title: D. melanogaster vigEP812 -/- RhiGFP, testis

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

description: rRNA-depleted total RNA

data_processing:
To evaluate the expression level of Stellate and Su(Ste) loci RNA-seq libraries were mapped to consensus sequences using bowtie version 1.1.0 (-l 150). Mapped reads were counted and normalized to the library depth.
Assembly: Ste and Su(Ste) consensuses, dm6
Supplementary files format and content: Xlsx file with counts reads mapped to Ste and Su(Ste) consensuses

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
Total RNA for RNA-seq libraries were isolated from vasEP812-/-, vasEP812+/-, and vasEP812-/-; rhi-GFP D. melanogaster gonads with ExtractRNA (Evrogen). RNA was depleted with Dynabeads MyOne Streptavidin C1 (Thermo Scientific Fisher) conjugated with synthesized anti-rDNA oligos.
RNA-seq libraries were generated using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760, NEB) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, NEB #E7335, and Set 2, NEB #E7500) according to the manufacturer's instructions and sequenced on the Illumina NovaSeq 6000 SP platform (100 bp runs).

value: testis


title: cuttagforHK16instbd4_oa10

status: Public on Aug 02 2024

type: SRA

city: BEIJING

first: xin

last: yu

state: Beijing

address: DATUN ROAD

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: genomic

data_processing:
use 'bedtools genomecov' scale bed file to normalize, and get scaled bedgraph file
use 'bedgraphtobbigwig'  transfer bdg file to bw file
use 'wigglettols' merge repeat bw file
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: human trophoblast stem cell

extract_protocol:
Briefly, cells were extracted from hTSCs, STBs in D1/D4 and STBs in D4 with acetate or oxamate by TrypLE. Each sample was subjected to two experimental replicates for different antibodies. The CUT&Tag reagents were from the CUT&Tag kit provided by Vazyme (https://www.vazyme.com/).
DNA library was amplified according to the genomic content and sequenced on the Illumina NovaSeq platform.

tag: cell type

value: TS cells culture in STB medium for syncytialization 4 day and treated with oxamate and acetate

tag: cell line

value: human trophoblast stem cell

tag: antibody


title: D. melanogaster vigEP812 -/-, testis

description: rRNA-depleted total RNA

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: cuttagforHK16instbd4_ox

value: TS cells culture in STB medium for syncytialization 4 day and treated with oxamate


title: Denuded, 22h, rep3

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description:
60
sample_60

data_processing:
Raw read QC was done using FastQC (v0.11.9)
UMI removal was done using UMI-tools (v1.1.2)
Deduplication was done in python (reads having the same UMI and miRNA sequence were grouped and a single representative was kept)
miRNA identification, novel candidate prediction and quantification was done using the miRPro (1.1.4) pipeline and miRBase (v22.1)
Assembly: Bos taurus ARS-UCD1.2 (ENSEMBL release 105)
Supplementary files format and content: counts_known_mature.tsv: tab separated miRNA expression counts for all samples
Supplementary files format and content: counts_novel_mature.tsv: tab separated novel miRNA candidate expression counts for all samples
Supplementary files format and content: novel_mature.fa: name and sequence of predicted novel mature miRNA candidates in fasta format

organism: Bos taurus

source_name: oocyte

extract_protocol:
Total RNA was extracted from oocytes using the miRNeasy Mini kit (Qiagen). To ensure the samples are DNA free, they were treated with RNase-Free DNase Set (Qiagen)
QIAseq miRNA Library Kit

value: oocyte

tag: treatment

value: Denuded

tag: maturation time


title: Coculture, 22h, rep3

description:
59
sample_59

value: Coculture


title: cuttagforHK16instbd4

value: TS cells culture in STB medium for syncytialization 4 day


title: CTRLsiKDM3B_H3K9me3_rep1

city: Boston

first: Kashish

last: Chetal

state: MA

address: 55 Fruit St

department: Molecular biology

country: USA

institute: MGH

description: Control siKDM3B H3K9me3 replicate 1

data_processing:
Sequencing reads were aligned against the hg19 reference genome using BWA (PMID: 20080505). Alignments were filtered for uniquely mapped reads and duplicates were removed.
ChIP over Input ratio coverage tracks were generated using deepTools (PMID: 27079975).
Peaks were called using HOMER (PMID: 20513432) with default parameters.

source_name: RPE

extract_protocol:
Cells were fixed with 1% formaldehyde for 13 minutes. After quenching and cell lysis, chromatin was sonicated using a Q800R3 sonicator (QSonica).
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Library Preparation Kit Set A and B with associated index barcode adapters. 1 ng or 30µL of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were cleaned up using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity D1000 DNA Kit.

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown


library_source: other

data_processing:
To evaluate the piRNA level and analyze ping-pong signature of piRNA for Stellate and Su(Ste) filtered small RNA fraction were mapped to consensus sequences using bowtie (-l 30). Mapped reads were normalized to the microRNA level.
Assembly: Ste and Su(Ste) consensuses, dm6
Supplementary files format and content: Xlsx file with counts reads mapped to Ste and Su(Ste) consensuses

molecule: other

extract_protocol:
Small RNAs of 18–29 nt in size from gonads of D. melanogaster vasEP812-/-, vasEP812+/-, vasEP812-/-; rhi-GFP, vasEP812/vasD1, mix of vasEP812/+ with vasD1/+, and vasEP812/vasD1; rhi-GFP were isolated with TRIzol Reagent (Invitrogen). Small RNA fraction (19–29 nt) was purified by 15% polyacrylamide gel
libraries were prepared using NEBNext Multiplex Small RNA Sample Prep Set for Illumina (E7300S) and sequenced on NovaSeq 6000 in 50 bp single-end mode.


title: cuttagforHK16instbd1

value: TS cells culture in STB medium for syncytialization one day


title: D. melanogaster vigEP812 -/-, testis


title: CBX, 22h, rep3

description:
57
sample_57

value: CBX


title: Control, 22h, rep3

description:
55
sample_55

value: control


title: D. melanogaster vigEP812 +/-, testis


title: cuttagforH3K27instbd4_oa10

description: bigwig file

data_processing:
use 'bedtools genomecov' scale bed file to normalize, and get scaled bedgraph file
use 'bedgraphtobbigwig'  transfer bdg file to bw file
use 'wigglettols' merge repeat bw file
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: Cut & Tag

source_name: placental trophoblast stem cells

extract_protocol: CUT&Tag seq of H3K27ac in TS, STB-D1, STB-D4, STB-D4 treated with oxamate, STB-D4 treated with oxamate and acetate

tag: agent

value: oxamate and acetate

value: placental trophoblast stem cells


title: cuttagforHK16ints

value: trophoblast stem cells


title: Denuded, 6h, rep3

description:
54
sample_54


title: D. melanogaster vigEP812 +/-, testis

description: rRNA-depleted total RNA

value: testis


title: cuttagforH3K27instbd4

description: bigwig file

value: oxamate


title: D. melanogaster vigEP812/vasD1 +/-, testis


title: Control, 6h, rep3

description:
49
sample_49


title: Coculture, 6h, rep3

description:
53
sample_53


title: cuttagforH3K27instbd4_ox

description: bigwig file


title: cuttagforH3K27instbd1

description: bigwig file


title: CBX, 6h, rep3

description:
51
sample_51


title: D. melanogaster vigEP812/vasD1 -/-, testis


title: D. melanogaster vigEP812/vasD1 -/- RhiGFP, testis


title: U373MG, non-infection, rep2

city: Seoul

first: Dohoon

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

department: Bioinformatics Institute

country: South Korea

institute: Seoul National University

data_processing:
ATAC-seq reads were preprocessed with Trim Galore! v0.6.7 and aligned to hg38 reference genome with BWA v0.7.17-r1188.
Alignment sorting and indexing were done by Sambamba v0.8.1.
Genomewide read depth signals (in RPKM) were computed by Deeptools v3.5.1. To avoid anomalous signals, we excluded ENCODE blacklist regions from the analysis.
MACS2 v2.2.7.1 was used to filter duplicate reads and call ATAC peaks.
Assembly: hg38
Supplementary files format and content: bigWig files for ATAC read depths (in RPKM).
Supplementary files format and content: BED files for ATAC-seq peak.

growth_protocol: U373MG cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; HyClone) with 10% fetal bovine serum (FBS; HyClone) and 1% (v/v) GlutaMAX-I (Gibco). Cells were incubated at 37°C under 5% CO2 atmosphere.

extract_protocol:
DNA was extracted using a Qiagen MinElute PCR purification Kit.
Transposed DNA fragments were amplified using Nextera DNA Flex kit.

treatment_protocol: Cells were lysed using cold lysis buffer. The nuclei concentration was determined using Countess II Automated Cell Counter and the nuclei morphology was examined using microscopy. Immediately after lysis, transposition reaction was performed. Nuclei of 50,000 cells were resuspended in the transposition reaction mix and were incubated at 37°C for 30min.

value: Glioblastoma

value: Non-infected


title: cuttagforH3K27ints

description: bigwig file


title: U373MG, non-infection, rep1


title: cuttagforH3K18instbd4_oa10

description:
cuttag_H3K18_stbdoa10_1&2
bigwig file

data_processing:
*library strategy: CUT&TAG
use 'bedtools genomecov' scale bed file to normalize, and get scaled bedgraph file
use 'bedgraphtobbigwig'  transfer bdg file to bw file
use 'wigglettols' merge repeat bw file
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol: NOT PROVIDED; REQUESTED

value: human trophoblast stem cell


title: Coculture, 1h, rep3

description:
47
sample_47

value: oocyte


title: U373MG, HCMV infected, rep2

value: HCMV infected


title: Denuded, 1h, rep3

description:
48
sample_48

value: Denuded


title: CBX, 1h, rep3

description:
45
sample_45


title: U373MG, HCMV infected, rep1


title: cuttagforH3K18instbd4

description:
cuttag_H3K18_stbd4_1&2
bigwig file


title: cuttagforH3K18instbd4_ox

description:
cuttag_H3K18_stbdox_1&2
bigwig file


title: Control, 0h, rep3

description:
41
sample_41


title: cuttagforH3K18ints

description:
cuttag_H3K18_ts_1&2
bigwig file

value: ts


title: Zona Incerta single nuclei, rep 2

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

library_source: transcriptomic single cell

data_processing:
The demultiplexing and quantification was performed with Cell Ranger v3.0.2. A modified reference with introns included was used, and the expected number of cells was set according to expectation.
Assembly: mm10
Supplementary files format and content: The processed data is in the form of gzipped MM matrices with expression (UMI count) matrices consistant with Cell Ranger filtered counts output

molecule: nuclear RNA

organism: Mus musculus

source_name: zona Incerta

growth_protocol: The 3 adult (8-12 week old) mice included in this snRNA-seq study were maintained on a C57Bl/6J genetic background, had ad libitum access to food and water, and were housed under a standard 12:12 hour light:dark cycle (lights on at 07:00, lights off at 19:00).

extract_protocol:
Mice were deeply anesthetized during the light phase of the cycle with saturated isofl-rane vapor and then rapidly decapitated. Each head was submerged in ice cold high sucrose, cutting artificial cerebrospinal fluid (ACSF; 194mM Sucrose, 30mM NaCl, 4.5mM KCl, 1.2mM NaH2PO4, 26 mM NaHCO3, 10mM D-(+)-Glucose, 8mM MgSO4, 0.2mM CaCl; 360 mOsm) saturated with 95% O2 and 5% CO2 and incubated for 1 minute prior to brain dissection and tis-sue slice preparation. 250µm sagittal slices spanning the mediolateral extent of the zona incerta (ZI) were prepared on a vibratome (Leica VT1200S) and the ZI was micro-dissected under ste-reoscopic guidance with the slices submerged in the same ice-cold high sucrose ACSF. Reflected light helped to identify anatomical landmarks (e.g. medial lemniscus, cerebral peduncle) that partially demarcated the boundaries of the ZI. The dissected tissue was then immediately submerged in room temperature RNAlater solution (Thermo Fisher Scientific, AM7020), before it was transferred to 4˚C overnight, and then frozen at -80˚C until further processing. Nuclei were isolated from RNAlater preserved tissues using a previously published method (Habib et al., 2017), except that the final suspension buffer was replaced with a blocking buffer consisting of 1x PBS, 0.5% BSA (Sigma, Cat# B8667-5ML) and 0.2 U/µl RNase inhibitor (Clontech, Cat #2313A) for the neuronal nuclei enrichment process described as follows. The nuclear pellet was resuspended in 600 µl blocking buffer and incubated on ice for 15 minutes followed by add-ing 1.2 µl Anti-NeuN Antibody (clone A60, Alexa Fluor®488 conjugated, EMD Millipore, Cat# MAB377X) and incubation on ice for another 15 minutes. The nuclei suspension was spun down at 500g and 4°C for 5 minutes followed by supernatant removal. The nuclear pellet was resus-pended in 500 µl resuspension buffer consisting of 1x PBS, 1% BSA (Sigma, Cat# B8667-5ML) and 0.2 U/µl RNase inhibitor (Clontech, Cat #2313A) followed by filtration through a 20 µm filter (Sysmex, Cat# 04-004-2325. 1 µl of Vybrant DyeCycle Violet nuclei stain (Invitrogen, Cat# V35003) was added before a SH800 cell sorter (SONY Biotechnology) for FANS by gating on forward and side scatter plot, and both Violet+ NeuN+ to collect the neuronal nuclei population.
Nuclei from each tissue sample were loaded (the number of nuclei per sample depended on the sorting yields) onto each channel of the 10x Chromium Chip B (10x Genomics, 1000073) followed by construction of  snRNA-seq libraries with the Chromium Single Cell 3' GEM, Library & Gel Bead v3 Kit (10x Genomics, 1000075) following vendor protocols. The final libraries were pooled and sequenced with a NextSeq500 75 cycle flow cell (Illumina, 20024906) with read length as 28 bases for read1, 55 bases for read2 and 8 bases for index1.
snRNA-seq

value: zona Incerta

value: Neuron

tag: genotype

value: Wild type


title: Zona Incerta single nuclei, rep 3


title: Denuded, 22h, rep2

description:
40
sample_40


title: cuttagforh3k9instbd4_oa10

description:
cuttag_h3k9_stbdoa10_1&2
bigwig file


title: Zona Incerta single nuclei, rep 1


title: Control, 1h, rep3

description:
43
sample_43


title: sgHerc1_Clone-E5-vehicle-3

city: Montreal

first: François

middle: Émile

last: Mercier

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Medicine

country: Canada

institute: McGIll University

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M25
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M25 transcript annotations
Assembly: GRCm38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

molecule: polyA RNA

source_name: MLL/AF9 Cas9-GFP (MA) lineestablished by sorting multipotent progenitors (Lineage-c-KithighSca-1-; LSK) from a male Cas9-GFP+/- donor with a MSCV-MLL/AF9-IRES-GFP construct

growth_protocol: RPMI1640 supplemented with 10% fetal bovine serum (FBS; Gibco), 100 I.U./ml penicillin, 100 mg/ml streptomycin (Gibco), 10 ng/ml recombinant mouse SCF (rmSCF), 6 ng/ml recombinant mouse interleukin 3 (rmIL-3)

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: MLL/AF9 cells were treated with either Cytarabine (200nM) or H20 for six hours. Cytarabine (U-19920A) Catalog No.S1648 (Selleckchem) and cells were subsequently collected in TRIzol (Invitrogen). Experiment was performed in biological replicates (N=3).

value: murine acute myeloid leukemia

value: C57BL/6J x 129 hybrid

value: H2O vehicle control


title: cuttagforH3K18instbd1

description:
cuttag_H3K18_stbd1_1&2
bigwig file


title: cuttagforh3k9instbd4_ox

description:
cuttag_h3k9_stbdox_1&2
bigwig file


title: CBX, 22h, rep2

description:
37
sample_37

value: CBX


title: cuttagforh3k9instbd4

description:
cuttag_h3k9_stbd4_1&2
bigwig file


title: sgHerc1_Clone-E5-vehicle-2

value: MLL/AF9 Cas9-GFP (MA) lineestablished by sorting multipotent progenitors (Lineage-c-KithighSca-1-; LSK) from a male Cas9-GFP+/- donor with a MSCV-MLL/AF9-IRES-GFP construct


title: Coculture, 22h, rep2

description:
39
sample_39

value: Coculture


title: Control, 22h, rep2

description:
35
sample_35

value: control


title: Exp_05_CD3

type: genomic

city: Linköping

first: Jyotirmoy

last: Das

address: Sandbäcksgatan 7

department: Medical Microbiology

country: Sweden

institute: Linkoping University

description: Household contact

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: GenomeStudio (version 1.8) Methylation module to detect cytosine methylation at single-base resolution.

label: Cy5 and Cy3

source_name: genomic DNA was isolated from alveolar lymphocyte cells

label_protocol: Standard Illumina protocol

extract_protocol: DNA from HLA-DR, CD3 and PBMC cells was extracted using AllPrep DNA/RNA Mini Kit from Qiagen, Germany.

tag: sample type

value: Sputum


title: sgHerc1_Clone-E5-vehicle-1


title: cuttagforh3k9instbd1

description:
cuttag_h3k9_stbd1_1&2
bigwig file


title: cuttagforh3k9ints

description:
cuttag_h3k9_ts_1&2
bigwig file


title: Coculture, 6h, rep2

description:
33
sample_33


title: Denuded, 6h, rep2

description:
34
sample_34


title: Exp_05_HLA-DR

description: Household contact

source_name: genomic DNA was isolated from alveolar macrophages cells


title: sgHerc1_Clone-E5-drug_6h-2

value: 200 nM cytarabine x 6 hours


title: sgHerc1_Clone-E5-drug_6h-3


title: WD39 iPSC-derived astrocytes, ropinirole hydrochloride 3

city: Kanagawa

first: Satoru

last: Morimoto

address: 3－25－10, Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Keio Regenerative Medicine Research Center (KRM)

country: Japan

institute: Keio University

description: SMART-seq

data_processing:
Quality Control of the sequences was performed by fastp (version 0.23.2, all arguments set to default).
Read counts were calculated by salmon (version 1.7.0, all arguments set to default), and the read count data outputs by salmon were processed by tximport (version 1.22.0).

source_name: WD39; CVCL_Y528

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen). 0.2 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: WD39; CVCL_Y528

value: iPSC-derived astrocytes

value: WT

value: ropinirole hydrochloride


title: CBX, 6h, rep2

description:
31
sample_31

value: oocyte


title: Exp_04_CD3

description: Household contact


title: WD39 iPSC-derived astrocytes, ropinirole hydrochloride 2

description: SMART-seq


title: sgHerc1_Clone-E5-drug_6h-1


title: WD39 iPSC-derived astrocytes, ropinirole hydrochloride 1

description: SMART-seq


title: sgCtrl-vehicle-3


title: Denuded, 1h, rep2

description:
28
sample_28

value: Denuded


title: Pat_03_CD3

description: Patient


title: Pat_02_HLA-DR

description: Patient


title: sgCtrl-vehicle-2


title: WD39 iPSC-derived astrocytes, non 3

description: SMART-seq

value: non


title: WD39 iPSC-derived astrocytes, non 2

description: SMART-seq


title: Pat_02_CD3

description: Patient


title: Pat_03_HLA-DR

description: Patient


title: Con_06_HLA-DR

description: Control

data_processing:
GenomeStudio (version 1.8) Methylation module to detect cytosine methylation at single-base resolution.
Unmethylated and methylated signal intensities


title: Con_06_CD3

description: Control


title: Con_04_PBMC

description: Control

source_name: genomic DNA was isolated from PBMC cells

value: Blood


title: Con_05_PBMC

description: Control


title: WD39 iPSC-derived astrocytes, non 1

description: SMART-seq


title: Control, 1h, rep2

description:
23
sample_23


title: Con_05_CD3

description: Control


title: Con_06_PBMC

description: Control


title: sgCtrl-drug_6h-2

value: murine acute myeloid leukemia


title: Con_05_HLA-DR

description: Control


title: shACSL6_2

city: Guangzhou

first: Ziyang

last: Wang

state: Guangdong

address: 58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MHCC97H cells were grown in DMEM supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

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

treatment_protocol: MHCC97H cells were infected with shNT or ACSL6 knockdown lentiviruses for 48 h, and then screened by puromycin for 3 days.

value: Human liver cancer cells

value: ACSL6 knockdown

value: infected with shACSL6


title: CBX, 1h, rep2

description:
25
sample_25

value: CBX


title: Control, 0h, rep2

description:
21
sample_21


title: sgCtrl-vehicle-1

value: MLL/AF9 Cas9-GFP (MA) lineestablished by sorting multipotent progenitors (Lineage-c-KithighSca-1-; LSK) from a male Cas9-GFP+/- donor with a MSCV-MLL/AF9-IRES-GFP construct

value: C57BL/6J x 129 hybrid

value: H2O vehicle control


title: sgCtrl-drug_6h-1

value: 200 nM cytarabine x 6 hours


title: sgCtrl-drug_6h-3


title: shACSL6_1


title: Denuded, 22h, rep1

description:
20
sample_20


title: shNT_2

value: Control

value: infected with shNT


title: NASH Liver, CDDO-Me, rep 4

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.12.0.3).
The 3' end of the sequenced read was trimmed by one nucleotide. Reads with more than 2 ambiguous nucleotides and reads with quality scores less than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.12.0.3).
Trimmed sequence reads were mapped to GRCm38 release-95 using CLC genomics workbench with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.12.0.3).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: Liver

extract_protocol:
Total RNA was isolated from the livers using the RNeasy Mini Kit (Qiagen). Polyadenylated mRNA was purified using oligo dT beads included in the NEBNext Poly (A) mRNA Magnet Isolation Module (New England Biolabs, NEB). Purified mRNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences included in NEBNext Multiplex Oligos for Illumina were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Bioanalyzer. The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NextSeq DNA sequencer with 75 bp paired-end cycle sequencing kit (Illumina).

value: Liver

tag: disease state

value: NASH (CDAHFD-treated)

tag: strain

value: WT

value: CDDO-Me 10 mg/kg


title: NASH Liver, CDDO-Me, rep 3


title: Coculture, 22h, rep1

description:
19
sample_19

value: oocyte

value: Coculture


title: KPNA2_IP_2

city: Lanzhou

first: Yuping

address: the first hospital of lanzhou university, Lanzhou, Gansu

description: KPNA2-binding peaks and motifs

data_processing:
After reads were aligned onto the genome with TopHat 2, only uniquely mapped reads were used for the following analysis
“ABLIRC” strategy was used to identify the binding regions of KPNA2 on the genome
Reads with at least 1 bp overlap were clustered as peaks. For each gene, computational simulation was used to randomly generate reads with the same number and lengths as reads in peaks. The outputting reads were further mapped to the same genes to generate random max peak height from overlapping reads.
The whole process was repeated 500 times. All the observed peaks with heights higher than those of random max peaks (p-value < 0.05) were selected. The IP and input samples were analyzed by the simulation independently, and the IP peaks that have overlapped with Input peaks were removed.
The target genes of IP were finally determined by the peaks and the binding motifs of IP protein were called by HOMER software
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

source_name: AGS

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from KPNA2-RNA complexes and another for the western blotting assay for KPNA2 immunoprecipitation.The KPNA2-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

value: AGS

value: epithelial cell


title: shNT_1

value: Human liver cancer cells


title: CBX, 22h, rep1

description:
17
sample_17


title: NASH Liver, CDDO-Me, rep 2


title: Control, 6h, rep2

description:
29
sample_29

value: control


title: NASH Liver, CDDO-Me, rep 1


title: Exp_04_HLA-DR

description: Household contact

value: Sputum


title: Control, 22h, rep1

description:
15
sample_15


title: Denuded, 6h, rep1

description:
14
sample_14

value: Denuded


title: NASH Liver, vehicle, rep 4

value: Vehicle


title: Coculture, 1h, rep2

description:
27
sample_27


title: KPNA2_Input_2

institute: the first hospital of lanzhou university

description: IgG-binding peaks

value: IgG


title: CBX, 6h, rep1

description:
11
sample_11

value: CBX


title: KPNA2_Input_1

description: IgG-binding peaks


title: NASH Liver, vehicle, rep 3


title: KPNA2_IP_1

description: KPNA2-binding peaks and motifs


title: NASH Liver, vehicle, rep 2


title: siCtrl_3rd

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13).
The short reads less than 16nt were also dropped. After that, clean reads were aligned to the GRch38 genome by tophat2 allowing 4 mismatches
Uniquely mapped reads were used for gene reads number counting and FPKM calculation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene read counts and FPKM values for each Sample

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

value: siNC


title: Control, 6h, rep1

description:
9
sample_9


title: NASH Liver, vehicle, rep 1


title: Coculture, 6h, rep1

description:
13
sample_13


title: siCtrl_2nd


title: Denuded, 1h, rep1

description:
8
sample_8


title: siCtrl_1st


title: Coculture, 1h, rep1

description:
7
sample_7


title: Control Liver, vehicle, rep 4

value: Control


title: Control Liver, vehicle, rep 3

value: Liver


title: Con_04_HLA-DR

description: Control


title: siKPNA2_3rd

value: KPNA2 knockdown


title: Con_04_CD3

description: Control


title: Con_03_HLA-DR

description: Control


title: CBX, 1h, rep1

description:
5
sample_5


title: siKPNA2_2nd


title: Con_03_CD3

description: Control


title: Con_03_PBMC

description: Control

value: Blood


title: Control, 1h, rep1

description:
3
sample_3


title: siKPNA2_1st


title: Control Liver, vehicle, rep 1

value: WT


title: Control Liver, vehicle, rep 2


title: Control, 0h, rep1

description:
1
sample_1

value: oocyte


title: tile7-interaction-selection-rep1_merge_R1

status: Public on Aug 01 2024

city: Copenhagen

first: Sven

last: Larsen-Ledet

state: N

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads from each lane were merged and resulting R1 and R2 fastq files were trimmed. The trimmed fastq files were used as input to Enrich2 that calculated a log ratio score for each variant using normalization to synonymous wild-type variants.
The abundance scores were rescaled between tiles to obtain a uniform distribution.
Assembly: AGAAAGGAAATGACTGCTGCATGTACACCAAGAAGAAGAATTATTAATTTGACATCAGTTTTGTCTTTGCAAGAAGAAATTAATGAACAAGGTCATGAAGTTTTGAGAGAAATGTTGCATAACCATTCTTTCGTTGGTTGTGTTAACCCACAATGGGCTTTAGCACAACATCAAACTAAGTTGTATTTGTTGAACACTACAAAGTTATCAGAAGAATTGTTTTATCAAATTTTAATCTATGATTTTGCTAATTTTGGTGTTTTAAGATTGTCTGAACCAGCACCATTATTTGATTTGGCTATGTTAGCATTGGATTCACCAGAATCTGGTTGGACAGAAGAAGATGGTCCAAAAGAAGGTTTAGCTGAATACATCGTTGAATTCTTGAAAAAGAAAGCTGAAATGTTGGCAGATTACTTCTCTTTGGAAATCGATGAAGAGGGTAATTTGATCGGTTTGCCATTGTTGATCGATAACTACGTTCCACCATTAGAAGGTTTGCCAATTTTCATTTTGAGATTGGCTACTGAAGTTAACTGGGATGAAGAAAAGGAATGTTTCGAATCATTGTCTAAGGAATGTGCAATGTTCTACTCAATCAGAAAGCAATACATTTCAGAAGAATCTACATTATCAGGTCAACAATCTGAAGTTCCAGGTTCTATTCCAAATTCATGGAAGTGGACTGTTGAACATATCGTTTACAAGGCTTTGAGATCTCATATTTTGCCACCAAAGCATTTCACTGAAGATGGTAACATCTTGCAATTGGCAAATTTGCCAGATTTGTACAAGGTTTTCGAAAGATGTTAA
Supplementary files format and content: A csv file with an abundance and PMS2 interaction score for each missense variant in the C-terminal domain of human MLH1, including standard errors and an epsilon score calculated by Enrich2.

organism:
Homo sapiens
synthetic construct

source_name: Yeast cells

growth_protocol: Following library transformations, yeast cells were expanded in SC-URA medium (for the abundance assay) or SC-LEU-TRP medium (for the interaction assay) until saturation.

extract_protocol:
For both abundance and interaction assays and all conditions, plasmid DNA was extracted from 9 OD units of yeast cells using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen).
Site saturation mutagensis libraries comprising MLH1 missense variants in the C-terminal domain of human MLH1 were prepared in each tile and cloned into pDONR221 by Twist Bioscience.
Site saturation mutagensis in tiles

treatment_protocol: For selection yeast cells were washed and grown on solid SC+HIS+LEU+MET medium with and without 200 uM methotrexate and 1 mM sulfanilamide at 30C for three days (for the abundance assay) or on solid SC-LEU and SC-LEU-HIS with 20 mM 3-Amino-1,2,4-triazole at 30C for two days (for the interaction assay). Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

value: Yeast cells

value: selection


title: tile7-interaction-selection-rep2


title: tile6-interaction-selection-rep3


title: tile6-interaction-selection-rep2


title: tile6-interaction-selection-rep1_merge_R1


title: tile7-interaction-control-rep3


title: tile7-interaction-control-rep2


title: tile6-interaction-control-rep1_merge_R1


title: tile7-interaction-control-rep1_merge_R1


title: tile5-interaction-selection-rep3


title: tile5-interaction-selection-rep2


title: tile6-interaction-control-rep2


title: tile6-interaction-control-rep3


title: Con_02_PBMC

description: Control


title: Con_02_CD3

description: Control


title: tile5-interaction-selection-rep1_merge_R1


title: Con_02_HLA-DR

description: Control


title: tile5-interaction-control-rep2


title: tile5-interaction-control-rep1_merge_R1


title: tile4-interaction-selection-rep3


title: Exp_03_HLA-DR

description: Household contact


title: Exp_03_CD3

description: Household contact


title: tile5-interaction-control-rep3


title: tile7-interaction-selection-rep3


title: Exp_02_HLA-DR

description: Household contact


title: tile4-interaction-selection-rep2


title: tile4-interaction-selection-rep1_merge_R1


title: Con_01_CD3

description: Control


title: Exp_02_PBMC

description: Household contact


title: Con_01_PBMC

description: Control


title: tile4-interaction-control-rep3


title: tile4-interaction-control-rep2


title: tile3-interaction-selection-rep2


title: tile3-interaction-selection-rep3


title: tile3-interaction-control-rep3


title: tile4-interaction-control-rep1_merge_R1


title: Exp_01_CD3

description: Household contact


title: tile3-interaction-selection-rep1_merge_R1


title: Con_01_HLA-DR

description: Control


title: Exp_03_PBMC

description: Household contact


title: tile2-interaction-selection-rep3


title: Exp_01_PBMC

description: Household contact


title: tile2-interaction-selection-rep2


title: Pat_01_CD3

description: Patient


title: Pat_01_PBMC

description: Patient


title: tile3-interaction-control-rep2


title: tile2-interaction-selection-rep1_merge_R1


title: Exp_02_CD3

description: Household contact


title: tile2-interaction-control-rep2


title: tile2-interaction-control-rep3


title: tile1-interaction-selection-rep1_merge_R1


title: tile1-interaction-selection-rep2


title: tile1-interaction-selection-rep3


title: tile1-interaction-control-rep1_merge_R1


title: tile1-interaction-control-rep3


title: tile2-interaction-control-rep1_merge_R1


title: Exp_01_HLA-DR

description: Household contact


title: tile7-abundance-selection-rep3


title: tile7-abundance-selection-rep1_merge_R1


title: tile6-abundance-selection-rep3


title: tile7-abundance-control-rep1_merge_R1


title: tile6-abundance-selection-rep1_merge_R1


title: tile6-abundance-selection-rep2


title: tile7-abundance-control-rep3


title: tile1-interaction-control-rep2


title: tile6-abundance-control-rep2


title: tile3-interaction-control-rep1_merge_R1


title: tile5-abundance-selection-rep2


title: tile7-abundance-selection-rep2


title: tile4-abundance-selection-rep1_merge_R1


title: tile5-abundance-control-rep2


title: tile5-abundance-control-rep3


title: tile5-abundance-selection-rep1_merge_R1


title: tile6-abundance-control-rep1_merge_R1


title: tile4-abundance-selection-rep2


title: tile4-abundance-selection-rep3


title: tile5-abundance-control-rep1_merge_R1


title: tile4-abundance-control-rep3


title: tile3-abundance-selection-rep1_merge_R1


title: tile3-abundance-selection-rep3


title: tile4-abundance-control-rep2


title: tile3-abundance-control-rep3


title: tile4-abundance-control-rep1_merge_R1


title: tile7-abundance-control-rep2


title: tile3-abundance-control-rep2


title: Pat_01_HLA-DR

description: Patient


title: tile3-abundance-control-rep1_merge_R1


title: tile2-abundance-selection-rep3


title: tile3-abundance-selection-rep2


title: tile6-abundance-control-rep3


title: tile2-abundance-selection-rep1_merge_R1


title: tile5-abundance-selection-rep3


title: tile2-abundance-control-rep2


title: tile2-abundance-control-rep1_merge_R1


title: tile1-abundance-selection-rep3


title: tile2-abundance-selection-rep2


title: tile1-abundance-selection-rep2


title: tile1-abundance-control-rep3


title: tile1-abundance-control-rep1_merge_R1


title: tile1-abundance-control-rep2


title: water treatment_rep2

city: 河南

first: 翟

last: 怡梦

address: 河南省濮阳市华龙区

institute: 翟怡梦

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Gene expression was calculated using Htseq software (V0.6.1), which calculated gene expression using FPKM (Fragments Per Kilo bases Per Million reads) (Mortazavi, 2008). FPKM is the expected number of fragments per kilobase per million base pairs of a transcriptional sequence. It also considers the impact of sequencing depth and gene length on fragments count, and is currently the most commonly used estimate of gene expression level method
Assembly: Vibrio parahaemolyticus RIMD2210633, complete genome (NC_004603.1; NC_004605.1)
Supplementary files format and content: gene expression (read counts and fpkm for each stra).

organism: Vibrio parahaemolyticus

growth_protocol: Vibrio parahaemolyticus was cultured in LB Broth (LB) medium at 37℃ overnight. The strain was diluted 1:100 in fresh medium and grew to the middle of the index (OD600 = 0.6).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
Subsequent library preparation was performed using 1ug total RNA. Libraries with different indexes are then multiplexed and loaded onto the Illumina X Ten instrument according to the manufacturer's instructions (Illumina, San Diego, CA, USA) or according to the manufacturer's instructions (MGI, Shenzhen, China).

treatment_protocol: The culture medium was divided into 2 parts and 1 mM CuSO4 and H2O were added, respectively. After 15 minutes of treatment, bacterial cells were collected for RNA extraction.

tag: phase

value: mid-exponential phase

value: water


title: water treatment_rep3


title: water treatment_rep1


title: copper treatment_rep2

value: copper


title: copper treatment_rep3


title: tile1-abundance-selection-rep1_merge_R1


title: SUV420i O4+ nOPC rep2

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
High-quality reads were aligned to the mouse reference genome (mm10) using the subread package toolset (Liao et al., 2013). The featureCounts program (Liao et al., 2014) was used to count mapped reads and DESeq2 was used for differential gene expression analysis. For the treatments samples, we performed paired DESeq2 samples processing.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each technical replicate

source_name: O4+ oligodendrocyte progenitor cells

growth_protocol: O4+ oligodendrocyte progenitor cells were extracted from the cortex of P5 and P60 mice. Isolated O4+ oligodendrocyte progenitors were cultured on poly-D-lysine (PDL; 0.1 mg/mL, Sigma, P6407) coated plates. The isolated primary OPCs were cultured in tissue-culture incubator (37C, 5% CO2) in SATO medium (Dulbecco’s modified Eagle’s medium (DMEM), 0.1 mg/mL bovine serum albumin (BSA, Sigma), 0.1 mg/mL apo-transferrin (Sigma), 16 μg/mL putrescine, 62.5 ng/mL progesterone (Sigma), 40 ng/mL sodium selenite (Sigma), 10 μg/mL insulin (Sigma), 1 mM sodium pyruvate (Gibco, Thermo Fisher Scientific), 5 μg/mL N-acetyl-cysteine (Sigma), 1% GlutaMAXTM Supplement (Gibco, Thermo Fisher Scientific), B27 Supplement (Gibco, Thermo Fisher Scientific), Trace Element B (Corning, Fisher), 10 ng/ml biotin (Sigma), 5 μM forskolin (Sigma)) supplemented with Platelet-Derived Growth Factor-AA (PDGF-AA; 30 ng/mL, PeproTech, 100-13A) and basic Fibroblast Growth Factor (bFGF; 30 ng/mL, Peprotech, 100-18B) for the first day. Half media change was performed on the second and all other days with SATO medium supplemented with PDGF-AA (20 ng/mL) and bFGF (20 ng/mL).

extract_protocol:
RNA from cells were extracted from at least three biological replicates for each condition using TRIzol (Invitrogen) extraction and isopropanol precipitation. RNA samples were resuspended in nuclease-free H2O and further purified with RNeasy Mini Kit (Qiagen,  74106) with on-column DNase treatment. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop.
For RNA-sequencing, approximately 85 ng of total RNA per sample was used for library construction with the Ultra-Low-RNA-seq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument according to the manufacturer’s instructions for 150 bp paired-end read runs.

treatment_protocol: Cultured progenitors were untreated or treated either with DMSO, KAT or SUV420 inhibitors for 48 hours in proliferation media.

value: O4+ oligodendrocyte progenitor cells

tag: age

value: postnatal day 5

tag: time

value: 48 hours


title: SUV420i O4+ nOPC rep3


title: SUV420i O4+ nOPC rep4


title: SUV420i O4+ nOPC rep1


title: SUV420i O4+ nOPC rep5


title: KATi O4+ nOPC rep5

description: nOPC-E-iKAT

value: 5 uM Garcinol 0.2 uM NU-9056


title: tile2-abundance-control-rep3

value: control


title: KATi O4+ nOPC rep3

description: nOPC-C-iKAT


title: DMSO O4+ nOPC rep5

description: nOPC-E-DMSO


title: KATi O4+ nOPC rep1

description: nOPC-A-iKAT


title: KATi O4+ nOPC rep2

description: nOPC-B-iKAT


title: DMSO O4+ nOPC rep4

description: nOPC-D-DMSO


title: KATi O4+ nOPC rep4

description: nOPC-D-iKAT


title: DMSO O4+ nOPC rep2

description: nOPC-B-DMSO


title: DMSO O4+ nOPC rep1

description: nOPC-A-DMSO


title: Untreated O4+ nOPC rep3

description: nOPC-E

value: Untreated


title: Untreated O4+ nOPC rep2

description: nOPC-D


title: Untreated O4+ nOPC rep1

description: nOPC-C


title: copper treatment_rep1


title: SUV420i O4+ aOPC rep1

value: postnatal day 60


title: SUV420i O4+ aOPC rep3


title: SUV420i O4+ aOPC rep4


title: KATi O4+ aOPC rep4

description: aOPC-D-iKAT


title: SUV420i O4+ aOPC rep2


title: DMSO O4+ aOPC rep2

description: aOPC-B-DMSO


title: DMSO O4+ aOPC rep4

description: aOPC-D-DMSO


title: KATi O4+ aOPC rep2

description: aOPC-B-iKAT


title: KATi O4+ aOPC rep1

description: aOPC-A-iKAT


title: Postnatal day 21 (P21) hypoxia, biological rep 2

type: RNA

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description:
mouse brain gene panel
HX2

hyb_protocol: A total of 497 genes were selected and assigned a 20-bit binary barcode which was used for generating MERFISH probes. Sections were washed with 1x PBS followed by Sample Prep Wash Buffer (Vizgen, PN 20300001). Sections were incubated in Formamide Wash Buffer (Vizgen, PN 20300002) for 30 min at 37°C, then incubated in the gene panel mix for 42-46 hr at 37°C. Sections were then incubated two times in Formamide Wash Buffer for 30 min each at 47°C, and washed with sample prep wash buffer for at least 2 min. Sections were coated in gel embedding solution (0.05% w/v ammonium persulfate, 0.05% v/v N,N,N’,N'-tetramethylethylenediamine in Gel Embedding Premix (Vizgen, PN 20300004)) and incubated at RT for 1.5 hr, cleared in 1:100 proteinase K in Clearing Premix (Vizgen, PN 20300003) at 37°C overnight or for a maximum of 7 days to clear lipids and proteins that may contribute to auto-fluorescence background noise. Prior to imaging, sections were washed two times with Sample Prep Wash Buffer, incubated in DAPI and PolyT Staining Reagent (Vizgen, PN 20300021) for 15 min on a rocking platform, incubated in Formamide Wash Buffer for 10 min, and washed again with Sample Prep Wash Buffer.

scan_protocol: Imaging was performed on the MERSCOPE platform (Vizgen, Cat: 10000001) according to manufacturer instructions.

data_processing: Transcript barcodes were read and matched assigned to the correct gene. MERFISH images were segmented using Vizgen's post-processing tool and Cellpose v2. DAPI and PolyT signals were used to delinate the cell boundaries. Individual RNA molecules were assigned to a cell based on whether they were positioned within the marked boundary. Anatomical segmentation was performed using the MERSCOPE Visualizer software. Cells for MERFISH were processed using the Seurat V5 package in R.

label: Gene targeting probes

source_name: Whole brain, perinatal hyopxia

label_protocol: Single-cell spatial transcriptomics was performed using a gene panel targeting 497 transcripts.

extract_protocol: Frozen brain were cryo-sectioned at 10 μm thickness at -21°C, and mounted onto MERSCOPE beaded coverslips. Sections were allowed to refreeze, and then fixed with 4% paraformaldehyde, diluted in 1x PBS for 15 minutes, washed with 1x PBS for 5 minutes each, then stored in 70% ethanol overnight.

value: Whole brain

value: perinatal hyopxia


title: Postnatal day 21 (P21) hypoxia, biological rep 3

description:
mouse brain gene panel
HX3


title: Postnatal day 21 (P21) normoxia, biological rep 2

description:
mouse brain gene panel
NX2

source_name: Whole brain, perinatal normoxia

value: perinatal normoxia


title: DMSO O4+ nOPC rep3

description: nOPC-C-DMSO

value: WT


title: Postnatal day 21 (P21) normoxia, biological rep 1

description:
mouse brain gene panel
NX1


title: Postnatal day 21 (P21) hypoxia, biological rep 1

description:
mouse brain gene panel
HX1


title: Untreated O4+ aOPC rep2

description: aOPC-D


title: Untreated O4+ aOPC rep1

description: aOPC-C


title: DMSO O4+ aOPC rep3

description: aOPC-C-DMSO


title: Rat Myocardium_24hr_rep1

city: Nanjing

first: Hejuan

last: Li

state: Nanjing

address: China Pharmaceutical University Xuanwumen Campus, No.24, Tongjiaxiang, Gulou Dis

institute: China Pharmaceutical University

description: Gene expression after MI and control

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

label: Cyanine 3-pCp

organism: Rattus norvegicus

source_name: myocardium

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Cryopulverization of tissue using the Biopulverizer.Homogenization using the Mini-Bead-Beater-16.Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C.Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: The rats in the MI group were opened to expose the heart, the left coronary artery was ligated, the chest was closed, sutured, and whether the modeling was successful or not was observed by electrocardiography and other observations after 24 h. The rats with successful MI modeling were taken. The control group was treated consistently except that the filling artery was not ligated.

value: myocardium

tag: time point

tag: gender

value: male


title: Rat Myocardium_0hr_rep2

description: Gene expression after MI and control


title: Rat Myocardium_24hr_rep2

description: Gene expression after MI and control


title: Rat Myocardium_0hr_rep3

description: Gene expression after MI and control


title: Rat Myocardium_24hr_rep3

description: Gene expression after MI and control


title: Liver tissue, EVs high dose group

first: Daye

last: Mun

description: L-EVH

data_processing:
The raw reads were used to remove the adapter sequence using Trimmomatic 0.38.
Mapping of preprocessed trimmed reads to a known reference genome using the HISAT2 program.
After read mapping, transcript assembly was performed using StringTie program.
As a result, expression profile values were obtained for each sample for known transcripts, and read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads), and TPM (Transcripts Per Kilobase Million) values were organized based on transcript/gene.
Assembly: mm10
Supplementary files format and content: text file includes FPKM values for all samples

source_name: liver

extract_protocol:
Tissue RNA was isolated using TRIzol reagent (Invitrogen, USA) and a RNeasy Plus kit (Qiagen, Hilden, Germany).
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, San Diego, CA, USA).

value: liver


title: Liver tissue, EVs low dose group

description: L-EVL


title: Liver tissue, NASH group

description: L-NASH


title: KATi O4+ aOPC rep3

description: aOPC-C-iKAT


title: Liver tissue, control group

description: L-CON


title: Rat Myocardium_0hr_rep1

description: Gene expression after MI and control


title: Colon tissue, EVs high dose group

description: C-EVH

source_name: colon

value: colon


title: Colon tissue, EVs low dose group

description: C-EVL


title: DMSO O4+ aOPC rep1

description: aOPC-A-DMSO


title: Postnatal day 21 (P21) normoxia, biological rep 3

description:
mouse brain gene panel
NX3


title: Colon tissue, control group

description: C-CON


title: Colon tissue, NASH group

description: C-NASH


title: Tumor, mtDSN-2-treated

city: Hangzhou

first: Lulu

last: Ren

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. After mapping with Cell Ranger (v7.0.0) on the mouse reference, downstream single-cell analyses were further performed using Seurat (v4.3.0). In silico doublet prediction and removal were performed using DoubletFinder. Cells with number of genes detected per cell > 8500 or < 200, and percentage of mitochondrial genes > 30% were removed from the dataset before the downstream analysis. After this initial filtering, we normalized the gene expression of each cell by the total expression before performing log-transformation. In the log-normalized data, we identified the top 2000 most highly variable genes and included them in principal component analysis and clustering analysis. Scaling was carried out by centering the expression of each gene before dividing the mean-centered expressions by the standard deviation. Cell cluster annotations were performed by manual annotation based on selected canonical markers via unsupervised clustering.
Assembly: mm10-2020-A
Supplementary files format and content: gene-barcode counts
Supplementary files format and content: gene files
Supplementary files format and content: cell barcode files

source_name: tumor

extract_protocol:
The cell suspension was prepared according to general protocols and loaded into Chromium microfluidic chips with 3’ (v3.1) chemistry and barcoded with a 10X Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
The sequencing libraries were constructed using a Chromium Single Cell 3’ (v3.1) reagent kit (10X Genomics) (Novogene). Illumina NovaSeq 6000 PE150 was used for sequencing following the manufacturer’s instructions.

value: tumor

value: tumor cells


title: Kidney, KO, infected day 7, biol rep3

city: Vienna

first: Philipp

last: Penninger

address: Dr. Bohr-Gasse 9

country: Austria

institute: Medical University of Vienna

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v2.8 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1). The reads were then mapped to Mus Musculus (GRCm38/mm10) using Hisat2 v2.0.5.
Read counting was done using featureCounts v1.5.0-p3.
Differential gene expression analysis was done using the DESeq2 v1.34.0 (Love MI, Huber W, Anders S, 2014)
Assembly: Mus Musculus (GRCm38/mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample and gene annotation

source_name: Kidney

growth_protocol: Kidneys were isolated directly from uninfected or 7-day infected mice and placed into TRIzol solution.

extract_protocol:
Total RNA extraction was done following the TRIzol standard protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end pairing, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Isolated kidneys from uninfected or systemically infected mice with C. albicans for 7 days.

value: Kidney

value: Bulk kidney cells

value: HDAC1 KO

value: C. albicans infected 7 days


title: Kidney, KO, infected day 7, biol rep1


title: Kidney, WT, infected day 7, biol rep4


title: Kidney, KO, uninfected, biol rep3

value: uninfected


title: Kidney, KO, uninfected, biol rep2


title: Kidney, KO, uninfected, biol rep1


title: Kidney, KO, infected day 7, biol rep4


title: Tumor, vehicle-treated


title: Kidney, WT, infected day 7, biol rep3


title: Kidney, WT, infected day 7, biol rep2


title: Kidney, WT, uninfected, biol rep3


title: Kidney, WT, infected day 7, biol rep1


title: Kidney, WT, uninfected, biol rep2


title: explant YZ9 2

city: New Haven

first: Jenna

middle: Michal

last: Bergmann

state: Connecticut

address: 333 Cedar Street, I-168

department: Genetics

institute: Yale University

description:
Y2
dom1222_YZ9_MesodermExplant_final_deseq2.csv

data_processing:
Flow Cell Preparation and Sequencing: Sample concentrations are normalized to 1.2 nM and loaded onto an Illumina NovaSeq flow cell at a concentration that yields 25 million passing filter clusters per sample. Samples are sequenced using 100bp paired-end sequencing on an Illumina NovaSeq according to Illumina protocols. The 10bp unique dual index is read during additional sequencing reads that automatically follow the completion of read 1. Data generated during sequencing runs are simultaneously transferred to the YCGA high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time.
Data Analysis and Storage: Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Base calls are transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis - sample de-multiplexing and alignment to the human genome - is performed using Illumina's CASAVA 1.8.2 software suite. The data are returned to the user if the sample error rate is less than 2% and the distribution of reads per sample in a lane is within reasonable tolerance.
Paired end reads were aligned using Star (v2.7.9a) to the mouse genome (GRCm38) using the Ensembl transcriptome (release 109) (Cunningham et al, 2022).
Analysis of differential gene expression was performed using DESeq2 (v1.40.1). To identify differentially regulated genes between samples for downstream analyses, we selected genes with log2 fold change greater than 0.7 or less than -0.7 and an adjusted p-value <0.01.
data processing step
Assembly: Ensembl GRCm38
Supplementary files format and content: Processed data files are in CSV format and contain differential epression analysis comparing treatment groups (PD and YZ9, respectively) to controls. These files also contain both raw and normalized counts for each sample included in the analysis.

source_name: E7.25 mesoderm explant

growth_protocol: For mesoderm isolation from E7.25 mouse embryos, we followed a modified protocol as described in Burdsal et al. (1993). Embryos were collected as described above. Extraembryonic tissue proximal to the amnion was removed, and the cup-shaped embryo was transferred to a dissociation media consisting of 0.5% Trypsin EDTA (Gibco) and 2.5% Pancreatin (Thermo Scientific Chemicals) for 15min in 4º. Embryos were washed with collection media (described earlier) and mesoderm tissue was dissected using insect pins (Roboz) attached to syringes. Explants were transferred to fibronectin-coated 18-well µ slides (Ibidi) plates and left to adhere for 3-4hr in media containing a 1:4 ratio of rat serum to embryo culture media (described earlier), prior to downstream experiments and/or chemical inhibitor treatments. For RNA sequencing, explants were cultured to 27h then scraped off with sterile insect pins and flash-frozen.

extract_protocol:
Total RNA was extracted from mesoderm explants using a PicoPureTM RNA Isolation Kit as per the manufacturer’s instructions (Applied Biosystems).
RNA Seq Library Prep: Using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420L) and a normalized RNA input between 200pg-50ng a template switching method is used to generate cDNAs. The NEB Ultra II FS workflow is used for fragmentation, end repair, dA-tailing, adapter ligation and PCR. Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: 10µM YZ9 or 1μM PD for 16 hours

value: E7.25 mesoderm explant


title: Kidney, WT, uninfected, biol rep1


title: explant PD 2

description:
P2
dom1222_PD1_MesodermExplant_final_deseq2.csv

value: PD


title: explant control 2

description:
C2
dom1222_PD1_MesodermExplant_final_deseq2.csv
dom1222_YZ9_MesodermExplant_final_deseq2.csv

value: control


title: PyMT, Auphen, replicate 1

city: South Bend

first: Verodia

last: Charlestin

state: IN

address: 1234 N. Notre Dame Ave

department: Chemistry and Biochemistry

institute: University of Notre Dame

data_processing:
Reads were mapped to human (genome GRCh38, transcriptome GRCh38.109) or mouse genomes (genome GRCm39, transcriptome GRCm39.109) using HISAT2, and then the number of reads uniquely mapped to each gene tallied using HTSeq.
When identifying differentially expressed (DE) genes, vehicle and Auphen treated samples were paired.
Next, we did differential expression (DE) analysis using edgeR using the likelihood ratio test (LRT). Low-expression genes whose average number of reads per sample < 2.0 were filtered out except for Aqp7/AQP7.
First condition = Vehicle; Second conditon = Auphen. A positive/negative log2FC means that the gene is up-regulated/down-regulated in the second condition compared to the first condition.), and log2CPM (log2 of the overall average expression, measured by log2 of counts per million. This number indicates whether the gene is a high-expression or low-expression gene, on average, over the two groups.).
Assembly: GRCh38, transcriptome GRCh38.109 and GRCm39, transcriptome GRCm39.109.
Supplementary files format and content: CSV file. The columns for each file are: GeneSymbol (the gene symbol), FDR (the false discovery rate or the adjusted p-value; set to 0.1 as a cutoff), pval (the unadjusted/original p-value), log2FC (log2 fold change.
Supplementary files format and content: A positive/negative log2FC means that the gene is up-regulated/down-regulated in the second condition compared to the first condition.), and log2CPM (log2 of the overall average expression, measured by log2 of counts per million. This number indicates whether the gene is a high-expression or low-expression gene, on average, over the two groups.).

source_name: Mouse; Mammary gland

growth_protocol: All cells were maintained at 37°C in humidified incubators with 5% CO2 at atmospheric oxygen levels. MCF-7 and PyMT cells were cultured in DMEM High Glucose media with 10% FBS.

extract_protocol:
RNA extraction was carried out with RNeasy Plus Mini Kit (Qiagen).Total RNA was evaluated with Agilent Tapestation 4150 system and RNA ScreenTape (Agilent Technologies). All samples had an RNA Integrity Number (RIN) of 9 or higher. Samples were quantitated with the Qubit RNA HS Assay Kit.
Total RNA input was normalized to 500 ng. mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and converted into an Illumina library using NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (New England BioLabs). Indexed libraries were quality assessed using Qubit dsDNA HS Assay Kit (Invitrogen) and Tapestation 4150 DNA HS 1000 Kit (Agilent Technologies). The individual libraries were normalized, and equal molar amounts were multiplexed. Molar concentration of the multiplex pool was determined with KAPA Library Quantification Kits for Illumina.

treatment_protocol: 100,000 cells/well were seeded in 6-well plates . After overnight incubation, the cells were treated with Auphen or Vehicle (DMSO)  for 72 h at determined IC50 concentrations (~4 uM and ~8 uM for MCF-7 and PyMT, respectively).

value: Mouse; Mammary gland

value: Vo-PyMT

value: epithelial cell

value: Auphen


title: explant control 1

description:
C1
dom1222_PD1_MesodermExplant_final_deseq2.csv
dom1222_YZ9_MesodermExplant_final_deseq2.csv

value: WT


title: PyMT, Vehicle, replicate 3

value: Vehicle


title: PyMT, Auphen, replicate 2


title: PyMT, Auphen, replicate 4


title: PyMT, Auphen, replicate 3


title: PyMT, Vehicle, replicate 4


title: PyMT, Vehicle, replicate 2


title: Kidney, KO, infected day 7, biol rep2


title: PyMT, Vehicle, replicate 1


title: fl_ctrl_systemic_5

city: Konstanz

first: Rebekka

last: Lambrecht

address: Universitaetsstrasse 10

country: Germany

institute: University of Konstanz

data_processing:
Raw reads were aligned to mouse genome (GRCm38) using STAR aligner and translated into read counts using FeatureCounts based on GENCODE gene annotation version M16
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text file with raw counts of each sample

source_name: primary keratinocytes from ear and dorsal skin

growth_protocol: K14-CreERTam x Cyp11b1L2/L2 (cKO) and Cyp11b1 L2/L2 mice (fl_ctrl) were held in groups of 2-6 animals in IVC cages in 12:12 h light/dark cycle with permanent access to water and standard chow diet ad libitum.

extract_protocol:
Keratinocytes were isolated from treated skin and enriched by FACS. Total RNA of 2 x10^6 sorted keratinocytes per sample was extracted using the RNeasy Plus Mini Kit (QIAGEN).
Illumina’s SmartSeq II library construction, NovaSeq 6000 (Illumina Inc.)

treatment_protocol: Keratinocyte-specific deletion of Cyp11b1 was induced by treating mice with tamoxifen for five consecutive days, either by intra-peritoneal (100 ul of 10 mg/ml) injection, here termed as systemic, or by topical application (ear: 20 ul, back: 100 ul), here termed as local.

value: Cyp11b1 L2/L2 (fl_ctrl)

value: tamoxifen intra-peritoneal


title: fl_ctrl_systemic_1

value: primary keratinocytes from ear and dorsal skin


title: fl_ctrl_local_7

value: tamoxifen topical


title: explant YZ9 1

description:
Y1
dom1222_YZ9_MesodermExplant_final_deseq2.csv


title: fl_ctrl_local_6


title: fl_ctrl_local_5


title: fl_ctrl_systemic_6


title: fl_ctrl_systemic_4


title: cKO_systemic_7

value: K14-CreERTam x Cyp11b1 L2/L2 (cKO)


title: cKO_systemic_6


title: fl_ctrl_systemic_3


title: explant PD 1

description:
P1
dom1222_PD1_MesodermExplant_final_deseq2.csv


title: cKO_systemic_5


title: cKO_systemic_4


title: fl_ctrl_local_3


title: cKO_systemic_2


title: cKO_local_2


title: cKO_local_3


title: cKO_local_7


title: cKO_local_4


title: A27_CBD0.325_24h

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: Mouse GRC39
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

source_name: hypothalamus

extract_protocol:
Standard procedure of TRIzol Reagent
Standard protocol of QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen)

value: hypothalamus

value: Adult Mouse Hypothalamus Cell Line mHypoA-2/12


title: A26_CBD0.325_24h


title: A29_CTR_24h


title: A25_CBD0.325_24h


title: A30_CTR_24h


title: A23_CBD0.75_24h


title: A24_CBD0.75_24h


title: fl_ctrl_local_1


title: A20_CBD1.5_24h


title: A17_CBD3_24h


title: A19_CBD1.5_24h


title: A21_CBD1.5_24h


title: A18_CBD3_24h


title: A15_CBD0.325_6h


title: cKO_local_5


title: A22_CBD0.75_24h


title: A10_CBD0.75_6h


title: A11_CBD0.75_6h


title: A12_CBD0.75_6h


title: A8_CBD1.5_6h


title: A14_CBD0.325_6h


title: A13_CBD0.325_6h


title: A28_CTR_24h


title: A9_CBD1.5_6h


title: A6_CBD3_6h


title: A7_CBD1.5_6h


title: A4_CBD3_6h


title: A5_CBD3_6h


title: A1_CTR_6h


title: A2_CTR_6h


title: Letrozole + anti-PD-1 rep 4

city: Dunedin

first: Sarah

last: Barber

address: 362 Leith Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Terminal version 2.12 and R studio version 2021.09.1+372
Adaptor sequences were trimmed from sequences using Bash through Terminal (parameter: <5% adaptor content)
Trimmed sequence reads were mapped to GRCm39/mm39 using the STAR alignment tool in Bash through Terminal with default parameters of STAR 2.7.10a
Read counts were extracted using Bash through Terminal
Normalisation was performed by estimating size factors using DESeq2 in R studio.
Assembly: GRCm39/mm39
Supplementary files format and content: .csv file contains normalised read counts for all samples

source_name: Mammary

growth_protocol: 5 x 105 SSM3 cells were injected into the fourth inguinal mammary gland of 129S6/SvEv mice aged 2-4 months and followed until tumours reached approximately 150 mm3

extract_protocol:
RNA was extracted using Qiagen All Prep DNA/RNA mini kit. 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Swift Rapid library prep kit following manufacturer's protocols

treatment_protocol: Mice received either an ovariectomy, if they were to be treated with letrozole, or a sham surgery. Mice that underwent an ovariectomy  received daily subcutaneous injections of 1 mg/kg letrozole resuspended in 5% ethanol in sterile saline for 25 days. Mice that underwent sham surgery received daily subcutaneous injections of 5% ethanol in sterile saline for 25 days. Mice in groups receiving either immune checkpoint inhibitor, anti-PD-1 (250 ug) or anti-PD-L1 (200 ug), received a single 0.08 mL IP injection on days 3, 5 and 7 post-surgery

value: Mammary

value: Letrozole and anti-PD-1


title: Letrozole + anti-PD-1 rep 5


title: Letrozole + anti-PD-1 rep 3


title: A3_CTR_6h


title: Letrozole + anti-PD-1 rep 2


title: Letrozole + anti-PD-1 rep 1


title: A16_CBD3_24h


title: Letrozole rep 4

value: Letrozole


title: Letrozole rep 5


title: Letrozole rep 2


title: Letrozole rep 3


title: Control + anti-PD-1 rep 5


title: Control + anti-PD-1 rep 4


title: Control + anti-PD-1 rep 3


title: Letrozole rep 1


title: Control rep 5


title: Control rep 3


title: Control + anti-PD-1 rep 2


title: Control rep 4


title: Control + anti-PD-1 rep 1


title: Adult HIF2A cKO CoE RNA-seq replicate 2

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 105 T. W. Alexander Drive

institute: NIEHS

data_processing:
The raw RNA-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using TopHat version 2.0.4
Assembly: mm10
Supplementary files format and content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

source_name: mouse uterus

growth_protocol: Adult mouse uterine tissues were colleclted from WT and HIF2A cKO control diestrus, control estrus.

extract_protocol:
RNA was extracted using Qiagen RNeasy kit with DNase on column treatment
RNA-seq libraries were generated using Illumina Tru-Seq RNA kit.

treatment_protocol: Mice were unexposed WT or HIF2A cKO control FVB/N mice

value: mouse uterus

value: FVB/N

value: 2 months

tag: Stage

value: estrus

value: HIF2A cKO


title: Adult HIF2A cKO CoE RNA-seq replicate 1


title: Adult HIF2A cKO CoE RNA-seq replicate 4


title: Adult HIF2A cKO CoD RNA-seq replicate 3

value: diestrus


title: Adult HIF2A cKO CoD RNA-seq replicate 2


title: Adult HIF2A cKO CoD RNA-seq replicate 4


title: Adult WT CoE RNA-seq replicate 4

value: WT


title: Adult HIF2A cKO CoD RNA-seq replicate 1


title: Adult WT CoE RNA-seq replicate 2


title: Adult WT CoE RNA-seq replicate 1


title: Control rep 1

value: Vehicle


title: Adult WT CoD RNA-seq replicate 1


title: Adult WT CoD RNA-seq replicate 2


title: Adult WT CoD RNA-seq replicate 3


title: Adult WT CoD RNA-seq replicate 4


title: 9257plusCKO_cil

city: Los Angeles

first: Kindra

middle: M

last: Kelly-Scumpia

state: CA

address: 615 Charles E Young Dr Rm 246

institute: UCLA

data_processing:
RNA-seq libraries were sequenced, single end 50bp on an Illumina HiSeq 3000.
RNA-seq fastq files were mapped using Hisat2. Only the uniquely mapped reads were kept for further analysis.
Uniquely aligned reads were used to quantify against exon in seqmonk to generated read counts matrix
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each file

source_name: skin

extract_protocol:
RNA was harvested using RNAeasy kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina's  TruSeq stranded RNA Sample Preparation Kit

treatment_protocol: Mice were treated with cilengitide; skin was wounded and harvested 14 days later

value: skin

value: Col5a1 CKO

value: cilengitde treatment and wounded


title: 4221plusCKO_cil


title: 3617plusCKO

value: vehicle treatment and wounded

value: Day 14


title: 4220plusCKO_cil


title: 4222plusCKO


title: 4192plusCKO


title: 4223plusCKO


title: 4193-WT3


title: Control rep 2


title: 3960plusCKO_cil


title: 3953-WT1


title: 4194-WT1


title: 3959-WT2


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep7

city: Nashville

first: Douglas

last: McMahon

state: Tennessee

address: Department of Biological Sciences/MRB III, Vanderbilt University

department: Department of Biological Sciences

institute: Vanderbilt University

description: LONG_pZT 0_7

data_processing:
Trim Galore 0.6.7 (Krueger et al., 2023) and Cutadapt 1.18 (Martin, 2011) used to remove adapter sequences and pairs that were either shorter than 20 bp or that had Phred scores less than 20
The Spliced Transcripts Alignment to a Reference (STAR v2.7.9a) application (Dobin et al., 2013) was used to perform sequence alignments and mapping
Assembly: mm39 (GRCm39) mouse genome reference and GENCODE comprehensive gene annotations (release M31)
Supplementary files format and content: HTSeq-formatted counts file (tsv)

source_name: suprachiasmatic nucleus

extract_protocol:
AllPrep DNA/RNA Micro Kit (Qiagen)
Stranded cDNA libraries were constructed using 200 ng of total RNA per sample and the NEBNext® Ultra™ II RNA Library Prep (NEB, Cat: E7765S) per manufacturer’s instructions, with mRNA enriched via poly-A-selection using oligoDT beads. Paired-end sequencing produced approximately 54.6 million reads per sample (total of 11.1 billion reads).

treatment_protocol: Mice used in this experiment were under Short (Hours Light: Hours Dark 8:16) or Long (LD 16:8) photoperiods from embryonic day zero (E0). Mice were weaned at postnatal day 21 (P21) per standard practice and remained in the same photoperiod until postnatal day 50 (P50, late adolescence). Male P50 mice were used for this experiment (see experimental design above).

value: suprachiasmatic nucleus

value: Wild type

tag: photoperioid

value: LONG

tag: projected zeitgeber_time

tag: timepoint clock_time

tag: circadian cycle

tag: replicate

tag: batch rna_extraction

tag: batch sequencing


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep10

description: SHORT_pZT 0_10

tag: tissue

tag: genotype

value: SHORT


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep11

description: SHORT_pZT 0_11


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep8

description: LONG_pZT 0_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep8

description: SHORT_pZT 4_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep9

description: SHORT_pZT 0_9


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep7

description: SHORT_pZT 16_7


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep8

description: SHORT_pZT 0_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep10

description: SHORT_pZT 4_10


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep9

description: LONG_pZT 20_9


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep10

description: SHORT_pZT 16_10


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep8

description: LONG_pZT 20_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep6

description: SHORT_pZT 16_6


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep8

description: SHORT_pZT 8_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep7

description: SHORT_pZT 8_7


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep10

description: SHORT_pZT 20_10


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep8

description: SHORT_pZT 20_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep9

description: SHORT_pZT 20_9


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep9

description: LONG_pZT 0_9


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep6

description: LONG_pZT 0_6


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep5

description: SHORT_pZT 8_5


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep6

description: SHORT_pZT 8_6


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep9

description: LONG_pZT 12_9


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep7

description: LONG_pZT 8_7


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep5

description: SHORT_pZT 12_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep12

description: LONG_pZT 8_12


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep5

description: LONG_pZT 12_5


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep8

description: SHORT_pZT 16_8


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep7

description: LONG_pZT 12_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep11

description: LONG_pZT 8_11


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep9

description: LONG_pZT 8_9


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep6

description: SHORT_pZT 4_6


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep9

description: SHORT_pZT 4_9


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep6

description: SHORT_pZT 12_6


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep8

description: LONG_pZT 8_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep7

description: SHORT_pZT 12_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep10

description: LONG_pZT 8_10


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep8

description: SHORT_pZT 12_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep9

description: SHORT_pZT 16_9


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep6

description: LONG_pZT 20_6


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep7

description: SHORT_pZT 4_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep4

description: LONG_pZT 20_4


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep16

description: LONG_pZT 4_16


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep5

description: LONG_pZT 20_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep14

description: LONG_pZT 4_14


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep13

description: LONG_pZT 4_13


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep12

description: LONG_pZT 4_12


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep5

description: LONG_pZT 0_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep7

description: LONG_pZT 20_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep8

description: LONG_pZT 12_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep9

description: SHORT_pZT 12_9


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep6

description: LONG_pZT 12_6


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep4

description: LONG_pZT 0_4


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep3

description: LONG_pZT 0_3


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep3

description: LONG_pZT 20_3


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep11

description: LONG_pZT 4_11


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep10

description: LONG_pZT 4_10


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep15

description: LONG_pZT 4_15


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep2

description: LONG_pZT 20_2


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep2

description: LONG_pZT 12_2


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep4

description: LONG_pZT 8_4


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep5

description: SHORT_pZT 20_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep6

description: LONG_pZT 8_6


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep6

description: SHORT_pZT 20_6


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep5

description: LONG_pZT 8_5


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep7

description: SHORT_pZT 20_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep3

description: LONG_pZT 12_3


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep7

description: SHORT_pZT 0_7


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep6

description: SHORT_pZT 0_6


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep4

description: LONG_pZT 12_4


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep9

description: LONG_pZT 4_9


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep3

description: LONG_pZT 8_3


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep8

description: LONG_pZT 4_8


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep1

description: LONG_pZT 8_1


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep7

description: LONG_pZT 4_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT8, rep2

description: LONG_pZT 8_2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep5

description: SHORT_pZT 0_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep6

description: LONG_pZT 4_6


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep5

description: LONG_pZT 4_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep4

description: LONG_pZT 4_4


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep2

description: LONG_pZT 0_2


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep3

description: LONG_pZT 4_3


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep1

description: LONG_pZT 4_1


title: suprachiasmatic nucleus, LONG photoperiod, pZT20, rep1

description: LONG_pZT 20_1


title: suprachiasmatic nucleus, LONG photoperiod, pZT4, rep2

description: LONG_pZT 4_2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep5

description: SHORT_pZT 4_5


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep4

description: SHORT_pZT 12_4


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep4

description: SHORT_pZT 4_4


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep1

description: SHORT_pZT 12_1


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep2

description: SHORT_pZT 12_2


title: suprachiasmatic nucleus, LONG photoperiod, pZT12, rep1

description: LONG_pZT 12_1


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep9

description: LONG_pZT 16_9


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep3

description: SHORT_pZT 20_3


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep8

description: LONG_pZT 16_8


title: suprachiasmatic nucleus, SHORT photoperiod, pZT12, rep3

description: SHORT_pZT 12_3


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep10

description: LONG_pZT 16_10


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep7

description: LONG_pZT 16_7


title: suprachiasmatic nucleus, LONG photoperiod, pZT0, rep1

description: LONG_pZT 0_1


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep6

description: LONG_pZT 16_6


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep1

description: SHORT_pZT 20_1


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep5

description: LONG_pZT 16_5


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep2

description: LONG_pZT 16_2


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep4

description: LONG_pZT 16_4


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep3

description: LONG_pZT 16_3


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep4

description: SHORT_pZT 0_4


title: suprachiasmatic nucleus, LONG photoperiod, pZT16, rep1

description: LONG_pZT 16_1


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep2

description: SHORT_pZT 0_2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep2

description: SHORT_pZT 20_2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep1

description: SHORT_pZT 0_1


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep4

description: SHORT_pZT 8_4


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep4

description: SHORT_pZT 16_4


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep5

description: SHORT_pZT 16_5


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep3

description: SHORT_pZT 16_3


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep2

description: SHORT_pZT 16_2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT20, rep4

description: SHORT_pZT 20_4


title: suprachiasmatic nucleus, SHORT photoperiod, pZT16, rep1

description: SHORT_pZT 16_1


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep3

description: SHORT_pZT 4_3


title: suprachiasmatic nucleus, SHORT photoperiod, pZT0, rep3

description: SHORT_pZT 0_3


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep2

description: SHORT_pZT 8_2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep1

description: SHORT_pZT 8_1


title: Kidney,control,20min3d,rep6

city: Guangzhou

first: FAN FAN

last: HOU

address: 1838 North Guangzhou Ave, Guangzhou

institute: Nanfang Hospital, Southern Medical University

data_processing:
Raw sequencing reads were filtered using FastQC (version 0.11.7).
Trimmed reads were aligned with the reference genome GRCm38 using Hisat2 (version 2.1.0).
Gene expression levels were calculated using Ballgown (version 2.10.0) and normalized by library size and gene length into FPKM. To reduce transcription noise, each gene with FPKM below 0.01 was dropped for further analyses. The differentially expressed genes (DEGs) were identified with up-regulated fold change ≥ 2 and FDR-adjusted P value < 0.05.
Assembly: GRCm38
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: Renal cortex

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Concentration and integrity of RNA for each sample was assessed by Agilent 2100 Bioanalyzer
RNA sequencing libraries were constructed by the Kapa Standard RNA-seq Library Prep Kit (Kapa Biosystems) and sequenced using Illumina X-ten/NovaSeq for 150 cycles.

value: Renal cortex

tag: Sex

value: male

tag: injury time

value: non

tag: sampling time_after_injury


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep1

description: SHORT_pZT 4_1


title: Kidney,IRI,20min3d,rep6

tag: strain


title: Kidney,IRI,20min3d,rep4


title: Kidney,control,20min3d,rep3


title: Kidney,control,20min3d,rep5


title: Kidney,IRI,20min3d,rep3


title: Kidney,control,20min3d,rep2


title: Kidney,IRI,20min3d,rep2


title: Kidney,control,20min3d,rep1


title: Kidney,IRI,20min3d,rep1


title: Kidney,control,20min1d,rep6


title: Kidney,IRI,20min1d,rep6


title: Kidney,IRI,20min1d,rep5


title: suprachiasmatic nucleus, SHORT photoperiod, pZT8, rep3

description: SHORT_pZT 8_3


title: Kidney,IRI,20min1d,rep4


title: Kidney,IRI,20min1d,rep3


title: Kidney,control,20min1d,rep4


title: Kidney,control,20min1d,rep3


title: Kidney,IRI,20min1d,rep2


title: suprachiasmatic nucleus, SHORT photoperiod, pZT4, rep2

description: SHORT_pZT 4_2


title: Kidney,control,20min3d,rep4


title: Kidney,IRI,20min3d,rep5


title: Kidney,control,20min1d,rep2


title: Kidney,control,20min1d,rep1


title: Kidney,IRI,40min3d,rep6


title: Kidney,control,40min3d,rep6


title: Kidney,IRI,20min1d,rep1


title: Kidney,control,40min3d,rep4


title: Kidney,control,40min3d,rep3


title: Kidney,IRI,40min3d,rep4


title: Kidney,IRI,40min3d,rep3


title: Kidney,control,40min3d,rep5


title: Kidney,IRI,40min3d,rep2


title: Kidney,control,40min3d,rep2


title: Kidney,control,40min3d,rep1


title: Kidney,control,40min1d,rep6


title: Kidney,control,20min1d,rep5


title: Kidney,IRI,40min1d,rep6


title: Kidney,control,40min1d,rep5


title: Kidney,IRI,40min1d,rep5


title: Kidney,control,40min1d,rep4


title: Kidney,IRI,40min1d,rep4


title: Kidney,IRI,40min1d,rep2


title: Kidney,control,40min1d,rep3


title: Kidney,IRI,40min1d,rep1


title: Kidney,control,40min1d,rep1


title: CD8 T AclyKO+Acss2i bio rep 4

city: Grand Rapids

first: Russell

last: Jones

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Isolated CD8 T cells were activated in VIM media with plate bound CD3/CD28 and IL-2 for 48 hours in the presence or absence of Acss2 inhibitor or acetate.

data_processing:
Reads were trimmed using TrimGalore v0.6.10 (Krueger et al., 2021) in paired-end mode with default parameters then aligned to the mm10 genome using ‘bwa mem’ v0.7.17 (Li, 2013), marking duplicate reads using SAMBLASTER v0.1.26 (Faust & Hall, 2014). For peak calling and differential accessibility analysis, alignments were quality-filtered, including removal of mitochondrial alignments, then deduplicated using ‘samtools view’ v1.17 (Li et al., 2009), with the parameters ‘-q 30 -F 2828 -f 2’ and ’-F 1024’ respectively. To call peaks centered at cut sites, BAM files were converted to BEDPE format using ‘bedtools bamtobed’ v2.30.0 (Quinlan & Hall, 2010), with the parameters ‘-bedpe -mate1’ followed by an AWK command to convert the resulting BEDPE file to BED format; ‘macs2 callpeak’ v2.2.7.1 (Zhang et al., 2008) was used with the parameters, ‘--keep-dup “all” -g mm -f “BED” --shift -75 --extsize 150 --nomodel --call-summits -B --SPMR’. Output bedgraph files were converted to BigWig format using bedGraphToBigWig from UCSCtools.
Assembly: mm10
Supplementary files format and content: BigWig, library size normalized read coverage centered at cut sites
Supplementary files format and content: NarrowPeak, peaks called by MACS2

source_name: CD8+ T cells

extract_protocol:
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed according to Grandi et al 2022. Transposition was done for 45 mins at 37C mixing at 800rpm.
Library quantification and amplification was performed according to Grandi et al 2022. Using the full DNA output for each sample from ATAC libraries were initially amplified for 5 cycles. qPCR on part of these amplfied libraries was used to determine the number of additional cycles of amplification (+9 cycles). Post amplification libraries were size selected using AMPure XP beads from Beckman Coulter (0.6x for upper cutoff and 1.2x for lower cutoff). Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell type

value: CD8+ T cells

value: Acly f/f Cd4Cre+

tag: treatment

value: Acss2 inhibitor


title: Kidney,IRI,40min3d,rep5


title: CD8 T AclyKO+Acss2i bio rep 1

growth_protocol: Isolated CD8 T cells were activated in VIM media with plate bound CD3/CD28 and IL-2 for 48 hours in the presence or absence of Acss2 inhibitor or acetate.


title: CD8 T AclyKO+Acss2i bio rep 3


title: CD8 T AclyKO+Acss2i bio rep 2


title: CD8 T AclyKO+Acet bio rep 3

value: Vehicle (DMSO)+1mM Acetate


title: CD8 T WT+Acss2i bio rep 3

value: Acly f/f Cd4Cre-


title: CD8 T AclyKO+Acet bio rep 4


title: CD8 T WT+Acss2i bio rep 4


title: CD8 T AclyKO bio rep 4

value: Vehicle (DMSO)


title: CD8 T WT+Acss2i bio rep 1


title: CD8 T AclyKO+Acet bio rep 1


title: CD8 T WT+Acss2i bio rep 2


title: CD8 T AclyKO+Acet bio rep 2


title: Kidney,IRI,40min3d,rep1


title: CD8 T AclyKO bio rep 1


title: CD8 T WT bio rep 2


title: Kidney,control,40min1d,rep2


title: CD8 T AclyKO bio rep 2


title: CD8 T WT bio rep 1


title: Kidney,IRI,40min1d,rep3


title: HM_VD_14

city: Frederiksberg C

first: Camilla

middle: Hartmann Friis

last: Hansen

address: Ridebanevej 9, 2nd floor

department: Faculty of Health Sciences

institute: University of Copenhagen

data_processing:
Illumina CASAVA software used for basecalling.
Adaptors trimmed with Fastp, filtered for low quality sequence and mapped to Mus Musculus(GRCm38/mm10) genome with HISAT2 v 2.0.5
Gene count file made using FeatureCounts v 1.5.0
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: adipose

extract_protocol:
Rneasy Lipid Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose

value: Male


title: CD8 T WT bio rep 3


title: CD8 T WT bio rep 4


title: HM_VD_9


title: HM_VD_8


title: HM_VD_7


title: HM_VD_10


title: HM_VD_6


title: CD8 T AclyKO bio rep 3


title: HM_VD_3


title: HM_VD_4


title: HM_VD_5


title: HM_VD_1


title: HM_CS_14


title: HM_CS_9


title: HM_CS_6


title: HM_CS_5


title: HM_CS_4


title: HM_CS_8


title: HM_CS_3


title: HM_CS_12


title: HM_CS_1