title: G1_ESC_A485_Micro-C_rep3

description:
Library name: G1_ESC_A485_rep3
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_A485_pool.hic
G1_ESC_A485_pool.mcool
G1_ESC_A485_compartment.bedgraph


title: P76

status: Public on Feb 16 2026

type: SRA

city: Valencia

first: Patricia

last: Diaz-Gimeno

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

country: Spain

institute: IIS La Fe / IVIRMA Global Research Alliance

description: Library name: P76

library_source: transcriptomic

data_processing:
Raw data were evaluated using FastQC. STAR was employed to align high-quality data using GRCh37/hg19 as a reference. Gene counts obtained using featureCounts.
Assembly: GRCh37/hg19
Supplementary files format and content: csv file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Endometrium

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were sequenced using the AmpliSeq for Illumina® Transcriptome Human Gene Expression Panel23 in a NextSeq 500/550 system.

tag: tissue

value: Endometrium

tag: treatment

value: In Vitro Fertilization


title: G1_ESC_A485_Micro-C_rep1

city: New York

first: UkJin

last: Lee

state: NY

address: 413 E 69th St

department: Sanford I. Weill Department of Medicine

country: USA

institute: Weill Cornell Medicine

description:
Library name: G1_ESC_A485_rep1
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_A485_pool.hic
G1_ESC_A485_pool.mcool
G1_ESC_A485_compartment.bedgraph

library_source: genomic

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using BWA-MEM algorithm from bwa (v0.7.17) with the following options: -5SP -T0.
Parse module of pairtools (v1.1.0) was used to filter high-quality valid read pairs with the with the following options: --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30. Dedup module of pairtools (v1.1.0) was used to remove PCR duplicates, followed by split module to generate ‘pairs’ file.
Juicer (v1.22.01)  was then used to generate a contact matrix in ‘hic’ format from ‘pairs’ file. For downstream analysis, ‘hic’ format was converted to ‘mcool’ format using HicConvertFormat of HiCExplorer (v3.0.1).
TAD, Compartment
Assembly: mm10
Supplementary files format and content: TAD, Compartment

molecule: genomic DNA

organism: Mus musculus

source_name: RAD21-dTAG cell line (Bruce-4 derived)

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 2,000,000 cells per replicate were collected and centrifuged at 300 × g for 5 min. The pellet was frozen at -80˚C for 30 min, thawed at RT, and resuspended in 1 mL PBS. Freshly prepared 10 µL of 0.3 M DSG (Sigma-Aldrich, 80424) in DMSO was added, and the samples were incubated with rotation at RT for 10 min. Subsequently, 27 µL of 37% formaldehyde (Sigma-Aldrich, 252549) was added, and the samples were incubated at RT for an additional 10 min. After centrifugation at 3,000 × g for 5 min at 4˚C, the pellets were washed with 200 µL of 1X wash buffer from Dovetail Micro-C kit (Cantata Bio, 210006).

extract_protocol:
The pellet was resuspended in 200 µL of MB1 buffer (50 mM NaCl, 10 mM Tris-HCl pH7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% v/v NP-40 alternative (MilliporeSigma, 492016), 1 X cOmplete EDTA-free protease inhibitor cocktail in ddH2O) and incubated on ice for 20 min. The samples were centrifuged at 1,750 × g for 5 min at 4˚C, and the pellets were washed with 200 µL of MB1 buffer.
The nuclei pellets were then resuspended in 200 µL of MB1 buffer, and 28 U of MNase (Worthinigton Biochemical Corporation, LS004798) was added. After brief vortexing, the samples were incubated at 37˚C for 20 min on a shaker at 1,000 rpm. The amount of MNase to use was determined based on a separate titration experiment. The samples were transferred onto ice and 1.6 µL of 500 mM EGTA was added to stop the digestion. The reaction was further incubated at 65˚C for 10 min for complete inactivation of MNase. The samples were centrifuged at 170 × g for 5 min at 4˚C, and the pellets were washed with 1 mL MB2 (50 mM NaCl, 10 mM Tris-HCl pH 7.6, 10 mM MgCl2 in ddH2O). The pellets were resuspended in 50 µL of 1X Nuclease Digestion Buffer from Dovetail Micro-C kit. To lyse the nuclei, 3 µL of 20% v/v SDS was added, and the samples were incubated at 22˚C for 15 min on a shaker at 1,250 rpm. The rest of the steps in Micro-C library preparation, including lysate quality control, proximity ligation, library preparation, ligation capture, and library amplification, were performed following Dovetail Micro-C kit user guide v1.2.

treatment_protocol: 0.05% v/v DMSO, 500 nM dTAG, or 20 µM A485.

tag: cell line

value: RAD21-dTAG cell line (Bruce-4 derived)

tag: cell type

value: Mouse embryonic stem cell

tag: genotype


title: MDAH, STAT3 siRNA + IL6, Rep3

city: Rochester

first: Esther

last: Rodman

state: Minnesota

address: 200 1st St SW

institute: Mayo Clinic

description:
Library name: MDAH_STAT3_siRNA_IL6_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

data_processing:
Reads were aligned using STAR (version 2.7.3a) and featureCounts (version 2.8.2) was used to assign mapped reads. Any gene with an RPKM < 1 in all samples were considered to be lowly expressed and removed from further analysis.
Assembly: hg38
Supplementary files format and content: .xlsx table file including raw counts and RPKM values for each sample

source_name: cell line

growth_protocol: MDAH and OVSAHO cells were maintained in phenol red free RPMI (#11835050, Gibco), containing 10% (v/v) FBS (#900-308, Gemini Bioproducts) and 1% (v/v) antibiotic/antimycotic (#15240-062, Gibco)

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy mini kit (#217004, Qiagen)
LibTruSeqStrmRNAv2(TSMRN)

treatment_protocol: MDAH and OVSAHO cells were plated at a density of 100,000 cells per well in 6 well plates and after 24 hours were transfected with 5 nM non-targeting (control), STAT1, or STAT3 siRNA with the addition of 5 nM Dharmafect Reagent 1 (Dharmacon) following the manufacture’s guidelines. Following 72 hours of transfection, siRNA containing media was removed and cells were treated with 30 ng/mL IL6, 10 ng/mL IFNγ, or vehicle (PBS) for 2 hours.

value: cell line

value: Endometrioid ovarian cancer

value: WT

value: STAT3 siRNA + IL6


title: P75

description: Library name: P75


title: hapo_newborn_cordblood_A1158

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

tag: Sex

value: Male

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: MDAH, STAT3 siRNA + IFNγ, Rep1

description:
Library name: MDAH_STAT3_siRNA_IFNY_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: STAT3 siRNA + IFNγ


title: G1_ESC_dTAG_Micro-C_rep3

description:
Library name: G1_ESC_dTAG_rep3
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_dTAG_pool.hic
G1_ESC_dTAG_pool.mcool
G1_ESC_dTAG_compartment.bedgraph

value: dTAG


title: hapo_newborn_cordblood_A1061


title: MDAH, STAT3 siRNA + Veh, Rep1

description:
Library name: MDAH_STAT3_siRNA_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: STAT3 siRNA + Veh


title: WT-1

city: LA

first: Peixian

last: Dong

state: California

address: 1450 Biggy St, NRT 5514, LA. CA

institute: USC

description: Library name: Normalized read count WT_P1

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized read out for each Sample

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy Plus mini kit (Qiagen). 1ug of total RNA was usedfor the construction of sequencing libraries.
RNAseq PolyA Selection + NEBNext Ultra II Directional

value: Spleen

value: Th17 cell


title: P72

description: Library name: P72

value: Endometrium


title: MDAH, STAT3 siRNA + IL6, Rep1

description:
Library name: MDAH_STAT3_siRNA_IL6_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_A1089


title: P8

description: Library name: P8

value: In Vitro Fertilization


title: hapo_newborn_cordblood_A1060

value: Female


title: hapo_newborn_cordblood_A1079


title: MDAH, STAT1 siRNA + IFNγ, Rep3

description:
Library name: MDAH_STAT1_siRNA_IFNY_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: STAT1 siRNA + IFNγ


title: hapo_newborn_cordblood_A1053


title: hapo_newborn_cordblood_A1055


title: hapo_newborn_cordblood_A1052


title: P69

description: Library name: P69


title: hapo_newborn_cordblood_A1054


title: G1_ESC_dTAG_Micro-C_rep2

description:
Library name: G1_ESC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_dTAG_pool.hic
G1_ESC_dTAG_pool.mcool
G1_ESC_dTAG_compartment.bedgraph

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell


title: hapo_newborn_cordblood_A1050


title: G1_ESC_dTAG_Micro-C_rep1

description:
Library name: G1_ESC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_dTAG_pool.hic
G1_ESC_dTAG_pool.mcool
G1_ESC_dTAG_compartment.bedgraph


title: P71

description: Library name: P71


title: P68

description: Library name: P68


title: MDAH, STAT3 siRNA + IL6, Rep2

description:
Library name: MDAH_STAT3_siRNA_IL6_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

value: Endometrioid ovarian cancer

value: WT


title: MDAH, STAT1 siRNA + IFNγ, Rep2

description:
Library name: MDAH_STAT1_siRNA_IFNY_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: G1_ESC_DMSO_Micro-C_rep3

description:
Library name: G1_ESC_DMSO_rep3
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_DMSO_pool.hic
G1_ESC_DMSO_pool.mcool
G1_ESC_DMSO_compartment.bedgraph
G1_ESC_DMSO_TAD-boundary.bed

value: DMSO


title: MDAH, STAT1 siRNA + Veh, Rep3

description:
Library name: MDAH_STAT1_siRNA_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: STAT1 siRNA + Veh


title: G1_ESC_DMSO_Micro-C_rep5

description:
Library name: G1_ESC_DMSO_rep5
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_DMSO_pool.hic
G1_ESC_DMSO_pool.mcool
G1_ESC_DMSO_compartment.bedgraph
G1_ESC_DMSO_TAD-boundary.bed


title: MDAH, STAT1 siRNA + IFNγ, Rep1

description:
Library name: MDAH_STAT1_siRNA_IFNY_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: P7657_1101

city: Stockholm

first: Andreas

last: Liontos

state: Stockholm

address: Svante Arrheniusväg 20C

department: Molecular Biosciences-The Wenner Gren Institute

country: Sweden

institute: Stockholm University

description:
single cell library
Smart-Seq2

library_source: transcriptomic single cell

data_processing:
Sequencing was done with Illumina 2500 HiSeq Rapid mode using paired-end (2x125 bp) and single-end (1x50 bp). For downstream analysis, we used the one strand sequencing out of paired-end libraries and trimmed the reads to 50 bp
High quality transcriptomic libraries were obtained after filtering, for doublet cells included in our experiment as sequencing controls, for cells obtaining less than 40% uniquely mapped reads, for cells that had number of detected genes outside mean ± 2s.d range and for cells whose GFP  expression ratio was lower than the GFP ration determined in embryonic epithelial cells.
The following single cells were removed as known doublets in our analysis: "P7657_1067", "P7657_1189", "P2661_1003", "P4730_1029". The following single cells were removed because they had <40% uniquely mapped reads: "P2272_1042", "P2661_1042", "P3504_1071", "P3504_1082", "P4730_1040", "P7657_1022", "P7657_1024", "P7657_1025", "P7657_1032", "P7657_1070".
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: raw count matrix and metadata files for the 464/478 single cells remaining after removal of doublet cells (4 cells removed) and removal of cells that failed uniquely map read filtering (10 cells removed) step.

source_name: lung

extract_protocol:
For full-length (Smart-Seq2) library preparation (Picelli et al., 2014), the left lungs were used for enzymatic digestion and right lungs were treated as described above for histological analysis. Briefly, we cut the lungs in small pieces using a razor blade and digested with elastase (Worthington, LS002292) and DNase I 0.5 mg/ml (Sigma-Aldrich, DN25) in HBSS (Gibco, 14175), at 37oC for 1 hour with rotation. Equal volume of HBSS++ [HBSS (Gibco, 14175), supplemented with 2% 0.2µm filtered FCS (Gibco, 10500), 0.1 M HEPES (Sigma-Aldrich, H0887), antibiotics (Gibco, 15240096) and EGTA 2 mM] was added and the suspension was mixed gently. Then cells were centrifuged at 800g for 10 minutes at 4oC. Supernatant was removed with a serological pipette and cells were resuspended in HBSS++. Viability was tested using trypan blue (Sigma-Aldrich, T8154) (1:1 dilution) and presence of fluorescence positive cells was evaluated using a normal fluorescence microscope. Just before sorting, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) in order to remove cell aggregates. For E16.5 lungs, after digestion, centrifuge and cell resuspension in HBSS++, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) and counted. We resuspented the cells in the proper amount of HBSS++ in order to obtain 20x106 cells/ml cell concentration. 100 µl of cell suspension were stained with 0.5 µl of anti-EpCam-PE antibody (Biolegend, 118205) and 0.5 µl anti-CD45-APC antibody (Biolegend, 103112). Replicates of the above reactions were set in separate tubes; in order to prevent the formation of cell aggregates, which is typical when we centrifuge large amount of epithelial cells.
For cell-sorting, we used a BD FACSARIA III cell-sorter, using 100 µm nozzle, applying single-cell sorting purity setting. For E16.5 lungs, EpCampos CD45neg cells were sorted. Cells from all other stages were isolated according to GFP expression.
Cell sorting and single-cell library preparation were done according to Smart Seq2 protocol (Picelli et al., 2013; Picelli et al., 2014) with some modifications. Cells were sorted in 96-well plates (Piko PCR Plates 24-well, Thermo Scientific, SPL0240 and Plate Frame for 24-well PikoPCR Plates, Thermo Scientific, SFR0241).  Each well contained Triton-X100 (0.2%) (Sigma-Aldrich, T9284-100ML), ERCC RNA Spike-In Mix (1:400.000) (Life-Technologies, 4456740), Oligo-dT30 VN (1,25uM) AAGCAGTGGTATCAACGCAGAGTAC (30 x T) VN, dNTPs (2.5mM/each) (Thermo Scientific-Fermentas, R0192) and Rnase Inhibitor (1U/ul) (Clontech, 2313A) in 4 µl final volume. After sorting, strips were covered with Axygen PCR-tube caps (VWR, PCR-02-FCP-C), centrifuged and placed on dry ice until storage at -80oC for further use. For cell culture cells were sorted into HBSS++ buffer and kept on ice until they were placed in culture.
Smart Seq2 protocol is optimal for cell lines and/or large human cells (Picelli et al., 2014). Mouse primary pulmonary cells are smaller and they contain smaller amount of RNA, as a result high amount of primer concatamers were formed during cDNA library preparation, compromising its efficiency. Our optimized protocol contains 50% less Oligo-dT30 VN and cDNA synthesis was divided into two steps, the first was without TSO LNA and the second contained 1µM TSO LNA and additional 40 U of SuperScript II RT (Thermo-Fisher Scientific, 18064071). Reaction lasted 30 minutes at 42oC. Then enzyme was deactivated at 70oC for 15 minutes. For Pre-Amplification PCR, we used the KAPA HiFi Hotstart ReadyMix (2x) (KAPA Biosystems, KK2602) and the ISPCR-primer AAGCAGTGGTATCAACGCAGAGT. PCR included 21 cycles and the total volume increased to 50ul in order to reduce the concentration of the unused Oligo-dT30 VN and TSO-LNA primers.
Tagmentation and indexed library amplification were done with Nextera® XT DNA Library Preparation Kit (Illumina, FC-131-1096) and Nextera® XT Index Kit (96 indexes, 384 samples), (Illumina, FC-131-1002) according to the manufacturer protocol (with 2.5 x volume reduction in all reactions). The quantity of the used library for tagmentation was 50 pg of the 500-9000 bp fraction of the library, as indicated by its Bioanalyzer profile.

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: P64

description: Library name: P64

tag: tissue

tag: treatment


title: G1_ESC_DMSO_Micro-C_rep2

description:
Library name: G1_ESC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_DMSO_pool.hic
G1_ESC_DMSO_pool.mcool
G1_ESC_DMSO_compartment.bedgraph
G1_ESC_DMSO_TAD-boundary.bed

tag: cell line

tag: cell type

tag: genotype


title: G1_ESC_DMSO_Micro-C_rep4

description:
Library name: G1_ESC_DMSO_rep4
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_DMSO_pool.hic
G1_ESC_DMSO_pool.mcool
G1_ESC_DMSO_compartment.bedgraph
G1_ESC_DMSO_TAD-boundary.bed


title: G1_ESC_DMSO_Micro-C_rep6

description:
Library name: G1_ESC_DMSO_rep6
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_DMSO_pool.hic
G1_ESC_DMSO_pool.mcool
G1_ESC_DMSO_compartment.bedgraph
G1_ESC_DMSO_TAD-boundary.bed


title: hapo_newborn_cordblood_A1048

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: P7

description: Library name: P7

value: Endometrium

value: In Vitro Fertilization


title: hapo_newborn_cordblood_A1027

value: Female


title: hapo_newborn_cordblood_A1040


title: P63

description: Library name: P63


title: P67

description: Library name: P67


title: MDAH, STAT1 siRNA + Veh, Rep1

description:
Library name: MDAH_STAT1_siRNA_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: MDAH, STAT1 siRNA + Veh, Rep2

description:
Library name: MDAH_STAT1_siRNA_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_D0876

value: Male


title: G1_ESC_DMSO_Micro-C_rep1

description:
Library name: G1_ESC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility
G1_ESC_DMSO_pool.hic
G1_ESC_DMSO_pool.mcool
G1_ESC_DMSO_compartment.bedgraph
G1_ESC_DMSO_TAD-boundary.bed

value: RAD21-dTAG cell line (Bruce-4 derived)

value: Mouse embryonic stem cell


title: hapo_newborn_cordblood_A1007


title: MDAH, STAT1 siRNA + IL6, Rep3

description:
Library name: MDAH_STAT1_siRNA_IL6_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line

value: Endometrioid ovarian cancer

value: WT

value: STAT1 siRNA + IL6


title: P61

description: Library name: P61


title: P62

description: Library name: P62


description:
Library name: Async-EpiLC-RAD21_EpiLC-22h_dTAG_rep1-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv

data_processing:
FASTQ files were aligned to the mouse genome (mm10) using Star aligner (v2.7.11a) with the default setting for paired-end reads. Samtools (v1.20) was used to process the aligned data, including transforming file formats, filtering low-quality reads, and sorting paired reads.
FeatureCounts from subread (v2.0.6) was used to count fragments that have both ends successfully aligned. Normalization of read counts was done in R using RPM and TPM methods. Genes with RPM > 1 in at least 2 samples were considered expressed.
Assembly: mm10
Supplementary files format and content: ".csv" for raw read counts and DESeq2-normalized read counts with batch correction.

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C.

extract_protocol:
Total RNA was extracted from 500,000 cells per sample using RNeasy Mini Kit (Qiagen, 74104), following the manufacturer’s instructions.
For M-to-G1 experiments, RNA-seq libraries were generated by Weill Cornell Medicine Genomics Resources Core Facility using NEBNext Ultra II Directional RNA library kit (New England Biolabs, E7760) and TruSeq Stranded mRNA library kit (Illumina, 20020595). For asynchronous experiments, RNA-seq libraries were generated by Novogene using their mRNA library preparation service with poly A enrichment.

value: Mouse epiblast-like cell

value: dTAG


title: MDAH, STAT1 siRNA + IL6, Rep2

description:
Library name: MDAH_STAT1_siRNA_IL6_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


description:
Library name: Async-EpiLC-RAD21_EpiLC-22h_dTAG_rep2-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


title: MDAH, STAT1 siRNA + IL6, Rep1

description:
Library name: MDAH_STAT1_siRNA_IL6_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_A1005


title: hapo_newborn_cordblood_A1017


title: P60

description: Library name: P60


title: hapo_newborn_cordblood_A1006


title: MDAH, Control siRNA + IFNγ, Rep3

description:
Library name: MDAH_Con_siRNA_IFNY_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Control siRNA + IFNγ


title: MDAH, Control siRNA + IFNγ, Rep2

description:
Library name: MDAH_Con_siRNA_IFNY_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: P59

description: Library name: P59


description:
Library name: Async-EpiLC-RAD21_EpiLC-3h_dTAG_rep2-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


title: hapo_newborn_cordblood_A1002


title: P58

description: Library name: P58


description:
Library name: Async-EpiLC-RAD21_EpiLC-22h_DMSO_rep1-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv

value: DMSO


title: MDAH, Control siRNA + IFNγ, Rep1

description:
Library name: MDAH_Con_siRNA_IFNY_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_A1001

value: cord clood


title: P57

description: Library name: P57


description:
Library name: Async-EpiLC-RAD21_EpiLC-22h_DMSO_rep2-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


title: hapo_newborn_cordblood_A0991

value: newborn


description:
Library name: Async-EpiLC-RAD21_EpiLC-3h_DMSO_rep4-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


description:
Library name: Async-EpiLC-RAD21_EpiLC-3h_dTAG_rep1-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


title: P51

description: Library name: P51


title: MDAH, Control siRNA + Veh, Rep2

description:
Library name: MDAH_Con_siRNA_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Control siRNA + Veh


title: P49

description: Library name: P49

value: Endometrium


title: MDAH, Control siRNA + Veh, Rep1

description:
Library name: MDAH_Con_siRNA_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


description:
Library name: Async-EpiLC-RAD21_EpiLC-3h_DMSO_rep3-batch2
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


title: MDAH, Control siRNA + Veh, Rep3

description:
Library name: MDAH_Con_siRNA_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: hapo_newborn_cordblood_A0989

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: whole blood cells


title: hapo_newborn_cordblood_A0983


title: P47

description: Library name: P47

value: In Vitro Fertilization


title: hapo_newborn_cordblood_A0976

value: Male


title: MDAH, Control siRNA + IL6, Rep3

description:
Library name: MDAH_Con_siRNA_IL6_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Control siRNA + IL6


description:
Library name: Async-EpiLC-RAD21_EpiLC-3h_DMSO_rep2-batch1
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv

value: RAD21-dTAG cell line (Bruce-4 derived)


title: P45

description: Library name: P45


description:
Library name: Async-EpiLC-RAD21_EpiLC-3h_DMSO_rep1-batch1
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv


title: MDAH, Control siRNA + IL6, Rep2

description:
Library name: MDAH_Con_siRNA_IL6_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: cell line


title: hapo_newborn_cordblood_A0969

value: Female


title: P43

description: Library name: P43


description:
Library name: Async-EpiLC-RAD21_ESC-3h_DMSO_rep2-batch1
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv

value: Mouse embryonic stem cell


title: MDAH, Control siRNA + IL6, Rep1

description:
Library name: MDAH_Con_siRNA_IL6_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Endometrioid ovarian cancer

value: WT


title: hapo_newborn_cordblood_A0955


title: OVSAHO, IFNγ Treatment, STAT3 (ChIP), Replicate 3

description:
Library name: OVSAHO_STAT3_IFNY_3
STAT3 (#CST9139, Cell Signaling)

data_processing:
Sequencing reads were normalized and aligned using the HiChIP pipeline(31), Burrows-Wheeler Alignment(32), and Picard tools (https://broadinstitute.github.io/picard/). MACS2(33) was used to call peaks with an FDR ≤ 1% and visualizations were generated using deeptools(34)
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were crosslinked using 1% formaldehyde (ThermoFisher, Waltham, MA) per 10 mL cell culture medium and placed on a rocker to mix for exactly 10 minutes at room temperature. Glycine (Fisher Scientific, Hampton, NH) was then added to a final concentration of 125 mM to each plate and mixed well by slowly swirling 10 times and incubated at room temperature for 5 minutes. Fixed cells were washed with cold 1X TBS (Bio Rad, Hercules, CA) and scraped into a 15 mL collection tube, centrifuged at 2500 rpm for 5 minutes at 4°C, and supernatant was removed. Another 3 mL of cold 1X TBS was added to each tube to wash, spun again at 2500 rpm for 5 minutes at 4°C, and supernatant was removed. For each treatment ChIP was performed with STAT1 (#SC417, Santa Cruz Biotechnology, Dallas, TX) and STAT3 (#CST9139, Cell Signaling, Danvers, MA) antibodies
Sequencing libraries were prepared using the Ribicon Genomics ThruPLEX DNA-seq kit (Takara Bio, Mountain View, CA) and sequencing was performed by the Mayo Clinic Genome Analysis Core using an Illumina HiSeq 4000.

treatment_protocol: 20 million MDAH and OVSAHO cells were plated in 150 mm dishes and after 24 hours treated in duplicate with vehicle (PBS, Gibco), 10 ng/mL IFNγ, or 30 ng/mL IL6 for 30 minutes.

value: OVSAHO

value: High grade serous ovarian cancer

value: 10ng/mL FNγ


description:
Library name: Async-EpiLC-RAD21_ESC-3h_DMSO_rep1-batch1
Novogene
Async-EpiLC-RAD21_rawCounts.csv
Async-EpiLC-RAD21_DESeqNormCounts.csv

value: DMSO


title: P42

description: Library name: P42


title: P39

description: Library name: P39


title: Fosl2_EpiLC_dTAG_4C-seq_rep1

description:
Library name: Fosl2_EpiLC_dTAG_rep2
Weill Cornell Medicine Genomics Resources Core Facility

data_processing:
Adapters were trimmed from paired-end reads using cutadapt (v4.8) with the following options: -j 0 -e 0.15 -m 40.
Filtered reads were aligned to the mouse genome (mm10) and normalized using  Pipe4C pipeline (Krijger P.H.L., Methods, 2020, PMID: 31351925).
Reads were depth normalized to 1 million cis reads, excluding the top 3 fragments with the highest reads aligned. Smoothening was performed using only non-blind fragments, with sliding bin normalization. Bin sizes of 5 kb were used for Klf4, and 10 kb Tbx3, Myc, and Fosl2, with a bin shift size of 1/20 of the bin size. Visualization of the 4C-seq data was done in R using ggplot2.
Assembly: mm10
Supplementary files format and content: ".bigWig" for 4C-seq tracks.
Library strategy: 4C-Seq

growth_protocol: RAD21-dTAG cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 2,000,000 cells per replicate were fixed with 1% w/v formaldehyde for 10 min at room temperature (RT) on a platform shaker, followed by quenching with 125 mM glycine for 5 minutes under the same conditions. Crosslinked cells were centrifuged at 500 × g for 5 min at 4˚C and were washed twice with ice-cold PBS. After the final wash and centrifuge, the pellet was snap-frozen before extraction.

extract_protocol:
The cell pellets were washed twice in PBS and resuspended in 300 μL of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1X cOmplete EDTA-free protease inhibitor cocktail) and incubated on ice for 20 min. Following centrifugation at 500 × g for 5 min at 4˚C, the pellet was resuspended in 50 μL of 0.5% SDS and incubated at 65˚C for 10 min on a shaker at 1,250 rpm. SDS was quenched by adding 150 μL of ddH2O and 25 μL of 10% v/v Triton X-100 at 37˚C for 15 min on a shaker at 1,250 rpm.
To initiate the first digestion, 25 μL of NEBuffer DpnII and 10 µL of DpnII enzyme were added, and the samples were incubated overnight at 37˚C on a shaker at 750 rpm. The following morning, an additional 2 µL of DpnII was added, and the samples were incubated for 2 hr. Digestion efficiency was confirmed using gel electrophoresis. The enzyme was then inactivated by incubating at 65˚C for 20 min. Once the samples cooled down, 645 µL of ddH2O, 120 µL of 10X T4 DNA ligase reaction buffer, 120 µL of 10% v/v Triton X-100, 12 µL of 10 mg/mL BSA, 1 µL of 2000 U/µL T4 DNA ligase, and 60 µL of 10 mM ATP were added to the samples. The ligation reaction was incubated overnight at 16˚C in a water bath in a cold room. The following morning, 0.5 µL of 2000 U/µL T4 DNA ligase and 30 µL of 10 mM ATP were added, and the samples were incubated at RT with rotation until the ligation efficiency was verified using gel electrophoresis. After confirming successful ligation, 60 µL of 20 mg/mL Proteinase K and 120 µL of 10% v/v SDS were added, and the samples were incubated at 65˚C for 3 min. Then, 130 µL of 5 M NaCl was added, and the samples were incubated overnight at 65˚C on a shaker at 5,000 rpm for reverse crosslinking. The following morning, 10 µL of 10 mg/mL RNase A was added, and the samples were incubated at 37˚C for 1 h. DNA was purified using phenol-chloroform extraction and ethanol precipitation, and the pellet was dissolved in 100 µL of 10 mM Tris-HCl pH 8.0. The second digestion was performed by adding 20 µL of 10X Buffer B, 10 µL of 10 U/µL Csp6I, and 80 µL of ddH2O, and incubating overnight at 37˚C on a shaker at 700 rpm. After confirming digestion efficiency the next morning, a second ligation was performed by adding 2,204 µL of ddH2O, 300 µL of 10X T4 DNA ligase buffer, 1 µL of 2000 U/mL T4 DNA ligase, and 300 µL of 10 mM ATP. The reaction was incubated overnight at 16˚C in a water bath in a cold room. DNA was purified using phenol-chloroform extraction and ethanol precipitation, resulting in the 4C template. Primers for 4C libraries were designed around the transcription start site of each gene of interest according to previously described criteria.60 Libraries were generated from the 4C template using the inverse PCR strategy. Briefly, the first round of PCR was performed in quadruplicate per sample, with 150 ng of 4C template used for each reaction in the quadruplicate, employing Expand Long Template PCR system. The PCR products were pooled to increase the library complexity. A second round of PCR was performed using the initial PCR library as a template, with overlapping primers to add P5/P7 sequencing primers and sample-specific indexes. SPRIselect beads were used for DNA size selection throughout the protocol.

treatment_protocol: 0.05% v/v DMSO or 500 nM dTAG.

value: Mouse epiblast-like cell

tag: viewpoint

value: dTAG


title: hapo_newborn_cordblood_A0949

value: cord clood

value: newborn


title: hapo_newborn_cordblood_A0957

value: whole blood cells


title: P44

description: Library name: P44

value: Endometrium

value: In Vitro Fertilization


title: Fosl2_EpiLC_DMSO_4C-seq_rep1

description:
Library name: Fosl2_EpiLC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)


title: OVSAHO, IFNγ Treatment, STAT3 (ChIP), Replicate 1

description:
Library name: OVSAHO_STAT3_IFNY_1
STAT3 (#CST9139, Cell Signaling)

value: cell line


title: hapo_newborn_cordblood_A0946

value: Female


title: hapo_newborn_cordblood_A0943

value: Male


title: P35

description: Library name: P35


title: P38

description: Library name: P38


title: P31

description: Library name: P31


title: OVSAHO, IL6 Treatment, STAT3 (ChIP), Replicate 3

description:
Library name: OVSAHO_STAT3_IL6_3
STAT3 (#CST9139, Cell Signaling)

value: 30ng/mL IL8


title: hapo_newborn_cordblood_A0939


title: Fosl2_ESC_dTAG_4C-seq_rep1

description:
Library name: Fosl2_ESC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell


title: OVSAHO, IL6 Treatment, STAT3 (ChIP), Replicate 2

description:
Library name: OVSAHO_STAT3_IL6_2
STAT3 (#CST9139, Cell Signaling)

value: OVSAHO

value: WT

value: 30ng/mL IL7


title: OVSAHO, IFNγ Treatment, STAT3 (Input)

description:
Library name: OVSAHO_STAT3_IFNY_Input
none

value: High grade serous ovarian cancer

value: 10ng/mL FNγ


title: hapo_newborn_cordblood_A0929


title: Fosl2_ESC_DMSO_4C-seq_rep1

description:
Library name: Fosl2_ESC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: DMSO


title: Myc_EpiLC_dTAG_4C-seq_rep1

description:
Library name: Myc_EpiLC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse epiblast-like cell

value: Myc

value: dTAG


title: P3

description: Library name: P3

value: Endometrium


title: OVSAHO, IFNγ Treatment, STAT3 (ChIP), Replicate 2

description:
Library name: OVSAHO_STAT3_IFNY_2
STAT3 (#CST9139, Cell Signaling)


title: Myc_EpiLC_DMSO_4C-seq_rep2

description:
Library name: Myc_EpiLC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility


title: hapo_newborn_cordblood_A0928

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: cord clood

value: newborn

value: whole blood cells


title: P29

description: Library name: P29

value: In Vitro Fertilization


title: Myc_EpiLC_DMSO_4C-seq_rep1

description:
Library name: Myc_EpiLC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)


title: OVSAHO, IL6 Treatment, STAT3 (ChIP), Replicate 1

description:
Library name: OVSAHO_STAT3_IL6_1
STAT3 (#CST9139, Cell Signaling)

value: cell line

value: 30ng/mL IL6


title: hapo_newborn_cordblood_A0927

value: Female


title: P26

description: Library name: P26


title: Myc_ESC_dTAG_4C-seq_rep1

description:
Library name: Myc_ESC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell


title: hapo_newborn_cordblood_A0905


title: OVSAHO, Vehicle Treatment, STAT3 (ChIP), Replicate 3

description:
Library name: OVSAHO_STAT3_Veh_3
STAT3 (#CST9139, Cell Signaling)

value: OVSAHO

value: WT

value: Vehicle (PBS)


title: OVSAHO, IL6 Treatment, STAT3 (Input)

description:
Library name: OVSAHO_STAT3_IL6_Input
none

value: High grade serous ovarian cancer

value: 30ng/mL IL5


title: P24

description: Library name: P24


title: Myc_ESC_DMSO_4C-seq_rep2

description:
Library name: Myc_ESC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility

value: Myc

value: DMSO


title: hapo_newborn_cordblood_A0885

value: Male


title: P23

description: Library name: P23

value: Endometrium


title: hapo_newborn_cordblood_A0878

value: cord clood

value: newborn


title: hapo_newborn_cordblood_A0875

value: whole blood cells


title: Myc_ESC_DMSO_4C-seq_rep1

description:
Library name: Myc_ESC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: RAD21-dTAG cell line (Bruce-4 derived)


title: Tbx3_ESC_dTAG_4C-seq_rep1

description:
Library name: Tbx3_ESC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: dTAG


title: P22

description: Library name: P22

value: In Vitro Fertilization


title: OVSAHO, Vehicle Treatment, STAT3 (ChIP), Replicate 1

description:
Library name: OVSAHO_STAT3_Veh_1
STAT3 (#CST9139, Cell Signaling)

value: cell line


title: Tbx3_ESC_DMSO_4C-seq_rep1

description:
Library name: Tbx3_ESC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility

value: Mouse embryonic stem cell


title: P21

description: Library name: P21


title: OVSAHO, Vehicle Treatment, STAT3 (ChIP), Replicate 2

description:
Library name: OVSAHO_STAT3_Veh_2
STAT3 (#CST9139, Cell Signaling)

value: OVSAHO


title: OVSAHO, Vehicle Treatment, STAT3 (Input)

description:
Library name: OVSAHO_STAT3_Veh_Input
none

value: WT


title: P20

description: Library name: P20


title: Klf4_ESC_dTAG_4C-seq_rep1

description:
Library name: Klf4_ESC_dTAG_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: hapo_newborn_cordblood_A0863


title: OVSAHO, IFNγ Treatment, STAT1 (ChIP), Replicate 2

description:
Library name: OVSAHO_STAT1_IFNY_2
STAT1 (#SC417, Santa Cruz Biotechnology)

value: 10ng/mL FNγ


title: P2

description: Library name: P2


title: Klf4_ESC_DMSO_4C-seq_rep2

description:
Library name: Klf4_ESC_DMSO_rep2
Weill Cornell Medicine Genomics Resources Core Facility


title: hapo_newborn_cordblood_A0857


title: OVSAHO, IFNγ Treatment, STAT1 (ChIP), Replicate 3

description:
Library name: OVSAHO_STAT1_IFNY_3
STAT1 (#SC417, Santa Cruz Biotechnology)

value: High grade serous ovarian cancer


title: P19

description: Library name: P19


title: Klf4_ESC_DMSO_4C-seq_rep1

description:
Library name: Klf4_ESC_DMSO_rep1
Weill Cornell Medicine Genomics Resources Core Facility


title: OVSAHO, IFNγ Treatment, STAT1 (ChIP), Replicate 1

description:
Library name: OVSAHO_STAT1_IFNY_1
STAT1 (#SC417, Santa Cruz Biotechnology)


title: hapo_newborn_cordblood_A0871

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Female


title: OVSAHO, IFNγ Treatment, STAT1 (Input)

description:
Library name: OVSAHO_STAT1_IFNY_Input
none


title: OVSAHO, IL6 Treatment, STAT1 (ChIP), Replicate 3

description:
Library name: OVSAHO_STAT1_IL6_3
STAT1 (#SC417, Santa Cruz Biotechnology)

value: 30ng/mL IL8


title: P13

description: Library name: P13


title: P17

description: Library name: P17


title: hapo_newborn_cordblood_A0844


title: hapo_newborn_cordblood_A0827


title: Astrocyte-RiboTag pulldown replicate 2

city: Atlanta

first: Christina

last: Ramelow

address: 615 Michael St RM 375

institute: Emory University

description:
Library name: Sample 53
/home/ec2-user/23238R-04-09_S9_L002_Aligned.sortedByCoord.out.bam

data_processing:
Global sequencing of 40 million paired-end reads per sample was completed using the Illumina-based platform at Admera Health. FASTQ files were evaluated for quality using FastQC and then mapped to the mouse genome, GRCm38 (mm10), or GRCh38, human genome (hg38), using the Spliced Transcripts Alignment to a Reference (STAR) (for mRNA-seq) or Bowtie 2 (for smRNA-seq) aligners with the paired-end option. The featureCounts package was used to generate a raw counts data matrix from mapped reads. Lowly abundant transcripts across all samples (average count value ≤ 10) were filtered out. After generating the filtered, raw counts data matrices, we used DESeq2 to normalize the matrices and perform differential gene ex-pression-based statistics.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file that includes raw counts for each sample.

molecule: polyA RNA

source_name: cortex

growth_protocol: Mouse microglia BV2 cells were cultured in 0.2 µm vacuum filter sterilized Dulbecco’s Modified Eagle Medium (DMEM) supplemented with high glucose and L-glutamine containing 1% penicillin-streptomycin, and 10% fetal bovine serum. BV2 cells were incubated in 100 mm cell culture dish at 37°C and 5% CO2 until reaching 80-90% confluency. Cells were treated with 100 ng/mL of LPS for 48 h and 200 µM of biotin for 24 h during the second day of LPS treatment. Human embryonic kidney 293 cells (HEK293) were cultured in DMEM containing 1% penicillin-streptomycin and 10% fetal bovine serum. HEK293 cells were incubated in 6-well cul-ture dishes in the same condition as the BV2 cells described above. At 30% confluency, HEK293 cells were infected with 3 µL of the two LVs generated (TurboID-NES, viral titer: 3.9x108 IU/mL or TurboID-noNES, viral titer: 1.7x109 IU/mL). LV-containing media was removed after 3 days, and successful infection was determined by cellular GFP signal using the ECHO Revolve fluores-cence microscope (Echo, USA) prior to lysis. HEK293 cells were grown to 80-90% confluency cells before biotin treatment (200 µM for 24 h). The 48 h LPS and 24 h biotin treatment paradigms were used to model similar treatment and labeling kinetics for in vivo SPARO studies.

extract_protocol:
After protein enrichment using streptavidin and A/B beads, RNA was extracted from the beads and bulk/g;obal cell or bulk cortical lysates using a miRNeasy Mini Kit (Qiagen Inc., 217004) following the manufacturer’s instructions. 1-3 ug of total RNA was used to generate cDNA libraries.
The SMART-Seq® v4 PLUS Kit (Takara Bio) was used following the manufacturer’s protocol. For small RNA-sequencing library preparation, a QIAseq miRNA NGS kit (Qiagen, 331565) was used.

treatment_protocol: BV2 cells were treated with 100 ng/mL of lipopolysaccharide (LPS) for 48 h and 200 mM of biotin for 24 h during the second day of LPS treatment. All mice were given tamoxifen (75 mg/kg) intraperitoneally (i.p.) for 5 days at 6 weeks of age and allowed 3 weeks of Cre recombination. After Cre recombination, TurboID mice were given water supplemented with biotin (37.5 mg/L) for 2 weeks until euthanasia at 3-4 months of age. RiboTag mice were euthanized at 2.5 months of age. For astrocyte-TurboID LPS studies, systemic LPS at 0.75mg/kg/dose x 5 days was given via i.p. injection during the first week of biotin water supplementation. Mice from each cohort were anesthetized using ketamine/xylazine (ketamine 87.5 mg/kg, xylazine 12.5 mg/kg) followed by transcardial perfusion with ice-cold PBS.

value: cortex

value: mature astrocyte

value: female

tag: batch


title: Astrocyte-RiboTag pulldown replicate 3

description:
Library name: Sample 54
/home/ec2-user/23238R-04-10_S10_L002_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0822

value: cord clood


title: OVSAHO, IL6 Treatment, STAT1 (ChIP), Replicate 2

description:
Library name: OVSAHO_STAT1_IL6_2
STAT1 (#SC417, Santa Cruz Biotechnology)

value: 30ng/mL IL7


title: P10

description: Library name: P10

value: Endometrium


title: P11

description: Library name: P11


title: Astrocyte-RiboTag pulldown replicate 1

description:
Library name: Sample 52
/home/ec2-user/23238R-04-08_S8_L002_Aligned.sortedByCoord.out.bam


title: OVSAHO, Vehicle Treatment, STAT1 (ChIP), Replicate 3

description:
Library name: OVSAHO_STAT1_Veh_3
STAT1 (#SC417, Santa Cruz Biotechnology)

value: Vehicle (PBS)


title: RiboTag pulldown replicate 1

description:
Library name: Sample 50
/home/ec2-user/23238R-04-06_S6_L002_Aligned.sortedByCoord.out.bam

value: male


title: OVSAHO, IL6 Treatment, STAT1 (ChIP), Replicate 1

description:
Library name: OVSAHO_STAT1_IL6_1
STAT1 (#SC417, Santa Cruz Biotechnology)

value: 30ng/mL IL6


title: RiboTag pulldown replicate 2

description:
Library name: Sample 51
/home/ec2-user/23238R-04-07_S7_L002_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0814

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_A0821

value: Male


title: OVSAHO, IL6 Treatment, STAT1 (Input)

description:
Library name: OVSAHO_STAT1_IL6_Input
none

value: cell line

value: OVSAHO

value: WT

value: 30ng/mL IL5


title: hapo_newborn_cordblood_A0801


title: hapo_newborn_cordblood_A0807


title: Astrocyte-RiboTag bulk replicate 3

description:
Library name: Sample 49
/home/ec2-user/23238R-04-05_S5_L002_Aligned.sortedByCoord.out.bam


title: OVSAHO, Vehicle Treatment, STAT1 (Input)

description:
Library name: OVSAHO_STAT1_Veh_Input
none

value: High grade serous ovarian cancer


title: Frontal Cortex, Tg2576 mouse control2

type: RNA

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression profiling of frontal cortex specimen of control Tg2576 mice

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Affymetrix GeneChip Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

label: biotin

source_name: Frontal cortex Tg2576 mouse control

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: Frontal cortex specimens were isolated from 18-month-old Tg2576 mice

extract_protocol: Total RNA was isolated from RNAlater-stabilized mouse frontal cortex specimens with the RNeasy Minii kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: Two groups of Tg2576 mice were analyzed. The treatment group received the GRK2 activity modulator CPD10 [1-(1,3-Benzodioxol-5-yl)-4-(cyclopropanecarbonyl)-3- hydroxy-2-phenyl-2H-pyrrol-5-one] for 6 months in drinking water (8 mg/kg/d) and the control group of Tg2576 mice received tap water.


title: Frontal Cortex, Tg2576 mouse control1


title: GSC20 cells treated with 6Gy radiation for scATAC-seq

city: Los Angeles

first: Khoi

last: Huynh

state: CA

address: 1441 Eastlake Ave

department: Radiation Oncology,Keck School of Medicine of USC

institute: University of Southern California

description: Library name: 3hr_6Gy_ATAC

library_source: genomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and data aggregation were performed using Cell Ranger software version 2.0.2 (available at 10x Genomics).
Assembly: human /hg38
Supplementary files format and content: Tab-separated value files showing cell barcodes, raw gene expression per cells, and raw fragment count per ATAC-seq peaks per cells

source_name: patient brain tumor-derived stem cell line

growth_protocol: All cells are cultured in standard neural basal medium (NBM), which consists of Corning DMEM/Hams F-12 50/50 mix, 1x B27 supplement, 20ng/mL EGF, 20ng/mL bFGF, and 1x anti-mycotic anti-bacterial solution

extract_protocol:
10x Multiomic extraction protocols
10x Multiomic library construction protocols

treatment_protocol: cells are irradiated with 2Gy or 6Gy radiation doses

value: Glioblastoma stem cell


title: hapo_newborn_cordblood_A0789


title: OVSAHO, Vehicle Treatment, STAT1 (ChIP), Replicate 2

description:
Library name: OVSAHO_STAT1_Veh_2
STAT1 (#SC417, Santa Cruz Biotechnology)


title: Astrocyte-RiboTag bulk replicate 1

description:
Library name: Sample 47
/home/ec2-user/23238R-04-03_S3_L002_Aligned.sortedByCoord.out.bam

value: cortex

value: mature astrocyte


title: GSC20 cells treated with 2Gy radiation for scATAC-seq

description: Library name: 3hr_2Gy_ATAC

value: patient brain tumor-derived stem cell line


title: hapo_newborn_cordblood_A0798

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: cord clood


title: hapo_newborn_cordblood_A0790

value: Female


title: Frontal Cortex, Tg2576 mouse treated2

description: Gene expression profiling of frontal cortex specimen of treated Tg2576 mice

source_name: Frontal cortex Tg2576 mouse treated


title: MDAH, IFNγ Treatment, STAT3 (ChIP), Replicate 2

description:
Library name: MDAH_STAT3_IFNY_2
STAT3 (#CST9139, Cell Signaling)

value: Endometrioid ovarian cancer

value: 10ng/mL FNγ


title: RiboTag bulk replicate 1

description:
Library name: Sample 45
/home/ec2-user/23238R-04-01_S1_L002_Aligned.sortedByCoord.out.bam

value: male


title: OVSAHO, Vehicle Treatment, STAT1 (ChIP), Replicate 1

description:
Library name: OVSAHO_STAT1_Veh_1
STAT1 (#SC417, Santa Cruz Biotechnology)

value: Vehicle (PBS)


title: GSC20 cells without radiation treatment for scATAC-seq

description: Library name: 3hr_0Gy_ATAC


title: RiboTag bulk replicate 2

description:
Library name: Sample 46
/home/ec2-user/23238R-04-02_S2_L002_Aligned.sortedByCoord.out.bam

value: female


title: Neuron-TurboID pulldown replicate 3

description:
Library name: Sample 44
/home/ec2-user/22082R-12-03_S9_L003_Aligned.sortedByCoord.out.bam

value: mature excitatory neuron


title: MDAH, IFNγ Treatment, STAT3 (ChIP), Replicate 1

description:
Library name: MDAH_STAT3_IFNY_1
STAT3 (#CST9139, Cell Signaling)

value: cell line


title: MDAH, IFNγ Treatment, STAT3 (ChIP), Replicate 3

description:
Library name: MDAH_STAT3_IFNY_3
STAT3 (#CST9139, Cell Signaling)


title: Astrocyte-RiboTag bulk replicate 2

description:
Library name: Sample 48
/home/ec2-user/23238R-04-04_S4_L002_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0782

value: Male

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_A0775


title: GSC20 cells treated with 2Gy radiation for scRNA-seq

description: Library name: 3hr_2Gy_GX


title: GSC20 cells treated with 6Gy radiation for scRNA-seq

description: Library name: 3hr_6Gy_GX


title: Frontal Cortex, Tg2576 mouse treated1


title: hapo_newborn_cordblood_A0768


title: MDAH, IL6 Treatment, STAT3 (ChIP), Replicate 3

description:
Library name: MDAH_STAT3_IL6_3
STAT3 (#CST9139, Cell Signaling)

value: WT

value: 30ng/mL IL8


title: GSC20 cells without radiation treatment for scRNA-seq

description: Library name: 3hr_0Gy_GX

value: Glioblastoma stem cell


title: Neuron-TurboID pulldown replicate 2

description:
Library name: Sample 43
/home/ec2-user/22082R-12-02_S0_L001_Aligned.sortedByCoord.out.bam

value: cortex


title: hapo_newborn_cordblood_A0760


title: MDAH, IFNγ Treatment, STAT3 (Input)

description:
Library name: MDAH_STAT3_IFNY_Input
none


title: MDAH, IL6 Treatment, STAT3 (ChIP), Replicate 2

description:
Library name: MDAH_STAT3_IL6_2
STAT3 (#CST9139, Cell Signaling)

value: 30ng/mL IL7


title: Patient BL1057; ATAC-seq

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: Library name: AT1057

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
Assembly: hg19
Supplementary files format and content: BigWig and peak text files (BED) were generated

source_name: Primary; Bladder resection; Non-muscle invasive; TaN0

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

tag: antibody


title: hapo_newborn_cordblood_A0754

value: cord clood


title: Neuron-TurboID pulldown replicate 1

description:
Library name: Sample 42
/home/ec2-user/22082R-12-01_S0_L001_Aligned.sortedByCoord.out.bam


title: MDAH, IL6 Treatment, STAT3 (ChIP), Replicate 1

description:
Library name: MDAH_STAT3_IL6_1
STAT3 (#CST9139, Cell Signaling)

value: 30ng/mL IL6


title: hapo_newborn_cordblood_A0771


title: Astrocyte-TurboID LPS pulldown replicate 2

description:
Library name: Sample 38
/home/ec2-user/21047FL-134-01-45_S18_L007_Aligned.sortedByCoord.out.bam

value: mature astrocyte

value: 0.75mg/kg/dose LPS, 5 d


title: Astrocyte-TurboID LPS pulldown replicate 4

description:
Library name: Sample 40
/home/ec2-user/21047FL-134-01-47_S20_L007_Aligned.sortedByCoord.out.bam


title: Astrocyte-TurboID LPS pulldown replicate 3

description:
Library name: Sample 39
/home/ec2-user/21047FL-134-01-46_S19_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1053; ATAC-seq

description: Library name: AT1053

source_name: Primary; Bladder biopsy; Non-muscle invasive; T1


title: MDAH, Vehicle Treatment, STAT3 (ChIP), Replicate 2

description:
Library name: MDAH_STAT3_Veh_2
STAT3 (#CST9139, Cell Signaling)

value: Endometrioid ovarian cancer


title: Astrocyte-TurboID LPS pulldown replicate 5

description:
Library name: Sample 41
/home/ec2-user/21047FL-134-01-48_S21_L007_Aligned.sortedByCoord.out.bam

value: male


title: hapo_newborn_cordblood_A0753

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Female


title: MDAH, IL6 Treatment, STAT3 (Input)

description:
Library name: MDAH_STAT3_IL6_Input
none

value: 30ng/mL IL5


title: Astrocyte-TurboID pulldown replicate 2

description:
Library name: Sample 35
/home/ec2-user/21047FL-134-01-42_S15_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0746


title: MDAH, Vehicle Treatment, STAT3 (ChIP), Replicate 3

description:
Library name: MDAH_STAT3_Veh_3
STAT3 (#CST9139, Cell Signaling)

value: cell line

value: Vehicle (PBS)


title: Patient BL1050; ATAC-seq

description: Library name: AT1050

source_name: Primary; Cystectomy; Non-muscle invasive; T1N0MX


title: hapo_newborn_cordblood_A0737

value: newborn


title: hapo_newborn_cordblood_A0752

value: whole blood cells


title: Astrocyte-TurboID pulldown replicate 1

description:
Library name: Sample 34
/home/ec2-user/21047FL-134-01-41_S14_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1049; ATAC-seq

description: Library name: AT1049

source_name: Primary; Cystectomy; Muscle invasive; T4N2


title: Astrocyte-TurboID pulldown replicate 3

description:
Library name: Sample 36
/home/ec2-user/21047FL-134-01-43_S16_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0747


title: Patient BL1046; ATAC-seq

description: Library name: AT1046

source_name: Primary; Cystectomy; Muscle invasive; T3bN2


title: Patient BL1068; Input

description: Library name: BL1068IN

value: Primary; Bladder resection; Non-muscle invasive; TaN0


title: MDAH, IFNγ Treatment, STAT1 (ChIP), Replicate 3

description:
Library name: MDAH_STAT1_IFNY_3
STAT1 (#SC417, Santa Cruz Biotechnology)

value: WT

value: 10ng/mL FNγ


title: hapo_newborn_cordblood_A0751


title: Patient BL1039; ATAC-seq

description: Library name: AT1039

source_name: Primary; Bladder biopsy; Muscle invasive; T3N0


title: Astrocyte-TurboID LPS pulldown replicate 1

description:
Library name: Sample 37
/home/ec2-user/21047FL-134-01-44_S17_L007_Aligned.sortedByCoord.out.bam

value: cortex


title: hapo_newborn_cordblood_D0776

value: Male


title: MDAH, Vehicle Treatment, STAT3 (ChIP), Replicate 1

description:
Library name: MDAH_STAT3_Veh_1
STAT3 (#CST9139, Cell Signaling)


title: Patient BL1009; ATAC-seq

description: Library name: AT1009

source_name: Primary; Cystectomy; Muscle invasive; T2N0Mx


title: MDAH, Vehicle Treatment, STAT3 (Input)

description:
Library name: MDAH_STAT3_Veh_Input
none


title: Patient BL1058; Input

description: Library name: BL1058IN

source_name: Primary; Cystectomy; -; TURBT

value: Primary; Cystectomy; -; TURBT


title: Astrocyte-TurboID LPS bulk replicate 4

description:
Library name: Sample 30
/home/ec2-user/21047FL-134-01-37_S10_L007_Aligned.sortedByCoord.out.bam

value: female


title: hapo_newborn_cordblood_A0729

value: cord clood


title: Patient BL1057; Input

description: Library name: BL1057IN


title: hapo_newborn_cordblood_A0736


title: MDAH, IFNγ Treatment, STAT1 (ChIP), Replicate 2

description:
Library name: MDAH_STAT1_IFNY_2
STAT1 (#SC417, Santa Cruz Biotechnology)


title: Aldh1l1-Cre pulldown replicate 1

description:
Library name: Sample 32
/home/ec2-user/21047FL-134-01-39_S12_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1063; Input

description: Library name: BL1063IN

source_name: Primary; Cystectomy; Muscle invasive; T2


title: hapo_newborn_cordblood_A0735


title: MDAH, IFNγ Treatment, STAT1 (ChIP), Replicate 1

description:
Library name: MDAH_STAT1_IFNY_1
STAT1 (#SC417, Santa Cruz Biotechnology)

source_name: cell line


title: Patient BL1056; Input

description: Library name: BL1056IN

source_name: Primary; Bladder resection; Muscle invasive; T3bN2


title: MDAH, IL6 Treatment, STAT1 (ChIP), Replicate 1

description:
Library name: MDAH_STAT1_IL6_1
STAT1 (#SC417, Santa Cruz Biotechnology)

value: 30ng/mL IL6


title: Aldh1l1-Cre pulldown replicate 2

description:
Library name: Sample 33
/home/ec2-user/21047FL-134-01-40_S13_L007_Aligned.sortedByCoord.out.bam


title: Astrocyte-TurboID LPS bulk replicate 5

description:
Library name: Sample 31
/home/ec2-user/21047FL-134-01-38_S11_L007_Aligned.sortedByCoord.out.bam

value: mature astrocyte

value: 0.75mg/kg/dose LPS, 5 d


title: MDAH, IFNγ Treatment, STAT1 (Input)

description:
Library name: MDAH_STAT1_IFNY_Input
none

value: Endometrioid ovarian cancer


title: hapo_newborn_cordblood_A0731

source_name: newborn cordblood


title: Astrocyte-TurboID LPS bulk replicate 1

description:
Library name: Sample 27
/home/ec2-user/21047FL-134-01-34_S7_L007_Aligned.sortedByCoord.out.bam

value: male


title: Astrocyte-TurboID LPS bulk replicate 3

description:
Library name: Sample 29
/home/ec2-user/21047FL-134-01-36_S9_L007_Aligned.sortedByCoord.out.bam


title: MDAH, IL6 Treatment, STAT1 (ChIP), Replicate 2

description:
Library name: MDAH_STAT1_IL6_2
STAT1 (#SC417, Santa Cruz Biotechnology)

value: cell line

value: 30ng/mL IL7


title: hapo_newborn_cordblood_A0728

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: newborn


title: Astrocyte-TurboID LPS bulk replicate 2

description:
Library name: Sample 28
/home/ec2-user/21047FL-134-01-35_S8_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0725

value: whole blood cells


title: MDAH, IL6 Treatment, STAT1 (Input)

description:
Library name: MDAH_STAT1_IL6_Input
none

value: 30ng/mL IL5


title: Patient BL1055; Input

description: Library name: BL1055IN

source_name: Primary; Bladder resection; Muscle invasive; T3aN0


title: Astrocyte-TurboID bulk replicate 2

description:
Library name: Sample 25
/home/ec2-user/21047FL-134-01-32_S5_L007_Aligned.sortedByCoord.out.bam

source_name: cortex


title: hapo_newborn_cordblood_A0704


title: Patient BL1054; Input

description: Library name: BL1054IN

source_name: Primary; Bladder biopsy; Non-muscle invasive; TaN0


title: hapo_newborn_cordblood_A0712


title: hapo_newborn_cordblood_A0700


title: Patient BL1040; ATAC-seq

description: Library name: AT1040

source_name: Primary; Bladder biopsy; Muscle invasive; T3aN0Mx


title: MDAH, Vehicle Treatment, STAT1 (Input)

description:
Library name: MDAH_STAT1_Veh_Input
none

value: WT

value: Vehicle (PBS)


title: Aldh1l1-Cre LPS bulk replicate 2

description:
Library name: Sample 23
/home/ec2-user/21047FL-134-01-30_S3_L007_Aligned.sortedByCoord.out.bam

value: cortex


title: MDAH, Vehicle Treatment, STAT1 (ChIP), Replicate 1

description:
Library name: MDAH_STAT1_Veh_1
STAT1 (#SC417, Santa Cruz Biotechnology)


title: Astrocyte-TurboID bulk replicate 3

description:
Library name: Sample 26
/home/ec2-user/21047FL-134-01-33_S6_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0695

value: Female


title: MDAH, Vehicle Treatment, STAT1 (ChIP), Replicate 2

description:
Library name: MDAH_STAT1_Veh_2
STAT1 (#SC417, Santa Cruz Biotechnology)


title: Aldh1l1-Cre LPS bulk replicate 1

description:
Library name: Sample 22
/home/ec2-user/21047FL-134-01-29_S2_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1053; Input

description: Library name: BL1053IN

value: Primary; Bladder biopsy; Non-muscle invasive; T1


title: hapo_newborn_cordblood_A0709

value: Male


title: Patient BL1048; Input

description: Library name: BL1048IN

source_name: Primary; Bladder biopsy; Non-muscle invasive; T1aNx


title: Patient BL1050; Input

description: Library name: BL1050IN

value: Primary; Cystectomy; Non-muscle invasive; T1N0MX


title: Astrocyte-TurboID bulk replicate 1

description:
Library name: Sample 24
/home/ec2-user/21047FL-134-01-31_S4_L007_Aligned.sortedByCoord.out.bam


title: MDAH, Vehicle Treatment, STAT1 (ChIP), Replicate 3

description:
Library name: MDAH_STAT1_Veh_3
STAT1 (#SC417, Santa Cruz Biotechnology)


title: hapo_newborn_cordblood_A0693

value: cord clood


title: Patient BL1049; Input

description: Library name: BL1049IN

value: Primary; Cystectomy; Muscle invasive; T4N2


title: batch_4,brain slices,patch-seq

city: Guangzhou

first: Ruifeng

last: Liu

state: Guangdong province

address: Jinsui Road, 7#

department: Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-sen University

description:
Library name: patch-seq_37 cells
Smart-seq2

data_processing:
The derived raw sequencing data were qualified with FastQC (FastQC v0.12.1), and some samples were trimmed with Trimmomatic (version 0.39) to remove the low-quality bases.
Then the clean data were aligned to the macaque reference genome (Ensembl Macaca fascicularis 5.0) using STAR (version 2.7.10a).
Finally, we calculated the gene expression using RSEM (v1.3.1)and created the gene expression matrix with a bash-based custom-made routine for further data analysis.
Assembly: MFA_5.0
Supplementary files format and content: patchseq raw count csv file, coma-delimited text file, column names are cell_ids , row names are gene symbols

organism: Macaca fascicularis

source_name: Brain

extract_protocol:
After patch clamp recording session, a gentle negative pressure (0.7-1.5 pounds per square inch) was applied to the pipette to aspirate the cell content into the pipette tip.
cDNA libraries for patch-seq RNA samples were prepared using Nextera XT DNA Library Preparation (Illumina, FC-131-1096) and Nextera XT Index Kit V2 Sets A (Illumina, FC-131-2001) following the manufacturer's instructions.

value: Brain

value: neurons


title: BV2-TurboID LPS pulldown replicate 3

description:
Library name: Sample 20
/home/ec2-user/21047FL-134-01-21_S20_L007_Aligned.sortedByCoord.out.bam

value: immature microglia

value: female

value: TurboID knockin

value: 100 ng/uL LPS; 48 h


title: batch_5,brain slices,patch-seq

description:
Library name: patch-seq_136 cells
Smart-seq2


title: hapo_newborn_cordblood_A0686

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_A0691


title: BV2-TurboID LPS pulldown replicate 2

description:
Library name: Sample 19
/home/ec2-user/21047FL-134-01-20_S19_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0675


title: Patient BL1045; Input

description: Library name: BL1045IN

source_name: Primary; Cystectomy; Muscle invasive; T4aN1


title: batch_1,brain slices,patch-seq

description:
Library name: patch-seq_81 cells
Smart-seq2

value: WT


title: BV2-TurboID LPS pulldown replicate 1

description:
Library name: Sample 18
/home/ec2-user/21047FL-134-01-19_S18_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0671


title: Patient BL1044; Input

description: Library name: BL1044IN

source_name: Primary; Bladder biopsy; Muscle invasive; T2aN0


title: MDAH, IL6 Treatment, STAT1 (ChIP), Replicate 3

description:
Library name: MDAH_STAT1_IL6_3
STAT1 (#SC417, Santa Cruz Biotechnology)

value: cell line

value: Endometrioid ovarian cancer

value: 30ng/mL IL8


title: 10xMulti_Pomc_5_HTO

city: Dallas

first: Li

last: Li

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: Library name: Pomc_5_HTO

library_source: other

data_processing:
Raw Fastq files were precessed using 10x Cellranger-ARC.
Assembly: mm10
Supplementary files format and content: Pomc.Joint.v2.rds : Merged data after QC in R format
Supplementary files format and content: feature_ref.csv : HTO&ADT barcode
Library strategy: CITE-seq

molecule: protein

source_name: Mediobasal Hypothalamus

extract_protocol:
Tissue preparation, dissociation, and nuclei extraction were described in a STAR Protocol (https://doi.org/10.1016/j.xpro.2023.102595). In this study, the ARH regions were dissected from four-week-old for Pomc-Cre; Sun1/sfGFP and Pomc-Cre; Otpfl/fl; Sun1/sfGFP mice, under a fluorescent dissecting microscope and stored at -80°C. Different genotype samples were separately homogenized with 1 ml homogenization buffer using a Dounce grinder pestle. The homogenate solutions were centrifuged at 500 g for 5 min in a swing bucket rotor, and the supernatants were removed. The nuclei were resuspended with 100 μl of wash buffer and incubated with different TotalSeq Hashtag antibodies against the nuclear pore complex (0.5 μl, MAb414; BioLegend) for 10 min. The nuclei suspensions were washed thrice with 1 ml wash buffer and spun down at 500 g for 5 min. After hashtagging each sample with the antibody, all samples were pooled together, and GFP-positive nuclei were sorted during FACS at the Flow Cytometry Core of UTSW Medical Center.
After sorting, the nuclei solution was adjusted to the desired concentration at 500–2,000 nuclei/μl, then proceeded with the 10× Multiome kit at the UTSW Next Generation Sequencing Core.

value: Mediobasal Hypothalamus

value: Pomc-Cre; R26LSL-Sun1-sfGFP; Otp-fl

value: KO

value: mixed sample


title: batch_3,brain slices,patch-seq

description:
Library name: patch-seq_28 cells
Smart-seq2


title: batch_2,brain slices,patch-seq

description:
Library name: patch-seq_70 cells
Smart-seq2


title: BV2-TurboID pulldown replicate 3

description:
Library name: Sample 17
/home/ec2-user/21047FL-134-01-18_S17_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1046; Input

description: Library name: BL1046IN

source_name: Primary; Cystectomy; Muscle invasive; T3bN2


title: Patient BL1042; Input

description: Library name: BL1042IN

source_name: Primary; Cystectomy; Muscle invasive; T4aN0MX


title: BV2-TurboID pulldown replicate 2

description:
Library name: Sample 16
/home/ec2-user/21047FL-134-01-17_S16_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1043; Input

description: Library name: BL1043IN

value: Primary; Cystectomy; Muscle invasive; T4aN0MX


title: hapo_newborn_cordblood_A0667

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Male

value: cord clood


title: BV2-TurboID pulldown replicate 1

description:
Library name: Sample 15
/home/ec2-user/21047FL-134-01-16_S15_L007_Aligned.sortedByCoord.out.bam

value: immature microglia


title: hapo_newborn_cordblood_A0669

value: Female


title: Patient BL1041; Input

description: Library name: BL1041IN

source_name: Primary; Cystectomy; Non-muscle invasive; T1


title: hapo_newborn_cordblood_A0664


title: BV2 LPS pulldown replicate 2

description:
Library name: Sample 14
/home/ec2-user/21047FL-134-01-14_S14_L007_Aligned.sortedByCoord.out.bam

value: female


title: Patient BL1040; Input

description: Library name: BL1040IN

value: Primary; Bladder biopsy; Muscle invasive; T3aN0Mx


title: 10xMulti_Pomc_4_HTO

description: Library name: Pomc_4_HTO


title: 10xMulti_Pomc_5_ATAC

description: Library name: Pomc_5_ATAC

data_processing:
Raw Fastq files were precessed using 10x Cellranger-ARC.
Assembly: mm10
Supplementary files format and content: Pomc.Joint.v2.rds : Merged data after QC in R format
Supplementary files format and content: feature_ref.csv : HTO&ADT barcode


title: hapo_newborn_cordblood_A0665

value: newborn


title: hapo_newborn_cordblood_A0660

value: whole blood cells


title: 10xMulti_Pomc_4_ATAC

description: Library name: Pomc_4_ATAC


title: BV2 LPS pulldown replicate 1

description:
Library name: Sample 13
/home/ec2-user/21047FL-134-01-13_S13_L007_Aligned.sortedByCoord.out.bam

value: WT


title: BV2-TurboID LPS bulk replicate 3

description:
Library name: Sample 12
/home/ec2-user/21047FL-134-01-12_S12_L007_Aligned.sortedByCoord.out.bam

value: TurboID knockin

value: 100 ng/uL LPS; 48 h


title: hapo_newborn_cordblood_A0659


title: 10xMulti_Pomc_5_GEX

description: Library name: Pomc_5_GEX


title: BV2-TurboID LPS bulk replicate 2

description:
Library name: Sample 11
/home/ec2-user/21047FL-134-01-11_S11_L007_Aligned.sortedByCoord.out.bam


title: 10xMulti_Pomc_4_GEX

description: Library name: Pomc_4_GEX


title: Patient BL1038; Input

description: Library name: BL1038IN

source_name: Primary; Cystectomy; Non-muscle invasive; pTisN0


title: Patient BL1037; Input

description: Library name: BL1037IN

source_name: Metastasis; Lymph node biopsy; Muscle invasive; T3bN0


title: hapo_newborn_cordblood_A0649


title: hapo_newborn_cordblood_A0656


title: BV2-TurboID LPS bulk replicate 1

description:
Library name: Sample 10
/home/ec2-user/21047FL-134-01-10_S10_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1039; Input

description: Library name: BL1039IN

source_name: Primary; Bladder biopsy; Muscle invasive; T3N0


title: Patient BL1052; Input

description: Library name: BL1052IN

source_name: Primary; Cystectomy; Non-muscle invasive; T1N0


title: BV2-TurboID bulk replicate 3

description:
Library name: Sample 9
/home/ec2-user/21047FL-134-01-09_S9_L007_Aligned.sortedByCoord.out.bam


title: 10xMulti_Pomc_3_GEX

description: Library name: Pomc_3_GEX

value: Pomc-Cre; R26LSL-Sun1-sfGFP

value: Ctrl&KO


title: Patient BL1034; Input

description: Library name: BL1034IN

source_name: Primary; Cystectomy; Muscle invasive; T4bN2


title: 10xMulti_Pomc_3_HTO

description: Library name: Pomc_3_HTO

value: Mediobasal Hypothalamus


title: BV2-TurboID bulk replicate 2

description:
Library name: Sample 8
/home/ec2-user/21047FL-134-01-08_S8_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1020; Input

description: Library name: BL1020IN

source_name: Primary; Cystectomy; Muscle invasive; T3aN0


title: Liver - restricted Glucose - uninfected - rep4

city: Frederiksberg

first: Björn

last: Klabunde

address: Dyrlægevej 68

country: Denmark

institute: Copenhagen University

description: Library name: L_897

data_processing:
The annotated gene information of porcine genome was obtained from Ensembl (release 99). The script htseq-count was used to generate a gene-count matrix, followed by analyses of DEGs using DESeq2.
Assembly: Sscrofa11.1
Supplementary files format and content: "Processed data Ketone experiment.xlsx", containing NCBI gene ID, sample ID (see Metadata file) and gene information. Results are depicted as read counts

organism: Sus scrofa

source_name: Liver

extract_protocol:
shock-frozen hepatic tissue was homogenized using gentleMACS™ Tubes (Miltenyi) and extracted using the QIAGEN Rneasy kit
RNA-Seq libraries were constructed using 1000 ng of RNA and the VAHTS mRNA-Seq V3 Library Prep Kit for Illumina (Vazyme). The libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads. Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Bioinformatics).

value: Liver


title: Patient BL1010; Input

description: Library name: BL1010IN

source_name: Primary; Cystectomy; Muscle invasive; T2aN0Mx


title: BV2-TurboID bulk replicate 1

description:
Library name: Sample 7
/home/ec2-user/21047FL-134-01-07_S7_L007_Aligned.sortedByCoord.out.bam


title: Liver - BHB treated - uninfected - rep4

description: Library name: L_896


title: 10xMulti_Pomc_3_ATAC

description: Library name: Pomc_3_ATAC

value: mixed sample


title: hapo_newborn_cordblood_A0636

source_name: newborn cordblood


title: hapo_newborn_cordblood_A0629


title: hapo_newborn_cordblood_A0638


title: Patient BL1009; Input

description: Library name: BL1009IN

source_name: Primary; Cystectomy; Muscle invasive; T2N0Mx


title: BV2 LPS bulk replicate 3

description:
Library name: Sample 6
/home/ec2-user/21047FL-134-01-06_S6_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0621


title: Liver - control - uninfected - rep2

description: Library name: L_895


title: hapo_newborn_cordblood_A0639


title: Patient BL1007; Input

description: Library name: BL1007IN

source_name: Metastasis; Lymph node biopsy; Muscle invasive; T3aN0Mx


title: Liver - BHB treated - infected - rep13

description: Library name: L_894


title: Patient BL1068; H3K4me2 ChIP

description: Library name: BL1068_H3K4me2

source_name: Primary; Bladder resection; Non-muscle invasive; TaN0

value: H3K4me2 antibody, Millipore C07030


title: BV2 LPS bulk replicate 1

description:
Library name: Sample 4
/home/ec2-user/21047FL-134-01-04_S4_L007_Aligned.sortedByCoord.out.bam


title: Liver - BHB treated - infected - rep12

description: Library name: L_893


title: BV2 LPS bulk replicate 2

description:
Library name: Sample 5
/home/ec2-user/21047FL-134-01-05_S5_L007_Aligned.sortedByCoord.out.bam


title: hapo_newborn_cordblood_A0620


title: Patient BL1047; Input

description: Library name: BL1047IN

source_name: Metastasis; Lung metastasis biopsy; Muscle invasive; T4a


title: BV2 bulk replicate 3

description:
Library name: Sample 3
/home/ec2-user/21047FL-134-01-03_S3_L007_Aligned.sortedByCoord.out.bam


title: Liver - restricted Glucose - infected - rep12

description: Library name: L_892


title: BV2 bulk replicate 2

description:
Library name: Sample 2
/home/ec2-user/21047FL-134-01-02_S2_L007_Aligned.sortedByCoord.out.bam


title: Patient BL1058; H3K4me2 ChIP

description: Library name: BL1058_H3K4me2

source_name: Primary; Cystectomy; -; TURBT

value: Primary; Cystectomy; -; TURBT


title: Liver - control - infected - rep13

description: Library name: L_891


title: hapo_newborn_cordblood_A0610

value: cord clood


title: Patient BL1057; H3K4me2 ChIP

description: Library name: BL1057_H3K4me2

value: Primary; Bladder resection; Non-muscle invasive; TaN0


title: Aldh1l1-Cre bulk replicate 1

description:
Library name: Sample 21
/home/ec2-user/21047FL-134-01-28_S1_L007_Aligned.sortedByCoord.out.bam

source_name: cortex

value: cortex

value: male


title: BV2 bulk replicate 1

description:
Library name: Sample 1
/home/ec2-user/21047FL-134-01-01_S1_L007_Aligned.sortedByCoord.out.bam

value: immature microglia

value: female


title: 28-AF-LA_H02_AF_LA

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

hyb_protocol: Array hibridisation was carried out at the QMUL Genome Centre following manufacturer specifications with Infinium MethylationEPIC v2.0 Kit.

scan_protocol: Array scanning was carried out at the QMUL Genome Centre following manufacturer specifications for Infinium MethylationEPIC v2.0 (GPL33022)

data_processing:
Methylation array data was processed to quantify methylation levels for a total of 930,698 CpG sites using the R Bioconductor package meffil (v1.3.6) (Min et al., 2018). Briefly, functional normalisation was applied to array intensity data (“.idat” files) to correct for between-array technical variation. As a quality control, sex of the individuals was properly assigned based on X and Y chromosome probes measurements and multidimensional scaling visualisation displayed clear grouping of anatomical side pairs per individual, confirming the expected inter-individual variability in DNAm signals. Low-quality and sex chromosome probes were removed.
*processed value definition: Methylation status was reported for all measured CpG sites as β-values ranging from 0 to 1 representing the fraction of DNAm signal compared to the total locus signal intensity.

label: biotin (ddCTP and ddGTP) and DNP (ddATP and ddUTP)

source_name: heart left atrium

label_protocol: Bisulfite treatment and subsequent amplification and hybridisation to methylation profiling microarray was performed by the QMUL Genome Centre. The Infinium MethylationEPIC v2.0 kit was used, providing coverage of approximately 930K CpGs, including RefSeq annotated genes, CpG islands and enhancer regions. Even and random distribution of biological groups across two chips of 8 samples each was assigned using the OSAT R Bioconductor package (Yan et al., 2012).

extract_protocol: Genomic DNA was isolated from 16 heart atrial biopsies (AF-LA, n=6; AF-RA, n=5; SR-LA, n=4; SR-RA, n=4) using the DNeasy Blood & Tissue Kit (Qiagen). DNA quality was determined with a NanoDrop Spectrophotometer.

value: heart left atrium

tag: disease state

value: atrial fibrillation


title: Patient BL1056; H3K4me2 ChIP

description: Library name: BL1056_H3K4me2

source_name: Primary; Bladder resection; Muscle invasive; T3bN2


title: Patient BL1063; H3K4me2 ChIP

description: Library name: BL1063_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T2


title: hapo_newborn_cordblood_A0609

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Male

value: newborn

value: whole blood cells


title: Liver - BHB treated - infected - rep11

description: Library name: L_890


title: hapo_newborn_cordblood_A0606


title: Patient BL1055; H3K4me2 ChIP

description: Library name: BL1055_H3K4me2

source_name: Primary; Bladder resection; Muscle invasive; T3aN0


title: Liver - control - infected - rep12

description: Library name: L_889


title: hapo_newborn_cordblood_A0597


title: 28-AF-RA_G02_AF_RA

source_name: heart right atrium

value: heart right atrium


title: Liver - BHB treated - infected - rep10

description: Library name: L_886


title: Liver - restricted Glucose - infected - rep11

description: Library name: L_887


title: Patient BL1054; H3K4me2 ChIP

description: Library name: BL1054_H3K4me2

source_name: Primary; Bladder biopsy; Non-muscle invasive; TaN0


title: Patient BL1053; H3K4me2 ChIP

description: Library name: BL1053_H3K4me2

source_name: Primary; Bladder biopsy; Non-muscle invasive; T1


title: hapo_newborn_cordblood_A0592


title: 45-SR-LA_E02_SR_LA

value: synus rhythm


title: hapo_newborn_cordblood_A0596

value: Female


title: Patient BL1052; H3K4me2 ChIP

description: Library name: BL1052_H3K4me2

source_name: Primary; Cystectomy; Non-muscle invasive; T1N0


title: hapo_newborn_cordblood_A0589


title: 2231-AF-LA_D02_AF_LA


title: 20-SR-LA_C02_SR_LA


title: hapo_newborn_cordblood_A0586


title: Liver - control - infected - rep10

description: Library name: L_880

source_name: Liver

value: Liver


title: Patient BL1050; H3K4me2 ChIP

description: Library name: BL1050_H3K4me2

source_name: Primary; Cystectomy; Non-muscle invasive; T1N0MX

value: H3K4me2 antibody, Millipore C07030


title: 2231-AF-RA_B02_AF_RA


title: Patient BL1049; H3K4me2 ChIP

description: Library name: BL1049_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T4N2


title: Liver - restricted Glucose - infected - rep10

description: Library name: L_882


title: 47-AF-LA_A02_AF_LA


title: Liver - restricted Glucose - uninfected - rep3

description: Library name: L_879


title: hapo_newborn_cordblood_A0585

source_name: newborn cordblood


title: hapo_newborn_cordblood_A0574


title: Patient BL1048; H3K4me2 ChIP

description: Library name: BL1048_H3K4me2

source_name: Primary; Bladder biopsy; Non-muscle invasive; T1aNx


title: Liver - control - infected - rep11

description: Library name: L_884


title: 12b-SR-LA_H01_SR_LA


title: Liver - BHB treated - uninfected - rep3

description: Library name: L_877


title: Patient BL1047; H3K4me2 ChIP

description: Library name: BL1047_H3K4me2

value: Metastasis; Lung metastasis biopsy; Muscle invasive; T4a


title: 45-SR-RA_G01_SR_RA


title: Liver - BHB treated - uninfected - rep2

description: Library name: L_874


title: Liver - restricted Glucose - uninfected - rep2

description: Library name: L_875


title: hapo_newborn_cordblood_A0573

value: cord clood


title: 313-AF-LA_F01_AF_LA


title: hapo_newborn_cordblood_A0569


title: Liver - restricted Glucose - infected - rep9

description: Library name: L_873


title: 18-AF-LA_E01_AF_LA


title: hapo_newborn_cordblood_A0563


title: hapo_newborn_cordblood_A0555


title: Liver - BHB treated - infected - rep9

description: Library name: L_872


title: hapo_newborn_cordblood_A0548


title: Patient BL1044; H3K4me2 ChIP

description: Library name: BL1044_H3K4me2

source_name: Primary; Bladder biopsy; Muscle invasive; T2aN0


title: Patient BL1042; H3K4me2 ChIP

description: Library name: BL1042_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T4aN0MX


title: Patient BL1043; H3K4me2 ChIP

description: Library name: BL1043_H3K4me2

value: Primary; Cystectomy; Muscle invasive; T4aN0MX


title: Liver - BHB treated - infected - rep8

description: Library name: L_869


title: 25-AF-LA_C01_AF_LA


title: hapo_newborn_cordblood_A0613


title: hapo_newborn_cordblood_A0541


title: 47-AF-RA_A01_AF_RA


title: Patient BL1040; H3K4me2 ChIP

description: Library name: BL1040_H3K4me2

source_name: Primary; Bladder biopsy; Muscle invasive; T3aN0Mx


title: 25-AF-RA_B01_AF_RA


title: Liver - restricted Glucose - infected - rep13

description: Library name: L_865


title: Patient BL1039; H3K4me2 ChIP

description: Library name: BL1039_H3K4me2

source_name: Primary; Bladder biopsy; Muscle invasive; T3N0


title: hapo_newborn_cordblood_A0535


title: Patient BL1041; H3K4me2 ChIP

description: Library name: BL1041_H3K4me2

source_name: Primary; Cystectomy; Non-muscle invasive; T1


title: RNA-seq of MFF-1 cells under hypoxic conditions sample 3

city: Zhuhai

first: Mincong

last: Liang

state: Guangdong

address: No. 2 Daxue Road

department: School of Marine Sciences

description: Library name: MFF-DY-3

data_processing:
Raw data were preprocessed and quality-controlled using fastp v0.24.0 with the parameters: “--detect_adapter_for_pe --dont_eval_duplication --cut_front --cut_tail --cut_right --cut_front_window_size 1 --cut_front_mean_quality 5 --cut_tail_window_size 1 --cut_tail_mean_quality 5 --cut_right_window_size 5 --cut_right_mean_quality 20 --length_required 50 --qualified_quality_phred 20 --unqualified_percent_limit 30”. The resulting clean data were aligned to the Siniperca chuatsi reference genome  using HISAT2 v2.2.1. Gene expression levels were then quantified using SAMtools v1.23 and StringTie v3.0.3.
Assembly: GCA_020085105.1
Supplementary files format and content: Tab-delimited text files containing raw gene counts and transcript counts for all samples, respectively.

organism: Siniperca chuatsi

source_name: MFF-1 cell line

growth_protocol: MFF-1 cells were cultured in 6-well plates in DMEM supplemented with 10% FBS until reaching 90–100% confluence.

extract_protocol:
After 72 h of treatment, the medium was removed, cells were washed twice with sterile PBS, and total RNA was collected following RNAiso Plus lysis.
After total RNA extraction, sequencing libraries were prepared according to the manufacturer’s instructions.

treatment_protocol: Cells were incubated for 72 hours in a humidified atmosphere maintained at either 21% O2 (normoxia control) or 3% O2 (hypoxia treatment).

value: MFF-1 cell line

value: Epithelial cells

value: Hypoxic conditions (3% O2)


title: Liver - restricted Glucose - infected - rep7

description: Library name: L_863


title: Liver - control - infected - rep9

description: Library name: L_864


title: hapo_newborn_cordblood_A0534


title: hapo_newborn_cordblood_A0539


title: Patient BL1038; H3K4me2 ChIP

description: Library name: BL1038_H3K4me2

source_name: Primary; Cystectomy; Non-muscle invasive; pTisN0


title: Liver - BHB treated - infected - rep7

description: Library name: L_862


title: RNA-seq of MFF-1 cells under hypoxic conditions sample 2

description: Library name: MFF-DY-2


title: hapo_newborn_cordblood_A0524


title: Patient BL1037; H3K4me2 ChIP

description: Library name: BL1037_H3K4me2

source_name: Metastasis; Lymph node biopsy; Muscle invasive; T3bN0


title: Liver - restricted Glucose - infected - rep6

description: Library name: L_861


title: RNA-seq of MFF-1 cells under normoxic conditions sample 3

description: Library name: MFF-CY-3

value: Normoxic conditions (21% O2)


title: Patient BL1034; H3K4me2 ChIP

description: Library name: BL1034_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T4bN2


title: Liver - BHB treated - infected - rep6

description: Library name: L_860


title: hapo_newborn_cordblood_A0510


title: hapo_newborn_cordblood_A0494


title: Liver - control - infected - rep8

description: Library name: L_858


title: RNA-seq of MFF-1 cells under normoxic conditions sample 1

description: Library name: MFF-CY-1


title: Liver - control - infected - rep7

description: Library name: L_856


title: Patient BL1010; H3K4me2 ChIP

description: Library name: BL1010_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T2aN0Mx


title: Patient BL1020; H3K4me2 ChIP

description: Library name: BL1020_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T3aN0


title: hapo_newborn_cordblood_A0493


title: hapo_newborn_cordblood_A0492


title: S. pombe, 30%wt+70%ΔmiaA, YES, 30°C, rep2

city: Berlin

first: Yu

last: Sun

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

description: Library name: S. pombe_30pwt_rep2

data_processing:
Read alignment was carried out using Bowtie2 with parameters -N 1 -L 6 to allow up to one mismatch per 6 nt seed. To assess reverse transcription-derived misincorporation patterns, the misincorporation rate at each nucleotide position was quantified using CoverageAnalyzer.
Assembly: Reference curation: The reference for S. pombe tRNATyr contains sequences of all unique mature tRNATyr and intron-containing tRNATyr  from GtRNAdb, and both 5’ and 3’ primer sequences were added. For E. coli, sequences of all unique tRNAs were from GtRNAdb, and primer sequences were added.
Supplementary files format and content: The processed data includes the following information: position, refbase, coverage, mm_ratio, a_mism, g_mism, t_mism, c_mism, and arrest_rate.

molecule: other

organism: Schizosaccharomyces pombe

source_name: strain: FY7385, FY7385 tit1DEL

growth_protocol: The S. pombe strains were grown in YES medium with or without 0.1 μM of queuine at 30°C and 140 rpm. The E. coli strains were grown in M9 medium at 37°C or 42°C and 180 rpm.

extract_protocol:
Extraction of small RNAs from cells: Small RNAs were extracted according to the manufacturer’s protocol (PureLink™ miRNA Isolation Kit (Invitrogen)) with some adjustments. Briefly, cells were suspended in 1 ml Trizol (Ambion). The samples were vortexed for 2 min after adding 0.2 ml chloroform and glass beads, and then were centrifuged at 16 000 rcf, 4°C for 15 min. After adding 215 µl ethanol to the upper phase, the samples were transferred to a spin cartridge and centrifuged at 12 000 rcf for 1 min. 700 µl of ethanol was added to the flow-through, and the samples were transferred to a new spin cartridge followed by centrifugation at 12 000 rcf for 1 min. After washing the cartridge with wash buffer, small RNAs were eluted with 50 µl of DEPC-treated water.
For ms2i6A modification detection, in brief, 500 ng of deacylated small RNAs were hybridized with 1 μl of 10 μM tRNATyr stem-loop primer using the following thermocycling program: 95°C for 2 min, 65°C for 30 s, followed by a gradual ramp to 4°C at 5°C per 30 s. After incubation on ice for 1 min, reverse transcription was performed in 20 μl reactions containing 100 μM dA/C/GTP, 12.5 μM dTTP, 100 nM RT-KTq I614Y enzyme, and RT buffer [50 mM Tris-HCl (pH 9.2), 16 mM (NH₄)₂SO₄, 2.5 mM MgCl₂, 0.1% Tween-20], and incubation at 55°C for 1 hour. Following reverse transcription, 5 μl of cDNA was used for PCR amplification in a 50 μl reaction containing 0.5 µM forward and reverse primers, 250 μM dNTPs, 2 mM MgCl2, 1 x Taq buffer with KCl, and 1.25 U Taq polymerase (Thermo Fisher). The thermal cycling conditions were: 96°C for 3 min; 40 cycles of 96°C for 30 s, 50°C for 45 s, and 72°C for 45 s; followed by a final extension at 72°C for 5 min. 3′-end primers included sample-specific barcodes for multiplexing. PCR products were resolved on a 2% agarose gel and purified using the QIAquick Gel Extraction Kit (Qiagen). The purified PCR products were pooled and submitted for Next-generation sequencing. For i6A modification detection, deacylated small RNAs were further treated with 0.5 M I2 for 20 min on ice. Following iodine treatment, saturated Na2S2O3 was added to the reaction mixture until the solution became colorless. Subsequently, saturated Na2CO3 was added dropwise until effervescence ceased. Upon completion of the reaction, small RNAs were purified using the RNA Clean & Concentrator Kit (ZYMO Research) according to the manufacturer’s instructions. Iodine-treated samples were then used for sequencing library preparation following the same protocol as described above for ms2i6A detection.

value: strain:FY7385, FY7385 tit1DEL

value: grown in YES medium at 30°C


title: RNA-seq of MFF-1 cells under normoxic conditions sample 2

description: Library name: MFF-CY-2


title: hapo_newborn_cordblood_A0516

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)


title: Patient BL1007; H3K4me2 ChIP

description: Library name: BL1007_H3K4me2

source_name: Metastasis; Lymph node biopsy; Muscle invasive; T3aN0Mx


title: S. pombe, 30%wt+70%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_30pwt_rep1


title: Liver - control - infected - rep5

description: Library name: L_853

source_name: Liver


title: Patient BL1009; H3K4me2 ChIP

description: Library name: BL1009_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T2N0Mx


title: Patient BL1068; H3K27ac ChIP

description: Library name: BL1068_H3K27ac

source_name: Primary; Bladder resection; Non-muscle invasive; TaN0

value: H3K27ac antibody, Diagenode C15410206


title: hapo_newborn_cordblood_A0489

source_name: newborn cordblood

value: newborn


title: S. pombe, 40%wt+60%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_40pwt_rep2


title: hapo_newborn_cordblood_A0481

value: Male

value: whole blood cells


title: Liver - BHB treated - uninfected - rep1

description: Library name: L_851


title: hapo_newborn_cordblood_A0474


title: Patient BL1063; H3K27ac ChIP

description: Library name: BL1063_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T2


title: Liver - control - uninfected - rep1

description: Library name: L_849


title: Liver - restricted Glucose - uninfected - rep1

description: Library name: L_848


title: hapo_newborn_cordblood_A0464


title: S. pombe, 40%wt+60%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_40pwt_rep1


title: hapo_newborn_cordblood_A0453


title: S. pombe, 50%wt+50%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_50pwt_rep2


title: Patient BL1056; H3K27ac ChIP

description: Library name: BL1056_H3K27ac

source_name: Primary; Bladder resection; Muscle invasive; T3bN2


title: S. pombe, 50%wt+50%ΔmiaA, YES, 30°C, rep3

description: Library name: S. pombe_50pwt_rep3


title: Liver - restricted Glucose - infected - rep5

description: Library name: L_846


title: Patient BL1057; H3K27ac ChIP

description: Library name: BL1057_H3K27ac

value: Primary; Bladder resection; Non-muscle invasive; TaN0


title: S. pombe, 50%wt+50%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_50pwt_rep1


title: Liver - BHB treated - infected - rep5

description: Library name: L_845


title: hapo_newborn_cordblood_A0442

value: Female


title: Liver - restricted Glucose - infected - rep8

description: Library name: L_871

value: Liver


title: Patient BL1055; H3K27ac ChIP

description: Library name: BL1055_H3K27ac

source_name: Primary; Bladder resection; Muscle invasive; T3aN0


title: S. pombe, 60%wt+40%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_60pwt_rep2


title: Patient BL1054; H3K27ac ChIP

description: Library name: BL1054_H3K27ac

source_name: Primary; Bladder biopsy; Non-muscle invasive; TaN0


title: RNA-seq of MFF-1 cells under hypoxic conditions sample 1

description: Library name: MFF-DY-1


title: Liver - restricted Glucose - infected - rep4

description: Library name: L_843


title: S. pombe, 60%wt+40%ΔmiaA, YES, 30°C, rep3

description: Library name: S. pombe_60pwt_rep3


title: Patient BL1058; H3K27ac ChIP

description: Library name: BL1058_H3K27ac

source_name: Primary; Cystectomy; -; TURBT

value: Primary; Cystectomy; -; TURBT


title: hapo_newborn_cordblood_A0428


title: Patient BL1053; H3K27ac ChIP

description: Library name: BL1053_H3K27ac

source_name: Primary; Bladder biopsy; Non-muscle invasive; T1


title: hapo_newborn_cordblood_A0426


title: S. pombe, 60%wt+40%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_60pwt_rep1


title: Liver - BHB treated - infected - rep4

description: Library name: L_842


title: Patient BL1052; H3K27ac ChIP

description: Library name: BL1052_H3K27ac

source_name: Primary; Cystectomy; Non-muscle invasive; T1N0


title: Liver - restricted Glucose - infected - rep3

description: Library name: L_838


title: S. pombe, 70%wt+30%ΔmiaA, YES, 30°C, rep3

description: Library name: S. pombe_70pwt_rep3


title: hapo_newborn_cordblood_A0419


title: Liver - control - infected - rep4

description: Library name: L_844


title: Patient BL1050; H3K27ac ChIP

description: Library name: BL1050_H3K27ac

source_name: Primary; Cystectomy; Non-muscle invasive; T1N0MX


title: hapo_newborn_cordblood_A0416


title: S. pombe, 70%wt+30%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_70pwt_rep2


title: Patient BL1049; H3K27ac ChIP

description: Library name: BL1049_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T4N2


title: S. pombe, 70%wt+30%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_70pwt_rep1


title: Liver - control - infected - rep3

description: Library name: L_834


title: Patient BL1048; H3K27ac ChIP

description: Library name: BL1048_H3K27ac

source_name: Primary; Bladder biopsy; Non-muscle invasive; T1aNx


title: Liver - BHB treated - infected - rep3

description: Library name: L_837


title: hapo_newborn_cordblood_A0412


title: Liver - restricted Glucose - infected - rep2

description: Library name: L_833


title: S. pombe, 80%wt+20%ΔmiaA, YES, 30°C, rep3

description: Library name: S. pombe_80pwt_rep3


title: Patient BL1047; H3K27ac ChIP

description: Library name: BL1047_H3K27ac

source_name: Metastasis; Lung metastasis biopsy; Muscle invasive; T4a


title: S. pombe, 80%wt+20%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_80pwt_rep2

source_name: strain: FY7385, FY7385 tit1DEL


title: Liver - BHB treated - infected - rep2

description: Library name: L_832


title: hapo_newborn_cordblood_A0402


title: Liver - control - infected - rep2

description: Library name: L_830


title: Patient BL1046; H3K27ac ChIP

description: Library name: BL1046_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T3bN2


title: S. pombe, 85%wt+15%ΔmiaA, YES, 30°C, rep3

description: Library name: S. pombe_85pwt_rep3


title: S. pombe, 80%wt+20%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_80pwt_rep1


title: hapo_newborn_cordblood_A0414


title: Patient BL1045; H3K27ac ChIP

description: Library name: BL1045_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T4aN1


title: hapo_newborn_cordblood_A0401


title: Liver - BHB treated - infected - rep1

description: Library name: L_828

source_name: Liver


title: Patient BL1044; H3K27ac ChIP

description: Library name: BL1044_H3K27ac

source_name: Primary; Bladder biopsy; Muscle invasive; T2aN0


title: S. pombe, 85%wt+15%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_85pwt_rep2


title: Patient BL1043; H3K27ac ChIP

description: Library name: BL1043_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T4aN0MX


title: hapo_newborn_cordblood_A0393

source_name: newborn cordblood


title: Liver - control - infected - rep1

description: Library name: L_826


title: hapo_newborn_cordblood_A0409