title: HSC from injured liver (12xCCl4) RS017

description:
HSC from injured liver (12xCCl4)
scRNA-seq (10x) on FACS-sorted-HSC

value: CCl4 (12 times)


title: Pou2af1+/+ CD8+ , 3

status: Public on Mar 24 2022

type: SRA

city: Montreal

first: Sylvie

last: Lesage

address: 2900 Bd Édouard-Montpetit

country: Canada

institute: Universite de Montreal

description:
Activated cells
CD8_WT_3

library_source: transcriptomic

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the GRCm38 reference genome (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
Raw reads extracted from STAR were normalized using DESeq2 v1.26.0
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized counts
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Mus musculus

source_name: Sorted CD8+ T cells

growth_protocol: Sorted T cells were activated in vitro for 2 days using anti-CD3 and anti-CD28 antibodies

extract_protocol:
Trizol
KAPA RNA HyperPrep PolyA (Roche)

tag: strain

tag: tissue

value: Spleen

tag: age

value: 12 weeks

tag: genotype/variation


title: HSC from normal liver (untreated) RS014

status: Public on Apr 07 2022

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

country: USA

institute: Columbia University

description:
HSC from normal liver (untreated)
scRNA-seq (10x) on FACS-sorted-HSC

data_processing:
10x genomics' cellranger software version 2.0.0 was used to process the data.
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
raw counts in the following formats: h5 and barcodes.tsv, genes.tsv, matrix.mtx
Genome_build: mm10

source_name: liver

extract_protocol:
For single cell RNA-seq of the whole liver, hepatic cell populations were obtained by perfusing and digesting the liver and enriched in non-parenchymal.
HSC were obtained perfusing and digesting the liver, followed by gradient centrifucation (Mederacke et al, Nat Protocol 2015) and FACS sorting for LratCre-induced TdTom.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina HiSeq and NovaSeq 6000 sequencing system instrument at the JP Sulzberger Columbia Genome Center.

treatment_protocol: Before HSC or whole liver cells isolation, mice were treated with one or multiple injection of CCl4  or were fed with a Fructose, Palmitate, Cholesterol and Trans-Fat (FPC) for 2 months after hydrodynamic tail vein injection of pT3-EF1α-TAZS89A plasmid in combination with sleeping beauty transposase SB13 or fed with a a L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline (CDAA-diet)

value: LratCre+, TdTom+ in C57BL/6J

tag: liver damage

tag: cell type

value: Hepatic Stellate Cells


title: Pou2af1+/- CD8+ , 2

description:
Activated cells
CD8_Het_2


title: Don1_3

status: Public on Mar 31 2022

city: New York

first: Daylon

last: James

address: 515 East 71st

institute: Weill Cornell Medicine

data_processing:
fastq files were processed using CellRangr count and individual libraries were aggregated using CellRangr aggr
Resultant features/barcodes file was imported into R Studio and used to generate a Seurat Object in Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature matrix and barcodes

organism: Homo sapiens

source_name: human antral follicle derived cells

growth_protocol: cells were isolated from primary patient derived ovarian follicles

extract_protocol:
cells were enzymatically separated and sorted by fluorescence activated cell sorting
RNA libraries were prepared for sequencing using version 3 10x Chromium library preparation kits

value: granulosa and stroma cells

tag: source

value: ovarian antral follicle

tag: follicle size

value: 3 mm


title: Pou2af1+/+ CD8+ , 4

description:
Activated cells
CD8_WT_4


title: Don1_2

value: 2 mm


title: Don1_1


title: Pou2af1+/+ CD8+ , 1

description:
Activated cells
CD8_WT_1


title: Don1_5

value: 4 mm


title: Pou2af1-/- CD4+ , 3

description:
Activated cells
CD4_KO_3

source_name: Sorted CD4+ T cells


title: Pou2af1-/- CD4+ , 2

description:
Activated cells
CD4_KO_2


title: Pou2af1-/- CD4+ , 1

description:
Activated cells
CD4_KO_1


title: Pou2af1+/- CD4+ , 3

description:
Activated cells
CD4_Het_3


title: Pou2af1+/+ CD4+ , 2

description:
Activated cells
CD4_WT_2


title: Pou2af1+/- CD4+ , 1

description:
Activated cells
CD4_Het_1


title: Pou2af1+/- CD4+ , 4

description:
Activated cells
CD4_Het_4


title: Pou2af1+/- CD8+ , 1

description:
Activated cells
CD8_Het_1


title: Pou2af1+/+ CD4+ , 1

description:
Activated cells
CD4_WT_1


title: Pou2af1+/+ CD4+ , 3

description:
Activated cells
CD4_WT_3


title: PTEC_mc_3DFlow_2_26

status: Public on Mar 20 2022

city: Mölndal

first: Julie

last: Williams

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

data_processing:
All samples were processed and analyzed using bcbio-nextgen pipeline v1.1.3 ( https://bcbio-nextgen.readthedocs.io ) where salmon was used for generating the raw gene count file.
Assembly: Hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: proximal tubule epithelial cells

growth_protocol: Human immortalized PTECs (RPTEC/TERT1; ATCC CRL4031) are cultured using the supplier’s specified protocol with some modifications. First, the PTECs are centrifuged at 200g for 4 min. Next, the cell suspension is pipetted through a 40-μm filter to obtain a single-cell suspension for accurate cell count. The cell media is modified to contain DMEM F-12 without glucose (pH 7.3 ± 0.05), NaHCO3 (1.2 mg/mL), D-glucose (100 mg/dL), ITS (1× concentration, 13146-5ML; Sigma), triiodothyronine (5 pM), sodium selenite (3.65 ng/mL), PGE1 (25 ng/mL), hydrocortisone (25 ng/mL), ascorbic acid (3.5 μg/mL), and EGF (10 ng/mL). The PTECs are cultured up to passage 20. Glomerular microvascular endothelial cells (HGECs, human primary; Cell Systems) are cultured according to the supplier’s specified protocol using their reagents. The HGECs are cultured up to passage 8.

extract_protocol:
RNA isolation is performed utilizing Qiagen’s miRNeasy Mini Kit according to manufacturer's protocol with minor modifications. Briefly, isolation is performed by injection of Qiazol lysing reagent through each channel on chip and then collection of the lysate. After homogenization via vortex mixing, the lysate is centrifuged for 15 min at 4°C to remove any unwanted gelatin-fibrin. Subsequent steps in the procedure followed the manufacturer’s protocol, including the on-column DNase digestion steps. The RNA quality is tested using a fragment analyzer (4200 TapeStation; Agilent). Only samples with an 8≤RINe≤ 10 are used.
The TrueSeq Stranded mRNA LT Sample Prep Kit (Illumina) was used to construct poly(A) selected RNA and then used for reverse transcription, generation of double stranded cDNA and subsequent library preparation and indexing to facilitate multiplexing. All libraries were quantified with the Fragment Analyzer using the standard sensitivity NGS kit (Agilent Technologies), pooled in equimolar concentrations and quantified with a Qubit Fluorometer (ThermoFisher Scientific) with the DNA Standard Sensitivity kit (ThermoFisher Scientific). The library pool was further diluted to 1.8pM and sequenced at >10M paired end reads/sample using the High Output reagent kit to 150 cycles on an Illumina NextSeq500. Three biological replicates were sequenced per sample.

value: hTERT-immortalized cell

tag: growing conditions

value: Flow

tag: co-culture

value: No


title: PTEC_mc_3DFlow_1_25


title: Pou2af1+/+ CD8+ , 2

description:
Activated cells
CD8_WT_2


title: PTEC_mc_3DFlow_5_28


title: H3K27ac_OSKM_D03_A_S14 (ChIP-seq)

status: Public on Apr 28 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: H3K27ac_OSKM_D03_A_S14 (ChIP-seq)

library_source: genomic

data_processing:
Fastq files were mapped to the mm9 reference using bwa [version 0.7.17-r1188].
The mapped reads were converted to BAM format and filtered by mapping quality (MAPQ) of >=10, retaining only properly aligned pairs (samtools -F 1796 flag)
Bigwig coverage tracks were generated using deepTools bamCoverage [version 3.4.1] with the following flags: --normalizeUsing RPGC -bs 50 -e 500 --effectiveGenomeSize 2150570000.
Coverage peaks were called using MACS [version 2.1.2] with flags -g mm --slocal=2000 --llocal=20000 --nomodel --extsize=300 -f BAMPE.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig generated using deepTools
Supplementary_files_format_and_content: bed genereted using MACS2

molecule: genomic DNA

source_name: OSKM reprogrammed stem cells

extract_protocol:
DNA was extracted using AMPure XP beads (Beckman Coulter Genomics, A63881). Chip sample libraries were prepared according to Illumina Genomic DNA protocol as described (Mikkelsen et al., 2007).
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Mendenhall et al., 2013). Briefly, cells were fixed for 10 min at RT with a final concentration of 0.8% formaldehyde. Formaldehyde was quenched with glycine for a final concentration of 125mM. The cells were then lysate with lysis buffer (100mM Tris-HCl, 300mM NaCl, 2% Triton® X-100, 0.2%v sodium deoxycholate, 10mM Cacl2) supplemented with EDTA free protease inhibitor Roche- 11873580001 for 20 min at Ice and the chromatin was digested by MNase (micrococcal nuclease)- Thermo Scientific™- 88216 for 20 min at 37OC. MNase was inactivated by 20mM EGTA. The fragmented chromatin was incubated with pre-bounded Dynabeads (A and G mix) - Invitrogen 10004D/ 10002D using H3K27ac antibody (Abcam, ab4729) and H3K4me2 antibody (Millipore, 07-030).  Samples were then washed twice with RIPA buffer, twice with RIPA high salt buffer (NaCl 360mM), twice with LiCl wash buffer (10mM Tris-Hcl, 250mM LiCl, 0.5% DOC, 1mM EDTA, 0.5% IGEPAL), twice with 10mM Tris-HCl pH=8. DNA was purified by incubating the samples with RNAse A (Thermo Scientific™ EN0531) for 30 min at 37OC followed by a 2 hours incubation with Proteinase K (Invitrogen™ 25530049). DNA was eluted by adding 2X concentrated elution buffer (10mM Tris-HCl, 300mM NaCl, 1% SDS, 2mM EDTA) and then reverse crosslinked overnight at 65OC.

tag: chip-seq antibody

tag: days from treatment

tag: reprogramming factors

value: OSKM

value: embryonic stem cells


title: PTEC_mc_3DFlow_4_27


title: Pou2af1-/- CD4+ , 4

description:
Activated cells
CD4_KO_4


title: PTEC_cc_TW_Plastic_3

value: Plastic

value: Yes


title: PTEC_cc_TW_gel_3

value: Gel


title: PTEC_cc_TW_gel_2


title: PTEC_cc_3DFlow_5_40


title: PTEC_cc_TW_Plastic_1


title: Pou2af1+/- CD4+ , 2

description:
Activated cells
CD4_Het_2

value: Spleen


title: PTEC_cc_3DFlow_4_39


title: Pou2af1+/+ CD4+ , 4

description:
Activated cells
CD4_WT_4

value: 12 weeks


title: PTEC_TW_gel_2_14


title: PTEC_cc_3DFlow_3_38


title: PTEC_cc_3DFlow_2_37


title: PTEC_cc_3DFlow_1_36


title: PTEC_TW_Plastic_2_02


title: PTEC_mc_3DFlow_6_29


title: PTEC_TW_gel_3_15


title: PTEC_TW_gel_1_13


title: PTEC_TW_Plastic_3_03


title: PTEC_TW_Plastic_1_01


title: ACBRI_mc_3DFlow_5_34

source_name: human glomerular endothelial cells

value: Primary glomerular endothelial cell


title: ACBRI_mc_3DFlow_4_33


title: PTEC_cc_TW_gel_1


title: PTEC_cc_TW_Plastic_2


title: ACBRI_mc_3DFlow_3_32


title: ACBRI_mc_3DFlow_6_35


title: ACBRI_cc_TW_gel_2


title: ACBRI_mc_3DFlow_2_31


title: ACBRI_mc_3DFlow_1_30


title: ACBRI_cc_TW_gel_3


title: ACBRI_cc_TW_Plastic_2


title: ACBRI_cc_TW_Plastic_1


title: ACBRI_cc_3DFlow_5_45


title: ACBRI_cc_3DFlow_4_44


title: ACBRI_cc_3DFlow_3_43


title: ACBRI_cc_3DFlow_2_42


title: ACBRI_cc_TW_Plastic_3


title: ACBRI_TW_Plastic_3_06


title: ACBRI_cc_3DFlow_1_41


title: ACBRI_TW_gel_2_17


title: Total Kidney 24 week old Clrf-KO1

status: Public on Mar 19 2022

city: Halifax

first: Francesca

last: Di Cara

state: Nova Scotia

address: 5850/5980 University Avenue

institute: Dalhousie University

data_processing:
The quality of the sequencing reads was inspected using FastQC tool V0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and reads with Phred quality score of 30 over 90% of the reads were retained utilizing the Fastx-toolkit V0.0.13 (http://hannonlab.cshl.edu/).
High-quality reads were mapped to the mouse GENCODE M25 annotation database (GRCm38.p6) using the STAR aligner V2.7.5a. STAR aligner was then used to remove duplicates, create transcriptome hits count tables, and generate wiggle files.
DESeq2 package V1.28.1 was used to remove hits with CPM values less than 1 and calculate differentially expressed genes with FDR-transformed P-value  > 0.05 and log fold change cutoff of 1.5.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files of FPKM values for all samples

source_name: Kidney

extract_protocol:
Total RNA was isolated from freshly frozen kidneys of three age- and sex-matched WT and Clr-f−/− mice at 7, 13, and 24 weeks of age using TRIzol (Thermo Fisher Scientific) and RNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA, USA).  RNA-seq was performed on the Illumina HiSeq 4000 platform, with paired-end reads, at > 30 × 10^6 read depth per
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: genotype

value: Clr-f-/-

value: 24 weeks


title: Total Kidney 24 week old Clrf-KO2


title: Total Kidney 13 week old Clrf-KO1

value: 13 weeks


title: Total Kidney 13 week old WT3

value: WT


title: Total Kidney 24 week old Clrf-KO3


title: ACBRI_TW_gel_3_18


title: ACBRI_TW_Plastic_2_05


title: Total Kidney 13 week old WT2


title: ACBRI_TW_gel_1_16


title: ACBRI_cc_TW_gel_1


title: Total Kidney 7 week old Clrf-KO2

value: 7 weeks


title: Total Kidney 7 week old WT3


title: Total Kidney 24 week old WT2


title: BIDC071 [methylation]

status: Public on Mar 18 2022

type: genomic

city: Vancouver

first: Janice

middle: M

last: Leung

state: BC

address: Room 166, 1081 Burrard Street

institute: Centre for Heart Lung Innovation, University of British Columbia

hyb_protocol: Unmethylated cytosine residues were converted to uracil using the EZ DNA Methylation Kit. The Illumina Infinium MethylationEPIC BeadChip microarray was used to profile 863,904 CpG sites.

scan_protocol: Recommended Illumina scanner setting

data_processing:
The methyl_signal_intensities.txt contains unmethylated and methylated signal intensities. R statistical software
the methyl_processed_data.txt contains 'Noob background corrected, BMIQ normalized beta values'

label: Cy5 and Cy3

source_name: Bronchial epithelium

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from bronchial epithelial brushings using the DNeasy Blood and Tissue Kit

tag: copd

value: N


title: Total Kidney 7 week old WT1


title: Total Kidney 24 week old WT3


title: BIDC072 [methylation]

value: Y


title: Total Kidney 13 week old Clrf-KO2


title: Total Kidney 13 week old Clrf-KO3


title: Total Kidney 24 week old WT1


title: Total Kidney 7 week old Clrf-KO3


title: Total Kidney 7 week old Clrf-KO1


title: Total Kidney 7 week old WT2


title: ACBRI_TW_Plastic_1_04

value: No


title: BIDC068 [methylation]


title: BIDC070 [methylation]


title: Total Kidney 13 week old WT1


title: BIDC057 [methylation]


title: BIDC066 [methylation]


title: BIDC065 [methylation]


title: BIDC067 [methylation]


title: BIDC063 [methylation]


title: BIDC061 [methylation]


title: BIDC059 [methylation]


title: BIDC031 [methylation]


title: BIDC055 [methylation]


title: BIDC062 [methylation]


title: BIDC046 [methylation]


title: BIDC053 [methylation]


title: BIDC047 [methylation]


title: BIDC064 [methylation]


title: BIDC054 [methylation]


title: BIDC043 [methylation]


title: BIDC060 [methylation]


title: BIDC058 [methylation]


title: BIDC028 [methylation]


title: BIDC051 [methylation]


title: BIDC027 [methylation]


title: BIDC049 [methylation]


title: BIDC022 [methylation]


title: BIDC025 [methylation]


title: BIDC045 [methylation]


title: BIDC042 [methylation]


title: BIDC032 [methylation]


title: BIDC024 [methylation]


title: BIDC050 [methylation]


title: BIDC021 [methylation]


title: BIDC019 [methylation]


title: BIDC020 [methylation]


title: BEC096 [methylation]


title: BEC085 [methylation]


title: BEC097 [methylation]


title: BEC089 [methylation]


title: BEC088 [methylation]


title: BEC071 [methylation]


title: BEC069 [methylation]


title: BEC084 [methylation]


title: BEC086 [methylation]


title: BEC081 [methylation]


title: BEC056 [methylation]


title: BEC063 [methylation]


title: BEC075 [methylation]


title: BEC064 [methylation]


title: BEC080 [methylation]


title: BEC068 [methylation]


title: BEC051 [methylation]


title: BEC053 [methylation]


title: BEC093 [methylation]


title: BEC062 [methylation]


title: BEC045 [methylation]


title: BEC046 [methylation]


title: BEC070 [methylation]


title: BEC043 [methylation]


title: BEC073 [methylation]


title: BEC042 [methylation]


title: BEC060 [methylation]


title: BEC041 [methylation]


title: BEC040 [methylation]


title: BEC039 [methylation]


title: BEC047 [methylation]


title: BEC038 [methylation]


title: BEC037 [methylation]


title: BEC035 [methylation]


title: BEC034 [methylation]


title: BEC032 [methylation]


title: BEC036 [methylation]


title: BEC027 [methylation]


title: BEC028 [methylation]


title: BEC031 [methylation]


title: BIDC066 [RNA-seq]

data_processing:
The raw sequencing reads were aligned to the human genome and quantified using the SALMON quasi-alignment approach
The voom function implemented in the Limma R package was used to normalise the counts to log2 counts per million (CPM).
Genes with low abundance (Log2 CPM <1 for 75% of the samples) were removed.
Genome_build: GRCh 37
Supplementary_files_format_and_content: comma-separated file include voom-normalized log2 CPM for each sample

source_name: Bronchial brush

extract_protocol:
Total RNA was extracted from the bronchial epithelial brushings by using the RNeasy Mini kit, paired end RNA sequencing was performed to a depth of 50 million reads using the Illumina Novaseq6000 platform
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bronchial epithelium


title: BIDC072 [RNA-seq]


title: BIDC060 [RNA-seq]


title: BIDC068 [RNA-seq]


title: BIDC067 [RNA-seq]


title: BIDC071 [RNA-seq]


title: BIDC070 [RNA-seq]


title: BIDC065 [RNA-seq]


title: BIDC064 [RNA-seq]


title: BIDC055 [RNA-seq]


title: BIDC063 [RNA-seq]


title: BIDC061 [RNA-seq]


title: BIDC059 [RNA-seq]


title: BIDC057 [RNA-seq]


title: BIDC058 [RNA-seq]


title: BIDC053 [RNA-seq]


title: BIDC054 [RNA-seq]


title: BIDC049 [RNA-seq]


title: BIDC047 [RNA-seq]


title: BIDC050 [RNA-seq]


title: BIDC051 [RNA-seq]


title: BIDC046 [RNA-seq]


title: BIDC045 [RNA-seq]


title: BIDC062 [RNA-seq]


title: BIDC032 [RNA-seq]


title: BIDC042 [RNA-seq]


title: BIDC028 [RNA-seq]


title: BIDC043 [RNA-seq]


title: BIDC027 [RNA-seq]


title: BIDC025 [RNA-seq]


title: BIDC022 [RNA-seq]


title: BIDC020 [RNA-seq]


title: BIDC021 [RNA-seq]


title: BIDC019 [RNA-seq]


title: BEC096 [RNA-seq]


title: BIDC024 [RNA-seq]


title: BEC088 [RNA-seq]


title: BEC089 [RNA-seq]


title: BEC097 [RNA-seq]


title: BEC085 [RNA-seq]


title: BEC081 [RNA-seq]


title: BEC086 [RNA-seq]


title: BEC080 [RNA-seq]


title: BEC093 [RNA-seq]


title: BEC075 [RNA-seq]


title: BEC073 [RNA-seq]


title: BEC070 [RNA-seq]


title: BEC069 [RNA-seq]


title: BEC064 [RNA-seq]


title: BIDC031 [RNA-seq]


title: BEC063 [RNA-seq]


title: BEC062 [RNA-seq]


title: BEC060 [RNA-seq]


title: BEC084 [RNA-seq]


title: BEC053 [RNA-seq]


title: BEC056 [RNA-seq]


title: C2C12 cells, gRc+H2O2 rep2

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: C2C12 cells were pretreated with gRc 10 uM for 18 h and then treated with H2O2 for 6 h (Pretreatment 18 h + H2O2 6 h = total 24 h)

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to mouse genome assembly GRCm38 via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with mouse gene annotation GRCm38.86.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

growth_protocol: C2C12 murine myoblasts (ATCC CRL-1772) were purchased from the ATCC (Manassas, VA, USA). Myoblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, CARLSBAD, CA, USA) containing 10% fetal bovine serum (FBS; Gibco Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen) at 37°C in an atmosphere of 5% CO2. For differentiation to C2C12 myotubes, myoblasts were cultured in DMEM containing 2% horse serum (HS; Gibco) for 5 days.

extract_protocol:
Total RNA was isolated from cells  using Maxwell (Promega) based method.
One 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.   The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

treatment_protocol: We obtained gRc and H2O2 solution from Sigma (St Louis, MO, USA). gRc was dissolved in 100% dimethyl sulfoxide (DMSO; Sigma) to a final concentration of 50 mM, filtered, and stored at -20°C until use. Myotubes were treated with vehicle (0.02% DMSO), 10 µM gRc, or 0.25 mM H2O2 for indicated times.

tag: cell line

value: myoblasts

tag: treatment

tag: treatment time

value: gRc 24h (pretreatment) + H2O2 6 h

tag: treatment dose

value: gRc 10 uM + H2O2 0.25mM


title: C2C12 cells, gRc rep3

description: C2C12 cells treated with gRc for 24 h

value: gRc

value: 10 uM


title: BEC046 [RNA-seq]

tag: tissue


title: C2C12 cells, Vehicle rep3

description: C2C12 cells treated with vehicle for 24 h

value: vehicle


title: BEC047 [RNA-seq]


title: BEC045 [RNA-seq]


title: C2C12 cells, Vehicle rep2


title: C2C12 cells, H2O2 rep2

description: C2C12 cells were pretreated with vehicle for 18 h and then treated with H2O2 for 6 h (Pretreatment 18 h + H2O2 6 h = total 24 h)

value: vehicle 18h (pretreatment)  + H2O2 6 h


title: BEC071 [RNA-seq]


title: BEC068 [RNA-seq]


title: BEC042 [RNA-seq]


title: BEC043 [RNA-seq]


title: C2C12 cells, gRc+H2O2 rep1


title: C2C12 cells, H2O2 rep1


title: BEC040 [RNA-seq]


title: C2C12 cells, gRc rep1

description: C2C12 cells treated with gRc for 24 h


title: BEC039 [RNA-seq]


title: BEC041 [RNA-seq]


title: C2C12 cells, gRc+H2O2 rep3


title: BEC038 [RNA-seq]


title: BEC035 [RNA-seq]


title: C2C12 cells, Vehicle rep1


title: BEC034 [RNA-seq]


title: C2C12 cells, H2O2 rep3


title: BEC027 [RNA-seq]


title: C2C12 cells, gRc rep2

description: C2C12 cells treated with gRc for 24 h


title: BEC036 [RNA-seq]


title: Liver Mettl3-deficient rep2

status: Public on Mar 09 2022

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi 44

country: China

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2.
FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes Entrez Gene ID and reads counts for each sample.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on liqid nitrogen, and total RNA was isolated with TRIzol reagent (Invitrogen) and performed using Ribo-Zero Gold rRNA Removal Kit (Illumina). The RNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: liver


title: Liver Mettl3-deficient rep3


title: BEC051 [RNA-seq]


title: Liver WT rep3

value: wild type


title: BEC037 [RNA-seq]


title: Liver Mettl3-deficient rep1


title: Liver Mettl3-deficient rep3_input

data_processing:
Illumina HiSeq raw sequencing read data that passed the Illumina chastity flter were used for the following analysis.
The IP and input trimmed reads were aligned to genome reference sequences using HISAT2 software (v2.1.0). Aligned reads were used for peak calling of the MeRIP regions, statistically signifcant MeRIP enriched regions (peaks) were identifed for each sample at a p value threshold of 0.05. The MeRIP enriched regions (peaks) were annotated by the overlapped gene using the newest Ensembl database.
Hierarchical clustering, scatter plots and volcano plots were performed for the methylated enriched regions analysis in R for statistical computing and graphics.
Genome_build: mm10
Supplementary_files_format_and_content: The fold enrichment within the peak in the IP sample compared with the input sample

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from mouse liver tissues with TRIzol reagent (Invitrogen) then subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit (61006, Invitrogen) following the manufacturers instructions. For m6A-immunoprecipitation (IP) samples, RNA fragmentation and immunoprecipitated of m6A-containing RNA fragments via anti-m6A antibody (202003, Synaptic System) were performed.
The input mRNA sample (Input) and purified mRNA sample (m6A-IP) were used for library construction by TruSeq Stranded mRNA Library Preparation kit (Illumina) according to the manufacturers instructions.


title: BEC032 [RNA-seq]


title: Liver WT rep2


title: Liver Mettl3-deficient rep1_input


title: Liver WT rep1


title: Liver Mettl3-deficient rep2_input


title: Liver Mettl3-deficient rep2_m6A-tagged


title: Liver WT rep3_input


title: Liver Mettl3-deficient rep1_m6A-tagged


title: Liver WT rep3_m6A-tagged


title: Liver WT rep2_input


title: BEC031 [RNA-seq]


title: Liver WT rep2_m6A-tagged


title: Liver WT rep1_input


title: Liver Mettl3-deficient rep3_m6A-tagged


title: Liver WT rep1_m6A-tagged


title: 4681-M

status: Public on Mar 01 2022

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: Whole blood of healthy control subject (Mother of 4681-P)

data_processing:
Trim-Galore! was used to perform adaptor trimming and filtering of raw reads.
Kallisto was used to align reads to the GENCODE 32 human transcriptome (Genome build hg38).
Transcript-level counts were summarized to gene level counts using tximport.
Genome_build: RNA-Seq reads aigned to GENCODE 32 human transcriptome (Genome build hg38)
Supplementary_files_format_and_content: Raw counts. Rownames represent genes (ENTREZ gene IDs), column names represent samples

source_name: Whole blood

extract_protocol:
Blood samples (EDTA tubes) were collected from all research subjects by venipuncture. DNA and RNA were extracted simultaneously from 1ml fresh whole blood, using the AllPrep DNA/RNA Mini kit (Qiagen).
Globin mRNAs were depleted from RNA samples using the GLOBINclear kit (Invitrogen). Stranded library preparation and eukaryotic transcriptome resequencing were performed using the BGISeq-500 next generation sequencing platform with paired end 100bp reads.

value: Control

value: Mother

tag: family

value: Discovery

tag: Sex

value: F

value: White


title: M-19-23

description: Whole blood of healthy control subject (Age/sex-matched control for 3425-P)

value: Age and sex matched donor

value: M


title: BEC028 [RNA-seq]

value: Bronchial epithelium

value: N


title: M-24-28

description: Whole blood of healthy control subject (Age/sex-matched control for 8658-P)


title: 4681-P

description: Whole blood of individual with Sotos syndrome

value: Case

value: Proband


title: F-16-20

description: Whole blood of healthy control subject (Age/sex-matched control for 5767-P)


title: 8658-P


title: 8658-F

description: Whole blood of healthy control subject (Father of 8658-P)

value: Father


title: 4681-F

description: Whole blood of healthy control subject (Father of 4681-P)


title: 7634-M

description: Whole blood of healthy control subject (Age/sex/race matched control of 9049-P)

value: Age/sex/race matched control

value: Validation


title: 6424-S

description: Whole blood of healthy control subject (Age and sex-matched sibling of 6424-P)

value: Age and sex matched sibling


title: 9049-P


title: 5767-P

value: Asian


title: 5996-P


title: 6424-P


title: 5996-S

description: Whole blood of healthy control subject (Age and sex-matched sibling of 5996-P)


title: 5530-P


title: 4834-P


title: 4834-M

description: Whole blood of healthy control subject (Mother of 4834-P)


title: 4834-F

description: Whole blood of healthy control subject (Father of 4834-P)


title: 3425-F

description: Whole blood of healthy control subject (Father of 3425-P)


title: 3077-P


title: 3077-S

description: Whole blood of healthy control subject (Age and sex-matched sibling of 3077-P)


title: 3425-P


title: 3077-M

description: Whole blood of healthy control subject (Mother of 3077-P and age/sex/race-matched control of 5530-P)

value: Mother and age and sex matched control


title: 5767-F

description: Whole blood of healthy control subject (Father of 5767-P)

value: Control


title: VM mouse #9

status: Public on Feb 11 2022

city: Worcester

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

institute: Umass Chan Medical

description:
samples processed with gentleMACS lung digestion kit
9_CD31_pos_A

data_processing:
1. For Quality Control, we use FastQC to create qc outputs. There are optional read quality filtering (trimmomatic), read quality trimming (trimmomatic), adapter removal (cutadapt) processes available.
1. Bowtie2/Bowtie/STAR is used to count or filter out common RNAs (eg. rRNA, miRNA, tRNA, piRNA etc.).
1. RSEM is used to align RNA-Seq reads to a reference transcripts and estimates gene and isoform expression levels. Alternatively, Kallisto used for quantifying abundances of transcripts based on pseudoalignments.
1. HISAT2, STAR and Tophat2 are used to align RNA-Seq reads to a genome. Optionally, counting reads to genomic features such as genes, exons, promoters and genomic bins could be done by featureCounts.
1. Genome-wide Bam analysis is done by RseQC, Picard.
Genome_build: mm10
Supplementary_files_format_and_content: a csv file output by DESeq2 containing expected counts for detected genes, differentially expressed genes are tested for by false discovery rate

source_name: Mouse lung FACS sorted for live CD45-EPCAM-PDGFRa-CD31+ endothelial cells

extract_protocol:
Lungs from mice were dissected and digested using the GentleMACS lung digestion kit. Samples were then FACS sorted for live CD45-EPCAM-PDGFRa-CD31+ directly into RLT buffer. Limited RNA（more than 200pg, high-quality）was amplified with oligo-dT and dNTPs, incubated at 72℃and immediately put back on ice, then reverse transcribed to cDNA based on polyA tail. The template was switched to the 5' end of the RNA and the full-length cDNA was generated by PCR. Agilent 2100 bioanalyzer instrument (Thermo Fisher Scientific, MA, USA) was used to determine the average molecule length of PCR product. Purified cDNA from previous steps was fragmented into small pieces with fragment buffer by PCR, and the product was purified and selected by the Agencourt AMPure XP-Medium kit (Thermo Fisher Scientific, USA). cDNA was quantified by Agilent Technologies 2100 bioanalyzer.
Oligo(dT)-attached magnetic beads were used to purified mRNA.   Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair-end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: cell type

value: Lung CD31+ endothelial cell

value: STING V154M mutant

value: lung


title: VM mouse #10

description:
samples processed with gentleMACS lung digestion kit
10_CD31_pos_A


title: WT mouse #5

description:
samples processed with gentleMACS lung digestion kit
5_CD31_pos_A

value: STING WT


title: VM mouse #8

description:
samples processed with gentleMACS lung digestion kit
8_CD31_pos_A


title: WT mouse #6

description:
samples processed with gentleMACS lung digestion kit
6_CD31_pos_A


title: VM mouse #3

description:
samples processed with gentleMACS lung digestion kit
3_CD31_pos_A


title: WT mouse #4

description:
samples processed with gentleMACS lung digestion kit
4_CD31_pos_A


title: Col0_TSS_RNA-seq_TSS_1

status: Public on Jan 21 2022

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed

Read counts on defined genomic regions were determined using bedtools v.2.25.0
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Read counts per genomic feature in a .bed file

organism: Arabidopsis thaliana

source_name: Chloroplast

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours and grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle

extract_protocol:
5μg of RNA isolated from enriched chloroplasts was digested with 6U of Terminator exonuclease
TSS RNA-Seq libraries were generated with SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian

value: wild type (Col-0)

tag: age

value: 14 days-old

value: 14 days-old seedlings

value: 0h formaldehyde crosslinking


title: WT mouse #1

description:
samples processed with gentleMACS lung digestion kit
1_CD31_pos_A


title: rpoB_ptChIP_1h_no_antibody_rpoB_no_antibody_3

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle. For four days-old plants they were grown on 0.5X MS plates under continuous light (100 umol m-2 s-1)

extract_protocol:
Five grams of rosette leaves were harvested and rinsed 3 times with ultra-pure water to eliminate soil debris and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a blender. The homogenate was filtered through two layers of miracloth, and the flow-through was centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer
ChIP-seq sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

value: 4h formaldehyde crosslinking

tag: chip antibody

value: no antibody


title: Col0_TSS_RNA-seq_TSS_3


title: Col0_TSS_RNA-seq_TSS_2


title: rpoB_ptChIP_4h_no_antibody_rpoB_no_antibody_2


title: Colo205_5% PC124 Ascites

status: Public on Feb 22 2022

type: RNA

city: Singapore

first: Johnny

middle: Chin-Ann

last: Ong

state: Singapore

address: 11 Hospital Drive

department: Division of Surgical Oncology

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression data from Colo-205 cells treated with 5% colorectal PC CFA medium for 24 hours

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray data was uploaded into the free programming software R (version 3.4.2) for processing and normalization.

label: biotin

source_name: Colo205 cell line treated with 5% of PC124 cell free ascites for 24 hours

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated using Qiagen Mini Kit (Qiagen) following the manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip Genome U133 Plus 2.0 array (Affymetrix).

tag: histology of cell line

value: Metastatic colorectal adenocarcinoma

tag: source of ascites

value: Patient diagnosed with peritoneal carcinomatosis of colorectal origin

value: 5% of PC124 cell free ascites


title: SNUC1_5% PC009 Ascites

description: Gene expression data from SNU-C1 cells treated with 5% colorectal PC CFA medium for 24 hours

source_name: SNUC1 cell line treated with 5% of PC009 cell free ascites for 24 hours

value: 5% of PC009 cell free ascites


title: SNUC1_5% PC124 Ascites

source_name: SNUC1 cell line treated with 5% of PC124 cell free ascites for 24 hours


title: Colo205_5% PC009 Ascites

source_name: Colo205 cell line treated with 5% of PC009 cell free ascites for 24 hours


title: SNUC1_0.1% PC124 Ascites

description: Gene expression data from SNU-C1 cells treated with 0.1% colorectal PC CFA medium for 24 hours

source_name: SNUC1 cell line treated with 0.1% of PC124 cell free ascites for 24 hours

value: 0.1% of PC124 cell free ascites


title: Colo205_0.1% PC124 Ascites

description: Gene expression data from Colo-205 cells treated with 0.1% colorectal PC CFA medium for 24 hours

source_name: Colo205 cell line treated with 0.1% of PC124 cell free ascites for 24 hours


title: rpoB_ptChIP_0h_no_antibody_rpoB_no_antibody_2


title: rpoB_ptChIP_1h_no_antibody_rpoB_no_antibody_2


title: rpoB_ptChIP_4h_no_antibody_rpoB_no_antibody_3


title: rpoB_ptChIP_1h_no_antibody_rpoB_no_antibody_1


title: rpoB_ptChIP_4h_input_rpoB_input_3

value: input


title: SNUC1_0.1% PC009 Ascites

source_name: SNUC1 cell line treated with 0.1% of PC009 cell free ascites for 24 hours

value: 0.1% of PC009 cell free ascites


title: rpoB_ptChIP_0h_no_antibody_rpoB_no_antibody_1


title: rpoB_ptChIP_1h_input_rpoB_input_3


title: VM mouse #7

description:
samples processed with gentleMACS lung digestion kit
7_CD31_pos_A

value: Lung CD31+ endothelial cell


title: rpoB_ptChIP_0h_input_rpoB_input_3


title: rpoB_ptChIP_0h_no_antibody_rpoB_no_antibody_3


title: rpoB_ptChIP_0h_input_rpoB_input_2


title: rpoB_ptChIP_4h_input_rpoB_input_2


title: rpoB_ptChIP_4h_rpoB_ChIP_3

value: a-RpoB (PhytoAB Cat.:PHY1239 Lot:9321A5)


title: rpoB_ptChIP_4h_input_rpoB_input_1


title: rpoB_ptChIP_4h_rpoB_ChIP_2


title: rpoB_ptChIP_0h_rpoB_ChIP_3


title: rpoB_ptChIP_1h_rpoB_ChIP_3


title: rpoB_ptChIP_0h_input_rpoB_input_1


title: rpoB_ptChIP_1h_input_rpoB_input_2


title: rpoB_ptChIP_1h_rpoB_ChIP_1


title: rpoB_ptChIP_1h_input_rpoB_input_1


title: HA_ptChIP_pTAC12-HA_1h_HA_ChIP_pTAC12-HA_2

value: 1h formaldehyde crosslinking


title: HA_ptChIP_pTAC12-HA_0h_HA_ChIP_pTAC12-HA_2


title: HA_ptChIP_pTAC12-HA_0h_HA_ChIP_pTAC12-HA_3


title: HA_ptChIP_pTAC12-HA_1h_HA_ChIP_pTAC12-HA_3


title: HA_ptChIP_Col0_1h_HA_ChIP_Col0_3


title: HA_ptChIP_pTAC12-HA_1h_HA_ChIP_pTAC12-HA_1


title: HA_ptChIP_Col0_4h_HA_ChIP_Col0_3


title: HA_ptChIP_Col0_0h_HA_ChIP_Col0_3


title: HA_ptChIP_pTAC12-HA_0h_HA_ChIP_pTAC12-HA_1


title: rpoB_ptChIP_1h_rpoB_ChIP_2


title: HA_ptChIP_Col0_4h_HA_ChIP_Col0_2


title: HA_ptChIP_Col0_16h_HA_ChIP_Col0_2

value: 16h formaldehyde crosslinking


title: rpoB_ptChIP_0h_rpoB_ChIP_1

value: wild type (Col-0)


title: HA_ptChIP_Col0_1h_HA_ChIP_Col0_2

value: 14 days-old


title: HA_ptChIP_Col0_0h_HA_ChIP_Col0_2

value: 14 days-old seedlings


title: HA_ptChIP_Col0_4h_HA_ChIP_Col0_1


title: rpoB_ptChIP_4h_rpoB_ChIP_1


title: HA_ptChIP_Col0_16h_HA_ChIP_Col0_1


title: HA_ptChIP_pTAC12-HA_4h_HA_ChIP_pTAC12-HA_3


title: rpoB_ptChIP_sig6-1_4_do_input_sig6-1_input_3

value: 4 days-old

value: 4 days-old seedlings


title: HA_ptChIP_pTAC12-HA_4h_HA_ChIP_pTAC12-HA_2

value: 4h formaldehyde crosslinking


title: rpoB_ptChIP_sig6-1_4_do_sig6_1_ChIP_3


title: rpoB_ptChIP_sig6-1_4_do_sig6_1_ChIP_2


title: HA_ptChIP_pTAC12-HA_4h_HA_ChIP_pTAC12-HA_1


title: HA_ptChIP_pTAC12-HA_16h_HA_ChIP_pTAC12-HA_2


title: rpoB_ptChIP_sig6-1_4_do_sig6_1_ChIP_1


title: HA_ptChIP_pTAC12-HA_16h_HA_ChIP_pTAC12-HA_1


title: rpoB_ptChIP_sig2-2_4_do_input_sig2-2_input_3


title: rpoB_ptChIP_sig2-2_4_do_input_sig2-2_input_1


title: rpoB_ptChIP_sig6-1_4_do_input_sig6-1_input_1


title: rpoB_ptChIP_sig2-2_4_do_input_sig2-2_input_2


title: rpoB_ptChIP_sig2-2_4_do_sig2-2_ChIP_2


title: rpoB_ptChIP_Col0_4_do_input_Col0_input_2


title: rpoB_ptChIP_sig2-2_4_do_sig2-2_ChIP_3


title: rpoB_ptChIP_sig2-2_4_do_sig2-2_ChIP_1


title: rpoB_ptChIP_Col0_4_do_input_Col0_input_3


title: HA_ptChIP_Col0_0h_HA_ChIP_Col0_1

value: 0h formaldehyde crosslinking


title: HA_ptChIP_Col0_1h_HA_ChIP_Col0_1


title: rpoB_ptChIP_Col0_4_do_input_Col0_input_1


title: rpoB_ptChIP_sig6-1_4_do_input_sig6-1_input_2


title: rpoB_ptChIP_Col0_4_do_Col0_ChIP_2


title: rpoB_ptChIP_Col0_14_do_input_Input_3


title: rpoB_ptChIP_Col0_14_do_input_Input_1


title: rpoB_ptChIP_Col0_14_do_ChIP_1


title: rpoB_ptChIP_Col0_14_do_ChIP_3


title: B6xSPRET-H3K27ac-90m-B2

status: Public on Jan 17 2022

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

data_processing:
Reads were trimmed with the paired-end option and with SLIDINGWINDOW:5:30 using Trimmomatic (Bolger et al., 2014).
Paired-end reads that survived trimming were re-paired using the bbmap utility (Bushnell 2014). Both unpaired and paired reads were concurrently mapped to the C57BL/6J and appropriate pseudogenome with bowtie2 using default parameters (Langmead and Salzberg, 2012).
Mapped reads were converted to .bam format with samtools view (Li et al., 2009) using the following options -h -b -F 3844 -q 10 and sorted by coordinate. Reads initially mapped to each pseudogenome were converted back to C57BL/6J coordinates by running Lapels (Huang et al., 2014).
For visualization purposes, mapped reads in .bam format were also converted to .bed format and unique reads were retained (with sort -k1,1 -k2,2n -k3,3n -u) and extended by 150 bp with bedtools slop -l 0 -r 150.
All samples were normalized to a depth of 10 million reads and read coverage was calculated by bedtools genomeCoverageBed. The output .bedgraph file was then converted with UCSC’s bedGraphtobigWig utility and all tracks displayed were visualized with the UCSC Genome Browser (GRCm38/mm10).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10 million mapped and in silico extended reads.

source_name: Primary mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in DMEM with 10% CCS.

extract_protocol:
Media was aspirated from MEFs and 2 mL or 15 mL crosslinking buffer (10 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) with 1% formaldehyde was added for 6-well or 15 cm dishes respectively. Cells were crosslinked by shaking gently for 10 min at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125mM and incubating for 5 min at room temperature while shaking. Cells were washed once in 2 mL or 15 mL PBS for 6-well or 15 cm dishes respectively. Cells were scraped and collected in 1 mL or 5 mL cold PBS for 6-well or 15 cm dishes respectively and pelleted by spinning at 1,000 g for 5 min at 4oC. Crosslinked MEFs per protocol above from 15 cm dishes were resuspended in 1 mL L1 buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X-100, 0.5% NP-40, 10% glycerol, 10 mM sodium butyrate) per 15 cm dish starting material and rotated for 10 min at 4oC to lyse cells. Nuclei were pelleted by spinning at 1,350 g for 5 min at 4oC and resuspended in 1 mL L2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 10 mM sodium butyrate) per 15 cm dish starting material and rotated for 10 min at room temperature. Nuclei were pelleted by spinning at 1,350 g for 5 min at 4oC and resuspended in 300 uL LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 10 mM sodium butyrate) per 15 cm dish starting material. Chromatin was sonicated with a Bioruptor Plus (Diagenode (Denville, NJ, USA)) on “high” power setting with an “on” interval of 30 sec and “off” interval of 45 sec for 36 cycles). DNA concentration was determined by taking 100 uL aliquot of sonicated chromatin, decrosslinking at 95oC for 15 min, and purifying with QIAquick PCR Purification Kit (QIAGEN 28104) and quantifying by Nanodrop. 1 ug of purified chromatin in 10% glycerol was run on 2% agarose gel and stained with ethidium bromide for 30 min to validate fragment size (typically within ~200-1,000 bp). The remainder of the sonicated chromatin was transferred to 1.5 mL tubes and centrifuged at 16,000 g for 10 min at 4oC to pellet insoluble debris. Triton X-100 was added to soluble chromatin to a final 1% concentration. Protein A Dynabeads (Thermo Fisher 10008D) were washed twice in 1 mL cold block solution (0.5% BSA (w/v), 1% Triton X-100, diluted in LB3 buffer). For coupling antibodies to beads, 15 uL bead slurry per IP were resuspended in 1.5 mL cold block solution and the appropriate amount of antibody (0.5 ug for anti-H3K27ac (Abcam (Waltham, MA, USA) ab4729), 0.5 ug for anti-H3K4me1 (Abcam ab8895), 0.5 ug for anti-H3K4me2 (Abcam ab7766), 0.5ug for anti-H3K4me3 (Abcam ab8580), 2 ug for anti-Fos (in-house generated antibody and Santa Cruz Biotechnology (Dallas, TX, USA) sc-7202X), 2 ug for anti-Tead1 (Abcam ab133533), 2 ug for anti-CTCF (Active Motif (Carlsbad, CA, USA) 61312), and 2 ug for anti-JunD (Santa Cruz Biotechnology sc74)) was added before rotating beads for >2 hrs at 4oC. For pre-clearing chromatin, 15 uL bead slurry was added to appropriate amount of chromatin (40 ug for histone modifications, 80 ug for transcription factors) and additional cold LB3 buffer with 1% Triton X-100 was added such that all samples had a final volume of 1.5 mL before rotating samples for > 2 hrs at 4oC. Pre-cleared chromatin was added to antibody-coupled beads and additional cold LB3 buffer with 1% Triton X-100 was added such that all samples had a final volume of 1.8 mL before rotating samples overnight at 4oC. 50 uL of pre-cleared chromatin was stored at -20oC for making input libraries. For all wash steps listed below, samples were rinsed with 1 mL cold wash buffer and rotated for 5 min at 4oC before separating beads with magnet and discarding supernatant. Samples were washed sequentially twice in low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), twice in LiCl buffer (250 mM LiCl, 1% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and once in TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA). Samples were eluted from beads by addition of 200 uL TE buffer with 1% SDS and incubating at 65oC for 30 min with brief vortexing every 10 min to mix. IP samples were placed on magnet and supernatant was transferred to new tubes. Input samples were also thawed and 150 uL TE buffer with 1% SDS was added. Both IP and input samples were decrosslinked by incubating at 65oC overnight. 10 ug RNase A (Sigma Aldrich (St. Louis, MO, USA) R6513) was added and samples were incubated at 37oC for 1 hr to digest RNA. 7 uL 20 ug/uL proteinase K (New England Biolabs P8107) was added and samples were incubated at 55oC for 2 hr to digest protein. DNA was extracted with 1 volume of 25:24:1 phenol-chloroform-isoamyl alcohol and purified with QIAquick PCR Purification Kit (QIAGEN 28104).
Libraries were prepared with the Ovation Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN (Redwood City, CA, USA) 0344NB-32) per manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 with 150 bp paired-end reads.

treatment_protocol: MEFs were starved for 26 hours in DMEM with 0.5% CCS and serum stimulated for the indicated times at a final concentration of 15% CCS.

value: Primary mouse embryonic fibroblasts

value: C57BL/6J x SPRET/EiJ F1 hybrid

value: wild-type

value: 90m stimulation with 15% CCS MEF media

tag: passage

value: Abcam ab4729

tag: experiment

value: ChIP-seq


title: B6xSPRET-H3K27ac-0m-B1

tag: genotype

value: starved with 0.5% CCS MEF media


title: B6xPWK-CTCF-cycling-B1

value: C57BL/6J x PWK/PhJ F1 hybrid

value: Active Motif 61312


title: B6xMOLF-H3K4me3-0m-B1

value: C57BL/6J x MOLF/EiJ F1 hybrid

value: Abcam ab8580


title: B6xMOLF-H3K27ac-10m-B2

value: 10m stimulation with 15% CCS MEF media


title: Renal tumor:R337

status: Public on Dec 29 2021

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Renal tumor:R337

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification were done using the quantMode geneCounts option.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: STAR GeneCounts

source_name: Renal tumor

extract_protocol:
kit RecoverAll ™ Total Nucleic Acid Isolation for FFPE (Ambion, Inc. Austin, TX, USA)
HiSeq 2000 sequencing system (Illumina, Inc. San Diego, CA, USA )

value: Renal tumor

tag: size

tag: furhman

tag: progression


title: Renal tumor:R334

description: Renal tumor:R334


title: Renal tumor:R331

description: Renal tumor:R331


title: Renal tumor:R335

description: Renal tumor:R335


title: Renal tumor:R329

description: Renal tumor:R329


title: Renal tumor:R326

description: Renal tumor:R326


title: Renal tumor:R327

description: Renal tumor:R327


title: Renal tumor:R325

description: Renal tumor:R325


title: Renal tumor:R324

description: Renal tumor:R324


title: rpoB_ptChIP_Col0_14_do_input_Input_2

value: wild type (Col-0)

value: 14 days-old

value: 14 days-old seedlings

tag: treatment

value: input


title: Renal tumor:R328

description: Renal tumor:R328


title: Renal tumor:R319

description: Renal tumor:R319


title: Renal tumor:R316

description: Renal tumor:R316


title: rpoB_ptChIP_Col0_14_do_ChIP_2

value: 4h formaldehyde crosslinking

value: a-RpoB (PhytoAB Cat.:PHY1239 Lot:9321A5)


title: Renal tumor:R321

description: Renal tumor:R321


title: Renal tumor:R314

description: Renal tumor:R314


title: Renal tumor:R313

description: Renal tumor:R313


title: Renal tumor:R315

description: Renal tumor:R315


title: Renal tumor:R311

description: Renal tumor:R311


title: Renal tumor:R309

description: Renal tumor:R309


title: B6xPWK-H3K4me1-90m-B1

value: Primary mouse embryonic fibroblasts

value: wild-type

value: Abcam ab8895


title: Renal tumor:R306

description: Renal tumor:R306


title: Renal tumor:R304

description: Renal tumor:R304


title: Renal tumor:R310

description: Renal tumor:R310


title: Renal tumor:R301

description: Renal tumor:R301


title: Renal tumor:R307

description: Renal tumor:R307


title: Renal tumor:R303

description: Renal tumor:R303


title: 6h progesterone treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-4 [ePRBoe P4-4]

status: Public on Dec 02 2021

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description:
NS50707.B8_20180510_093058.L001
NOVA0030.B8_20180510_093058.L001

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20 using "filterPE.pl"
Reads were aligned to mm10 genome using TopHat version 2.0.4, and assembled using Cufflinks version 2.0.2
BigWig file was generated from normalized bedgraph file of each sample using bedGraphToBigWig. Scores represent normalized mapped read coverage.
Differential expression was calculated using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample

growth_protocol: The female mice were fed with normal chow, and housed with its female littermates until 8 weeks old.

extract_protocol:
RNA was extracted using Trizol and aqueophase separation method, and futher purified by Qiagen Rneasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The females were mated with stud males and dissected at pregnancy day 4

value: Whole uterus

tag: surgery

value: Ovariectomy for 2 weeks

value: 6 h progesterone treatment


title: Renal tumor:R298

description: Renal tumor:R298

tag: tissue


title: Renal tumor:R300

description: Renal tumor:R300


title: 6h progesterone treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-1 [ePRBoe P4-1]

description:
NS50707.B5_20180510_093058.L001
NOVA0030.B5_20180510_093058.L001


title: 6h progesterone treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-3 [ePRBoe P4-3]

description:
NS50707.B7_20180510_093058.L001
NOVA0030.B7_20180510_093058.L001


title: 6h oil treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-3 [ePRBoe oil-3]

description:
NS50707.B3_20180510_093058.L001
NOVA0030.B3_20180510_093058.L001

value: 6 h oil treatment


title: 6h progesterone treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-2 [ePRBoe P4-2]

description:
NS50707.B6_20180510_093058.L001
NOVA0030.B6_20180510_093058.L001


title: 6h oil treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-1 [ePRBoe oil-1]

description:
NS50707.B1_20180510_093058.L001
NOVA0030.B1_20180510_093058.L001


title: 6h oil treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-2 [ePRBoe oil-2]

description:
NS50707.B2_20180510_093058.L001
NOVA0030.B2_20180510_093058.L001


title: 6h oil treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-2 [ePRAoe oil-2]

description:
NS50707.A2_20180510_093058.L001
NOVA0030.A2_20180510_093058.L001


title: 6h oil treated PgrcrePgrBLsL/+ mouse uterus, bioreplicate-4 [ePRBoe oil-4]

description:
NS50707.B4_20180510_093058.L001
NOVA0030.B4_20180510_093058.L001


title: 6h oil treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-3 [ePRAoe oil-3]

description:
NS50707.A3_20180510_093058.L001
NOVA0030.A3_20180510_093058.L001


title: 6h oil treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-4 [ePRAoe oil-4]

description:
NS50707.A4_20180510_093058.L001
NOVA0030.A4_20180510_093058.L001


title: 6h progesterone treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-1 [ePRAoe P4-1]

description:
NS50707.A5_20180510_093058.L001
NOVA0030.A5_20180510_093058.L001


title: 6h progesterone treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-2 [ePRAoe P4-2]

description:
NS50707.A6_20180510_093058.L001
NOVA0030.A6_20180510_093058.L001


title: 6h progesterone treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-3 [ePRAoe P4-3]

description:
NS50707.A7_20180510_093058.L001
NOVA0030.A7_20180510_093058.L001


title: Pgrcre/+Foxo1f/f uterine luminal epithelium, bioreplicate 3 [Foxo1dd LE-3]

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20 using "filterPE.pl"
Agilgn reads to mm10 genome using STAR aligner (V2.5.2b)
Count reads mapped to each gene using featureCounts ( v1.5.0-p1) function in Subread program
A DGEList object were created from the count matrix, normalization factors were calculated, and low-expressed genes (with max CPM<1) were filtered in edgeR package (v3.28.0)
Differential gene expression using R package "DESeq2" (DESeq2_1.12.4).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using featureCounts ( v1.5.0-p1) function in Subread program

tag: genotype/variation

tag: tissue collection

value: Laser capture

tag: timing

value: Pregnancy day 4

value: Uterine luminal epithelium


title: 6h oil treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-1 [ePRAoe oil-1]

description:
NS50707.A1_20180510_093058.L001
NOVA0030.A1_20180510_093058.L001


title: Foxo1f/f uterine luminal epithelium, bioreplicate 3 [Foxo1ff LE-3]

source_name: Foxo1f/f uterine luminal epithelium


title: Pgrcre/+Foxo1f/f uterine luminal epithelium, bioreplicate 2 [Foxo1dd LE-2]


title: Pgrcre/+Foxo1f/f uterine luminal epithelium, bioreplicate 1 [Foxo1dd LE-1]


title: Foxo1f/f uterine luminal epithelium, bioreplicate 2 [Foxo1ff LE-2]


title: Foxo1f/f uterine luminal epithelium, bioreplicate 1 [Foxo1ff LE-1]


title: 6h progesterone treated PgrcrePgrALsL/+ mouse uterus, bioreplicate-4 [ePRAoe P4-4]

description:
NS50707.A8_20180510_093058.L001
NOVA0030.A8_20180510_093058.L001


title: Wnt7acre uterine luminal epithelium, bioreplicate 2 [Wnt7acre LE-2]

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20 using "filterPE.pl"
Agilgn reads to mm10 genome using STAR aligner (V2.5.2b)
Count reads mapped to each gene using featureCounts ( v1.5.0-p1) function in Subread program
A DGEList object were created from the count matrix, normalization factors were calculated, and low-expressed genes (with max CPM<1) were filtered in edgeR package (v3.28.0)
Differential expression analysis was performed using Limma-Voom procedure (R package limma, v3.42.2),  with batch (refers to different sequencing runs) added to the end of the call to model matrix to adjust for batch in the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using featureCounts ( v1.5.0-p1) function in Subread program

source_name: Wnt7acre uterine luminal epithelium


title: Wnt7acre/+PgrALsL/+ uterine luminal epithelium, bioreplicate 3 [ePRAoe LE-3]


title: Wnt7acre/+PgrALsL/+ uterine luminal epithelium, bioreplicate 1 [ePRAoe LE-1]


title: Wnt7acre/+PgrBLsL/+ uterine luminal epithelium, bioreplicate 2 [ePRBoe LE-2]


title: Wnt7acre uterine luminal epithelium, bioreplicate 1 [Wnt7acre LE-1]


title: Wnt7acre/+PgrBLsL/+ uterine luminal epithelium, bioreplicate 1 [ePRBoe LE-1]


title: Wnt7acre/+PgrBLsL/+ uterine luminal epithelium, bioreplicate 3 [ePRBoe LE-3]


title: Input for H3K27AC ChIP

description: 6_02E3_00A3NIEHS_Input_Nr2f2-pool_mm_i86

data_processing:
75-nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the mouse genome mm9 using the BWA algorithm.
Only the unique tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: Uterus

growth_protocol: The female mice were fed with normal chow, and housed with its female littermates until 6 weeks old.

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

value: Pregnancy day 3.5

value: Uterus


title: Wildtype H3K27AC ChIP

description: 1_02PR_00C6NIEHS_Uteri-D3.5_H3K27Ac_mm_i86


title: Input for PGR ChIP

value: Pgrcre/+

value: 1h progesterone treatment


title: Pgrcre/-PgrALsL/+ PGR ChIP-Seq

value: Pgrcre/-PgrALsL/+

value: PGR


title: Pgrcre/-PgrBLsL/+ PGR ChIP-Seq

value: Pgrcre/-PgrBLsL/+


title: Pgrcre/+ PGR ChIP-Seq


title: MCY_Adult2

status: Public on Nov 17 2021

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

description: scRNA-seq (2 females)

data_processing:
scRNA-seq data were demultiplexed, aligned to the mouse genome, version mm10, and UMI-collapsed with the Cellranger toolkit (version 3.0.1, 10X Genomics). We excluded cells with fewer than 500 detected genes (where each gene had to have at least one UMI aligned). Gene expression was represented as the fraction of its UMI count with respect to total UMI in the cell and then multiplied by 10,000. For bulk RNA-seq, adaptor sequences were cut using CutAdapt and trimmed reads shorter than 30bp were discarded. Trimmed data were aligned to mouse reference genome mm10 using STAR (79), with uniquely mapping rates greater than 80%. HTseq-count  was used to count the number of reads mapped to each gene. Then data were loaded into the R platform where further statistical analyses occurred. Counts of genes were normalized and differentially expressed genes (p-value < 0.05, fold-change > 1.35) was determined in the DESeq2 package . Relationship among samples was assessed by principal component analysis (PCA) of DESeq2 normalized counts.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices

source_name: Long bones

growth_protocol: All mice were kept in an SPF facility operated in a 12-hour light/dark cycle.

extract_protocol: Chromium Controller (10X Genomics) with the Single Cell 3’ v2 kit, Chromium Single cell 3' Reagent Kits v2

treatment_protocol: Normal feeding

tag: strain

value: Bone marrows and bone fragments

tag: cell type

value: CD45-Ter119-Tie2-Lepr-Cre+ cells

value: Normal feeding


title: MCY_Adult

data_processing:
scRNA-Seq data were processed using the Cell Ranger pipelines (version 3.0.1, 10x Genomics) for sample demultiplexing, read mapping (mm10/GRCm38), barcode processing and single-cell transcript counting. We excluded low-quality cells with fewer than 500 detected genes (each gene must have at least one UMI aligned) and contaminating cells. Gene expression in each cell was represented as transcripts per 10k transcripts (TP10K), representing the fraction of each gene's UMI count with respect to total UMIs in the cell and multiplied by 10,000.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices

extract_protocol:
Chromium Controller (10x Genomics) with the Single Cell 3’ v2 kit
Chromium Single cell 3' Reagent Kits v2

treatment_protocol: Nomal feeding

tag: stain

value: Nomal feeding

tag: age


title: 786-O A21_rV5_IP

status: Public on Oct 29 2021

city: Berkeley

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description:
A21_rV5_IP
Homozygous cell line with endogenous CTCF loci tagged with an auxin-inducible degron

data_processing:
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --normalizeTo1x 2913022398 --extendReads 300 --ignoreDuplicates -of bigwig) to normalize read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on HIF2-2a peaks called by MACS2 across all 786O cell lines, subtracted of V5 peaks called by MACS2 in WT 786O cells (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing WT 786O enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to 1x sequencing depth; merged duplicates)

source_name: Clear cell renal cell carcinoma

growth_protocol: Human 786-O ccRCC cells were cultured at 37°C with 5% CO2 in 4.5 g/L glucose DMEM (ThermoFisher, Waltham, MA, #10566016) supplemented with 10% Fetal Bovine Serum (HyClone, Logan, UT, Cat. #SH30396.03, lot #AE28209315), 1 mM Sodium Pyruvate (ThermoFisher #11360070) and 100 U/mL Penicillin-Streptomycin (ThermoFisher #15140122). Cells were subcultured at a ratio of 1:4 to 1:12 every 2 to 4 days for no longer than 30 days.

extract_protocol:
Cell pellets were thawed and resuspended in 2 ml of cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) w/ protease inhibitors and incubated for 10’ on ice. Lysates were centrifuged for 10’ at 4000 rpm and nuclear pellets resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS) w/ protease inhibitors, incubated on ice for 10’, and sonicated to obtain DNA fragments around 500 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 150 peak incident power, 10 cycles 30” on and 30" off). Sonicated lysates were cleared by centrifugation and chromatin (400 ug per antibody) was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) w/ protease inhibitors to a final concentration of 0.8 ug/ul.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645) according to manufacturer instructions with a few modifications. 20 ng of ChIP input DNA (as measured by Nanodrop) and 25 ul of the immunoprecipitated DNA were used as a starting material and the recommended reagents’ volumes were cut in half. The NEBNext Adaptor for Illumina was diluted 1:10 in Tris/NaCl, pH 8.0 (10 mM Tris-HCl pH 8.0, 10 mM NaCl) and the ligation step extended to 30’. After ligation, a single purification step with 0.9X volumes of Agencourt AMPure XP PCR purification beads (Beckman Coulter A63880) was performed, eluting DNA in 22 ul of 10 mM Tris-HCl pH 8.0. 20 ul of the eluted DNA were used for the library enrichment step, performed with the KAPA HotStart PCR kit (Roche Diagnostics KK2502) in 50 ul of total reaction volume (10 ul 5X KAPA buffer, 1.5 ul 10 mM dNTPs, 0.5 ul 10 uM NEB Universal PCR primer, 0.5 ul 10 uM NEB index primer, 1 ul KAPA polymerase, 16.5 ul nuclease-free water and 20 ul sample). Samples were enriched with 9 PCR cycles (98 'C, 45”; [98 'C, 15”; 60 'C, 10”] x 9; 72 'C, 1’; 4 'C, hold), purified with 0.9 volumes of AMPure XP PCR purification beads and eluted with 33 ul of 10 mM Tris-HCl pH 8.0. Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. Libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (50-bp, single end-reads).

treatment_protocol: Cells were expanded to two 15-cm dishes and cross-linked 5’ at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10’ and pellets were flash-frozen.

tag: cell line

value: V5-Halo-HIF-1b endogenous knock-in, clone A21

tag: chip antibody

value: V5 (Abcam ab9116)


title: 786-O A21_HIF2a_IP

description:
A21_HIF2a_IP
Homozygous clonal cell line with endogenous HIF-1b loci tagged with V5 and Halo moieties

value: HIF-2a (Novus Biologicals NB100-122)


title: 786-O A21_HIF1b_IP

description:
A21_HIF1b_IP
Homozygous clonal cell line with endogenous HIF-1b loci tagged with V5 and Halo moieties

value: HIF-1b (Novus Biologicals NB100-124)


title: 786-O A21_input

description:
A21_input
Homozygous clonal cell line with endogenous HIF-1b loci tagged with V5 and Halo moieties


title: 786-O A31_HIF1b_IP

description:
A31_HIF1b_IP
Homozygous clonal cell line with endogenous HIF-2a loci tagged with V5 and Halo moieties

value: V5-Halo-HIF-2a endogenous knock-in, clone A31


title: WCM1358 REDV rep3

status: Public on Oct 01 2021

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.7 software used for basecalling.
All reads were independently aligned with STAR_2.4.0f141 for sequence alignment against the human genome sequence build hg19, downloaded via the UCSC genome browser [http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/], and SAMTOOLS v0.1.1942 for sorting and indexing reads. Cufflinks (2.0.2)43 was used to estimate the expression values (FPKMS), and GENCODE v1944 GTF file for annotation. The gene counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: WCM1358 prostate cancer organoid

extract_protocol:
RNA was extracted from frozen material for RNA-sequencing (RNA-seq) using the Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit (cat. # AS1280))
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-sequencing and data processing of synthetic organoids was performed according to the protocol described earlier by our group. Briefly, RNA was extracted from frozen material for RNA-sequencing (RNA-seq) using the Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit (cat. # AS1280)). Specimens were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2. RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized from total RNA using Superscript III (Invitrogen). Sequencing was then performed on HiSeq 2000, or HiSeq 2500.

tag: donor

value: Castration resistant prostate cancer (CRPC)

value: REDV


title: 786-O A31_rV5_IP

first: Robert

description:
A31_rV5_IP
Homozygous clonal cell line with endogenous HIF-1b loci tagged with V5 and Halo moieties

tag: genotype


title: 786-O A31_HIF2a_IP

description:
A31_HIF2a_IP
Homozygous clonal cell line with endogenous HIF-2a loci tagged with V5 and Halo moieties


title: 10x: PBMC_cDNA

status: Public on Oct 15 2021

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: Prox-seq analysis of PBMCs using 10x pipeline

data_processing:
Sequencing data was aligned using a custom Java program (https://github.com/tay-lab/Prox-seq) to identify the Prox-seq probe barcodes. The list of probe barcodes is in Proxseq_probe_barcodes.xlsx
Count data was analyzed in Python and RStudio. Cells with fewer total UMI count lower than 10 were discarded.
Protein data caclulated from PLA count data was used to cluster the cells in Seurat v4.0.4
Genome_build: Human GRCh38
Supplementary_files_format_and_content: tab-separated text file

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMCs are kept in RPMI media with 10% FBS

extract_protocol:
PLA products were extracted from single cells following 10x pipeline
Sequencing library was prepared from PLA products using PCR

value: Primary human white blood cells

tag: donor type

value: Healthy donor

tag: passages

tag: molecule subtype

value: polyA RNA


title: Wnt7acre/+PgrALsL/+ uterine luminal epithelium, bioreplicate 2 [ePRAoe LE-2]

value: Laser capture

value: Pregnancy day 4

value: Uterine luminal epithelium


title: Wnt7acre uterine luminal epithelium, bioreplicate 3 [Wnt7acre LE-3]


title: RNAseq_whole_tissue_duodenum_mYopM_rep3

status: Public on Sep 24 2021

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

data_processing:
RNA-seq: RNA-seq reads were mapped with STAR to the mm10 reference genome with default parameters. Read counts were assessed with HOMER’s analyzeRepeats with the option rna and parameters -noadj and -condenseGenes. Differential gene expression was assessed with DESeq2 using HOMER’s getDiffExpression.pl using a false discovery rate (FDR) of 5% and a fold change of 2. Metascape was used for analyzing enriched GO terms. ATAC-seq: ATAC-seq reads were mapped with STAR to the mm10 reference genome with default parameters. For all pairwise comparisons per treatment group IDR was run and only replicates passing IDR threshold were kept. All peaks that pass IDR threshold and could be found in all replicates were used for follow up analysis. Motif enrichment analysis was perfomed using HOMER.
ATAC-seq: ATAC-seq reads were mapped with STAR to the mm10 refernece genome with default parameters. All samples were processed using the Irreproducibility Discover Rate (IDR) pipeline using HOMER as peak caller with parameters -style factor -center -F 0 -L 0 -C 0 -fdr 0.01 -minDist 200 -size 200.The IDR threshold was set to 0.05. Only replicates that passed were used to defined peak set and only peaks that were found in all replicates were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-seq sample or number of reads per open region for each ATAC-seq sample

source_name: whole tissue samples from duodenum

extract_protocol:
Mice were euthanized with CO2, perfused via the left ventricle of the heart with 10 ml of PBS, siLP, liLP, lung and skin were collected and placed in cold complete medium (RPMI 1640 supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1 mM nonessential amino acids, 20 mM HEPES, 50 mM b-mercaptoethanol, 100 U/mL penicillin, 100 mg/mL streptomycin). For siLP and liLP, Peyer’s patches and mesenteric adipose tissue was removed. Tissues were open and wash in cold PBS to remove feces. Tissues were cut into 1-2 cm segments and treated with complete RPMI medium containing 5mM EDTA and 0.145 mg/ml dithiothreitol for 20 min at 37°C with constant stirring. Tissues were shake vigorously for 1 min, further digested with 10 ml 500 mg/ml DNase I (Sigma-Aldrich) and 100 mg/ml Liberase TL (Roche) with continuous stirring at 37°C.
Whole tissue RNA-seq: 3 cm of intestinal segments from duodenum, jejunum and ileum was collected and extensively washed with PBS to clean out feces. Samples were homogenized by beads beating with TRIzol in tubes containing 28mm beads and TRIzol (Thermofisher). RNA was extracted according to TRIzol protocol. cDNA was synthesized with the Ultralow V4 kit (Clonetech) and sequencing libraries were subsequently prepared with the Nextera XT DNA prep kit (Illumina).
Epithelial cells RNA-seq: Epithelial cells were sorted into RNA lysis buffer and RNA was extracted according to manufactoring instructions (Qiagen). RNA library was prepared using the NuGen mRNA-seq kit with mouse probes.
Epithelial cells ATAC-seq: Cells were pelleted by centrifugation at 500 g for 5 min at 4°C. Supernatant was removed, and cell pellet was resuspended with 45ul transpose mixture (25 ml Tagment DNA Buffer, 2.5 ml Tagment DNA enzyme, 0.5 ml 1% digitonin and 17 ml H2O ) and incubated for 30min at 37°C with agitation at 300 rpm. Transposed DNA was purified using QIAGEN MinElute Reaction Cleanup Kit and purified DNA was eluted in 10ul elution buffer. Transposed fragments were amplified with 10-15 cycle by PCR based on amplification curve. Once the libraries were purified by QIAGEN PCR cleanup kit, sample were further sequenced single-end on HiSeq 2500.

treatment_protocol: For YopM: Mice fasted overnight (12-16 hours) in new cages were orally administrated with 200 ml of overnight culture yopM suspension (~2 x 107 colony forming unit (CFU)).

tag: treatment

value: maternal YopM

tag: organ

value: duodenum (gut)


title: RNAseq_whole_tissue_duodenum_mCtrl_rep2

value: maternal control


title: RNAseq_whole_tissue_duodenum_mYopM_rep2


title: RNAseq_whole_tissue_duodenum_mCtrl_rep1


title: RNAseq_whole_tissue_duodenum_mCtrl_rep3


title: RNAseq_whole_tissue_duodenum_mCtrl_rep4


title: RNAseq_whole_tissue_duodenum_mYopM_rep1


title: RNAseq_epithelial_cells_E16_5_mIL6_rep4

source_name: epithelial cells from gut

value: maternal IL6

value: whole gut


title: RNAseq_epithelial_cells_E16_5_mIL6_rep3


title: RNAseq_epithelial_cells_E16_5_mIL6_rep5


title: RNAseq_epithelial_cells_E16_5_mIL6_rep2


title: RNAseq_epithelial_cells_E16_5_mIL6_rep1


title: RNAseq_epithelial_cells_E16_5_mCtrl_rep5


title: RNAseq_epithelial_cells_E16_5_mCtrl_rep4


title: RNAseq_epithelial_cells_E16_5_mCtrl_rep3


title: RNAseq_epithelial_cells_E16_5_mCtrl_rep2


title: RNAseq_epithelial_cells_E16_5_mCtrl_rep1


title: single_cell_RNAseq_epithelial_stemcells_gut_lane2_HTO_data

data_processing:
HTO were assigned to each single cell. Data was normalized, and lanes were combined using the scTransform function from Seurat. Data is displayed as uniform manifold approximation and projection (UMAP) using 25 dimensions. Intestinal cell subsets from each cluster were defined by the top 25 differentially expressed genes using published dataset. Gene expression within each cluster were compared between offspring delivered by control or IL-6-exposed dams using Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat R object

source_name: HTO barcode data for epithelial stemcells from gut processed on lane2

extract_protocol:
Mice were euthanized with CO2, perfused via the left ventricle of the heart with 10 ml of PBS, siLP, liLP, lung and skin were collected and placed in cold complete medium (RPMI 1640 supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1 mM nonessential amino acids, 20 mM HEPES, 50 mM b-mercaptoethanol, 100 U/mL penicillin, 100 mg/mL streptomycin). For siLP and liLP, Peyer’s patches and mesenteric adipose tissue was removed. Tissues were open and wash in cold PBS to remove feces. Tissues were cut into 1-2 cm segments and treated with complete RPMI medium containing 5mM EDTA and 0.145 mg/ml dithiothreitol for 20 min at 37°C with constant stirring. Tissues were shake vigorously for 1 min, further digested with 10 ml 500 mg/ml DNase I (Sigma-Aldrich) and 100 mg/ml Liberase TL (Roche) with continuous stirring at 37°C.
2.5 x 10^4 of EpCAM+ intestinal epithelial cells were isolated by Sony MA900 cell sorter with from each sample. All samples were labelled with TotalSeqA hash tags (Biolegend), pooled, encapsulated into droplets using Chromium Single Cell Controller (10X Genomics) and libraries were prepared using Chromium Single Cell 3 Reagent Kits v3 (10X Genomics). Controller was overloaded with 2.5 x 10^4 cells per lane. The mRNA was prepared following the 10X Genomic user guide, while HTO library was prepared according to published guidelines

treatment_protocol: For YopM: Mice fasted overnight (12-16 hours) in new cages were orally administrated with 200 ml of overnight culture yopM suspension (~2 x 10^7 colony forming unit (CFU)).

tag: tissue

value: epithelial stem cells


title: single_cell_RNAseq_epithelial_stemcells_gut_lane1_mRNA_data

source_name: mRNA data for epithelial stemcells from gut processed on lane1


title: single_cell_RNAseq_epithelial_stemcells_gut_lane2_mRNA_data

source_name: mRNA data for epithelial stemcells from gut processed on lane2


title: single_cell_RNAseq_epithelial_stemcells_gut_lane1_HTO_data

source_name: HTO barcode data for epithelial stemcells from gut processed on lane1


title: ATACseq_whole_tissue_E16_5_mIL6_rep3

source_name: whole tissue sample from gut


title: ATACseq_whole_tissue_E16_5_mIL6_rep2


title: ATACseq_whole_tissue_E16_5_mIL6_rep1


title: ATACseq_whole_tissue_E16_5_mCtrl_rep2


title: ATACseq_whole_tissue_E16_5_mCtrl_rep3


title: ATACseq_whole_tissue_E16_5_mCtrl_rep1


title: ATACseq_duodenum_mIL6_LGR5pos_rep2

source_name: LGR5 positive epithelial cells from the duodenum


title: ATACseq_duodenum_mCtrl_LGR5pos_rep3


title: ATACseq_duodenum_mIL6_LGR5pos_rep3


title: ATACseq_duodenum_mCtrl_LGR5pos_rep2


title: WT_2

status: Public on Aug 18 2021

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description:
Wild type ribosome footprinting
RPKMS_WT_NOT4_Not5.xlsx

data_processing:
For the Ribo-Seq samples, all fastq files were adapter stripped using cutadapt. Only trimmed reads were retained, with a minimum length of 20 and a quality cutoff of 2 reads were retained if the trimmed size was between 28 and 31.
Reads were mapped, using default parameters, with HISAT2  to R64-1-1, using Ensembl release 84 gtf for transcript definitions. For the mapping, only primary alignments were retained and reads were removed if they mapped to rRNA, tRNA and dubious ORFs or non-genic regions. Reads mapping to UTRs were retained.
A full set of 6692 CDS sequences were established for R64-1-1 Ensembl release 84 and extended by  UTR sequences. The filtered reads were then mapped to this transcriptome with bowtie2, using default parameters.
The P-site position of each read was predicted by riboWaltz and confirmed by inspection (reads were generally shifted 15 bases from the 3’ end). Counts were made by aggregating P-sites overlapping with the CDS and RPKMs were then generated through normalising by CDS length and total counts for the sample.
Genome_build: R64-1-1
Supplementary_files_format_and_content: RPKM

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae cells

growth_protocol: Yeast were grown in YPD to mid-log phase in accordance with standard protocols.

extract_protocol:
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)

treatment_protocol: Cells were harvested and extracts were perpared and processed as described for S. pombe samples in Subtelny et al., 2014 (GSE52809)

tag: genotype/variation

value: wild type


title: rpoB_ptChIP_Col0_4_do_Col0_ChIP_1

source_name: Chloroplast

value: wild type (Col-0)

value: 4 days-old

value: 4 days-old seedlings

value: 4h formaldehyde crosslinking

value: a-RpoB (PhytoAB Cat.:PHY1239 Lot:9321A5)


title: WT_1


title: ATACseq_duodenum_mIL6_LGR5pos_rep1


title: NGT_CTL_30h_i08

status: Public on Aug 17 2021

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz

data_processing:
1) Reads were trimmed using Trim_Galore! (v0.4.3) on default settings
2) Trimmed reads were aligned using STAR (v2.5.3a) aligner with Ensembl human annotation (GRCh38, release 92)
3) Gene read coverages were counted using featureCounts from subread (v1.5.2) package
4) The lowly expressed genes were discarded from downstream analysis using filterByExpr function from edgeR package (v3.32.1) resulting 18,482 genes for downstream analysis
5) Batch effect caused by "individuals" are removed from CPM values by using removeBatchEffect function from limma (v3.46.0)
6) Batch effect removed logCPM values are used for rhythmicity and differential rhythmicity analysis by RAIN (v1.20.0) and DODR (v0.99.3), respectively
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts and logCPM (log counts per million) values (batch effect caused by individuals are removed)

source_name: Primary myotubes from vastus lateralis

growth_protocol: Primary myoblasts from skeletal muscle biopsies from men with NGT and T2D were grown in DMEM/F12+Glutamax with 16% FBS and 1% Antibiotic-Antimycotic (100X). Differentiation was induced at 80% confluence, by incubating the cells for 4-5 days in fusion medium consisting of 76% DMEM Glutamax with 25 mmol/l glucose, 20% M199 (5.5 mmol/l), 2% HEPES and 1% Antibiotic-Antimycotic (100X), with 0.03 μg/ml zinc sulfate and 1.4 mg/ml Vitamin B12, with a further addition of 100 μg/ml apo-transferrin and 0.286 IU/ml insulin prior to use. Experiments were performed on differentiated myotubes after an additional 3-5 days incubation in the same media containing 2% FBS (post fusion media).

extract_protocol:
Cells were lysed and RNA extracted using E.Z.N.A.® Total RNA Kit I (SKU: R6834-01, Omega Bio-tek, GA, USA). RNA was checked for quality using the Agilent RNA 600 nano kit and Bioanalyser instrument (Agilent Technologies, Santa Clara, CA). Aliquots of RNA (1 µg) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina).
Ribosomal RNA was removed from the sample using 35 µl rRNA removal beads (Illumina) on a magnetic plate followed by clean-up of the ribosomal-depleted RNA with 193 µl Agencourt RNAClean XP beads (Beckman Coulter), 70% ethanol wash and elution into 10 µl Elution buffer (Illumina). The RNA sample was fragmented for 4 min at 94°C in Elute, Prime, Fragment High Mix (Illumina) and then subjected to first strand cDNA synthesis with 1 µl Superscript III reverse transcriptase (Life Technologies) per sample using a thermocycler programmed to 25°C for 10 min, 50°C for 15 min and 70°C for 15 min. Second strand cDNA was synthesized by addition of Second Strand Marking Master Mix and samples were incubated at 16°C for 60 min. Samples were subject to another bead clean up prior to A-tailing and ligation of adapters as per kit instructions (Illumina). Following a third bead clean-up, samples were enriched for DNA fragments by amplification using the Illumina PCR Primer Cocktail and PCR Master Mix, subjected to 98°C for 30 min, followed by a pre-defined cycle (98°C for 10 s, 60°C for 30 s and 72°C for 30 s) that was repeated 3-15 times, based on each individual sample, and finally incubated for 5 min at 72°C. Samples were cleaned, and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyser instrument.
Libraries were subjected to 100-bp single-end sequencing on the X Ten platform (Illumina) at the Beijing Genomics Institute (BGI), Hong Kong, China. Approximately 20 million reads/sample were assigned to genes with 18,482 genes surviving the expression threshold.

treatment_protocol: After post fusion, DMEM with 5.5 mmol/l glucose was used in the post fusion medium to create a low glucose condition. After 22 hrs, cells were synchronized by serum shock (media containing 50% FBS, 2 hrs) and then switched back to low glucose media. Skeletal muscle myotubes from men with either T2D or NGT were lysed at 6-hr intervals from 12 hrs to 54 hrs. Zeit-time (ZT) was determined as time after synchronization.  All transfections were performed using 250ng of plasmid DNA total. Treatment conditions: all cells received 5uM Rosiglitazone 48hrs post-transfection.

tag: disease

value: NGT

value: CTL

tag: group

tag: time

tag: individual


title: NGT_CTL_54h_i08


title: NGT_CTL_42h_i08


title: NGT_CTL_12h_i08


title: NGT_CTL_18h_i08


title: NGT_CTL_48h_i08


title: NGT_CTL_36h_i08


title: NGT_CTL_54h_i12


title: NGT_CTL_42h_i12


title: NGT_CTL_24h_i08


title: NGT_CTL_30h_i12


title: NGT_CTL_54h_i09


title: NGT_CTL_18h_i09


title: NGT_CTL_30h_i09


title: ATACseq_duodenum_mCtrl_LGR5pos_rep1

tag: strain


title: NGT_CTL_36h_i09


title: NGT_CTL_48h_i09


title: NGT_CTL_24h_i09


title: NGT_CTL_12h_i09


title: NGT_CTL_54h_i10


title: NGT_CTL_30h_i10


title: NGT_CTL_24h_i12


title: NGT_CTL_48h_i12


title: NGT_CTL_18h_i10


title: NGT_CTL_12h_i12


title: NGT_CTL_42h_i04


title: NGT_CTL_30h_i04


title: NGT_CTL_54h_i04


title: NGT_CTL_18h_i04


title: NGT_CTL_24h_i04


title: NGT_CTL_48h_i04


title: NGT_CTL_48h_i10


title: NGT_CTL_12h_i04


title: NGT_CTL_36h_i10


title: NGT_CTL_24h_i10


title: NGT_CTL_12h_i10


title: NGT_CTL_42h_i10


title: NGT_CTL_42h_i01


title: NGT_CTL_18h_i01


title: NGT_CTL_54h_i11


title: NGT_CTL_48h_i01


title: NGT_CTL_42h_i11


title: NGT_CTL_12h_i01


title: NGT_CTL_36h_i01


title: NGT_CTL_36h_i12


title: NGT_CTL_48h_i11


title: NGT_CTL_18h_i11


title: NGT_CTL_36h_i11


title: NGT_CTL_24h_i11


title: NGT_CTL_36h_i04


title: rpoB_ptChIP_Col0_4_do_Col0_ChIP_3

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed

Read counts on defined genomic regions were determined using bedtools v.2.25.0
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Read counts per genomic feature in a .bed file

tag: age


title: Spatial transcriptomics of a human brain metastasis (patient 26)

status: Public on Aug 04 2021

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Visium spatial transcriptomics of a human brain metastasis (patient 26)

data_processing:
spaceranger v 1.2.0 for alignment
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature-barcode matrices from space ranger
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5: processed data in feature-barcode matrix format
Supplementary_files_format_and_content: spatial.tar: tar archive includes processed output from Space Ranger with spatial information

source_name: tumor

extract_protocol:
Surgically resected brain metastases were embedded in OCT and flash frozen in a dry ice/5-methylbutane bath.
Libraries were prepared according to the manufacturer's protocols

tag: primary tumor

value: breast carcinoma

tag: visium gene expression slideserial number


title: Spatial transcriptomics of a human brain metastasis (patient 27)

description: Visium spatial transcriptomics of a human brain metastasis (patient 27)

value: lung adenocarcinoma


title: NGT_CTL_12h_i11


title: NGT_CTL_54h_i01


title: Spatial transcriptomics of a human brain metastasis (patient 16)

description: Visium spatial transcriptomics of a human brain metastasis (patient 16)

value: melanoma


title: B6xSPRET-Fos-90m-B1

data_processing:
Reads were trimmed with the paired-end option and with SLIDINGWINDOW:5:30 using Trimmomatic (Bolger et al., 2014).
Paired-end reads that survived trimming were re-paired using the bbmap utility (Bushnell 2014). Both unpaired and paired reads were concurrently mapped to the C57BL/6J and appropriate pseudogenome with bowtie2 using default parameters (Langmead and Salzberg, 2012).
Mapped reads were converted to .bam format with samtools view (Li et al., 2009) using the following options -h -b -F 3844 -q 10 and sorted by coordinate. Reads initially mapped to each pseudogenome were converted back to C57BL/6J coordinates by running Lapels (Huang et al., 2014).
For visualization purposes, mapped reads in .bam format were also converted to .bed format and unique reads were retained (with sort -k1,1 -k2,2n -k3,3n -u) and extended by 150 bp with bedtools slop -l 0 -r 150.
All samples were normalized to a depth of 10 million reads and read coverage was calculated by bedtools genomeCoverageBed. The output .bedgraph file was then converted with UCSC’s bedGraphtobigWig utility and all tracks displayed were visualized with the UCSC Genome Browser (GRCm38/mm10).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10 million mapped and in silico extended reads.

source_name: Primary mouse embryonic fibroblasts

tag: cell type

value: Primary mouse embryonic fibroblasts

value: C57BL/6J x SPRET/EiJ F1 hybrid

value: wild-type

value: 90m stimulation with 15% CCS MEF media

tag: passage

tag: chip antibody

value: Santa Cruz sc-7202X

tag: experiment

value: ChIP-seq


title: Spatial transcriptomics of a human brain metastasis (patient 15)

description: Visium spatial transcriptomics of a human brain metastasis (patient 15)


title: NGT_CTL_30h_i01


title: NGT_CTL_30h_i11


title: DL_59_CR_Sox2_8hrs_rep1

status: Public on Jul 29 2021

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
Library strategy: CUT&RUN
Mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: Embryonic stem cell line

growth_protocol: Cells were maintained at a density of 1 million cells per 10cm gelatinized plates at 37ºC x% O2, x% CO2 in 2i media (50% DMEM/F12, 50% Neurobasal, Penicillin-Streptomycin, GlutaMAX, 2-Mercaptoethanol, N2, B27, 0.3nM PD0325901, 0.1nM CHIR9902, and 2x105units/mL LIF).

extract_protocol:
Cells were harvested using accutase and 100,000 cells per replicate, per time point, were subjected to CUT&TAG and CUT&RUN. Blastocysts were fixed in 0.1% PFA and subjected to CUT&RUN by physically transferring the embryos into different CUT&RUN buffers under a dissection microscope.
DNA was issolated using phenol-chloroform extraction. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0. For CUT&TAG, DNA (20µl) was mixed with 5X Q5 reaction buffer (10µl), Q5 polymerase (0.5µl), dNTPs (1µl), nuclease free water (16µl), and an equimolar mixture of an universal i5 and a uniquely barcoded i7 primer (2.5µl) , using different barcodes for each sample. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x105units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time. Blastocysts were collected from 4-5 weeks old C57BL/6N females six days after PMSG/HCG injections. Blastocysts were used right away to profile E3.5 embryos, after removing the zona pellucida using acid tyrode’s solution. E4.5 embryos were isolated seven days after PMSG/HCG injections, and only blastocysts without any zona pellucida were used. Embryos were manipulated in 1% agar-coated 4-well dishes (ThermoFisher scientific, Nunc 4-Well Dishes for IVF) throughout the protocol.

tag: cell line

value: Embryonic stem cells

tag: time point

value: 8 hour post doxycycline

tag: transgene

value: Stem cells have TRE:GATA6-DSREd2

tag: antibody

tag: assay

value: CUT&RUN


title: DL_60_CR_Sox2_8hrs_rep2


title: DL_57_CR_Sox2_4hrs_rep1

value: 4 hour post doxycycline


title: DL_58_CR_Sox2_4hrs_rep2


title: DL_56_CR_Sox2_2hrs_rep2

value: 2 hour post doxycycline


title: DL_54_CR_Sox2_0hrs_rep2

value: 0 hour no doxycycline


title: DL_53_CR_Sox2_0hrs_rep1


title: DL_55_CR_Sox2_2hrs_rep1


title: DL_51_CR_Nanog_8h_rep2

value: NANOG


title: DL_50_CR_Nanog_8h_rep1


title: DL_49_CR_Nanog_4h_rep2


title: DL_47_CR_Nanog_2h_rep2


title: DL_48_CR_Nanog_4h_rep1


title: DL_45_CR_Nanog_0h_rep2


title: DL_46_CR_Nanog_2h_rep1


title: Spatial transcriptomics of a human brain metastasis (patient 24)

description: Visium spatial transcriptomics of a human brain metastasis (patient 24)

value: renal cell carcinoma (clear cell)


title: DL_44_CR_Nanog_0h_rep1


title: Spatial transcriptomics of a human brain metastasis (patient 19)

description: Visium spatial transcriptomics of a human brain metastasis (patient 19)

value: lung adenocarcinoma