title: PrSCshc

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

data_processing:
Bowtie2 version 2.1.0 was used for mapping to the human genome hg19 transcript set.
RSEM v1.2.15 was used to calculate the count and estimate the gene expression level.
Trimmed Mean of M-values (TMM) method in the edgeR package was used for gene  expression normalization.
Genome_build: hg19

source_name: PrSC

growth_protocol: PrSC cells were culture in T-medium supplemented with 10% FBS and 1% P/S

extract_protocol:
The total RNA was extracted by RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed on an Illumina HiSeq 3000 for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: Stable overexpressed MAOB in PrSC cells were achieved by infection of MAOB lentiviral expression construct by insertion of the coding region of MAOB in pLVX-AcGFP-N1 vector containing a puromycin-resistant gene. Stable knockdown of MAOB in PrSC cells were achieved by infection of lentivirus expressing a shRNA targeting the MAOB coding region, with a non-targeting shRNA as control, followed by antibiotic selection.

value: PrSC

value: Control

tag: sample type

value: Human prostate stromal cell line


title: PrscNEG

status: Public on Nov 10 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: PrSCshB2

value: shRNA-based MAOB stable knockdown


title: PrSCshB4


title: human-Healthy_2

city: hefei，anhui，china

first: jian-xiong

last: wang

state: anhui

address: No. 218，Ji-xi Road，Hefei 230022, Anhui, China.

country: China

institute: Hospital

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: Whole blood cell

growth_protocol: In this case-control study, 3 healthy humans and 5 patients with AS who met the modified New York 1984 criteria. they were all recruited from the Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui Medical University. Clinical records were collected and questionnaire were interviewed by professional rheumatologists. All patients were first diagnosed and they were excluded from the study if with infectious diseases, serious kidney diseases, serious liver diseases, endocrine disorders. Moreover, significant data missing, treated with steroid or any nonsteroidal anti-inflammatory drugs (NSAIDs) or disease-modifying anti-rheumatic drugs (DMARDs) within the past were also eliminated. In this study, each participant provided the informed consent to participate, and study was performed in accordance with the Declaration of Helsinki

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

tag: cell type

value: Whole blood cell

tag: disease state

value: healthy control


title: GEX_EXP20000722_Sample_01

city: Boston

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

institute: Brigham and Women's Hospital

description: GEX

data_processing:
Base Calling TCR BCL to TCR FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling GEX BCL to GEX FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling ADT BCL to ADT FASTQ via Cell Ranger 3.1.0 with the flag "--delete-undetermined" in addition to the standard settings.
Base Calling tetramer BCL to tetramer FASTQ file via bcl2fastq2 version v2.20.0 with the flags "--minimum-trimmed-read-length 0 --mask-short-adapter-reads 0" in addition to the standard settings.
TCR Read Counts: FASTQ to vdj counts via Cell Ranger 3.1.0 using the standard settings.
GEX Read Counts: FASTQ to gene expression counts via Cell Ranger 3.1.0 using the standard settings.
Tetramer FASTQ to Tetramer counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
ADT FASTQ to ADT counts via extracting tetramer barcode from uniquely observed tetramer UMI reads using python script
TCR VDJ counts paired with tetramer and ADT counts via common hydrogel barcode using python script
VDJ and tetramer counts separated via hashtags using Seurat 4.0.3
Dehashed VDJs selected for functional assays.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: The processed data files conform to the hfad AnnData format: https://anndata.readthedocs.io/en/latest/anndata.AnnData.html
Supplementary_files_format_and_content: Metadta for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_CIPHER_2021_11_04_Supplemental_Sample_to_HTO.xlsx"

source_name: CD8+ T cells

extract_protocol:
PBMCs were thawed, and CD8+ T cells were enriched by magnetic-activated cell sorting (MACS) using a CD8+ T Cell Isolation Kit (Miltenyi) following the manufacturers protocol. The CD8+ T cells were then stained with 1 nM final concentration tetramer library in the presence of 2 mg/mL salmon sperm DNA in PBS with 0.5% BSA solution for 20 minutes. Cells were then labeled with anti-TCR antibody-derived tag (ADT, IP26, Biolegend) for 15 minutes followed by washing. Tetramer bound cells were then labeled with phycoerythrin (PE) conjugated anti-DKDDDDK-Flag antibody (BioLegend) followed by dead cell discrimination using 7-amino-actinomycin D (7-AAD). The live, tetramer positive cells were sorted using a Sony MA900 Sorter (Sony). Tetramer positive cells were counted by Nexcelom Cellometer (Lawrence, MA, USA) using AOPI stain following manufacturer’s recommended conditions. Single-cell encapsulations were generated utilizing 5’ v1 Gem beads from 10x Genomics (Pleasanton, CA, USA) on a 10x Chromium controller and downstream TCR, and Surface marker libraries were made following manufacturer recommended conditions. All libraries were quantified on a BioRad CFX 384 (Hercules, CA, USA) using Kapa Biosystems (Wilmington, MA, USA) library quantified kits and pooled at an equimolar ratio. TCRs, surface markers, and tetramer generated libraries were sequenced on Illumina (San Diego, CA, USA) NextSeq550 instruments. Sequencing data were processed using the Cell Ranger Software Suite (Version 3). Samples were demultiplexed and unique molecular identifier (UMI) counts were quantified for TCRs, tetramers, and gene expression.
10X Chromium 5' single-cell

tag: tissue

value: PBMC

tag: subject

tag: cohort

value: convalescent


title: human-AS_patient_5

value: ankylosing spondylitis (AS)


title: human-AS_patient_4


title: human-AS_patient_3


title: follicular_granulosa_cell_layers-F5_RNA-seq_replicate_5

city: chengdu

first: hua

last: kui

address: No 211 Huimin Road

institute: Sichuan Agricultural University

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F5-5

data_processing:
TPM-submission.xlsx: bulk-RNAseq reads were aligned to the galGal6 using kallisto version 0.44.0 ,then tpm and counts matrixs were generated using R version 3.6.1.
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx: bulk-RNAseq reads were aligned to the galGal6 using kallisto version 0.44.0 ,then tpm and counts matrixs were generated using R version 3.6.1.
SWF.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1
F1.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1
POF.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1
ATAC-SWF_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1.
ATAC-F1_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1.
ATAC-POF_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1.
IP-SWF_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms.
IP-F1_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms.
IP-POF_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms.
F1.POF.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms.
SWF.F1.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms.
SWF.POF.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms.
Genome_build: galGal6
Supplementary_files_format_and_content: bulk-RNAseq (xlsx files)
Supplementary_files_format_and_content: single cell RNAseq (matrix.h5 files)
Supplementary_files_format_and_content: ATAC-seq (peaks.xls files)
Supplementary_files_format_and_content: chip-seq (AllEnhancers.table.txt files)
Supplementary_files_format_and_content: single cell RNAseq (silico.bulk.DEG.result.by.DEseq2.txt files)

organism: Gallus gallus

source_name: granulosa cells

extract_protocol:
total RNA was extracted from each sample using RNAiso Plus reagent (TaKaRa, Otsu, Shiga, Japan) following the manufacturer’s instructions.
Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5min at 95 °C before PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
We estimated the integrity and quality of total RNA using a Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA) with an RNA 6000 Nano kit. Subsequently, 30 strand-specific libraries (total of 10 stages with three biological replicates in each stage) were generated after depleting rRNA by the Ribo-Zero™ Gold Kit (Illumina, San Diego, CA, USA) and then sequenced on the Illumina HiSeq X Ten platform (Illumina Inc., San Diego, CA, USA) with a paired-end sequencing length of 150 bp (PE150) at Novogene Corporation (Beijing, China).

value: granulosa cells

tag: breed

value: Luhua hens

tag: developmental stage

value: preovulatory follicles

tag: age

value: 31 weeks

tag: follicle growth stage


title: PrscMAOB

value: MAOB stable overexpressed


title: human-AS_patient_2


title: GEX_EXP20000683_Sample_07

description: GEX


title: GEX_EXP20000683_Sample_01

description: GEX


title: follicular_granulosa_cell_layers-F5_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F5-4


title: follicular_granulosa_cell_layers-F5_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F5-3


title: PBMCs, COVID-19 patient, sand-100-1P

type: RNA

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

description: Isolation of Human peripheral blood mononuclear cells (PBMCs) obtained from COVID-19 patient

hyb_protocol: 30-100ng RNA were hybridized following CodeSet hybridization Setup Protocol (MAN-10056-03) On the Prep Station was selected the High Sensitivity protocol .

scan_protocol: Samples were analyzed with the nCounter Digital Analyzer. The data Resolution selected was Max ( max resolution takes 555 images per sample).

data_processing: RCC files were analyzed using nSolver analysis software (Version 4.0) as the manufacturer’s protocols. Negative and positive controls included in probe sets were used for background thresholding and a geometric mean of internal reference genes used for normalization. Normalized counts were further analyzed by MATLAB R2019b.

label: biotin

source_name: PBMC

label_protocol: According to the manufacturer's protocol

growth_protocol: growth protocol was not conducted

extract_protocol: Total RNA was extracted from PBMCs isolated from peripheral blood, using Qiazol (Qiagen, Hilden, Germany), purified from DNA contamination through a DNase I (Qiagen) digestion step, and further enriched by Qiagen RNeasy columns profiling (Qiagen). The quantity and purity of the RNA was assessed with the NanoDrop spectrophotometer. The quality of the RNA was controlled with the Bioanalyzer.

treatment_protocol: treatment protocol was not conducted

value: COVID-19 patient


title: human-AS_patient_1


title: PBMCs, COVID-19 patient, sand-009-1P

value: COVID-19 patient with Cancer


title: PBMCs, COVID-19 patient, sand-011-1P


title: GEX_EXP20000654_Sample_06

description: GEX


title: GEX_EXP20000654_Sample_05

description: GEX


title: GC cells_ARV125nM_3

city: Shanghai

first: Xinmei

last: Liao

state: Shanghai

address: 800 Dongchuan RD

department: department of instrument science and engineering

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: gastric cancer cells

growth_protocol: Cells were cultured in DMEM-medium at 37 °C with 5% CO2, contained 100 U/ml penicillin-streptomycin and 10% fetal bovine serum (FBS).

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

treatment_protocol: ARV-825 were incubated with cells for 48h.

value: treated with ARV-825 for 48h


title: follicular_granulosa_cell_layers-F5_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F5-6


title: follicular_granulosa_cell_layers-F5_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F5-1


title: GEX_EXP20000654_Sample_04

description: GEX


title: follicular_granulosa_cell_layers-F5_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
F5-2


title: GC cells_ARV125nM_2


title: GC cells_ARV125nM_1


title: GEX_EXP20000683_Sample_08

description: GEX


title: PBMCs, COVID-19 patient, sand-007-1P


title: GEX_EXP20000654_Sample_03

description: GEX


title: follicular_granulosa_cell_layers-LYF_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LYF-6

value: prehierarchical follicles

value: LYF


title: follicular_granulosa_cell_layers-LYF_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LYF-5


title: PBMCs, healthy control, sand-HD7

description: Isolation of Human peripheral blood mononuclear cells (PBMCs) obtained from healthy control


title: PBMCs, COVID-19 patient, sand-006-1P


title: PBMCs, healthy control, sand-HD6


title: GEX_EXP20000654_Sample_02

description: GEX


title: GC cells_ARV_0nM_2

value: untreated


title: follicular_granulosa_cell_layers-LYF_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LYF-4


title: PBMCs, COVID-19 patient, sand-010-1P


title: PBMCs, COVID-19 patient, sand-008-1P


title: HEC2-3

city: Beijing

first: zhongyi

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

institute: CAU(China Agricultural University)

data_processing:
Analyses of the transcriptome data were performed on the BMKCloud platform  (www.biocloud.net).
HISAT2 software used to compare the sequenced Reads to the reference genome (Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature methods, 2015, 12(4): 357-360.).
Differentially expressed genes (DEGs) were calculated using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi:10.1186/s13059-014-0550-8.). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. The false discovery rate (FDR) less than 0.05 and the fold change larger than 1.5 as were set as the threshold.
Genome_build: ChineseLong_v2 (http://cucurbitgenomics.org/organism/2)
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Cucumis sativus

source_name: cucumber

extract_protocol:
The RNA of the sample was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: female bud

tag: Stage

value: 7 days before anthesis

tag: genotype


title: GC cells_ARV_0nM_1


title: follicular_granulosa_cell_layers-LYF_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LYF-3


title: HEC2-2


title: P1SMLC6: Passage 1 DMSO-treated smooth muscle-like cells 6

city: La Jolla

first: Benjamin

middle: D

last: Gastfriend

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Basecalling was performed by the Illumina NovaSeq 6000
FASTQ files were aligned and transcripts quantified using RSEM (v1.3.3) calling bowtie2 (v2.4.2)
Genome_build: hg38
Supplementary_files_format_and_content: An Excel spreadsheet containing raw counts and TPM values is provided

source_name: Human induced pluripotent stem cells

extract_protocol:
Cells were lysed using Buffer RLT (Qiagen) supplemented with 1% beta-mercaptoethanol. RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer instructions.
First-strand cDNA synthesis (with polyA enrichment) was performed using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio), followed by 9 cycles of PCR amplification. Libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina).

value: smooth muscle-like cells

tag: passage number

value: DMSO

tag: differentiation (sample pairing)


title: PBMCs, COVID-19 patient, sand-005-1P

value: PBMC


title: GC cells_ARV_0nM_3


title: HEC2-1


title: P3CHIR6: Passage 3 CHIR-treated endothelial cells 6

value: endothelial cells

value: CHIR


title: follicular_granulosa_cell_layers-POF_ChIP-seq-Input_replicated_2

library_source: genomic

molecule: genomic DNA

extract_protocol:
Chicken ovarian GCs were washed twice in cold PBS buffer and cross-linked with 1% formaldehyde for 10 minutes at room temperature and then quenched by adding glycine (125 mmol/L final concentration). Afterwards, samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). Then 2ul chromatin was saved at -20°C for input DNA, and 100ul chromatin was used for immunoprecipitation by Anti-flag (14793, Cell Signaling Technology). A total of 5 μg of antibody was used in the immunoprecipitation reactions at 4 °C overnight. The next day, 30 μL of protein beads were added and the samples were further incubated for 3 h. The beads were next washed once with 20 mM Tris/HCL (pH 8.1), 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS; twice with 10 mM Tris/HCL (pH 8.1), 250 mM LiCl, 1 mMEDTA, 1% NP-40, 1% deoxycholic acid; and twice with TE buffer 1× (10 mM Tris-Cl at pH 7.5. 1 mM EDTA). Bound material was then eluted from the beads in 300 μL of elution buffer (100 mM NaHCO3, 1% SDS), treated first with RNase A (final concentration 8 μg/mL) during 6 h at 65°C and then with proteinase K (final concentration 345 μg/mL) overnight at 45°C.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing (NOVA-5143, Bioo Scientific) and sequenced on a Illumina Xten with PE 150 method.
We performed H3K27ac (a canonical histone marks of enhancers) ChIP-seq for 2 replicates in each of three stages, including SWF, F1, and POF. Briefly, chicken ovarian granulosa cells were washed twice in cold PBS buffer and cross-linked with 1% formaldehyde for 10 minutes at room temperature and then quenched by addition of glycine (125 mmol/L final concentration). Afterwards, samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). 2ul chromatin was saved at -20°C for input DNA, and 100ul chromatin was used for immunoprecipitation by Anti-flag (14793, Cell Signaling Technology).5 μg of antibody was used in the immunoprecipitation reactions at 4 °C overnight. The next day, 30 μL of protein beads was added and the samples were further incubated for 3 h. The beads were next washed once with 20 mM Tris/HCL (pH 8.1), 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS; twice with 10 mM Tris/HCL (pH 8.1), 250 mM LiCl, 1 mMEDTA, 1% NP-40, 1% deoxycholic acid; and twice with TE buffer 1× (10 mM Tris-Cl at pH 7.5. 1 mM EDTA). Bound material was then eluted from the beads in 300 μL of elution buffer (100 mM NaHCO3, 1% SDS), treated first with RNase A (final concentration 8 μg/mL) during 6 h at 65°C and then with proteinase K (final concentration 345 μg/mL) overnight at 45°C. Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing (NOVA-5143, Bioo Scientific) and sequenced on Illumina Xten with PE 150 method.

value: granulosa cells

value: Luhua hens

value: postovulatory follicles

value: POF

tag: chip antibodies


title: P1SMLC3: Passage 1 DMSO-treated smooth muscle-like cells 3


title: XM-3

value: wild type


title: XM-2


title: PBMCs, COVID-19 patient, sand-004-1P

value: COVID-19 patient


title: follicular_granulosa_cell_layers-LYF_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LYF-1

value: 31 weeks


title: follicular_granulosa_cell_layers-LYF_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LYF-2

value: prehierarchical follicles


title: follicular_granulosa_cell_layers-SYF_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SYF-5

value: SYF


title: XM-1


title: follicular_granulosa_cell_layers-SYF_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SYF-4


title: Crown_4

city: Xinxiang

first: Miao

last: Zhao

state: Henan

address: Jianshe east road

department: Life sciences college

institute: Henan Normal University

data_processing:
Getting rid of low quality reads
Getting rid of reads which proportion of N
Getting rid of reads with 5' primer contaminants and reads without the insert fragments
Getting rid of reads without 3' primer
Getting rid of reads with poly A
Getting rid of reads shorter than 18nt
Supplementary_files_format_and_content: sequences and count values

organism: Triticum aestivum

source_name: Crown

growth_protocol: Winter wheat Shimai 22 was grown in the fileld at Wheat Experimental Station of Henan Normal University. The crown tissues were collected at different stages, and snap frozen in liquid nitrogen.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacture's protocol.
Small RNA libraries were prepared by following the BGISEQ's protocol.

treatment_protocol: samples were collected at different growth stages.

value: crown tissue colleected at jointing stage


title: P3DMSO6: Passage 3 DMSO-treated endothelial cells 6


title: Crown_3

value: crown tissue colleected at spring greenup stage


title: follicular_granulosa_cell_layers-SYF_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SYF-3


title: follicular_granulosa_cell_layers-F1_ChIP-seq-Input_replicated_2

value: preovulatory follicles

value: Anti-flag (14793, Cell Signaling Technology)


title: follicular_granulosa_cell_layers-SYF_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SYF-2


title: follicular_granulosa_cell_layers-F1_ChIP-seq-Input_replicated_1


title: P3DMSO3: Passage 3 DMSO-treated endothelial cells 3

value: DMSO


title: follicular_granulosa_cell_layers-POF_ChIP-seq-Input_replicated_1


title: P3DMSO2: Passage 3 DMSO-treated endothelial cells 2


title: follicular_granulosa_cell_layers-SYF_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SYF-6


title: P3CHIR3: Passage 3 CHIR-treated endothelial cells 3


title: follicular_granulosa_cell_layers-SYF_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SYF-1


title: Crown_1

value: crown tissue collected at the three leaf stage


title: PBMCs, COVID-19 patient, sand-003-1P

description: Isolation of Human peripheral blood mononuclear cells (PBMCs) obtained from COVID-19 patient

value: PBMC


title: follicular_granulosa_cell_layers-LWF_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LWF-6

value: LWF


title: P3CHIR2: Passage 3 CHIR-treated endothelial cells 2

value: endothelial cells

value: CHIR


title: follicular_granulosa_cell_layers-POF_ChIP-seq-H3K27ac_replicated_2

value: granulosa cells

value: Luhua hens

value: postovulatory follicles


title: sciTIP multiplexed_F121-9 mESCs and human HCT116 cells

city: Tallahassee

first: Daniel

middle: A

last: Bartlett

state: Florida

address: 319 Stadium Drive

department: Biological Sciences

institute: Florida State University

description:
sciTIP multiplexed H3K27me3, H3K27ac, H3K9me3, RNAPII and CTCF in F121-9 mESCs
sciTIP multiplexed H3K27me3, H3K27ac, and H3K9me3 in HCT116 cells

data_processing:
Library strategy: TIP-seq
Basecalls perfomed using RTA3
For sciTIP-seq only, fastq files were demultiplexed to single cell fastq files based on unique combinations of r5, i5, and i7 barcodes using a custom script.
Reads were aligned to the mm10 or hg38 genome assembly using bowtie2 version 2.3.4.1 with the following configurations "--very-sensitive-local -p 28 --no-mixed --no-discordant --reorder -I 10 -X 700 -q --passthrough"
Mapped reads were filtered by mapping quality (MAPK>10) and PCR duplicates were removed using SAMtools version 1.9.
Reads were binned into 100 bp (bulk) or 5kb (sciTIP) genomic windows using Bedtools coverage version 2.26.0 with setting "-counts"
Genome_build: mm10/hg38
Supplementary_files_format_and_content: bigWig files contain read counts binned into 100 bp genomic windows.  sciTIP-seq Tab-delimited text file includes cell embeddings for each cell. Each column refers to a single cell and each row refers to a genomic bin.

organism:
Homo sapiens
Mus musculus

source_name: Cast X 129 F121-9 hybrid mouse ES cells and HCT116

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% FBS according to ATCC’s instruction. F121-9 mouse embryonic stem cell were cultured in 2i media on gelatin-coated dish as described in (PMID:29735606).

extract_protocol:
Cell cultures were harvested and rinsed once with an equal volume of room temperature PBS. Cells were moved to a 2 mL tube and washed twice with room temperature Wash buffer (20mM HEPES, pH 7.5; 150mM NaCl; 0.5mM Spermidine, 1x Protease inhibitor cocktail) before counting with a hemocytometer and aliquoting cells into fresh 1.5 mL LoBind Eppendorf tubes containing 1mL room temperature wash buffer. 10 µL of pre-washed Concanavalin A-coated magnetic beads slurry was added to aliquots of washed cells and rotated for 10 minutes at room temperature to allow beads to bind to cells. Bead-bound cells were incubated with primary antibody [1:100] in 100 µL Antibody buffer (Wash Buffer + 0.01% digitonin, 2mM EDTA, and 1%BSA) overnight at 4°C with rotation. Antibody buffer was removed and replaced with 100 µL Dig-Wash buffer (Wash buffer + 0.01% digitonin) containing Guinea pig anti-Rabbit IgG secondary antibody [1:100] and rotated for 1 hr at room temperature. Cells were washed twice in 1 mL Dig-Wash buffer and then resuspended in 100 µL Dig-300 buffer (0.01% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail) containing pA-Tn5 [1:100] loaded with ME-A/B adapters (CUT&Tag) or ME-T7 adapters (TIP-seq) and incubated at room temperature with rotation for 1 hr to allow pA-Tn5 to bind to antibody-bound sites. Cells were washed 3 times with 1 mL Dig-300 buffer to remove unbound pA-Tn5. Tagmentation was activated by resuspension in 100 µL Tag buffer (Dig-300 Buffer + 10 mM MgCl2) for 1h at 37°C and was terminated by adding 3.3 µL of 0.5M EDTA. Cells were mixed with 2 µL 10% SDS (0.2% final) and 0.84 µL 20 mg/mL proteinase K and incubated at 50°C for 30 min or overnight at 37°C before being purified using 2.0x volume SPRI beads (Beckman; A63881).
CUT&Tag: CUT&Tag libraries were prepared by mixing tagmented DNA with 2 µL of uniquely barcoded i5 and i7 primers and 25 µL of NEBNext HiFi 2× PCR Master mix (NEB; M0541L) and PCR amplified using the following thermocycler program: 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 (12-15 cycles). Amplified libraries were cleaned-up and size selected using 1.1× volume SPRI beads, washed 2x with 80% EtOH, and eluted into 30 µL 10 mM Tris pH 8.0.       TIP-seq: TIP-seq libraries were prepared by mixing tagmented DNA with 2 ml of NEB 5x Taq master mix (NEB; M0285) and incubating at 72 °C for 3 mins for gap-filling. In vitro transcription was performed using the NEB HiScribe T7 high yield synthesis kit (NEB; E2040S) by adding 2mL of each 100mM NTP, 2 mL 10x T7 reaction buffer, 2 mL T7 polymerase mix and 0.3 mL RNase Inhibitor and incubating at 37*C for 16-19 hrs. RNA was purified by adding 2.0x volume SPRI binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris-HCl, 1 mM EDTA) to reactivate the bead’s binding capacity. After washing twice with 80% EtOH and removing all liquid, residual EtOH was dried from RNA and SPRI beads for 3 minutes before being resuspended in 9 mL RNase-free water. First-strand synthesis was primed by adding 2.5 mL of 20 µM random hexamer to sample and incubating at 70*C for 3 mins, then immediately placing on ice. First strand synthesis was performed using SMART MMLV RTase kit (Takara; 639524) by adding 4 mL of 5x first-strand synthesis buffer, 2 mL of 10mM dNTP mix, 2 mL of 100 mM DTT, and 0.5 mL SMART MMLV RTase. Samples were mixed well and incubated at 22*C for 10 mins, 42*C for 60 min, then terminated at 70*C for 10 min. 1mL of a 1:10 dilution of 5U/µL RNase H was added and incubated at 37*C for 20 mins to degrade RNA in cDNA-RNA hybrids. Second strand synthesis was primed by adding 2.5 µL of 20 µM sss_scnXTv2 oligo (anneals to transposon directly downstream of T7 promoter TSS) and heating sample to 65*C for 2 minutes and placing immediately on ice. Second-strand synthesis was performed by adding 5.9 mL of NEB 5x Taq master mix (NEB;M0285) and incubating at 72*C for 8 mins, then cooling on ice. cDNA was purified by addition of 2.0x SPRI binding buffer, washed twice in 80% EtOH, and resuspended in 7mL water. Fragmentation and 3’-end adapter tagging of cDNA was performed by adding 2 µL TAPS buffer and 2 µL 0.7µM Tn5 (loaded with ME-B adapters only), incubated at 55*C for 6 minutes, and then briefly cooled on ice prior to adding GuHCl (4M final conc.) and vortexing to degrade Tn5. DNA was purified again by adding 2.0x volume SPRI binding buffer, washing twice with 80% EtOH, and Eluting DNA off of beads into 16 µL water. Eluent was moved to a fresh tube, this time leaving behind SPRI beads to discard.  PCR reactions were prepared by adding 20 µL NEBNext 2x master mix (NEB; M0541L), 2 µL of 10 µM standard Nextera index primers, 2 µL of 10 µM standard i7 Nextera indexes, for total vol of 40 µL. The optimal number of PCR cycles were determined as performed in Buenrostro et al. (7-9 cycles). Post PCR libraries were SPRI purified and left-side size selected by 0.85x volume SPRI beads (>200bp).

value: mouse ES cells and human HCT116 cells

tag: antibody

value: Mouse [H3K27me3 (Cell Signaling; 9733); H3K9me3 (Abcam; ab8898); H3K27ac (Abcam; ab4729); CTCF (Millipore; 07-729); RNAPII-Ser2Ph (Cell Signaling; 13499); Guinea pig anti-Rabbit IgG (Antibodies-Online; ABIN101961)] and Human [H3K27me3 (Cell Signaling; 9733); H3K9me3 (Abcam; ab8898); H3K27ac (Abcam; ab4729); Guinea pig anti-Rabbit IgG (Antibodies-Online; ABIN101961)]


title: follicular_granulosa_cell_layers-SWF_ChIP-seq-Input_replicated_1

value: prehierarchical follicles

value: 31 weeks

value: SWF


title: P1WNT3: Passage 1 Wnt7a/b-treated endothelial cells 3

tag: cell line


title: follicular_granulosa_cell_layers-LWF_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LWF-5


title: P1WNT5: Passage 1 Wnt7a/b-treated endothelial cells 5

tag: treatment


title: Crown_2

value: crown tissue colleected at winter dormancy stage


title: follicular_granulosa_cell_layers-LWF_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LWF-4

tag: cell type


title: follicular_granulosa_cell_layers-SWF_ChIP-seq-Input_replicated_2


title: follicular_granulosa_cell_layers-LWF_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LWF-3


title: follicular_granulosa_cell_layers-F1_ChIP-seq-H3K27ac_replicated_2

value: preovulatory follicles


title: P1WNT2: Passage 1 Wnt7a/b-treated endothelial cells 2


title: follicular_granulosa_cell_layers-F1_ChIP-seq-H3K27ac_replicated_1

value: Anti-flag (14793, Cell Signaling Technology)


title: follicular_granulosa_cell_layers-LWF_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LWF-2


title: P1CHIR5: Passage 1 CHIR-treated endothelial cells 5


title: follicular_granulosa_cell_layers-LWF_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
LWF-1


title: follicular_granulosa_cell_layers-SWF_ChIP-seq-H3K27ac_replicated_1


title: P1CHIR3: Passage 1 CHIR-treated endothelial cells 3


title: P1WNT6: Passage 1 Wnt7a/b-treated endothelial cells 6


title: P1CHIR2: Passage 1 CHIR-treated endothelial cells 2


title: follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_6

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SWF-6


title: follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_5

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SWF-5


title: HepG2_Sup_Cy3

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

description: Raw data file:  HepG2.txt

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar human m6A-mRNA&lncRNA Epitranscriptomic Microarray (v1, Arraystar).

scan_protocol: After washing, slides were scanned with the 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.
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: hepatocellular carcinoma cells (Sup)

label_protocol: Briefly, the total RNAs were immunoprecipitated with anti-N6-methyadenosine (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 labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: All cell lines were cultured under an atmosphere of 5% CO2 at 37°C. HepG2 were cultured in DMEM (GIBCO) medium. The medium is supplemented with 10% fetal bovine serum (FBS, GIBCO), penicillin (100 U/ml), and streptomycin (100 mg/ml).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The HepG2 cells were exposed to Fluid shear stress for 8h and the static cultured HepG2 used as control

value: hepatocellular carcinoma cell line HepG2

tag: passage

value: control

tag: rip antibody

tag: fraction

value: supernatant RNA


title: follicular_granulosa_cell_layers-F1_ATAC-seq

extract_protocol:
Cryopreserved samples grinded into powders in liquid nitrogen after washed with 0.09% NaCl solution. Lysis buffer were added to the powders and incubated on ice for 10 min on the rotation mixer. Cell suspension was filtered with 40 um cell strainer and then washed with cold PBS buffer three times to collect the cell nuclei.
Approximate 50,000 nuclei were allocated to perform tagmentation according to the standard protocols96 and Tn5 transposed DNA was purified by AMPure DNA magnetic beads. Next, average 11 cycles of PCR were performed with transposed DNA and amplified libraries were run on an Agilent TapeStation 2200 (Agilent Technologies) using a D5000 DNA ScreenTape to assess quality by visualizing nucleosomal laddering. The final libraries were submitted for sequencing on the Illumina HiSeq X Ten platform (San Diego, CA, United States) with 150 PE mode.
An improved ATAC-seq protocol compatible with cryopreserved samples was employed (Corces et al., 2017, Fujiwara et al., 2019). Cryopreserved samples grinded into powders in liquid nitrogen after washed with 0.09% NaCl solution. Lysis buffer were added to the powders and incubated on ice for 10 min on the rotation mixer. Cell suspension was filtered with 40 um cell strainer and then washed with cold PBS buffer three times to collect the cell nuclei. Approximate 50,000 nuclei were allocated to perform tagmentation according to standard protocols (Corces M R et al., 2017) and Tn5 transposed DNA were purified by AMPure DNA magnetic beads. Next, average 11 cycles of PCR were performed with transposed DNA and amplified libraries were run on an Agilent TapeStation 2200 (Agilent Technologies) using a D5000 DNA ScreenTape to assess quality by visualizing nucleosomal laddering.


title: follicular_granulosa_cell_layers-POF_ATAC-seq

value: POF


title: FSS-HepG2_IP_Cy5

description: Raw data file:  FSS-HepG2.txt

source_name: hepatocellular carcinoma cells (IP)

value: Fluid shear stress

value: anti-N6-methyadenosine (m6A) antibody

value: immunoprecipitated RNA


title: HepG2_IP_Cy5

description: Raw data file:  HepG2.txt


title: follicular_granulosa_cell_layers-SWF_ATAC-seq

value: granulosa cells

value: Luhua hens


title: FSS-HepG2_Sup_Cy3

description: Raw data file:  FSS-HepG2.txt


title: P1CHIR6: Passage 1 CHIR-treated endothelial cells 6

value: endothelial cells

value: CHIR


title: follicular_granulosa_cell_layers-SWF_ChIP-seq-H3K27ac_replicated_2

value: prehierarchical follicles


title: follicular_granulosa_cell_layers-POF_single-cell_RNA_sequencing

description:
POF.filtered_feature_bc_matrix.h5
F1.POF.silico.bulk.DEG.result.by.DEseq2.txt
SWF.POF.silico.bulk.DEG.result.by.DEseq2.txt

molecule: polyA RNA

extract_protocol:
The separated GC layers were washed in ice-cold RPMI1640 and dissociated using Multi-tissue dissociation kit 2 (Miltenyi Catalog No.130-110-203) from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminate.
scRNA-seq libraries were prepared following the standard protocols by Beijing SeekGene BioSciences Co., Ltd (Beijing, China). Libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics).
Libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then loaded to the sample well in Chromium Next GEM Chip G. Subsequently Gel Beads and Partitioning Oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 53℃ for 45 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Bar code and Unique Molecular Index.

value: postovulatory follicles

value: 31 weeks


title: P1DMSO3: Passage 1 DMSO-treated endothelial cells 3

value: DMSO


title: follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_2

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SWF-2

value: SWF


title: follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_3

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SWF-3


title: follicular_granulosa_cell_layers-F1_single-cell_RNA_sequencing

description:
F1.filtered_feature_bc_matrix.h5
F1.POF.silico.bulk.DEG.result.by.DEseq2.txt
SWF.F1.silico.bulk.DEG.result.by.DEseq2.txt


title: P1DMSO2: Passage 1 DMSO-treated endothelial cells 2


title: P1DMSO6: Passage 1 DMSO-treated endothelial cells 6


title: follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_1

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SWF-1


title: follicular_granulosa_cell_layers-SWF_single-cell_RNA_sequencing

description:
SWF.filtered_feature_bc_matrix.h5
SWF.F1.silico.bulk.DEG.result.by.DEseq2.txt
SWF.POF.silico.bulk.DEG.result.by.DEseq2.txt


title: follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_4

description:
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx
TPM-submission.xlsx
SWF-4


title: Mix3T3-293T (ATAC-seq)

status: Public on Nov 09 2021

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
For sequenced Microwell-ATAC-seq library, we integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ using Drop-seq tools. Then, snaptools was used to pre-process the Microwell-ATAC-seq datasets.
Demultiplexed sequencing reads are aligned to the merged hg19-mm10 genome reference (provided by Drop-seq group, GSE63269) using bwa-mem in pair-end mode with default parameter settings.
For cell quality control, the single nucleus accessibility profile containing the top 10,000 cells sorted by the total number of unique mapping reads were obtained after this pre-procession. The corresponding protocol is available at https://github.com/r3fang/SnapTools.
The fragment size distribution was evaluated using insertion size of the aligned bam. TSS enrichment were calculated using deeptools bamCoverage and computeMatrix command with the corresponding reference.
Nonduplicate fragment endpoints for each cell were used for peak calling in each sample by use of MACS2 callpeak command with parameters “–shift -100 –extsize 200 –nomodel”.
Genome_build: hg19-mm10 genome
Supplementary_files_format_and_content: bw & bed, contains the coverage of DNA fragments for peak calling

source_name: 3T3 cell and 293T cell

extract_protocol: Library preparations were performed with the Microwell-ATAC-seq protocol

tag: culture medium

value: 10% DMEM

tag: protocol

value: fragmentation by Tn5


title: WT_R108_rep4

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description:
nodules_fpkm.txt
R108_4

data_processing:
The quality of the fastq files were validated with fastqc
Sequence reads were trimmed for adapter and repetitive sequences with Cutadept
The resulting reads from the raw fastq data were quality controlled and and mapped to the M. truncatula reference genome version 4.0 with STAR
The FPKM (Fragments per kilobase per million mapped reads) values were calculated with featureCounts in R package Rsubread
Genome_build: Mt4.0v1
Supplementary_files_format_and_content: tab separated files with the corresponding expression values

organism: Medicago truncatula

source_name: root nodule

growth_protocol: M. truncatula seeds were scarified with concentrated sulfuric acid for 6 min, followed by washing several times with ice-cold sterilized water. The seeds were then surface-sterilized for 3 min in 10% sodium hypochlorite solution and rinsed by sterilized water for 5 times. The seeds were imbibed at 4°C for 3 days and germinated on water agar plates. For hairy root transformed assays, plants were grown in sterile conditions in controlled environment rooms at 22 °C (16 h light/8 h dark) on filter paper-lined mod-FP media in sealed plates. For nodulation assays in trays, M. truncatula seedlings were grown in terragreen/sharp sand mix (1:1) for seven days and inoculated with 5 mL S. meliloti  (OD600, 0.02).

extract_protocol:
Total RNA from roots overexpressing NIN or GFP and nodules was isolated using RNeasy PlantMini Kit (Qiagen) and Spectrum™ Plant Total RNA Kit (Sigma-Aldrich) respectively following the manufacturer’s instructions.
The library was constructed with Illumina TruSeq® Stranded mRNA HT kit

treatment_protocol: M. truncatula seedlings were grown in terragreen/sharp sand mix (1:1) for seven days and then inoculated with 5 mL S. meliloti. For NIN overexpression, seedlings were transformed with LjUBI:NIN-CDS and LjUBI-GFP construct using Agrobacterium rhizogenes mediated hairy root transformation, plants were regenerated on plates under non symbiotic conditions, transformed roots were harvested after 3 weeks

tag: genoytpe

value: wild type ecotype R108

value: Sinorhizobium meliloti


title: P1DMSO5: Passage 1 DMSO-treated endothelial cells 5


title: WT_R108_rep1

description:
nodules_fpkm.txt
R108_1


title: nin-16_rep4

description:
nodules_fpkm.txt
nin_16_4

value: nin-16 mutant in R108 wild type background


title: WT_R108_rep3

description:
nodules_fpkm.txt
R108_3


title: WT_R108_rep2

description:
nodules_fpkm.txt
R108_2


title: Aged_Germ_Free_mouse_2

city: Saint Louis

last: Link

state: MO

address: 660 S. Euclid Avenue

department: Oncology

institute: Washington University in St. Louis

description: gene expression from aged GF HSCs

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul). The hybridization solutions were applied to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4846A-026655). Hybridization was carried out at 65C for 20 hours. Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). Raw images were first passed-through quality control tools from the Bioconductor package of R. Array intensity data were then background adjusted, and quantile normalized. To test for differential expression, the linear models for Microarray data (limma) package was used.

organism: Mus musculus

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul). The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes. Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol. cDNAs were quantitated on a Nanodrop spectrophotometer.

growth_protocol: Germ-free C57BL/6J mice were housed in a sterile environment of plastic flexible film isolators. Specific pathogen-free mice were maintained under standard pathogen-free conditions.

extract_protocol: Cell sorting was performed using a Sony iCyt Synergy SY3200 (Synergy) cell sorter. The hematopoietic stem/progenitor cell (HSPC) panel included PE-Cy7-conjugated anti-CD117 (2B8); PerCP-Cy5.5-conjugated anti-Ly-6A/E; PE-conjugated anti-CD150 (TC15-12F12.2) BV421-conjugated anti-CD48 (HM48-1) and the following APC-Cy7-conjugated antibodies: anti-CD3e (145-2C11), anti-B220 (RA3-6B2), anti-Gr1 (RB6-8C5), anti-Ter119 (TER-119), anti-CD11b (M1/70), and anti-NK1.1 (PK136). Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations. RNA transcripts were first amplified by WTA2 kit (Sigma Aldrich). 2ng of total RNA (14ul) was amplified according to manufacturer’s protocol.

treatment_protocol: Mice were not treated

tag: strain

value: sorted phenotypic Hematopoietic Stem Cell

tag: germ status

value: Germ Free

tag: age

value: 12 months


title: Aged_Germ_Free_mouse_3

description: gene expression from aged GF HSCs


title: Aged_Specific_Pathogen_Free_mouse_2

description: gene expression from aged SPF HSCs

value: Specific Pathogen Free


title: dnf1-2_rep4

description:
nodules_fpkm.txt
dnf1_4

value: dnf1-2 mutant in A17 wild type background


title: Aged_Specific_Pathogen_Free_mouse_3

description: gene expression from aged SPF HSCs

source_name: OCV


title: nin-16_rep2

description:
nodules_fpkm.txt
nin_16_2


title: dnf1-2_rep2

description:
nodules_fpkm.txt
dnf1_2


title: dnf1-2_rep3

description:
nodules_fpkm.txt
dnf1_3


title: follicular_granulosa_cell_layers-POF_ChIP-seq-H3K27ac_replicated_1

value: granulosa cells

tag: breed

value: Luhua hens

tag: developmental stage

tag: follicle growth stage

value: POF

value: Anti-flag (14793, Cell Signaling Technology)


title: dnf1-2_rep1

description:
nodules_fpkm.txt
dnf1_1


title: WT_A17_rep4

description:
nodules_fpkm.txt
A17_4

value: wild type ecotype jemalong A17


title: Aged_Germ_Free_mouse_1

description: gene expression from aged GF HSCs


title: WT_A17_rep1

description:
nodules_fpkm.txt
A17_1


title: WT_A17_rep2

description:
nodules_fpkm.txt
A17_2


title: WT_A17_rep3

description:
nodules_fpkm.txt
A17_3


title: Aged_Specific_Pathogen_Free_mouse_1

description: gene expression from aged SPF HSCs


title: nin-16_rep3

description:
nodules_fpkm.txt
nin_16_3


title: pLjUBI:GFPcontrol_forNIN_rep1

source_name: regenerated root structure

value: wild type ecotype jemalong A17 cultivar Jester transformed with pLjUBI:NIN

value: no treatment


title: pLjUBI:GFPcontrol_forNIN_rep2


title: pLjUBI:NIN_rep3


title: pLjUBI:GFPcontrol_forNIN_rep3


title: pLjUBI:NIN_rep4


title: nin-16_rep1

description:
nodules_fpkm.txt
nin_16_1


title: pLjUBI:NIN_rep2


title: pLjUBI:NIN_rep1


title: H441_PRMT5i_1

city: San Diego

first: Tao

last: Xie

address: 10770 science Center Dr.

department: ORD

institute: Pfizer Inc

data_processing:
Sequencing reads were mapped to human genome using STAR(2.5.3) and quantified using RSEM (1.3.0) gencode v25 mapped to GRCh37
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw counts from RSEM in a tab-delimited text format

source_name: Cancer cell line

growth_protocol: Cancer cells were grown in recommanded groeth mediun overnight at 37 degC, 5% CO2

extract_protocol:
Cancer cells treated with PRMT5i/DMSO were preserved in RNALater (Qiagen) reagent and sent to WuXi NextCode for RNA isolation and sequencing at 100MM read depth).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with PRMT5i at 30uM or DMSO (0.1%) for 72 hours.

tag: replicate


title: H441_PRMT5i_3


title: H441_DMSO_2

value: DMSO


title: H441_DMSO_1


title: A427_PRMT5i_3


title: A427_PRMT5i_2


title: A427_PRMT5i_1


title: A427_DMSO_3


title: A427_DMSO_1


title: H1975_PRMT5i_3


title: H1975_PRMT5i_1


title: H1975_DMSO_3


title: H1975_DMSO_1


title: H1975_PRMT5i_2


title: H1975_DMSO_2


title: No_betaine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For Illunima platform cellbarcode: In read1, the bases 1-6,22-27,43-48,92-101 merge (28bp); UMI: In read1, the　bases　84-91 (8bp). For MGI platform (rep1-plate1-2, rep1-plate2-2, rep2-plate1-1, rep2-plate1-2, rep2-plate2-1, rep2-plate2-2) cell barcode: In read1, the bases 1-18, 27-36 merge (28bp), UMI: In read1, the bases 19-26 (8bp). For MGI platform (rep1-plate1-1, rep1-plate2-1) cell barcode: In read1, the bases 1-18, 33-42 merge (28bp), UMI: In read1, the bases 25-32 (8bp).
ScRNA-seq reads were aligned to the mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
Supplementary_files_format_and_content: The file chemical_annotation.xlsx is the  metadata file with the cell barcode, cluster, perturbation information for rep1 and rep2.

growth_protocol: H9 human embryonic stem cells (ESCs) were maintained in mTeSRTM1 media (STEMCELL Technologies) on 6-well tissue culture plates coated with Matrigel (BD Bioscience) routinely.

extract_protocol: Library preparations were performed with the Microwell-seq 2.0 protocol

treatment_protocol: Day 0, 96-well plate was coated using 50 μL Matrigel (25 μg protein/well). The 96-well plate was incubated at room temperature for 1 hour. H9 cells were dissociated into single-cell suspension with Accutase (Gibco) and resuspended in 1 mL mTeSR™1 (with 10 μg Y-27632). Excess Matrigel solution was removed from the well and 5000 cells (200μL) were seeded per well using a multi-channel pipettor. Cells were pipetted up and down several times with the multi-channel pipettor. After mixing, the plate was undisturbed inside the bench for 10 min. Then the plate was incubated at 37°C and 5% CO2 with 95% humidity overnight. Day 1, culture medium was removed and 100 μL fresh mTeSR™1 (with 25 μg protein/well Matrigel) was added. The plate was incubated at 37°C and 5% CO2 with 95% humidity overnight. Day 2, a full medium change was performed using 100 μL fresh mTeSR™1. Day 3, a full medium change was performed using 200 μL fresh E6 (STEMCELL Technologies) with different compounds (47 perturbations + 1 vehicle, two repetitions). Day 5, cells were dissociated into single-cell suspension with Accutase. Cells were collected into a 96-well PCR plate for washing and fixation. The fixed cells were stored at -80℃.

value: 10% DMEM


title: H441_PRMT5i_2


title: betaine


title: NaCl


title: primer_plus


title: 45um


title: Lysis_5


title: KCl


title: Lysis_1


title: SQLE_24h_d252

city: Los Angeles

first: Zulema

middle: R.

last: Garcia

address: 18033 Le Conte Ave 52-121, Center for Heath Sciences

institute: University of California, Los Angeles

data_processing:
Samples were mapped to hg38 using STAR/2.7.9a with parameters --runThreadN 2 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
The raw counts table was generated using subread/2.0.3 featurecounts function with parameters -T 8 -p
Genome_build: hg38
Supplementary_files_format_and_content: Table with log normalized gene counts for every gene and every sample

source_name: pbmc

growth_protocol: Monocytes were seeded at 500,000 cells/well in a 24-well plate and differentiated in M-CSF (50 ng/ml) (R&D Systems, cat. # 216MC025/CF) for 5 day in RPMI with 10% FCS at 37°C.

extract_protocol:
RNA were extracted using Trizol RNA extraction protocol and Qiagen RNeasy Micro Kit .
We quantified the RNA concentration and quality using TapeStation.

treatment_protocol: Macrophages were then stimulated with M-CSF (50 ng/ml) (R&D Systems, cat. # 216MC025/CF), IL-4 (20ng/mL) (Peprotech, cat. # 200-04), and squalene (1 mM) (Thermofisher Scientific, cat.# S3626-100ML) for 1 days.

value: SQLE

value: macrophages


title: H441_DMSO_3


title: A427_DMSO_2


title: primer_minus


title: Testicular_Sample_3411_R1

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on May 2015
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 normalized counts for each Sample.

source_name: Testis

growth_protocol: Primary isolated macrophage without further culture.

extract_protocol:
The testis, epididymis and brian were cut in small pieces and enzymatically digested by a solution containing RPMI1640 (ThermoFisher) + 1 mg/mL Collagenase II (Sigma) + 50μg/mL DNase I (Sigma) for 40 min at 37oC. Then they were passed through 70 μm cell strainers and the generated single cell suspensions undergone erythrocyte lysis on ice. Single cell suspensions from  testes and epididymides were pooled in a separate tube. Cells from brains, epididiymides, and testes were resuspended into 40% isotonic Percoll (GE Healthcare, Uppsala, Sweden) at a density of 1.072 g/ml in PBS containing 3% FCS. Cells were collected from 1.06 and 1.072 g/ml layers after centrifugation and resuspended. RBCs were lysed in RBC lysis buffer (Qiagen). The cells were blocked with FC-block and stained with antibodies against CD45, Ly6c, CD11b, CD11c, CD11b and F4/80. Macrophage populations were identified and sorted as live (DAPI-), CD45+ Ly6c- CD11c-, CD11b+ F4/80+. The sorted cells were collected in RPMI medium containing 10% FCS.
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries

treatment_protocol: No treatment.

tag: genetic background

tag: mouseid

tag: tissue

value: Testis


title: 28um

tag: cell type


title: IL4_24h_d252

tag: treatment


title: media_24h_d252

value: media (mcsf)


title: SQLE_24h_d0000


title: Lysis_2


title: media_24h_d0000


title: DPP4_pos_isoproterenol3

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

data_processing:
Reads with phred quality scores <20 and <35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HISAT (v2.0.1) using default settings.
Duplicates were marked using Sambamba version 0.6.6.
Aligned reads were quantified using ‘featurecount’ (v1.4.6).
Generatin of normalized counts and analysis of differential gene expression was done using the R package DEseq2 (v1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: text file of normalized counts for every sample and every gene

source_name: Adipose tissue PDGFRb+ cells

growth_protocol: Adipose tissue PDGFRb+ cells were isolated by flow cytometry and cultured in DMSO/F12 media supplemented with 10% FBS + pen/strep antibiotics prior to the treatment.

extract_protocol:
Total RNA of treated cells was extracted using RNAqueous micro RNA isolation kit. 500ng total RNA of each sample was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Libray Prep Kit following manufacturer's instructions.

treatment_protocol: Cultured adipose tissue PDGFRb+ cells were treated with vehicle(PBS) or 10mM isoproterenol for 4 hours.

tag: subpopulation

value: DPP4_pos APC

value: isoproterenol (10mM)


title: IL4_24h_d0000


title: DPP4_pos_isoproterenol1


title: DPP4_pos_isoproterenol2


title: DPP4_pos_vehicle4

value: vehicle(PBS)


title: DPP4_pos_vehicle1


title: DPP4_pos_vehicle2


title: DPP4_pos_vehicle3


title: Mix3T3-293T

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: mix genome (human hg19 and mouse mm10), Homo_sapiens.GRCH39, Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

tag: cell line


title: DPP4_neg_isoproterenol4

value: DPP4_neg APC


title: DPP4_neg_isoproterenol3


title: DPP4_neg_vehicle4


title: DPP4_neg_vehicle3


title: DPP4_neg_isoproterenol2


title: DPP4_neg_vehicle2


title: ISO_p-CREB_5%_input

data_processing:
Trimgalore version 0.4.1 was used to remove adaptor sequences and to remove reads shorter than 35bp or with phred quality scores less than 20
Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.4.2
Qualified (MAPQ quality score>30) mappable reads were retained using Samtools version 1.8
Peak calling was performed using MACS version 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: peak files in bigwig format

extract_protocol:
Treated DPP4+ APCs were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37 °C and quenched in 125 mM glycine in PBS for 5 minutes at 4 °C. DPP4+ cells were then lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) to obtain nuclear material. Crude nuclear pellets were collected by centrifugation and then lysed by incubation in lysis buffer containing 5 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]. Chromatin fragmentation (200-500 bp length) was performed at 4 °C by Bioruptor 300 using the setting of 10 cycles of 30 seconds on and 60 seconds off. Soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) and pre-cleared using Protein G Sepharose 4 Fast Flow (GE Healthcare Bio-sciences, #17-0618-01) for 1 hour at 4 °C. Pre-cleared samples were incubated with anti-phospho-CREB antibody (Cell Signaling Technology, #9198) at 4 °C overnight. Antibody-protein-DNA complexes were captured by incubation with Protein G Sepharose 4 Fast Flow (GE Healthcare Bio-sciences, #17-0618-01) at 4 °C for 2 hours. Immunoprecipitated material was consecutively washed with low salt wash buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), high salt wash buffer (20 mM Tris-HCl pH 7.9, 2mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), LiCl wash buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, and Protease inhibitor cocktail [Sigma, #P8340]), and 1x Tris-EDTA (TE). After elution (100 mM NaHCO3, 1% SDS), the immunoprecipitated material was digested with RNase (Roche, #11119915001) and proteinase K (ThermoFisher Scientific, #EO0491) prior to the purification and concentration of the immunoprecipitated genomic DNA by ChIP DNA Clean & Concentrator kit (Zymo Research, #D5201). 50ng immunoprecipitated DNA of each sample was used for the construction of sequencing libraries.
DNA libraries were prepared for sequencing using NEBNext NGS DNA Libray Preparation for Illumina Kit following manufacturer's instructions.

tag: antibody

value: anti-phospho-CREB


title: DPP4_neg_isoproterenol1


title: DPP4_pos_RT4

extract_protocol:
Adipose tissue PDGFRb+ cells were isolated by flow cytometry, and total RNA was extracted using RNAqueous micro RNA isolation kit. 500ng total RNA of each sample was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Libray Prep Kit following manufacturer's instructions

tag: temperature

value: room temperature (22°C)


title: ISO_p-CREB_IP


title: DPP4_pos_isoproterenol4


title: DPP4_pos_RT5


title: DPP4_pos_RT1


title: Veh_p-CREB_5%_input


title: DPP4_pos_RT3


title: Veh_p-CREB_IP


title: DPP4_pos_CE5

value: cold exposure (6°C)


title: DPP4_pos_CE1


title: DPP4_pos_CE3


title: DPP4_pos_CE2


title: DPP4_pos_RT2


title: DPP4_neg_RT4


title: DPP4_neg_RT5


title: DPP4_neg_CE5


title: DPP4_neg_RT2


title: DPP4_neg_RT1


title: DPP4_neg_CE4


title: DPP4_neg_CE3


title: DPP4_neg_vehicle1


title: DPP4_neg_CE1


title: DPP4_neg_CE2


title: Fed_Crtc2 rep 3

city: Jupiter

first: Jerome

last: Nwachukwu

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

data_processing:
Primary data analysis including base calling and quality scoring was performed in real-time on the NextSeq 500 platform.
fastq files were generated on BaseSpace (Illumina) using FASTQ Generation Version: 1.0.0
Reads were aligned to the Ensembl Mus musculus GRCm38.83.chr.gtf genome (mm10) assembly using HISAT2 v2.0.5
Sorting and indexing was performed using SAMtools v1.7
The featureCounts program in Subread v1.6.1 was used to count reads
Differential expression analysis was performed using DESeq2 v1.18.1
Genome_build: mm10
Supplementary_files_format_and_content: A matrix table containing the raw counts of sequencing reads for each gene

source_name: tibialis anterior muscle

extract_protocol:
TA muscles were removed, flash frozen on dry ice, and RNA was extracted using TRIzol™ reagent (Invitrogen). The RNA was cleaned up using the RNeasy kit (Qiagen). Sequencing libraries were constructed using an NEBNext Ultra II directional kit (New England Biolabs).
Sequencing libraries were constructed using standard Illumina TruSeq Stranded mRNA library prep protocol

tag: Sex

value: male

value: 13 weeks

value: tibialis anterior

tag: transduction

tag: diet

value: Fed ad libitum


title: Fed_Crtc2 rep 2

tag: strain

tag: age


title: Fed_Crtc2 rep 1


title: Fed_GFP rep 2

value: GFP


title: DPP4_pos_CE4


title: Fed_GFP rep 3


title: ADF_Crtc2 rep 3

value: Alternate day fasting


title: DPP4_neg_RT3


title: Fed_GFP rep 1


title: ADF_Crtc2 rep 1


title: ADF_GFP rep 1


title: ADF_GFP rep 2


title: ADF_Crtc2 rep 2


title: PBMCs, 6101_D3

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description: 6101 Day 3

data_processing:
Each sample was mapped to the Human Ensembl reference genome GRCh38 using the fast alignment tool HISAT2 v2.1.0 with default settings and library type set to RF (1).
Genes in GRCh38 were quantified used HTSeq v0.9.0 using default settings for paired reads and library type set to reverse.
edgeR, an R Bioconductor package, with R version 4.0, was used for differential gene analysis comparing various sample groups with a gene expression filter of > 1 CPM counts in at least half the samples in a given group.
Genome_build: GRCh38
Supplementary_files_format_and_content: htseq_counts.txt, Metadata.xlsx

source_name: PBMC

extract_protocol:
Total PBMC were isolated using CPT blood tubes (BD) per manufacturer's instructions.  Total RNA from Days 0, 3 and 7 post-vaccination was isolated, ribosomal RNA depleted (Ribo-zero Gold) and sequenced using the Illumina TruSeq platform.
Approximately 37 to 61 million reads per sample were collected and were mapped to the Human Ensembl reference genome GRCh38 using the fast alignment tool HISAT2 v2.1.0.

treatment_protocol: Children were immunized with the quadrivalent vaccine IIV ((either Fluzone (Sanofi Pasteur) or Fluarix (GlaxoSmithKline) as determined by their health insurance provider)).

value: PBMC

tag: patient id

tag: time

value: 3 days post-vaccination


title: PBMCs, 7024_D3

description: 7024 Day 3


title: PBMCs, 7017_D3

description: 7017 Day 3


title: PBMCs, 6105_D3

description: 6105 Day 3


title: PBMCs, 7107_D3

description: 7107 Day 3


title: ADF_GFP rep 3


title: PBMCs, 5066_D3

description: 5066 Day 3


title: PBMCs, 5266_D3

description: 5266 Day 3


title: PBMCs, 7152_D0

description: 7152 Day 0

value: pre-vaccination


title: PBMCs, 6112_D0

description: 6112 Day 0


title: PBMCs, 7107_D0

description: 7107 Day 0


title: PBMCs, 6113_D0

description: 6113 Day 0


title: PBMCs, 6113_D3

description: 6113 Day 3


title: PBMCs, 7152_D3

description: 7152 Day 3


title: PBMCs, 6105_D0

description: 6105 Day 0


title: PBMCs, 6101_D0

description: 6101 Day 0


title: PBMCs, 5066_D0

description: 5066 Day 0


title: PBMCs, 5266_D0

description: 5266 Day 0


title: PBMCs, 7017_D0

description: 7017 Day 0


title: PBMCs, 6040_D7

description: 6040 Day 7

value: 7 days post-vaccination


title: PBMCs, 6114_D7

description: 6114 Day 7


title: PBMCs, 6006_D7

description: 6006 Day 7


title: PBMCs, 6112_D3

description: 6112 Day 3


title: PBMCs, 7024_D0

description: 7024 Day 0


title: PBMCs, 5040_D7

description: 5040 Day 7


title: PBMCs, 5001_D7

description: 5001 Day 7


title: PBMCs, 5050_D7

description: 5050 Day 7


title: PBMCs, 6114_D0

description: 6114 Day 0


title: PBMCs, 6006_D0

description: 6006 Day 0


title: PBMCs, 5001_D0

description: 5001 Day 0


title: PBMCs, 6040_D0

description: 6040 Day 0


title: PBMCs, 5050_D0

description: 5050 Day 0


title: SeD2

city: Nanjing

first: Yang

last: Ping

address: 321 Zhongshan Road

institute: nanjing drum tower hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed reads (pass Illumina quality  filter, trimmed 3’-adaptor bases by cutadapt [4]  ) were aligned to cytoplasmic mature-tRNA sequences  from GtRNAdb and also including the mitochondrial tRNA sequences from mitotRNAdb using BWA [5]  software. For tRNA alignment, the maximum mismatch was 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Serum of  SLE(Systemic Lupus Erythematosus) with LN (Lupus nephritis)

extract_protocol:
The heavy decoration of tsRNAs by RNA modification is a main problem while constructing a small RNA sequence library. To construct a total RNA library, the following changes were made, 3’-aminoacyl was deacylated, and 3’-cP (2’, 3’-cyclic phosphate) was removed from 3’-OH to facilitate 3’ adaptor ligation. 5’-OH (hydroxyl group) was phosphorylated to 5’ -P for ligating a 5’- adaptor. m1A and m3C demethylated to facilitate reverse transcription.
The integrity of the RNA samples was validated using Agarose gel electrophoresis. Quantification of the RNA samples was achieved by using NanoDrop ND-1000 instrument. The removal of the RNA modifications, the main issue during construction of RNA sequence library, was carried out by adopting the pretreatment strategy as explianed. Agilent 2100 Bioanalyzer was used to quantify the completed libraries. Based on the quantification outcomes, the libraries were mixed in equal quantities for sequencing operation.
For sequencing the single stranded DNAs were needed. To achieve that o.1 M NaOH solution was used to denature the DNA fragments in well mixed libraries. The single stranded DNA with 1.8pM concentration was loaded onto the reagent cartridge. NextSeq system using NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) was used for sequencing operation following the guidelines provided by the production company. Sequencing operation included 50 cycles.

tag: disease state

value: Systemic Lupus Erythematosus with LN


title: PBMCs, 5040_D0

description: 5040 Day 0


title: ExD2

source_name: Serum exosome of SLE(Systemic Lupus Erythematosus) with LN(Lupus nephritis)


title: SeE

source_name: Serum of healthy control

value: healthy control


title: KellyXeno_223_veh

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Mouse reads were filtered using hisat2 v2.1 in paired-end mode against the mm9 revision of the mouse genome.  Remaining reads were aligned to a reference genome containing the hg19 revision of the human reference and the sequences of ERCC spike-in probes.
Expression was quantified using sorted BAMs, a gene reference built using ERCC sizes and RefSeq genes downloaded 7/15/2017, and htseq-count with parameters -I gene_id –stranded=reverse -f bam -m intersection-strict.
Genome_build: hg19
Supplementary_files_format_and_content: Count files represent the counts of reads assigned to each listed gene by htseq-count

source_name: Neuroblastoma

growth_protocol: Eight-week-old female NSG mice were subcutaneously implanted with 2.5 × 106 Kelly cells in 50% matrigel/PBS. Animals were treated with vehicle (n=4) or JQAD1 (n=4) at 40 mg/kg I.P. daily for 14 days. These animals were sacrificed at day 14, following which tumor was extracted, and divided for immunohistochemical analysis or analysis of RNA expression by RNAseq.

extract_protocol: Total RNA was extracted from control, A485 or JQAD1 treated Kelly cells using Trizol reagent (Ambion). Prior to extraction, samples were subjected to exogenous spike-in of synthetic ERCC RNA controls (Ambion). Samples were treated with RNAse-free DNAse I and spin purified using the Qiagen RNeasy Kit (Qiagen). Purified RNA samples were subjected to library construction with poly-adenylation preparation and sequencing using the Illumina NextSeq 5000 (paired end, 75bp reads).

treatment_protocol: Mice were injected intraperitoneally daily with DMSO solubilized in 10% hydroxypropyl β-cyclodextrin (Sigma-Aldrich) in sterile water as a matched 40mg/kg vehicle dose.

tag: sample type

value: Kelly xenografted into mouse

tag: cell line source

value: Kelly

value: Neuroblastoma

value: vehicle


title: ExD1

source_name: Serum exosome of SLE(Systemic Lupus Erythematosus) without LN(Lupus nephritis)

value: Systemic Lupus Erythematosus


title: KellyXeno_215_veh


title: KellyXeno_217_JQAD_40

treatment_protocol: Mice were injected intraperitoneally with 40 mg/kg (R,S)-JQAD1 solubilized in 10% hydroxypropyl β-cyclodextrin (Sigma-Aldrich) in sterile water, daily.


title: KellyXeno_219_JQAD_40


title: Kelly_24h_JQAD1_r2

data_processing:
RNA-seq reads were aligned to a reference index containing the sequences of the hg19 revision of the human reference genome and the ERCC spike-in probes using hisat 2.1.0. Expression was quantified using sorted BAMs, a gene reference built using ERCC sizes and RefSeq genes downloaded 7/15/2017, and htseq-count with parameters -I gene_id –stranded=reverse -f bam -m intersection-strict.
hg19
Supplementary_files_format_and_content: Count files represent the counts of reads assigned to each listed gene by htseq-count

growth_protocol: Neuroblastoma cell lines were cultured in RPMI media containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin and validated to be free of Mycoplasma species by routine testing.

extract_protocol: Total RNA was extracted from control, A485 or JQAD1 treated Kelly cells using Trizol reagent (Ambion). Prior to extraction, samples were subjected to exogenous spike-in of synthetic ERCC RNA controls (Ambion). Samples were treated with RNAse-free DNAse I and spin purified using the Qiagen RNeasy Kit (Qiagen). Purified RNA samples were subjected to library construction with poly-adenylation preparation and sequencing using the Illumina NextSeq 500 (paired end, 75bp reads).

treatment_protocol: Cells were treated with 1000 nM concentrations of JQAD1 for 24h before harvesting

value: JQAD1 24 h


title: Kelly_24h_A485_r2

treatment_protocol: Cells were treated with 1000 nM concentrations of A485 for 24h before harvesting


title: Kelly_24h_JQAD1_r1


title: Kelly_24h_JQAD1_r3


title: KellyXeno_210_veh


title: KellyXeno_220_JQAD_40


title: KellyXeno_213_veh


title: Kelly_24h_A485_r1


title: Kelly_24h_A485_r3


title: Kelly_DMSO_r3

value: DMSO


title: Kelly_DMSO_r1


title: Kelly_DMSO_r2


title: SeD1

source_name: Serum of SLE(Systemic Lupus Erythematosus) without LN(Lupus nephritis)


title: ExE

source_name: Serum exosome of healthy control


title: Kelly_JQAD_0h_H3K27ac_r1

data_processing:
Reads were aligned to the dm6 reference genome using bowtie -k 1 --best.  Non-mapping reads were aligned to the hg19 reference genome using bowtie -k 2 -m 2 --best -l 75 --chunkmbs 256
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are normalized to millions of reads mapped to the fly genome

extract_protocol: For each ChIP, 10 μg of antibody was added to 3 ml of sonicated nuclear extract. Illumina sequencing, library construction and ChIP-seq analysis methods were previously described (Mansour et al. Science, 2014)

value: JQAD 0h

tag: chip antibody

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: antibody lot


title: Kelly_JQAD_0h_H3K27ac_r2

tag: treatment

tag: cell line

tag: cell type


title: Kelly_JQAD_24h_H3K27ac_r1

value: JQAD 24h


title: Kelly_JQAD_0h_Input

value: none (input)


title: Kelly_JQAD_24h_Input


title: Kelly_JQAD_6h_H3K27ac_r1

value: JQAD 6h


title: Kelly_JQAD_6h_H3K27ac_r2


title: Kelly_JQAD_6h_Input


title: Kelly_EP300_MWZ5393 [Lab: Look]

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1


title: Kelly_JQAD_24h_H3K27ac_r2


title: BE2C_EP300_MWZ5393 [Lab: Look]


title: Kelly_CBP_2_MWZ5968 [Lab: Look]

value: CBP

value: Cell Signaling


title: POSR2 H3K27ac Replicate 1

city: Cambridge

middle: Robert

last: Goulet

state: MA

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

description:
POSR2 H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt

data_processing:
ChIP-seq fastq: Cutadapt (v.1.12) was used to remove adaptor sequences from reads. Reads were filtered with FASTX-Toolkit (v0.0.12) including options -Q 33, -p 90, and q 20.  Reads were then aligned to the hg19 genome using STAR (v2.5.2b) with the following parameters: --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, --outFilterMultimapNmax 1.
Raw Counts tables: Number of reads for given set of genomic coordinates was tabulated using the featureCounts function in the Rsubread R package (v. 1.34.7)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain total read depth normalized signal. txt-MACS2 contain narrowpeak calls for JUNB ChIP-seq data, and refinePeaks summits of H3K27ac ChIP-seq with +/- 500 bp window. txt-DESEQ2 contains all results from differential signal analysis by DESeq2 for regions of H3K27ac signal enrichment. txt-Raw_counts represent the unnormalized read counts used for DESeq2 analyses.

source_name: Pleural effusion

growth_protocol: Low passage SUM-229PE and isolated subpopulations were cultured in Ham’s F-12 Media (Gibco cat. # 11765-054) with 5% fetal bovine serum (VWR cat. # 97068-085), 5 ug/mL insulin (Gibco cat. # 12585-014), 1 ug/mL hydrocortisone (Sigma cat. # H0396), 1% penicillin-streptomycin solution (Gibco cat. # 15140-014) and 5 mM HEPES (Corning cat. # 25-060-CI)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature, then quenched for five minutes using 1 mM Glycine. Media was discarded and cells were scraped on ice using a cell lifter. Cells were centrifuged 3K RPM at 4C, then supernatant was aspirated and the pellet was flash frozen in liquid nitrogen. Antibody was conjugated to Protein A Dynabeads (Life Technologies cat. # 1002D) for 4 hours at 4C in PBS + 0.5% BSA. Crosslinked pellets were resuspended in lysis buffer 1 to permeabilize plasma membrane, and centrifuged for 5 minutes at 4C at 200 x g. Nuclei were resuspended in lysis buffer, and centrifuged for 5 minutes at 4C at 200 x g. Chromatin was resuspended in sonication buffer, sonication beads added and chromatin was sonicated at 4C for 15 cycles; 30 seconds on, 30 seconds off. Beads were then washed three times with a low salt sonication buffer, then washed once with a high salt sonication buffer, then washed once with a LiCl wash buffer, then washed once with TE buffer. Fragmented chromatin was eluted from the beads with elution buffer at 65C for 15 minutes, vortexing every two minutes. Eluted chromatin and Dynabeads were placed on the magnet, and eluted chromatin was transferred to a fresh tube. Crosslinking was reversed by incubating the eluted chromatin at 65C overnight. The following day, 0.2 ug/mL RNase A (Sigma cat. # R4642) was added to the samples and incubated for 1 hr at 37C. Protein in the sample was digested using 0.2 ug/mL Proteinase K (Ambion cat. # 25530-015) at 55C. Fragmented DNA was purified using the Qiagen MinElute Kit (Qiagen cat. # 28004).
50 ng of DNA was used for library preparation using the KAPA stranded HyperPrep Kit (Roche cat. # 07962347001) and Illumina TruSeq Indexed Adapters according to the manufacturer’s instructions. Dual size selection was performed after 18 cycles of PCR amplification of the cDNA library according to manufacturer recommendations. A multiplexed pool of 12 libraries was sequenced using the 75-cycle NextSeq 500/550 High Output v2 sequencing kit (Illumina cat. # FC-404-2005) on the Illumina NextSeq500 to yield approximately 3.5 x 107 reads per sample.

treatment_protocol: DMSO Control, Acute 30 nM Trametinib for 24 hrs, Chronic 10 nM Trametinib for 0-5 weeks

value: Triple-Negative Breast Cancer Cell Line

tag: passages

tag: subpopulation

value: POSR

value: H3K27ac (Active Motif cat. # 39133)


title: POS Chronic D14 H3K27ac Replicate 2

description:
POS Chronic D14 H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_POS_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt

value: POS

value: Chronic Trametinib D14


title: Kelly_AP2_SCBT_MWZ7150 [Lab: Look]

value: Kelly

value: Neuroblastoma

value: Santa Cruz


title: BE2C_CBP_2_MWZ5968 [Lab: Look]


title: POS Chronic D0 H3K27ac Replicate 1

description:
POS Chronic D0 H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_POS_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt

value: Chronic Trametinib D0


title: POSR2 H3K27ac Replicate 2

description:
POSR2 H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POS Acute Tram H3K27ac Replicate 2

description:
POS Acute Tram H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt

value: Acute Trametinib


title: POSR2 H3K27ac Input

description:
POSR2 H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POS Acute Tram H3K27ac Input

description:
POS Acute Tram H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt


title: POSR1 H3K27ac Replicate 2

description:
POSR1 H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POS Acute DMSO JUNB Replicate 1

description:
POS Acute DMSO JUNB Replicate 1
macs2-JUNB_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt
Raw_counts-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt

value: DMSO

value: JUNB (Cell Signaling cat. #3753S)


title: POSR1 H3K27ac Replicate 1

description:
POSR1 H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POSR1 H3K27ac Input

description:
POSR1 H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POS Chronic D14 H3K27ac Input

description:
POS Chronic D14 H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_POS_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt


title: POS Chronic D14 H3K27ac Replicate 1

description:
POS Chronic D14 H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_POS_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt


title: POS Chronic D0 H3K27ac Replicate 2

description:
POS Chronic D0 H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_POS_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt


title: BE2C_ASCL1_MWZ5393 [Lab: Look]


title: POS Chronic D0 H3K27ac Input

description:
POS Chronic D0 H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_POS_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Chronic_Day14_Tram_POS_Day0_DMSO_control.txt


title: POS Acute Tram H3K27ac Replicate 3

description:
POS Acute Tram H3K27ac Replicate 3
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt


title: POS Acute DMSO JUNB Replicate 2

description:
POS Acute DMSO JUNB Replicate 2
macs2-JUNB_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
DESeq2-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt
Raw_counts-JUNB_regions_of_enrichment_POS_DMSO_NEG_DMSO_control.txt


title: POS Acute DMSO H3K27ac Input

description:
POS Acute DMSO H3K27ac Input
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POS Acute Tram H3K27ac Replicate 1

description:
POS Acute Tram H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt


title: NEG Chronic D14 H3K27ac Replicate 1

description:
NEG Chronic D14 H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_NEG_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt

value: NEG


title: NEG Chronic D0 H3K27ac Replicate 2

description:
NEG Chronic D0 H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_NEG_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt


title: POS Acute DMSO H3K27ac Replicate 3

description:
POS Acute DMSO H3K27ac Replicate 3
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: POS Acute DMSO H3K27ac Replicate 1

description:
POS Acute DMSO H3K27ac Replicate 1
macs2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control_union.txt
macs2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
DESeq2-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_Acute_Tram_POS_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POS_NEG_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_POSR_POS_DMSO_control_union.txt


title: NEG Chronic D14 H3K27ac Replicate 2

description:
NEG Chronic D14 H3K27ac Replicate 2
macs2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_NEG_Day0_DMSO_control_union.txt
DESeq2-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt
Raw_counts-H3K27ac_regions_of_enrichment_NEG_Chronic_Day14_Tram_NEG_Day0_DMSO_control.txt


title: Uncontrolled 200536850032_B

city: Taipei

first: Yungling

middle: Leo

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Uncontrolled

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Initial quality assessment of the whole genome gene expression data was performed using Illumina’s GenomeStudio Gene Expression module (San Diego, CA). Raw expression data were applied by log2‐transformation and quantile‐transformation.

source_name: whole blood

label_protocol: Standard Illumina protocol

extract_protocol: RNA samples were isolated from whole blood and then extracted by Direct-zolTM RNA MiniPrep (Zymo Research).

tag: gender

value: male


title: Controlled 200536850007_I

description: Controlled

value: female


title: Uncontrolled 3999927049_C

description: Uncontrolled


title: Uncontrolled 9999593126_K

description: Uncontrolled


title: Uncontrolled 9999593126_J

description: Uncontrolled


title: Controlled 200536850007_A

description: Controlled


title: Controlled 200536850032_C

description: Controlled


title: Uncontrolled 3999927051_G

description: Uncontrolled


title: Uncontrolled 200536850007_L

description: Uncontrolled


title: Controlled 3999545107_H

description: Controlled


title: Controlled 3999545107_L

description: Controlled


title: Controlled 3999545107_I

description: Controlled


title: Uncontrolled 3999927051_L

description: Uncontrolled