title: Replicate 1 NanoDam

description: NanoDan Cph Rep1

value: CphYFP x UAS-NanoDam x esgTS

value: Cph NanoDam


title: MNase-input.wrap-seq.rep2

status: Public on Oct 28 2024

type: SRA

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
Paired-end reads were trimmed for adaptor sequence using cutadapt v4.3 with parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -n 2 -m 35 -q 30 –pairfilter = any
Trimed reads were mapped to mm10 using Bowtie2 v2.5.1  with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal.
Duplicates were marked using picard MarkDuplicates v2.27.5 with default parameters and removed using samtools view v1.17  with parameters: -f 2 -F 1024 -q 10.
Unique pair-end reads in bam format was converted to bed format grouped according to fragment length using a custom python script.
Mouse genome was segmented in to non-overlapping 100 kb bins. Then, within each genomic bin, fragment from each fragment length group were counted by annotateBed from bedtools v2.30.0. Fragment length groups used includes 50-80 bp, 80-90 bp, 90-100 bp, 100-110 bp, 110-120 bp, 120-130 bp, 130-140 bp, 140-150 bp, 150-160 bp, 160-250 bp or 50-140bp, 140-250bp. Then when a fragment length break point (X bp) is chosen, nucleosome wrapping score (NRS) is computed as the relative deviation between the number (a) of fragments within X~250 bp and the number (b) of fragments within 50~X bp, expressed as NRS(X) = (a-b)/(a+b). Then the genome-wide NRS was transformed as z-score to derive genome-wide nucleosome wrapping index (NRI).
Assembly: mm10
Supplementary files format and content: bedgraphs of Nucleosome wrapping score and nucleosome wrapping index, or replication timing
Supplementary files format and content: bed of nucleosome wrapping domains and RT domains

molecule: genomic DNA

organism: Mus musculus

source_name: Inner cell mass

growth_protocol: Mouse ES cells (R1) were cultured in the medium with 80% DMEM (EmbryoMax, SLM-220-B), 15% FBS (Hyclone, SH30070.03), Nonessential amino acids (EmbryoMax, TMS-001-C), 2-Mercaptoethanol (EmbryoMax, ES-007-E), L-glutamine (EmbryoMax, TMS-002-C), Nucleosides (EmbryoMax, ES-008-D), Pen/Strep (EmbryoMax, TMS-AB-2C) and 1000U/ml leukemia inhibitory factor (LIF) (ESGRO, ESG1107) in standard incubator with 5% CO2 at 37 °C.

extract_protocol:
Cell pellet of ~1x10^7 cells was resuspended in 1 mL nuclei extraction buffer (10 Mm Hepes, PH 7.5; 300 mM NaCl; 3 mM MgCl2; 0.5% IGEPAL CA-630; 0.1% SDS) with EDTA-free protease inhibitor cocktail (Roch, 05892791001) and incubate on ice for min. Then cell pellet was washed once with buffer A (10 mM Tris, PH 7.5; 10 KCl; 60 mM NaCl; 3 mM MgCl2) with EDTA-free protease inhibitor cocktail.
Chromatin was crosslink reversed by heating at 65 °C for 6 hours, and DNA were extracted using a standard phenol-chloroform extraction procedure. For paired-end sequencing, libraries without size selection were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L).
Illumina libraries were sequenced on a DNBSEQ-T7 (MGI) platform with PE150 model.

treatment_protocol: For wrapping-seq, mouse ES cells plated for about 48 hours were directly crosslinked with 1% formaldehyde in PBS for 10 min at room temperature, then quenched by 125 mM glycine, and scraped off from the dish with a cell scraper. Then the cells were washed with cold PBS for twice and the cell pellet were stored at -80 °C.

tag: tissue

value: Inner cell mass

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype

value: wild type


title: 0618ADSC_H3K27ac_rep1,CUT&Tag

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

data_processing:
*library strategy: Cut&Tag
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was calculated using MACS2 while peak calling.
Assembly: hg19
Supplementary files format and content: .bw file containing merged signal intensity of each sample

organism: Homo sapiens

source_name: Adipose tissue

extract_protocol:
Approximately 1 x 10^5 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol. Briefly, harvest fresh cultures and count 1 x 10^5 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4C. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 ℃ for 1 h and then performed DNA extraction with DNA extraction beads.
For extracted DNA, combinate i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and Illumina sequencing.

value: Adipose tissue

value: adult human adipose derived mesenchymal stromal cells

tag: antibody


title: tumor positive, scRNA-seq

city: Seoul

first: Minsu

country: South Korea

institute: Catholic University of Korea

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcode processing and gene counting were performed using the Cell Ranger software v5.0.0 single pipeline with the mm10-2020-A and vdj-GRCm38-alts-ensembl-5.0.0 reference genomes.
Assembly: mm10
Supplementary files format and content: Output files of 10x Cell Ranger software: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: total RNA

source_name: tissue

extract_protocol:
Lung tissue collected from the mouse was minced and dissociated for 40 minutes at 37°C using the Tumor Dissociation Kit, mouse (Miltenyi Biotec, Bergisch Gladbach, Germany). The digested tissue was filtered through a 70-μm strainer to obtain a single cell suspension. Total RNA capture and cDNA amplification were performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell 5p RNA library v2 protocol, 10x Genomics). Briefly, Single-cell suspensions were loaded onto the 10x Chromium system targeting 7,000 cells. For each single cell, total RNA from the cell lysate contained in gel bead-in-emulsion (GEM) was captured with UMI and 10x barcoded gel bead and then reverse transcribed to cDNA. The barcoded cDNAs were pooled and amplified.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 5p RNA library v2 protocol, 10x Genomics).

value: tissue

tag: strain

tag: age

value: 9 weeks old


title: MNase-input.wrap-seq.rep1


title: Replicate 2 NanoDam

city: Heidelberg

first: Stefan

last: Peidli

state: BW

address: Meyerhofstraße 1

department: Genome Biology

country: Germany

institute: European Molecular Biology Laboratory

description: NanoDan Cph Rep2

data_processing:
Reads were trimmed using trim_galore (v0.6.10, DOI:10.5281/zenodo.7598955) with settings for illumina reads, removing 10bp from both the 5’ and 3’ ends of all reads, and requiring a minimal read length of 36bp.
Trimmed reads were then aligned to the Drosophila Melanogaster genome using a precompiled bowtie index (BDGP6) and bowtie2 (v2.5.4, DOI:10.1038/nmeth.1923) while allowing for maximum single mismatches.
Resulting alignment files were filtered for uniquely mapped reads, converted to bam, sorted, and indexed using samtools (v1.20, DOI:10.1093/bioinformatics/btp352).
We used MACS2 (v2.2.9.1, DOI:10.1101/496521) for peak calling while filtering out peaks with FDR>0.05. Peaks were then annotated with CHIPseeker (v1.38.0, DOI:10.1093/bioinformatics/btv145) and a genome annotation file from Ensembl (index BDGP6.46.110).
Additionally, a GATC signal was obtained by binning the genome into consecutive GATC sites using a custom python script and a GFF of sites obtained from damidseq_pipeline doi:10.1093/bioinformatics/btv386, then calculating fold-changes of the NanoDam Cph signal with respect to the control for each replicate respectively.
Tracks were plotted using pyGenomeTracks do:10.1038/s41467-017-02525-w, di: 10.1093/bioinformatics/btaa692. The entire workflow was implemented using snakemake (v8.14.0, DI: 10.12688/f1000research.29032.1).
Assembly: BDGP6
Supplementary files format and content: SAMPLE_ID.bw contains read coverage converted to bigwig file for plotting in IGV
Supplementary files format and content: SAMPLE_ID_peaks.broadPeak contains broad peaks called by MACS2
Supplementary files format and content: SAMPLE_ID_peaks.xls also contains broad peaks called by MACS2
Supplementary files format and content: SAMPLE_ID_vs_CONTROL_ID_peaks.broadPeak and similar files contain MACS2 peaks with the respective control samples as a contrast
Library strategy: NanoDam

organism: Drosophila melanogaster

source_name: intestine

growth_protocol: To perform Cph NanoDam in the intestine, we crossed a CphYFP; UAS-NanoDam line with esgTS. As control, we crossed UAS-NanoDam line with esgTS. Flies were reared at 18°C. Adult flies aged between 3-5 days were shifted to 29°C for 17hrs.

extract_protocol:
30 Midguts where dissected in ice-cold PBS, taking care to remove Malpighian tubules, hindgut and proventriculus and samples were frozen in -80°C. DNA was extracted from dissected midgut and methylated fragments were isolated with DpnI and DpnII digestion.
Methylated fragments were then amplified with PCR and sonicated in order to generate libraries suitable for sequencing. Sequencing was performed using single end 86 bp reads with a using a Nextseq 550 at the Deep Sequencing Facility, BioQuant, Heidelberg University.

value: intestine

tag: replicate

value: biol rep 2

tag: treatment


title: Superficial Sample_11

city: Daegu

first: Taehee

last: Jo

address: 1035 Dalgubeol daero

department: Department of Plastic and Reconstructive Surgery

institute: Keimyung University Dongsan Hospital

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level. Gene expression estimation was performed by RSEM v.1.3.1
Read count and FPKM(Fragment per Kilobase of transcript per Million mapped reads) were calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts, RPKM and FPKM values for each Sample.

source_name: superficial adipose tissue (SSAT)

extract_protocol:
The tissues were then homogenized with appropriate volume of Trizol reagent (Invitrogen, USA) in independent bead containing safe lock tubes. After Trizol/chloroform extraction, the aqueous phase was mixed with 100% EtOH, and then loaded onto RNeasy column (Qiagen, USA). The RNA extraction process was continued according to the manufacturer’s protocol.
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, USA)

tag: gender

value: female

value: superficial adipose tissue (SSAT)


title: H4.wrap-seq.rep1


title: Hep 3B-CMTM4-KD-1

type: RNA

city: Nanning

first: Xuefeng

last: Guo

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road

department: 1.	Department of Epidemiology and Health Statistics

institute: Xuefeng Guo

description: Hep 3B, CMTM4 KO, Y9663-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Hep 3B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA .

growth_protocol: Hep3B cells were grown in DMEM medium (Invitrogen) containing 10% FBS and incubated at 37℃ in a humidified CO2 incubator.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

treatment_protocol: shRNAs were transfected into Hep3B cells with Lipofectamine 3000 (Invitrogen) according to the instructions of the manufacturer.

value: Hep 3B

value: CMTM4 Knockdown


title: rpr.hid_3

city: Hangzhou

first: qiang

last: zhao

address: 866 Yuhangtang Rd, Hangzhou

institute: Zhejiang University

data_processing:
The clean reads were mapped to the Drosophila genome sequence using Hisat2 with default parameters.
Assembly: dm6
Supplementary files format and content: csv file "FeatureCounts.cvs" of raw counts for each sample
Supplementary files format and content: csv file "DEseq2_rpr_vs_ctrl.csv" after DESeq2 for each sample

source_name: tracheal progenitors at 1hr APF

extract_protocol:
The white pupae were dissected in cold PBS and a single cluster of progenitors from Tr5 metamere were subjected to RNA extraction using the RNeasy Micro Kit from Qiagen. Total RNA from each sample was used for sequencing library preparation. Three biological replicates were performed for each genotype or treatment.
The SMART-Seq v4 Ultra low input RNA Kit was used for first-strand and second strand cDNA synthesis and double-stranded cDNA end repair. Double strand cDNAs were purified using the AMPure XP from Beckman Coulter, subjected to tagmentation and ligated to adaptors. Finally, the libraries were generated by PCR enrichment of the adaptor-ligated DNA.

value: tracheal progenitors at 1hr APF

value: normal diet;29C for 24h


title: flag-3

city: Guangzhou

first: Xueying

last: Chen

address: 58 Zhongshan Road II

department: Department of Endocrinology and Diabetes Center

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

description: lncRNA-Seq

data_processing:
Illumina novaseq6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensembl_release104 whole genome using HISAT2 with parameters -rna-strandness RF.
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: Ensembl_release104
Supplementary_files_format_and_content: Tab-delimited text files include counts and FPKM values for each Sample.

source_name: HEK 293 cells

growth_protocol: DMEM with 10% FBS and 1% PS.

extract_protocol:
Cell lysates were obtained by RIP-assay kit (MBL,NO.RN1001), of which the RNA profile were enriched with antibody.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: The full length of human FUS was cloned into pLVX-C-FLAG-mCMV-ZsGreen-IRES-Puro vector, which the HEK293 cells were infected.

value: HEK 293

value: Flag-tagged FUS overexpression

tag: rip antibody

value: Anti-DDDDK-tag mAb (MBL, No.M185-3L)


title: tumor negative, scRNA-seq

description: 10x Genomics

value: 8 weeks old


title: H4.wrap-seq.rep2

value: Inner cell mass

value: embryonic stem cell

value: wild type


title: WT_T+S (4W)

city: Daejeon

first: Jeongwoon

last: Choi

address: 291, Daehak-ro, Yuseong-gu

institute: Institute of basic science

data_processing:
The FastQ sequencing files were processed by bioinformatic pre-processing using the cloud based Seven Bridges Platform environment (Seven Bridges Genomics).
The BD Rhapsody WTA Analysis Pipeline app was utilized to generate csv-files including cell codes and gene lists for each individual sample.
The preprocessed count matrix was imported into R version 4.0.3 using Seurat version 3.2.3. Following quality control filtering, the samples were normalized and scaled.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Assembly: GRCm38

source_name: Lymph node

extract_protocol:
After sorting cells using MACS, single-cell suspensions were processed on the BD Rhapsody system following the manufacturer's protocols.
cDNA libraries were constructed using BD Rhapsody™ Whole Transcriptome Analysis (WTA) Amplification Kit (BD)

value: Lymph node

value: Endothelial cell

tag: sample type

value: 2'3'-cGAMP-challenged tumor-draining lymph nodes 4 weeks after tumor cell implantation


title: Parental Daoy 1

city: Greenwood

first: Heather

last: Flanagan-Steet

state: South Carolina

address: 113 Gregor Mendel Cir.

department: J.C. Self Research Institute

country: USA

institute: Greenwood Genetic Center

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCh38
Supplementary files format and content: csv text file contains raw gene hit counts for each sample

molecule: polyA RNA

source_name: Daoy

growth_protocol: All cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% FBS, Pen/Strep, 2mM L-glutamine in humidified CO2 incubator

extract_protocol:
Cells were washed twice with ice cold PBS buffer, scraped and collected in 1.5 mL TRIzol reagent (Thermo), and flash frozen in liquid nitrogen. Frozen samples were shipped on dry ice to Azenta Life Sciences to complete RNA extraction, library extraction, and sequencing.
Libraries for RNA-seq were generated by Azenta Life Sciences. In short, mRNA was selected through poly-A enrichment, fragmented, and randomly primed. First and second strand cDNA synthesis was performed, followed by end repair, 5' phosphorylation, and dA-tailing. Finally, adapters were ligated and enriched via PCR prior to sequencing.

treatment_protocol: The GNPTAB knockout cell clones were generated by Synthego (Redwood City, California USA) using DAOY medulloblastoma cells using a single guide RNA (CACGTAGAGCCCATACCTGT).  Two cell clones (labeled D3 and E4) were identified following Sanger sequencing and shown to bear compound heterozygous alterations in GNPTAB, with clone D3 carrying multiple deletions (-2/-2/-1 bp)[934-935delCC + 933-934delTC + 933delT], while clone E4 harbors a single-nucleotide insertion and a single nucleotide deletion (-1/+1 bp) [934delC + 933_934insN]

value: Daoy

value: WT


title: rpr.hid_1


title: flag-2

description: lncRNA-Seq


title: MNase.10min


title: WT_T (4W)

value: PBS

value: Tumor-draining lymph nodes 4 weeks after tumor cell implantation


title: flag-1

description: lncRNA-Seq


title: control_3


title: H3.wrap-seq.rep2-2


title: WT_T+S (2W)

value: 2'3'-cGAMP-challenged tumor-draining lymph nodes 2 weeks after tumor cell implantation


title: control_2

value: tracheal progenitors at 1hr APF


title: total-3

description: lncRNA-Seq


title: total-2

description: lncRNA-Seq


title: control_1

value: normal diet;29C for 24h


title: H3.wrap-seq.rep2-1


title: WT_T (2W)

value: Tumor-draining lymph nodes 2 weeks after tumor cell implantation


title: Control

value: Normal lymph nodes


title: H3.wrap-seq.rep1-2


title: H3.wrap-seq.rep1-1


title: total-1

description: lncRNA-Seq

value: HEK 293

value: Flag-tagged FUS overexpression


title: rpr.hid_2


title: 220810-YXH-LT2-H02

status: Public on Oct 27 2024

city: shanghai

first: Yu

last: Xianhong

institute: Mobidrop

data_processing:
Library quality control, barcode processing, mapping, peak calling, cell calling, and report generation are all analyzed by MobiVision V1.1(https://www.mobidrop.com/support).
Assembly: GRCh38,GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Cricetulus griseus
Mus musculus

source_name: human+mouse+hamster

extract_protocol:
Cell was permeated with detergent and incubated with PATn5 to cut chromatin DNA and ligate adaptors.The tagmented DNA was purified for library preparation
Single cell libraries preparation for ChIP-seq was performed as in CoBATCH with minor modification.

value: Human + mouse + hamster


title: H9,RNA-seq

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .csv file containing FPKM values of each gene in each sample.

source_name: embryonic

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7775). Fragmented and randomly primed 2 x150 bp pairedend libraries were sequenced using Illumina HiSeq X Ten.

value: embryonic

value: human embryonic stem cell


title: H1,RNA-seq


title: hADSCs-0618_rep1,RNA-seq

value: Adipose tissue

value: adult human adipose derived mesenchymal stromal cells


title: hADSCs-0618_rep2,RNA-seq


title: 230418C-S-YXH-L02

organism:
Homo sapiens
Mus musculus

source_name: human+mouse

value: Human + mouse


title: hADSCs-0605_rep1,RNA-seq


title: hADSCs-1013_rep1,RNA-seq


title: hADSCs-1217_rep2,RNA-seq


title: Vibrio algalinolyticus biofilm scRNA-seq

city: Xiamen

first: qiu

last: li

address: No. 185, Yinjiang Road, Jimei District, Xiamen City, Fujian Province

institute: Jimei University

data_processing:
Reads were processed using the VITAseer v1.0 pipeline with default and recommended parameters.First, primer sequences and capture adpator sequences were trimmed in raw  sequencing data. Then for each Read1, we extracted UMI (8 nts) and cell-specific barcode (20 nts) and merged sequenced barcodes that can be uniquely assigned to the same accepted barcode with a Hamming distance of 1 nts or less. Read2 was used to generate the gene  expression matrix by the STARsolo module in STAR(2.7.10a) .  The valid bacteria were identified by STARsolo.
Assembly: Vibrio algalinolyticus
Supplementary files format and content: gene matrix:barcodes.tsv.gz,features.tsv.gz,matrix.mtx.gz

organism: Vibrio alginolyticus

source_name: Vibrio algalinolyticus biofilm

extract_protocol:
The prepared bacteria suspension was permaeablized and blocked for single-stranded DNA-blocking. Random primers were then added for the reverse transcription of total RNA inside the cell. Subsequently, the generated cDNA fragments were ligated to adaptors inside the bacteria. The reverse-transcribed single-bacteria suspension and reagents, along with barcode beads containing cell barcodes and UMIs, were mixed. The mixture underwent encapsulation, capturing and barcoding using the VITAcruizer DP400 instrument. The resulting product underwent extension, resulting in barcoded cDNA strands.
PCR amplification was conducted using the cDNA as the template. The purified products after cDNA amplification were then used to constructed a standard next-generation sequencing library. The constructed single-cell library contained P5 and P7 adapters and was sequenced on a Xplus sequencer (Illumina) with 150 bp paired-end reads.

value: Vibrio algalinolyticus biofilm


title: hADSCs-1217_rep1,RNA-seq


title: hADSCs-0809_rep1,RNA-seq


title: hADSCs-0509_rep2,RNA-seq


title: hADSCs-1003_rep1,RNA-seq


title: hADSCs-0809_rep2,RNA-seq


title: hADSCs-0509_rep1,RNA-seq


title: SID6-1013-V4_rep2,RNA-seq

source_name: induced from hADSC

value: induced from hADSC


title: SID6-1013-V4-WA4_rep2,RNA-seq


title: hCiPSCs-1013-A#,RNA-seq

value: human chemically induced pluripotent stem cells


title: SID6-1013-V4-WA4_rep1,RNA-seq


title: hCiPSCs-0618-2#,RNA-seq


title: SID6-1013-V4_rep1,RNA-seq


title: hADSCs-1013,RNA-seq


title: hCiPSCs-1013-D#,RNA-seq


title: K562_H3K27ac_1K_cells-Input

city: Shanghai

first: Xiaodong

last: Zhao

address: 800 Dongchuan RD

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed using Trimmomatic (version 0.38).
Bowtie (version 1.2.2) was used to align the clean reads to the reference genome (hg19 for human and mm10 for mouse).
The uniquely mapped reads after the removal of duplicates were used for the downstream analysis.
Peaks were obtained using MACS (version 2.1.1) with corresponding input samples.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: The bigwig files were generated with the function bamCoverage from DeepTools27 using with the following parameters (--binSize 200 and --smoothLength 1,000), and binSize 1,000 was used when processing MeDIP data.

growth_protocol: K562 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Penicillin-Streptomycin.

extract_protocol:
Chromatin DNA was sonicated and ChIP DNA was enriched with antibody.
Libraries were prepared as 2cChIP-seq or 2cMeDIP-seq protocol described.

tag: number of cells

tag: chip antibody


title: hCiPSCs-0618-1#,RNA-seq


title: 220810-YXH-LT2-H03


title: 220810-YXH-LT2-H01


title: K562_H3K27ac_10_cells_2cChIP-seq_Rep2


title: K562_H3K27ac_10_cells_2cChIP-seq_Rep1


title: hADSCs-1013_rep2,RNA-seq


title: K562_H3K27ac_50_cells_2cChIP-seq_Rep2


title: K562_H3K27ac_100_cells_2cChIP-seq_Rep1


title: K562_H3K27ac_1K_cells_2cChIP-seq_Rep2


title: K562_H3K27ac_1K_cells_2cChIP-seq_Rep1


title: K562_H3K27ac_100_cells_2cChIP-seq_Rep2


title: K562_H3K4me3_1K_cells-Input


title: K562_H3K4me3_10_cells_2ChIP-seq_Rep2


title: K562_H3K4me3_50_cells_2cChIP-seq_Rep2


title: K562_H3K4me3_10_cells_2ChIP-seq_Rep1


title: K562_H3K4me3_100_cells_2cChIP-seq_Rep1


title: K562_H3K4me3_1K_cells_2cChIP-seq_Rep2


title: K562_H3K4me3_50_cells_2cChIP-seq_Rep1


title: K562_H3K4me3_100_cells_2cChIP-seq_Rep2


title: ESC_H3K4me3_exp2_cell95

data_processing:
Sequenced reads were trimmed and filtered by cutadapt (v 2.10) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with default parameters.
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Bigwig files were generated from bam files using deeptools (v 3.3.0) bamCoverage, with parameter of "--binSize 1 --normalizeUsing BPM --skipNonCoveredRegions".
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage.

growth_protocol: Mouse embryonic stem cells were cultured in KnockOut DMEM supplemented with 15% (vol/vol) FBS, and human LIF at 37°C with 5% CO2.

extract_protocol:
Tn5 transposition was set up by incubation at 37°C for 50 min and 55°C for 10 min. After brief sonication, soluble chromatin was used for following ChIP experiments.DNA was reverse crosslinked and extracted by phenol/chloroform/isoamylalcohol.
Following single-cell 2cChIP protocol

value: embryo (blastocyst)


title: ESC_H3K4me3_exp2_cell96


title: ESC_H3K4me3_exp2_cell93


title: ESC_H3K4me3_exp2_cell91


title: ESC_H3K4me3_exp2_cell89


title: K562_H3K4me3_1K_cells_2cChIP-seq_Rep1


title: ESC_H3K4me3_exp2_cell94


title: ESC_H3K4me3_exp2_cell90


title: K562_H3K27ac_50_cells_2cChIP-seq_Rep1


title: ESC_H3K4me3_exp2_cell83


title: ESC_H3K4me3_exp2_cell84


title: ESC_H3K4me3_exp2_cell82


title: ESC_H3K4me3_exp2_cell86


title: ESC_H3K4me3_exp2_cell85


title: ESC_H3K4me3_exp2_cell78


title: ESC_H3K4me3_exp2_cell79


title: ESC_H3K4me3_exp2_cell81


title: ESC_H3K4me3_exp2_cell77


title: ESC_H3K4me3_exp2_cell75


title: ESC_H3K4me3_exp2_cell76


title: ESC_H3K4me3_exp2_cell92


title: ESC_H3K4me3_exp2_cell69


title: ESC_H3K4me3_exp2_cell74


title: ESC_H3K4me3_exp2_cell70


title: ESC_H3K4me3_exp2_cell71


title: ESC_H3K4me3_exp2_cell87


title: ESC_H3K4me3_exp2_cell88


title: ESC_H3K4me3_exp2_cell67


title: ESC_H3K4me3_exp2_cell72


title: ESC_H3K4me3_exp2_cell68


title: ESC_H3K4me3_exp2_cell63


title: ESC_H3K4me3_exp2_cell62


title: ESC_H3K4me3_exp2_cell65


title: ESC_H3K4me3_exp2_cell80


title: ESC_H3K4me3_exp2_cell59


title: ESC_H3K4me3_exp2_cell58


title: ESC_H3K4me3_exp2_cell61


title: ESC_H3K4me3_exp2_cell60


title: ESC_H3K4me3_exp2_cell57


title: ESC_H3K4me3_exp2_cell55


title: ESC_H3K4me3_exp2_cell54


title: ESC_H3K4me3_exp2_cell53


title: ESC_H3K4me3_exp2_cell56


title: ESC_H3K4me3_exp2_cell51


title: ESC_H3K4me3_exp2_cell73


title: ESC_H3K4me3_exp2_cell52


title: ESC_H3K4me3_exp2_cell49


title: ESC_H3K4me3_exp2_cell50


title: ESC_H3K4me3_exp2_cell64


title: ESC_H3K4me3_exp2_cell47


title: ESC_H3K4me3_exp2_cell66


title: ESC_H3K4me3_exp2_cell46


title: ESC_H3K4me3_exp2_cell48


title: ESC_H3K4me3_exp2_cell41


title: ESC_H3K4me3_exp2_cell39


title: ESC_H3K4me3_exp2_cell43


title: ESC_H3K4me3_exp2_cell42


title: ESC_H3K4me3_exp2_cell40


title: ESC_H3K4me3_exp2_cell38


title: ESC_H3K4me3_exp2_cell37


title: Leaves, Se_48h3

city: zhengzhou

first: jinke

last: hu

state: henan

address: Zhengzhou City, Henan Province

institute: zhengzhou

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: TM-1
Supplementary_files_format_and_content: txt file includes FPKM values and counts for each Sample

organism: Medicago sativa

source_name: leaves

extract_protocol:
Total RNA was isolated and purified from plant leaf tissue at three times (0, 12, and 48 h) under 100 mg kg-1 Se (IV) treatment using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina at the (lc-bio, China) following of the merchant's recommended protocol.
The paired-end libraries was 300 bp ( ± 50 bp)

value: leaves

value: treated with selenium for 48 hours


title: ESC_H3K4me3_exp2_cell44


title: Leaves, Se_48h2


title: ESC_H3K4me3_exp2_cell35


title: ESC_H3K4me3_exp2_cell34


title: Leaves, Se_48h1


title: ESC_H3K4me3_exp2_cell36


title: Leaves, Se_12h3

value: treated with selenium for 12 hours


title: Leaves, Se_12h2


title: ESC_H3K4me3_exp2_cell33


title: Leaves, Se_12h1


title: ESC_H3K4me3_exp2_cell32


title: Leaves, Se_0h3

value: treated with selenium for 0 hour


title: ESC_H3K4me3_exp2_cell30


title: ESC_H3K4me3_exp2_cell45


title: Leaves, Se_0h2


title: ESC_H3K4me3_exp2_cell29


title: Leaves, Se_0h1


title: ESC_H3K4me3_exp2_cell26


title: ESC_H3K4me3_exp2_cell27


title: ESC_H3K4me3_exp2_cell24


title: Zebrafish, Riboseq, M-sphere-5

city: qingdao

first: yizhuang

last: zhang

address: binhai road

institute: Shandong university

data_processing:
Each library was amplified by a 11-cycle PCR, and 150 bp paired-end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data.
Assembly: GRCz10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C

extract_protocol:
Total RNAs were extracted from WT and Mrbm24a embryos at 4-cell sphere 24-hpf stage, using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: whole embryo

tag: Stage

value: sphere stage

value: embryonic cell


title: Zebrafish, Riboseq, M-sphere-4


title: ET_SR31133_3

city: Minneapolis

first: Lei

middle: Justan

last: Zhang

state: MN

address: 312 Church Street SE

department: Department of Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

data_processing:
Quality control on raw sequence data for each sample was performed with FastQC
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (GRCm38) as reference.
Gene quantification was done via Feature Counts for raw read counts.
Differentially expressed genes (DEGs) were identified using the R package edgeR.
Assembly: GRCm38
Supplementary files format and content: excel file includes raw counts for each sample

source_name: MEFs

growth_protocol: MEFs were grown at a 1:1 ratio of Dulbecco’s Modification of Eagles Medium (supplemented with 4.5 g/L glucose and L-glutamine) and Ham’s F10 medium, supplemented with 10% fetal bovine serum, penicillin, streptomycin and non-essential amino acid. WT MEFs were induced senescence by treating with hydrogen peroxide H2O2 (200 μM) or etoposide (2 μM) for 24 h, followed by 5 days in normal culture media.

extract_protocol:
Trizol RNA extraction
Illumina TruSeq Stranded Total RNA Library Prep kit

treatment_protocol: Cells were treated with fisetin (5 μM), or SR29384 (5 μM) or SR31133 (5 μM).

value: MEFs

value: WT

tag: senescence inducer

value: Etoposide


title: ESC_H3K4me3_exp2_cell28


title: ET_DMSO_3

value: DMSO


title: ESC_H3K4me3_exp2_cell20


title: ESC_H3K4me3_exp2_cell25


title: ET_SR31133_2


title: Zebrafish, Riboseq, M-sphere-1


title: Zebrafish, Riboseq, M-sphere-2


title: ET_SR29384_3


title: ESC_H3K4me3_exp2_cell21


title: ESC_H3K4me3_exp2_cell23


title: ESC_H3K4me3_exp2_cell31


title: ET_SR29384_2


title: Zebrafish, Riboseq, M-4cell-5

value: 4-cell stage


title: ESC_H3K4me3_exp2_cell18


title: ET_Fisetin_2

value: Fisetin (5 µM)


title: Zebrafish, Riboseq, M-4cell-4


title: ESC_H3K4me3_exp2_cell16


title: ESC_H3K4me3_exp2_cell15


title: ESC_H3K4me3_exp2_cell22


title: ESC_H3K4me3_exp2_cell13


title: ET_Fisetin_3


title: Zebrafish, Riboseq, M-4cell-2


title: ET_SR31133_1


title: ESC_H3K4me3_exp2_cell19


title: ESC_H3K4me3_exp2_cell11


title: ESC_H3K4me3_exp2_cell12


title: ET_SR29384_1


title: Zebrafish, RNAseq, M-24HPF-4

value: 24 hpf stage


title: ESC_H3K4me3_exp2_cell17


title: ESC_H3K4me3_exp2_cell5


title: ESC_H3K4me3_exp2_cell7


title: ET_Fisetin_1


title: ESC_H3K4me3_exp2_cell6


title: ESC_H3K4me3_exp2_cell9


title: Zebrafish, RNAseq, M-24HPF-3


title: ET_DMSO_2


title: H2O2_SR31133_3


title: ESC_H3K4me3_exp2_cell4


title: ET_DMSO_1


title: ESC_H3K4me3_exp2_cell8


title: Zebrafish, RNAseq, M-24HPF-2


title: H2O2_SR29384_3


title: ESC_H3K4me3_exp2_cell2


title: ESC_H3K4me3_exp2_cell3


title: Zebrafish, RNAseq, Sibling-sphere-4

value: wild type


title: Zebrafish, RNAseq, M-24HPF-1


title: H2O2_Fisetin_3


title: ESC_H3K4me3_exp2_cell1


title: ESC_H3K4me3_exp1_cell95


title: Zebrafish, RNAseq, Sibling-sphere-3


title: ESC_H3K4me3_exp2_cell10


title: ESC_H3K4me3_exp1_cell96


title: H2O2_DMSO_3


title: Zebrafish, RNAseq, Sibling-sphere-1


title: ESC_H3K4me3_exp1_cell93


title: Zebrafish, RNAseq, Sibling-4cell-4


title: ESC_H3K4me3_exp1_cell90


title: ESC_H3K4me3_exp1_cell92


title: ESC_H3K4me3_exp1_cell89


title: H2O2_SR31133_2


title: ESC_H3K4me3_exp1_cell91


title: H2O2_DMSO_2


title: Zebrafish, RNAseq, Sibling-4cell-2


title: Zebrafish, RNAseq, Sibling-4cell-1


title: ESC_H3K4me3_exp1_cell87


title: H2O2_Fisetin_2


title: ESC_H3K4me3_exp1_cell88


title: Zebrafish, RNAseq, lSibling-24HPF-5


title: Zebrafish, Riboseq, M-4cell-3


title: ESC_H3K4me3_exp1_cell85


title: H2O2_SR31133_1


title: ESC_H3K4me3_exp1_cell94


title: ESC_H3K4me3_exp1_cell84


title: Zebrafish, RNAseq, lSibling-24HPF-4


title: ESC_H3K4me3_exp1_cell86


title: Zebrafish, RNAseq, lSibling-24HPF-3


title: H2O2_SR29384_1


title: H2O2_Fisetin_1


title: H2O2_SR29384_2


title: pACYC177 plasmid / fast_in/slow Luciferase rep 2

city: Baltimore

first: Vincent

middle: J

last: Hilser

state: Maryland

address: 3400 N Charles St

department: Biology

institute: The Johns Hopkins University

description:
Replicate 2
RNA treated with MNase
FinS_2

data_processing:
Library strategy: Ribo-Seq
fastx_clipper 0.0.13.2 to remove the adapter from the end with parameters: -Q33 -a CTGTAGGCACCATCAAT -l 21 -c -n -v -i input_file -o trimmed.fq
rRNA and tRNA sequences were removed using bowtie2 2.2.9 with parameters: bowtie2 -x rrna_db -U trimmed.fq --very-sensitive -t --quiet -p 8 --un filtered.fq > /dev/null
Reads were mapped to the E. coli genome (NC_000913.3) using bowtie2 2.2.9 with parameters: bowtie2 -x genome_db -U filtered.fq -S aligned.sam -D 20 -R 3 -N 1 -L 20 -i S,1,0.5 -p 8 --no-hd -t -a --un unaligned.fq
Procedure, written in Perl, which corrects sequencing errors and merges identical reads (Martens et al., 2015). Using the list of proteins and their corresponding genomic map points from PTT files, each gene was scanned for mapped reads and the totals were recorded to a new file. Reads mapped to tufA and tufB were merged, and an additional scan was performed to assign reads to ssrA.
Differential gene expression analysis was performed using DeSeq2 1.12.3 and R 3.3.1 (Love et al., 2014).
Genome_build: E. coli genome: NC_00913.3
Genome_build: Additional files for pACYC177 vectors (3 genes: ampR (bla), Luc (optional), kanR)
Supplementary_files_format_and_content: Integer sequencing reads assigned to each genomic feature, formatted as a matrix of values, with rows corresponding to genomic features and columns corresponding to experiments

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol:
MOPS minimal medium (Neidhardt et al., 1974) plates (0.6% glycerol, 0.2% casamino acids, 100 μg/ml ampicillin) were streaked with E. coli MG1655 (Yale CGSC # 6300; F-, λ-, rph-1) cells bearing one of the pACYC177-derived plasmids and grown at 37°C (Table S1). Glycerol and casamino acids, rather than glucose, were added to minimize catabolite repression while avoiding amino acid starvation. Overnight cultures were prepared by inoculating 2.5 ml of MOPS medium, with 1 mM IPTG, from a plate, and grown overnight, shaking at 37°C at 250 RPM. Under these conditions, cells typically grow with a doubling time of 50 min.
200 ml of minimal medium medium, in pre-warmed 2 L flasks, were inoculated by diluting the overnight cultures more than one thousandfold and set to shake at 37°C in an Innova 40 incubator shaker (New Brunswick Scientific) at 200 RPM.

extract_protocol:
Once the cultures reached an OD600 of 0.40 - 0.65 (measured using a Shimadzu UV-1800 spectrophotometer; 1 OD600 = 6 x 108 cells / mL) they were filtered through a pre-warmed 0.22 μm nitrocellulose filter paper and 90 mm glass filtration system (Kontes) with vacuum (Whatman cat. no. 7182-009); the filtration took about 1 min. The apparatus was rapidly disassembled, and the cells were immediately scraped from the filter paper, using a pre-warmed scoopula, and submerged into a 50 ml Falcon tube (Corning cat. no. 352070) filled with liquid nitrogen (LN2). The cells were then transferred to a mortar immersed in, and containing, LN2 and 600 μl of cell lysis buffer (10 mM MgCl2, 100 mM NH4Cl, 20 mM Tris-HCl pH 8.0, 0.1% Nonidet P40, 0.4% Triton X-100, 500 μg/ml chloramphenicol) were dripped in. The cells were pulverized with the chilled mortar and pestle, whereupon the LN2 was allowed to boil off. The remaining powder was scraped with a chilled spatula into a chilled 1.5 ml Eppendorf tube and stored at -80°C overnight.
Cell lysates were centrifuged 15 min at 14,000 RPM and 4°C, and the clarified supernatant was transferred to a 1.5 ml Eppendorf tube. Between 250 μl and 500 μl of supernatant were then treated with 2.0 μl of micrococcal nuclease (Life Technologies cat. no. EN0181) and 5 mM CaCl2 and incubated 1 h while gently rotating at room temperature. The reactions were quenched using 6 mM EGTA and then transferred to 3.5 ml thickwall polycarbonate ultracentrifuge tubes (Beckman Coulter cat. no. 349622). The samples were underlaid with 2.0 ml of 1 M sucrose and centrifuged 6.5 h on a Beckman XL-80K ultracentrifuge at 55,000 RPM and 4°C in a SW55 rotor. Following removal of the liquid, the invisible pellets were re-suspended with 700 μl of Qiazol reagent, and RNA was extracted as directed by the miRNEasy kit (Qiagen cat. no. 217004).
Samples were denatured at 70°C and then subjected to electrophoresis on a 15% polyacrylamide TBE-urea gel 65 min at 200 V. The gel was then stained using SYBR gold and imaged with a blue light transilluminator. Gel slices were taken from the regions corresponding to lengths between 20 to 45 nt, as indicated by 10 bp ladder (Invitrogen cat. no. 10821015) and RNA size markers (5′-AUGUACACGGAGUCGAGCUCAACCCGCAACGCGA-(Phos)-3′ and 5′-AUGUACACGGAGUCGACCCAACGCGA-(Phos)-3′). The samples were then prepared as directed in Ingolia et al. (Ingolia et al., 2012), with modifications: ProtoScript II reverse transcriptase (New England Biolabs cat no. M0368) was used for reverse transcription, and different biotinylated oligonucleotides were used for the removal of E. coli rRNA sequences (Li et al., 2014). The library was sequenced on an Illumina HiSeq 2500 by the Johns Hopkins University Genetic Resources Core Facility. Each bacterial strain was processed in duplicate or triplicate.

tag: vector backbone

tag: insert

value: fast_in/slow Luciferase


title: THLE-3 cells, ICR, single, MeHgCl, rep3

city: Cheonan

first: Jihye

last: Park

address: 119 Dan-daero, Dongnam-gu

institute: Dankook University

data_processing:
Potentially present sequencing adapters and low-quality bases present in the low reads were trimmed using Skewer (version 0.2.2)
The cleaned high-quality reads were mapped to the reference genome using BS-seeker2 software (version 2.1.2). A 10% mis-mapping rate was allowed, as the alignment is performed with reference to certain specified genic regions of the genome sequence.
BS-seeker2 was used to determine the methylation levels from the mapping result.
Assembly: H19 DMR: hg38_ct_locations11p155_5937 range=chr11:1998143-1998554 ICR: NC_000011.10: Homo sapiens chromosome 11, GRCh38.p14 Primary Assembly
Supplementary files format and content: tab-delimited text file includes methylation levels for each Sample (H19-DMR)
Supplementary files format and content: tab-delimited text file includes methylation levels for each Sample (ICR)

growth_protocol: THLE-3 cells were cultured in BEGM Bronchial Epithelial Cell Growth Basal Medium supplemented with 10% FBS, 1% antibiotic antimycotic solution, 5 ng/mL human recombinant EGF, 70 ng/mL phosphoethanolamine, and the additives from the BEGM Bullet Kit . Culture plates were maintained at 37°C in humidified 5% CO2 atmosphere, and the passage number for exposure assessment was four to five.

extract_protocol:
The gDNA was extracted using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer's protocol
Bisulfite modification of the 2 μg of gDNA was performed using the EZ DNA methylation-lightning kit. The bisulfite-converted DNA was amplified to a 387-bp sequence element harboring 21 CpG sites located at the H19 DMR and a 348-bp element involving 17 CpG sites at the ICR using TaKaRa EX Taq DNA polymerase. The library was prepared according to Illuminaâs recommendations and sequenced using the 300-cycle MiSeq reagent kit V3 (paired end, 2 Ã 300 bp) on an Illumina MiSeq instrument (Illumina Inc., San Diego, CA, USA) for BSAS analysis.

treatment_protocol: The cells were seeded at a density of approximately 4-6 × 104 cells/cm2 in 90-mm plates one day prior to metal exposure. Subsequent treatments involved either individual or combined exposure to oAs, CdCl2, and MeHgCl, or a control condition using sterile distilled water for 72 hours.

tag: cell line

value: hepatic epithelial cells

value: toxic metal exposure

value: MeHgCl


title: pACYC177 plasmid / fast_in/slow Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
FinS_1


title: WT_SR31133_3

tag: cell type

value: no inducer


title: H2O2_DMSO_1

tag: genotype


title: THLE-3 cells, ICR, single, MeHgCl, rep2


title: ESC_H3K4me3_exp1_cell79

tag: tissue

value: embryo (blastocyst)


title: WT_Fisetin_3


title: ESC_H3K4me3_exp1_cell77

tag: strain


title: pACYC177 plasmid / fast/slow Luciferase rep 3

description:
Replicate 3
RNA treated with MNase
FS_3

value: fast/slow Luciferase


title: THLE-3 cells, ICR, single, CdCl2, rep2


title: THLE-3 cells, ICR, single, CdCl2, rep3


title: pACYC177 plasmid / slow_in/fast Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
SinF_2

value: slow_in/fast Luciferase


title: pACYC177 plasmid / slow_in/fast Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
SinF_1


title: THLE-3 cells, ICR, single, MeHgCl, rep1


title: ESC_H3K4me3_exp1_cell78

tag: age


title: ESC_H3K4me3_exp1_cell83


title: WT_DMSO_3


title: pACYC177 plasmid / fast/slow Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
FS_2


title: ESC_H3K4me3_exp1_cell82


title: ESC_H3K4me3_exp1_cell76


title: THLE-3 cells, ICR, single, CdCl2, rep1


title: WT_SR29384_3


title: pACYC177 plasmid / fast/slow Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
FS_1


title: ESC_H3K4me3_exp1_cell75


title: WT_SR31133_2


title: ESC_H3K4me3_exp1_cell80


title: THLE-3 cells, ICR, single, oAs, rep3

value: oAs


title: ESC_H3K4me3_exp1_cell81


title: ESC_H3K4me3_exp1_cell74


title: WT_Fisetin_2

value: MEFs


title: ESC_H3K4me3_exp1_cell73


title: THLE-3 cells, ICR, single, oAs, rep2


title: pACYC177 plasmid / slow/fast Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
SF_2

value: slow/fast Luciferase


title: pACYC177 plasmid / fast Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
F_2

value: fast Luciferase


title: pACYC177 plasmid / fast Luciferase rep 3

description:
Replicate 3
RNA treated with MNase
F_3


title: WT_DMSO_2

value: WT

value: DMSO


title: ESC_H3K4me3_exp1_cell70


title: ESC_H3K4me3_exp1_cell71


title: THLE-3 cells, ICR, single, control, rep3

value: control


title: THLE-3 cells, ICR, single, control, rep1


title: WT_SR29384_1


title: pACYC177 plasmid / slow/fast Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
SF_1


title: WT_SR31133_1


title: THLE-3 cells, ICR, combined, CdCl2 + MeHgCl, rep3

value: CdCl2 + MeHgCl


title: ESC_H3K4me3_exp1_cell72


title: ESC_H3K4me3_exp1_cell69


title: pACYC177 plasmid / harmonized Luciferase rep 3

description:
Replicate 3
RNA treated with MNase
H_3

value: harmonized Luciferase


title: THLE-3 cells, ICR, single, control, rep2


title: WT_SR29384_2


title: WT_DMSO_1


title: THLE-3 cells, ICR, combined, CdCl2 + MeHgCl, rep2


title: ESC_H3K4me3_exp1_cell68


title: pACYC177 plasmid / harmonized Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
H_2


title: pACYC177 plasmid / fast Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
F_1


title: pACYC177 plasmid / slow/fast Luciferase rep 3

description:
Replicate 3
RNA treated with MNase
SF_3


title: THLE-3 cells, ICR, single, oAs, rep1


title: THLE-3 cells, ICR, combined, CdCl2 + MeHgCl, rep1


title: FRG5

city: New York

first: Kelechi

last: Ndukwe

state: NY

address: 695 Park Ave, New York, NY 10065

institute: Hunter College City University of New York Graduate Center

description: Female, TgF-344AD transgenic rat, RG2833 chow

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript (RGSC 6.0/rn6) set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15[2]. TMM (trimmed mean of M-values) was used to normalize the gene expression.
Differentially expressed genes were identified using the edgeR program[3].
Assembly: rn6
Supplementary files format and content: rsem_count.txt => Expected read count produced by RSEM for each gene in each sample.
Supplementary files format and content: TMM_normalized_reads_count_per_million.txt => Normalized gene expression data by TMM method

organism: Rattus norvegicus

source_name: Left Hippocampus Brain

extract_protocol:
RNA was isolated by RNeasy Mini Kit from Qiagen
Kapa Stranded mRNA Kit (Roche, cat. KK8421) to generate strand-specific RNA-seq libraries

treatment_protocol: RG2833 drug was incoporated into the Purina RodentChow. With 750 mg RG2833 per kg of rodent chow. The amount of food per rat was calculated by the wieght of the food consumed per rat. Food Dye (FD&C Blue Dye #1) used to differential the normal chow and RG2833 food

value: Left Hippocampus Brain

value: female

value: Tg-AD


title: WT_Fisetin_1

value: Fisetin (5 µM)


title: ESC_H3K4me3_exp1_cell67


title: ESC_H3K4me3_exp1_cell66


title: pACYC177 plasmid / harmonized Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
H_1


title: THLE-3 cells, ICR, combined, oAs + CdCl2, rep3

value: hepatic epithelial cells

value: toxic metal exposure

value: oAs + CdCl2


title: FRG4


title: pACYC177 plasmid / WT Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
W_2

source_name: pACYC177 plasmid / WT Luciferase rep 2

value: WT Luciferase


title: THLE-3 cells, ICR, combined, oAs + CdCl2, rep2


title: FRG2


title: ESC_H3K4me3_exp1_cell64

value: embryo (blastocyst)


title: FRG1


title: ESC_H3K4me3_exp1_cell63


title: THLE-3 cells, ICR, combined, oAs + CdCl2, rep1


title: F5

description: Female, TgF-344AD transgenic rat, rodent chow

value: No Treatment


title: pACYC177 plasmid / WT Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
W_1

source_name: pACYC177 plasmid / WT Luciferase rep 1


title: THLE-3 cells, ICR, combined, control, rep3


title: pACYC177 plasmid / slow Luciferase rep 2

description:
Replicate 2
RNA treated with MNase
S_2

value: slow Luciferase


title: THLE-3 cells, ICR, combined, control, rep2


title: pACYC177 plasmid / slow Luciferase rep 3

description:
Replicate 3
RNA treated with MNase
S_3


title: F4


title: ESC_H3K4me3_exp1_cell62


title: THLE-3 cells, ICR, combined, control, rep1


title: ESC_H3K4me3_exp1_cell61


title: pACYC177 plasmid / slow Luciferase rep 1

description:
Replicate 1
RNA treated with MNase
S_1


title: F3


title: pACYC177 plasmid / WT Luciferase rep 3

description:
Replicate 3
RNA treated with MNase
W_3

source_name: pACYC177 plasmid / WT Luciferase rep 3


title: ESC_H3K4me3_exp1_cell60


title: THLE-3 cells, H19-DMR, single, MeHgCl, rep3

value: MeHgCl


title: FRG3


title: pACYC177 plasmid / no insert rep 3

description:
Replicate 3
RNA treated with MNase
C_3

source_name: pACYC177 plasmid / no insert rep 3


title: ESC_H3K4me3_exp1_cell65


title: F2


title: THLE-3 cells, H19-DMR, single, MeHgCl, rep2


title: ESC_H3K4me3_exp1_cell59


title: pACYC177 plasmid / no insert rep 2

description:
Replicate 2
RNA treated with MNase
C_2

source_name: pACYC177 plasmid / no insert rep 2


title: MRG5

description: Male, TgF-344AD transgenic rat, RG2833 chow

treatment_protocol: RG2833 drug was incoporated into the Purina RodentChow. With 750 mg RG2833 per kg of rodent chow. The amount of food per rat was calculated by the wieght of the food consumed per rat.

value: male


title: THLE-3 cells, H19-DMR, single, MeHgCl, rep1


title: MRG4


title: pACYC177 plasmid / no insert rep 1

description:
Replicate 1
RNA treated with MNase
C_1

source_name: pACYC177 plasmid / no insert rep 1


title: F1


title: MRG3


title: THLE-3 cells, H19-DMR, single, CdCl2, rep2


title: ESC_H3K4me3_exp1_cell57


title: ESC_H3K4me3_exp1_cell58


title: ESC_H3K4me3_exp1_cell55


title: ESC_H3K4me3_exp1_cell56


title: Pre-menstrual sample E4

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Transcriptomic maps of paired-end reads were generated using STAR v2.5 against the hg38 reference genome.
Assembly: hg38
Supplementary files format and content: Count data in .TXT format

source_name: Endometrium

extract_protocol:
RNA was harvested and extracted from whole tissues using the phenol-chloroform method using STAT-60. Quality control, library preparation and sequencing were performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
Quantified libraries were pooled and sequenced on Illumina platform HiSeq 4000, according to effective library concentration and data amount.

value: Endometrium

tag: progesterone (nmol/l)

tag: bmi

tag: previous live_births

tag: first trimester_losses


title: Pre-menstrual sample E3


title: Pre-menstrual sample E2


title: ESC_H3K4me3_exp1_cell54


title: MRG2

tag: gender

tag: treatment


title: THLE-3 cells, H19-DMR, single, CdCl2, rep1


title: THLE-3 cells, H19-DMR, single, oAs, rep3

value: oAs


title: Pre-menstrual sample E1


title: ESC_H3K4me3_exp1_cell53


title: THLE-3 cells, H19-DMR, single, oAs, rep2


title: MRG1


title: Late secretory sample D4


title: M5.

description: Male, TgF-344AD transgenic rat, rodent chow


title: THLE-3 cells, H19-DMR, single, oAs, rep1


title: Late secretory sample D3


title: ESC_H3K4me3_exp1_cell52


title: ESC_H3K4me3_exp2_cell14


title: M4.


title: THLE-3 cells, H19-DMR, single, CdCl2, rep3


title: THLE-3 cells, H19-DMR, single, control, rep3

value: WT

value: control


title: ESC_H3K4me3_exp1_cell51


title: M3.

value: Left Hippocampus Brain


title: ESC_H3K4me3_exp1_cell50


title: Late secretory sample D1


title: M2.


title: Late secretory sample D2


title: Mid secretory sample C4


title: M1.


title: THLE-3 cells, H19-DMR, single, control, rep1


title: THLE-3 cells, H19-DMR, combined, CdCl2 + MeHgCl, rep3

value: CdCl2 + MeHgCl


title: Differentiated_FGSC_RNA-seq_Rep2

data_processing:
RNA-seq read files (fastq files) were checked for quality by FastQC and adapter trimming was done with Trim Galore.
Trimmed reads were mapped to the reference reference genome mm10 retaining only uniquely mapped reads by using the hisat2(v2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: Raw count of gene abundance was calculated from the mapped reads using featureCounts.

source_name: differentiated female germline stem cells

growth_protocol: FGSCs in logarithmic phase were digested with 0.5% trypsin and suspended in differentiation medium (FGSC culture medium with all supplements except GDNF, EGF and LIF, but including 10 ng/mL bone morphogenetic protein 4 (BMP4, PeproTech) and 10 μM Retinoic acid (RA, Sigma)). Single cells of FGSCs were cultured on monolayer granulosa cells at 37°C in a 5% CO2 incubator for 3 days.

extract_protocol:
Cells were lysed in hypotonic lysis buffer (Clontech, 635013), and the polyadenylated mRNAs were captured by the PolyT primers.
Following  Smart-seq2 protocol as described previously

tag: developmental stage

value: Premeiotic interphase

value: Retinoic acid

tag: Sex

value: female


title: Mid secretory sample C3


title: ESC_H3K4me3_exp1_cell48


title: Mid secretory sample C2


title: THLE-3 cells, H19-DMR, combined, CdCl2 + MeHgCl, rep2

value: hepatic epithelial cells

value: toxic metal exposure


title: ESC_H3K4me3_exp1_cell45


title: ESC_H3K4me3_exp1_cell46


title: Differentiated_FGSC_RNA-seq_Rep1

value: differentiated female germline stem cells


title: Early secretory sample B4


title: THLE-3 cells, H19-DMR, combined, CdCl2 + MeHgCl, rep1


title: GV_5mc_300_cells [Input]

source_name: GV oocyte

extract_protocol:
Genomic DNA extracted using GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma, G1N10)
Libraries were prepared as 2cMeDIP-seq protocol described.

tag: medip antibody

value: GV oocyte


title: GV_5mc_300_cells_2cMeDIP-seq_Rep2


title: THLE-3 cells, H19-DMR, combined, oAs + CdCl2, rep2

value: oAs + CdCl2


title: ESC_H3K4me3_exp1_cell49

value: embryo (blastocyst)


title: THLE-3 cells, H19-DMR, single, control, rep2


title: ESC_H3K4me3_exp1_cell43


title: Early secretory sample B3


title: Early secretory sample B2


title: THLE-3 cells, H19-DMR, combined, oAs + CdCl2, rep1


title: GV_5mc_300_cells_2cMeDIP-seq_Rep1


title: ESC_H3K4me3_exp1_cell42


title: Differentiated_FGSC_5mc_100_cells-Input

growth_protocol: Differentiated FGSCs were induced as we previously described with minor modifications [Zou et al., Cell proliferation, 2019]. FGSCs were cultured in differentiation medium (FGSC culture medium with all supplements except GDNF, EGF and LIF, but including 10 ng/ml BMP4 and 10μM RA).

extract_protocol:
gDNA was harvested using AllPrep DNA/RNA Mini Kit (Qiagen) and sonicated with a sonicator and MeDIP DNA was isolated with antibody.
Libraries were prepared as 2cChIP-seq or 2cMeDIP-seq protocol described.

value: Differentiated FGSC

tag: number of cells


title: Mid secretory sample C1


title: Early secretory sample B1


title: ESC_H3K4me3_exp1_cell41


title: ESC_H3K4me3_exp1_cell44


title: Differentiated_FGSC_5mc_100_cells_2cMeDIP-seq_Rep2


title: Anovulatory sample A4


title: THLE-3 cells, H19-DMR, combined, control, rep2


title: THLE-3 cells, H19-DMR, combined, control, rep3


title: THLE-3 cells, H19-DMR, combined, oAs + CdCl2, rep3


title: Differentiated_FGSC_5mc_100_cells_2cMeDIP-seq_Rep1


title: THLE-3 cells, H19-DMR, combined, control, rep1


title: FGSC_5mc_1K_cells-Input

source_name: FGSC

growth_protocol: FGSCs were cultured in minimum essential medium (MEM)-α containing 10 % FBS and several growth factors as in our previous report [Zhang et al. Genome Biology 2016].

value: FGSC


title: Anovulatory sample A3

value: Endometrium


title: ESC_H3K4me3_exp1_cell40


title: FGSC_5mc_10K_cells-Input


title: ESC_H3K4me3_exp1_cell39


title: ESC_H3K4me3_exp1_cell38


title: eif5a1/2 morpholino 3

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

data_processing:
Data was analyzed using Dr. Tom
Assembly: GRCz11
Supplementary files format and content: excel file with tpm and read counts
Supplementary files format and content: excel file with fold change and q-value

source_name: whole body

extract_protocol:
RNA was extracted using a trizol-chloroform protocol
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3'end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3'end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

treatment_protocol: zebrafish were treated with morpholino and RNA was extracted 24 hours later

value: whole body

value: eif5a1/2 morpholino


title: Anovulatory sample A1


title: FGSC_5mc_200K_cells-Input


title: ESC_H3K4me3_exp1_cell37


title: NT siRNA 8-bromo-cAMP + MPA treated 3

description: S3 NT cAMP-treated

data_processing:
Transcriptomic maps of paired-end reads were generated using STAR v2.5 against the hg38 reference genome using default settings with gencode.v38 as annotation file.
Assembly: hg38
Supplementary files format and content: Count data in .TXT format

source_name: Endometrial cells

extract_protocol:
RNA was purified through columns using the RNAEasy mini kits supplied by Qiagen according to manufacturer's instructions. RNA quality was examined using the Agilent Bioanalyser 2100.
Libraries were prepared using the Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions. Paired-end sequencing was performed on Illumina HiSeq 4000.

value: Endometrial cells

value: NT siRNA 8-bromo-cAMP + MPA treated


title: eif5a1/2 morpholino 2


title: FGSC_5mc_50_cells_2cMeDIP-seq_Rep2


title: FGSC_5mc_50_cells_2cMeDIP-seq_Rep1


title: ESC_H3K4me3_exp1_cell36


title: ESC_H3K4me3_exp1_cell35


title: dhps morpholino 2

value: dhps morpholino


title: FGSC_5mc_200_cells_2cMeDIP-seq_Rep2


title: ESC_H3K4me3_exp1_cell34


title: FGSC_5mc_200_cells_2cMeDIP-seq_Rep1


title: Control morpholino 3

value: Control morpholino


title: FGSC_5mc_1K_cells_2cMeDIP-seq_Rep2


title: GIPC siRNA Untreated 3

description: S3 GIPC Untreated

value: GIPC siRNA Untreated


title: Anovulatory sample A2


title: ESC_H3K4me3_exp1_cell32


title: APPL1 siRNA Untreated 3

description: S3 APPL1 Untreated

value: APPL1 siRNA Untreated


title: ESC_H3K4me3_exp1_cell33


title: Control morpholino 1


title: eif5a1/2 morpholino 1


title: ESC_H3K4me3_exp1_cell47


title: ESC_H3K4me3_exp1_cell31


title: NT siRNA Untreated 3

description: S3 NT Untreated

value: NT siRNA Untreated


title: GIPC siRNA PGE2+MPA treated 3

description: S3 GIPC Treated

value: GIPC siRNA PGE2+MPA treated


title: FGSC_5mc_1K_cells_2cMeDIP-seq_Rep1


title: APPL1 siRNA PGE2+MPA treated 3

description: S3 APPL1 Treated

value: APPL1siRNA PEG2+MPA treated


title: ESC_H3K4me3_exp1_cell30


title: BA18 brain ED11

city: Norman

first: Alexandra

last: Bentz

state: OK

address: 730 Van Vleet Oval

institute: University of Oklahoma

data_processing:
Reads were trimmed using fastp (version 0.20.1) with parameters “-l 17 --detect_adapter_for_pe -g -p”
RNA-Seq reads were quantified to the reference tree swallow transcriptome obtained previously by our laboratory (Bentz et al. 2019) using Salmon (version 1.9.0)
Assembly: tree swallow transcriptome obtained previously by our laboratory (Bentz et al. 2019)
Supplementary files format and content: Tab-delimited text file of raw RNA-seq read count values for each Sample

organism: Tachycineta bicolor

source_name: whole brain

extract_protocol:
Quick-DNA/RNA Microprep Plus Kit (Zymo Research)
xGen RNA Library kit (Integrated DNA Technologies, USA)

value: whole brain

value: embryonic day 11

value: high density


title: Control morpholino 2


title: dhps morpholino 1


title: NT siRNA 8-bromo-cAMP + MPA treated 2

description: S2 NT cAMP-treated


title: ESC_H3K4me3_exp1_cell29

value: embryo (blastocyst)


title: GIPC siRNA PGE2+MPA treated 2

description: S2 GIPC Treated


title: NT siRNA PGE2+MPA treated 3

description: S3 NT Treated

value: NT siRNA PGE2+MPA treated


title: FGSC_5mc_200K_cells_2cMeDIP-seq_Rep2

value: FGSC


title: SW42 brain ED11


title: FGSC_5mc_10K_cells_2cMeDIP-seq_Rep1


title: ESC_H3K4me3_exp1_cell27


title: ESC_H3K4me3_exp1_cell28


title: CN10 brain ED11

value: low density


title: FGSC_5mc_200K_cells_2cMeDIP-seq_Rep1


title: GP12 brain ED11


title: SW64 brain ED11


title: NT siRNA PGE2+MPA treated 2

description: S2 NT Treated


title: FGSC_5mc_10K_cells_2cMeDIP-seq_Rep2


title: dhps morpholino 3

value: whole body


title: ESC_H3K4me3_exp1_cell26


title: GIPC siRNA Untreated 2

description: S2 GIPC Untreated

value: Endometrial cells


title: SW62 brain ED11


title: ESC_H3K4me3_exp1_cell25


title: SW22 brain ED11


title: pACYC177 plasmid / WT Luciferase rep 1

description: W

data_processing:
fastx_clipper 0.0.13.2 to remove the adapter from the end with parameters: -Q33 -a CTGTAGGCACCATCAAT -l 21 -c -n -v -i input_file -o trimmed.fq
rRNA and tRNA sequences were removed using bowtie2 2.2.9 with parameters: bowtie2 -x rrna_db -U trimmed.fq --very-sensitive -t --quiet -p 8 --un filtered.fq > /dev/null
Reads were mapped to the E. coli genome (NC_000913.3) using bowtie2 2.2.9 with parameters: bowtie2 -x genome_db -U filtered.fq -S aligned.sam -D 20 -R 3 -N 1 -L 20 -i S,1,0.5 -p 8 --no-hd -t -a --un unaligned.fq
Procedure, written in Perl, which corrects sequencing errors and merges identical reads (Martens et al., 2015). Using the list of proteins and their corresponding genomic map points from PTT files, each gene was scanned for mapped reads and the totals were recorded to a new file. Reads mapped to tufA and tufB were merged, and an additional scan was performed to assign reads to ssrA.
Differential gene expression analysis was performed using DeSeq2 1.12.3 and R 3.3.1 (Love et al., 2014).
Genome_build: E. coli genome: NC_00913.3
Genome_build: Additional files for pACYC177 vectors (3 genes: ampR (bla), Luc (optional), kanR)
Supplementary_files_format_and_content: Integer sequencing reads assigned to each genomic feature, formatted as a matrix of values, with rows corresponding to genomic features and columns corresponding to experiments

organism: Escherichia coli

extract_protocol:
Total mRNA was extracted using the hot acid phenol chloroform reaction as follows. Acid phenol chloroform (5:1, pH 4.5) was heated to 65°C. After clarified lysates were heated to 65°C, SDS was added to a final concentration of 1%, followed by the addition of 1 volume of hot acid phenol chloroform.
The samples were incubated for 5 min at 65°C with frequent vortexing. The samples were then placed on ice for 5 min, and then centrifuged for 2 min at 14,000 RPM at room temperature. The aqueous (upper) phase was then recovered to a new tube, and a second extraction with hot acid phenol chloroform was performed. After the addition of 1 volume of chloroform:isoamyl alcohol (24:1), the samples were vortexed for 1 min at room temperature, then centrifuged for 1 min at 14,000 RPM. Finally, the aqueous phase was transferred to a clean microcentrifuge tube.
The aqueous (upper) phase was then recovered to a new tube, and a second extraction with hot acid phenol chloroform was performed. After the addition of 1 volume of chloroform:isoamyl alcohol (24:1), the samples were vortexed for 1 min at room temperature, then centrifuged for 1 min at 14,000 RPM. Finally, the aqueous phase was transferred to a clean microcentrifuge tube.
The RNA was then precipitated using isopropanol, as described above. The ribosomal RNA was removed using the MicrobExpress kit (ThermoFisher cat. no. AM1905) as described per the instructions. The samples were then purified using ethanol precipitation by adding 35 μl of 3 M NaAc-, 1 μl Glycoblue, and 7 μl glycogen, and then 1175 μl of ice cold ethanol. After thorough mixing, the samples were chilled at -80°C for 1 h, then centrifuged for 30 min at 4°C at 14,000 RPM. The supernatant was removed, and 750 μl of ice cold 70% ethanol was added. After mixing, the samples were centrifuged for 5 min at 4°C at 14,000 RPM, and a second washing with 70% ethanol was performed. The samples were air dried for 5 min, then resuspended in 25 μl Tris EDTA. After 15 min at room temperature, the samples were vortexed to resuspend the RNA and then spun briefly to collect the liquid within the tubes.
The MEGA Clear kit (ThermoFisher cat. no. AM1908) was then used to remove small RNAs. 75 μl of elution solution was added to each sample, followed by gentle and thorough mixing. 350 μl of binding was added, and after gentle mixing by pipetting, 250 μl of 100% ethanol was added. Following purification using the spin columns included with the kit, the samples were eluted in a final volume of 50 μl. RNA was then hydrolyzed by adding 50 μl of hydrolysis solution (44 M NaHCO3, 6 mM Na2CO3, 1 mM EDTA) and incubation at 95°C for 25 min. The samples were then precipitated using ethanol, and sequencing libraries were prepared as described above, skipping the rRNA removal step, and were sequenced in an Illumina Hi-Seq 2500. Sequencing data were analyzed using the same pipeline as described below.

tag: vector backbone

tag: insert

value: WT Luciferase


title: pACYC177 plasmid / slow Luciferase rep 1

description: S

value: slow Luciferase


title: pACYC177 plasmid / fast Luciferase rep 1

description: F

value: fast Luciferase


title: pACYC177 plasmid / harmonized Luciferase rep 1

description: H

value: harmonized Luciferase


title: pACYC177 plasmid / no insert rep 1

description: C


title: APPL1 siRNA Untreated 2

description: S2 APPL1 Untreated

tag: cell type

value: APPL1 siRNA Untreated


title: ESC_H3K4me3_exp1_cell23


title: ESC_H3K4me3_exp1_cell24


title: APPL1 siRNA PGE2+MPA treated 2

description: S2 APPL1 Treated


title: GIPC siRNA PGE2+MPA treated 1

description: S1 GIPC Treated


title: ESC_H3K4me3_exp1_cell22


title: GP4 brain ED11


title: CC10 brain ED11


title: ESC_H3K4me3_exp1_cell21


title: BA21 brain ED11


title: NT siRNA PGE2+MPA treated 1

description: S1 NT Treated


title: GP16 brain ED11


title: ESC_H3K4me3_exp1_cell20


title: CS9 brain ED11


title: APPL1 siRNA PGE2+MPA treated 1

description: S1 APPL1 Treated


title: ESC_H3K4me3_exp1_cell19


title: ESC_H3K4me3_exp1_cell18


title: NT siRNA 8-bromo-cAMP + MPA treated 1

description: S1 NT cAMP-treated

value: NT siRNA 8-bromo-cAMP + MPA treated


title: CS3 brain ED11


title: NT siRNA Untreated 1

description: S1 NT Untreated

value: NT siRNA Untreated


title: CC22 brain ED11


title: ESC_H3K4me3_exp1_cell17


title: ESC_H3K4me3_exp1_cell16


title: PC 12 cell line-Se & MPP+ treatment_rep3

city: Wuhan

first: Xiang

last: Li

state: China

address: Donghu Road

department: Neurosurgery

institute: Wuhan University, China

data_processing:
Illumina high-throughput sequencing data was dealt with bcl2fastq and converted into sequenced reads
Raw reads were filtered by removing adapter-contamination reads, low-quality reads and reads with >5% ploy-N. Q30
HISAT2 (v2.2.1) was used to build index from fasta files
HISAT2 (v2.2.1) alignement was applied to map reads to index
Samtools (v1.8) was used to convert sam files to bam files along with sorting
HTseq-count (v0.13.5) was used to get the expression set of 9 samples
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with fpkm for every gene and every sample

source_name: differentiated PC12 cells

growth_protocol: The rat pheochromocytoma cell line PC12 (Procell Life Science & Technology, Wuhan, China) was cultured in the 1640 medium with 5% fetal bovine serum, 5% horse serum and 1% penicillin-streptomycin (Gibco, Australia) in 5% CO2 at 37°C. For differentiation, cells were grown in the 1640 medium, containing 10% fetal bovine serum, 1% penicillin-streptomycin and 100 ng/ml nerve growth factor (Sigma-Aldrich, St. Louis, USA) for 5 days. The differentiated PC12 cells were cultured in the normal growth medium and were prepared for the subsequent experiments.

extract_protocol:
Total RNA was extracted from normal control PC12 cells, MPP+ (1500 μM) treatment PC12 cells and Se (20 μM) + MPP+ (1500 μM) treatment PC12 cells by using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)
RNA purity and concentration was checked with Nano Photometer® spectrophotometer (IMPLEN, Westlake Village, CA, USA) and Qubit® RNA Assay kits (Thermo Fisher Scientific, Waltham, MA, USA), respectively. In addition, RNA integrity and quantity were assessed with the RNA Nano 6000 LabChip Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA), and the RNA integrity number (RIN) values were greater than nine.  One microgram of total RNA was used to consume ribosomal RNA by Ribo-off rRNA Depletion Kit (Vazyme Biotech). Subsequently, the RNA was broken into 200-300 bp and used for reverse transcription of the first-strand cDNA. Following the instructions of VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech), the cDNA libraries were constructed by paired-end sequencing.

treatment_protocol: For each group, the medium was replaced with serum-free 1640 medium with or without various concentrations of Na2SeO3 (Se4+) (Sigma), which is the source of Se. Differentiated PC12 cells were incubated with Se for 48h. Again, the differentiated PC12 cells were cultured in serum-free medium for 24h. Subsequently, the medium was replaced with serum-free 1640 medium with or without various concentrations of MPP+ (Sigma) and these cells were incubated for 24h. The desired concentration for combination treatment was carefully chosen by exposing PC12 cells to Se and MPP+. For sequencing, in the normal control group, PC12 cells were cultured in serum-free medium for 48h. In the MPP+ group, PC12 cells were cultured in serum-free medium for 24h, then incubated with MPP+ (1500 μM) for 24h. In the Se + MPP+ group, PC12 cells were exposed to Se (20 μM) for 24h, then incubated with MPP+ (1500 μM) for 24h

tag: cell line

value: exposed to Se for 24h, and then incubated with MPP+ for 24h


title: ESC_H3K4me3_exp1_cell15

tag: tissue


title: PC 12 cell line-Se & MPP+ treatment_rep2


title: ESC_H3K4me3_exp1_cell14

tag: strain


title: NT siRNA Untreated 2

description: S2 NT Untreated


title: GIPC siRNA Untreated 1

description: S1 GIPC Untreated

value: GIPC siRNA Untreated


title: PC 12 cell line-Se & MPP+ treatment_rep1


title: ESC_H3K4me3_exp1_cell13

tag: age


title: PC 12 cell line-MPP+ treatment_rep3

value: treated with MPP+ for 24 hours


title: ESC_H3K4me3_exp1_cell12


title: PC 12 cell line-MPP+ treatment_rep2


title: ESC_H3K4me3_exp1_cell11


title: S2D2,scRNA-seq

city: Beijing

first: Jingxiao

last: Cao

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

institute: Peking University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: induced from hADSC

extract_protocol:
Cells were harvested and resuspended at 1 x 106 cells per milliliter in PBS supplemented with 0.04% BSA.
Using Single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension containing 300-600 living cells per microliter was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. On an S1000TM Touch Thermal Cycler (Bio Rad), captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEM. These steps were carried out at 53 °C for 45 minutes, followed by 85 °C for 5 minutes, and held at 4 °C. Single-cell RNA sequencing libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics) and sequenced by IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150).

value: induced from hADSC


title: S2D4,scRNA-seq

description: 10x Genomics


title: S3D6,scRNA-seq

description: 10x Genomics


title: S1D6,scRNA-seq

description: 10x Genomics


title: S3D10,scRNA-seq

description: 10x Genomics


title: PC 12 cell line-MPP+ treatment_rep1


title: ESC_H3K4me3_exp1_cell10

extract_protocol:
Tn5 transposition was set up by incubation at 37°C for 50 min and 55°C for 10 min. After brief sonication, soluble chromatin was used for following ChIP experiments.DNA was reverse crosslinked and extracted by phenol/chloroform/isoamylalcohol.
Following single-cell 2cChIP protocol

value: embryo (blastocyst)


title: PC 12 cell line-control_rep3


title: PV, M3

city: Boston

first: Bo

last: Zhu

state: MA

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

description:
raw_counts.tab
deseq2_normalized_counts.tab

data_processing:
Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2
Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads.
Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2
Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package.
Assembly: GRCz11
Supplementary files format and content: Raw read counts in a TAB delimited file
Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file

source_name: follicle

extract_protocol:
TRIzol reagent for RNA extraction
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: AB

value: follicle

value: pre-vitellogenin

tag: genotype


title: S1D4,scRNA-seq

description: 10x Genomics


title: ESC_H3K4me3_exp1_cell9


title: APPL1 siRNA Untreated 1

description: S1 APPL1 Untreated


title: L-AOPP 50µM 2h, IPyA 100nM 1h (085)

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

country: Japan

institute: Yokohama City University

description: L-AOPP 50µM 2h→IPyA 100nM 1h

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix Gene Array Scanner 2500A with the original setting (This means that scanning steps are conducted at a high level of sensitivity to focus on those genes that function in hormone signaling, because their transcripts are relatively less abundant. Under these conditions, signals of highly abundant transcripts may reach saturation)

data_processing: MAS5.0 signal

organism: Arabidopsis thaliana

source_name: L-AOPP 50µM 2h, then treated with IPyA 100nM 1h

label_protocol: One-cycle target labeling reagents (Affymetrix)

growth_protocol: Four-day-old Arabidopsis seedlings were grown at 22 degrees under continuous light.

extract_protocol: guanidine-hydrochloride method

treatment_protocol: The seedlings were treated with or without 50 µM AOPP for 3 h. Alternatively, the seedlings were treated with AOPP for 2 h, and then treated with or without 1 µM IAA or IPyA for additional 1 h.

value: seedling


title: L-AOPP 50µM 2h, IAA 1µM 1h (080)

description: L-AOPP 50µM 2h→IAA 1µM 1h

source_name: L-AOPP 50µM 2h, then treated with IAA 1µM 1h


title: PV, M2


title: ESC_H3K4me3_exp1_cell8

data_processing:
Sequenced reads were trimmed and filtered by cutadapt (v 2.10) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with default parameters.
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Bigwig files were generated from bam files using deeptools (v 3.3.0) bamCoverage, with parameter of "--binSize 1 --normalizeUsing BPM --skipNonCoveredRegions".
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage.


title: THLE-3 cells, CH, CdCl2 + MeHgCl

data_processing:
Sequence reads were trimmed with Trim Galore (version 0.6.6) to eliminate potential adapter sequences and low-quality reads
Reads were then aligned to the human genome version GRCh38 using the STAR aligner (version 2.7.9a)
Gene expression levels were normalized by calculating the number of fragments per kilobase of transcript per million mapped reads (FPKM) with StringTie (version 2.1.7b)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: hepatic epithelial cells

value: toxic metal exposure

value: CdCl2 + MeHgCl


title: L-AOPP 50µM 2h, IAA 1µM 1h (070)

description: L-AOPP 50µM 2h→IAA 1µM 1h

value: L-AOPP 50µM 2h, then treated with IAA 1µM 1h


title: Mock (078)

description: Mock

source_name: Mock

value: Mock


title: ESC_H3K4me3_exp1_cell7


title: S3D3,scRNA-seq

description: 10x Genomics


title: L-AOPP 50µM 3h (083)

description: L-AOPP 50µM 3h

source_name: L-AOPP 50µM 3h

value: L-AOPP 50µM 3h


title: PV, WT3


title: THLE-3 cells, AC, oAs + CdCl2

value: oAs + CdCl2


title: L-AOPP 50µM 3h (079)

description: L-AOPP 50µM 3h


title: S1D0.5,scRNA-seq

description: 10x Genomics


title: L-AOPP 50µM 2h, IAA 1µM 1h (084)

description: L-AOPP 50µM 2h→IAA 1µM 1h


title: L-AOPP 50µM 3h (069)

description: L-AOPP 50µM 3h


title: PV, WT2


title: L-AOPP 50µM 2h, IPyA 100nM 1h (081)

description: L-AOPP 50µM 2h→IPyA 100nM 1h

value: L-AOPP 50µM 2h, then treated with IPyA 100nM 1h


title: L-AOPP 50µM 2h, IPyA 100nM 1h (071)

description: L-AOPP 50µM 2h→IPyA 100nM 1h


title: Mock (068)

description: Mock


title: THLE-3 cells, AC, control

value: WT

value: control


title: Mock (082)

description: Mock


title: THLE-3 cells, CH, control


title: PC 12 cell line-control_rep1


title: PC 12 cell line-control_rep2


title: PV, M1


title: PV, WT1


title: ESC_H3K4me3_exp1_cell4


title: M1d-2

city: Tianjin

first: Lanyu

last: Jia

address: No. 354, Beima Road, Hongqiao District, Tianjin

institute: Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China

description: Gene expression in MCAO rat after 1d

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array V2 (8x15K, Arraystar) and incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: MCAO model

label_protocol: Enriched circRNAs were amplified and transcribed into fluorescent cDNA using an Arraystar Super RNA Labeling Kit by a random priming method according to the Arraystar Super RNA Labeling protocol (Arraystar Super RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA was extracted by Trizol reagent (#15596018CN; Invitrogen). RNA quantity and quality were assessed at A260/A280 nm by NanoDrop (Wilmington, DE, USA) and Agilent 2100 (Palo Alto, CA, USA). Total RNAs were digested using Rnase R (#RNR07250; Epicentre) to eliminate linear RNAs and enrich circRNAs.

treatment_protocol: A permanent rat middle cerebral artery occlusion (MCAO) model was established. The right middle cerebral artery of the rat was blocked by Longa intracavitary suture method, and the diameter of the nylon suture was 0.205 mm (Longa ZE, Stroke, 1989, 20 (1): 84-91). Shuigou acupoint was acupunctured immediately after MCAO. The positioning was based on the animal acupoint map of Hua Xingbang. A half-inch needle was used to obliquely puncture 2 mm below the nasal septum of the rat, and a needle was inserted about 2 mm below the site as a reference electrode. The Shuigou acupoint was connected to the positive electrode of the electroacupuncture instrument, and the reference electrode was connected to the negative electrode. A 15Hz/2mA sparse-dense wave was used for 20 minutes. The blank group did not have an external suture inserted and did not receive electroacupuncture intervention. The rest of the steps were the same. The rats were anesthetized with 10% chloral hydrate (3.5ml/Kg) intraperitoneally and then perfused by heart. After complete perfusion, the brain was removed by decapitation. The brain tissue in the middle cerebral artery blood supply area on the infarct side was cut, and a part of it was used for chip experiments.

value: male

value: Brain tissue

value: 8 weeks


title: M1d-3

description: Gene expression in MCAO rat after 1d


title: ESC_H3K4me3_exp1_cell3

value: embryo (blastocyst)


title: PG_HE_8mpf_2

description:
HE_PG_8mpf_2
counts_raw.tab
counts_normalized.tab

value: AB

value: follicle

value: primary growth

value: HE (cdkn1a +/-)


title: ESC_H3K4me3_exp1_cell6


title: ESC_H3K4me3_exp1_cell2


title: Central lens epithelial cells, replicate 1

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

description:
HPS1_Capsule_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx
HPS1_Fibers_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx

data_processing:
Trimmed for quality and adapter content with Trim Galore! Version 0.6.6 Call:  trim_galore -o $TRIMDIR --length 85 --paired --clip_R2 3 --phred33 --cores 8
Aligned to RN45S5 transcript to reduce ribosomal content using HISAT2 2.2.1: hisat2 -p8 --verbose --phred33 --dta --fr
Convert rRNA Alignments to BAM samtools 1.9/htslib 1.9: samtools view -@ 8 -bS
sort rRNA Alignments samtools 1.9/htslib 1.9:samtools sort -n -@ 8 -m 12G
Extracted reads that don't align to RN45S5 using bedtools v2.29.2: bedtools bamtofastq
Aligned non-ribosomal reads to Human Genome using HISAT2 2.2.1: hisat2 -p8 --verbose --phred33 --dta --fr --rna-strandness RF
Counted reads aligning to genomic features in the Ensembl v104 GTF File using HTSeq Count 0.13.5: htseq-count -i gene_id -r pos -f bam -s reverse -m union --type exon
Assembled a DGEList object from all study samples, edgeR version 3.34.1
For each pairwise contrast, extracted a subset dgelist containing only samples  participating in that contrast
Filtered low counts using edgeR's filterByExpr with default settings for each contrast. edgeR version 3.34.1
Calculated TMM scaling factors edgeR's calcNormFactors with default settings, for each contrast. edgeR version 3.34.1
Estimated robust dispersions  for each contrast using "estimateDisp(dgelist, robust=TRUE)".  edgeR version 3.34.1
Analyzed differential gene expression in each pairwise contrastusing edgeR's exact test.  edgeR version 3.34.1
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: The processed data files are excel workbooks that contain the raw count matrix for the target contrast (all features in the GTF File) and tables of differential expression statistics.

source_name: lens

growth_protocol: 24 Hour injury samples were cultured under the following conditions: capsular bag was cultured in medium (RPMI-1640 with 5% fetal calf serum (FCS), 1% 10,000 units penicillin, 10 mg and 25 mg amphotericin B per mL for 24 hours. streptomycin

extract_protocol:
RNA was extracted using the Qiagen RNeasy Kit
SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian
Primer directed ribosomal depletion

treatment_protocol: Ex-vivo micro

tag: donor

tag: lens

value: b

value: M


title: PG_HE_8mpf_1

description:
HE_PG_8mpf_1
counts_raw.tab
counts_normalized.tab


title: ESC_H3K4me3_exp1_cell1


title: B-3

description: Gene expression in healthy rat after 1d

source_name: Blank control group


title: Central lens epithelial cells,  replicate 3

value: a


title: B-2

description: Gene expression in healthy rat after 1d


title: M1d-1

description: Gene expression in MCAO rat after 1d


title: Central lens epithelial cells, replicate 2

value: F


title: Equatorial lens epithelial cells, 24 hours post injury replicate 3

description:
HPS1_Capsule_24vs0H_Pairwise_Exact_Test_Differential_Expression.xlsx
HPS1_Capsule_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx


title: PG_WT_8mpf_2

description:
WT_PG_8mpf_2
counts_raw.tab
counts_normalized.tab

value: WT (cdkn1a +/+)


title: PG_WT_8mpf_3

description:
WT_PG_8mpf_3
counts_raw.tab
counts_normalized.tab


title: X22117

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to hg38 genome using Space Ranger's default settings.
Gene expression level of Ensembl coding genes were quantified using Space Ranger's default settings.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: spatial transcriptome

source_name: Endometrial biopsy

extract_protocol:
Human endometrial biopsies fixed in formalin and embedded in parafin were sectioned and H&E stained directly on 10X Genomics Visium Gene Expression slides and imaged using an EVOS (M7000) at 10x magnification. Tissues were permeabilised and RNA was subjected to spatial transcriptomics as per manufactuers protocols.
Human whole transcriptome probe panels, consisting of a pair of specific probes for each targeted gene, were added to the tissue. These probe pairs hybridize to their gene target and are then ligated to one another. The ligation products are released from the tissue upon RNase treatment and permeabilization. The ligated probe pairs bind with spatially barcoded oligonucleotides present on the Capture Area. All the probes captured by primers on a specific spot share a common Spatial Barcode. Libraries are generated from the probes and sequenced and the Spatial Barcodes are used to associate the reads back to the tissue section images for spatial mapping of gene expression.

value: Endometrial biopsy


title: X22118


title: Equatorial lens epithelial cells, 24 hours post injury replicate 2


title: PG_WT_8mpf_1

description:
WT_PG_8mpf_1
counts_raw.tab
counts_normalized.tab


title: Equatorial lens epithelial cells, 24 hours post injury replicate 1


title: X22114


title: PG_HE_8mpf_3

description:
HE_PG_8mpf_3
counts_raw.tab
counts_normalized.tab


title: Equatorial lens epithelial cells, 0 hours post injury replicate 3

description:
HPS1_Capsule_24vs0H_Pairwise_Exact_Test_Differential_Expression.xlsx
HPS1_Capsule_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx
HPS1_Fibers_vs_Capsule_Pairwise_Exact_Test_Differential_Expression.xls


title: Equatorial lens epithelial cells, 0 hours post injury replicate 2


title: A1d-1

description: Gene expression in MCAO rat after  1 d-acupuncture treatment

source_name: MCAO model,Electroacupuncture intervention,20 min


title: KO-2

city: Yangzhou

first: Ling

last: Ling

address: 136 Jiangyang Road

department: Medical College

institute: Yangzhou university

data_processing:
First, Raw Reads were filtered and high quality sequences (Clean Reads) were obtained. All subsequent analyses were based on Clean Reads, which included reference genome comparison, gene expression analysis, differential analysis and enrichment analysis.
Assembly: This is a transcriptome data.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Primary cell

extract_protocol:
Total RNA isolation was performed using TriZol Reagent.
After the library was qualified with Qubit3.0 and Agilent 2100, high-throughput sequencing platform was used for sequencing, and the sequencing strategy was PE150.

value: fetal livers from embryos at embryonic day 14.5

value: Embryonic hepatocyte

value: Gata1 3'UTR knockout

value: untreated


title: KO-3


title: B-1

description: Gene expression in healthy rat after 1d

value: male

value: Brain tissue


title: X19421


title: PG_HE_50dpf_3

description:
PG_HE_3
counts_raw.tab
counts_normalized.tab


title: X22112


title: PG_HE_50dpf_2

description:
PG_HE_2
counts_raw.tab
counts_normalized.tab


title: KO-1


title: Equatorial lens epithelial cells, 0 hours post injury replicate 1


title: X19276


title: WT-3

value: wide type


title: Cortical fiber cells,  replicate 3

description:
HPS1_Fibers_vs_Capsule_Pairwise_Exact_Test_Differential_Expression.xls
HPS1_Fibers_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx


title: PG_WT_50dpf_3

description:
PG_WT_3
counts_raw.tab
counts_normalized.tab

value: AB


title: A1d-2

value: 8 weeks


title: WT-2


title: Cortical fiber cells, replicate 2


title: X18576


title: PG_WT_50dpf_2

description:
PG_WT_2
counts_raw.tab
counts_normalized.tab

value: follicle

value: primary growth


title: A1d-3


title: Cortical fiber cells, replicate 1

value: b


title: PG_WT_50dpf_1

description:
PG_WT_1
counts_raw.tab
counts_normalized.tab


title: X17158