title: OP3

value: peripheral blood mononuclear cells


title: kidney biopsy [GSM3524459 re-analysis]

status: Public on Sep 04 2024

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

molecule: total RNA

organism: Homo sapiens

source_name: kidney 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 heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
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: rej7aaclust (nr, minor, tcmr1, tcmr2, eabmr, fabmr, labmr)

value: NR

tag: tissue

value: kidney biopsy


title: kidney biopsy [GSM3524494 re-analysis]

value: FABMR


title: OP2

type: SRA

city: Xi'an

first: Xuzhao

last: Bian

state: Shaan'xi

address: No.28 Xianning West Road

country: China

institute: xi'an jiaotong university

library_source: transcriptomic

data_processing:
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow:FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * TranscriptLength(kb)}}
Assembly: GRCh38 (hg38)
Supplementary files format and content: normalized_data.xls
Supplementary files format and content: raw_counts.xls

molecule: polyA RNA

source_name: peripheral blood mononuclear cells

extract_protocol:
Peripheral blood was collected into an anticoagulant tube, and peripheral blood mononuclear cells (PBMCs) were isolated using a commercial Lymphocyte Separation Medium (Beyotime, China) by centrifugation at 700g for 30 minutes.
For library preparation and sequencing, each RNA sample, with an input quantity of 1 μg, underwent library construction using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, Shanghai, China), as per the provided protocol.

tag: cell type

tag: disease

value: Hemorrhagic Fever with Renal Syndrome


title: SBC-3, siCtrl, RNA-seq rep.2

city: Montreal

first: Thomas

middle: Francis

last: Duchaine

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

data_processing:
Adapter sequences, low-quality ends (phred quality < 15), and short reads (< 35 nt) were removed using Cutadapt v4.2.
Reads were mapped to the hg38 Ensembl v104 genome assembly using STAR v2.7.5a.
Gene-level stranded-reads counts were quantified using featureCounts (Subread v2.0.3).
Normalization and differential expression were performed using the R package DESeq2 v1.38.1.
Assembly: hg38 Ensembl v104
Supplementary files format and content: tab-delimimted text file contains gene information and counts for each sample

growth_protocol: SBC-3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS). Cells were incubated in a humidified environment at 37 °C with 5 % CO2.

extract_protocol:
Total RNA from mammalian cells was prepared using Trizol reagent according to the manufacturer's instructions.
RNA libraries were prepared with the KAPA RNA HyperPrep Kit (Roche) according to the manufacturer’s instructions using 100 ng poly(A)-selected RNA for mRNA sequencing and Illumina universal adapters.

treatment_protocol: siRNAs and ASOs (10 nM) were reverse transfected into SBC-3 cells with Lipofectamine RNAiMAX according to the manufacturer’s instructions. Cells were harvested 72 h post-transfection.

tag: cell line

value: Small cell lung cancer

tag: genotype

value: WT

tag: treatment

value: siCtrl


title: Kidney, fibroblasts, Trf1+/+; Col1a2-CreERT2, RGQ00329

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
Obtained reads were single-end 86bp. Read adaptors and poly(A) tails were removed with bbduk.sh, following the Lexogen recommendations. Reads were then analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm39) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1, using the mouse gene annotation from GENCODE (vM26.GRCm39.Ensembl103). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Tabulated text file with DESeq2 normalized counts

organism: Mus musculus

source_name: Kidney

growth_protocol: Not applicable

extract_protocol:
Mice were euthanized after 8 weeks and kidneys were extracted.  To isolate fibroblasts populations in Col1a2 -CreERT2 mice, kidneys were collected in PBS, minced, and digested with 2.5 mg/ml type I collagenase (Thermo Fisher, 17100017), 2.5 mg/ml dispase II (Thermo Fisher, 17105041), and 50 ng/ml DNAse I (Roche, 10104159001) at 37 °C for 20 min to create a homogeneous cell suspension. Cell suspensions were passed through a 70 μm filter (Cultek, 45352350) to remove any undigested tissue. To remove erythroid cells, cell suspensions and blood samples were incubated for 10 min on ice in blood erythrocyte lysis buffer (Qiagen, 79217). Before analysis, cell suspensions were treated with PBS 0.04% Ultrapure BSA (Thermo Fisher, AM216). Cells were incubated at 4 °C for 30 min with anti-mouse CD29-PE (clone: HMB1-1, 1:00) (Milteneyi Biotec, 130-102-994)  and anti t-RFP (EVN-AB233, Evrogen; 1:00) for fibroblasts isolation respectively. Chicken anti-Rabbit Alexa 647 (A21443, Invitrogen;1:400) was used as a secondary control against t-RFP Thermo Fisher, A21443. Isolated cells were collected on a mix of NEBNext® Cell Lysis Buffer (New England Biolabs, E6428A) and Murine RNase Inhibitor (New England Biolabs, E6429A) in DNA LoBIND tubes (Eppendorf, 0030108051), using a BD FACSAria IIu cell sorter (BD Biosciences).
500 cells per sample were were processed with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. Briefly, extracts obtained by sample suspension in cell lysis buffer were submitted to an oligo(dT) primed reverse transcription with a template switching reaction. Double stranded cDNA production was performed by limited-cycle PCR. Sequencing libraries were completed with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805). These libraries are non-directional or non-stranded. The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.
Single read 86bp

treatment_protocol: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to six-to eight-week-old male and female Trf1+/+ KFP+/t Cre+/t and Trf1lox/lox KFP+/t Cre+/t mice for three times a week for 8 weeks

value: Kidney

value: fibroblasts

value: Trf1+/+; Col1a2-CreERT2

value: Tamoxifen


title: SBC-3, siCtrl, RNA-seq rep.1


title: kidney biopsy [GSM3524427 re-analysis]


title: EP2/EP4KO NK cells, CM-treated, stimulated with anti-NK1.1, rep2

city: Munich

first: Anna-Marie

last: Pedde

address: Ismaningerstr. 22

department: Institute of Molecular Immunology

country: Germany

institute: Klinikum rechts der Isar, TU Munich

data_processing:
Data was processed using the published Drop-seq pipeline to map raw sequence reads to the reference genome and to generate transcript counts.
Reference genome (GRCm38) was used for alignment.
Transcript and gene definitions were used according to the GENCODE M25.
DESeq2 R package was utilized to identify differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Txt file is tab delimited table with raw sequence counts of each sample.

source_name: splenic NK cells

growth_protocol: Murine NK cells were isolated from spleen and cultured in low doses of IL-2 and IL15:IL15Ra for 5 days.

extract_protocol:
RNA from NK cells was isolated using the NEB Monarch Total RNA Miniprep Kit.
RNA extract from mouse NK cells was used for construction of bulk 3’ mRNA-seq libraries as previously described (Parekh et al. 2016). In brief, RNA of individual samples was reversely transcribed by a Maxima RTpolymerase using oligo-dT primers containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5′ ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al., the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition.

treatment_protocol: 1x10e5 NK cells were seeded in 200ul RPMI supplemented with IL-2 and the respective treatments for indicated periods of time.

value: splenic NK cells

value: CM control 1h + aNK1.1 stimulation 4h


title: kidney biopsy [GSM3525438 re-analysis]

value: EABMR


title: ZIC3 KO_C1, long-read, biol rep 3 of 3

city: Indianapolis

first: John

middle: Robert

last: Wells

state: IN

address: 1044 W Walnut St

department: Department of Medical & Molecular Genetics

country: USA

institute: Indiana University School of Medicine

description:
ZIC3_KO_C1_ONT_Flowcell_BiolRep3
ZIC3_KO_3
Long_Read_Log_CPM_EdgeR.txt

data_processing:
For the short-read RNA-seq, results were aligned to the GRCh38/hg38 reference genome using two passes of the Spliced Transcripts Alignment to a Reference (STAR) aligner, version 2.7.10b and visualized in the Integrated Genomics Viewer (IGV).
For the long-read RNA-seq, the following software was used: MinKNOW v22.12.5, Bream v7.4.8, Configuration v5.4.7, Guppy v6.4.6, MinKNOW Core v5.4.3. Bases were called using Guppy v6.4.6 running the super-accurate basecalling model, 450 bp setting. The fastq files from each of the three flow cells were merged together based on the sequencing barcode. Results were aligned to the GRCh38/hg38 reference genome using minimap2 and visualized in IGV. Differential expression analysis was conducted using the R package edgeR (version 4.0.2) comparing undifferentiated ZIC3 WT, ZIC3 AtoG_C1, and ZIC3 KO_C1 H1-OCT4-eGFP cells.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for all short-read RNA-seq samples - Short_Read_Raw_Counts_All_Samples.txt
Supplementary files format and content: tab-deliminated text file includes log_CPM values for all long-read RNA-seq samples - Long_Read_Log_CPM_EdgeR.txt

growth_protocol: Wildtype, ZIC3 c.1224+3286A>G, and ZIC3 knockout (KO) H1-OCT4-EGFP cells were cultured following the WiCell Feeder Independent Stem Cell Protocols using geneticin (G418 sulfate; Gibco) standard operating procedure 208 version 2.0. Briefly, 6-well plates (Corning) were coated with Matrigel® Matrix (growth factor reduced) diluted in DMEM/F-12, HEPES media (Invitrogen). After thawing, cell lines were cultured in Matrigel®-coated 6-well plates with mTeSR1 media (STEMCELL Technologies Inc.). Cells were maintained in mTeSR1 media for an additional 24 h, then replaced with mTeSR1 media supplemented with 100 µg/mL of geneticin (mTeSR1-G). Cells were dissociated using Versene solution (Gibco) and collected for further experiments.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) followed by column purification with the RNeasy MinElute Cleanup kit (Qiagen).
Short-read RNA-seq was completed by the Indiana University School of Medicine Center for Molecular Genomics. Total RNA was extracted from wildtype, ZIC3 AtoG_C1, ZIC3 AtoG_C2, ZIC3 KO_C1, and ZIC3 KO_C2 H1-OCT4-EGFP cells. The RNA integrity number (RIN) was determined using an Agilent TapeStation (Agilent Technologies) followed by an RNA purification step with the KAPA RNA HyperPrep kit (Roche). cDNA libraries were prepared using the NovaSeq 6000 SP Reagent kit v1.5 (300 cycles) and sequenced using the NovaSeq 6000 (Illumina) with 2 x 150 bp paired-end reads.   Long-read RNA-seq was performed by the Genome Access Technology Center at Washington University in St. Louis. Total RNA was extracted from control (ZIC3 WT) (n=3), ZIC3 AtoG_C1 (n=3), and ZIC3 KO_C1 (n=3) H1-OCT4-EGFP cells and the RIN determined with an Agilent Bioanalyzer (Agilent Technologies). Sequencing libraries were prepared with the PCR-cDNA Barcoding kit SQK-PCB111.24 (Oxford Nanopore Technologies) and the Agilent Bioanalyzer (Agilent Technologies) served for quality assessment. Cell samples were pooled together on three PromethION R9.4.1 flow cells (50 fM/flow cell) and sequenced in a PromethION 24 A100 (Oxford Nanopore Technologies) for 90 h.

treatment_protocol: Undifferentiated - cultured in mTeSR1 media supplemented with 100 µg/mL of geneticin. Three short-read RNA-seq samples also received 100 µg/mL cyloheximide (CHX) for 6 hr prior to RNA extraction.

value: human embryonic stem cell

value: ZIC3 c.190_200delinsG (ZIC3 KO_C1)


title: ZIC3 KO_C1, long-read, biol rep 2 of 3

description:
ZIC3_KO_C1_ONT_Flowcell_BiolRep2
ZIC3_KO_2
Long_Read_Log_CPM_EdgeR.txt

value: Undifferentiated - cultured in mTeSR1 media supplemented with 100 µg/mL of geneticin


title: OP1

value: peripheral blood mononuclear cells


title: kidney biopsy [GSM3524308 re-analysis]

value: NR

value: kidney biopsy


title: chr2_Rep1-Rep5 and yfp_Rep1-Rep5

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

library_source: transcriptomic single cell

data_processing:
FASTQ files were deconvoluted and transcript abundance was estimated using zUMIs v2.9.6 and GENCODE vM26 annotations. Bases 1-66 were extracted from the R1 file, corresponding to cDNA sequence, and for the R2 file, bases 1-10 represented UMI, and bases 11-18, 49-56, and 87-94 represented the three barcodes. Internally, zUMIs performs a two-pass alignment using STAR v2.7.3a  with the additional parameter "--limitSjdbInsertNsj 2000000". Barcodes and UMIs were also filtered for quality using "num_bases=1, phred=10”. We then generated cellx x genes matricies.
Data were then imported into R v3.6 and Seurat objects were created for each individual sample before being merged. Cells were filtered such that there were at least 1000 UMIs and 500 genes detected, and fewer than 10% of the transcripts were mitochondrially contributed.
Data were then scaled and normalized using scTransform and integrated using Seurat. Clusters were identified using Louvain-Jaccard clustering with multilevel refinement (resolution=2) performed on the top 100 PCs
Marker genes of each cluster were identified using the FindMarkers function in Seurat, and differential expression analysis was performed using RNA CPMs in R using Wilcoxon Rank Sum test. Differentially expressed genes were considered significant with nominal p-value < 0.01.
Assembly: GRCm39
Supplementary files format and content: SCTransform normalized expression values
Supplementary files format and content: Raw counts as reported by zUMIs, converted to a matrix

source_name: Dentate gyrus

growth_protocol: Single or double transgenic young adult mice (6-12 weeks, males and females) were used and randomly assigned to experimental groups. C57BL/6J, Chat-IRES-Cre were obtained from Jackson laboratory stock #(006410) and Nestin-GFP mice (Mignone et al., 2004) were obtained from Dr. Grigori Enikolopov at Stony Brook University. All Chat-IRES-Cre animals used in this study were heterozygous and came from a breeding of a homozygous Chat-IRES-Cre animal with a wild type C57Bl/6J. Animals were group housed and bred in a dedicated husbandry facility with 12 hour /12 hour light-dark cycles with food and water ad libitum and received veterinary supervision. Animals that were exposed to surgical procedures were moved to a separate satellite housing facility for recovery with the same light-dark cycle. Animals were sacrificed at the same time for each experiment which was around 5:00 PM to 7:00 PM. No immune deficiencies or other health problems were observed in these mouse lines, and all animals were experimentally and drug naive before use. All animal procedures followed the NIH Guide for Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill.

extract_protocol:
The Dentate Gyrus was dissected from animals that were injected with AAV5-EF1a-DIO-hChR2(H134R)-eYFP and allowed to recover. Animals were then stimulated using the stimulation protocol described previously. After stimulation, animals were transcardially perfused using ice cold PBS solution. The brain was then removed and placed in ice cold PBS and sliced bilaterally across the sagittal midline. Each hemisphere was then taken and the DG was dissected carefully in ice cold PBS. To ensure that mostly stimulated DG tissue was used for sequencing experiments, only the upper half or dorsal DG was then collected. Both Dorsal DG sections from each animal were then placed in a cryogenic tube and flash frozen and placed in -80°C.
Single-nucleus RNA sequencing was performed following the SPLiT-seq method with minor modifications (Rosenberg et al., 2018). Nuclei isolated from flash frozen DGs was performed as previously described (Su et al., 2017, Qian et al. 2020). Briefly, tissue was thawed, minced and homogenized using a tissue grinder in a 1 mL of HB buffer (1 mM DTT), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor, 0.3% IGEPAL-630, 0.25 M sucrose, 25 mM MgCl2, 20 mM Tricine-KOH) for 5 to 10 strokes, then filtered through a 40 mm strainer, under layered with a cushion buffer (0.5 mM MgCl2, 0.5 mM DTT, EDTA-free protease inhibitor, 0.88 M sucrose) to prevent damage to nuclei, and centrifuged at 2800 g for 10 minutes in a swinging bucket centrifuge at 4°C. Pellets of Nuclei were collected. Nuclei were then centrifuged for 3 mins at 500 g at 4°C. The pellet was resuspended in 1 mL of cold PBS-RI (1x PBS + 0.05 U/ml RNase Inhibitor). The nuclei were passed through a 40 mm strainer. 3 mL of cold 1.33% formaldehyde solution was then added to 1 mL of cells. Nuclei were fixed for 10 mins before adding 160 mL of 5% Triton X-100. We then permeabilized nuclei for 3 mins and centrifuged at 500 g for 3 mins at 4°C. Nuclei were resuspended in 500 mL of PBS-RI before adding 500 mL of cold 100 mM Tris-HCl pH 8. Then, nuclei were spun down at 500 g for 3 mins at 4°C and resuspended in 300 mL of cold 0.5 X PBS-RI. Finally, nuclei were again passed through a 40 mm strainer and then counted on a hemocytometer, diluted to 1,000,000 cells/ml. mRNA from single nuclei were tagged 3 rounds with barcoded primers, with in-cell ligations using T4 DNA ligase.   Plates were incubated for 30 mins at 37°C with gentle shaking (50 rpm) to allow hybridization and ligation to occur. The ligation products were purified with Dynabeads MyOne Streptavidin C1 beads. After washing beads once with 10 mM Tris and 0.1% Tween-20 solution and once with water, beads were resuspended into a solution containing 110 mL of 2X Kapa HiFi HotStart Master Mix, 8.8 mL of 10 mM stocks of primers BC_0062 and BC_0108, and 92.4 mL of water. PCR thermocycling was performed as follows: 95°C for 3 mins, then five cycles at 98°C for 20 s, 65°C for 45 s, 72°C for 3 mins. After these five cycles, Dynabeads were removed from PCR solution and EvaGreen dye was added at a 1X concentration. Samples were again placed in a qPCR machine with the following thermocycling conditions: 95°C for 3 mins, cycling at 98°C for 20 s, 65°C for 20 s, and then 72°C for 3 mins, followed by a single 5 mins at 72°C after cycling. Once the qPCR signal began to plateau, reactions were removed.   PCR reactions were purified using a 0.8X ratio of KAPA Pure Beads and cDNA concentration was measured using a qubit. For tagmentation, a Nextera XT Library Prep Kit was used. 600 pg of purified cDNA was diluted in water to a total volume of 5 ml.10 mL of Nextera TD buffer and 5 mL of Amplicon Tagment enzyme were added to bring the total volume to 20 ml. After mixing by pipetting, the solution was incubated at 55°C for 5 mins. A volume of 5 mL of neutralization buffer was added and the solution was mixed before incubation at room temperature for another 5 mins. PCR was then performed with the following cycling conditions: 95°C for 30 s, followed by 12 cycles of 95°C for 10 s, 55°C for 30 s, 72°C for 30 s, and 72°C for 5 mins after the 12 cycles. 40 mL of this PCR reaction was removed and purified with a 0.7X ratio of SPRI beads to generate an Illumina-compatible sequencing library.
SPLiT-seq

treatment_protocol: In order to stimulate cholinergic afferents from either the Medial Septum or Diagonal Band, we used optogenetics to carefully control the firing frequency and duration of activity. For neurogenesis experiments animals were stimulated for 3 days using an 8hz paradigm. Laser intensity was set to 5 mWh and fired at 1 ms pulses for a total of 30 seconds every 5.5 minutes. There were a total of about 11 five minute stimulations per hour for 8 hours total so mice received 88 five minute simulations during the each day. This stimulation paradigm has been previously used in (Bao et al. 2018) and was shown to have circuit specific effects for a distinct circuit projecting from the MS/DB.

tag: strain

value: Chr2 or yfp


title: MOLM13_ZNF740_Knockout_ZNF740

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

library_source: genomic

data_processing:
Raw CUT&RUN reads were subjected to adapter removal (cutadapt 2.10) and mapped genome hg38 (bowtie2 2.4.1) using --end-to-end --very-sensitive -–no-mixed -–no-discordant --phred33 -I 10 -X 700 parameters. Bigwig files were generated by bamCoverage (version 3.3.0).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: Cells were cultured in RPMI-1640 medium supplement with 10% FBS and 1% Pen-Strep.

extract_protocol:
CUT&RUN DNA was prepared using CUTANA pAG-MNase for CUT&RUN (Epicypher), following the manufacturer’s instructions.
Library construction was performed using the NEBNext Ultra II DNA Library Prep Kit from NEB (E7645S).

treatment_protocol: Lentiviral vector LRG2.1_Neo (Addgene,125593) was used to express sgRNAs. Lentiviral particles were prepared using HEK293FT cells and infected into AML cell lines, followed by antibiotics selection. Gene knockout was confirmed by Western blotting for each experiment.

value: ZNF740 Knockout


title: EP2/EP4KO NK cells, CM-treated, stimulated with anti-NK1.1, rep1


title: ZIC3 KO_C1, long-read, biol rep 1 of 3

description:
ZIC3_KO_C1_ONT_Flowcell_BiolRep1
ZIC3_KO_1
Long_Read_Log_CPM_EdgeR.txt


title: kidney biopsy [GSM3525103 re-analysis]


title: Kidney, fibroblasts, Trf1+/+; Col1a2-CreERT2, RGQ00334


title: MOLM13_ZNF740_Knockout_IgG


title: EP2/EP4KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep3

value: PGE2 1h + aNK1.1 stimulation 4h


title: ZIC3 AtoG_C1, long-read, biol rep 3 of 3

description:
ZIC3_AtoG_C1_ONT_Flowcell_BiolRep3
ZIC3_AtoG_3
Long_Read_Log_CPM_EdgeR.txt


title: MOLM13_Luciferase_Knockout_ZNF740

value: Luciferase Knockout


title: kidney biopsy [GSM3524212 re-analysis]


title: MOLM13_Luciferase_Knockout_IgG


title: ZIC3 AtoG_C1, long-read, biol rep 2 of 3

description:
ZIC3_AtoG_C1_ONT_Flowcell_BiolRep2
ZIC3_AtoG_2
Long_Read_Log_CPM_EdgeR.txt


title: kidney biopsy [GSM3524073 re-analysis]

value: Minor


title: EP2/EP4KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep2


title: EP2/EP4KO NK cells, CM-treated, stimulated with anti-NK1.1, rep3


title: EP2/EP4KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep1


title: ZIC3 AtoG_C1, long-read, biol rep 1 of 3

description:
ZIC3_AtoG_C1_ONT_Flowcell_BiolRep1
ZIC3_AtoG_1
Long_Read_Log_CPM_EdgeR.txt


title: OCI-AML2_ZNF740_Knockout_ZNF740


title: ZIC3 WT, long-read, biol rep 3 of 3

description:
ZIC3_WT_ONT_Flowcell_BiolRep3
ZIC3_WT_3
Long_Read_Log_CPM_EdgeR.txt

value: ZIC3 wildtype (ZIC3 WT)


title: EP2/EP4KO NK cells, untreated, stimulated with anti-NK1.1, rep3

value: untreated 1h + aNK1.1 stimulation 4h


title: OCI-AML2_ZNF740_Knockout_IgG


title: kidney biopsy [GSM3524909 re-analysis]


title: EP2/EP4KO NK cells, untreated, stimulated with anti-NK1.1, rep2


title: OCI-AML2_Luciferase_Knockout_ZNF740


title: ZIC3 WT, long-read, biol rep 2 of 3

description:
ZIC3_WT_ONT_Flowcell_BiolRep2
ZIC3_WT_2
Long_Read_Log_CPM_EdgeR.txt


title: EP2/EP4KO NK cells, untreated, stimulated with anti-NK1.1, rep1


title: ZIC3 WT, long-read, biol rep 1 of 3

description:
ZIC3_WT_ONT_Flowcell_BiolRep1
ZIC3_WT_1
Long_Read_Log_CPM_EdgeR.txt


title: kidney biopsy [GSM3525276 re-analysis]


title: EP2/EP4KO NK cells, CM-treated, unstimulated, rep3

value: CM control 5h


title: MOLM13_ZNF740_Knockout_replicate1

data_processing:
The paired-end reads were mapped to the human genome (hg38) using STAR with default parameters. The read counts were used for DESeq2 to define differentially expressed genes.
Assembly: hg38

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen, Germany).
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).


title: OCI-AML2_Luciferase_Knockout_IgG


title: kidney biopsy [GSM3525278 re-analysis]


title: H9C2 cells，OGD/R + si-CIRBP group, biol rep 2

city: shenzhen

first: Qiang

last: Zhang

state: Guangdong

address: 628 Zhenyuaan Rd.

department: Emergency medicine

institute: The seventh Affiliated Hospital of Sun Yat sen University

data_processing:
The raw data was achieved by sequenceing of  Illumina hiseqtm 2000 and Soapnuke software （version 1.5.2）is used to obtain valid sequences
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
Bowtie software (version: 2.3.3.1) is used to align effective sequences with the reference genome of corresponding species,Cufflinks software (version: 2.2.1) is used to assemble transcripts to obtain new transcripts，and Rsem (version: 1.3.1) is used to quantify gene expression
Assembly: reference sequence used for read alignment
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent according to the manufacturer’s protocol. 1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
After extracting total RNA from the sample and passing quality inspection, enrich the eukaryotic mRNA using magnetic beads with Oligo(dT) (if it is prokaryotic, use a kit to remove rRNA). Add fragmentation reagents and use a thermocycler to fragment the mRNA into short fragments. Synthesize first-strand cDNA using the fragmented mRNA as a template, and then prepare a reaction system for the synthesis of second-strand cDNA. Purify, repair sticky ends, and add a base "A" to the 3' end of the cDNA, followed by adapter ligation using a kit. Perform fragment size selection and PCR amplification to construct the library. After the constructed library passes quality inspection using the Agilent 2100 Bioanalyzer and Qubit, perform sequencing using the Illumina sequencer.

value: Rat Astrocytes

value: OGD/R + si-CIRBP


title: MOLM13_Luciferase_Knockout_replicate2


title: H9C2 cells，OGD/R + si-CIRBP group, biol rep 1


title: EP2/EP4KO NK cells, PGE2-treated, unstimulated, rep3

value: splenic NK cells

value: PGE2 5h


title: kidney biopsy [GSM3525033 re-analysis]


title: kidney biopsy [GSM3525138 re-analysis]

value: FABMR


title: H9C2 cells，OGD/R +si-NC group, biol rep 3

value: OGD/R + si-NC


title: OCI-AML2_ZNF740_Knockout_replicate2


title: EP2/EP4KO NK cells, PGE2-treated, unstimulated, rep2


title: EP2/EP4KO NK cells, CM-treated, unstimulated, rep1


title: kidney biopsy [GSM3524140 re-analysis]


title: kidney biopsy [GSM3525087 re-analysis]


title: H9C2 cells，OGD/R +si-NC group, biol rep 2


title: EP2/EP4KO NK cells, PGE2-treated, unstimulated, rep1


title: kidney biopsy [GSM3524007 re-analysis]


title: OCI-AML2_ZNF740_Knockout_replicate1


title: EP2/EP4KO NK cells, untreated, unstimulated, rep3

value: untreated 5h


title: H9C2 cells，OGD/R + si-CIRBP group, biol rep 3


title: EP2/EP4KO NK cells, CM-treated, unstimulated, rep2


title: OCI-AML2_Luciferase_Knockout_replicate2


title: H9C2 cells，OGD/R +si-NC group, biol rep 1


title: MOLM13_ZNF740_Knockout_replicate2


title: H9C2 cells，OGD/R + CIRBP group, biol rep 3

value: OGD/R  + CIRBP


title: kidney biopsy [GSM3525131 re-analysis]

value: NR

value: kidney biopsy


title: EP2/EP4KO NK cells, untreated, unstimulated, rep2


title: OCI-AML2_Luciferase_Knockout_replicate1


title: H9C2 cells，OGD/R + CIRBP group, biol rep 2


title: kidney biopsy [GSM3525512 re-analysis]


title: EP2/EP4KO NK cells, untreated, unstimulated, rep1


title: H9C2 cells，OGD/R + CIRBP group, biol rep 1


title: kidney biopsy [GSM3525270 re-analysis]


title: EP2KO NK cells, CM-treated, stimulated with anti-NK1.1, rep4

value: CM control 1h + aNK1.1 stimulation 4h


title: Donor3-Wound7

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

description: Fresh frozen spatial transcriptomics sequencing

data_processing:
The raw spatial sequence data were processed using the standard Space Ranger pipeline (version 1.2) with the GRCh38 human reference genome and GENCODE v38 gene annotations and visualized by BBrowser (BioTuring) and Seurat R package.
Assembly: GRCh38
Supplementary files format and content: _filtered_feature_bc_matrix.h5: contain spatial barcodes, genes IDs, and gene expression count data in matrix
Supplementary files format and content: _spatial_images.zip: contain aligned fiducials of image, image of tissue and spots, scalefactors in jsonformat, hi-res and low-res images, and list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatialseq_metadata_acutewound.txt:spot and cluster annotation file
Library strategy: spatial transcriptomics

source_name: Skin

extract_protocol:
Fresh frozen tissues were embedded in the OCT, and were cryosectioned in 10 µm with cryostat.
The spatial transcriptomics libraries sequencing was prepared with 10X Genomics Visium Spatial Gene Expression Slide & Reagents Kit according to manufacturers' construction.

tag: time point

value: day 7

tag: donor

tag: Sex

value: Male

tag: age

value: Skin


title: Donor3-Wound30

value: day 30


title: H9C2 cells，OGD/R + NC group, biol rep 3

value: OGD/R +NC


title: kidney biopsy [GSM3523930 re-analysis]

value: LABMR


title: kidney biopsy [GSM3524803 re-analysis]


title: H9C2 cells，OGD/R + NC group, biol rep 2

value: Rat Astrocytes


title: Donor3-Wound1

value: day 1


title: kidney biopsy [GSM3525574 re-analysis]


title: EP2KO NK cells, CM-treated, stimulated with anti-NK1.1, rep3

value: splenic NK cells


title: EP2KO NK cells, CM-treated, stimulated with anti-NK1.1, rep2


title: kidney biopsy [GSM3524479 re-analysis]

value: EABMR


title: H9C2 cells，OGD/R + NC group, biol rep 1


title: EP2KO NK cells, CM-treated, stimulated with anti-NK1.1, rep1


title: Donor3-Skin


title: kidney biopsy [GSM3524523 re-analysis]


title: EP2KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep4

value: PGE2 1h + aNK1.1 stimulation 4h


title: Donor2-Wound30

value: Female


title: kidney biopsy [GSM3524908 re-analysis]


title: Donor2-Wound7


title: OIR PIA P20biol repl 8

city: Minneapolis

first: Ellen

middle: Coley

last: Ingolfsland

state: MN

address: 516 Delaware St SE

institute: University of Minnesota

data_processing:
Sequencing reads were mapped to the rat reference genome (Rattus_norvegicus.Rnor_6.0.98) using Hisat2.
Genes differentially expressed were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Rattus_norvegicus.Rnor_6.0.98
Supplementary files format and content: RawCounts.txt

source_name: Retina

extract_protocol:
RNA was extracted from individual whole retina using the RNAqueous kit (Invitrogen).
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mRNA Protocols at the University of Minnesota Genomic Center (UMGC)

treatment_protocol: OIR was induced using the Penn 50/10 rat OIR model. PIA was induced by facial vein phlebotomy to a hematocrit of 18%. Room air controls were reared in normoxia. Non-anemic pups did not receive phlebotomy but instead received a prick to the scruff of the neck that did not induce bleeding.

value: Retina

value: WT

value: OIR PIA


title: OIR PIA P20 biol repl 7


title: EP2KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep3


title: kidney biopsy [GSM3523920 re-analysis]

value: NR

value: kidney biopsy


title: kidney biopsy [GSM3524774 re-analysis]


title: OIR PIA P20 biol repl 6


title: EP2KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep2


title: OIR PIA P20 biol repl 5


title: Donor2-Skin


title: EP2KO NK cells, PGE2-treated, stimulated with anti-NK1.1, rep1


title: MOLM13_Luciferase_Knockout_replicate1

value: Luciferase Knockout


title: Donor2-Wound1


title: kidney biopsy [GSM3525500 re-analysis]


title: EP2KO NK cells, untreated, stimulated with anti-NK1.1, rep4

value: untreated 1h + aNK1.1 stimulation 4h


title: Donor1-Wound30

value: Male

value: Skin


title: OIR PIA P20 biol repl 4


title: OIR PIA P20 biol repl 2


title: Donor1-Wound1


title: Donor1-Wound7

value: day 7


title: EP2KO NK cells, untreated, stimulated with anti-NK1.1, rep2


title: kidney biopsy [GSM3524124 re-analysis]


title: OIR PIA P20 biol repl 1


title: kidney biopsy [GSM3524626 re-analysis]


title: Donor1-Skin


title: EP2KO NK cells, untreated, stimulated with anti-NK1.1, rep1


title: OIR non-anemic P20 biol repl 8

value: OIR


title: kidney biopsy [GSM3524534 re-analysis]


title: EP2KO NK cells, CM-treated, unstimulated, rep4

value: CM control 5h


title: kidney biopsy [GSM3525117 re-analysis]


title: OIR non-anemic P20 biol repl 6


title: OIR non-anemic P20 biol repl 7


title: kidney biopsy [GSM3524145 re-analysis]


title: kidney biopsy [GSM3525468 re-analysis]


title: EP2KO NK cells, CM-treated, unstimulated, rep1


title: OIR non-anemic P20 biol repl 5


title: kidney biopsy [GSM3525059 re-analysis]


title: EP2KO NK cells, untreated, stimulated with anti-NK1.1, rep3


title: OIR non-anemic P20 biol repl 4


title: EP2KO NK cells, PGE2-treated, unstimulated, rep4

value: PGE2 5h


title: kidney biopsy [GSM3524179 re-analysis]


title: OIR non-anemic P20 biol repl 3


title: OIR non-anemic P20 biol repl 2


title: kidney biopsy [GSM3524594 re-analysis]


title: kidney biopsy [GSM3525313 re-analysis]


title: EP2KO NK cells, PGE2-treated, unstimulated, rep2

value: splenic NK cells


title: kidney biopsy [GSM3524303 re-analysis]


title: kidney biopsy [GSM3524290 re-analysis]


title: OIR non-anemic P20 biol repl 1


title: kidney biopsy [GSM3525612 re-analysis]


title: EP2KO NK cells, PGE2-treated, unstimulated, rep1


title: Room air PIA P20 biol repl 4

value: PIA


title: EP2KO NK cells, CM-treated, unstimulated, rep3


title: EP2KO NK cells, untreated, unstimulated, rep4

value: untreated 5h


title: ZIC3 KO_C2, short-read RNA-seq, biol rep 1 of 1

description:
ZIC3_KO_C2_BiolRep1
Zic3_Spl_2_Chx
Short_Read_Raw_Counts_All_Samples.txt

value: human embryonic stem cell

value: Undifferentiated - cultured in mTeSR1 media supplemented with 100 µg/mL of geneticin


title: OIR PIA P20 biol repl 3

value: Retina

value: WT


title: Room air PIA P20 biol repl 3


title: kidney biopsy [GSM3524201 re-analysis]

value: NR


title: EP2KO NK cells, untreated, unstimulated, rep3


title: ZIC3 KO_C1, short-read, biol rep 1 of 1

description:
ZIC3_KO_C1_BiolRep1
Zic3_Spl_2
Short_Read_Raw_Counts_All_Samples.txt

value: ZIC3 c.190_200delinsG (ZIC3 KO_C1)


title: kidney biopsy [GSM3524105 re-analysis]

value: EABMR

value: kidney biopsy


title: Room air PIA P20 biol repl 2


title: EP2KO NK cells, CM-treated, unstimulated, rep2


title: ZIC3 AtoG_C2, short-read, CHX treated, biol rep 1 of 1

description:
ZIC3_AtoG_C2_CHX_BiolRep1
Zic3_Spl_1_Chx
Short_Read_Raw_Counts_All_Samples.txt

value: Undifferentiated - cultured in mTeSR1 media supplemented with 100 µg/mL of geneticin and 100 µg/mL cyloheximide (CHX) for 6 hr


title: Room air PIA P20 biol repl 1


title: kidney biopsy [GSM3524272 re-analysis]


title: EP2KO NK cells, untreated, unstimulated, rep2


title: EP2KO NK cells, PGE2-treated, unstimulated, rep3


title: EP2KO NK cells, untreated, unstimulated, rep1


title: ZIC3 AtoG_C2, short-read, biol rep 1 of 1

description:
ZIC3_AtoG_C2_BiolRep1
Zic3_Spl_1
Short_Read_Raw_Counts_All_Samples.txt


title: ZIC3 AtoG_C1, short-read, CHX treated, biol rep 1 of 1

description:
ZIC3_AtoG_C1_CHX_BiolRep1
Zic3_KO_2
Short_Read_Raw_Counts_All_Samples.txt


title: kidney biopsy [GSM3524497 re-analysis]


title: WT NK cells, CM-treated, stimulated with anti-NK1.1, rep4

value: CM control 1h + aNK1.1 stimulation 4h


title: kidney biopsy [GSM3525492 re-analysis]


title: ZIC3 AtoG_C1, short-read, biol rep 1 of 1

description:
ZIC3_AtoG_C1_BiolRep1
Zic3_KO_1
Short_Read_Raw_Counts_All_Samples.txt


title: WT NK cells, CM-treated, stimulated with anti-NK1.1, rep3


title: Room air control P20 biol repl 2


title: Room air control P20 biol repl 3


title: kidney biopsy [GSM3524579 re-analysis]


title: Room air control P20 biol repl 1


title: kidney biopsy [GSM3524707 re-analysis]


title: WT NK cells, CM-treated, stimulated with anti-NK1.1, rep2


title: OIR PIA P15 biol repl 4

value: OIR PIA


title: WT NK cells, CM-treated, stimulated with anti-NK1.1, rep1


title: ZIC3 WT, short-read, biol rep 1 of 1

description:
ZIC3_WT_BiolRep1
WT
Short_Read_Raw_Counts_All_Samples.txt

value: ZIC3 wildtype (ZIC3 WT)


title: ZIC3 WT, short-read, CHX treated, biol rep 1 of 1

description:
ZIC3_WT_CHX_BiolRep1
WT_Chx
Short_Read_Raw_Counts_All_Samples.txt


title: Huh7_KLF5_CUTTAG

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: hg38
Supplementary files format and content: wig files were generated using deepTools.
Library strategy: CUT&Tag

source_name: liver

growth_protocol: Huh 7 was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8)；Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit. Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 3000 platform (Illumina, CA, USA); CUT&Tag was performed according to the manufacturer’s protocol (Novoprotein, Shanghai, China).
For the ChIPseq, input amounts of DNA was converted into high quality libraries for next-generation sequencing on the Illumina platform using the NEBNext Ultra II DNA Library Prep Kit. Bead based size selection was performed for final library size selection to obtain ChIP-seq libraries containing fragments of 250 bp to 500 bp.  For the RNA-seq, the sequencing library was prepared using an Illumina mRNA-seq sample preparation kit and was then subjected to paired-end sequencing on the Illumina HiSeq platform.  CUT&Tag was performed according to the manufacturer's protocol (Novoprotein, Shanghai, China). The DNA was mixed with a universal i5 and a uniquely barcoded i7 primer. The sample was placed in a Thermocycler for PCR, and post-PCR clean-up was performed by bead based size selection and cleanup.

treatment_protocol: For cultures with different concentrations of choline, custom DMEM without choline chloride (BasalMedia, Shanghai, China) was used, with 10% FBS replaced by B-27 (Thermo Fisher Scientific, IL, USA), and the choline chloride used for supplementation was obtained from Sigma‒Aldrich (MO, USA). siRNAs targeting KLF5 and negative control siRNAs (siNCs) were procured from RiboBio (Guangzhou, China). Cells were transfected with the specified targeted or control siRNA at a final concentration of 75 nM using Lipofectamine RNAiMAX reagent (Invitrogen, CA, USA). After 48 hours of transfection, the cells were collected for further experiments.

value: liver

value: HCC cells

tag: chip antibody

value: Huh7 cells were treated with 15μM choline for 48 hours


title: WT NK cells, PGE2-treated, stimulated with anti-NK1.1, rep3

value: splenic NK cells

value: PGE2 1h + aNK1.1 stimulation 4h


title: OIR PIA P15 biol repl 3


title: WT NK cells, PGE2-treated, stimulated with anti-NK1.1, rep4


title: kidney biopsy [GSM3524028 re-analysis]


title: OIR PIA P15 biol repl 2


title: WT NK cells, PGE2-treated, stimulated with anti-NK1.1, rep2


title: Huh7_15_me_Input_ChIP

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: hg38
Supplementary files format and content: wig files were generated using deepTools.


title: Room air control P20 biol repl 4


title: OIR PIA P15 biol repl 1


title: kidney biopsy [GSM3525169 re-analysis]


title: kidney biopsy [GSM3524875 re-analysis]


title: Huh7_15_H3K4me1_ChIP

value: H3K4me1, Cell Signaling Technology, 5326S


title: WT NK cells, PGE2-treated, stimulated with anti-NK1.1, rep1


title: Huh7_0_me_Input_ChIP

value: Huh7 cells were treated with 0μM choline for 48 hours


title: OIR non-anemic P15 biol repl 4

value: Retina

value: OIR


title: WT NK cells, untreated, stimulated with anti-NK1.1, rep4

value: WT

value: untreated 1h + aNK1.1 stimulation 4h


title: Huh7_0_H3K4me1_ChIP


title: kidney biopsy [GSM3524336 re-analysis]

value: NR


title: OIR non-anemic P15 biol repl 3


title: WT NK cells, untreated, stimulated with anti-NK1.1, rep3


title: kidney biopsy [GSM3525008 re-analysis]

value: kidney biopsy


title: Huh7_15_ac_Input_ChIP


title: kidney biopsy [GSM3525639 re-analysis]


title: OIR non-anemic P15 biol repl 2


title: WT NK cells, untreated, stimulated with anti-NK1.1, rep2


title: OIR non-anemic P15 biol repl 1


title: WT NK cells, untreated, stimulated with anti-NK1.1, rep1


title: kidney biopsy [GSM3524066 re-analysis]


title: Huh7_15_H3K27ac_ChIP

value: H3K27ac, Active motif, 39133


title: Huh7_0_ac_Input_ChIP


title: kidney biopsy [GSM3524276 re-analysis]


title: kidney biopsy [GSM3524776 re-analysis]

value: LABMR


title: Room air PIA P15 biol repl 3

value: PIA


title: Room air PIA P15 biol repl 2


title: WT NK cells, CM-treated, unstimulated, rep3

value: CM control 5h


title: Huh7_0_H3K27ac_ChIP

value: liver


title: WT NK cells, CM-treated, unstimulated, rep2


title: WT NK cells, CM-treated, unstimulated, rep4


title: kidney biopsy [GSM3524095 re-analysis]


title: kidney biopsy [GSM3523947 re-analysis]


title: Huh7_15

value: HCC cells

value: Huh7 cells were treated with15μM choline and transfected with siNC using Lipofectamine RNAiMAX for 48 hours


title: Room air Control P15 biol repl 4


title: Huh7_0

value: Huh7 cells were treated with 0μM choline and transfected with siNC using Lipofectamine RNAiMAX for 48 hours


title: WT NK cells, CM-treated, unstimulated, rep1

value: splenic NK cells


title: SBC-3, siSFPQ-3, PRO-seq rep.2

description:
siSFPQ-3-2
PRO-seq_siSFPQ-vs-siCtrl_norm-reads.csv

library_source: other

data_processing:
Unique Molecular Identifiers (UMIs) of 6 nt were extracted from read pairs using UMI-tools.
Adapter sequences were removed using Cutadapt 1.14 and an additional nucleotide was removed from the end of read 1 using Seqtk.
Paired-end reads were mapped to a genome index combining the spike (dm6) and primary (hg38) genomes using Bowtie2.
spike and primary reads were independently deduplicated using UMI-tools.
Reads mapping to hg38 were sorted via SAMtools 1.3.1.
Normalization and differential expression were performed using the R package DESeq2 v1.38.1. For each sample, the PRO-seq signal was calculated from the annotated transcription start site (TSS) to 150 nt downstream, using the hg38 Ensembl v99 gene annotation and the proTSScall script from the Nascent Transcription Core (Harvard).
Assembly: hg38 Ensembl v99
Supplementary files format and content: semicolumn-delimimted text file contains DESeq2 result matrix (including log2(Fold change) and p-adjust) as well as DESeq2 normalized counts for each sample
Supplementary files format and content: tab-delimimted text file contains counts for transcriptionally repressed genes upon SFPQ knockdown (KD) for each sample. The counts are given per bin of 10 bp in a region spanning from 1 kb before the TSS to 1 kb after the transcription end site (TES).
Supplementary files format and content: tab-delimimted text file contains counts for transcriptionally activated genes upon SFPQ KD for each sample. The counts are given per bin of 10 bp in a region spanning from 1 kb before the TSS to 1 kb after the TES.
Supplementary files format and content: tab-delimimted text file contains counts for transcriptionally non-affected genes upon SFPQ KD for each sample. The counts are given per bin of 10 bp in a region spanning from 1 kb before the TSS to 1 kb after the TES.
Library strategy: PRO-seq

molecule: other

extract_protocol:
Nascent RNA was extracted using Trizol reagent according to the manufacturer's instructions.
RNA libraries were prepared by the Nascent Transcriptomic Core at Harvard Medical School.

treatment_protocol: siRNAs and ASOs (10 nM) were reverse transfected into SBC-3 cells with Lipofectamine RNAiMAX according to the manufacturer’s instructions. Cells were harvested and permeabilized 72 h post-transfection.

value: Small cell lung cancer

value: SFPQ knockdown

value: siSFPQ


title: kidney biopsy [GSM3524502 re-analysis]


title: Room air Control P15 biol repl 3

value: Retina


title: Room air PIA P15 biol repl 4

value: WT


title: WT NK cells, PGE2-treated, unstimulated, rep2

value: PGE2 5h


title: Room air Control P15 biol repl 2


title: WT NK cells, untreated, unstimulated, rep4

value: untreated 5h


title: WT NK cells, PGE2-treated, unstimulated, rep4


title: kidney biopsy [GSM3525590 re-analysis]

value: NR

value: kidney biopsy


title: SBC-3, siSFPQ-2, PRO-seq rep.2

description:
siSFPQ-2-2
PRO-seq_siSFPQ-vs-siCtrl_norm-reads.csv


title: kidney biopsy [GSM3524887 re-analysis]

value: EABMR


title: Room air Control P15 biol repl 1


title: kidney biopsy [GSM3524710 re-analysis]


title: Huh7_15_siKLF5

value: KLF5 knockdown

value: Huh7 cells were treated with15μM choline and transfected with sKLF5 using Lipofectamine RNAiMAX for 48 hours


title: WT NK cells, untreated, unstimulated, rep3


title: SBC-3, siSFPQ-2, PRO-seq rep.1

description:
siSFPQ-2-1
PRO-seq_siSFPQ-vs-siCtrl_norm-reads.csv


title: WT NK cells, untreated, unstimulated, rep2


title: Zebrafish, 3 somite stage embryo, gpc4 mutant, replicate 3

city: Oxford

first: Amélie

middle: M

last: Julé

address: Roosevelt Drive, Headington

country: United Kingdom

institute: Kennedy Institute of Rheumatology (KIR)

description: 10x Genomics; processed files are Cellranger (v6.1.0) filtered feature matrices

data_processing: FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger (version 6.1.0).

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (Danio rerio) embryos were raised at 28.5C in E3 medium, and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.

extract_protocol:
Embryos were dechorionated with a ~10 min incubation in 1 mg/mL Pronase, washed 3x in embryo medium, and dissociated on ice in 200 uL DPBS (without Ca2+ and Mg2+) with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation, cells were passed through a 70 um cell strainer, and cell counts and viability were measured. After droplet encapsulation, barcoding, and library preparation using the 10X Genomics Chromium Single Cell 3’ kit (version 3), data were sequenced on an Illumina NovaSeq 6000 sequencer.
Droplet encapsulation, barcoding, and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3’ kit (version 3)

value: whole embryo

value: Tubingen

tag: developmental stage

value: 3 somite stage


title: kidney biopsy [GSM3525113 re-analysis]


title: SBC-3, siCtrl, PRO-seq rep.2

description:
siCtrl-2
PRO-seq_siSFPQ-vs-siCtrl_norm-reads.csv

value: siCtrl


title: Room air PIA P15 biol repl 1

value: PIA


title: kidney biopsy [GSM3524727 re-analysis]


title: Zebrafish, 3 somite stage embryo, dact1-/-;dact2-/- compound mutant, replicate 3


title: SBC-3, siCtrl, PRO-seq rep.1

description:
siCtrl-1
PRO-seq_siSFPQ-vs-siCtrl_norm-reads.csv

value: Small cell lung cancer


title: kidney biopsy [GSM3525034 re-analysis]


title: Zebrafish, 3 somite stage embryo, WT, replicate 4


title: LI CD45 of Tph2 KO 4

city: boston

first: Hailong

address: 181 longwood ave

institute: Brigham and Women's Hospital, Harvard Medical School

description:
Large intestine lamina propria CD45 of Tph2 KO 4
Count_LI_CD45.txt

data_processing:
For data analysis, reads were trimmed using Trim Galore with automatic adapter sequence detection.
Then, trimmed reads were mapped to the mouse reference genome (mm10) and annotated using STAR v2.7.3a with default parameter.
The number of mapped reads to each gene were counted by featureCounts of the Subread package using mouse GENCODE annotation M25 (GRCm38.p6).
Assembly: mm10
Supplementary files format and content: Feature counts table

source_name: FACS sorted CD45 cell from large intestine

extract_protocol:
FACS sorted immune cells were lysed in Trizol (15596018, Invitrogen), and RNA was extracted with the RNeasy mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep kit (50-196-5308, Roche) or NEBNext Multiplex Oligos for Illumina kit (E7335L, NEB).

value: KO


title: SBC-3, siSFPQ-3, PRO-seq rep.1

description:
siSFPQ-3-1
PRO-seq_siSFPQ-vs-siCtrl_norm-reads.csv

value: SFPQ knockdown

value: siSFPQ


title: IMA, woman 6, snRNAseq

city: Montréal

first: Pauline

last: Mury

state: QC

address: 5000 rue Bélanger

institute: Montreal Heart Institute

description: 10X Genomics

data_processing:
Fastq files were processed using CellRanger (10X Genomics, version 7.0.1) to decompose cell barcodes and align cDNA sequences against the human genomic reference (hg19) provided by 10X Genomics
Assembly: hg19
Supplementary files format and content: hdf5 file containing counts, and metadata on the rows (genes) and columns (cells)

molecule: nuclear RNA

source_name: mammary artery

extract_protocol:
Thoracic arteries were harvested in operating room and snap frozen within 15min and stored at -80oC. Frozen segments were processed using GentleMACS Octo Dissociator and its nuclei lysis buffer, according the the manufacturer's instructions. Nuclei were then washed, filtered (70µm and 20µm) and resuspended in PBS-BSA 0.1%.
Libraries were prepared using the Next GEM Single Cell 3' Dual Indexing kit (10X Genomics) using a Chromium Controller instrument to generate single-nuclei gel bead-in-emulsion (GEMs). Then, GEMs were reverse transcribed into cDNAs that were then amplified and cleaned up using SPRIselect Reagent Kit (Beckman Coulter). The barcoded sequencing libraries were constructed by enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

value: mammary artery

tag: group

value: woman

value: coronary artery disease (CAD)


title: Zebrafish, 3 somite stage embryo, gpc4 mutant, replicate 2


title: kidney biopsy [GSM3524592 re-analysis]

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

extract_protocol:
All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
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).

value: NR


title: IMA, man 6, snRNAseq

description: 10X Genomics

value: man


title: Zebrafish, 3 somite stage embryo, dact1-/-;dact2-/- compound mutant, replicate 2


title: LI CD45 of Tph2 KO 2

description:
Large intestine lamina propria CD45 of Tph2 KO 2
Count_LI_CD45.txt

value: FACS sorted CD45 cell from large intestine


title: kidney biopsy [GSM3524291 re-analysis]

value: kidney biopsy


title: Zebrafish, 3 somite stage embryo, WT, replicate 3

value: WT


title: IMA, woman 5, snRNAseq

description: 10X Genomics


title: LI CD45 of Tph2 KO 1

description:
Large intestine lamina propria CD45 of Tph2 KO 1
Count_LI_CD45.txt


title: IMA, man 5, snRNAseq

description: 10X Genomics


title: kidney biopsy [GSM3524816 re-analysis]

value: FABMR


title: Zebrafish, 3 somite stage embryo, gpc4 mutant, replicate 1

value: whole embryo

value: Tubingen


title: LI CD45 of Tph2 WT 4

description:
Large intestine lamina propria CD45 of Tph2 WT 4
Count_LI_CD45.txt


title: kidney biopsy [GSM3524798 re-analysis]


title: Zebrafish, 3 somite stage embryo, dact1-/-;dact2-/- compound mutant, replicate 1

value: 3 somite stage


title: LI CD45 of Tph2 WT 3

description:
Large intestine lamina propria CD45 of Tph2 WT 3
Count_LI_CD45.txt


title: IMA, man 4, snRNAseq

description: 10X Genomics


title: WT NK cells, untreated, unstimulated, rep1

value: splenic NK cells

value: untreated 5h


title: kidney biopsy [GSM3524639 re-analysis]

value: LABMR


title: Zebrafish, 3 somite stage embryo, WT, replicate 2


title: LI CD45 of Tph2 KO 3

description:
Large intestine lamina propria CD45 of Tph2 KO 3
Count_LI_CD45.txt

value: KO


title: LI CD45 of Tph2 WT 2

description:
Large intestine lamina propria CD45 of Tph2 WT 2
Count_LI_CD45.txt


title: IMA, woman 3, snRNAseq

description: 10X Genomics


title: kidney biopsy [GSM3523957 re-analysis]

value: EABMR


title: kidney biopsy [GSM3524877 re-analysis]


title: Zebrafish, 3 somite stage embryo, WT, replicate 1


title: IMA, man 3, snRNAseq

description: 10X Genomics

value: mammary artery


title: LI CD45 of Tph2 WT 1

description:
Large intestine lamina propria CD45 of Tph2 WT 1
Count_LI_CD45.txt


title: kidney biopsy [GSM3524763 re-analysis]


title: kidney biopsy [GSM3525329 re-analysis]


title: SI CD45 of Tph2 KO 4

description:
Small intestine lamina propria CD45 of Tph2 KO 4
Count_SI_CD45.txt

source_name: FACS sorted CD45 cell from small intestine


title: IMA, man 2, snRNAseq

description: 10X Genomics


title: LNCaP_H3K27me3

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: LNCaP

growth_protocol: LNCaP,PC3 and DU145 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were fixed with 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: LNCaP

value: prostate cancer

value: H3K27me3 (ACTIVE MOTIF,#39155)


title: DU145_WT

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: DU145_WT.txt

growth_protocol: DU145 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).


title: IMA, woman 4, snRNAseq

description: 10X Genomics

value: woman

value: coronary artery disease (CAD)


title: kidney biopsy [GSM3524381 re-analysis]

value: NR

value: kidney biopsy


title: SI CD45 of Tph2 KO 2

description:
Small intestine lamina propria CD45 of Tph2 KO 2
Count_SI_CD45.txt

value: FACS sorted CD45 cell from small intestine


title: PC3_Hi-C

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Hi-C reads were processed using HiC-Pro2.11.1.
Aligned reads are converted to hic file by juicer-tools version1.9.8.
Supplementary_files_format_and_content: .hic
Assembly: hg19

growth_protocol: LNCaP,PC3 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol: Hi-C experiment was conducted using Mbo I, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547). After proximity ligation and fragmentation by COVARIS S220, the sequencing library was generated from fragmented DNA using KAPA HyperPrep Kits following the manufacturer's instructions.


title: IMA, woman 1, snRNAseq

description: 10X Genomics


title: SI CD45 of Tph2 KO 1

description:
Small intestine lamina propria CD45 of Tph2 KO 1
Count_SI_CD45.txt


title: kidney biopsy [GSM3524311 re-analysis]


title: kidney biopsy [GSM3524636 re-analysis]


title: SI CD45 of Tph2 WT 4

description:
Small intestine lamina propria CD45 of Tph2 WT 4
Count_SI_CD45.txt

value: WT


title: IMA, man 1, snRNAseq

description: 10X Genomics

value: man


title: DU145_Hi-C

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Hi-C reads were processed using HiC-Pro2.11.1.
Aligned reads are converted to hic file by juicer-tools version1.9.8.
Assembly: hg19
Supplementary files format and content: .hic


title: human adjacent normal cervix tissue, patient 3

city: Tianjin

first: Jia

last: Xu

address: No.94 Weijin Road

department: School of Medicine

institute: Nankai University

description: adjacent normal cervix tissue of patient 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Reference genome (hg38) and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

growth_protocol: Uterine cervical specimens (including tumor tissues and adjacent normal tissues) were resected from 3 clinical patients in Department of Obstetrics and Gynecology of The Seventh Medical Center of Chinese PLA General Hospital immediately after radical hysterectomy.

extract_protocol:
Total RNA from 3 patients was extracted by Trizol (Invitrogen, CA, USA) according to the manufacturer’s protocol. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

treatment_protocol: These specimens were stored at -80℃ and were used for RNA sequencing  within 1 week.

value: female

tag: tumor stage

value: Laparoscopic radical hysterectomy + bilateral adnexectomy + pelvic lymph node resection


title: SI CD45 of Tph2 WT 3

description:
Small intestine lamina propria CD45 of Tph2 WT 3
Count_SI_CD45.txt


title: LNCaP_Hi-C


title: Sample_SG9_R3,HR,3

city: Dijon

first: Stéphane

last: GUYOT

address: 1 Esplanade Erasme

country: France

institute: Institut Agro Dijon

data_processing:
Differential expression analysis was performed using the DESeq2 package operating in the R environment. Separate analysis was made for all annotated reads, including non-mRNA species, or taking into account of only yeast mRNAs.
Assembly: Saccharomyces cerevisiae S288c
Supplementary files format and content: tab-delimited text files

organism: Saccharomyces cerevisiae

growth_protocol: 48h at 25°C in YPD medium, with gentle periodic agitation (to reach the stationary growth phase)

extract_protocol:
Yeast total RNA was extracted using hot acid phenol and quantified using a Nanodrop2100 (ThermoFisher Scientific). RNA quality was checked by capillary electro-phoresis on a Bioanalyzer 2100 (Agilent). RNA was treated with 1 MBU of Base-line-ZEROTM DNAse (ref#DB0715K, Epicentre) for 20 min at 37 °C followed by a phe-nol/chloroform and chloroform extraction. RNA was precipitated in 3 volumes of Ethanol (96% v/v) using 0.3M AcONa and 15 µg of glycoblue. After a wash with EtOH (80% v/v), the pellet was resuspended in 101 µl of RNAse-free H2O.
After RNA quantification and quality control, 4.5 µg of each RNA (DNAseI-treated) was used for polyA+ isolation using NEBNext Oligo d(T)25 Magnetic beads kit (ref#E7490, NEB) following the manufacturer’s instructions. Enrichment of the polyA+ fraction was checked by capillary electrophoresis on Bioanalyzer 2100. 1 ng of each rRNA-depleted RNA was converted to a library with the Scriptseq V2 RNA-Seq kit (ref#SSV21106, Illumina) using the manufacturer’s instructions. After 15 cycles of PCR amplification, the libraries were purified using the Agencourt AMPure XP beads (ref#A63880, Beckman Coulter) at a ratio of 0.9x. Library quality was assessed using a High Sensivity DNA chip on a Bioanalyzer 2100. Library quantification was performed using a fluorometer (Qubit 2.0 fluorometer, Invitrogen).
RNAseq. Libraries were multiplexed and subjected for high-throughput sequencing using an Illu-mina HiSeq 1000 instrument with 50 bp single-end read runs and loaded at 12 pM per lane. Quality of sequencing reads was evaluated by FastQC. Raw sequencing reads were trimmed by Trimmomatic V0.32 with the following parameters: adapt-ers/TruSeq3-SE.fa:2:30:10, LEADING:30, TRAILING:30, SLIDINGWINDOW:4:15, MINLEN:17, and AVGQUAL:30. Trimmed reads were aligned to the SacCer3 assembly of S. cerevisiae genome using Bowtie2 in sensitive-local mode. This generated a *.sam file that was sorted and converted to *.bam with subsequent removal of non-mapped reads. Visu-alization was performed in Integrative Genomics Viewer (IGV: https://igv.org)

treatment_protocol: no treatement (CTL) or heat shock (HS, from 25°C to 50°C at the rate of 50°C/min followed by 30 min at 50°C before rapid recovery at 25°C) or heat ramp (HR,  from 25°C to 50°C at the rate of 0.5°C/min followed by 30 min at 50°C before rapid recovery at 25°C). Three independent biological replicates (meaning three independent cultures) were run.

value: Wild Type

value: Heat Ramp


title: human adjacent normal cervix tissue, patient 2

description: adjacent normal cervix tissue of patient 2

value: Laparoscopic radical hysterectomy + bilateral salpingectomy + pelvic lymph node resection


title: kidney biopsy [GSM3525439 re-analysis]

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

institute: University of Alberta


title: human cervical cancer tissue, patient 3

description: cervical cancer tissue of patient 3

source_name: cervical cancer tissue of patient 3

value: cervical cancer tissue of patient 3


title: SI CD45 of Tph2 WT 2

description:
Small intestine lamina propria CD45 of Tph2 WT 2
Count_SI_CD45.txt


title: Sample_SG7_R1,HR,1


title: kidney biopsy [GSM3524102 re-analysis]


title: kidney biopsy [GSM3524611 re-analysis]


title: kidney biopsy [GSM3525312 re-analysis]

value: Minor


title: Enteric neuron of infant mice 4

description:
Entericneuron_barcodes.tsv.gz
Entericneuron_features.tsv.gz
Entericneuron_matrix.mtx.gz

data_processing:
Data analysis was performed using the 10× Genomics Cloud Analysis Cell Ranger pipeline and Seurat v4.3.0 with the SCT normalization method.
Low quality cells were removed by the parameters nfeature_RNA > 500, nCount_RNA > 2000 & nCount_RNA < 50000, and percent.mt < 5. To generate UMAPs,
we integrated our data with published small intestine data in  Drokhlyansky et al20 and performed a principal component analysis (PCA) using RunPCA function (npcs=50), and then cell clusters were identified using FindNeighbors (dims=1:15) and FindClusters (resolution=0.4) functions.
RunUMAP function (dims=1:15, n.neighbors=15, min.dist=0.3, spread=1) was used to create UMAP plots. The cell-type assignment was performed using clustifyr R package (v1.8.0, clustifyr50) based on the cell-types presented in Drokhlyansky et al20.
Assembly: mm10
Supplementary files format and content: Entericneuron_barcodes.tsv.gz
Supplementary files format and content: Entericneuron_features.tsv.gz
Supplementary files format and content: Entericneuron_matrix.mtx.gz

source_name: Enteric neuron

extract_protocol:
10 × Genomics protocol was performed on single sorted enteric nucleus
Library was generated using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X) according to the manufacturer’s protocol

value: Enteric neuron


title: kidney biopsy [GSM3524520 re-analysis]


title: human cervical cancer tissue, patient 2

description: cervical cancer tissue of patient 2

source_name: cervical cancer tissue of patient 2

value: cervical cancer tissue of patient 2


title: IMA, woman 2, snRNAseq

description: 10X Genomics

value: mammary artery


title: Sample_SG5_Ch2,HS,2

value: Heat Shock


title: Sample_SG6_Ch3,HS,3


title: human adjacent normal cervix tissue, patient 1

description: adjacent normal cervix tissue of patient 1

value: Robot-assisted laparoscopic radical hysterectomy + bilateral salpingectomy + pelvic lymph node resection


title: human cervical cancer tissue, patient 1

description: cervical cancer tissue of patient 1

source_name: cervical cancer tissue of patient 1

value: cervical cancer tissue of patient 1


title: kidney biopsy [GSM3524959 re-analysis]

source_name: kidney biopsy

value: LABMR

value: kidney biopsy


title: Enteric neuron of infant mice 3


title: kidney biopsy [GSM3524619 re-analysis]

value: NR


title: Sample_SG4_Ch1,HS,1


title: Enteric neuron of infant mice 2


title: GBM39-ER_Paired_Hi-C_DNA

city: La Jolla

first: Yang

last: Xie

state: CA

address: Rm.2071, 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

description: 10XMultiome, single-cell Hi-C

data_processing:
All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files are demultiplexed using cellranger-arc v2.0.0. Hi-C and RNA modalities were preprocessed using cellranger-atac v2.0.0 and cellranger v6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei from DNA modality, we filtered barcodes based on the per cell contacts number, and then further selected nuclei by pairing pass-filtered nuclei from both Hi-C and RNA modality.
Assembly: hg38
Supplementary files format and content: For Hi-C modality, processed data are provided in .pairs format, each line represents a unique contact, with cell barcodes corresponding to left- and right-side of the contacts being recorded as extra columns in pairs file. For RNA modality, raw cells-by-gene matrices are provided. Valid cells information is provided as metadata in the supplementary file.

growth_protocol: As described previously, patient-derived xenograft (PDX) model GBM39 (Mayo Clinic Hospital) was cultured in DMEM/F12 (ThermoFisher, 11320033), 20ng/mL EGF (STEMCELL Technologies, 78006), 20ng/ml FGF (STEMCELL Technologies, 78134.1), 10% B27 Supplement without Vitamin A (ThermoFisher, 12587010), and 1% penicillin-streptomycin solution at 37°C with 5% CO2. GBM39-ER was under continuous treatment with 5µM erlotinib (LC Laboratories, E-4007). GBM39 cell lines were cultured as neurospheres.

extract_protocol:
Cells were crosslinked in 1% formaldehyde, which was diluted from 37% formaldehyde with 1× PBS (pH=7.4), and incubated at room temperature for 10 min. After crosslinking, the reactions were quenched in 200 mM glycine and incubated at room temperature for 5 min. Quenched reactions were spun down at 1,000g for 5 min at 4°C, resuspended using 1% BSA in 1× PBS (pH=7.4) to wash twice, and then aliquoted 1 million cells into each tube. The cells were pelleted once again at 1,000g for 5 min, removed supernatant, and flash frozen in liquid nitrogen, and finally stored indefinitely at -80°C.
Following user guide of Chromium Next GEM Single Cell Multiome ATAC + Gene Expression.


title: Sample_SG8_R2,HR,2


title: Sample_SG3_C3,CTL,3

value: Control


title: SI CD45 of Tph2 WT 1

description:
Small intestine lamina propria CD45 of Tph2 WT 1
Count_SI_CD45.txt

value: FACS sorted CD45 cell from small intestine

value: WT


title: Enteric neuron of infant mice 1


title: Sample_SG2_C2,CTL,2

value: Wild Type


title: kidney biopsy [GSM3524599 re-analysis]


title: LI epithelium of Tph2 KO 3

source_name: Intestinal epithelium

extract_protocol:
Purified intestinal epithelial cells were lysed in Trizol (15596018, Invitrogen), and RNA was extracted with the RNeasy mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep kit (50-196-5308, Roche) or NEBNext Multiplex Oligos for Illumina kit (E7335L, NEB).

value: Intestinal epithelium

value: KO


title: GBM39_Paired_Hi-C_DNA

description: 10XMultiome, single-cell Hi-C

growth_protocol: As described previously, patient-derived xenograft (PDX) model GBM39 (Mayo Clinic Hospital) was cultured in DMEM/F12 (ThermoFisher, 11320033), 20ng/mL EGF (STEMCELL Technologies, 78006), 20ng/ml FGF (STEMCELL Technologies, 78134.1), 10% B27 Supplement without Vitamin A (ThermoFisher, 12587010), and 1% penicillin-streptomycin solution at 37°C with 5% CO2. GBM39 cell lines were cultured as neurospheres.


title: kidney biopsy [GSM3525584 re-analysis]


title: GBM39-ER_Droplet_Hi-C_10xATAC_v1.1

description: 10XATAC_v1.1, single-cell Hi-C

data_processing:
All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files were demultiplexed and pre-processed using cellranger-atac v2.0.0. To select high-quality nuclei from DNA modality, we filtered cells based on the per cell contacts number.
Assembly: hg38
Supplementary files format and content: Processed data are provided in .pairs format, each line represents a unique contact, with cell barcodes corresponding to left- and right-side of the contacts being recorded as extra columns in pairs file. Valid cells information is provided as metadata in the supplementary file.

source_name: patient-derived xenograft (PDX) model GBM39

extract_protocol:
Cells were crosslinked in 1% formaldehyde, which was diluted from 37% formaldehyde with 1× PBS (pH=7.4), and incubated at room temperature for 10 min. After crosslinking, the reactions were quenched in 200 mM glycine and incubated at room temperature for 5 min. Quenched reactions were spun down at 1,000g for 5 min at 4°C, resuspended using 1% BSA in 1× PBS (pH=7.4) to wash twice, and then aliquoted 1 million cells into each tube. The cells were pelleted once again at 1,000g for 5 min, removed supernatant, and flash frozen in liquid nitrogen, and finally stored indefinitely at -80°C.
Following user guide of Chromium Next GEM Single Cell ATAC Reagent Kits v1.1

value: GBM39-ER was under continuous treatment with 5µM erlotinib (LC Laboratories, E-4007)


title: kidney biopsy [GSM3525452 re-analysis]


title: LI epithelium of Tph2 KO 2


title: Sample_SG1_C1,CTL,1


title: GBM39_Droplet_Hi-C_10xATAC_v1.1

description: 10XATAC_v1.1, single-cell Hi-C

value: patient-derived xenograft (PDX) model GBM39


title: LI epithelium of Tph2 KO 1


title: U2OS, iCLIP, irradiated, rep2

city: Seville

first: Patrick

last: Toolan-Kerr

address: Calle Américo Vespucio 24 Edificio

institute: University of Seville

data_processing:
Mapping , crosslinking position and quantification was carried out using the iCLIP Nextflow analysis pipeline (https://app.flow.bio/)
GENCODE was used as the reference transcriptome annotation.
Assembly: Hg38
Supplementary files format and content: fastq of raw sequencing files
Supplementary files format and content: tsv files containing crosslinks per annotated transcript.

source_name: Bone

growth_protocol: U2OS cells were in DMEM  supplemented with  10% FBS and antibiotics

extract_protocol:
Total RNAs were extracted using Rneasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using the iCLIP protocol. Lee, F. C. Y. et al. An improved iCLIP protocol. bioRxiv, 2021.2008.2027.457890 (2021). https://doi.org/10.1101/2021.08.27.457890.

value: Bone

value: Osteosarcoma

value: 5 Gy X-Ray, Recovery 4h


title: kidney biopsy [GSM3524807 re-analysis]

value: EABMR


title: U2OS, iCLIP, irradiated, rep1


title: LI epithelium of Tph2 WT 3


title: COLO320DM_Droplet_Hi-C_10xATAC_v2

description: 10XATAC_v2, single-cell Hi-C

growth_protocol: COLO320DM was maintained in RPMI-1640 supplemented with 10% FBS (ThermoFisher, S11550H) and 1% penicillin-streptomycin (ThermoFisher, 15140122). Media was refreshed every 3-4 days, and cells were passaged once per week using Accutase (VWR, AT104) for dissociation.

extract_protocol:
Cells were crosslinked in 1% formaldehyde, which was diluted from 37% formaldehyde with 1× PBS (pH=7.4), and incubated at room temperature for 10 min. After crosslinking, the reactions were quenched in 200 mM glycine and incubated at room temperature for 5 min. Quenched reactions were spun down at 1,000g for 5 min at 4°C, resuspended using 1% BSA in 1× PBS (pH=7.4) to wash twice, and then aliquoted 1 million cells into each tube. The cells were pelleted once again at 1,000g for 5 min, removed supernatant, and flash frozen in liquid nitrogen, and finally stored indefinitely at -80°C.
Following user guide of Chromium Next GEM Single Cell ATAC Reagent Kits v2


title: COLO320HSR_Droplet_Hi-C_10xATAC_v2

description: 10XATAC_v2, single-cell Hi-C

growth_protocol: COLO320HSR was maintained in RPMI-1640 supplemented with 10% FBS (ThermoFisher, S11550H) and 1% penicillin-streptomycin (ThermoFisher, 15140122). Media was refreshed every 3-4 days, and cells were passaged once per week using Accutase (VWR, AT104) for dissociation.


title: U2OS, iCLIP, control, rep2

value: No treatment


title: LI epithelium of Tph2 WT 2


title: kidney biopsy [GSM3523984 re-analysis]

value: FABMR


title: Cell line mixing_Droplet_Hi-C_10xATAC_v2

description: 10XATAC_v2, single-cell Hi-C

data_processing:
All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files were demultiplexed and pre-processed using cellranger-atac v2.0.0. To select high-quality nuclei from DNA modality, we filtered cells based on the per cell contacts number.
Assembly: mix (hg38 + mm10)
Supplementary files format and content: Processed data are provided in .pairs format, each line represents a unique contact, with cell barcodes corresponding to left- and right-side of the contacts being recorded as extra columns in pairs file. Valid cells information is provided as metadata in the supplementary file.

growth_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in high glucose DMEM (Sigma-Aldrich, D6429) supplemented with 10% fetal bovine serum (FBS; Omega Scientific, FB-02) and 1% Penicillin-Steptomycin-Glutamine (ThermoFisher Scientific, 10378016) at 37°C with 5% CO2. K562 cells were cultured at 37°C, 5% CO2 in RPMI-1640 (ATCC, 30-2001) supplemented with 1% Penicillin-Steptomycin-Glutamine and 10% FBS. GM12878 cells were cultured at 37°C, 5% CO2 in RPMI-1640 supplemented with 1% Penicillin-Steptomycin-Glutamine and 15% FBS.


title: U2OS, iCLIP  control, rep1


title: DU145_NSD2

value: prostate cancer

value: NSD2 (abcam,#ab75359)


title: LI epithelium of Tph2 WT 1


title: kidney biopsy [GSM3525623 re-analysis]

value: kidney biopsy


title: PLK2-FLAG3

city: Hangzhou

first: Junjie

address: Huancheng East 208

department: Pharmacy

institute: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine

data_processing:
1.Data filtering  The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). 2.RNA identification  Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. 3.Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis) with Q Value≤0.05 (or FDR ≤0.001). 4.Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Sample Lysis 1.Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 2.Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 3.Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 4.Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. RNA Purification 1.Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 2.Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 3.Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 4.Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 5.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 6.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 7.Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 8.Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 9.Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: epithelial cells

value: overexpression PLK2-FLAG


title: kidney biopsy [GSM3525239 re-analysis]


title: SI epithelium of Tph2 KO 3


title: PLK2-FLAG2

value: WT


title: kidney biopsy [GSM3524983 re-analysis]

value: NR


title: kidney biopsy [GSM3525422 re-analysis]


title: SI epithelium of Tph2 KO 1

value: Intestinal epithelium


title: DU145_H3K27ac

value: H3K27ac (ACTIVE MOTIF,#91193)


title: SI epithelium of Tph2 KO 2

value: KO


title: kidney biopsy [GSM3524773 re-analysis]


title: DU145_H3K36me2


title: PLK2-D223N3

value: overexpression PLK2(D223N)-FLAG


title: DU145_H3K4me3

value: H3K4me3 (ACTIVE MOTIF,#39159)


title: SI epithelium of Tph2 WT 3


title: DU145_H3K27me3

value: H3K27me3 (ACTIVE MOTIF,#39155)


title: PLK2-D223N2


title: SI CD45 of Tph2 KO 3

description:
Small intestine lamina propria CD45 of Tph2 KO 3
Count_SI_CD45.txt

value: FACS sorted CD45 cell from small intestine


title: kidney biopsy [GSM3525408 re-analysis]

value: EABMR


title: PLK2-D223N1


title: kidney biopsy [GSM3524878 re-analysis]


title: SI epithelium of Tph2 WT 1


title: LI epithelium of Tph2 KO 4

description:
Large intestinal epithelium of Tph2 KO 4
Count_Tph2_LI_IEC_Co.txt

source_name: Large intestinal epithelium

value: Large intestinal epithelium

value: Tph2 KO


title: kidney biopsy [GSM3524085 re-analysis]

value: FABMR


title: FLAG3

value: overexpression FLAG Vector


title: PLK2-FLAG1


title: PC3_H3K27me3

value: LNCaP

value: prostate cancer


title: FLAG2

value: epithelial cells


title: LI epithelium of Tph2 KO 3

description:
Large intestinal epithelium of Tph2 KO 3
Count_Tph2_LI_IEC_Co.txt


title: kidney biopsy [GSM3525589 re-analysis]

value: kidney biopsy


title: PC3_NSD2

value: NSD2 (abcam,#ab75359)


title: FALG1

value: WT


title: kidney biopsy [GSM3524979 re-analysis]

value: LABMR


title: kidney biopsy [GSM3524415 re-analysis]


title: kidney biopsy [GSM3525358 re-analysis]

value: NR


title: PC3_H3K36me2


title: shHSPA13_TGFb_3

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
The fastq data were cleaned with the Fastx-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the default protocol by the manufacturer. The Blastn (http://blast.ncbi.nlm.nih.gov/) was used to annotated the mRNA. The Bowtie ( http://bowtie-bio.sourceforge.net/index.shtml ) was used to mapped the sequences to reference gennome.
Assembly: hg38
Supplementary files format and content: Raw counts

source_name: human embryonic stem cells -derived retinal pigment epithelium cells

extract_protocol:
The  total RNA  of the cells was isolated by TRIzol® Reagent (Invitrogen)
then the construction of cDNA library was performed by Illumina TruSeq Small RNA sample prep kit. The target PCR products were purified through 6% Novex TBE PAGE gel and the quality was checked by TBS380 (Picogreen). Then PCR amplification was performed and the generated clusters were sequenced by Illumina HiSeq platform.


title: SI epithelium of Tph2 WT 2

value: Intestinal epithelium


title: LI epithelium of Tph2 KO 1

description:
Large intestinal epithelium of Tph2 KO 1
Count_Tph2_LI_IEC_Co.txt


title: DU145_H3K4me1


title: kidney biopsy [GSM3525000 re-analysis]

value: Minor


title: shHSPA13_TGFb_2

value: human embryonic stem cells -derived retinal pigment epithelium cells


title: Donor3, Wound30

description:
single cell transcriptomics sequencing
PWH28D30
cell_metadata.txt

data_processing:
The single-cell sequence data were mapped with CellRanger (version 5.0.1) to a manually built human reference genome GRCh38 with annotation file GENCODE version 38. The low-quality cells expressing <500 genes, >20% mitochondrial genes, and <1000 gene counts were filtered out. We excluded mitochondrial and hemoglobin genes, as well as genes expressed in fewer than 10 cells. The Scrublet (v0.2.3) and DoubletFinder (v2.0.3) were further performed on each sample to detect potential doublets. Cell doublets identified by overlaps of two tools or in the same cluster with well-known markers of distinct cell types were also excluded from the analysis.
Data normalization and scaling were performed using the SCTransform package with regressing out the mitochondrial percentage and cell cycle effects. Top 4000 variable genes were used for principal component analysis (PCA). The batch effect of sample-to-sample variation was corrected using top 40 PCs as input of the RunHarmony function when integrating data. Uniform Manifold Approximation and Projection (UMAP) and k-nearest neighbors graph were generated using the RunUMAP and FindNeighbors functions inside Seurat (v4), respectively. The major cell clusters were identified using the Louvain graph-based algorithm with a resolution of 0.8, which resulted in 27 clusters. The differentially expressed genes among clusters were calculated using the FindAllMarkers functions with the MAST method. Genes with adjusted Pvalue<0.05, log fold change>0.25, and detected in at least 25 percent of cells were considered significantly high in the cluster. The clusters were annotated according to the top 20 marker genes of each cluster and documented signature genes of different cell types.
Assembly: GRCh38
Supplementary files format and content: zip files: contain the raw counts of gene expression, cell barcodes, and gene IDs.
Supplementary files format and content: txt file: cell and cluster annotation information

source_name: Skin

extract_protocol:
The healthy volunteers were enrolled at the Karolinska University Hospital, Stockholm, Sweden. To study the gene expression patten of human acute wound, 2-3 full-thickness skin wounds were made by using 3-mm biopsy punch at the upper buttock area of each donor. On day1, day7 or day30, the wound edge tissues were collected by using a 6-mm biopsy punch and snap-frozen for the following studies. Written informed consent was obtained from all donors for the collection and use of tissues for research. This study was approved by the Stockholm Regional Ethics Committee and conducted according to the Declaration of Helsinki’s principles.
Wound skin tissues were incubated with 5U/ml Dispase II at 4°C overnight. The epidermis was separated from dermis by tweezers gently and incubated in 0.025% Trypsin/ EDTA (Thermo Fisher) for 10-15 minutes at 37 ℃. The dermal cell suspension was prepared using the whole skin dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions. To capture as many cell types as possible, equal amounts of epidermal and dermal cells were mixed. The red blood cells and dead cells were depleted by Red Blood Cell Removal Solution (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec), respectively. After cleaning, viable cells were loaded onto the Chromium Controller (10X Genomics). Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics). The libraries were subsequently sequenced on an Illumina Novaseq6000 platform to achieve an average of approximately 50K read-pairs per cell.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

tag: individual

value: Skin

value: skin wound day 30


title: LNCaP_H3K36me2


title: LI epithelium of Tph2 WT 4

description:
Large intestinal epithelium of Tph2 WT 4
Count_Tph2_LI_IEC_Co.txt

data_processing:
For data analysis, reads were trimmed using Trim Galore with automatic adapter sequence detection.
Then, trimmed reads were mapped to the mouse reference genome (mm10) and annotated using STAR v2.7.3a with default parameter.
The number of mapped reads to each gene were counted by featureCounts of the Subread package using mouse GENCODE annotation M25 (GRCm38.p6).
Assembly: mm10
Supplementary files format and content: Feature counts table

value: Large intestinal epithelium


title: shHSPA13_TGFb_1


title: Donor3, Wound7

description:
single cell transcriptomics sequencing
PWH28D7
cell_metadata.txt

value: skin wound day 7


title: LNCaP_NSD2


title: LI epithelium of Tph2 WT 3

description:
Large intestinal epithelium of Tph2 WT 3
Count_Tph2_LI_IEC_Co.txt


title: shHSPA13_3


title: LI epithelium of Tph2 WT 2

description:
Large intestinal epithelium of Tph2 WT 2
Count_Tph2_LI_IEC_Co.txt


title: kidney biopsy [GSM3524410 re-analysis]

tag: rej7aaclust (nr, minor, tcmr1, tcmr2, eabmr, fabmr, labmr)

value: FABMR


title: Donor3, Wound1

description:
single cell transcriptomics sequencing
PWH28D1
cell_metadata.txt

tag: tissue

value: skin wound day 1


title: LI epithelium of Tph2 KO 2

description:
Large intestinal epithelium of Tph2 KO 2
Count_Tph2_LI_IEC_Co.txt

value: Tph2 KO


title: LI epithelium of Tph2 WT 1

description:
Large intestinal epithelium of Tph2 WT 1
Count_Tph2_LI_IEC_Co.txt


title: kidney biopsy [GSM3525304 re-analysis]


title: shHSPA13_2


title: Donor3, Skin

description:
single cell transcriptomics sequencing
PWH28D0
cell_metadata.txt

value: intact skin


title: shHSPA13_1


title: kidney biopsy [GSM3524402 re-analysis]


title: kidney biopsy [GSM3524669 re-analysis]


title: shControl_3

value: shControl


title: Donor4, Wound30

description:
single cell transcriptomics sequencing
PWH27D30
cell_metadata.txt


title: SI epithelium of Tph2 KO 4

description:
Small intestinal epithelium of Tph2 KO 4
Count_Tph2_SI_IEC_Co.txt

source_name: Small intestinal epithelium

value: Small intestinal epithelium


title: SI epithelium of Tph2 KO 3

description:
Small intestinal epithelium of Tph2 KO 3
Count_Tph2_SI_IEC_Co.txt


title: shControl_2


title: kidney biopsy [GSM3524060 re-analysis]

value: kidney biopsy


title: Donor4, Wound7

description:
single cell transcriptomics sequencing
PWH27D7
cell_metadata.txt


title: SI epithelium of Tph2 KO 2

description:
Small intestinal epithelium of Tph2 KO 2
Count_Tph2_SI_IEC_Co.txt


title: shControl_1


title: kidney biopsy [GSM3525525 re-analysis]


title: kidney biopsy [GSM3525135 re-analysis]

value: EABMR


title: Donor4, Skin

description:
single cell transcriptomics sequencing
PWH27D0
cell_metadata.txt


title: kidney biopsy [GSM3525132 re-analysis]


title: shCon_TGFb_3

value: shCon


title: Donor4, Wound1

description:
single cell transcriptomics sequencing
PWH27D1
cell_metadata.txt


title: SI epithelium of Tph2 KO 1

description:
Small intestinal epithelium of Tph2 KO 1
Count_Tph2_SI_IEC_Co.txt


title: SI epithelium of Tph2 WT 4

description:
Small intestinal epithelium of Tph2 WT 4
Count_Tph2_SI_IEC_Co.txt

value: WT


title: kidney biopsy [GSM3524757 re-analysis]


title: SI epithelium of Tph2 WT 3

description:
Small intestinal epithelium of Tph2 WT 3
Count_Tph2_SI_IEC_Co.txt


title: Donor5, Wound7

description:
single cell transcriptomics sequencing
PWH26D7
cell_metadata.txt


title: Donor5, Wound1

description:
single cell transcriptomics sequencing
PWH26D1
cell_metadata.txt


title: shCon_TGFb_1


title: kidney biopsy [GSM3523985 re-analysis]


title: SI epithelium of Tph2 WT 2

description:
Small intestinal epithelium of Tph2 WT 2
Count_Tph2_SI_IEC_Co.txt


title: kidney biopsy [GSM3524876 re-analysis]

value: NR


title: SI epithelium of Tph2 WT 1

description:
Small intestinal epithelium of Tph2 WT 1
Count_Tph2_SI_IEC_Co.txt