: GNE-495 + DMSO, biol rep 3, tech rep 2

description:
Library name: Sample33
GNE-495 + DMSO, biol rep 3, tech rep 2

value: GNE-495 + DMSO


title: PTX, biol rep 3, tech rep 1

description:
Library name: Sample26
PTX, biol rep 3, tech rep 1

value: PTX


title: DMSO, biol rep 3, tech rep 2

description:
Library name: Sample31
DMSO, biol rep 3, tech rep 2

value: DMSO


title: PTX, biol rep 3, tech rep 2

description:
Library name: Sample32
PTX, biol rep 3, tech rep 2


title: JNK-IN-8 + DMSO, biol rep 3, tech rep 1

description:
Library name: Sample29
JNK-IN-8 + DMSO, biol rep 3, tech rep 1


title: JNK-IN-8 + PTX, biol rep 3, tech rep 2

description:
Library name: Sample36
JNK-IN-8 + PTX, biol rep 3, tech rep 2


title: GNE-495 + PTX, biol rep 3, tech rep 1

description:
Library name: Sample28
GNE-495 + PTX, biol rep 3, tech rep 1


title: GNE-495 + DMSO, biol rep 3, tech rep 1

description:
Library name: Sample27
GNE-495 + DMSO, biol rep 3, tech rep 1


title: DMSO, biol rep 3, tech rep 1

description:
Library name: Sample25
DMSO, biol rep 3, tech rep 1


title: JNK-IN-8 + PTX, biol rep 2, tech rep 2

description:
Library name: Sample24
JNK-IN-8 + PTX, biol rep 2, tech rep 2

value: Batch 2


title: GNE-495 + DMSO, biol rep 2, tech rep 1

description:
Library name: Sample15
GNE-495 + DMSO, biol rep 2, tech rep 1


title: JNK-IN-8 + DMSO, biol rep 2, tech rep 2

description:
Library name: Sample23
JNK-IN-8 + DMSO, biol rep 2, tech rep 2


title: GNE-495 + PTX, biol rep 2, tech rep 2

description:
Library name: Sample22
GNE-495 + PTX, biol rep 2, tech rep 2


title: PTX, biol rep 2, tech rep 2

description:
Library name: Sample20
PTX, biol rep 2, tech rep 2


title: DMSO, biol rep 2, tech rep 1

description:
Library name: Sample13
DMSO, biol rep 2, tech rep 1


title: DMSO, biol rep 2, tech rep 2

description:
Library name: Sample19
DMSO, biol rep 2, tech rep 2


title: PTX, biol rep 1, tech rep 2

description:
Library name: Sample8
PTX, biol rep 1, tech rep 2

value: Batch 1


title: JNK-IN-8 + DMSO, biol rep 2, tech rep 1

description:
Library name: Sample17
JNK-IN-8 + DMSO, biol rep 2, tech rep 1


title: GNE-495 + PTX, biol rep 1, tech rep 1

description:
Library name: Sample4
GNE-495 + PTX, biol rep 1, tech rep 1


title: GNE-495 + PTX, biol rep 2, tech rep 1

description:
Library name: Sample16
GNE-495 + PTX, biol rep 2, tech rep 1


title: GNE-495 + DMSO, biol rep 2, tech rep 2

description:
Library name: Sample21
GNE-495 + DMSO, biol rep 2, tech rep 2


title: GNE-495 + DMSO, biol rep 1, tech rep 1

description:
Library name: Sample3
GNE-495 + DMSO, biol rep 1, tech rep 1


title: JNK-IN-8 + PTX, biol rep 1, tech rep 2

description:
Library name: Sample12
JNK-IN-8 + PTX, biol rep 1, tech rep 2


title: DMSO, biol rep 1, tech rep 1

description:
Library name: Sample1
DMSO, biol rep 1, tech rep 1


title: PTX, biol rep 2, tech rep 1

description:
Library name: Sample14
PTX, biol rep 2, tech rep 1


title: PTX, biol rep 1, tech rep 1

description:
Library name: Sample2
PTX, biol rep 1, tech rep 1


title: GNE-495 + PTX, biol rep 1, tech rep 2

description:
Library name: Sample10
GNE-495 + PTX, biol rep 1, tech rep 2


title: GNE-495 + DMSO, biol rep 1, tech rep 2

description:
Library name: Sample9
GNE-495 + DMSO, biol rep 1, tech rep 2


title: JNK-IN-8 + PTX, biol rep 1, tech rep 1

description:
Library name: Sample6
JNK-IN-8 + PTX, biol rep 1, tech rep 1


title: DMSO, biol rep 1, tech rep 2

description:
Library name: Sample7
DMSO, biol rep 1, tech rep 2


title: JNK-IN-8 + DMSO, biol rep 1, tech rep 1

description:
Library name: Sample5
JNK-IN-8 + DMSO, biol rep 1, tech rep 1


title: JNK-IN-8 + DMSO, biol rep 1, tech rep 2

description:
Library name: Sample11
JNK-IN-8 + DMSO, biol rep 1, tech rep 2


title: JNK-IN-8 + PTX, biol rep 2, tech rep 1

description:
Library name: Sample18
JNK-IN-8 + PTX, biol rep 2, tech rep 1


title: NC-2

first: Ruizhe

last: He

address: No. 639, Zhizaoju Road

institute: Shanghai Jiao Tong University

description:
Library name: Sample6
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: NC2

data_processing:
For the animals wounds tissue, raw reads were firstly processed using fastp (v0.22.0) and the low  quality reads were removed to obtain the clean reads. The clean reads were mapped to the  reference genome using HISAT2 (v2.1.0). FPKM of each gene was calculated and the read  counts of each gene were obtained by featureCounts. PCA analysis were performed using R  (v 3.2.0) to evaluate the biological duplication of samples.                                                                     For the cell lines, the raw data was handled by Skewer and data quality was checked by FastQC (v0.11.2). Clean reads were aligned to the referance genome using STAR(2.5.3a). The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using StringTie (v1.3.1c). Differentially expression genes(DEGs) were determined by DEGseq2(v1.16.1).
Assembly: GRCh38 / mRatBN7.2
Supplementary files format and content: txt files include FPKM values for each sample

source_name: Skin wound margin tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the  manufacturer’s protocol.
For the animals wounds tissue, the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OBiO Technology Corp., Ltd. (Shanghai, China). Then, the libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end  reads were generated.                                                                                For the cell lines, libraries were constructed using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China), and sequencing was carried out using the Illumina NovaSeq X Plus instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: Skin wound margin tissue

value: negative control


title: L-4

description:
Library name: Sample4
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: L4

value: L-chirality hydroge


title: NC-1

description:
Library name: Sample5
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: NC1


title: L-3

description:
Library name: Sample3
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: L3


title: NC-4

description:
Library name: Sample8
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: NC4


title: L-2

description:
Library name: Sample2
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: L2


title: L-1

description:
Library name: Sample1
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: L1


title: PIM_174_7

city: Saint-Paul-lez-Durance

first: Thien-Phong

last: Vu Manh

address: CEA Cadarache, Zone Cité des Énergies BIAM

department: BIAM

institute: CNRS

description: Library name: Sample 47

data_processing:
Sample raw reads were mapped to an indexed swine reference genome (Ensembl Sscrofa11.1) and transcript abundances were quantified using Kallisto (v0.46.2). Quality of the reads as well as the results of Kallisto mapping were assessed using fastqc and multiqc. Data pre-processing and analysis were performed using R (v4.4.2), all samples together and also separately for the PAM and the PIM samples. Gene annotation was retrieved using the BiomaRt package (2.62.1 with Ensembl genes v110). After TMM normalization, hierarchical clustering as well as principal component analyses revealed a dominant batch effect linked to animals or harvesting days. This batch effect was then corrected using the ComBat-seq package applied to raw transcript counts .
Assembly: Ensembl Sscrofa11.1
Supplementary files format and content: ComBat_norm_all_samples.csv: Tab-delimited .csv file includes ComBat corrected normalized data for each sample
Supplementary files format and content: log2_norm_ComBat_PAM_data.csv: Tab-delimited .csv file includes ComBat corrected log2 normalized data for PAM samples
Supplementary files format and content: log2_norm_ComBat_PIM_data.csv: Tab-delimited .csv file includes ComBat corrected log2 normalized data for PIM samples

organism: Sus scrofa

source_name: lung parenchyma

extract_protocol:
PAM were sorted from BAL samples and PIM, cDC and moDC were sorted from PAR samples. After sorting, approximately 300,000 PAM and 100,000 PIM were collected for each condition.A range between 63,000 and 100,000 were collected for moDC and cDC.  Total RNA was obtained from 63,000-100,000 sorted PAM, PIM, moDC, cDC of four pigs (two females and two males) using the PicoPure RNA Isolation Kit (Thermo Fisher, KIT0204) following manufacturer’s instructions. RNA quantity was determined using a Nanodrop 1000 (Thermo Fisher) and an Agilent Bioanalyzer (Agilent), with RIN values ranging from 7.1-9.6 and concentrations ranging from 0.11-21.61 ng/uL.
RNA-seq libraries were generated from 1ng of total RNA per sample, using a NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs) following the manufacturer’s instructions. Amplified cDNA quality and quantity were assessed using an Agilent Technologies 2200 TapeStation with high sensitivity D5000 tape. For library preparation, 2ng of amplified cDNA per sample were used. Library quality was assessed using an Agilent Technologies 2200 TapeStation with D1000 tape. Libraries were quantified by RT-qPCR using a NGS Library Quantification kit (Takara Bio) following the manufacturer’s instructions. A total of 47 cDNA libraries were diluted to 10 nM, pooled, and submitted to Novogene for 150-bp paired-end sequencing on a NovaSeq 6000 S4 lane (Illumina).

treatment_protocol: Lung bronchoalveolar lavage (BAL) and parenchyma (PAR) samples were isolated from two male and two female animals between 8-12 weeks of age were used. For each pig, thirty million enriched mononuclear pahgocytes (MNP) from both BAL and PAR were infected with NC134 and NC174 at MOI=1 or left uninfected in 50 ml falcon tubes for 12h. Infections were synchronized and after 12h cells were washed and stained with a five-color flow cytometry staining to sort AM, PIM, monocyte derived dendritic cells (moDC) and classical DC (cDC),

value: lung parenchyma

value: pulmonary intravascular macrophage

value: WT

tag: time

value: F


title: PIM_174_6

description: Library name: Sample 46

value: M


title: PIM_134_3

description: Library name: Sample 40


title: PIM_174_3

description: Library name: Sample 44


title: PIM_Mock_6

description: Library name: Sample 38

value: Mock


title: PIM_134_6

description: Library name: Sample 42


title: PAM_174_4

description: Library name: Sample 33

source_name: broncho alveolar lavage

value: broncho alveolar lavage

value: porcine alveolar macrophage


title: PAM_174_6

description: Library name: Sample 34


title: PIM_174_4

description: Library name: Sample 45


title: PIM_134_4

description: Library name: Sample 41


title: PAM_174_3

description: Library name: Sample 32


title: PAM_134_7

description: Library name: Sample 31


title: PAM_134_6

description: Library name: Sample 30


title: PAM_174_7

description: Library name: Sample 35


title: PIM_Mock_4

description: Library name: Sample 37


title: NC-3

description:
Library name: Sample7
gene_fpkm-Rat tissue.txt
column name in gene_fpkm-Rat tissue.txt: NC3


title: PIM_Mock_3

description: Library name: Sample 36


title: moDC_174_7

description: Library name: Sample 23

value: monocyte-derived DC


title: PAM_Mock_3

description: Library name: Sample 24


title: moDC_174_4

description: Library name: Sample 21


title: PAM_134_4

description: Library name: Sample 29


title: PAM_134_3

description: Library name: Sample 28


title: PAM_Mock_6

description: Library name: Sample 26


title: PAM_Mock_4

description: Library name: Sample 25


title: PIM_Mock_7

description: Library name: Sample 39


title: PAM_Mock_7

description: Library name: Sample 27


title: moDC_134_7

description: Library name: Sample 19


title: moDC_134_4

description: Library name: Sample 17


title: moDC_134_6

description: Library name: Sample 18


title: moDC_134_3

description: Library name: Sample 16


title: moDC_Mock_3

description: Library name: Sample 12


title: moDC_Mock_7

description: Library name: Sample 15


title: moDC_Mock_6

description: Library name: Sample 14


title: cDC_134_7

description: Library name: Sample 8

value: classical DC


title: PIM_134_7

description: Library name: Sample 43


title: cDC_174_4

description: Library name: Sample 10


title: cDC_Mock_7

description: Library name: Sample 4


title: cDC_174_6

description: Library name: Sample 11


title: cDC_Mock_3

description: Library name: Sample 1


title: moDC_Mock_4

description: Library name: Sample 13


title: cDC_134_4

description: Library name: Sample 6


title: cDC_174_3

description: Library name: Sample 9


title: DKO_ES_RNA_D6-BMP4_Rep2

first: Robin

last: Rondon

address: 15 rue Hélène Brion

institute: Institut Jacques Monod / CNRS UMR7592 / Universite Paris Cite

description: Library name: Sample 213

data_processing:
ATAC:Reads in raw files were pre trimmed to 36bp using Trimmomatic (Bolger et al., 2014) (v0.39)
ATAC/CUT&Tag data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.87) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Tag using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
RNA-Seq:PCR duplicate removal, trimming, and read alignement on mm10 genome was performed by BGI. Processed bigwig files were generated from BAM files using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
Assembly: mm10
Supplementary files format and content: Bigwig format. ATAC-Seq-CUT&Tag-RNA-Seq: CPM-normalized counts.

extract_protocol:
Total RNA was extracted from the cells with NucleoSpin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions.
Stranded mRNA libraries were generated by BGI, followed by paired-end 100 bp sequencing on a DBNSEQ-G400.
All information is included as columns in the SAMPLES section above
All information is included as columns in the SAMPLES section above

value: ES cell

value: DKO

value: neuronal differentiation - BMP4


title: cDC_134_6

description: Library name: Sample 7


title: cDC_Mock_6

description: Library name: Sample 3


title: CRPR2

city: Houston

first: Jinho

last: Jang

address: 1755 Wyndale Street

institute: MD Anderson Cancer Center

hyb_protocol: Followed Xenium In Situ Gene Expression protocol from the manufacturer (CG000582)

scan_protocol: Followed Xenium Analyzer User Guide (CCG000584)

data_processing: Data were processed with the Xenium Analyzer (10x Genomics) and imported into R for further processing using Seurat (v4.4.0), including quality control, normalization, and object construction.

label: Xenium Mouse Probe Set

source_name: Small Cell Lung Cancer

label_protocol: Followed Xenium In Situ for FFPE - Tissue Preparation Guide from the manufacturer (CG000578)

growth_protocol: C57BL/6 mice were purchased from the Jackson Laboratory (Maine, USA). Compound transgenic mice Rb1lox/lox Trp53lox/lox Rbl2lox/lox (RPR2) mice have been previously described. For SCLC tumor induction, the lungs of 10-week-old mice were infected with adenoviral Cre via intratracheal instillation as previously described. Multiple cohorts of independent litters were analyzed to control for background effects, and both male and female mice were used. Ad-Cracd-Cre particles were produced in the Vector Development Laboratory at Baylor College of Medicine. Mice were euthanized by CO2 asphyxiation followed by cervical dislocation at the indicated time

extract_protocol: Mouse SCLC and allograft tumors were decontaminated under the dissecting microscope by removing any normal and connective tissues. Then, tumors were transferred to a dry dish and minced into pieces with blades. The tissue was digested in Leibovitz’s medium (Invitrogen) with 2 mg/mL Collagenase Type I (Worthington), 2 mg/mL Elastase (Worthington), and 2 mg/mL DNase I (Worthington) at 37 °C for 45 min. The tissue was triturated with a pipet every 15 min of digestion until homogenous. The digestion was stopped with FBS (Invitrogen) to a final concentration of 20%. The cells were filtered with a 70 μm cell strainer (Falcon) and spun down at 5,000 r/min for 1 min. The cell pellet was resuspended in red blood cell lysing buffer (Sigma) for 3 min, spun down at 5,000 r/min for 1 min, and washed with 1 mL ice-cold Leibovitz’s medium with 10% FBS. Cells were resuspended in 1 mL ice-cold Leibovitz’s medium with 10% FBS and filtered with a cell strainer (20 μm). Dead cells were removed with a Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Live cells were collected for 10´ Genomics library preparation.

value: Small Cell Lung Cancer

tag: model

value: GEMM (Cracd, Rb1, Trp53, and Rbl2 KO)


title: moDC_174_6

description: Library name: Sample 22


title: P3--_ES_RNA_D6-BMP4_Rep2

description: Library name: Sample 210


title: moDC_174_3

description: Library name: Sample 20


title: RPR2

value: GEMM (Rb1, Trp53, and Rbl2 KO)


title: P7--_ES_RNA_D6-BMP4_Rep3

description: Library name: Sample 208


title: P3--_ES_RNA_D6-BMP4_Rep3

description: Library name: Sample 211


title: P7--_ES_RNA_D6-BMP4_Rep2

description: Library name: Sample 207


title: DKO_ES_RNA_D6+BMP4_Rep3

description: Library name: Sample 202

value: neuronal differentiation + BMP4


title: cDC_Mock_4

description: Library name: Sample 2

value: lung parenchyma


title: cDC_134_3

description: Library name: Sample 5


title: WT_ES_RNA_D6-BMP4_Rep2

description: Library name: Sample 204


title: DKO_ES_RNA_D6+BMP4_Rep2

description: Library name: Sample 201


title: DKO_ES_RNA_D6+BMP4_Rep1

description: Library name: Sample 200


title: WT_ES_RNA_D6-BMP4_Rep3

description: Library name: Sample 205


title: P3--_ES_RNA_D6+BMP4_Rep1

description: Library name: Sample 197


title: P3--_ES_RNA_D6+BMP4_Rep3

description: Library name: Sample 199


title: P3--_ES_RNA_D6+BMP4_Rep2

description: Library name: Sample 198


title: DKO_ES_RNA_D6-BMP4_Rep3

description: Library name: Sample 214


title: P7--_ES_RNA_D6+BMP4_Rep3

description: Library name: Sample 196


title: DKO_ES_RNA_D6-BMP4_Rep1

description: Library name: Sample 212


title: P7--_ES_RNA_D6-BMP4_Rep1

description: Library name: Sample 206


title: P7--_ES_RNA_D6+BMP4_Rep1

description: Library name: Sample 194


title: P3--_ES_RNA_D6-BMP4_Rep1

description: Library name: Sample 209


title: WT_ES_RNA_D6+BMP4_Rep3

description: Library name: Sample 193


title: WT_ES_RNA_D6+BMP4_Rep2

description: Library name: Sample 192


title: WT_ES_RNA_D6+BMP4_Rep1

description: Library name: Sample 191


title: FLAG-P3_ES_FLAG_D5+BMP4_Rep2

description: Library name: Sample 184

library_source: genomic

data_processing:
ATAC:Reads in raw files were pre trimmed to 36bp using Trimmomatic (Bolger et al., 2014) (v0.39)
ATAC/CUT&Tag data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.87) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Tag using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
RNA-Seq:PCR duplicate removal, trimming, and read alignement on mm10 genome was performed by BGI. Processed bigwig files were generated from BAM files using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
Assembly: mm10
Supplementary files format and content: Bigwig format. ATAC-Seq-CUT&Tag-RNA-Seq: CPM-normalized counts.
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
We performed CUT&Tag according with the protocol described in (Kaya-Okur et al., 2020), closely following the procedure described in “Bench top CUT&Tag V.2” (S Kaya-Okur and Henikoff, 2019). We used 500 000 per sample cells per sample and the anti-FLAG (Sigma-Aldrich F3165-5MG; 1/50) for CUT&Tag on transcription factors, or 200 000 nuclei that were previously fixed and frozen following the procedure described in(Kaya-Okur et al., 2020) with anti-H3K4me2 (Abcam ab176878; 1/100), anti-H3K27me3 (Cell Signaling 9733S; 1/100) primary antibodies. The primaries antibodies were incubated overnight at 4ºC on a rotator. Samples were then incubated with a secondary anti-rabbit IgG (ABIN6923140) or anti-mouse IgG (ABIN6923141) at room temperature on a rotator. After an incubation of 1h at room temperature with a homemade purified pA-TN5 complex, the Tn5 enzyme tagmentation reaction was performed by adding a buffer containing MgCl2 to the samples and incubating for 1h at 37°C. To stop tagmentation and solubilize DNA fragments, we added 10 μL 0.5M EDTA, 3 μL 10% SDS and 2.5 μL 20 mg/mL Proteinase K to each sample and samples were incubated at 50°C for 1h. Purified DNA was obtained by phenol/chloroform extraction and precipitated with 100% ethanol and centrifugation. The DNA pellet was washed in 80% ethanol, spun down and air-dried before being resuspended in 25µl of 1mM Tris-HCl pH8.0.
Nextera primers or indexed primers were used to perform PCR. Library quality was assessed using 4200 TapeStation system (Agilent) and paired-end, 100 bp sequencing on a DBNSEQ-G400 was performed by BGI.
All information is included as columns in the SAMPLES section above
All information is included as columns in the SAMPLES section above

value: Day 5


title: FLAG-P7_ES_FLAG_D5+BMP4_Rep1

description: Library name: Sample 187


title: FLAG-P7_ES_FLAG_D5+BMP4_Rep2

description: Library name: Sample 188


title: WT_ES_RNA_D6-BMP4_Rep1

description: Library name: Sample 203

value: WT


title: FLAG-P7_ES_FLAG_D5-BMP4_Rep2

description: Library name: Sample 190


title: FLAG-P3_ES_FLAG_D5-BMP4_Rep1

description: Library name: Sample 185


title: FLAG-P3_ES_FLAG_D5-BMP4_Rep2

description: Library name: Sample 186


title: FLAG-P7_ES_FLAG_D5-BMP4_Rep1

description: Library name: Sample 189


title: WT_ES_FLAG_D5+BMP4_Rep2

description: Library name: Sample 182


title: WT_ES_FLAG_D5+BMP4_Rep1

description: Library name: Sample 181


title: DKO_ES_H3K4me2_D6+BMP4_Rep2

description: Library name: Sample 179


title: DKO_ES_H3K4me2_D6+BMP4_Rep3

description: Library name: Sample 180


title: P3--_ES_H3K4me2_D6+BMP4_Rep3

description: Library name: Sample 177


title: FLAG-P3_ES_FLAG_D5+BMP4_Rep1

description: Library name: Sample 183


title: P3--_ES_H3K4me2_D6+BMP4_Rep2

description: Library name: Sample 176


title: DKO_ES_H3K4me2_D6+BMP4_Rep1

description: Library name: Sample 178


title: P7--_ES_H3K4me2_D6+BMP4_Rep1

description: Library name: Sample 172


title: WT_ES_H3K4me2_D6+BMP4_Rep2

description: Library name: Sample 170


title: P7--_ES_H3K4me2_D6+BMP4_Rep2

description: Library name: Sample 173


title: WT_ES_H3K4me2_D6+BMP4_Rep1

description: Library name: Sample 169


title: P7--_ES_H3K4me2_D6+BMP4_Rep3

description: Library name: Sample 174


title: P3--_ES_H3K4me2_D6+BMP4_Rep1

description: Library name: Sample 175


title: DKO_ES_H3K4me2_D6-BMP4_Rep3

description: Library name: Sample 168


title: DKO_ES_H3K4me2_D6-BMP4_Rep2

description: Library name: Sample 167


title: P3--_ES_H3K4me2_D6-BMP4_Rep2

description: Library name: Sample 164


title: WT_ES_H3K4me2_D6+BMP4_Rep3

description: Library name: Sample 171


title: DKO_ES_H3K4me2_D6-BMP4_Rep1

description: Library name: Sample 166


title: P3--_ES_H3K4me2_D6-BMP4_Rep1

description: Library name: Sample 163


title: P3--_ES_H3K4me2_D6-BMP4_Rep3

description: Library name: Sample 165


title: P7--_ES_H3K4me2_D6-BMP4_Rep1

description: Library name: Sample 160


title: P7--_ES_H3K4me2_D6-BMP4_Rep2

description: Library name: Sample 161


title: WT_ES_H3K4me2_D6-BMP4_Rep1

description: Library name: Sample 157


title: WT_ES_H3K4me2_D6-BMP4_Rep2

description: Library name: Sample 158


title: DKO_ES_H3K4me2_D5-BMP4_Rep3

description: Library name: Sample 156


title: WT_ES_H3K4me2_D6-BMP4_Rep3

description: Library name: Sample 159


title: DKO_ES_H3K4me2_D5+BMP4_Rep3

description: Library name: Sample 154


title: DKO_ES_H3K4me2_D3_Rep2

description: Library name: Sample 152

value: neuronal differentiation

value: Day 3


title: DKO_ES_H3K4me2_D3_Rep3

description: Library name: Sample 155


title: DKO_ES_H3K4me2_D5+BMP4_Rep2

description: Library name: Sample 151


title: P7--_ES_RNA_D6+BMP4_Rep2

description: Library name: Sample 195


title: 9089-JF-3

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 9089-JF-3

data_processing:
“BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCh38
Supplementary files format and content: cellranger output format

source_name: skin

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722286172/support-documents/CG000331_Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_RevF.pdf

value: skin

value: skin cells

value: Les


title: 9089-JF-4

description: Library name: 9089-JF-4


title: 9089-JF-2

description: Library name: 9089-JF-2


title: DKO_ES_H3K4me2_D5+BMP4_Rep1

city: Paris

description: Library name: Sample 148


title: 9089-JF-5

description: Library name: 9089-JF-5


title: 8972-JF-2

description: Library name: 8972-JF-2


title: 9089-JF-1

description: Library name: 9089-JF-1


title: P3--_ES_H3K4me2_D5-BMP4_Rep3

description: Library name: Sample 147


title: 8972-JF-1

description: Library name: 8972-JF-1


title: P7--_ES_H3K4me2_D6-BMP4_Rep3

description: Library name: Sample 162


title: P3--_ES_H3K4me2_D3_Rep3

description: Library name: Sample 146


title: 8956-JF-4

description: Library name: 8956-JF-4

value: Nonles


title: 8956-JF-3

description: Library name: 8956-JF-3


title: P3--_ES_H3K4me2_D5+BMP4_Rep3

description: Library name: Sample 145


title: P3--_ES_H3K4me2_D3_Rep2

description: Library name: Sample 143


title: 8956-JF-2

description: Library name: 8956-JF-2


title: P3--_ES_H3K4me2_D5+BMP4_Rep2

description: Library name: Sample 142


title: 8956-JF-1

description: Library name: 8956-JF-1


title: DKO_ES_H3K4me2_D5-BMP4_Rep2

description: Library name: Sample 153


title: 8787-JF-1

description: Library name: 8787-JF-1


title: 8740-JF-4

description: Library name: 8740-JF-4


title: DKO_ES_H3K4me2_D3_Rep1

description: Library name: Sample 149


title: 8740-JF-3

description: Library name: 8740-JF-3


title: 8740-JF-2

description: Library name: 8740-JF-2


title: P7--_ES_H3K4me2_D5-BMP4_Rep3

description: Library name: Sample 138


title: P7--_ES_H3K4me2_D5+BMP4_Rep3

description: Library name: Sample 136


title: 8693-JF-5

description: Library name: 8693-JF-5


title: P7--_ES_H3K4me2_D3_Rep3

description: Library name: Sample 137


title: 8693-JF-4

description: Library name: 8693-JF-4


title: 8693-JF-3

description: Library name: 8693-JF-3


title: P7--_ES_H3K4me2_D3_Rep2

description: Library name: Sample 134


title: P3--_ES_H3K4me2_D5-BMP4_Rep2

description: Library name: Sample 144


title: P7--_ES_H3K4me2_D5-BMP4_Rep1

description: Library name: Sample 132


title: 8687-JF-4

description: Library name: 8687-JF-4

value: Control


title: 8687-JF-3

description: Library name: 8687-JF-3


title: P7--_ES_H3K4me2_D3_Rep1

description: Library name: Sample 131

value: ES cell


title: 8787-JF-2

description: Library name: 8787-JF-2


title: 8687-JF-2

description: Library name: 8687-JF-2


title: WT_ES_H3K4me2_D5-BMP4_Rep3

description: Library name: Sample 129


title: P3--_ES_H3K4me2_D5+BMP4_Rep1

description: Library name: Sample 139


title: WT_ES_H3K4me2_D3_Rep3

description: Library name: Sample 128


title: 8557-JF-6

description: Library name: 8557-JF-6


title: P3--_ES_H3K4me2_D5-BMP4_Rep1

description: Library name: Sample 141


title: P7--_ES_H3K4me2_D5-BMP4_Rep2

description: Library name: Sample 135


title: WT_ES_H3K4me2_D5+BMP4_Rep3

description: Library name: Sample 127


title: 8687-JF-1

description: Library name: 8687-JF-1


title: WT_ES_H3K4me2_D5-BMP4_Rep2

description: Library name: Sample 126


title: 8557-JF-3

description: Library name: 8557-JF-3


title: 8557-JF-5

description: Library name: 8557-JF-5


title: 8557-JF-2

description: Library name: 8557-JF-2


title: WT_ES_H3K4me2_D5+BMP4_Rep2

description: Library name: Sample 124


title: 8374-JF-3

description: Library name: 8374-JF-3


title: WT_ES_H3K4me2_D5-BMP4_Rep1

description: Library name: Sample 123


title: 8557-JF-1

description: Library name: 8557-JF-1


title: WT_ES_H3K4me2_D3_Rep2

description: Library name: Sample 125


title: P7--_ES_H3K4me2_D5+BMP4_Rep2

description: Library name: Sample 133


title: DKO_ES_H3K4me2_D5-BMP4_Rep1

description: Library name: Sample 150

value: DKO


title: P3--_ES_H3K4me2_D3_Rep1

description: Library name: Sample 140


title: 8374-JF-2

description: Library name: 8374-JF-2


title: 8374-JF-1

description: Library name: 8374-JF-1


title: 8557-JF-4

description: Library name: 8557-JF-4


title: DKO_ES_H3K27me3_D3_Rep3

description: Library name: Sample 120


title: P7--_ES_H3K4me2_D5+BMP4_Rep1

description: Library name: Sample 130


title: DKO_ES_H3K27me3_D3_Rep2

description: Library name: Sample 119


title: 8272-JF-3

description: Library name: 8272-JF-3


title: 8740-JF-1

description: Library name: 8740-JF-1


title: 8272-JF-1

description: Library name: 8272-JF-1


title: 8205-JF-6

description: Library name: 8205-JF-6


title: WT_ES_H3K4me2_D3_Rep1

description: Library name: Sample 122


title: P3--_ES_H3K27me3_D3_Rep3

description: Library name: Sample 117


title: 8205-JF-5

description: Library name: 8205-JF-5


title: 8205-JF-4

description: Library name: 8205-JF-4


title: P3--_ES_H3K27me3_D3_Rep1

description: Library name: Sample 115


title: 8205-JF-2

description: Library name: 8205-JF-2


title: P7--_ES_H3K27me3_D3_Rep3

description: Library name: Sample 114


title: 8205-JF-3

description: Library name: 8205-JF-3


title: WT_ES_H3K4me2_D5+BMP4_Rep1

description: Library name: Sample 121


title: auricular chrondroytes, cultured in HATG-Alg bioink, 9 weeks, rep3

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: HATGA1g_9W_rep3

data_processing:
NovaSeq 6000: Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing.
Reads were aligned to the reference genome using the STAR (version 2.7.3a) with parameters --outFilterType BySJout,  --outFilterMultimapNmax 20, --alignSJoverhangMin = 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --alignIntronMin 20,  --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMmultNmax 1, --outSAMtype BAM SortedByCoordinate and --outSAMunmapped Within KeepPairs
Alignments overlapping genes from the TxDb.Hsapiens.UCSC.hg38.knownGene Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.TxDb.Hsapiens.UCSC.hg38.knownGene , version 3.15.0) were quantified using the qCount function with parameter orientation = “opposite” from the QuasR Bioconductor package (version 1.34.0)
Assembly: GRCh38/hg38
Supplementary files format and content: Comma-seperated text file with gene annotation (ENTREZID, number of exonic bases, ENSEMBL gene ID, gene symbol) and raw counts for each gene and sample.

source_name: auricular cartilage graft

growth_protocol: Primary human auricular chondrocytes (hAUR) were expanded by seeding them at a density of 3'000 cells cm-2 to passage 3. Two protocols for the expansion and graft culture were used:  1) HATG protocol: hAUR were expanded in the presence of  DMEM containing 10% v/v FBS and 10 µg mL-1 gentamicin (basal medium). hAUR at passage 3 were combined with the HATG bioink (1.5% HATG, 1.5% HA, 2.0% sNAG nanofibrils) and cultured in chondrogenic medium consisting of DMEM 31966, 50 µg mL–1 L-ascorbate-2-phosphate, 40 µg mL–1 L-proline, 10 µg mL–1 gentamycin, 1% ITS+ (ITS+ Premix Universal Culture Supplement, Corning) and 10 ng mL-1 TGF-b3 for 3 and 9 weeks.  2) HATG-Alg protocol: hAUR were expanded in the presence of  DMEM containing 10% v/v FBS, 10 µg mL-1 gentamicin, 10 ng mL-1 FGF-2 and 10 ng mL-1 TGF-b3. hAUR at passage 3 were combined with the HATG-Alg bioink (0.5% HATG, 0.25% Alg, 1.5% HA, 2.0% sNAG nanofibrils) and cultured in chondrogenic medium consisting of DMEM 31966, 50 µg mL–1 L-ascorbate-2-phosphate, 40 µg mL–1 L-proline, 10 µg mL–1 gentamycin, 1% ITS+ (ITS+ Premix Universal Culture Supplement, Corning) and 10 ng mL-1 TGF-b3 for 3 and 9 weeks.

extract_protocol:
HATG and HATG-Alg constructs were snap frozen in liquid nitrogen and subjected to cryopulverization. The powder was collected in 1.4 mL TRIzol Reagent (Invitrogen, 15596026), and RNA was isolated according to the manufacturer’s specifications. RNA concentration was determined using the Qubit RNA High Sensitivity (HS) Kit (Invitrogen, Q32852). RNA quality and integrity were assessed using a 2100 Bioanalyzer (Agilent Technologies) with the RNA 6000 Pico Kit (Agilent, 5067-1514), and only samples with an RNA Integrity Number (RIN) > 9 were used for library preparation. RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, RS-122-2202) with 100 ng of total RNA per sample. Libraries were uniquely dual-indexed using the TruSeq UDI system (Illumina) and sequenced on a NovaSeq 6000 with 50 bp paired-end to a depth of ~ 20 million fragments per sample.
Illumina TruSeq Stranded Total RNA Library Prep Kit (Cat. No. RS-122-2202)

value: auricular cartilage graft

value: auricular chondrocytes

value: HATG-Alg bioink

value: 9 weeks


title: auricular chrondroytes, cultured in HATG-Alg bioink, 9 weeks, rep2

description: Library name: HATGA1g_9W_rep2


title: 8205-JF-1

description: Library name: 8205-JF-1


title: WT_ES_H3K27me3_D3_Rep3

description: Library name: Sample 111


title: P7--_ES_H3K27me3_D3_Rep1

description: Library name: Sample 112


title: WT_ES_H3K27me3_D3_Rep2

description: Library name: Sample 110


title: WT_ES_H3K27me3_D3_Rep1

description: Library name: Sample 109


title: auricular chrondroytes, cultured in HATG-Alg bioink, 9 weeks, rep1

description: Library name: HATGA1g_9W_rep1


title: P7--_ES_H3K27me3_D3_Rep2

description: Library name: Sample 113


title: auricular chrondroytes, cultured in HATG bioink,9 weeks, rep3

description: Library name: HATG_9W_rep3

value: HATG bioink


title: DKO_ES_H3K27me3_D3_Rep1

description: Library name: Sample 118


title: DKO_ES_H3K27me3_D6-BMP4_Rep3

description: Library name: Sample 108

value: neuronal differentiation - BMP4


title: auricular chrondroytes, cultured in HATG bioink, 9 weeks, rep2

description: Library name: HATG_9W_rep2


title: auricular chrondroytes, cultured in HATG bioink, 9 weeks, rep1

description: Library name: HATG_9W_rep1


title: DKO_ES_H3K27me3_D6-BMP4_Rep2

description: Library name: Sample 107


title: DKO_ES_H3K27me3_D6-BMP4_Rep1

description: Library name: Sample 106


title: P3--_ES_H3K27me3_D3_Rep2

description: Library name: Sample 116


title: auricular chrondroytes, cultured in HATG-Alg bioink, 3 weeks, rep3

description: Library name: HATGA1g_3W_rep3

value: 3 weeks


title: P3--_ES_H3K27me3_D6-BMP4_Rep3

description: Library name: Sample 105


title: auricular chrondroytes, cultured in HATG-Alg bioink, 3 weeks, rep2

description: Library name: HATGA1g_3W_rep2


title: Adult mouse liver, F3-TBT, replicate6, CTCF, ChIP

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: TBT.normalized.bw.gz

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus. FASTQ reads (150 + 150 paired-end) were generated from the BCL files using Illumina bcl2fastq for NovaSeq.
ChIP-seq FASTQ reads were subjected to trimGalore with -q 20 --trim1 --paired options.
ChIP-seq FASTQ reads were aligned to the mGRC38/mm10 mouse genome reference sequence using STAR with options --alignIntronMax 1 --alignEndsType EndToEnd for suppression of splicing-aware mapping.
Uniquely mapped reads were extracted from BAM files using Sambamba markdup with -r option.
Normalized bigWig files were generated from merged BAM files for exposure (DMSO or TBT, 6 BAM files in each group) using deepTools bamCoverage with options --ignoreForNormalization chrM chrX --binSize 10 --effectiveGenomeSize 2652783500 --normalizeUsing RPGC --outFileFormat bigwig.
Assembly: mGRC38/mm10
Supplementary files format and content: bigWig files containing normalized ChIP-seq coverages for DMSO and TBT treatment groups.

source_name: F3 adult liver

extract_protocol:
Liver tissue (50 mg) were dispersed into single cell suspension and fixed in 1% paraformaldehyde for 10 minutes. Nuclei were isolated using a detergent mixture (0.5% Nonidet P-40, 0.25% Triton X-100) followed by chromatin extraction by sonication. The fragmented chromatin specimens were subjected to anti-CTCF immunoprecipitation, and crosslinking was reversed by by heat, and released genomic DNA was purified using the QIAquick PCR cleanup kit.
ChIP-seq libraries were prepared from 30 ng ChIP-enriched genomic DNA using New England Biolabs NEXNext Ultra II Kit (E7645). Libraries were indexed using the NEBNext Multiplex Oligos for Illumina KIT (E7600), amplified 10 cycles, and purified using AMPure beads. The peak size of the libraries were determined to be 380 bp using Agilent Tapestation (HSD1000 tape).

value: F3 adult liver

value: male

tag: chip antibody

value: anti-CTCF (abcam ab128873)

value: F0 exposure to TBT


title: auricular chrondroytes, cultured in HATG-Alg bioink, 3 weeks, rep1

description: Library name: HATGA1g_3W_rep1


title: P3--_ES_H3K27me3_D6-BMP4_Rep2

description: Library name: Sample 104


title: P7--_ES_H3K27me3_D6-BMP4_Rep2

description: Library name: Sample 101


title: P3--_ES_H3K27me3_D6-BMP4_Rep1

description: Library name: Sample 103


title: P7--_ES_H3K27me3_D6-BMP4_Rep3

description: Library name: Sample 102


title: auricular chrondroytes, cultured in HATG bioink, 3 weeks, rep3

description: Library name: HATG_3W_rep3


title: Adult mouse liver, F3-TBT, replicate4, CTCF, ChIP

description: TBT.normalized.bw.gz


title: P7--_ES_H3K27me3_D6-BMP4_Rep1

description: Library name: Sample 100


title: WT_ES_H3K27me3_D6-BMP4_Rep3

description: Library name: Sample 99

value: WT


title: WT_ES_H3K27me3_D6-BMP4_Rep1

description: Library name: Sample 97


title: auricular chrondroytes, cultured in HATG bioink, 3 weeks, rep2

description: Library name: HATG_3W_rep2


title: Adult mouse liver, F3-TBT, replicate3, CTCF, ChIP

description: TBT.normalized.bw.gz


title: DKO_ES_H3K27me3_D6+BMP4_Rep3

description: Library name: Sample 96

value: neuronal differentiation + BMP4


title: POINT-seq dTAG-U170K plus dTAG rep2

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Insitute

country: United Kingdom

institute: University of Exeter

description: Library name: Sample 4

data_processing:
Adapters removed from sequencing reads using Trim Galore 0.6.5dev (Cutadapt v2.9)
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings)
Removal of unmapped and multimapped reads (MAPQ <30) using SAMTools v.1.13
Merge biological replicates using BamTools v2.5.1
Split reads by strand using SAMTools v1.13
Bigwig files were generated from split strand BAM files using the bamCoverage of Deeptools v3.5.0
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged replicates

molecule: nuclear RNA

growth_protocol: HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
RNA for POINT-Seq was extracted using a protocol designed by Nojima et al., 2021.
RNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: colorectal carcinoma

value: plus dTAGv-1


title: DKO_ES_H3K27me3_D6+BMP4_Rep1

description: Library name: Sample 94

value: ES cell


title: DKO_ES_H3K27me3_D6+BMP4_Rep2

description: Library name: Sample 95

value: DKO


title: POINT-seq dTAG-U170K plus dTAG rep1

description: Library name: Sample 3


title: P3--_ES_H3K27me3_D6+BMP4_Rep3

description: Library name: Sample 93


title: P3--_ES_H3K27me3_D6+BMP4_Rep2

description: Library name: Sample 92


title: POINT-seq dTAG-U170K minus dTAG rep2

description: Library name: Sample 2

value: minus dTAGv-1


title: P3--_ES_H3K27me3_D6+BMP4_Rep1

description: Library name: Sample 91


title: Adult mouse liver, F3-TBT, replicate1, CTCF, ChIP

description: TBT.normalized.bw.gz


title: Adult mouse liver, F3-DMSO, replicate6, CTCF, ChIP

description: DMSO.normalized.bw.gz

value: F0 exposure to DMSO


title: P7--_ES_H3K27me3_D6+BMP4_Rep3

description: Library name: Sample 90


title: POINT-seq dTAG-U170K minus dTAG rep1

description: Library name: Sample 1


title: P7--_ES_H3K27me3_D6+BMP4_Rep2

description: Library name: Sample 89


title: Adult mouse liver, F3-DMSO, replicate5, CTCF, ChIP

description: DMSO.normalized.bw.gz


title: P7--_ES_H3K27me3_D6+BMP4_Rep1

description: Library name: Sample 88


title: Adult mouse liver, F3-TBT, replicate5, CTCF, ChIP

description: TBT.normalized.bw.gz


title: Adult mouse liver, F3-DMSO, replicate4, CTCF, ChIP

description: DMSO.normalized.bw.gz


title: WT_ES_H3K27me3_D6+BMP4_Rep3

description: Library name: Sample 87


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus dTAG U1 AMO rep2

description: Library name: Sample 8

extract_protocol:
Chromatin-associated RNA was extracted using Trizol reagent from fractionated nuclei
DNA-free & rRNA-free RNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: U1 AMO, plus dTAGv-1


title: WT_ES_H3K27me3_D6-BMP4_Rep2

description: Library name: Sample 98


title: WT_ES_H3K27me3_D6+BMP4_Rep2

description: Library name: Sample 86


title: auricular chrondroytes, cultured in HATG bioink, 3 weeks, rep1

description: Library name: HATG_3W_rep1

value: auricular cartilage graft

value: auricular chondrocytes


title: Adult mouse liver, F3-TBT, replicate2, CTCF, ChIP

description: TBT.normalized.bw.gz


title: WT_ES_H3K27me3_D6+BMP4_Rep1

description: Library name: Sample 85


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus dTAG U1 AMO rep1

description: Library name: Sample 7


title: DKO_ES_H3K27me3_D5-BMP4_Rep3

description: Library name: Sample 84

value: neuronal differentiation - BMP4

value: Day 5


title: Adult mouse liver, F3-DMSO, replicate3, CTCF, ChIP

description: DMSO.normalized.bw.gz

value: F3 adult liver


title: Adult mouse liver, F3-DMSO, replicate2, CTCF, ChIP

description: DMSO.normalized.bw.gz

value: male


title: DKO_ES_H3K27me3_D5+BMP4_Rep3

description: Library name: Sample 83


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus dTAG U1 AMO rep2

description: Library name: Sample 6

value: U1 AMO, minus dTAGv-1


title: Adult mouse liver, F3-DMSO, replicate1, CTCF, ChIP

description: DMSO.normalized.bw.gz

value: anti-CTCF (abcam ab128873)


title: DKO_ES_H3K27me3_D5+BMP4_Rep2

description: Library name: Sample 81


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus dTAG U1 AMO rep1

description: Library name: Sample 5


title: DKO_ES_H3K27me3_D5-BMP4_Rep1

description: Library name: Sample 80


title: DKO_ES_H3K27me3_D5+BMP4_Rep1

description: Library name: Sample 79


title: KP

data_processing:
Read alignment and data processing were performed using bowtie2, picard, and samtools.
Assembly: mm10 mouse reference genome.
Supplementary files format and content: Bigwig files containing read coverage information.
Library strategy: CUT&Run

source_name: KP

extract_protocol:
Library preparation for CUT&RUN was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (M0544S), incorporating Illumina barcodes with 12 cycles of amplification.
The libraries were sequenced on the Illumina NovaSeq platform at Novogene USA, with a read length of 150 base pairs for paired-end reads, and a sequencing depth of 30 million read pairs.

value: KP

value: Cracd^WT Kras^G12D Trp53^fl/fl


title: CKP

source_name: CKP

value: CKP

value: Cracd^KO Kras^G12D Trp53^fl/fl


title: P3--_ES_H3K27me3_D5-BMP4_Rep3

description: Library name: Sample 78

value: ES cell


title: P3--_ES_H3K27me3_D5+BMP4_Rep3

description: Library name: Sample 77

value: neuronal differentiation + BMP4


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus dTAG control AMO rep2

description: Library name: Sample 4

value: colorectal carcinoma

value: control AMO, plus dTAGv-1