title: dual RNA-seq, uLCFA gavage, 2, sample number 9

city: Geneva

first: Aleksander

last: Czauderna

address: Rue Michel-Servet 1

department: PATIM

country: Switzerland

institute: University of Geneva

description:
Library name: AC105S9_OALA
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis

data_processing:
Raw sequence reads were filtered using Trimmomatic (Bolger et al., 2014), sequentially aligned to the mouse genome to remove mouse-derived sequences and then to each of the 4 CBBP genomes using bowtie2 (Langmead and Salzberg, 2012). BAM files obtained were analyzed using R. Reads were assigned to genes using featureCounts (Liao et al., 2014), and analyzed using ‘DeSeq2’ (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: processed files are counts tables of the host (mouse) and microbes (4mix members) (.txt)

organism:
Mus musculus
mouse gut metagenome

source_name: Mus musculus and microbial consortium, mainly B. thetaiotaomicron, P. distasonis, B. producta, E. bolteae

extract_protocol:
microbial DNA for 16S-seq was extracted with PureLink Microbiome DNA kit (Invitrogen), microbial RNA extracted with RNeasy PowerMIcrobiome kit (Qiagen), host RNA extracted with trizol (Invitrogen)
16S-seq - custom library preparation protocol, dual RNA-seq libraries were prepared using Illumina Stranded Total RNA Prep kit with the Ribo-zero Plus, and they were sequenced using the Illumina NovaSeq 6000 with single read 100bp.

treatment_protocol: ip injection (Flagellin) or oral gavage (oleic acid, linoleic acid)

value: cecal tissue and cecal pouch contents

value: mammalian and bacterial cells

value: uLCFAs


title: male offspring / benzene exposed mother library#14

status: Public on Jul 03 2025

type: SRA

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

country: USA

institute: Van Andel Institute

library_source: transcriptomic

data_processing:
Adapter and low-quality sequences were trimmed from the reads using Trim Galore v0.6.0 (Krueger et al., 2021) with the ‘--paired’ parameter.
Trimmed reads were aligned to the mm10 genome with GENCODE M24 gene annotations (Frankish et al., 2019), using STAR v2.7.8a (Dobin et al., 2013) with the parameters ‘--twopassMode Basic’, and ‘--quantMode GeneCounts’ to generate the read counts per gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited files containing per-gene read counts as calculated by STAR.

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
Prior to RNA extraction, tissue samples were stored in RNAlater at -80°C. 1 mL TRIzol Reagent (Life Technologies, 15596026) was added per 50-100 mg of tissue in screw cap tubes containing 3 mm Zirconium Beads (OPS Diagnostics, BAWZ 3000-300-23). Tissue was homogenized using the FastPrep-24 system on high for 30 seconds and visually observed for tissue disruption, performing additional homogenizations as needed. 200 ul chloroform (Sigma-Aldrich, 319988) was added and samples were centrifuged at 12,000 x g for 15 minutes at 4°C. The upper aqueous phase was transferred to new Eppendorf tubes followed by RNA precipitation using 500 ul ice cold isopropanol (Sigma-Aldrich, 190764) and 2 ul GlycoBlue (ThermoFisher, AM9516) for pellet visualization. Samples were then centrifuged at 12,000 x g for 15 minutes at 4°C. Supernatant was removed and discarded. The samples were washed twice with 75% ethanol (Fisher Scientific, 111000200), using a 5-minute 7,500 x g centrifugation each round for pellet collection. The pellet was air dried for 10 minutes and resuspended in 20 ul RNase-free water (Life Technologies, AM9938). Samples were incubated at 60°C for 5 minutes, then stored at -80°C.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA). Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA)). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 30M raw paired-reads per transcriptome.

tag: tissue

value: hypothalamus

tag: genotype

tag: litter

tag: Sex

value: Male

tag: treatment

value: Benzene


title: female offspring / benzene exposed mother library#17

value: Female


title: dual RNA-seq, uLCFA gavage, 1, sample number 8

description:
Library name: AC105S8_OALA
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis

tag: cell type


title: dual RNA-seq, PBS gavage, 2, sample number 2

description:
Library name: AC105S2_PBS
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis

value: PBS


title: female offspring / control mother library #29

value: Control


title: dual RNA-seq, PBS gavage, 1, sample number 1

description:
Library name: AC105S1_PBS
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, Flagellin ip, 2, sample number 8

description:
Library name: S8_FLAG
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis

value: Flagellin


title: dual RNA-seq, Flagellin ip, 3, sample number 9

description:
Library name: S9_FLAG
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, Flagellin ip, 4, sample  number 10

description:
Library name: S10_FLAG
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, PBS ip, 3, sample number 16

description:
Library name: S16_PBS
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, Flagellin ip, 1, sample number 7

description:
Library name: S7_FLAG
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, PBS ip, 4, sample number 17

description:
Library name: S17_PBS
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, PBS ip, 2, sample number 15

description:
Library name: S15_PBS
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: dual RNA-seq, PBS ip, 1, sample number 14

description:
Library name: S14_PBS
BP - B. producta, EB - E. bolteae, BT - B. thetaiotaomicron, PD - P. distasonis


title: ChIP for H3K4me3 in RpA70-EGFP (wt) embryos staged at NC14 replicate ID= rep2

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description:
Library name: wt_ChIP-H3K4me3_NC14_rep2
H3K4me3 ChIP at NC14

library_source: genomic

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates
Duplicate-marked mapped reads were imported into R, discarding duplicates, and keeping only reads with map-quality scores of 10 or greater. Wiggle files were generated by calculating the average number of mapped reads within 10 bp windows, and normalizing to millions of reads in the overall sample. Peaks were called using MACS2. Broad polycomb domains were called using STAN.
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: wiggle files for merged replicates are provided . Data represents counts per million normalized average reads per 10 bp genomic bin
Supplementary files format and content: Coverage files for merged replicates for all ChIP experiments are provided in bigwig format. Peak calls for Cg, GAF, Pho, and E(z) are provided in .bed format. Broad polycomb domains are provided in .bed format.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
For ChIP experiments, embryos were crosslinked (Heptane/PBS/formaldehyde, 15 minutes) and sorted by stage prior to homogenization in RIPA buffer and sonication. Sonicated chromatin samples were subjected to immunoprecipiation with the indicated antibodies.
ChIP libraries: following IP but prior to washes, antibody-chromatin complexes were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 40 minutes at 37 degrees C. Following tagmentation, beads were washed and subjected to PCR with barcoding primers (Buenrostro, 2013).

value: embryo

tag: chip antibody

tag: developmental stage


title: ChIP for H3K4me3 in RpA70-EGFP (wt) embryos staged at NC14 replicate ID= rep1

description:
Library name: wt_ChIP-H3K4me3_NC14_rep1
H3K4me3 ChIP at NC14


title: ChIP for H3K4me2 in RpA70-EGFP (wt) embryos staged at NC14 replicate ID= rep2

description:
Library name: wt_ChIP-H3K4me2_NC14_rep2
H3K4me2 ChIP at NC14


title: TreeShrew_Male

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

description:
Library name: Sample 2
10x Genomics

library_source: transcriptomic single cell

data_processing:
the 10X Cell Ranger pipeline (version 7.2.0) was used to demultiplex
Assembly: a custom “pre-mRNA” reference genome created from the published tree shrew database (http://www.treeshrewdb.org/)
Supplementary files format and content: H5 file; feature-barcode matrices

molecule: polyA RNA

organism: Tupaia belangeri

source_name: Superficial superior colliculus

extract_protocol:
Brains were rapidly dissected, cooled in ice-cold Hibernate-A for 1.5 minutes, transferred to PBS, and prepared under a dissecting microscope. The cortex and cerebellum were removed to expose the superior colliculus (SC). The sSC was visualized coronally, micro-dissected by knife cuts along its visually approximated anatomical borders, and processed into a single-nucleus suspension using a published detergent-mechanical lysis protocol (Matson et al., 2018). Briefly, the sSC was homogenized in a lysis buffer, and cell nuclei were purified by density gradient centrifugation. After resuspension, nuclei were labeled with propidium iodide (Propidium Iodide Ready Flow™ Reagent, Invitrogen, catalog # R37169) and then counted with a CellDrop automated cell counter (DeNovix, Delaware, USA).
We used the 10X Genomics Chromium Next GEM 3’ kit v3.1 according to the manufacturer’s protocol (user guide revision D) to encapsulate each nucleus’s poly-adenylated RNA and then process the poly-adenylated RNA into cDNA sequencing libraries. We then sequenced the cDNA libraries by Illumina Next-Seq 2000 to an average of 29,857 mean reads per cell.

value: Superficial superior colliculus

value: male

value: Neural cells

value: WT

tag: age

value: 2-4 months

tag: batch


title: TreeShrew_Female

description:
Library name: Sample 1
10x Genomics

value: female


title: ChIP for H3K4me2 in RpA70-EGFP (wt) embryos staged at NC14 replicate ID= rep1

description:
Library name: wt_ChIP-H3K4me2_NC14_rep1
H3K4me2 ChIP at NC14


title: ChIP for H3K4me1 in RpA70-EGFP (wt) embryos staged at NC14 replicate ID= rep1

description:
Library name: wt_ChIP-H3K4me1_NC14_rep1
H3K4me1 ChIP at NC14


title: Nsd1_hKO_placenta_1

city: saga

first: Musashi

last: Kubiura-Ichimaru

country: Japan

institute: Saga university

description:
Library name: Nsd1_+/-_Placenta_rep1
Wild-type vs Nsd1-knockout placenta samples

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: placenta

growth_protocol: C3H 10T1/2 mesenchymal 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). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma).
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: placenta


title: WT_placenta_3

description:
Library name: WT_Placenta_rep_3
Wild-type vs Nsd1-knockout placenta samples


title: Nsd1_hKO_placenta_3

description:
Library name: Nsd1_+/-_Placenta_rep3
Wild-type vs Nsd1-knockout placenta samples


title: WT_placenta_2

description:
Library name: WT_Placenta_rep_2
Wild-type vs Nsd1-knockout placenta samples


title: Nsd1_hKO_brain_3

description:
Library name: Nsd1_+/-_Brain_rep3
Wild-type vs Nsd1-knockout brain samples

source_name: brain

value: brain


title: Nsd1_hKO_placenta_2

description:
Library name: Nsd1_+/-_Placenta_rep2
Wild-type vs Nsd1-knockout placenta samples


title: Nsd1_hKO_brain_2

description:
Library name: Nsd1_+/-_Brain_rep2
Wild-type vs Nsd1-knockout brain samples


title: WT_placenta_1

description:
Library name: WT_Placenta_rep_1
Wild-type vs Nsd1-knockout placenta samples


title: WT_brain_3

description:
Library name: WT_Brain_rep_3
Wild-type vs Nsd1-knockout brain samples


title: WT_brain_2

description:
Library name: WT_Brain_rep_2
Wild-type vs Nsd1-knockout brain samples


title: WT_brain_1

description:
Library name: WT_Brain_rep_1
Wild-type vs Nsd1-knockout brain samples


title: Nsd1_hKO_brain_1

description:
Library name: Nsd1_+/-_Brain_rep1
Wild-type vs Nsd1-knockout brain samples


title: HCT116_AB-2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: ZsGreen fluorescence-positive

data_processing:
Sequencing was performed on HiSeqSeq 3000 platform in a 100 or 125-base single-end mode.
Illumina RTA2 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Homo sapiens

source_name: HCT116 cells

extract_protocol:
Total RNA was extracted from cells with TRIzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: cell line

value: HCT116 cells


title: HCT116_AB-3

description: ZsGreen fluorescence-positive


title: HCT116_AB-1

description: ZsGreen fluorescence-positive


title: 3_d-

description: ZsGreen fluorescence-negative


title: 2_d-

description: ZsGreen fluorescence-negative


title: 1_d-

description: ZsGreen fluorescence-negative


title: ChIP for RNAPol2 in zld; RpA70GFP (zld) embryos staged at NC14E replicate ID= rep2

description:
Library name: zld_ChIP-RNAPol2_NC14E_rep2
RNA Pol2 (CTD pSer5) ChIP in zelda mutants at NC14 early

value: zld; RpA70GFP


title: ChIP for RNAPol2 in w; RpA70GFP (wt) embryos staged at NC14E replicate ID= rep2

description:
Library name: wt_ChIP-RNAPol2_NC14E_rep2
RNA Pol2 (CTD pSer5) ChIP at NC14 early

value: w; RpA70GFP


title: ChIP for RNAPol2 in zld; RpA70GFP (zld) embryos staged at NC14E replicate ID= rep1

description:
Library name: zld_ChIP-RNAPol2_NC14E_rep1
RNA Pol2 (CTD pSer5) ChIP in zelda mutants at NC14 early


title: ChIP for H3K4me1 in RpA70-EGFP (wt) embryos staged at NC14 replicate ID= rep2

description:
Library name: wt_ChIP-H3K4me1_NC14_rep2
H3K4me1 ChIP at NC14


title: tazKO5dpf2

city: Cleveland

first: Usua

last: Oyarbide

state: Ohio

address: Cleveland Clinic, Lerner Research Institute NE6-205

institute: Cleveland Clinic

description: Library name: sample 5

data_processing:
Sequencing reads generated from the Illumina platform were assessed for quality and trimmed for adapter sequences using TrimGalore! v0.4.2 (Babraham Bioinformatics), a wrapper script for FastQC and cutadapt.  Reads that passed quality control were aligned to the zebrafish reference genome (GRCz11.112) using the STAR aligner v2.5.3.
The aligned reads were analyzed for differential expression using Cufflinks v2.2.1, a RNASeq analysis package which reports the fragments per kilobase of exon per million fragments mapped (FPKM) for each gene using annotations from ZFin (v2024.08.19) annotation for GRCz11. Differential analysis was performed using the cuffdiff command in a pairwise manner for each group.  Differential genes were identified using a significance cutoff of q-value < 0.05 (FDR < 5% using Benjamini Hochberg adjustment for multiple-testing correction).  PCA and heatmap visualization was done using ClustVis.
Assembly: GRCz11
Supplementary files format and content: FPKM values and p and q values

organism: Danio rerio

source_name: whole larvae

extract_protocol: RNA was harvested using TRIzol, following the manufacturer's instructions. RNA quality was assesed by a bioanalyzer

value: whole larvae

tag: time point

value: 5 dpf

value: taz mutant


title: tazKO5dpf1

description: Library name: sample 4


title: wt5dpf3

description: Library name: sample 3

value: taz wildtype


title: wt5dpf2

description: Library name: sample 2


title: wt5dpf1

description: Library name: sample 1


title: ChIP for RNAPol2 in w; RpA70GFP (wt) embryos staged at NC14E replicate ID= rep1

description:
Library name: wt_ChIP-RNAPol2_NC14E_rep1
RNA Pol2 (CTD pSer5) ChIP at NC14 early


title: tazKO5dpf3

description: Library name: sample 6


title: liver biopsy [liver770]

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: liver biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: rejection archetype groups (nr,tcmr,nkrl,injury)

value: NR

value: liver biopsy


title: liver biopsy [liver767]


title: liver biopsy [liver774]


title: liver biopsy [liver764]


title: liver biopsy [liver773]

value: TCMR


title: liver biopsy [liver763]

value: Injury


title: liver biopsy [liver769]


title: liver biopsy [liver766]


title: liver biopsy [liver756]


title: liver biopsy [liver757]


title: liver biopsy [liver765]


title: liver biopsy [liver755]


title: liver biopsy [liver759]


title: liver biopsy [liver762]


title: liver biopsy [liver772]


title: liver biopsy [liver768]


title: liver biopsy [liver760]


title: liver biopsy [liver771]


title: liver biopsy [liver753]


title: liver biopsy [liver776]


title: liver biopsy [liver751]


title: liver biopsy [liver758]


title: liver biopsy [liver750]


title: liver biopsy [liver754]


title: liver biopsy [liver752]


title: liver biopsy [liver775]


title: liver biopsy [liver749]


title: liver biopsy [liver761]


title: liver biopsy [liver748]


title: liver biopsy [liver747]


title: liver biopsy [liver746]


title: liver biopsy [liver741]


title: liver biopsy [liver742]


title: liver biopsy [liver743]


title: liver biopsy [liver738]


title: liver biopsy [liver737]


title: liver biopsy [liver745]


title: liver biopsy [liver733]


title: liver biopsy [liver740]


title: liver biopsy [liver736]


title: liver biopsy [liver725]

value: NKRL


title: liver biopsy [liver734]


title: liver biopsy [liver724]


title: liver biopsy [liver744]


title: liver biopsy [liver730]


title: liver biopsy [liver731]


title: liver biopsy [liver722]


title: liver biopsy [liver732]


title: liver biopsy [liver726]


title: liver biopsy [liver729]


title: liver biopsy [liver723]


title: liver biopsy [liver721]


title: liver biopsy [liver735]


title: liver biopsy [liver719]


title: liver biopsy [liver727]


title: liver biopsy [liver720]


title: liver biopsy [liver717]


title: liver biopsy [liver712]


title: liver biopsy [liver718]


title: liver biopsy [liver715]


title: liver biopsy [liver728]


title: liver biopsy [liver716]


title: liver biopsy [liver709]


title: liver biopsy [liver714]


title: liver biopsy [liver710]


title: liver biopsy [liver713]


title: liver biopsy [liver707]


title: liver biopsy [liver711]


title: liver biopsy [liver708]


title: liver biopsy [liver703]


title: liver biopsy [liver706]


title: liver biopsy [liver700]


title: liver biopsy [liver697]


title: liver biopsy [liver704]


title: liver biopsy [liver702]


title: liver biopsy [liver705]


title: liver biopsy [liver693]


title: liver biopsy [liver696]


title: liver biopsy [liver701]


title: liver biopsy [liver694]


title: liver biopsy [liver695]


title: liver biopsy [liver698]


title: liver biopsy [liver699]


title: liver biopsy [liver690]


title: liver biopsy [liver691]


title: liver biopsy [liver692]


title: liver biopsy [liver687]


title: liver biopsy [liver682]


title: liver biopsy [liver689]


title: liver biopsy [liver683]


title: liver biopsy [liver680]


title: liver biopsy [liver684]


title: liver biopsy [liver678]


title: liver biopsy [liver688]


title: liver biopsy [liver681]


title: liver biopsy [liver677]


title: liver biopsy [liver685]


title: liver biopsy [liver686]


title: liver biopsy [liver679]


title: liver biopsy [liver675]


title: liver biopsy [liver671]


title: liver biopsy [liver676]


title: liver biopsy [liver668]


title: liver biopsy [liver672]


title: liver biopsy [liver669]


title: liver biopsy [liver673]


title: liver biopsy [liver670]


title: liver biopsy [liver663]


title: liver biopsy [liver674]


title: liver biopsy [liver739]


title: liver biopsy [liver664]


title: liver biopsy [liver665]


title: liver biopsy [liver661]


title: liver biopsy [liver667]


title: liver biopsy [liver658]


title: liver biopsy [liver657]


title: liver biopsy [liver655]


title: liver biopsy [liver666]


title: liver biopsy [liver656]


title: liver biopsy [liver654]


title: liver biopsy [liver648]


title: liver biopsy [liver659]


title: liver biopsy [liver652]


title: liver biopsy [liver651]


title: liver biopsy [liver653]


title: liver biopsy [liver662]


title: liver biopsy [liver660]


title: liver biopsy [liver645]


title: liver biopsy [liver647]


title: liver biopsy [liver644]


title: liver biopsy [liver643]


title: liver biopsy [liver638]


title: liver biopsy [liver641]


title: liver biopsy [liver640]


title: liver biopsy [liver642]


title: liver biopsy [liver650]


title: liver biopsy [liver636]


title: liver biopsy [liver649]


title: liver biopsy [liver633]


title: liver biopsy [liver635]


title: liver biopsy [liver637]


title: liver biopsy [liver639]


title: liver biopsy [liver646]


title: liver biopsy [liver634]


title: liver biopsy [liver631]


title: liver biopsy [liver630]


title: liver biopsy [liver628]


title: liver biopsy [liver621]


title: liver biopsy [liver625]


title: liver biopsy [liver626]


title: liver biopsy [liver620]


title: liver biopsy [liver629]


title: liver biopsy [liver632]


title: liver biopsy [liver627]


title: liver biopsy [liver623]


title: liver biopsy [liver622]


title: liver biopsy [liver624]


title: liver biopsy [liver617]


title: liver biopsy [liver619]


title: liver biopsy [liver616]


title: liver biopsy [liver615]


title: liver biopsy [liver613]


title: liver biopsy [liver610]


title: liver biopsy [liver618]


title: liver biopsy [liver605]


title: liver biopsy [liver609]


title: liver biopsy [liver612]


title: liver biopsy [liver608]


title: liver biopsy [liver607]


title: liver biopsy [liver602]


title: liver biopsy [liver606]


title: liver biopsy [liver603]


title: liver biopsy [liver600]


title: liver biopsy [liver614]


title: liver biopsy [liver598]


title: liver biopsy [liver604]


title: liver biopsy [liver594]


title: liver biopsy [liver599]


title: liver biopsy [liver601]


title: liver biopsy [liver596]


title: liver biopsy [liver595]


title: liver biopsy [liver597]


title: liver biopsy [liver611]


title: liver biopsy [liver592]


title: liver biopsy [liver591]


title: liver biopsy [liver589]


title: liver biopsy [liver588]


title: liver biopsy [liver590]


title: liver biopsy [liver586]


title: liver biopsy [liver585]


title: liver biopsy [liver593]


title: liver biopsy [liver587]


title: liver biopsy [liver575]


title: liver biopsy [liver576]


title: liver biopsy [liver583]


title: liver biopsy [liver579]


title: liver biopsy [liver577]


title: liver biopsy [liver582]


title: liver biopsy [liver573]


title: liver biopsy [liver580]


title: liver biopsy [liver581]


title: liver biopsy [liver584]


title: liver biopsy [liver570]


title: liver biopsy [liver572]


title: liver biopsy [liver566]


title: liver biopsy [liver568]


title: liver biopsy [liver564]


title: liver biopsy [liver571]


title: liver biopsy [liver562]


title: liver biopsy [liver578]


title: liver biopsy [liver567]


title: liver biopsy [liver561]


title: liver biopsy [liver565]


title: liver biopsy [liver560]


title: liver biopsy [liver563]


title: liver biopsy [liver559]


title: liver biopsy [liver556]


title: liver biopsy [liver569]


title: liver biopsy [liver558]


title: liver biopsy [liver574]


title: liver biopsy [liver557]


title: liver biopsy [liver555]


title: liver biopsy [liver551]


title: liver biopsy [liver546]


title: liver biopsy [liver550]


title: liver biopsy [liver552]


title: liver biopsy [liver549]


title: liver biopsy [liver554]


title: liver biopsy [liver548]


title: liver biopsy [liver545]


title: liver biopsy [liver547]


title: liver biopsy [liver540]


title: liver biopsy [liver541]


title: liver biopsy [liver532]


title: liver biopsy [liver538]


title: liver biopsy [liver537]


title: liver biopsy [liver553]


title: liver biopsy [liver539]


title: liver biopsy [liver535]


title: liver biopsy [liver529]


title: liver biopsy [liver542]


title: liver biopsy [liver544]


title: liver biopsy [liver543]


title: liver biopsy [liver526]


title: liver biopsy [liver528]


title: liver biopsy [liver530]


title: liver biopsy [liver533]


title: liver biopsy [liver534]


title: liver biopsy [liver525]


title: liver biopsy [liver527]


title: liver biopsy [liver524]


title: liver biopsy [liver520]


title: liver biopsy [liver516]


title: liver biopsy [liver512]


title: liver biopsy [liver531]


title: liver biopsy [liver523]


title: liver biopsy [liver521]


title: liver biopsy [liver519]


title: liver biopsy [liver513]


title: liver biopsy [liver515]


title: liver biopsy [liver506]


title: liver biopsy [liver511]


title: liver biopsy [liver510]


title: liver biopsy [liver509]


title: liver biopsy [liver501]


title: liver biopsy [liver508]


title: liver biopsy [liver517]


title: liver biopsy [liver518]


title: liver biopsy [liver507]


title: liver biopsy [liver522]


title: liver biopsy [liver505]


title: liver biopsy [liver498]


title: liver biopsy [liver495]


title: liver biopsy [liver494]


title: liver biopsy [liver514]


title: liver biopsy [liver504]


title: liver biopsy [liver499]


title: liver biopsy [liver502]


title: liver biopsy [liver500]


title: liver biopsy [liver497]


title: liver biopsy [liver496]


title: liver biopsy [liver493]


title: liver biopsy [liver492]


title: liver biopsy [liver503]


title: liver biopsy [liver485]


title: liver biopsy [liver489]


title: liver biopsy [liver488]


title: liver biopsy [liver490]


title: liver biopsy [liver477]


title: liver biopsy [liver484]


title: liver biopsy [liver476]


title: liver biopsy [liver486]


title: liver biopsy [liver491]


title: liver biopsy [liver482]


title: liver biopsy [liver481]


title: liver biopsy [liver483]


title: liver biopsy [liver480]


title: liver biopsy [liver475]


title: liver biopsy [liver479]


title: liver biopsy [liver478]


title: liver biopsy [liver467]


title: liver biopsy [liver466]


title: liver biopsy [liver469]


title: liver biopsy [liver471]


title: liver biopsy [liver470]


title: liver biopsy [liver473]


title: liver biopsy [liver465]


title: liver biopsy [liver456]


title: liver biopsy [liver468]


title: liver biopsy [liver453]


title: liver biopsy [liver454]


title: liver biopsy [liver461]


title: liver biopsy [liver463]


title: liver biopsy [liver460]


title: liver biopsy [liver462]


title: liver biopsy [liver536]


title: liver biopsy [liver472]


title: liver biopsy [liver457]


title: liver biopsy [liver459]


title: liver biopsy [liver455]


title: liver biopsy [liver451]


title: liver biopsy [liver440]


title: liver biopsy [liver452]


title: liver biopsy [liver448]


title: liver biopsy [liver442]


title: liver biopsy [liver446]


title: liver biopsy [liver445]


title: liver biopsy [liver450]


title: liver biopsy [liver447]


title: liver biopsy [liver443]


title: liver biopsy [liver449]


title: liver biopsy [liver444]


title: liver biopsy [liver487]


title: liver biopsy [liver441]


title: liver biopsy [liver439]


title: liver biopsy [liver437]


title: liver biopsy [liver438]


title: liver biopsy [liver435]


title: liver biopsy [liver434]


title: liver biopsy [liver431]


title: liver biopsy [liver432]


title: liver biopsy [liver430]


title: liver biopsy [liver428]


title: liver biopsy [liver427]


title: liver biopsy [liver425]


title: liver biopsy [liver424]


title: liver biopsy [liver422]


title: liver biopsy [liver436]


title: liver biopsy [liver419]


title: liver biopsy [liver423]


title: liver biopsy [liver417]


title: liver biopsy [liver418]


title: liver biopsy [liver420]


title: liver biopsy [liver433]


title: liver biopsy [liver429]


title: liver biopsy [liver416]


title: liver biopsy [liver411]


title: liver biopsy [liver426]


title: liver biopsy [liver410]


title: liver biopsy [liver414]


title: liver biopsy [liver413]


title: liver biopsy [liver412]


title: liver biopsy [liver415]


title: liver biopsy [liver421]


title: liver biopsy [liver407]


title: liver biopsy [liver406]


title: liver biopsy [liver403]


title: liver biopsy [liver409]


title: liver biopsy [liver402]


title: liver biopsy [liver405]


title: liver biopsy [liver408]


title: liver biopsy [liver401]


title: liver biopsy [liver399]


title: liver biopsy [liver397]


title: liver biopsy [liver400]


title: liver biopsy [liver398]


title: liver biopsy [liver395]


title: liver biopsy [liver396]


title: liver biopsy [liver404]


title: liver biopsy [liver392]


title: liver biopsy [liver387]


title: liver biopsy [liver394]


title: liver biopsy [liver388]


title: liver biopsy [liver393]


title: liver biopsy [liver386]


title: liver biopsy [liver390]


title: liver biopsy [liver384]


title: liver biopsy [liver389]


title: liver biopsy [liver385]


title: liver biopsy [liver382]


title: liver biopsy [liver391]


title: liver biopsy [liver381]


title: liver biopsy [liver380]


title: liver biopsy [liver383]


title: liver biopsy [GSM5774270 re-analysis]


title: liver biopsy [liver378]


title: liver biopsy [GSM5774268 re-analysis]


title: liver biopsy [GSM5774265 re-analysis]


title: liver biopsy [GSM5774267 re-analysis]


title: liver biopsy [GSM5774271 re-analysis]


title: liver biopsy [liver376]


title: liver biopsy [GSM5774272 re-analysis]


title: liver biopsy [GSM5774266 re-analysis]


title: liver biopsy [liver377]


title: liver biopsy [liver379]


title: liver biopsy [GSM5774264 re-analysis]


title: liver biopsy [liver374]


title: liver biopsy [GSM5774260 re-analysis]


title: liver biopsy [GSM5774262 re-analysis]


title: liver biopsy [GSM5774269 re-analysis]


title: liver biopsy [GSM5774261 re-analysis]


title: liver biopsy [liver372]


title: liver biopsy [liver458]


title: liver biopsy [liver375]


title: liver biopsy [liver371]


title: liver biopsy [GSM5774259 re-analysis]


title: liver biopsy [liver368]


title: liver biopsy [GSM5774256 re-analysis]


title: liver biopsy [GSM5774257 re-analysis]


title: liver biopsy [liver370]


title: liver biopsy [liver373]


title: liver biopsy [liver369]


title: liver biopsy [GSM5774258 re-analysis]


title: liver biopsy [GSM5774254 re-analysis]


title: liver biopsy [GSM5774255 re-analysis]


title: liver biopsy [liver365]


title: liver biopsy [GSM5774263 re-analysis]


title: liver biopsy [GSM5774252 re-analysis]


title: liver biopsy [liver366]


title: liver biopsy [GSM5774251 re-analysis]


title: liver biopsy [GSM5774248 re-analysis]


title: liver biopsy [GSM5774241 re-analysis]


title: liver biopsy [GSM5774239 re-analysis]


title: liver biopsy [GSM5774250 re-analysis]


title: liver biopsy [liver367]


title: liver biopsy [GSM5774242 re-analysis]


title: liver biopsy [GSM5774249 re-analysis]


title: liver biopsy [GSM5774244 re-analysis]


title: liver biopsy [GSM5774253 re-analysis]


title: liver biopsy [GSM5774236 re-analysis]


title: liver biopsy [GSM5774246 re-analysis]


title: liver biopsy [liver363]


title: liver biopsy [GSM5774247 re-analysis]


title: liver biopsy [GSM5774231 re-analysis]


title: liver biopsy [GSM5774237 re-analysis]


title: liver biopsy [GSM5774230 re-analysis]


title: liver biopsy [GSM5774232 re-analysis]


title: liver biopsy [GSM5774234 re-analysis]


title: liver biopsy [GSM5774235 re-analysis]


title: liver biopsy [GSM5774224 re-analysis]


title: liver biopsy [GSM5774227 re-analysis]


title: liver biopsy [liver364]


title: liver biopsy [GSM5774240 re-analysis]


title: liver biopsy [GSM5774228 re-analysis]


title: liver biopsy [GSM5774222 re-analysis]


title: liver biopsy [GSM5774238 re-analysis]


title: liver biopsy [GSM5774225 re-analysis]


title: liver biopsy [GSM5774220 re-analysis]


title: liver biopsy [liver360]


title: HTR8/SVneo cells, siTET13

city: Jinan

first: Chao

last: Fan

address: No. 9-7, Jiang Shui Quan Road, Lixia District

country: China

institute: Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University

description:
Library name: Sample 6
siTET1_vs_Con_gene.FPKM.txt: siTET13

data_processing:
Illunima Casava 1.8 was sued for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic-0.39
Trimmed sequence reads were mapped to GRCh38 using HISAT2(2.2.1) with default parameter
Assembly: hg38
Supplementary files format and content: table-delimited txt file includes FPKM values for each sample

growth_protocol: The HTR8/SVneo cells were cultured with RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and 1% penicillin and streptomycin at 37°C and 5% CO2.

extract_protocol:
RNA were extracted using the RNAsimple Total RNA Kit (Tiangen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by U-mRNAseqLibraryPrepKit (Kaitaibio) according to the manufacturer's procedure.

treatment_protocol: When cells reached 70% confluence, 40 pmol siTET1 and 8 μL of Lipofectamine® RNAiMAX transfection reagent were mixed in Opti-MEM™ medium (Invitrogen) and used to knock down TET1.

value: trophoblast cells

value: TET1 knockdown


title: liver biopsy [GSM5774245 re-analysis]


title: liver biopsy [GSM5774226 re-analysis]


title: liver biopsy [GSM5774219 re-analysis]


title: liver biopsy [GSM5774217 re-analysis]


title: liver biopsy [liver357]


title: liver biopsy [liver362]


title: liver biopsy [GSM5774223 re-analysis]


title: liver biopsy [liver359]


title: liver biopsy [GSM5774221 re-analysis]


title: HTR8/SVneo cells, siTET12

description:
Library name: Sample 5
siTET1_vs_Con_gene.FPKM.txt: siTET12


title: liver biopsy [GSM5774216 re-analysis]


title: liver biopsy [GSM5774229 re-analysis]


title: liver biopsy [liver361]


title: liver biopsy [GSM5774213 re-analysis]


title: liver biopsy [GSM5774215 re-analysis]


title: HTR8/SVneo cells, siTET11

description:
Library name: Sample 4
siTET1_vs_Con_gene.FPKM.txt: siTET11


title: HTR8/SVneo cells, Con3

description:
Library name: Sample 3
siTET1_vs_Con_gene.FPKM.txt: Con3

value: WT


title: liver biopsy [GSM5774211 re-analysis]


title: liver biopsy [liver358]


title: HTR8/SVneo cells, Con1

description:
Library name: Sample 1
siTET1_vs_Con_gene.FPKM.txt: Con1


title: SUM44PE_TAMR_3

city: Columbus

first: Daniel

last: Stover

state: OH

address: Biomedical Research Tower, Room 512, 460 W. 12th Avenue

institute: Ohio State University Comprehensive Cancer Center

description: Library name: SUM44_T3

data_processing:
Data processing and pathway analysis was performed by Novogene
Assembly: hg38
Supplementary files format and content: FPKM values for each samples

growth_protocol: Parental and TAMR MB134 cells were grown in a 1:1 ratio of Dulbecco’s modified Eagle’s medium (DMEM; Gibco, USA) and Leibovitz’s L-15 medium (Gibco, USA), supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin. Parental and TAMR SUM44 cell lines were cultured in Ham’s F-12 (Gibco,USA) supplemented with 1 g/L bovine serum albumin, 5 mM ethanolamine, 10 mM HEPES, 1μg/mL hydrocortisone, 5 μg/mL insulin, 50 nM sodium selenite, 5 μg/ mL apo-transferrin and 10 nM triodo-L-thyronine. MB134TAMR and SUM44TAMR cells were maintained in media containing 100 nM and 500 nM 4-OHT respectively.

extract_protocol:
Total RNA was extracted from exponentially growing cells using Trizol (Invitrogen, USA) following manufacturer’s protocol
polyA enrichment library preparation

treatment_protocol: ILC cell lines MDA-MB-134-VI (MB134) (ATCC, USA) and SUM44PE (SUM44) (Asterand, USA) were used to develop the tamoxifen-resistant (TAMR) cells by continuously exposing them to 100 to 500 nM of 4-hydroxy tamoxifen (4-OHT) for over 6 months.

value: Lobular breast cancer

value: Tamoxifen-resistant


title: HTR8/SVneo cells, Con2

description:
Library name: Sample 2
siTET1_vs_Con_gene.FPKM.txt: Con2


title: liver biopsy [GSM5774214 re-analysis]


title: liver biopsy [GSM5774212 re-analysis]


title: liver biopsy [liver356]


title: SUM44PE_TAMR_2

description: Library name: SUM44_T2


title: SUM44PE_TAMR_1

description: Library name: SUM44_T1


title: MDA-MB-134-VI_TAMR_2

description: Library name: MB134_T2


title: liver biopsy [GSM5774209 re-analysis]


title: SUM44PE_Parental_1

description: Library name: SUM44_P1


title: liver biopsy [liver353]


title: SUM44PE_Parental_3

description: Library name: SUM44_P3


title: liver biopsy [GSM5774218 re-analysis]


title: liver biopsy [liver350]


title: MDA-MB-134-VI_TAMR_1

description: Library name: MB134_T1


title: liver biopsy [GSM5774207 re-analysis]


title: liver biopsy [liver354]


title: liver biopsy [GSM5774208 re-analysis]


title: MDA-MB-134-VI_TAMR_3

description: Library name: MB134_T3


title: liver biopsy [liver351]


title: liver biopsy [GSM5774206 re-analysis]


title: liver biopsy [liver349]


title: MDA-MB-134-VI _Parental_1

description: Library name: MB134_P1


title: MDA-MB-134-VI _Parental_3

description: Library name: MB134_P3


title: liver biopsy [liver355]


title: EOC649, sensitive, scRNA-seq

city: Helsinki

first: Daria

last: Afenteva

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: EOC649_sensitive
10x Genomics

data_processing:
The Cell Ranger v.6.0.1 pipeline (10x Genomics) was used for demultiplexing, alignment, barcode processing, and unique molecular identifier (UMI) quantification.
Assembly: GRCh38.d1.vd1
Supplementary files format and content: The raw count matrix and cell annotation file are provided as tsv.gz files.

source_name: Omentum

extract_protocol:
Tumor specimens were incubated overnight in a mixture of collagenase and hyaluronidase (Department of Pathology, University of Turku) to obtain single-cell suspensions.
Library construction was performed according to the manufacturer's (10x Genomics) protocols for indicated assay chemistries (v2, v3, and v3.1).

value: Omentum

tag: sample group

value: chemo-sensitive

tag: subject status

value: patient diagnosed with ovarian high-grade serous carcinoma (HGSC)

value: Chemo-naïve


title: MDA-MB-134-VI _Parental_2

description: Library name: MB134_P2


title: EOC115, refractory, scRNA-seq

description:
Library name: EOC115_refractory
10x Genomics

source_name: Peritoneum

value: Peritoneum

value: chemo-refractory


title: liver biopsy [liver352]


title: EOC204, refractory, scRNA-seq

description:
Library name: EOC204_refractory
10x Genomics

source_name: Mesentery

value: Mesentery


title: liver biopsy [GSM5774243 re-analysis]


title: liver biopsy [liver344]


title: C918shc

city: Tianjin

first: Jing

last: Mo

state: Tianjin

address: 22 Qixiangtai Road, Heping District

department: Pathology

institute: Tianjin medical university

description:
Library name: Melanoma_shNC
Column name in Melanoma_shSE1VSMelanoma_shNC_Gene_differential_expression: Melanoma_shNC
Melanoma_shSE1VSMelanoma_shNC_Gene_differential_expression.xlsx

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38.ensemblV101
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: Melanoma

growth_protocol: Human breast cancer cell line MDA-MB-231, glioma cell line H4, and melanoma cell line C918  were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin, and maintained at 37°C in 5% CO₂.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Total RNA was isolated and purified from samples using TRIzol (Thermofisher, 15596018) per the manufacturer's protocol. RNA quantity and purity were assessed with a NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and integrity was evaluated via Bioanalyzer 2100 (Agilent, CA, USA). Samples with concentration >50 ng/μL, RIN value >7.0, and total RNA >1 μg were used for downstream processes. PolyA-containing mRNA was specifically captured through two rounds of purification with oligo(dT) magnetic beads (Dynabeads Oligo (dT), cat.25-61005, Thermo Fisher, USA). The captured mRNA was fragmented at 94℃ for 5 - 7 minutes a using magnesium RNA fragmentation kit (NEBNext Magnesium RNA Fragmentation Module, cat.E6150S, USA). cDNA was synthesized from fragmented RNA using reverse transcriptase (Invitrogen SuperScript II Reverse Transcriptase, cat.1896649, CA, USA). E. coli DNA polymerase I (NEB, cat.m0209, USA) and RNase H (NEB, cat.m0297, USA) were employed for second - strand synthesis, incorporating dUTP Solution (Thermo Fisher, cat.R0133, CA, USA) and blunting the ends. An A - base was added to each end to facilitate adapter ligation with T - overhangs. Magnetic beads were used for size selection and purification. The second strand was digested with UDG enzyme (NEB, cat.m0280, MA, US), followed by PCR amplification: 3 minutes at 95℃, 8 cycles of 15 seconds at 98℃, 15 seconds at 60℃, and 30 seconds at 72℃, with a final 5 - minute extension at 72℃, generating a 300bp ±50bp strand - specific library. Finally, the library was sequenced on an illumina Novaseq 6000 (LC Bio Technology CO.,Ltd. Hangzhou, China) using PE150 mode.

treatment_protocol: Lentivirus production and transduction were performed using the Lenti-Pac HIV Expression Packaging Kit  by co-transfecting 293T cells.  Transduced cells were selected with puromycin and/or neomycin. SERPINE1 shRNA and control shRNA were purchased from GENECHEM.

value: Melanoma

value: Melanoma cell

value: wt


title: C918shSE1

description:
Library name: Melanoma_shSE1
Column name in Melanoma_shSE1VSMelanoma_shNC_Gene_differential_expression: Melanoma_shSE1
Melanoma_shSE1VSMelanoma_shNC_Gene_differential_expression.xlsx


title: liver biopsy [liver348]

value: NR

value: liver biopsy


title: H4shc

description:
Library name: Glioma_shNC
Column name in Glioma_shSE1VSGlioma_shNC_Gene_differential_expression: Glioma_shNC
Glioma_shSE1VSGlioma_shNC_Gene_differential_expression.xlsx

source_name: Glioma

value: Glioma

value: Glioma cell


title: EOC1127, sensitive, scRNA-seq

description:
Library name: EOC1127_sensitive
10x Genomics


title: liver biopsy [liver345]


title: liver biopsy [liver343]

value: TCMR


title: 231shSE1

description:
Library name: BreastC_shSE1
Column name in BreastC_shSE1VSBreastC_shNC_Gene_differential_expression: BreastC_shSE1
BreastC_shSE1VSBreastC_shNC_Gene_differential_expression.xlsx

source_name: Breast cancer

value: Breast cancer

value: Breast cancer cell


title: HiC data for COLO320-DM mitotic cell line, triptolide-treated, BiolRep 2

city: New York

first: John

last: Maciejowski

state: NY

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: Library name: Sample 14

data_processing:
Reads were trimmed of the 5' end adapter sequences using Cutadapt (version 2.4), aligned to the hg38 genome using bowtie2 (version 2.4.4), and all valid pairs were filtered for using HiC-Pro (version 3.1.0).
Assembly: hg38
Supplementary files format and content: Files containing sequences of all valid pairs in .hic format.

extract_protocol:
Cells were sorted to obtain asynchronous or mitotic samples. Cells were frozen at -80C in 1-4 million cell pellets and DNA was extracted with an Arima HiC kit (Arima, A510008).
200 ng of DNA was used to generate libraries using the Arima HiC kit in conjunction with the Arima Library prep module.

value: colorectal cancer cell line

value: nocodazole arrest, triptolide


title: SUM44PE_Parental_2

description: Library name: SUM44_P2

value: Lobular breast cancer


title: 231shc

description:
Library name: BreastC_shNC
Column name in BreastC_shSE1VSBreastC_shNC_Gene_differential_expression: BreastC_shNC
BreastC_shSE1VSBreastC_shNC_Gene_differential_expression.xlsx


title: liver biopsy [GSM5774205 re-analysis]


title: liver biopsy [GSM5774203 re-analysis]

value: NKRL


title: liver biopsy [GSM5774202 re-analysis]


title: liver biopsy [GSM5774204 re-analysis]


title: H4shSE1

description:
Library name: Glioma_shSE1
Column name in Glioma_shSE1VSGlioma_shNC_Gene_differential_expression: Glioma_shSE1
Glioma_shSE1VSGlioma_shNC_Gene_differential_expression.xlsx


title: liver biopsy [liver342]


title: liver biopsy [GSM5774200 re-analysis]


title: HiC data for COLO320-DM mitotic cell line, DMSO-treated, BiolRep 2

description: Library name: Sample 12

value: nocodazole arrest, DMSO


title: liver biopsy [liver346]


title: HiC data for HCT116 mitotic cell line, BiolRep 1

description: Library name: Sample 9

value: nocodazole arrest


title: HiC data for HCT116 mitotic cell line, BiolRep 2

description: Library name: Sample 10


title: HiC data for COLO320-DM mitotic cell line, DMSO-treated, BiolRep 1

description: Library name: Sample 11


title: HiC data for HCT116 asynchronous cell line, BiolRep 2

description: Library name: Sample 8


title: HiC data for COLO320-DM mitotic cell line, triptolide-treated, BiolRep 1

description: Library name: Sample 13


title: HiC data for HCT116 asynchronous cell line, BiolRep 1

description: Library name: Sample 7


title: HiC data for COLO320-HSR mitotic cell line

description: Library name: Sample 6


title: liver biopsy [GSM5774201 re-analysis]


title: liver biopsy [GSM5774198 re-analysis]


title: liver biopsy [GSM5774210 re-analysis]


title: HiC data for COLO320-DM mitotic cell line, BiolRep 2

description: Library name: Sample 4


title: HiC data for COLO320-DM mitotic cell line, BiolRep 1

description: Library name: Sample 3


title: HiC data for COLO320-HSR asynchronous cell line

description: Library name: Sample 5


title: liver biopsy [GSM5774197 re-analysis]


title: liver biopsy [liver347]


title: MCF-7,Z8KO,ER,EtOH,rep2

city: ShangHai

first: HongJie

last: Shen

address: Dongan road 131

institute: Fudan University

description: Library name: MCF7 Z8KO EtOH ER ChIP rep2

data_processing:
Trimed reads were aligned to the hg19 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: hg19
Supplementary files format and content: Genome coverage bigwig files

growth_protocol: MCF-7 and HeLa cells were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS, Gibco #10099141C), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010) at 37℃ with 5% CO2.  For E2 stimulaiton, cells were shifted to Phenol Red-free RPMI-1640 Medium (Hyclone #SH30605) containing 10% Charcoal Stripped Fetal Bovine Serum (Viva Cell #3830-0050), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1% Glutamine (Hyclone #SH30034) . For EGF stimulation, cells were shifted to DMEM containing 0.5% fetal bovine serum,  (FBSGibco #16000-044), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010).

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: For E2 stimulation, when the density of MCF-7 cells was up to 40%, DMEM was changed to Phenol Red-free RPMI-1640 with 10% Charcoal Stripped Fetal Bovine Serum for 72 h. Final concentration of 100 nM 17β-estradiol (E2) were added into the cell culture medium, cells were incubated in 37 °C for 1 h. For EGF stimulation, when the density of HeLa cells was up to 70%, 10% FBS contained DMEM was changed to 0.5% FBS contained DMEM for 48h. Final concentration of 50ng/mL EGF were added to the cell culture medium, cells were incubated in 37℃ for 40min. For transcription inhibitor treatment, after the cell were cultured in  Phenol Red-free RPMI-1640 for 66h, 1μM Flavopiridol or 1μM Triptolide was added into the culture medium for 6h, 100nM E2 was added into the culture medium at the 5th hour and co-culture with transcription inhibitor for 1h.

value: EtOH

value: ER (Bethyl, A300-498A)


title: liver biopsy [GSM5774196 re-analysis]

value: Injury


title: liver biopsy [GSM5774193 re-analysis]


title: MCF-7,Z8KO,ER,E2,rep2

description: Library name: MCF7 Z8KO E2 ER ChIP rep2


title: liver biopsy [GSM5774192 re-analysis]


title: liver biopsy [GSM5774191 re-analysis]


title: MCF-7,WT,ER,E2,rep2

description: Library name: MCF7 WT E2 ER ChIP rep2

value: WT


title: liver biopsy [GSM5774187 re-analysis]

value: NR


title: liver biopsy [GSM5774188 re-analysis]

value: liver biopsy


title: liver biopsy [GSM5774195 re-analysis]


title: liver biopsy [GSM5774186 re-analysis]


title: liver biopsy [GSM5774194 re-analysis]


title: liver biopsy [GSM5774189 re-analysis]


title: liver biopsy [GSM5774190 re-analysis]


title: MCF-7,WT,ER,EtOH,rep2

description: Library name: MCF7 WT EtOH ER ChIP rep2


title: liver biopsy [GSM5774184 re-analysis]


title: MCF-7,Z8KO,ZMYND8,normal,rep2

description: Library name: MCF7 Z8KO ZMYND8 ChIP rep2

value: normal medium

value: ZMYND8 (Bethyl, A302-090A)


title: MCF-7,WT,ZMYND8,normal,rep2

description: Library name: MCF7 WT ZMYND8 ChIP rep2


title: HiC data for COLO320-DM asynchronous cell line, BiolRep 1

description: Library name: Sample 1


title: HeLa,Z8KO,ZMYND8,rep2

description: Library name: HeLa Z8KO ZMYND8 ChIP rep2

source_name: HeLa

value: HeLa


title: HiC data for COLO320-DM asynchronous cell line, BiolRep 2

description: Library name: Sample 2


title: liver biopsy [GSM5774183 re-analysis]

value: TCMR


title: HeLa,WT,ZMYND8,rep2

description: Library name: HeLa WT ZMYND8 ChIP rep2


title: liver biopsy [GSM5774181 re-analysis]


title: MCF-7,Z8KO,ER,E2,rep1

description: Library name: MCF7 Z8KO E2 ER ChIP rep1


title: liver biopsy [GSM5774185 re-analysis]


title: liver biopsy [GSM5774182 re-analysis]


title: MCF-7,WT,ZMYND8,normal,rep1

description: Library name: MCF7 WT ZMYND8 ChIP rep1


title: liver biopsy [GSM5774199 re-analysis]


title: MCF-7,WT,ER,E2,rep1

description: Library name: MCF7 WT E2 ER ChIP rep1


title: liver biopsy [GSM5774179 re-analysis]


title: liver biopsy [GSM5774175 re-analysis]


title: liver biopsy [GSM5774176 re-analysis]


title: MCF-7,WT,ER,EtOH,rep1

description: Library name: MCF7 WT EtOH ER ChIP rep1


title: MCF-7,Z8KO,ZMYND8,normal,rep1

description: Library name: MCF7 Z8KO ZMYND8 ChIP rep1


title: MCF-7,Z8KO,ER,EtOH,rep1

description: Library name: MCF7 Z8KO EtOH ER ChIP rep1


title: liver biopsy [GSM5774172 re-analysis]


title: Synovium, Ankle, Control, Sample 8

city: Aurora

first: Julia

last: Matthias

state: Colorado

department: Orthopedic Surgery

institute: University of Colorado - Anschutz Medical Campus

description:
Library name: S192
Column name in raw data and FPKMs file: S192

data_processing:
Base-calling & Quality Control:
Base-calling was performed using Illumina’s onboard software to convert raw sequencing signals into nucleotide sequences. The raw sequencing data were generated in FASTQ format, which includes sequenced reads and corresponding quality scores. Quality control was performed using in-house Perl scripts to remove reads containing adapter sequences, poly-N (>10% unresolved bases), or low-quality bases (>50% bases with QPhred ≤ 5). Quality metrics, including Q20, Q30, and GC content, were calculated to assess sequencing quality.
Alignment:
Reads were aligned to the GRCh38/hg38 human reference genome using HISAT2 v2.0.5, with the reference genome index generated from gene model annotation files. HISAT2 was chosen for its ability to incorporate splice junction databases for improved alignment accuracy.
Filtering:
During preprocessing, low-quality reads, adapter-containing sequences, and ambiguous base calls were filtered out.
Quantification & Normalization:
Gene expression levels were quantified using featureCounts v1.5.0-p3, which counted reads mapped to each gene. Expression values were normalized using Fragments Per Kilobase of transcript per Million mapped reads (FPKM), accounting for sequencing depth and gene length.
Assembly: GRCh38/hg38 human reference genome
Supplementary files format and content: raw_counts_all_samples.xls includes raw counts for each sample. FPKMs_all_samples.txt includes FPKM values for each sample

source_name: Ankle Synovium

extract_protocol:
Following operative removal of the tissue, samples were immediately flash-frozen in liquid nitrogen and stored at -80ºC. RNA was extracted using TRIzol™ following the manufacturer’s suggested protocol (ThermoFisher) and purified (GeneJET RNA Purification Kit).
Messenger RNA was purified using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis with dUTP for a directional library or dTTP for a non-directional library. Libraries were quantified using Qubit and real-time PCR, while size distribution was assessed with a Bioanalyzer.

value: Ankle Synovium

value: Control Ankle Synovium

value: Outerbridge 0


title: HeLa,Z8KO,ZMYND8,rep1

description: Library name: HeLa Z8KO ZMYND8 ChIP rep1


title: liver biopsy [GSM5774170 re-analysis]


title: liver biopsy [GSM5774180 re-analysis]


title: HeLa,WT,ZMYND8,rep1

description: Library name: HeLa WT ZMYND8 ChIP rep1


title: Synovium, Ankle, Control, Sample 7

description:
Library name: S169
Column name in raw data and FPKMs file: S169

value: Outerbridge 1


title: liver biopsy [GSM5774178 re-analysis]


title: liver biopsy [GSM5774177 re-analysis]


title: Synovium, Ankle, Control, Sample 4

description:
Library name: S137
Column name in raw data and FPKMs file: S137


title: Synovium, Ankle, Control, Sample 6

description:
Library name: S147
Column name in raw data and FPKMs file: S147


title: Synovium, Ankle, Control, Sample 5

description:
Library name: S145
Column name in raw data and FPKMs file: S145


title: liver biopsy [GSM5774165 re-analysis]


title: Synovium, Ankle, Control, Sample 3

description:
Library name: S110
Column name in raw data and FPKMs file: S110


title: liver biopsy [GSM5774171 re-analysis]

value: NKRL


title: liver biopsy [GSM5774169 re-analysis]


title: liver biopsy [GSM5774168 re-analysis]


title: liver biopsy [GSM5774174 re-analysis]


title: liver biopsy [GSM5774167 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 25

description:
Library name: A202
Column name in raw data and FPKMs file: A202

value: End-stage Ankle Osteoarthritis

value: Outerbridge 4


title: Synovium, Ankle, Control, Sample 2

description:
Library name: S105
Column name in raw data and FPKMs file: S105


title: Synovium, Ankle, Control, Sample 1

description:
Library name: S183
Column name in raw data and FPKMs file: S183


title: Synovium, End-stage Ankle Osteoarthritis, Sample 23

description:
Library name: A195
Column name in raw data and FPKMs file: A195


title: Synovium, End-stage Ankle Osteoarthritis, Sample 26

description:
Library name: A136
Column name in raw data and FPKMs file: A136


title: Synovium, End-stage Ankle Osteoarthritis, Sample 22

description:
Library name: A184
Column name in raw data and FPKMs file: A184


title: Synovium, End-stage Ankle Osteoarthritis, Sample 21

description:
Library name: A176
Column name in raw data and FPKMs file: A176


title: liver biopsy [GSM5774166 re-analysis]


title: liver biopsy [GSM5774163 re-analysis]


title: liver biopsy [GSM5774162 re-analysis]


title: liver biopsy [GSM5774161 re-analysis]


title: liver biopsy [GSM5774173 re-analysis]


title: liver biopsy [GSM5774159 re-analysis]


title: liver biopsy [GSM5774160 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 19

description:
Library name: A99
Column name in raw data and FPKMs file: A99


title: Synovium, End-stage Ankle Osteoarthritis, Sample 20

description:
Library name: A122
Column name in raw data and FPKMs file: A122


title: Synovium, End-stage Ankle Osteoarthritis, Sample 18

description:
Library name: A69
Column name in raw data and FPKMs file: A69


title: liver biopsy [GSM5774164 re-analysis]


title: liver biopsy [GSM5774157 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 24

description:
Library name: A196
Column name in raw data and FPKMs file: A196


title: Synovium, End-stage Ankle Osteoarthritis, Sample 17

description:
Library name: A68
Column name in raw data and FPKMs file: A68


title: liver biopsy [GSM5774156 re-analysis]


title: liver biopsy [GSM5774155 re-analysis]


title: liver biopsy [GSM5774154 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 16

description:
Library name: A67
Column name in raw data and FPKMs file: A67


title: liver biopsy [GSM5774151 re-analysis]


title: liver biopsy [GSM5774152 re-analysis]


title: liver biopsy [GSM5774158 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 14

description:
Library name: A62
Column name in raw data and FPKMs file: A62


title: Synovium, End-stage Ankle Osteoarthritis, Sample 13

description:
Library name: A60
Column name in raw data and FPKMs file: A60


title: Synovium, End-stage Ankle Osteoarthritis, Sample 11

description:
Library name: A37
Column name in raw data and FPKMs file: A37


title: Synovium, End-stage Ankle Osteoarthritis, Sample 12

description:
Library name: A56
Column name in raw data and FPKMs file: A56


title: liver biopsy [GSM5774150 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 8

description:
Library name: A24
Column name in raw data and FPKMs file: A24


title: Synovium, End-stage Ankle Osteoarthritis, Sample 10

description:
Library name: A3
Column name in raw data and FPKMs file: A3


title: Synovium, End-stage Ankle Osteoarthritis, Sample 15

description:
Library name: A64
Column name in raw data and FPKMs file: A64


title: Synovium, End-stage Ankle Osteoarthritis, Sample 9

description:
Library name: A25
Column name in raw data and FPKMs file: A25


title: Synovium, End-stage Ankle Osteoarthritis, Sample 6

description:
Library name: A22
Column name in raw data and FPKMs file: A22


title: Synovium, End-stage Ankle Osteoarthritis, Sample 5

description:
Library name: A16
Column name in raw data and FPKMs file: A16


title: Synovium, End-stage Ankle Osteoarthritis, Sample 7

description:
Library name: A2
Column name in raw data and FPKMs file: A2


title: liver biopsy [GSM5774143 re-analysis]


title: liver biopsy [GSM5774147 re-analysis]


title: liver biopsy [GSM5774153 re-analysis]


title: liver biopsy [GSM5774144 re-analysis]


title: liver biopsy [GSM5774148 re-analysis]


title: liver biopsy [GSM5774146 re-analysis]


title: liver biopsy [GSM5774145 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 4

description:
Library name: A139
Column name in raw data and FPKMs file: A139


title: liver biopsy [GSM5774139 re-analysis]


title: liver biopsy [GSM5774142 re-analysis]


title: liver biopsy [GSM5774140 re-analysis]


title: liver biopsy [GSM5774141 re-analysis]


title: Synovium, End-stage Ankle Osteoarthritis, Sample 1

description:
Library name: A186
Column name in raw data and FPKMs file: A186


title: Activated Neonate 3

city: New Haven

first: Carrie

middle: L

last: Lucas

state: CT

address: 300 Cedar St., TAC S625D

institute: Yale School of Medicine

description:
Library name: Sample 20
C3_D2stimulated

data_processing:
100 paired-end fragments were trimmed using fastp software.
Trimmed fragments were mapped to the human transcriptome with Gencode annotation GRCh38 using STAR and in parallel transcript level expression was quantified using SALMON.
Gene-length normalized counts were then used to generate batch corrected counts using ComBat-seq package in R.
Gene level differential expression analysis was performed using DESeq2 package in R.
Assembly: hg38
Supplementary files format and content: tab-delimted text file includes raw counts for each sample

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated using density gradient centrifugation. Blood samples were diluted 1:1 with phosphate-buffered saline (PBS) and carefully layered onto lymphoprep medium (StemCell) in a 50 mL conical tube. Following centrifugation for 20 min at 20°C at 824 RCF/G with no deceleration, the PBMC layer was collected and washed twice with complete RPMI media. For the isolation of CD8+ T cells, PBMCs were subjected to positive bead selection using CD8+ microbeads (Miltenyi Biotec) according to the manufacturer’s instructions. Isolated CD8+ T cells were then sorted using a BD FACSAria flow cytometer (BD Biosciences) to obtain live naive cells defined as DAPI-CD8+CD45RA+CCR7+.

extract_protocol:
The RNeasy Plus Mini Kit (Qiagen) was used following the manufacturer’s protocol. RNA quality was assessed using a Bioanalyzer (Agilent Technologies), and only samples with an RNA Integrity Number (RIN) > 7 were used for library preparation.
Libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina) and sequenced on NovaSeq.

treatment_protocol: CD8+ T cells were cultured in 96-well plates or 24-well plates (for RNA seq and TEM) coated with anti-CD3 antibodies (Clone: OKT3, BioLegend, Catalog no. 317326) at a concentration of 5 μg/mL (coated overnight at 4C and washed twice with PBS prior to cell plating). Soluble anti-CD28 (BioLegend, Catalog no. 302943, 1 μg/mL) was added to the cultures to provide a second signal for T cell activation and proliferation. Cells were maintained in complete RPMI-1640 media supplemented with 10% FBS and 1% penicillin-streptomycin and 100 units/mL IL-2 (Prometheus). Total RNA was extracted from freshly isolated naïve CD8+ T cells (baseline) and naïve CD8 T cells that were activated with plated anti-CD3 and soluble anti-CD28 for 2 days and then re-stimulated with PMA and ionomycin for four hours (stimulated).

value: blood

value: CD8 T cell

value: Male

value: TCR activation


title: liver biopsy [GSM5774138 re-analysis]

value: NR


title: Activated Neonate 4

description:
Library name: Sample 21
C4_D2stimulated

value: Female


title: Synovium, End-stage Ankle Osteoarthritis, Sample 2

description:
Library name: A120
Column name in raw data and FPKMs file: A120


title: Activated Neonate 1

description:
Library name: Sample 18
C1_D2stimulated


title: Activated Neonate 2

description:
Library name: Sample 19
C2_D2stimulated


title: liver biopsy [GSM5774136 re-analysis]

value: liver biopsy


title: liver biopsy [GSM5774137 re-analysis]


title: liver biopsy [GSM5774135 re-analysis]

value: Injury


title: Activated Adult 3

description:
Library name: Sample 16
A3_D2stimulated


title: Synovium, End-stage Ankle Osteoarthritis, Sample 3

description:
Library name: A123
Column name in raw data and FPKMs file: A123


title: Activated Adult 2

description:
Library name: Sample 15
A2_D2stimulated


title: Activated Adult 1

description:
Library name: Sample 14
A1_D2stimulated


title: liver biopsy [GSM5774132 re-analysis]


title: liver biopsy [GSM5774134 re-analysis]


title: liver biopsy [GSM5774131 re-analysis]


title: liver biopsy [GSM5774130 re-analysis]


title: Neonate 6

description:
Library name: Sample 12
C6_baseline


title: liver biopsy [GSM5774128 re-analysis]


title: Activated Adult 4

description:
Library name: Sample 17
A4_D2stimulated


title: Neonate 4

description:
Library name: Sample 10
C4_baseline


title: liver biopsy [GSM5774133 re-analysis]


title: Neonate 2

description:
Library name: Sample 8
C2_baseline


title: Neonate 3

description:
Library name: Sample 9
C3_baseline


title: liver biopsy [GSM5774129 re-analysis]


title: Neonate 1

description:
Library name: Sample 7
C1_baseline


title: Neonate 5

description:
Library name: Sample 11
C5_baseline


title: Adult 6

description:
Library name: Sample 6
A6_baseline


title: liver biopsy [GSM5774149 re-analysis]


title: liver biopsy [GSM5774127 re-analysis]


title: Adult 5

description:
Library name: Sample 5
A5_baseline


title: liver biopsy [GSM5774126 re-analysis]


title: liver biopsy [GSM5774125 re-analysis]


title: Adult 3

description:
Library name: Sample 3
A3_baseline


title: Neonate 7

description:
Library name: Sample 13
C7_baseline


title: Adult 4

description:
Library name: Sample 4
A4_baseline


title: liver biopsy [GSM5774124 re-analysis]


title: liver biopsy [liver341]


title: liver biopsy [liver340]


title: liver biopsy [GSM5774121 re-analysis]


title: Adult 2

description:
Library name: Sample 2
A2_baseline


title: liver biopsy [GSM5774122 re-analysis]


title: Adult 1

description:
Library name: Sample 1
A1_baseline


title: liver biopsy [GSM5774120 re-analysis]


title: Homo sapiens,T. gondii infected,24h,Infected_IP RNA,rep1

city: Nanjing

last: gao

state: Jiangsu

address: Longmian Street num101

institute: Nanjingmedicaluniversity

description: Library name: Infected1_IP

data_processing:
Base calling software: BCL convert
Data filter: fastp，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2
Peak calling diffpeak : R package: exomePeak
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie
Differential Expression Analysis :R package: edgeR
Motif: HOMER
Assembly: eg GRCH38
Supplementary files format and content: Control_IPVSControl_input_peak.xlsx,Infected_IPVSInfected_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: InfectedVSControl_diffPeak_result.xlsx, which contained the result of differential methylation sites
Supplementary files format and content: 4_genes_fpkm_expression.txt, which contained the expression information of various genes in various samples (Expression profile)
Library strategy: MeRIP-Seq

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). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Approximately more than 25 μg of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA).
Following purification, the ribosomal-depleted RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86 ℃ 7 min. Then the cleaved RNA fragments were incubated for 2 h 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). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are amplified with PCR by the following conditions: initial denaturation at 95 ℃ for 3 min; 8 cycles of denaturation at 98 ℃ for 15 sec, annealing at 60 ℃ for 15 sec, and extension at 72 ℃ for 30 sec; and then final extension at 72 ℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: macrophage

value: T. gondii RH strain infected 24h


title: Homo sapiens,T. gondii infected,24h,Infected_input RNA,rep2

description: Library name: Infected2_input


title: liver biopsy [liver339]

value: TCMR


title: liver biopsy [GSM5774119 re-analysis]


title: liver biopsy [GSM5774118 re-analysis]


title: Homo sapiens,T. gondii infected,24h,Infected_input RNA,rep1

description: Library name: Infected1_input


title: liver biopsy [GSM5774123 re-analysis]


title: liver biopsy [GSM5774116 re-analysis]


title: Homo sapiens,Control_IP RNA,rep2

description: Library name: Control2_IP


title: Homo sapiens,Control_input RNA,rep2

description: Library name: Control2_input


title: Homo sapiens,Control_IP RNA,rep1

description: Library name: Control1_IP


title: liver biopsy [GSM5774115 re-analysis]


title: liver biopsy [GSM5774117 re-analysis]


title: HeLa,H3K27Ac,EGF,rep2

description: Library name: WT_EGF_H3K27Ac_ChIP_rep2

treatment_protocol: For E2 stimulation, when the density of MCF-7 cells was up to 40%, DMEM was changed to Phenol Red-free RPMI-1640 with 10% Charcoal Stripped Fetal Bovine Serum for 72 h. Final concentration of 100 nM 17β-estradiol (E2) were added into the cell culture medium, cells were incubated in 37 °C for 1 h. For EGF stimulation, when the density of HeLa cells was up to 70%, 10% FBS contained DMEM was changed to 0.5% FBS contained DMEM for 48h. Final concentration of 50ng/mL EGF were added to the cell culture medium, cells were incubated in 37℃ for 20min. For transcription inhibitor treatment, after the cell were cultured in  Phenol Red-free RPMI-1640 for 66h, 1μM Flavopiridol or 1μM Triptolide was added into the culture medium for 6h, 100nM E2 was added into the culture medium at the 5th hour and co-culture with transcription inhibitor for 1h.

value: HeLa

value: WT

value: H3K27Ac (Millipore, 07-360)

value: EGF


title: Homo sapiens,T. gondii infected,24h,Infected_IP RNA,rep2

description: Library name: Infected2_IP


title: Homo sapiens,Control_input RNA,rep1

description: Library name: Control1_input


title: HeLa,H3K4me1,PBS,rep2

description: Library name: WT_PBS_H3K4me1_ChIP_rep2

value: H3K4me1 (ActiveMotif, 39297)

value: PBS


title: HeLa,H3K4me1,EGF,rep2

description: Library name: WT_EGF_H3K4me1_ChIP_rep2


title: liver biopsy [GSM5774113 re-analysis]


title: HeLa,H3K27Ac,PBS,rep2

description: Library name: WT_PBS_H3K27Ac_ChIP_rep2


title: liver biopsy [GSM5774114 re-analysis]

value: NKRL


title: liver biopsy [GSM5774112 re-analysis]


title: HeLa,ZMYND8,EGF,rep2

description: Library name: WT_EGF_ZMYND8_ChIP_rep2

value: ZMYND8(Bethyl, A302-090A)


title: HeLa,ZMYND8,PBS,rep2

description: Library name: WT_PBS_ZMYND8_ChIP_rep2


title: HeLa,H3K27Ac,EGF,rep1

description: Library name: WT_EGF_H3K27Ac_ChIP_rep1


title: liver biopsy [GSM5774109 re-analysis]


title: liver biopsy [GSM5774111 re-analysis]


title: liver biopsy [GSM5774107 re-analysis]


title: liver biopsy [GSM5774108 re-analysis]


title: HeLa,H3K4me1,EGF,rep1

description: Library name: WT_EGF_H3K4me1_ChIP_rep1


title: liver biopsy [GSM5774104 re-analysis]


title: liver biopsy [GSM5774110 re-analysis]


title: MCF-7,Z8KO,H3K4me3,E2,rep2

description: Library name: MCF7_Z8KO_E2_H3K4me3_ChIP_rep2


title: HeLa,H3K4me1,PBS,rep1

description: Library name: WT_PBS_H3K4me1_ChIP_rep1


title: HeLa,ZMYND8,EGF,rep1

description: Library name: WT_EGF_ZMYND8_ChIP_rep1


title: liver biopsy [GSM5774103 re-analysis]


title: HeLa,ZMYND8,PBS,rep1

description: Library name: WT_PBS_ZMYND8_ChIP_rep1


title: liver biopsy [GSM5774105 re-analysis]


title: MCF-7,Z8KO,H3K14Ac,E2,rep2

description: Library name: MCF7_Z8KO_E2_H3K14Ac_ChIP_rep2

value: H3K14Ac (abcam,ab52946)


title: MCF-7,Z8KO,H3K14Ac,EtOH,rep2

description: Library name: MCF7_Z8KO_EtOH_H3K14Ac_ChIP_rep2

value: EtOH


title: HeLa,H3K27Ac,PBS,rep1

description: Library name: WT_PBS_H3K27Ac_ChIP_rep1


title: MCF-7,Z8KO,Pol2,E2,rep2

description: Library name: MCF7_Z8KO_E2_Pol2_ChIP_rep2

value: Pol 2 (Biolegend,664906)


title: MCF-7,Z8KO,Pol2,EtOH,rep2

description: Library name: MCF7_Z8KO_EtOH_Pol2_ChIP_rep2


title: MCF-7,WT,H3K4me3,E2,rep2

description: Library name: MCF7_WT_E2_H3K4me3_ChIP_rep2


title: liver biopsy [GSM5774099 re-analysis]


title: liver biopsy [GSM5774096 re-analysis]


title: liver biopsy [GSM5774098 re-analysis]

value: NR


title: liver biopsy [GSM5774092 re-analysis]

value: liver biopsy


title: liver biopsy [GSM5774095 re-analysis]


title: liver biopsy [GSM5774093 re-analysis]


title: liver biopsy [GSM5774091 re-analysis]


title: MCF-7,WT,H3K4me3,EtOH,rep2

description: Library name: MCF7_WT_EtOH_H3K4me3_ChIP_rep2


title: liver biopsy [GSM5774090 re-analysis]


title: liver biopsy [GSM5774101 re-analysis]

value: Injury


title: liver biopsy [GSM5774102 re-analysis]


title: MCF-7,Z8KO,H3K4me3,EtOH,rep2

description: Library name: MCF7_Z8KO_EtOH_H3K4me3_ChIP_rep2


title: MCF-7,WT,H3K14Ac,E2,rep2

description: Library name: MCF7_WT_E2_H3K14Ac_ChIP_rep2


title: liver biopsy [GSM5774088 re-analysis]


title: MCF-7,WT,H3K14Ac,EtOH,rep2

description: Library name: MCF7_WT_EtOH_H3K14Ac_ChIP_rep2


title: liver biopsy [GSM5774086 re-analysis]


title: MCF-7,WT,Pol2,E2,rep2

description: Library name: MCF7_WT_E2_Pol2_ChIP_rep2


title: MCF-7,WT,H3K27Ac,EtOH,rep2

description: Library name: MCF7_WT_EtOH_H3K27Ac_ChIP_rep2


title: MCF-7,WT,H3K27Ac,E2,rep2

description: Library name: MCF7_WT_E2_H3K27Ac_ChIP_rep2


title: liver biopsy [GSM5774106 re-analysis]


title: MCF-7,WT,H3K4me1,E2,rep2

description: Library name: MCF7_WT_E2_H3K4me1_ChIP_rep2


title: MCF-7,WT,H3K4me1,EtOH,rep2

description: Library name: MCF7_WT_EtOH_H3K4me1_ChIP_rep2


title: liver biopsy [GSM5774079 re-analysis]


title: MCF-7,WT,ZMYND8,triptolide,rep2

description: Library name: MCF7_WT_triptolide_ZMYND8_ChIP_rep2

value: ZMYND8 (Bethyl, A302-090A)


title: MCF-7,WT,Pol2,EtOH,rep2

description: Library name: MCF7_WT_EtOH_Pol2_ChIP_rep2


title: MCF-7,WT,ZMYND8,EtOH,rep2

description: Library name: MCF7_WT_EtOH_ZMYND8_ChIP_rep2


title: MCF-7,WT,ZMYND8,flabvopiridol,rep2

description: Library name: MCF7_WT_flavopiridol_ZMYND8_ChIP_rep2


title: liver biopsy [GSM5774075 re-analysis]


title: liver biopsy [GSM5774083 re-analysis]


title: MCF-7,WT,ZMYND8,E2,rep2

description: Library name: MCF7_WT_E2_ZMYND8_ChIP_rep2


title: liver biopsy [GSM5774077 re-analysis]


title: liver biopsy [GSM5774081 re-analysis]


title: liver biopsy [GSM5774082 re-analysis]


title: liver biopsy [GSM5774085 re-analysis]


title: liver biopsy [GSM5774074 re-analysis]


title: MCF-7,Z8KO,H3K4me3,EtOH,rep1

description: Library name: MCF7_Z8KO_EtOH_H3K4me3_ChIP_rep1


title: liver biopsy [GSM5774071 re-analysis]


title: MCF-7,Z8KO,H3K14Ac,E2,rep1

description: Library name: MCF7_Z8KO_E2_H3K14Ac_ChIP_rep1


title: MCF-7,Z8KO,H3K14Ac,EtOH,rep1

description: Library name: MCF7_Z8KO_EtOH_H3K14Ac_ChIP_rep1


title: liver biopsy [GSM5774094 re-analysis]


title: liver biopsy [GSM5774069 re-analysis]


title: MCF-7,Z8KO,Pol2,E2,rep1

description: Library name: MCF7_Z8KO_E2_Pol2_ChIP_rep1


title: MCF-7,Z8KO,H3K4me3,E2,rep1

description: Library name: MCF7_Z8KO_E2_H3K4me3_ChIP_rep1


title: liver biopsy [GSM5774068 re-analysis]


title: liver biopsy [GSM5774073 re-analysis]


title: EOC153, sensitive, scRNA-seq

description:
Library name: EOC153_sensitive
10x Genomics

value: Omentum

value: chemo-sensitive

value: patient diagnosed with ovarian high-grade serous carcinoma (HGSC)

value: Chemo-naïve


title: MCF-7,Z8KO,Pol2,EtOH,rep1

description: Library name: MCF7_Z8KO_EtOH_Pol2_ChIP_rep1


title: liver biopsy [GSM5774064 re-analysis]


title: MCF-7,WT,H3K4me3,E2,rep1

description: Library name: MCF7_WT_E2_H3K4me3_ChIP_rep1

value: WT


title: liver biopsy [GSM5774063 re-analysis]


title: liver biopsy [GSM5774066 re-analysis]


title: EOC3, refractory, scRNA-seq

description:
Library name: EOC3_refractory
10x Genomics

value: Peritoneum

value: chemo-refractory


title: EOC372, sensitive, scRNA-seq

description:
Library name: EOC372_sensitive
10x Genomics


title: EOC136, sensitive, scRNA-seq

description:
Library name: EOC136_sensitive
10x Genomics

value: Mesentery


title: EOC87, refractory, scRNA-seq

description:
Library name: EOC87_refractory
10x Genomics


title: tSAECs MoCu TGFb 5

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description: Library name: tSAECs_MoCu_TGFb_5

data_processing:
Demultiplexing was conducted using bcl2fastq2 v2.20.0.422 from Illumina. Other pre-processing was performed as previously described (PMID: 29231921).
Assembly: GRCh38.86
Supplementary files format and content: Tab-separated count matrix file containing combined raw counts of all 70 samples.

source_name: lung

growth_protocol: Primary healthy human lung airway epithelial cells (SAECs, Lonza) were used in passages 2-3. They were expanded in flasks on type I collagen (Corning) pre-coated cell culture flasks in PneumaCult-Ex Plus Medium (STEMCELL Technologie) until confluency of around 80%. For air-liquid-interface cultivation and differentiation, 30 000 cells/well SAECs were seeded on collagen-coated transwells and grown until confluency in PneumaCul-Ex Plus Medium. Airlift was conducted by changing medium to PneumaCul-ALI Medium (STEMCELL Technologies) and exposing cells apically to air. Healthy human lung fibroblasts (LF, Lonza) were used in passages 4-7. They were expanded in flasks in Fibroblast Basal Medium with FGM2- Fibroblast Growth Medium BulletKit (Lonza) until confluency of around 70%.

extract_protocol:
Chronically injured and acutely injured SAECs were cultivated as previously described and lysed in RLT plus buffer (Qiagen). Total RNA was isolated and purified using the MagMAXTM 96 Total RNA Isolation Kit (Thermo Fisher) following manufacturer’s instruction. Total RNA was assessed for quantity using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (Thermo Fisher) and quality using the Standard Sensitivity RNA Analysis DNF-471 Kit (Agilent) on a 48-channel Fragment Analyzer (Agilent).
Samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). A total of 200 ng RNA was used for library construction using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs). RNA-seq libraries were processed on a Biomek i7 Hybrid instrument (Beckman Coulter) using 12 PCR cylces following manufacturer’s instruction instead of SRPIselect beads). Final RNA-seq libraries were then quantified by the High Sensitivity dsDNA Quanti- iT Assay Kit (Thermo Fisher) on a BioTek Synergy HTX (Agilent). And assessed for their size distribution and adapter dimer presence using the High Sensitivity Small Fragment DNF-477 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR and pooled. Additionally, PhiX Control v3 (Illumina) was spiked in. The pooled libraries were clustered on a Paired-End Flow Cell and sequenced on a HiSeq 4000 Sequencing System (Illumina) with dual index, paired-end reads at 75 bp length. Read parameters: Rd1: 76 bp, Rd2: 8 bp, Rd3: 8 bp, Rd4: 76 bp with an average sequencing depth of around 30 million pass-filter reads per sample.

treatment_protocol: SAECs were differentiated in air liquid interface on transwells for 10 days until differentiated cells were initially observed. Afterwards, ALI SAECs were treated for 14 days with 1 ng/ml TGF-β1 (Biotechne) to induce chronic injury on SAECs. For the acute injury model, ALI SAECs were cultivated for 14 days without any stimuli. After 14 days, both, SAECs for chronic and acute injury were transferred into cocultures with human lung fibroblasts +/- 1 ng/ml TGF-β1 and +/- PTX3 in the basolateral chamber for additional 3 days. Before setting up the coculture, both, SAECs and LFs were starved for 6-8 h in normal DMEM (GibcoTM).

value: lung

value: airway epithelial cells

tag: injury model

value: chronic

value: TGFb

tag: culture format

value: mono culture


title: liver biopsy [GSM5774070 re-analysis]

tag: tissue


title: liver biopsy [GSM5774062 re-analysis]

value: NR


title: MCF-7,WT,H3K14Ac,E2,rep1

description: Library name: MCF7_WT_E2_H3K14Ac_ChIP_rep1

tag: genotype

value: H3K14Ac (abcam,ab52946)


title: tSAECs MoCu TGFb 4

description: Library name: tSAECs_MoCu_TGFb_4


title: tSAECs MoCu TGFb 2

description: Library name: tSAECs_MoCu_TGFb_2


title: tSAECs MoCu TGFb 3

description: Library name: tSAECs_MoCu_TGFb_3


title: liver biopsy [GSM5774060 re-analysis]

value: liver biopsy


title: MCF-7,WT,H3K14Ac,EtOH,rep1

description: Library name: MCF7_WT_EtOH_H3K14Ac_ChIP_rep1

value: EtOH


title: liver biopsy [GSM5774065 re-analysis]

value: Injury


title: liver biopsy [GSM5774061 re-analysis]


title: MCF-7,WT,Pol2,E2,rep1

description: Library name: MCF7_WT_E2_Pol2_ChIP_rep1

value: Pol 2 (Biolegend,664906)


title: MCF-7,WT,Pol2,EtOH,rep1

description: Library name: MCF7_WT_EtOH_Pol2_ChIP_rep1


title: tSAECs MoCu Control 4

description: Library name: tSAECs_MoCu_Control_4

value: control


title: liver biopsy [GSM5774059 re-analysis]


title: liver biopsy [GSM5774057 re-analysis]


title: liver biopsy [GSM5774058 re-analysis]


title: MCF-7,WT,H3K4me3,EtOH,rep1

description: Library name: MCF7_WT_EtOH_H3K4me3_ChIP_rep1


title: tSAECs MoCu Control 3

description: Library name: tSAECs_MoCu_Control_3


title: tSAECs MoCu Control 5

description: Library name: tSAECs_MoCu_Control_5


title: tSAECs MoCu Control 1

description: Library name: tSAECs_MoCu_Control_1


title: tSAECs LFs CoCu TGFb 5

description: Library name: tSAECs_LFs_CoCu_TGFb_5

value: airway epithelial cells, fibroblasts

value: co culture


title: MCF-7,WT,H3K27Ac,EtOH,rep1

description: Library name: MCF7_WT_EtOH_H3K27Ac_ChIP_rep1

value: WT

value: H3K27Ac (Millipore, 07-360)


title: MCF-7,WT,H3K27Ac,E2,rep1

description: Library name: MCF7_WT_E2_H3K27Ac_ChIP_rep1


title: tSAECs LFs CoCu TGFb 4

description: Library name: tSAECs_LFs_CoCu_TGFb_4


title: tSAECs LFs CoCu TGFb 3

description: Library name: tSAECs_LFs_CoCu_TGFb_3


title: liver biopsy [GSM5774056 re-analysis]

value: TCMR


title: MCF-7,WT,H3K4me1,E2,rep1

description: Library name: MCF7_WT_E2_H3K4me1_ChIP_rep1

value: H3K4me1 (ActiveMotif, 39297)


title: tSAECs MoCu TGFb 1

description: Library name: tSAECs_MoCu_TGFb_1

value: lung

value: airway epithelial cells


title: MCF-7,WT,H3K4me1,EtOH,rep1

description: Library name: MCF7_WT_EtOH_H3K4me1_ChIP_rep1


title: liver biopsy [GSM5774055 re-analysis]


title: tSAECs LFs CoCu Control 5

description: Library name: tSAECs_LFs_CoCu_Control_5

value: chronic


title: tSAECs LFs CoCu TGFb 1

description: Library name: tSAECs_LFs_CoCu_TGFb_1

value: TGFb


title: liver biopsy [GSM5774054 re-analysis]

value: NR


title: tSAECs LFs CoCu Control 4

description: Library name: tSAECs_LFs_CoCu_Control_4


title: MCF-7,WT,ZMYND8,triptolide,rep1

description: Library name: MCF7_WT_triptolide_ZMYND8_ChIP_rep1

value: ZMYND8 (Bethyl, A302-090A)


title: liver biopsy [GSM5774053 re-analysis]

value: liver biopsy


title: tSAECs LFs CoCu Control 3

description: Library name: tSAECs_LFs_CoCu_Control_3


title: liver biopsy [GSM5774052 re-analysis]


title: MCF-7,WT,ZMYND8,flabvopiridol,rep1

description: Library name: MCF7_WT_flavopiridol_ZMYND8_ChIP_rep1

value: EtOH


title: nSAECs MoCu TGFb 5

description: Library name: nSAECs_MoCu_TGFb_5

value: acute

value: mono culture


title: MCF-7,WT,ZMYND8,E2,rep1

description: Library name: MCF7_WT_E2_ZMYND8_ChIP_rep1


title: tSAECs LFs CoCu Control 2

description: Library name: tSAECs_LFs_CoCu_Control_2

value: control


title: liver biopsy [GSM5774051 re-analysis]


title: tSAECs MoCu Control 2

description: Library name: tSAECs_MoCu_Control_2


title: tSAECs LFs CoCu Control 1

description: Library name: tSAECs_LFs_CoCu_Control_1

value: airway epithelial cells, fibroblasts


title: nSAECs MoCu TGFb 2

description: Library name: nSAECs_MoCu_TGFb_2


title: MCF-7,WT,ZMYND8,EtOH,rep1

description: Library name: MCF7_WT_EtOH_ZMYND8_ChIP_rep1


title: tSAECs LFs CoCu TGFb 2

description: Library name: tSAECs_LFs_CoCu_TGFb_2

value: co culture


title: nSAECs MoCu TGFb 3

description: Library name: nSAECs_MoCu_TGFb_3


title: nSAECs MoCu TGFb 1

description: Library name: nSAECs_MoCu_TGFb_1


title: nSAECs MoCu Control 5

description: Library name: nSAECs_MoCu_Control_5


title: MCF-7, ZMYND8-KO, E2, chrRNA, rep2

description:
Library name: ZMYND8KO_E2_chrRNAseq_rep2
treated with E2 for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA

library_source: other

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads.
The remaining reads were aligned to human rRNA and mouse rRNA using Bowtie2 v2.5.1 with parameters "--very-sensitive-local --no-unal -I 1 -X 1000 ", the output reads were aligned to the hg19 genome using STAR v2.7.5c with parameter “-outFilterMultimapNmax 1 -outBAMsortingBinsN 100 ”.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: Genome coverage bigwig files

molecule: other

growth_protocol: MCF-7 cells were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS, Gibco #10099141C), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010) at 37℃ with 5% CO2.  For E2 stimulaiton, cells were shifted to Phenol Red-free RPMI-1640 Medium (Hyclone #SH30605) containing 10% Charcoal Stripped Fetal Bovine Serum (Viva Cell #3830-0050), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1% Glutamine (Hyclone #SH30034) .

extract_protocol:
chrRNAs were isolated and extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Strand specific chrRNA libraries were prepared according to VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazymes, #NR604-01).

treatment_protocol: For E2 stimulation, when the density of MCF-7 cells was up to 40%, DMEM was changed to Phenol Red-free RPMI-1640 with 10% Charcoal Stripped Fetal Bovine Serum for 72 h. Final concentration of 100 nM 17β-estradiol (E2) were added into the cell culture medium, cells were incubated in 37 °C for 1 h.


title: nSAECs MoCu Control 3

description: Library name: nSAECs_MoCu_Control_3


title: MCF-7, ZMYND8-KO, EtOH, chrRNA, rep2

description:
Library name: ZMYND8KO_EtOH_chrRNAseq_rep2
treated with EtOH for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA


title: nSAECs MoCu Control 4

description: Library name: nSAECs_MoCu_Control_4


title: liver biopsy [GSM5774048 re-analysis]


title: liver biopsy [GSM5774049 re-analysis]

value: Injury


title: nSAECs MoCu Control 2

description: Library name: nSAECs_MoCu_Control_2


title: MCF-7, WT, E2, chrRNA, rep2

description:
Library name: WT_E2_chrRNAseq_rep2
treated with E2 for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA

value: WT


title: liver biopsy [GSM5774047 re-analysis]


title: liver biopsy [GSM5774046 re-analysis]


title: nSAECs LFs CoCu TGFb 5

description: Library name: nSAECs_LFs_CoCu_TGFb_5


title: nSAECs LFs CoCu TGFb 4

description: Library name: nSAECs_LFs_CoCu_TGFb_4


title: nSAECs MoCu Control 1

description: Library name: nSAECs_MoCu_Control_1


title: nSAECs LFs CoCu TGFb 1

description: Library name: nSAECs_LFs_CoCu_TGFb_1


title: nSAECs LFs CoCu TGFb 2

description: Library name: nSAECs_LFs_CoCu_TGFb_2


title: MCF-7, ZMYND8-KO, EtOH, chrRNA, rep1

description:
Library name: ZMYND8KO_EtOH_chrRNAseq_rep1
treated with EtOH for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA


title: MCF-7, ZMYND8-KO, E2, chrRNA, rep1

description:
Library name: ZMYND8KO_E2_chrRNAseq_rep1
treated with E2 for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA


title: nSAECs LFs CoCu Control 5

description: Library name: nSAECs_LFs_CoCu_Control_5


title: nSAECs LFs CoCu TGFb 3

description: Library name: nSAECs_LFs_CoCu_TGFb_3


title: nSAECs LFs CoCu Control 3

description: Library name: nSAECs_LFs_CoCu_Control_3


title: nSAECs LFs CoCu Control 4

description: Library name: nSAECs_LFs_CoCu_Control_4


title: liver biopsy [GSM5774050 re-analysis]


title: nSAECs LFs CoCu Control 2

description: Library name: nSAECs_LFs_CoCu_Control_2


title: MCF-7, WT, E2, chrRNA, rep1

description:
Library name: WT_E2_chrRNAseq_rep1
treated with E2 for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA


title: nSAECs LFs CoCu Control 1

description: Library name: nSAECs_LFs_CoCu_Control_1


title: liver biopsy [GSM5774043 re-analysis]

value: TCMR


title: liver biopsy [GSM5774044 re-analysis]


title: liver biopsy [GSM5774041 re-analysis]


title: LFs tSAECs CoCu TGFb 4

description: Library name: LFs_tSAECs_CoCu_TGFb_4


title: liver biopsy [GSM5774042 re-analysis]

value: NKRL


title: DMD3_WiCell_scRNAseq

city: Bochum

first: Holm

last: Zaehres

state: NRW

address: Universitaetsstr. 150

department: Institute of Anatomy

institute: Ruhr University Bochum

description:
10x Genomics
sample4_DMD3

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.1a) used for human reference genome (hg38) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Assembly: hg38
Supplementary files format and content: tsv files include UMI counts for each cell barcode and genes

source_name: iPSC-derived skeletal muscle organoid

extract_protocol:
Organoid 12 weeks post differentiation were dissociated into single cells upon incubation for 1hr with solution containing papain and EDTA. Upon dissociation, we estimated the cell number and viability; then cells were resuspended on solution containing 0.5% BSA in PBS to reach concentration of 390 cells per ul.
The cDNA library was prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), Single Cell B Chip Kit (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics).

value: iPSC-derived skeletal muscle organoid

value: DMD WiCell iPSC line

value: 12 weeks


title: LFs tSAECs CoCu TGFb 2

description: Library name: LFs_tSAECs_CoCu_TGFb_2

value: lung

value: chronic

value: TGFb


title: MCF-7, WT, EtOH, chrRNA, rep2

description:
Library name: WT_EtOH_chrRNAseq_rep2
treated with EtOH for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA


title: DMD2_(Beckman)_scRNAseq

description:
10x Genomics
sample3_DMD2

value: DMD2 iPSC line


title: LFs tSAECs CoCu TGFb 3

description: Library name: LFs_tSAECs_CoCu_TGFb_3


title: LFs tSAECs CoCu Control 5

description: Library name: LFs_tSAECs_CoCu_Control_5


title: LFs tSAECs CoCu TGFb 1

description: Library name: LFs_tSAECs_CoCu_TGFb_1


title: LFs tSAECs CoCu Control 3

description: Library name: LFs_tSAECs_CoCu_Control_3


title: MCF-7, WT, EtOH, chrRNA, rep1

description:
Library name: WT_EtOH_chrRNAseq_rep1
treated with EtOH for 1h, cells were fractionated to extract the chromatin-associated fraction of RNA

value: EtOH


title: LFs tSAECs CoCu Control 4

description: Library name: LFs_tSAECs_CoCu_Control_4


title: liver biopsy [liver338]

value: NR

value: liver biopsy


title: liver biopsy [GSM5774039 re-analysis]


title: LFs tSAECs CoCu Control 2

description: Library name: LFs_tSAECs_CoCu_Control_2

value: control