title: E9

city: Chengdu

first: nanwei

last: tong

address: No. 37, Guoxue Alley, Wuhou District

department: Department of Endocrinology and Metabolism

institute: West China Hospital of Sichuan University

description:
Library name: sample 43
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 9

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

source_name: epididymal white adipose tissue

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: epididymal white adipose tissue

value: male


title: E7

status: Public on Dec 04 2025

type: SRA

country: China

description:
Library name: sample 41
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 7

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: Sex


title: E8

description:
Library name: sample 42
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 8


title: Ngn2_C11C_SETD1A_del_mutant [EX16KI_11M1]

city: New Brunswick

first: Zhiping

last: Pang

state: New Jersey

address: 89 French Street Floor 3, Room 3233

department: Child Health Institute of New Jersey

country: USA

institute: Rutgers University

data_processing:
Raw fastq sequencing files were aligned with human reference genome (hg38) using HISAT2 for patient-specific mutation and STAR for frameshif mutation.
Raw counts of expressed genes were extracted using featureCounts from the Rsubread package.
Assembly: hg38
Supplementary files format and content: Samples x genes, raw counts

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Ngn2-iN cultures are fed with Neurobasal medium with 5%FBS and three growth factors (BDNF, GDNF and NT3).

extract_protocol:
Total RNA was prepared using Qiagen Rneasy kits, followed by poly(A) selection using oligo-dT magnetic beads.
Illumina TruSeq 3' RNA Library kits were used.

tag: cell line

tag: cell type

tag: genotype

value: SETD1A heterozygous mutant c.4582-2delAG (del)


title: E6

description:
Library name: sample 40
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 6


title: Ngn2_C11C_SETD1A_del_control [EX16KI_11C3]

value: Control


title: Ngn2_C11C_SETD1A_del_control [EX16KI_11C1]


title: E4

description:
Library name: sample 38
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 4


title: Ngn2_C11C_SETD1A_del_control [EX16KI_11C2]


title: E5

description:
Library name: sample 39
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 5


title: Chondrocytes, Input

city: Nanchang

first: Jinghong

last: Yuan

state: Jiangxi

address: No.1 Minde Road

institute: The Secondly Affiliated Hospital of Nanchang University

library_source: genomic

data_processing:
The samples were diluted to a final concentration of 8 pM and cluster generation was performed on the Illumina cBot, following NovaSeq 6000 S4 Reagent Kit manufacturer’s instructions.
Sequencing was performed on Illumina NovaSeq 6000 using NovaSeq 6000 S4 Reagent Kit (300 cycles), according to the manufacturer’s instructions.
Images analysis and base calling à Solexa CHASTITY quality filter à Human genome (UCSC hg19) alignment à Peak detection à Peak annotation.
Statistically significant ChIP-enriched regions (peaks) detected by MACS were identified by comparison of IP_vs_input or comparison to a Poisson background model, using a p-value threshold of 0.0001. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each comparison. The following list only shows part of IP_vs_input_1e-4_10_30_peaks.xls results.
Assembly: hg19
Supplementary files format and content: wig, bed, xlsx

molecule: genomic DNA

source_name: Chondrocytes

extract_protocol:
The purity and concentration of DNA samples were determined with Qubit® Fluorometer. Results are provided in this report.
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer's instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

value: Chondrocytes

tag: chip antibody


title: Ngn2_CD07_SETD1A_del_mutant [EX16KI_7M2]


title: Chondrocytes, ZNF-148_CHIP

value: ZNF-148 (Santa Cruz,sc-398148X)


title: Ngn2_CD07_SETD1A_del_mutant [EX16KI_7M3]


title: Ngn2_CD07_SETD1A_del_mutant [EX16KI_7M1]


title: TILs WIOG Day14_1

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

country: South Korea

institute: CHA Bundang Medical Center

description:
D14 WIOG_SC245
Day 14 WIOG TILs-rep1

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (hg19) using HISAT v2.1.0 (KIM et al, 2015) and then, transcript assembly of known transcripts was processed by StringTie v1.3.4d (Pertea, Mihaela, et al., 2015, 2016).
Based on the result of that, expression abundance of transcript and gene were calculated as read count or TPM value per sample.
The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes).
WIOG The fold change was calculated between WIO group and WIOG group. The statistical significances were calculated using ANOVA
Assembly: The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from the NCBI.
Supplementary files format and content: FPKM, TPM values of genes for 6 samples, 3 from day 14 WIO and 3 from day 14.

source_name: Tumor infiltrating lymphocyte

growth_protocol: Following tumor processing, single cells were cultured in complete medium (CM) for 14 days. CM for culturing TILs consisted of 1:1 mixture of RPMI1640 medium with GlutaMAX (Gibco) supplemented with 10% human serum albumin (Sigma Aldrich, St.Louis, MO, USA), 100 U/ mL penicillin and 100 μg/mL streptomycin (Gibco), 55µM 2-mercaptoethanol (Gibco) and AIM-V medium (Gibco).

extract_protocol:
RNA of sorted cells at Day 0 and Day 14 was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
In order to construct cDNA libraries, we used the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., San Diego, CA, USA). The protocol comprised polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription, and 100 nt paired-end sequencing using Illumina NovaSeq 6000 (Illumina, Inc)

treatment_protocol: TILs were expanded in four conditions with IL-2 (Peprotech, Cranbury, NJ, USA): (1) control (W group), (2)anti-PD1 antibody (WI group), (3) anti-PD1 antibody + IL-15 + IL-21 (WIO group), (4) anti-PD1 antibody + IL-15 + IL-21 +anti-GITR antibody (BPS Bioscience, San Diego, CA, USA) (WIOG group).

tag: source

value: Ovarian tumor

value: Tumor infiltrating lymphocyte

tag: culture day

tag: treatment

value: cultured with anti-GITR (WIOG group)


title: E3

description:
Library name: sample 37
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 3


title: E1

description:
Library name: sample 35
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 1


title: E2

description:
Library name: sample 36
HFD, 60% fat+SZ-A（600 mg/kg/day), replicate biosample 2


title: Ngn2_CD07_SETD1A_del_control [EX16KI_7C3]


title: Ngn2_CD07_SETD1A_del_control [EX16KI_7C2]


title: Ngn2_C11C_SETD1A_del_mutant [EX16KI_11M3]


title: D7

description:
Library name: sample 33
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 7


title: Ngn2_CD07_SETD1A_del_control [EX16KI_7C1]


title: D6

description:
Library name: sample 32
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 6


title: Ngn2_C11C_SETD1A_del_mutant [EX16KI_11M2]


title: D8

description:
Library name: sample 34
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 8


title: D5

description:
Library name: sample 31
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 5


title: D3

description:
Library name: sample 29
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 3


title: Normal_P4_m6a_input

city: Kunming

first: Li

last: He

state: Yunnan

address: No. 295 Xichang Road

institute: First Affiliated Hospital of Kunming Medical University

data_processing:
FastQC (version 0.11.9) was used to access the base quality of raw data and trim_galore (version 0.0.1) was used to trim the adaptor and low-quality reads with parameters -q 25 --phred33 --length 40 -e 0.1 --stringency 3.
After quality control, the remaining reads were mapped to the reference genome (hg19).
Peaks were called using R package ‘MeRIPtools’ with the significance cut-off q-value <=0.05 and a consensus peak that requires peak to be called in at least 2 samples in 5 AK/SCC or 3 samples in 10 normal.
Bigwig files adjusted by input data were all generated using deeptools (version 3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: MeRIP-seq

source_name: skin

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RNA Integrity Number (RIN) >7.0. Poly(A) RNA is purified from 30μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, USA) using two rounds of purification. Then the poly(A)RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, USA) under 86℃ for 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630).
The IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, USA), RNase H (NEB, USA) and dUTP Solution (Thermo Fisher, USA). An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec, and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: skin

value: Normal


title: Normal_P4_m6a_IP


title: D1

description:
Library name: sample 27
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 1


title: C9

description:
Library name: sample 26
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 9


title: Normal_P3_m6a_IP


title: C7

description:
Library name: sample 24
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 7


title: Normal_P1_m6a_input


title: Normal_P2_m6a_input


title: C6

description:
Library name: sample 23
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 6


title: C8

description:
Library name: sample 25
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 8


title: cSCC_P5_m6a_input

value: cSCC


title: C5

description:
Library name: sample 22
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 5


title: C3

description:
Library name: sample 20
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 3


title: cSCC_P5_m6a_IP


title: Normal_P2_m6a_IP


title: cSCC_P4_m6a_input


title: Normal_P5_m6a_input


title: C2

description:
Library name: sample 19
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 2


title: cSCC_P4_m6a_IP


title: Normal_P1_m6a_IP


title: cSCC_P3_m6a_input


title: D4

description:
Library name: sample 30
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 4


title: Normal_P5_m6a_IP


title: C4

description:
Library name: sample 21
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 4


title: C1

description:
Library name: sample 18
HFD, 60% fat+SZ-A（200 mg/kg/day), replicate biosample 1


title: B9

description:
Library name: sample 16
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 9


title: Normal_P3_m6a_input


title: cSCC_P3_m6a_IP


title: cSCC_P2_m6a_input


title: B8

description:
Library name: sample 15
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 8


title: B7

description:
Library name: sample 14
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 7


title: cSCC_P1_m6a_input


title: B6

description:
Library name: sample 13
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 6


title: B5

description:
Library name: sample 12
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 5


title: cSCC_P1_m6a_IP


title: B4

description:
Library name: sample 11
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 4


title: B3

description:
Library name: sample 10
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 3


title: Normal_P10_m6a_input


title: Normal_P9_m6a_input


title: Normal_P8_m6a_input


title: Normal_P9_m6a_IP


title: B2

description:
Library name: sample 9
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 2


title: A7

description:
Library name: sample 7
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 7


title: A5

description:
Library name: sample 5
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 5


title: A4

description:
Library name: sample 4
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 4


title: B10

description:
Library name: sample 17
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 10


title: Normal_P7_m6a_input


title: A3

description:
Library name: sample 3
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 3


title: A6

description:
Library name: sample 6
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 6


title: Normal_P8_m6a_IP


title: A2

description:
Library name: sample 2
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 2


title: AK_P10_m6a_input

value: AK


title: 20240320-LC-2_BC27

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

description: RNA-seq of  homo sapiens: lung cancer patient's plasma; Provided by Beijing chest hospital capital medical university.

data_processing:
Adapt cut  fastq files were merged by reverse R1 file using seqtk  merge. The combine files were sequentially mapped to human transcriptome by STAR STAR_2.5.3a_modified (parameters: —outSAMmultNmax 1 --outSAMtype BAM Unsorted): spike-in, univec, rRNA, MT_rRNA, MT_mRNA, MT_tRNA, chrM.all, mRNA, lncRNA, pseudogene, tRNA,srpRNA, snoRNA,snRNA, Y_RNA, misc_RNA, tucpRNA, exon, intron, intergenic
feature were summarized by featurecounts.
Assembly: hg38

source_name: plasma

extract_protocol:
Peripheral whole blood samples were collected from individuals before therapy or surgery using EDTA-coated vacutainer tubes. Plasma was separated within 2 hr after collection by centrifuge at 1,900 g for 10 min at 4 ℃. All plasma samples were aliquoted and stored at -80°C. CfRNAs were extracted using QIAzol Lysis Reagent (QIAGEN, Beijing, China), and DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China). End repair and polyadenylation were performed using E. coli Poly(A) Polymerase (NEB, Beijing, China), and T4 Polynucleotide Kinase (NEB, Beijing, China).
Reverse transcription and libraries were prepared according to DETECTOR-seq protocol with minor modifications by replacing original TSO with uracil-containing TSO and extra digestion with Uracil-DNA Glycosylase (NEB, Beijing, China) after reverse transcription. Library quantification was performed by Qubit dsDNA HS Kit. Library fragment size and quality were checked using Agilent 2100 Bioanalyzer. Libraries were sequenced on MGI Tech DNBSEQ-T7 with PE150.

value: plasma

tag: condition

value: Benign


title: A1

description:
Library name: sample 1
SD，10% fat, 20% protein, 70% carbohydrate, replicate biosample 1


title: Normal_P10_m6a_IP


title: Normal_P6_m6a_IP


title: stTW3

city: Wuhan

first: xinran

last: zhao

address: No. 169, Donghu Road, Wuchang District

department: Department of Stomatology

institute: Zhongnan Hospital of Wuhan University

description:
Library name: sample 18
Stiff-TW group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

tag: sample group

value: Stiff-TW group


title: AK_P10_m6a_IP


title: Normal_P7_m6a_IP


title: stTW2

description:
Library name: sample 17
Stiff-TW group, replicate biosample 2


title: AK_P9_m6a_input


title: cSCC_P2_m6a_IP


title: B1

description:
Library name: sample 8
HFD，60% fat, 20% protein, 20% carbohydrate, replicate biosample 1


title: AK_P9_m6a_IP


title: stTW1

description:
Library name: sample 16
Stiff-TW group, replicate biosample 1


title: Normal_P6_m6a_input


title: stmito3

description:
Library name: sample 15
Stiff+mito group, replicate biosample3

value: Stiff+mito group


title: stmito2

description:
Library name: sample 14
Stiff+mito group, replicate biosample2


title: AK_P7_m6a_input


title: stmito1

description:
Library name: sample 13
Stiff+mito group, replicate biosample1


title: AK_P8_m6a_IP


title: st3

description:
Library name: sample 12
Stiff group, replicate biosample 3

value: Stiff group


title: AK_P7_m6a_IP


title: AK_P6_m6a_input


title: st1

description:
Library name: sample 10
Stiff group, replicate biosample 1


title: soTW2

description:
Library name: sample 8
Soft-TW group, replicate biosample 2

value: Soft-TW group


title: AK_P6_m6a_IP


title: st2

description:
Library name: sample 11
Stiff group, replicate biosample 2


title: soTW3

description:
Library name: sample 9
Soft-TW group, replicate biosample 3


title: cSCC_P5_atac

data_processing:
FastQC (version 0.11.9) was used to access the base quality of raw data and trim_galore (version 0.0.1) was used to trim the adaptor and low-quality reads with parameters -q 25 --phred33 --length 40 -e 0.1 --stringency 3.
After quality control, the remaining reads were mapped to the reference genome (hg19) using bwa (version 0.7.17-r1188). High mapping quality reads with MAPQ>=30 were remained and then duplicated reads were filtered by sambamba (version 0.8.2).
Peak calling was performed by using MACS2 (version 2.2.6) with parameters -g hs --nomodel --shift 100 --extsize 200 -q 0.05.
Promoter ATAC signal levels were used to represent the accessibility of genes which were obtained by calculating the TPM within the 1kb range of the upstream and downstream tss.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
1 ml of 1 XHB buffer was added into the tissue sample, after grinding and filtering, filtrate was centrifuged at 4℃ 500×g for 5 min, and then supernatant was discarded, density gradient centrifugation for 10 min, nucleus suspension was obtained. 50,000 nuclei were taken and resuspended in Tn5 transposase reaction mixture. The transposition reaction was incubated at 37℃ for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.


title: Normal_P1_atac


title: cSCC_P2_atac


title: somito3

description:
Library name: sample 6
Soft+mito group, replicate biosample 3

value: Soft+mito group


title: cSCC_P4_atac


title: soTW1

description:
Library name: sample 7
Soft-TW group, replicate biosample 1


title: cSCC_P1_atac


title: somito1

description:
Library name: sample 4
Soft+mito group, replicate biosample 1


title: AK_P8_m6a_input


title: so3

description:
Library name: sample 3
Soft group, replicate biosample 3

value: Soft group


title: Normal_P7_atac


title: Normal_P6_atac


title: Normal_P8_atac


title: Normal_P2_atac


title: somito2

description:
Library name: sample 5
Soft+mito group, replicate biosample 2


title: so1

description:
Library name: sample 1
Soft group, replicate biosample 1


title: so2

description:
Library name: sample 2
Soft group, replicate biosample 2


title: Sample 3, WT BMDMs, IL-4-stimulated M2, 48 hours

city: Cleveland

first: Brian

middle: A

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

department: Pathology

institute: Case Western Reserve University School of Medicine

description: Library name: WT3_M2_48

data_processing:
Transcripts Assembly: Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Different expression analysis of mRNAs: StringTie was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2 between two different groups (and by R package edgeR between two samples). The mRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed mRNAs.
Assembly: mus musculus v101
Supplementary files format and content: Excel spreadsheet with gene names, FPKM values, and associated statistics

source_name: bone marrow

growth_protocol: Mice were sacrificed via CO2 inhalation according to an IACUC protocol approved by CWRU. Nested microcentrifuge tubes were prepared with a hole poked in the inner tube. Femurs were spun in the inner tube for 10 minutes at 2,000xg to spin out marrow. Bone marrow pellets were resuspended in BMDM media, counted, and plated in 10 cm petri dishes at 5 million cells per plate. Cells were plated in 7.5 mL BMDM media and 2.5 mL L929-conditioned media. Cells were incubated at 37°C and 5% CO2. Media was supplemented on Day 3 via addition of 2 mL BMDM media and 1 mL L929-conditioned media per plate. All media was removed from plates on Day 6 and replaced with 7.5 mL fresh BMDM media and 2.5 mL fresh L929-conditioned media. Cells were washed with 1X PBS (Gibco, Thermo Fisher Scientific), scraped, and utilized for experiments on Day 7.

extract_protocol:
Rneasy total RNA extraction according to the manufacturer's protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification.
After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature, followed by first strand synthesis, second strand synthesis with dUTP, end repair, 3'adenylation, adapt ligation, UDG treatment, and finally PCR. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: Cells were seeded following harvest on day 7 as described above. Polarization growth was in media containing 25% L929-conditioned media. Cells were polarized to M2-like utilizing 20 ng/mL IL-4 (R&D Systems). Polarizations were carried out for 48 hours at 37°C and 5% CO2.

value: bone marrow

value: bone marrow-derived macrophages

value: macrophage

value: C57Bl/6 wild type

value: derived with 25% L929 conditioned media, polarized with 20ng/ml IL-4 for 48 hours

tag: batch


title: Sample 2, WT BMDMs, IL-4-stimulated M2, 48 hours

description: Library name: WT2_M2_48


title: AK_P7_atac

value: skin


title: AK_P6_atac


title: Sample 1, WT BMDMs, IL-4-stimulated M2, 48 hours

description: Library name: WT1_M2_48


title: HEPG2-PAOA-igg

city: Shanghai

first: Liang

last: Li

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126). Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly, 100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: Human Liver Cancer

value: lipid overload-induced


title: Sample 3, CD22 knockout BMDMs, IL-4-stimulated M2, 48 hours

description: Library name: KO3_M2_48

value: C57Bl/6 global CD22 knockout


title: Sample 2, CD22 knockout BMDMs, IL-4-stimulated M2, 48 hours

description: Library name: KO2_M2_48


title: HEPG2-PAOA


title: HEPG2-DMSO-igg

value: mock-induced


title: Sample 1, CD22 knockout BMDMs, IL-4-stimulated M2, 48 hours

description: Library name: KO1_M2_48


title: HEPG2-DMSO


title: Wildtype rep1, Cerebellum, NeuroD1 (ChIP)

city: Nashville

first: Lei

last: Chen

state: TN

address: 465 21st Ave. South

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

description: Library name: Cerebellum_Wildtype_NeuroD1_rep1, ChIP

data_processing:
ChIP-seq reads were initially processed using Cutadapt to remove sequencing adapter sequences, followed by alignment of the sequences to the mouse mm10 genome with Bowtie2.
The aligned results were then converted into BAM files using Samtools and filtered to exclude reads aligning to mitochondrial DNA and regions on the blacklist.
PCR duplicates were removed utilizing Picard's MarkDuplicates tool.
Peaks were called in comparison with IgG ChIP-seq controls using MACS2.
Reproducible peaks were identified using the Irreproducible Discovery Rate method.
Assembly: mm10
Supplementary files format and content: BigWig (except for IgG and Input samples)

source_name: Cerebella

extract_protocol:
Cerebellar tissue  was sectioned into small pieces approximately 0.5 mm in size. Subsequently, these fragments were digested with a cold protease cocktail solution, which contained cold protease (Sigma-Aldrich) (5mg/ml) and Dnase (Sigma-Aldrich) (2.5mg/ml), for 15 minutes in a water bath maintained at 6℃, with gently pipetting to mechanically dissociate the tissues every five minutes during this period. After dissociation, the digestion enzyme mixtures were passed through a 40μm filter (Miltenyi Biotech) and washed twice by 1XPBS solution. The BD FACS Aria III cell sorter was used to purify GCPs based on the intensity of Atoh1-GFP fluorescence at the single-cell level.
ChIP-seq was followed by the ChIPmentation protocol(Xu et al., 2020). In brief, purified cells were cross-linked with 1% formaldehyde/PBS solution at room temperature for 15 minutes before quenching with 250 mM glycine. For co-repressor(Sin3A and Hdac1) ChIP assays, an additional protein cross-linking step using 2mM disuccinimidyl glutarate was incorporated. Chromatin was subsequently fragmented to the size of 200~1000bp by sonication for 21 seconds using a Diagenode One device (Diagenode, NJ). Soluble chromatin was then obtained and incubated overnight at 4°C with the target antibody. Afterward, Dynabeads Protein A/G (10001D/10003D, Thermo Fisher Scientific, MA) were added for two hours to capture the antibody-chromatin complexes. Unbound chromatin were removed through multiple washes following a high-salt buffter, low-salt buffer, LiCl buffer, and 10mM Tris buffter sequence to ensure specificity of binding to the beads. Subsequently, an on-bead tagmentation step were performed using transposase Tn5 (20034197, Illumina, CA) to facilitate the ligation of sequencing adapters to the DNA. The DNA was then eluted from the beads and purified using AMPure XP Beads (A63880, Beckman Coulter, IN). Finally, the ChIP DNA was amplified to generate a sequencing library with Illumina Nextera DNA CD Indexes (20018707, Illumina, CA). All libraries are sequenced and performed at multiplex Paired-End 150 bp on a Illumina NovaSeq 600 at Vanderbilt Technologies for Advanced Genomics.

value: Cerebella

value: Mouse Cerebellar Cells

value: Wildtype


title: STM + PAOA-IP biol rep 1

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
ChIP-seq reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
Libraries were prepared via xGen™ssDNA & Low-Input DNA Library Prep Kit


title: Wildtype, Cerebellum, (Input)

description: Library name: Cerebellum_Wildtype_Input, INPUT


title: STM + PAOA-IgG biol rep 1


title: STM + PAOA-IgG biol rep 2


title: STM + PAOA-IP biol rep 2


title: STM + Mock-IP biol rep 2


title: Wildtype, Cerebellum, IgG (ChIP)

description: Library name: Cerebellum_IgG, ChIP


title: Wildtype rep1, Cerebellum, Hdac1 (ChIP)

description: Library name: Cerebellum_Wildtype_Hdac1_rep1, ChIP


title: Wildtype rep2, Cerebellum, Hdac1 (ChIP)

description: Library name: Cerebellum_Wildtype_Hdac1_rep2, ChIP


title: STM + Mock-IP biol rep 1


title: NeuroD1 KO rep1, Cerebellum, Sin3A (ChIP)

description: Library name: Cerebellum_NeuroD1-KO_Sin3A_rep1, ChIP

value: NeuroD1 LacZ/LacZ


title: NeuroD1 KO rep2, Cerebellum, Sin3A (ChIP)

description: Library name: Cerebellum_NeuroD1-KO_Sin3A_rep2, ChIP


title: STM + Mock-IgG biol rep 2


title: AK_P8_atac

value: AK


title: AK_P10_atac


title: Wildtype rep2, Cerebellum, Sin3A (ChIP)

description: Library name: Cerebellum_Wildtype_Sin3A_rep2, ChIP


title: Wildtype rep1, Cerebellum, Sin3A (ChIP)

description: Library name: Cerebellum_Wildtype_Sin3A_rep1, ChIP


title: Mock + PAOA-IP biol rep 2


title: NeuroD1 control rep2, GCP, H3K27ac (ChIP)

description: Library name: GCP_NeuroD1-control_H3K27ac_rep2, ChIP

value: Mouse Granule cell precursors

value: Atoh1 M1GFP/+


title: Wildtype rep2, Cerebellum, NeuroD1 (ChIP)

description: Library name: Cerebellum_Wildtype_NeuroD1_rep2, ChIP


title: Mock + PAOA-IP biol rep 1


title: Mock + PAOA-IgG biol rep 2


title: NeuroD1 control rep1, GCP, H3K27ac (ChIP)

description: Library name: GCP_NeuroD1-control_H3K27ac_rep1, ChIP


title: Mock + PAOA-IgG biol rep 1


title: NeuroD1 KO rep2, GCP, H3K27ac (ChIP)

description: Library name: GCP_NeuroD1-KO_H3K27ac_rep2, ChIP

value: NeuroD1 LacZ/LacZ; Atoh1 M1GFP/+


title: Sin3A CKO, GCP, IgG (ChIP)

description: Library name: GCP_Sin3A-CKO_IgG, ChIP

value: Sin3A F/F; Atoh1-Cre; Atoh1 M1GFP/+


title: NeuroD1 KO rep1, GCP, H3K27ac (ChIP)

description: Library name: GCP_NeuroD1-KO_H3K27ac_rep1, ChIP


title: Mock + Mock-IP biol rep 1


title: Sin3A CKO rep2, GCP, H3K27ac (ChIP)

description: Library name: GCP_Sin3A-CKO_H3K27ac_rep2, ChIP


title: Control rep2, GCP, H3K27ac (ChIP)

description: Library name: GCP_Control_H3K27ac_rep2, ChIP


title: Mock + Mock-IP biol rep 2


title: Sin3A CKO rep1, GCP, H3K27ac (ChIP)

description: Library name: GCP_Sin3A-CKO_H3K27ac_rep1, ChIP


title: Control rep1, GCP, H3K27ac (ChIP)

description: Library name: GCP_Control_H3K27ac_rep1, ChIP


title: r2_ST_BRM014_H3K14ac

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
adapter and quality trimming; cutadapt
genomic alignment; bowtie2
peakcalling; Genrich
read counts and normalization; DiffBind
bigwig generation; deeptools
Assembly: GENCODE V38
Supplementary files format and content: Genrich peaks considering all matched replicates and inputs
Supplementary files format and content: Bigwig of ChIP signal

source_name: placenta

extract_protocol:
The cells were fixed with 1% formaldehyde (ThermoFisher, 28908) for 7 minutes at room temperature. The reaction was quenched by 0.125M glycine. The cells were harvested in PBS containing 1x complete EDTA-free Protease inhibitor cocktail (Sigma Aldrich, 5056489001), centrifuged, and resuspended in ice-cold immunoprecipitation (IP) buffer. IP buffer was freshly made by 2:1 mixture of SDS buffer (100mM NaCl, 50mM Tris pH8, 5mM EDTA pH8, 0.5% SDS) and TritonX buffer (100mM NaCl, 100mM Tris pH 8.6, 5mM EDTA pH8, 5% TritonX) and 1x complete EDTA-free Protease inhibitor cocktail. Sonication was performed using Bioruptor Pico (Diagenode) at 4°C for 23 cycles, 15 seconds ON/ 30 seconds OFF. 30µg (for transcription factors) and 10µg (for histone modifications) of chromatin (DNA equivalent) were immunoprecipitated at 4°C overnight with primary antibodies. Detailed information on antibodies is provided in Table X. at the end of this chapter. Spike in chromatin (Active Motif, 53083) and Spike in antibody (Active Motif, 61686) were used for normalization of sample processing bias, technical variation, and monitoring of inhibitory effects. Protein G Dynabeads (Invitrogen, 10004D) were blocked in IP buffer supplemented with 1mg/mL BSA (New England Biolabs, B9000S) and yeast tRNA for 60 minutes at 4°C. Next, the beads were washed and added to the immunoprecipitation reaction for 3 hours at 4°C. The samples were washed with low salt buffer (50mM HEPES pH7.5, 140mM NaCl, 1%TritonX, 1x complete EDTA-free Protease inhibitor cocktail), high salt buffer (50mM HEPES pH7.5, 500mM NaCl, 1%TritonX, 1x complete EDTA-free Protease inhibitor cocktail) and TE buffer. Each sample was eluted in 200µL of ChIP elution buffer (100Mm NaHCO3, 1%SDS) and de-crosslinked using 0.2M NaCl at 65°C, 600 rpm overnight. On the next day, the samples were treated with RNAse A (60 minutes at 37°C, 600 rpm) and Proteinase K (30 min at 65°C). The samples were purified with MinElute PCR purification kit (QIAGEN). The DNA content was quantified by QUBIT dsDNA HS assay kit (ThermoFisher, Q33230). 10ng of DNA per sample was used for library preparation using NEBNext Ultra II DNA library preparation master mix (New England Biolabs, E7645).
NEBnext Ultra II

value: placenta

value: ST

value: WT

value: Forskolin + BRM014


title: Control, GCP, IgG (ChIP)

description: Library name: GCP_Control_IgG, ChIP


title: Mock + Mock-IgG biol rep 1

value: Human Liver Cancer


title: r2_ST_H3K14ac

value: Forskolin


title: GEMM_Placebo_3

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: Library name: Sample 20

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

source_name: Oviductal tissue

extract_protocol:
Total RNA was extracted using a Qiagen miRNAeasy mini kit (Qiagen 1038703) according to the manufacturer's protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: Female 6-8 week old Ovgp1-iCreERT2; BPRN-het mice were implanted with slow-release (90 day) hormone pellets MPA (25 mg),P4(25mg), E2+P4 (0.05 mg 17β-estradiol + 25 mg P4) and placebo control ( 25mg) subcutaneously under the dorsal skin.  Three days later, mice were treated transiently with Tamoxifen (TAM, 0.2g/kg body weight, on day 1 and day 3) to induce Cre-mediated recombination of the floxed TSG alleles in the oviductal epithelium. After14 days post TAM treatment, mouse oviductal tissues were harvested to obtain RNAs for RNA-seq.

value: Oviductal tissue

value: Ovgp1-iCreERT2; Brca1flox/+, Trp53 flox/+, Rb1 flox/+, Nf1 flox/+,

value: Placebo and TAM-induced gene deletion


title: GEMM_Placebo_1

description: Library name: Sample 18


title: r2_SR_BRM014_H3K14ac

value: hTSC


title: STM + Mock-IgG biol rep 1


title: r2_SR_H3K14ac


title: GEMM_Placebo_2

description: Library name: Sample 19


title: r1_ST_BRM014_H3K14ac


title: r1_ST_H3K14ac


title: GEMM_P4_3

description: Library name: Sample 17

value: P4 and TAM-induced gene deletion


title: r1_SR_BRM014_H3K14ac


title: GEMM_P4_2

description: Library name: Sample 16


title: r3_ST_BRM014_H3K4me3

description: H3K4me3_STinh_215360vs215358_215384vs215382_223311_223308_def.narrowPeak


title: r1_SR_H3K14ac


title: GEMM_noPwithTAM_4

description: Library name: Sample 14

value: TAM-induced gene deletion


title: GEMM_P4_1

description: Library name: Sample 15


title: Mock + Mock-IgG biol rep 2


title: r3_ST_BRM014_H3K27ac

description: H3K27ac_STinh_223275vs215358_223283vs215382_223310_223308_def.narrowPeak


title: GEMM_noPwithTAM_2

description: Library name: Sample 12


title: L-A-CDM4

city: Kansas City

first: Hongmin

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

institute: The University of Kansas Medical Center

description: Library name: Sample 32

data_processing:
RNA-Seq was sequenced as 75bp single reads on Illumina NextSeq 550 machine
Raw reads weredemultiplexed into Fastq format allowing up to one mismatch.
Reads were aligned to mouse reference genome (GRCm38.90) , using HISAT v.2.1.0.13.
TPM values were generated using HTSeq (version v0.6.0).
Pairwise differential expression analysis was performed using R package edgeR between the young and aged groups in control and EtOH conditions.
Assembly: mm10
Supplementary files format and content: Excell file includes raw counts for each sample

source_name: liver

extract_protocol:
Livers and hippocampus tissures were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared with standard Illumina protocol

treatment_protocol: young (3-month-old) and aged WT mice (22-month-old) were subjected to the Gao-Binge alcohol model.

value: liver

tag: strain

value: Control

tag: age


title: L-A-CDM3

description: Library name: Sample 31


title: r3_ST_BRM014_HMinput


title: r3_ST_BRM014_H2BK20ac

description: H2B_STinh_223274vs215358_223280vs215376_223309_223308_a500.narrowPeak


title: L-A-CDM2

description: Library name: Sample 30


title: GEMM_noPwithTAM_1

description: Library name: Sample 11


title: L-A-CDM1

description: Library name: Sample 29


title: L-A-EDE3

description: Library name: Sample 27

value: EtOH


title: r3_ST_BRM014_BRG1

description: BRG1_STinh_215357vs215355_215375vs215373_223307vs223305_a20_ATACmode.narrowPeak


title: GEMM_noPnoTAM_4

description: Library name: Sample 10

value: No treatment


title: L-A-EDE2

description: Library name: Sample 26


title: L-A-EDE4

description: Library name: Sample 28


title: L-A-EDE1

description: Library name: Sample 25


title: r3_ST_BRM014_TFinput


title: L-Y-CDM4

description: Library name: Sample 24


title: GEMM_noPnoTAM_2

description: Library name: Sample 8


title: r3_ST_BRM014_BRM

description: BRM_STinh_215356vs215355_215374vs215373_223306vs223305_a20_ATACmode.narrowPeak


title: L-Y-CDM3

description: Library name: Sample 23


title: r3_ST_H3K4me3

description: H3K4me3_ST_215354vs215352_215378vs215376_223304_223301_def.narrowPeak


title: GEMM_noPnoTAM_3

description: Library name: Sample 9


title: L-Y-CDM1

description: Library name: Sample 21


title: L-Y-EDE3

description: Library name: Sample 19


title: L-Y-EDE4

description: Library name: Sample 20


title: GEMM_MPA_3

description: Library name: Sample 6

value: MPA and TAM-induced gene deletion


title: GEMM_noPwithTAM_3

description: Library name: Sample 13


title: r3_ST_HMinput

value: placenta


title: GEMM_MPA_2

description: Library name: Sample 5


title: L-Y-EDE1

description: Library name: Sample 17


title: H-A-CDM4

description: Library name: Sample 16

source_name: hippocampus

value: hippocampus


title: r3_ST_H2BK20ac

description: H2B_ST_223272vs215352_223282vs215382_223302_223301_a500.narrowPeak

value: ST

value: WT


title: L-Y-EDE2

description: Library name: Sample 18


title: r3_ST_BRG1

description: BRG1_ST_215351vs215349_215381vs215379_223300vs223298_a20_ATACmode.narrowPeak


title: H-A-CDM3

description: Library name: Sample 15


title: GEMM_E2P4_4

description: Library name: Sample 3

value: E2+P4 and TAM-induced gene deletion


title: H-A-EDE3

description: Library name: Sample 11


title: GEMM_E2P4_2

description: Library name: Sample 2


title: H-A-CDM2

description: Library name: Sample 14


title: H-A-EDE4

description: Library name: Sample 12


title: r3_ST_TFinput

value: Forskolin


title: H-A-EDE2

description: Library name: Sample 10


title: H-A-EDE1

description: Library name: Sample 9


title: r3_ST_H3K27ac

description: H3K27ac_ST_215354vs215352_215378vs215376_223303_223301_def.narrowPeak


title: H-Y-CDM2

description: Library name: Sample 6


title: Case_Gcm1

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

description: Library name: Case_Gcm1

data_processing:
The raw sequencing data were examined using the illumina analysis pipeline.
Using Bowtie2, the data were aligned to the Mus musculus reference genome (University of California, Santa Cruz, mm10).
The data were further analyzed through the ChIP-seq analysis based on the model (MACS) program (https://github.com/taoliu/MACS).
The enriched binding peaks were identified after normalization with the control input.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Supplementary files format and content: bigWig, narrowPeak

source_name: C57BL/6 mouse embryonic stem cells

growth_protocol: DMEM, UltraPure™ distilled water (Invitrogen, USA), 1 mM glucose, 0.1 mM nonessential amino acids, 0.1 mM glutamate, 15% FBS, 0.1 mM β-mercaptoethanol (Life Technologies, USA), 1000 U/ml leukemia inhibitory factor (Millipore, USA)  Cells were cultured at 37C at 5% CO2.

extract_protocol:
C57BL/6 mESCs were seeded into culture dishes precoated with MEFs cultured in DMEM supplemented with 0.1 mM nonessential amino acids, 0.1 mM glutamate, and 10% fetal bovine serum (FBS) (Invitrogen, USA) overnight.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 30 cycles on the thermocycler. Post amplification libraries were size selected at 250-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Folate power (Sigma–Aldrich, USA) was dissolved in Dulbecco’s modified Eagle’s medium (DMEM) 10X without folic acid (Sigma–Aldrich, USA) and with 3.7%. filtered sodium hydrogen carbonate (Beijing ChemicalReagent Company, China). The final concentration of 4 mg/L folate as a normal control while the folatedeficient group was treated simply by DMEM without folate.

value: C57BL/6 mouse embryonic stem cells

value: Folate-deficient


title: H-Y-CDM3

description: Library name: Sample 7


title: GEMM_noPnoTAM_1

description: Library name: Sample 7

value: Oviductal tissue

value: Ovgp1-iCreERT2; Brca1flox/+, Trp53 flox/+, Rb1 flox/+, Nf1 flox/+,


title: r3_SR_BRM014_H3K27ac

description: H3K27ac_SRinh_223271vs215346_223279vs215370_223296_223294_def.narrowPeak

value: hTSC


title: r3_SR_BRM014_H3K4me3

description: H3K4me3_SRinh_215348vs215346_215372vs215370_223297_223294_def.narrowPeak


title: L-Y-CDM2

description: Library name: Sample 22


title: GEMM_MPA_1

description: Library name: Sample 4


title: H-Y-EDE4

description: Library name: Sample 4


title: Con_Gcm1

description: Library name: Con_Gcm1

value: CON


title: H-Y-EDE2

description: Library name: Sample 2


title: r3_SR_BRM014_HMinput


title: r3_ST_BRM

description: BRM_ST_215350vs215349_215380vs215379_223299vs223298_a20_ATACmode.narrowPeak


title: H-Y-EDE3

description: Library name: Sample 3


title: H-A-CDM1

description: Library name: Sample 13


title: H-Y-EDE1

description: Library name: Sample 1


title: Con input

description: Library name: Con input


title: r3_SR_BRM014_BRG1

description: BRG1_SRinh_215345vs215343_215369vs215367_223293vs223291_a20_ATACmode.narrowPeak


title: r3_SR_BRM014_BRM

description: BRM_SRinh_215344vs215343_215368vs215367_223292vs223291_a20_ATACmode.narrowPeak


title: ileum_HPE_P337_rep1

city: Chapel Hill

first: Matthew

last: Niederhuber

state: NC

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

data_processing:
Nextflow (v23.10.1) and nf-core/rnaseq (v3.14.0)
Adapter trimming with Trim Galore! (v0.6.7)
Alignment with STAR (v2.7.9a)
Transcript quantification with Salmon (v1.10.1)
Assembly: Sscrofa11.1
Supplementary files format and content: Salmon quantification files with estimated TPM

organism: Sus scrofa

source_name: Neonata ileal monolayers

growth_protocol: The collected ileum was opened longitudinally along the antimesenteric border and then sub-sectioned into 1 cm pieces. Crypt isolation was completed as previously published apart from a shorter duration of incubation (20 minutes) in the first dissociation reagent.  Crypts were then plated for organoid culture which was performed as previously described. Enteroids were grown until reaching an adequate size to provide a sufficient number of cells for monolayer creation. Enteroids were dissociated from 3D Matrigel matrix using the protocol described by Van der Hee and colleagues with minor deviations. Briefly, ice-cold DMEM/F12 medium (ThermoFisher Scientific, Waltham, MA)  was applied to Matrigel patties, which were then transferred to 15 mL conical tubes and centrifuged for 5 min at 250xg. The supernatant was removed, and 2.5 mL of TrypLE Express dissociation media (Gibco) was added to the pellet, thoroughly mixed with repetitive pipetting, and then allowed to incubate for 10 min at 37C. After incubation, 8mL of 20% FBS in 80% culture media, was added to the vial which was then centrifuged at 600xg for 6 minutes. The supernatant was again removed, and the remaining cell pellet resuspended in the necessary volumes of culture media with 20% FBS (200 uL per monolayer).  Cells were quantified using a Cellometer Auto 2000 (Nexcelom) and plated onto 0.5% Matrigel-coated plates at a density of 78,125 – 100,000 cells/cm2. Monolayers were supplemented with FBS-enriched culture media and growth factor combination as previously published. Monolayers were grown until visual confluence.

extract_protocol:
Once nearly confluent (> 90%), monolayers were harvested for bulk RNA sequencing using the RNeasy ® Plus Mini Kit and protocol for total RNA extraction (Qiagen, Valencia, CA). Baseline yield and quality were determined (NanoDrop Technologies, Thermo Fisher Scientifid, Waltham, MA; 260/280 = 2.09 to 2.12). To further confirm quality, samples were evaluated for RNA Integrity Number (RIN) score (10 for all samples, RNA ScreenTape®, TapeStation Analysis Software 4.1, Agilent Technologies, Santa Clara, CA).
Samples were then submitted for bulk RNA sequencing which was performed through a series of steps including RNA Quantification and Normalization using the DeNovix RNA Fluorescence Assay, mRNA-Seq library preparation (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina), library quantification and normalization (DeNovix DNA Fluorescence Assay), library quality control (Agilent Bioanalyzer HS DNA Kit).

treatment_protocol: At the time of plating, wells were either treated with media alone (Control) or Human Placental Extract (HPE) (0.075 mg/mL). Monolayers were imaged daily to evaluate progress to confluence with daily replenishment of media, growth factors, and treatment prior to imaging. The percent confluence was recorded at each day and compared between HPE-treated and untreated monolayers (paired T-test or Wilcoxon test).

value: Neonata ileal monolayers

value: Human Placental Extract


title: 688M PDA cells, shKdm8, hypoxia, replicate 2

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

institute: Rutgers Cancer Institute of New Jersey

description:
Library name: Sample 8
Column name in "Kdm8KD_count_090522.txt": X688_shKdm8_Hyp_2

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 sequencer (paired-end 2x150bp, Novogene). Reads were mapped to the mm39 genome build using the STAR aligner (v2.7.5a). Reads counts at both transcript and gene levels were derived using htseq-count (--stranded=no --type=exon --mode=intersection-nonempty --idattr=gene_id or transcript_id) and scaled into transcripts per million using the R package “GenomicFeatures” and the NCBI RefSeq mm39 assembly.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file with raw counts per sample

source_name: Pancreatic

growth_protocol: PDA 688M cells expressing the control or Kdm8-targeting shRNA (shKdm8) were maintained in DMEM media with 10% FBS and antibiotics in humidified 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from PDA 688M cells using RNeasy Mini kit (Qiagen).
The Illumina sequencing libraries were built using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: PDA 688M cells were either cultured in normoxia (atmospheric O2) or hypoxia (<0.5% O2) for 48 hours prior to total RNA extraction.

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells

value: hypoxia


title: ileum_HPE_P337_rep2


title: H-Y-CDM4

description: Library name: Sample 8

value: Control


title: ileum_control_P337_rep2


title: 688M PDA cells, shKdm8, hypoxia, replicate 1

description:
Library name: Sample 7
Column name in "Kdm8KD_count_090522.txt": X688_shKdm8_Hyp_1


title: ileum_control_P337_rep1


title: r3_SR_BRM014_TFinput

value: placenta


title: 688M PDA cells, shGFP, hypoxia, replicate 2

description:
Library name: Sample 6
Column name in "Kdm8KD_count_090522.txt": X688_shGFP_Hyp_2


title: ileum_HPE_P342_rep2


title: ileum_HPE_P342_rep3


title: r3_SR_H3K4me3

description: H3K4me3_SR_215342vs215364_215366vs215340_223290_223287_def.narrowPeak


title: ileum_HPE_P342_rep1


title: H-Y-CDM1

description: Library name: Sample 5

value: hippocampus


title: r3_SR_BRM014_H2BK20ac

description: H2B_SRinh_223270vs215346_223278vs215370_223295_223294_a500.narrowPeak

value: WT


title: 688M PDA cells, shGFP, hypoxia, replicate 1

description:
Library name: Sample 5
Column name in "Kdm8KD_count_090522.txt": X688_shGFP_Hyp_1


title: ileum_control_P342_rep3


title: Case_input

description: Library name: Case_input


title: ileum_control_P342_rep2


title: ileum_control_P342_rep1


title: 688M PDA cells, shKdm8, normoxia, replicate 2

description:
Library name: Sample 4
Column name in "Kdm8KD_count_090522.txt": X688_shKdm8_Nor_2

value: normoxia


title: r3_SR_H2BK20ac

description: H2B_SR_215327_223312vs215340_223276vs215364_223288_223287_a500.narrowPeak


title: ileum_HPE_P336_rep2


title: 688M PDA cells, shGFP, normoxia, replicate 2

description:
Library name: Sample 2
Column name in "Kdm8KD_count_090522.txt": X688_shGFP_Nor_2


title: r3_SR_HMinput


title: ileum_control_P336_rep1


title: 688M PDA cells, shKdm8, normoxia, replicate 1

description:
Library name: Sample 3
Column name in "Kdm8KD_count_090522.txt": X688_shKdm8_Nor_1


title: r3_SR_BRG1

description: BRG1_SR_215339vs215337_215363vs215361_223286vs223284_a20_ATACmode.narrowPeak


title: 688M PDA cells, shGFP, normoxia, replicate 1

description:
Library name: Sample 1
Column name in "Kdm8KD_count_090522.txt": X688_shGFP_Nor_1


title: ileum_control_P336_rep2


title: ileum_HPE_P336_rep1


title: ileum_HPE_P335_rep1


title: ileum_HPE_P335_rep2


title: Tomato+lin- cancer cells isolated from mouse PTC308 (lung metastasis)

description:
Library name: Sample 11
Sample ID is L308 in processed files

library_source: transcriptomic single cell

data_processing:
Fastq files were mapped to a custom mm39 genome build (GRCm39 release 108 with the Tomato transcript) using the 10X CellRanger pipeline (v6.0.2). To exclude Jurkat cells in samples A252, A147, and L254, reads were also mapped to the GRCh38 genome reference. We used Seurat (v4) and custom R scripts for the identification of cell clusters, differential genes, and all the downstream cell state analyses. Briefly, CellRanger output sparse matrices were merged and read counts were normalized after removing potential doublets, dying cells, and Jurkat cells based on GRCm39 transcript count, mitochondria percent, and GRCh38 transcriptomic features, respectively. Distinct clusters of malignant cells were uncovered using SNN modularity optimization-based approach following linear transformation of data and dimensionality reduction. To calculate gene signature scores, we performed single sample GSEA using the GSVA r package (v4.4.2). For RNA velocity analysis, we inferred the latent time and estimated differential kinetics using scVelo (v0.3.3). Briefly, mapped bam files from the CellRanger pipeline were used to generate spliced and non-spliced expression matrices using default velocyto run10x command. Preprocessing was performed to compute first- and second-order moments for velocity estimation and subsequently the full splicing kinetics using the scv.tl.velocity() function. We then projected the velocity or latent time estimates onto the UMAPs for visualization.
Assembly: mm39
Supplementary files format and content: Seurat object with both scaled data and raw counts (n=32,878 cells in total); fully annotated metadata also include latent time, gene signature scores, Kdm8-Seq scores, and KrasBC-Seq results for subsets of the cells. All the spiked in Jurkat cells were removed.

growth_protocol: Cells were ex vivo isolated from spontaneous PDA tumors.

extract_protocol: Single-cell RNA-seq libraries were prepared using the 10X 5’ v2 dual indexed kit according to the user guide. In 3 metastatic lesions, we spiked in different numbers of Jurkat cells due to low cell counts of sorted Tomato-pos malignant cells (A252, A147, and L254). Following cDNA amplification, the cDNA pool was split and used for scRNA-Seq library construction, Kdm8-Seq, and KrasBC-Seq.

value: PTC;Kdm8-KO (CRISPR)


title: ileum_control_P335_rep1


title: ileum_control_P335_rep2


title: r3_SR_TFinput


title: r3_SR_BRM

description: BRM_SR_215338vs215337_215362vs215361_223285vs223284_a20_ATACmode.narrowPeak


title: ileum_HPE_P333_rep2


title: GEMM_E2P4_1

description: Library name: Sample 1

value: E2+P4 and TAM-induced gene deletion


title: D2

description:
Library name: sample 28
HFD, 60% fat+SZ-A（400 mg/kg/day), replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: epididymal white adipose tissue

value: male


title: ileum_HPE_P333_rep1


title: Tomato+lin- cancer cells isolated from mouse PTC147 (primary PDA tumor)

description:
Library name: Sample 9
Sample ID is T417 in processed files


title: ileum_control_P333_rep1


title: Tomato+lin- cancer cells isolated from mouse PTC308 (primary PDA tumor)

description:
Library name: Sample 10
Sample ID is T308 in processed files


title: r2_ST_H3K27ac

description: H3K27ac_ST_215354vs215352_215378vs215376_223303_223301_def.narrowPeak

value: ST

value: Forskolin


title: ileum_control_P333_rep2


title: Tomato+lin- cancer cells isolated from mouse PTC254 (primary PDA tumor)

description:
Library name: Sample 8
Sample ID is T254 in processed files


title: ileum_HPE_P332_rep2


title: r2_ST_BRM014_H3K27ac

description: H3K27ac_STinh_223275vs215358_223283vs215382_223310_223308_def.narrowPeak

value: Forskolin + BRM014


title: r3_SR_H3K27ac

description: H3K27ac_SR_215328_223313vs215340_223277vs215364_223289_223287_def.narrowPeak

value: hTSC


title: Tomato+lin- cancer cells isolated from mouse PTC252 (primary PDA tumor)

description:
Library name: Sample 7
Sample ID is T252 in processed files


title: r2_ST_BRM014_H2BK20ac

description: H2B_STinh_223274vs215358_223280vs215376_223309_223308_a500.narrowPeak


title: Tomato+lin- cancer cells isolated from mouse PTC218 (primary PDA tumor)

description:
Library name: Sample 6
Sample ID is T218 in processed files


title: r2_SR_BRM014_H3K27ac

description: H3K27ac_SRinh_223271vs215346_223279vs215370_223296_223294_def.narrowPeak


title: Homo liver-hepatocellular carcinoma-rep3

type: RNA

description: Samples were obtained from patients undergoing surgery for HCC at the Eastern Hepatobiliary Surgery Hospital (Shanghai, China).

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar Human circRNA Epitranscriptomic Microarray (8x15K, Arraystar)

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 1 out of 10 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated circRNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

label: Cy3, Cy5

source_name: Hepatocellular carcinoma

label_protocol: Briefly, the total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol.

growth_protocol: Patient samples were obtained following informed consent according to an established protocol approved by the Ethics Committee of Eastern Hepatobiliary Surgery Hospital. Permission was obtained from the Ethics Committee of Eastern Hepatobiliary Surgery Hospital to submit the data to GEO.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis.

treatment_protocol: Patient samples were collected immediately after HCC resection for total RNA isolation and microarray assess.

tag: gender

value: female

tag: excessive alcohol intake

value: no

tag: hbsag

value: negative

tag: hcv infection

value: yes

tag: hyperlipemia

tag: hypertension

value: positive

tag: bmi

tag: bclc stage

value: A


title: Homo liver-hepatocellular carcinoma-rep2


title: Tomato+lin- cancer cells isolated from mouse PTC254 (lung metastasis)

description:
Library name: Sample 5
Sample ID is L254 in processed files

tag: tissue

value: Pancreatic

tag: cell line

tag: cell type

value: pancreatic ductal adenocarcinoma cells

tag: genotype


title: Homo liver-paracarcinoma tissue-rep5

source_name: Para-carcinoma tissue


title: Homo liver-hepatocellular carcinoma-rep1

value: B


title: r2_SR_BRM014_H2BK20ac

description: H2B_SRinh_223270vs215346_223278vs215370_223295_223294_a500.narrowPeak

value: placenta

value: WT

tag: treatment


title: Homo liver-paracarcinoma tissue-rep4


title: Homo liver-paracarcinoma tissue-rep3


title: Tomato+lin- cancer cells isolated from mouse PTC218 (lung metastasis)

description:
Library name: Sample 4
Sample ID is L218 in processed files

value: PTC;Kdm8-KO (CRISPR)


title: Tomato+lin- cancer cells isolated from mouse PTC147 (ascites)

description:
Library name: Sample 3
Sample ID is A417 in processed files


title: r2_SR_H3K27ac


title: Homo liver-paracarcinoma tissue-rep1


title: ileum_HPE_P332_rep1

value: Neonata ileal monolayers

value: Human Placental Extract


title: r1_ST_BRM014_H3K27ac


title: kidney, FSGS, untreated, rep3

city: Hangzhou

first: Cao

last: Jiawei

address: No. 1630 Huan Ding Road, Shangcheng District

institute: Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University

description:
Library name: Sample 6
M3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Ensembl_v104
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: kidney

value: underwent unilateral nephrectomy of left kidneyunderwent unilateral nephrectomy of left kidney and injected with  adriamycin


title: Tomato+lin- cancer cells isolated from mouse PTC218 (ascites)

description:
Library name: Sample 1
Sample ID is A218 in processed files


title: r2_SR_H2BK20ac

description: H2B_SR_215327_223312vs215340_223276vs215364_223288_223287_a500.narrowPeak

value: hTSC


title: kidney, FSGS, untreated, rep2

description:
Library name: Sample 5
M2

value: underwent unilateral nephrectomy of left kidney and injected with  adriamycin


title: r1_ST_BRM014_H2BK20ac

value: ST

value: Forskolin + BRM014


title: ileum_control_P332_rep1


title: Homo liver-hepatocellular carcinoma-rep4

value: male

value: no

value: negative


title: r2_ST_H2BK20ac

description: H2B_ST_223272vs215352_223282vs215382_223302_223301_a500.narrowPeak

value: Forskolin


title: kidney, FSGS, untreated, rep1

description:
Library name: Sample 4
M1


title: Tomato+lin- cancer cells isolated from mouse PTC252 (ascites)

description:
Library name: Sample 2
Sample ID is A252 in processed files

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells


title: Homo liver-hepatocellular carcinoma-rep5

value: positive

value: A


title: Kdm8KO 688M PDA cells, Kdm8-W412N, hypoxia, clone 04

description:
Library name: Sample 16
Column name in "Kdm8expr_count_110323.txt": Hyp_KO4_W412N

growth_protocol: PDA 688M cells were maintained in DMEM media with 10% FBS and antibiotics in humidified 5% CO2 at 37C

treatment_protocol: Two Kdm8 knockout PDA 688M cell clones re-expressing wildtype Kdm8, the catalytically dead variant Kdm8-H319A, or the two hypermorphic variants Kdm8-W308Y or W412N were either cultured in normoxia (atmospheric O2) or hypoxia (<0.5% O2) for 48 hours prior to total RNA extraction.

value: hypoxia


title: r1_ST_H3K27ac

description: H3K27ac_ST_215354vs215352_215378vs215376_223303_223301_def.narrowPeak

value: placenta

value: WT


title: Kdm8KO 688M PDA cells, Kdm8-W412N, hypoxia, clone 03

description:
Library name: Sample 15
Column name in "Kdm8expr_count_110323.txt": Hyp_KO3_W412N


title: kidney, control, untreated, rep1

description:
Library name: Sample 1
C1

value: kidney

value: injected with saline


title: r1_ST_H2BK20ac


title: Kdm8KO 688M PDA cells, Kdm8-W412N, normoxia, clone 04

description:
Library name: Sample 14
Column name in "Kdm8expr_count_110323.txt": Nor_KO4_W412N

value: normoxia


title: treatment1

city: kunming

first: Xingyou

last: Deng

state: --- Select One ---

address: 120 Guanghua Street, Kunming City, Yunnan Province

institute: Yunnan Provincial Hospital of Traditional Chinese Medicine

description: Library name: Sample9

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. DESeq2 padj<=0.05 |log2FoldChange|>=1.0.
Assembly: mRatBN7.2

source_name: joint

extract_protocol:
Trizol (Ambition/Invitrogen, USA)
RNA libraries for RNA-seq were prepared using VAHTS Universal V5 RNA-seq Library Prep  Kit following manufacturer's protocols.

value: joint


title: r1_SR_BRM014_H3K27ac

value: hTSC


title: treatment3

description: Library name: Sample11


title: Kdm8KO 688M PDA cells, Kdm8-W412N, normoxia, clone 03

description:
Library name: Sample 13
Column name in "Kdm8expr_count_110323.txt": Nor_KO3_W412N


title: r1_SR_BRM014_H2BK20ac


title: model1

description: Library name: Sample5


title: model2

description: Library name: Sample6


title: model4

description: Library name: Sample8


title: model3

description: Library name: Sample7


title: Kdm8KO 688M PDA cells, Kdm8-W308Y, hypoxia, clone 03

description:
Library name: Sample 11
Column name in "Kdm8expr_count_110323.txt": Hyp_KO3_W308Y


title: Sham4

description: Library name: Sample4


title: Sham3

description: Library name: Sample3


title: Sham2

description: Library name: Sample2


title: r2_ST_BRG1

description: BRG1_ST_215351vs215349_215381vs215379_223300vs223298_a20_ATACmode.narrowPeak

value: ST


title: Kdm8KO 688M PDA cells, Kdm8-W308Y, hypoxia, clone 04

description:
Library name: Sample 12
Column name in "Kdm8expr_count_110323.txt": Hyp_KO4_W308Y


title: kidney, control, untreated, rep3

description:
Library name: Sample 3
C3


title: Kdm8KO 688M PDA cells, Kdm8-W308Y, normoxia, clone 03

description:
Library name: Sample 9
Column name in "Kdm8expr_count_110323.txt": Nor_KO3_W308Y


title: r2_ST_H3K4me3

description: H3K4me3_ST_215354vs215352_215378vs215376_223304_223301_def.narrowPeak


title: Kdm8KO 688M PDA cells, Kdm8-W308Y, normoxia, clone 04

description:
Library name: Sample 10
Column name in "Kdm8expr_count_110323.txt": Nor_KO4_W308Y


title: r2_ST_HMinput


title: treatment4

description: Library name: Sample12


title: r2_ST_BRM

description: BRM_ST_215350vs215349_215380vs215379_223299vs223298_a20_ATACmode.narrowPeak


title: scATAC-seq Sample 3 WT 20mo

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

description: Library name: WT_20mo_3_ATAC

library_source: genomic single cell

data_processing:
Cell Ranger ARC (cellranger-arc) from 10x Genomics was used to pricess Chromium Single Cell Multiome ATAC + Gene Expression (GEX) sequencing data. BCL files from from the Illumina NovaSeq were demultiplexed into paired-end, gzip-compressed FASTQ files using the default parameters of cellranger-arc mkfastq. Following this, the cellranger-arc count function was employed for read alignment, filtering, barcode counting, peak calling, and the quantification of both ATAC and GEX molecules. The rat genome mRatBN7 and its annotated transcriptome was used as a reference for alignment. Only confidently mapped reads with valid barcoes, unique molecular identities (UMIs) and non-PCR duplicates were retained. Spatial sequencing data was processed using Space Ranger from 10x Genomics.
Assembly: mRatBN7
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each sample from filtered_feature_bc_matrix folder for RNA-seq component.
Supplementary files format and content: Cell Ranger output files: fragments.tsv.gz for each sample for ATAC-seq component
Supplementary files format and content: Space Ranger output files: aligned_fiducials.jpg.gz, detected_tissue_image.jpg.gz, scalefactors_json.json.gz, tissue_hires_image.png.gz, tissue_lowres_image.png.gz, tissue_positiones_list.csv.gz for spatial information for each sample and barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz for sequencing information for each sample

source_name: scATAC-seq data from the hippocampus of a WT rat at 20 months of age

extract_protocol:
Hippocampus from 10-month and 20-month-old female McGill-R955-hTau transgenic rat and age-matching WT controls were dissected and snap-frozen at -80°C until further use. The tissues were minced and homogenized, and single-nuclei were isolated following 10x Genomics protocol (Pleasanton, CA, CG000505). Briefly, frozen tissues were minced, lysed, and dissociated in lysis buffer and then filtered on Nuclei Isolation Column by centrifugation. Nuclei pellets were washed with debris removal buffer, and nuclei were resuspended with 50 µL resuspension buffer. Nuclei concentration was determined with Luna-FL cell counter (Logos Biosystems, Annandale, VA). For tissues used for Spatial sequencing: 10-month and 20-month-old females McGill-R955-hTau transgenic rat and age-matching WT controls were perfused with 10% formalin, and the fixed brains were embedded in OCT compound, coronally sectioned at 10 µm using CryoStar NX50 cryotome (Epredia Kalamazoo, MI) and mounted onto microscope slides. Tissue sections were transferred onto the fiducial frames of a Visium Spatial Gene Expression slide (PN-2000233, 10x Genomics, Pleasanton, CA) using the Visium CytAssist.
Using the 10x Genomics Chromium Controller and following downstream protocols, RNA and ATAC libraries were generated on a cell-by-cell basis using microfluidic partitioning to capture single cells and prepare barcoded, next-generation sequencing (NGS) libraries. The mRNA and ATAC libraries were sequenced using a NovaSeq 6000 system (Illumina, San Diego, CA) targeting at minimum 80,000 and 50,000 reads per cell for mRNA and ATAC, respectively.  For spatial sequencing: The tissues underwent spatial barcoding, and cDNA library was generated from the tissue mRNA as outlined in the Visium Spatial Gene Expression User Guide (CG000239, 10x Genomics). The mRNA transcriptome was mapped to a 55 µm spatial resolution, corresponding to 1-10 cells per spot. The mRNA library was sequenced using a Nextseq 2000 platform.

value: Hippocampus


title: scATAC-seq Sample 2 WT 20mo

description: Library name: WT_20mo_2_ATAC


title: Kdm8KO 688M PDA cells, Kdm8-H319A, hypoxia, clone 04

city: New Brunswick

description:
Library name: Sample 8
Column name in "Kdm8expr_count_110323.txt": Hyp_KO4_CD


title: treatment2

description: Library name: Sample10


title: r2_ST_TFinput


title: scATAC-seq Sample 1 WT 20mo

description: Library name: WT_20mo_1_ATAC


title: scATAC-seq Sample 3 Tau 20mo

description: Library name: Tau_20mo_3_ATAC

source_name: scATAC-seq data from the hippocampus of a mutant Tau rat at 20 months of age


title: r2_ST_BRM014_H3K4me3

description: H3K4me3_STinh_215360vs215358_215384vs215382_223311_223308_def.narrowPeak

value: Forskolin + BRM014


title: scATAC-seq Sample 1 Tau 20mo

description: Library name: Tau_20mo_1_ATAC


title: scATAC-seq Sample 2 Tau 20mo

description: Library name: Tau_20mo_2_ATAC


title: scATAC-seq Sample 3 WT 10mo

description: Library name: WT_10mo_3_ATAC

source_name: scATAC-seq data from the hippocampus of a WT rat at 10 months of age


title: Kdm8KO 688M PDA cells, Kdm8-WT, hypoxia, clone 04

description:
Library name: Sample 4
Column name in "Kdm8expr_count_110323.txt": Hyp_KO4_WT


title: Sham1

description: Library name: Sample1


title: scATAC-seq Sample 2 WT 10mo

description: Library name: WT_10mo_2_ATAC


title: Kdm8KO 688M PDA cells, Kdm8-H319A, normoxia, clone 03

description:
Library name: Sample 5
Column name in "Kdm8expr_count_110323.txt": Nor_KO3_CD


title: scATAC-seq Sample 1 WT 10mo

description: Library name: WT_10mo_1_ATAC


title: r2_ST_BRM014_BRM

description: BRM_STinh_215356vs215355_215374vs215373_223306vs223305_a20_ATACmode.narrowPeak


title: r2_ST_BRM014_BRG1

description: BRG1_STinh_215357vs215355_215375vs215373_223307vs223305_a20_ATACmode.narrowPeak


title: scATAC-seq Sample 2 Tau 10mo

description: Library name: Tau_10mo_2_ATAC

source_name: scATAC-seq data from the hippocampus of a mutant Tau rat at 10 months of age


title: Kdm8KO 688M PDA cells, Kdm8-WT, hypoxia, clone 03

description:
Library name: Sample 3
Column name in "Kdm8expr_count_110323.txt": Hyp_KO3_WT


title: scATAC-seq Sample 3 Tau 10mo

description: Library name: Tau_10mo_3_ATAC


title: r2_ST_BRM014_HMinput


title: scATAC-seq Sample 1 Tau 10mo

description: Library name: Tau_10mo_1_ATAC


title: r2_ST_BRM014_TFinput


title: Homo liver-paracarcinoma tissue-rep2

description: Samples were obtained from patients undergoing surgery for HCC at the Eastern Hepatobiliary Surgery Hospital (Shanghai, China).

value: male

value: no

value: negative

value: yes


title: Kdm8KO 688M PDA cells, Kdm8-WT, normoxia, clone 04

description:
Library name: Sample 2
Column name in "Kdm8expr_count_110323.txt": Nor_KO4_WT

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells


title: snRNA-seq Sample 2 WT 20mo

description: Library name: WT_20mo_2_RNA

molecule: nuclear RNA

source_name: snRNA-seq data from the hippocampus of a WT rat at 20 months of age


title: r2_SR_BRM014_H3K4me3

description: H3K4me3_SRinh_215348vs215346_215372vs215370_223297_223294_def.narrowPeak


title: snRNA-seq Sample 1 WT 20mo

description: Library name: WT_20mo_1_RNA


title: snRNA-seq Sample 3 WT 20mo

description: Library name: WT_20mo_3_RNA


title: Kdm8KO 688M PDA cells, Kdm8-WT, normoxia, clone 03

description:
Library name: Sample 1
Column name in "Kdm8expr_count_110323.txt": Nor_KO3_WT


title: snRNA-seq Sample 2 Tau 20mo

description: Library name: Tau_20mo_2_RNA

source_name: snRNA-seq data from the hippocampus of a mutant Tau rat at 20 months of age


title: snRNA-seq Sample 3 Tau 20mo

description: Library name: Tau_20mo_3_RNA


title: Kdm8KO 688M PDA cells, Kdm8-H319A, normoxia, clone 04

description:
Library name: Sample 6
Column name in "Kdm8expr_count_110323.txt": Nor_KO4_CD


title: r2_SR_BRM014_HMinput

source_name: placenta


title: snRNA-seq Sample 1 Tau 20mo

description: Library name: Tau_20mo_1_RNA


title: Kdm8KO 688M PDA cells, Kdm8-H319A, hypoxia, clone 03

description:
Library name: Sample 7
Column name in "Kdm8expr_count_110323.txt": Hyp_KO3_CD

value: hypoxia


title: HSCs, treatment4

city: shanghai

first: yajie

last: peng

address: dongan road 130

institute: fudan university

description:
Library name: Sample7
Colume name in raw_counts_All_Samples.txt:treatment4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore
Trimmed sequence reads were mapped to mm10 using Hisat2
Read count extraction were performed using featureConts
Read count normalization and differential expression analysis were performed using DESeq2
Assembly: mm10
Supplementary files format and content: Excel fle includes raw counts for each Sample

source_name: HSCs

growth_protocol: Immortalized HSCs were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 μg/mL penicillin and streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from using Trizol. 200ng of total RNA was used for the construction of  sequencing libraries.
RNA libraries for RNA-seg were prepared using VAHTS® Universal V8 RNA-seg Library Prep Kit for Illumina

treatment_protocol: Cells were treated with GDF10 recombinant protein (200 ng/ml) 24 hours.

value: HSCs

tag: time

value: 24 hours


title: snRNA-seq Sample 3 WT 10mo

description: Library name: WT_10mo_3_RNA

source_name: snRNA-seq data from the hippocampus of a WT rat at 10 months of age


title: r2_SR_BRM014_BRG1

description: BRG1_SRinh_215345vs215343_215369vs215367_223293vs223291_a20_ATACmode.narrowPeak

value: placenta

value: WT


title: r2_SR_BRM014_BRM

description: BRM_SRinh_215344vs215343_215368vs215367_223292vs223291_a20_ATACmode.narrowPeak


title: HSCs, treatment3

description:
Library name: Sample6
Colume name in raw_counts_All_Samples.txt:treatment3

value: Cells were treated with GDF10 recombinant protein (200 ng/ml)


title: r2_SR_BRM014_TFinput


title: snRNA-seq Sample 2 Tau 10mo

description: Library name: Tau_10mo_2_RNA

source_name: snRNA-seq data from the hippocampus of a mutant Tau rat at 10 months of age


title: snRNA-seq Sample 3 Tau 10mo

description: Library name: Tau_10mo_3_RNA


title: HSCs, treatment1

description:
Library name: Sample4
Colume name in raw_counts_All_Samples.txt:treatment1


title: snRNA-seq Sample 1 WT 10mo

description: Library name: WT_10mo_1_RNA


title: HSCs, treatment2

description:
Library name: Sample5
Colume name in raw_counts_All_Samples.txt:treatment2


title: snRNA-seq Sample 2 WT 10mo

description: Library name: WT_10mo_2_RNA


title: NRK-49F, TGFb, 48h, siHoxc8, rep2

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

description:
Library name: NRK49F_TGFb_siHoxc8_2
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".

data_processing:
Reads were trimmed using Trim Galore
Aligned to the rat reference genome (rn6) using Bowtie (v2.3.5.1).
Visualization of ChIP-seq data, including heatmaps and profile plots, was conducted using deepTools
For RNA, gene quantification was performed with featureCounts
Assembly: rat reference genome (rn6)
Supplementary files format and content: bigwig
Supplementary files format and content: FPKM table

source_name: cell line

growth_protocol: NRK-49F cells were procured from the American Type Culture Collection (ATCC) and maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO) supplemented with 4.5 g/L glucose and 10% fetal calf serum (Viva cells) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cells using TRIzol, and its integrity was evaluated using a Qubit 4 analyzer.ChIP enriched DNA fragments were extracted and evaluated using a Qubit 4 analyzer.
The DNA fragments were utilized for library amplification using a VAHTS Universal Library Prep Kit (ND601, Vazyme) following the manufacturer’s instructions.

treatment_protocol: Prior to treatment, NRK-49F cells were starved for 24 hours with DMEM containing 0.2% FBS and then exposed to 5 ng/μL of TGF-β1 (240-B, R&D Systems). For methionine restriction (MetR) treatment, the medium was composed of Eagle's balanced salt solution 10x (E7510, Sigma-Aldrich), MEM vitamins solution 100x (M6895, Sigma-Aldrich), NaHCO3, dialyzed FBS (04-011-1B, Viva cells), MilliQ water, and amino acids at the following concentrations: L-methionine (Met, 200 μM for Ctrl, 30 μM for MetR).

value: cell line

value: Fibroblast


title: HSCs, ctrl3

description:
Library name: Sample3
Colume name in raw_counts_All_Samples.txt:ctrl3

value: PBS


title: NRK-49F, TGFb, 48h, siHoxc8, rep1

description:
Library name: NRK49F_TGFb_siHoxc8_1
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".


title: r2_SR_HMinput

value: hTSC


title: r2_SR_H3K4me3

description: H3K4me3_SR_215342vs215364_215366vs215340_223290_223287_def.narrowPeak


title: HSCs, ctrl2

description:
Library name: Sample2
Colume name in raw_counts_All_Samples.txt:ctrl2


title: NRK-49F, TGFb, 48h, MetR, rep2

description:
Library name: NRK49F_TGFb_MetR_2
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".

value: TGFb+MetR


title: NRK-49F, TGFb, 48h, MetR, rep1

description:
Library name: NRK49F_TGFb_MetR_1
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".


title: r2_SR_BRG1

description: BRG1_SR_215339vs215337_215363vs215361_223286vs223284_a20_ATACmode.narrowPeak


title: Rned500/p600, bio-repeat 4

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
The single-end, 76-bp raw sequencing reads for each sample were aligned to the reference genome and transcriptome of E. coli. (GCF_000005845.2; ASM584v2) using STAR (v 2.7.10)
The read counts of 4,626 genes, including 92 spike-in ERCC RNAs, were estimated by RSEM (v1.3.3)
The spike-in ERCC RNAs as the internal control showed the highly correlation (> 0.9) with the input concentration. Subsequently, the read-count-per-gene measurements were normalized across all samples using ERCC RNAs according to the method in Potts AH et. al.
The normalization factors, k values, were calculated for the 24 most abundant RNAs in the ERCC spike-in (top 6 abundances from each A, B, C and D group) from a WT sample, R419-R-177_S1, and the geometric average of these was then used as the library normalization factor.
Assembly: ASM584v2
Supplementary files format and content: tab-delimited text file includes raw read counds for each sample

organism: Escherichia coli K-12

source_name: bacterial cell

growth_protocol: Overnight E. coli liquid culture were stab into 0.35 % soft agar plate and incubate at 30 ℃ for 24 h. Plasmid ectopic expressed proteins are under the transcription control of rne native promoter.

extract_protocol:
To extract RNA from plate culture, we collected ~ 3 to 4 ml of soft-agar into 50 ml falcon tube. Bacterial enzymatic activity was stop by incubating in 8 ml of stop solution for 3 min. Soft-agar that contained bacterial cells were pelleted by centrifugation at 12,000 rpm, 5 min, 4 ℃. After that, agar pellets were resuspended in 4 ml of KJ medium and 4 ml of lysis buffer. To lyse the bacteria in soft-agar, the mixture was boiled in hot water for 3 min. Total RNE were extracted by adding 4 ml of acid phenol (pH 4.5) and mixed thoroughly by slowly inverting the tube ~ 30 times. Total RNA were extracted in aqueous phase by centrifugation at 4000 g, 1 h, 4 ℃. Total RNA were precipitated in 1 volume of isopropanol and 1/10 volume of 3 M sodium acetate (pH 7.8) at – 20 ℃ for at least 2 h as described above. All RNA samples were maintained in isopropanol at – 20 ℃ before further experiments.
five ug total RNA with ERCC control RNA were prepared for libraries using  Ribominus bacteria 2.0  Kit (ThermoFisher A47335) and Illumina TruSeq total  RNA standard Sample Prep protocol.RNAseq on Illumina NextSeq 500 platform as single read 75 bp.

treatment_protocol: Stop solution (95 % EtOH, 5 % phenol saturated with buffer, pH 6.6-7.9) was added to plate culture to stop all enzymatic activity before sujected for RNA isolation.

value: bacterial cell

tag: phenotype

value: high catalytic activity N-terminal RNase E (Rne1-599)


title: r2_SR_BRM

description: BRM_SR_215338vs215337_215362vs215361_223285vs223284_a20_ATACmode.narrowPeak


title: HSCs, ctrl1

description:
Library name: Sample1
Colume name in raw_counts_All_Samples.txt:ctrl1


title: NRK-49F, TGFb, 48h, rep1

description:
Library name: NRK49F_TGFb_1
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".

value: TGFb


title: Prrx1 Knockdown Pericyte Replicate 4

city: Changsha

first: Zhishang

last: Meng

address: No 139 Renmin Middle Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description:
Library name: Si-4
Prrx4 knockdown pericyte sample under hypoxia

data_processing:
Raw reads were quality-filtered using fastp (v0.20.0) to remove low-quality reads and obtain clean reads. data processing step Clean reads were mapped to the mouse reference genome (mm10) using HISAT2 (v2.2.1) with default parameters. data processing step Read counts for each gene were obtained using HTSeq-count (v0.12.4).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing gene IDs and raw counts for all samples.

source_name: Mouse retina

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 10296010) according to the manufacturer's protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions. Sequencing was performed by OE Biotech Co., Ltd. (Shanghai, China).

value: Mouse retina

value: primary cell

value: retinal microvascular primary pericytes

value: Prrx1 knockdown

value: hypoxia + siRNA-mediated Prrx1 knockdown

tag: batch


title: r2_SR_TFinput


title: Prrx1 Knockdown Pericyte Replicate 3

description:
Library name: Si-3
Prrx3 knockdown pericyte sample under hypoxia


title: snRNA-seq Sample 1 Tau 10mo

description: Library name: Tau_10mo_1_RNA

value: Hippocampus


title: r1_ST_BRM014_H3K4me3

description: H3K4me3_STinh_215360vs215358_215384vs215382_223311_223308_def.narrowPeak

value: placenta

value: ST

value: Forskolin + BRM014


title: NRK-49F, control, rep1

description:
Library name: NRK49F_Control_1
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".

value: cell line

value: Control


title: Prrx1 Knockdown Pericyte Replicate 2

description:
Library name: Si-2
Prrx2 knockdown pericyte sample under hypoxia


title: Rned500/p600, bio-repeat 1


title: r1_ST_BRM014_HMinput

value: WT


title: NRK-49F, control, rep2

description:
Library name: NRK49F_Control_2
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".

value: Fibroblast


title: Rned500/p500, bio-repeat 3

value: low catalytic activity N-terminal RNase E (Rne1-499)


title: NRK-49F, siHoxc8, TGFb, Pol II Ser2P ChIP

description: Library name: siHoxc8_TGFb_S2P


title: ileum_control_P332_rep2

source_name: Neonata ileal monolayers

value: Neonata ileal monolayers


title: NRK-49F, siHoxc8, TGFb, Pol II ChIP

description: Library name: siHoxc8_TGFb_PolII


title: Control Pericyte Replicate 3

description:
Library name: NC-3
Control pericyte sample under hypoxia

value: wild-type

value: hypoxia


title: r1_ST_BRM014_BRM

description: BRM_STinh_215356vs215355_215374vs215373_223306vs223305_a20_ATACmode.narrowPeak


title: r1_ST_BRM014_BRG1

description: BRG1_STinh_215357vs215355_215375vs215373_223307vs223305_a20_ATACmode.narrowPeak


title: Rned500/p500, bio-repeat 2

value: bacterial cell


title: NRK-49F, TGFb, 48h, rep2

description:
Library name: NRK49F_TGFb_2
The FPKM value of all RNA-seq samples were in one same file "All_sample_FPKMs.txt".

value: TGFb


title: Rned500/p600, bio-repeat 2

value: high catalytic activity N-terminal RNase E (Rne1-599)


title: Control Pericyte Replicate 2

description:
Library name: NC-2
Control pericyte sample under hypoxia

value: Mouse retina

value: primary cell

value: retinal microvascular primary pericytes


title: NRK-49F, siHoxc8, TGFb, Input

description: Library name: siHoxc8_TGFb_Input


title: Rned500/p600, bio-repeat 3


title: Rned500/p500, bio-repeat 1


title: r1_ST_BRM014_TFinput

value: placenta


title: Control Pericyte Replicate 1

description:
Library name: NC-1
Control pericyte sample under hypoxia


title: NRK-49F, siHoxc8, TGFb, Hoxc8 ChIP

description: Library name: siHoxc8_TGFb_HOXC8


title: Rned500/p500, bio-repeat 4


title: Rned500/pFL, bio-repeat 4

value: full-length RNase E


title: NRK-49F, siControl, TGFb, Pol II Ser2P ChIP

description: Library name: siCtrl_TGFb_S2P

value: siControl+TGFb


title: Prrx1 Knockdown Pericyte Replicate 1

description:
Library name: Si-1
Prrx1 knockdown pericyte sample under hypoxia

value: Prrx1 knockdown

value: hypoxia + siRNA-mediated Prrx1 knockdown


title: NRK-49F, siControl, TGFb, Pol II ChIP

description: Library name: siCtrl_TGFb_PolII

value: cell line