title: E5.fastq.gz

city: Hangzhou

first: zuorui

last: xie

address: Zhejiang Gongshang University

institute: ZFM

data_processing:
DNA from different samples was extracted using the CTAB
Samples were sequenced on an Illumina NovaSeq platform according to the manufacturer's recommendations, provided by LC-Bio.
Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean tags according to the fqtrim(v0.94).
Chimeric sequences were filtered using Vsearch software(v2.3.4).
After dereplication using DADA2,we obtained feature table and feature sequence.
Assembly: V3-V4 region of the 16S rRNA gene
Supplementary files format and content: ASV_table*: Feature tables and feature sequences obtained by removing background noise.
Supplementary files format and content: alpha_diversity*: Reflects species richness and uniformity as well as sequencing depth.
Supplementary files format and content: clean_data_stat: Double-ended stitching, quality control, and chimera filtering of raw dismounted data.

source_name: colon faeces

extract_protocol:
DNA from different samples was extracted using the CTAB according to manufacturer ’s instructions
16S rRNA gene high-throughput sequencing of the V3-V4 region was performed by LC-Bio Technology Co., Ltd, Hang Zhou, Zhejiang Province, China.

value: colon faeces

value: ICR

value: saline by gavage


title: E4.fastq.gz

status: Public on Nov 30 2022

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: strain

tag: treatment


title: Con3

city: Shanghai

first: Dianyin

last: Yang

address: 150, Jimo Road, Pudong District

institute: Shanghai East hospital

library_source: transcriptomic

data_processing:
After sequencing on Illumina Novaseq 6000 sequencer, double-end reads were harvested. q30 was used for quality control, and cutadapt software (v1.9.3) was used to de-join and remove low quality reads to obtain high quality reads. circRNA, LncRNA and mRNA were analyzed separately using different methods.
circRNA: High quality reads were compared to the reference genome/transcriptome using STAR software (v2.5.1b), and circular RNA detection and identification were performed using DCC software (v0.4.4)
The identified circular RNAs were also annotated using the circBase database and Circ2Traits. Data normalization and differentially expressed circRNA screening were then performed using edgeR software (v3.16.5). GO and KEGG analysis of the genes from which the differential circRNAs originated was also performed.
LncRNA & mRNA: using hisat2 software (v2.1), high quality reads were aligned to the human reference genome (UCSC HG19).Then, FPKM of transcript-level LncRNA and gene-level mRNA were obtained using cuffdiff software (part of the cufflinks software suite) guided by gtf gene annotation files.
(Fragments per kilobase of exon per million fragments mapped) values as expression profiles of LncRNA and mRNA, and ploidy changes and p-values between two/groups of samples were calculated to screen for differentially expressed LncRNA and mRNA.
Based on the proximity relationship, the target genes of LncRNAs were predicted, and GO and KEGG pathway analysis of target genes were performed. GO and KEGG pathway analysis of differential mRNAs were also performed.
Assembly: HG19
Supplementary files format and content: excel format

molecule: total RNA

organism: Homo sapiens

source_name: plasma

extract_protocol:
RNA was extracted using trizol reagent
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA)

value: plasma

tag: disease state

value: healthy

value: untreated


title: GFP_Crush-rep-4

city: Los Angeles

first: Yuyan

last: Cheng

state: CA

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

country: USA

institute: UCLA

data_processing:
For RNA-seq, raw sequenced reads were mapped to the reference genome Mus musculus (mm10) refSeq (refFlat) using STAR with default parameter.
Data quality was assessed on base-quality calls, nucleotide composition of sequences, insert sizes, per cent of uniquely aligned reads and transcript coverage using custom scripts and Picard Tools.
Total counts of read fragments aligned to candidate gene regions were derived using the Salmon program with mouse mm10 refSeq (refFlat table) as a reference.
Differential expression analysis was conducted with limma-voom.
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene counts in tsv format

source_name: Dorsal Root Ganglion Neurons

extract_protocol:
Samples were dissociated in papain, followed by FACS sorting. For RNA-seq, RNA from 5,000 – 10,000 FACS-sorted DRG neurons were isolated with RNeasy Micro Kit (Qiagen), and RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), following manufacturers’ protocols.
The cDNA was fragmented to 300 base pairs (bp) using the Covaris M220 (Covaris), and then the manufacturer’s instructions were followed for end repair, adaptor ligation, and library amplification. The libraries were quantified by the Qubit dsDNA HS Assay Kit (Molecular Probes); Library size distribution and molar concentration of cDNA molecules in each library were determined by the Agilent High Sensitivity DNA Assay on an Agilent 2200 TapeStation system.

value: Crush

tag: genotype

value: wild-type


title: Con2


title: GFP_Naive-rep-1

value: Naive


title: Vv3 (RNA-seq)

city: Zhengzhou

first: Gao-Pu

last: Zhu

state: Henan

address: No. 3, Weiwu Road

department: Non-timber Forest Research and Development Center

institute: Chinese Academy of Forestry

data_processing:
A cDNA library constructed by technology from the pooled RNA from all samples of grape was sequenced run with Illumina 4000 sequence platform.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) Vitis vinifera reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.
HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
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.
The miRNA-seq raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs.
The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
To predict the genes targeted by most aboundant miRNAs, computational target prediction algorithms (TargetFinder) were used to identify miRNA binding sites. The GO terms and KEGG Pathway of most aboundant miRNA targets were also annotated
Raw sequencing reads were obtained using Illumina's software to remove adaptors and low quality reads. The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline .
The degradome reads were mapped to the mRNA downloaded from www （ JGI , NCBI or other databases,or mapped to the species transcripts from transcriptome  sequencing） . Only the perfect matching alignment(s) for the given read would be kept for degradation analysis .
The degradation group sequence can match different numbers of reads on different sites on the same mRNA, and the predicted sequences at these sites may haven't corresponding miRNAs. The degradation group sequence can match different numbers of reads on different sites on the same mRNA, and the predicted sequences at these sites may haven't corresponding miRNAs. Detailed results with specific alignment information form a long_outfile file with AlignmentScore (Targetfinder penalty), AlignmentRange (pairing site), CleaveageSite (cutting site), Category (segmentation),P-value (P value), Raw_reads, Rep_Norm_reads (matches that match multiple sites for site normalization). Without alignment information, only AlignmentScore (Targetfinder score), AlignmentRange (pairing site), CleaveageSite (cutting site), Category (type), P-value (P value), Raw_reads, Rep_Norm_reads are listed. The (multi-site normalized reads) information is a simple list of miRNA and target gene relationships for the "Degradome_result.xlsx" file.
All resulting reads (t-signature) were reverse-complemented and aligned to the miRNA identified in our study.
All the identified targets were subjected to BlastX analysis to search for similarity, and then to GO analysis to uncover the miRNA-gene regulatory network on the basis of biological process ,cellular component and molecular function .
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-37/plants/gtf/vitis_vinifera v37
Supplementary_files_format_and_content: mRNA include FPKM values for each Sample ;miRNA expression use the norm values for each Sample.

organism: Vitis vinifera

source_name: Vitis vinifera

growth_protocol: Both grafted types of plants had grown in the same area for 25 years

extract_protocol:
In harvest season, the samples were selected that quick-frozen in liquid nitrogen, and stored at below 80°C until use. Total RNA and small RNA were extracted using Polysaccharide Polyphenol Plant MicroRNA Extraction Kit (LabHelper, Beijing, China) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no special treatment

tag: type

value: Self-root Vitis vinifera

tag: time

value: 25 years

value: LEAF, PHLOEM, BERRY


title: Amino acid starvation_rep2

city: Ibaraki

first: Tomonori

last: Kimura

state: Osaka

address: 7-6-8 Saito-Asagi

department: Center for Rare Disease Research

country: Japan

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

description: small RNA

data_processing:
The sequenced read was mapped to the human tRNA sequences using Blast version 2.2.26, and was aligned to the 25 nucleotides of 3' end of tRNA sequences without any mismatches.
The aligned read with 3'-end CCA was regarded to be derived from charged tRNA, whereas the read ended with 3'-end CC was from uncharged tRNA. Charging ratios were determined as 3'-end CCA–aligned reads over the sum of 3'-end CCA– and CC–aligned reads. Abundancy ratio of tRNA isodecoder was calculated based on the sum of 3'-end CCA– and CC–aligned reads of each isodecoder.
Genome_build: hg19
Supplementary_files_format_and_content: Individual alignment files mapping tRNA to isodecoder with read counts

source_name: TIG-1 cells

growth_protocol: TIG-1 20 (JCRB0501) cells from JCRB were grown in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was extracted once the cells reached 70-90% confluency. Small RNA was isolated using Isogen2. After ethanol precipitation, periodate oxidation of small RNA was carried out in 100 mM NaOAc/HOAc, pH 5.2, freshly prepared 50 mM NaIO4 at 27°C for 30 minutes. The reaction was quenched with 100 mM glucose for 5 minutes at 27°C. tRNA was then purified by denaturing 15% PAGE(5M Urea, 1× TBE), and eluted from the gel overnight in TE.   For β-elimination and deacylation, tRNA was treated in 150 mM Tris-HCl, pH 9.0, at 37 °C for 30 min. tRNA was demethylated as previously described (Zheng 2015).
RNA libraries were prepared for sequencing using NEBNext Small RNA Library Prep Set for Illumina.

treatment_protocol: Both replicates were incubated with amino acid free medium for 15h and one replicate was suplemented with amino acids.

tag: cell line

tag: tissue for primary cancer

value: Lung

tag: cell type

value: fetal lung


title: E6.fastq.gz


title: E3.fastq.gz


title: GFP_Crush-rep-3


title: GFP_Naive-rep-3


title: E2.fastq.gz


title: GFP_Crush-rep-2


title: Con1


title: E1.fastq.gz


title: LS411N-BR/tet-MUC1shRNA_DOX+3

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
LS411NBR_Gene_TPM.csv
LS411N-BR_DOXpositive_3

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: GRCh38.74
Supplementary files format and content: csv files represent TPMs for all samples

growth_protocol: LS411N cells were cultured in RPMI medium with 10% FBS.LS411N-BR cells were cultured in RPMI medium with 10% FBS and 4uM BRAF inhibitor.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline for inducible model.

tag: brafi resistance

value: resistant to BRAF inhibitors

value: Colon Cancer

tag: puromycin resistance

value: resistant

tag: shRNA

value: MUC1 shRNA

value: DOX

value: MUC1-C knockdown


title: B6.fastq.gz

value: colon faeces

value: ICR

value: eriocitrin by gavage


title: A9_Naive-rep-6

value: a9k1 overexpression


title: LS411N-BR/tet-MUC1shRNA_DOX+2

description:
LS411NBR_Gene_TPM.csv
LS411N-BR_DOXpositive_2


title: Vv2 (RNA-seq)


title: IgG control ChIP-seq data of the KAT7 (HBO1) ChIP-seq experiment

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
ChIP-seq reads were aligned to the USCS mm10 using Bowtie2.
The aligned ChIP-Seq libraries were sorted using samtools and duplicates reads were marked but not removed using MarkDuplicates from Picard Tools.
The ChIP-seq libraries were then GC corrected using Benjamini’s and Speed’s method implemented in the correctGCBias function by the deepTools program.
ChIP-Seq libraries were then merged across biological replicates for the H3K14ac and KAT7 markers using the merge command from the sambamba software.
The genomic regions for gene bodies used for ChIp-Seq gene counts were obtained as follows: the gene bodies were taken from the RNA-Seq analysis reported in submission XX and only genes with an average expression across replicates larger than 0 were considered and with an available Symbol in the NCBI annotation.
The source of the other genomic regions used to compute ChIp-Seq counts were obtained as described in the method of the publication in section "Chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) and analysis".
ChIP-Seq counts over all the considered genomic regions were computed using the R package featureCounts with the following command: featureCounts(path_to_bamfiles,       ignoreDup=FALSE,nthreads=10,isPairedEnd=FALSE,minMQS=0,annot.ext=genomic_region.gtf)
One combined processed data file, "combined_genomic_regions_chipseq_rpkm_NSPCs.csv", has been created with the ChIP-Seq read counts of the merged libraries.
Assembly: mm10
Supplementary files format and content: combined_genomic_regions_chipseq_rpkm_NSPCs.csv. CSV file with ChIP-Seq raw counts and RPKM over various genomic regions. There are columns with read counts and RPKM counts repsectively for each merged ChIP-Seq library, one for KAT7 and H3K14ac; a unique "RegionID" identifier (Gene Id, Enhancer number etc..); "Chr", "Start" and "End" of the genomic region; "Strand" when available; "Lenght" of the genomic region;"RegionName", name used for plotting; and "ExprLevel05" which indicated the Genes used to distinguish genes in the top 5%, bottom 5% and other range of expression. "ExprLevel05"  is only available for RegionName: "Promoter", "Gene Body" and "Post TES".
Supplementary files format and content: Some raw ChIP-Seq files don't have pre-processed files since the corresponding aligned bamfiles were simply explored in SeqMonk and no binning of counts was used for analysis.

source_name: Mouse neural stem and progenitor cells (NSPCs)

growth_protocol: E14.5 embryonic cortices and ganglionic eminences were dissected, washed in PBS, digested with pancreatin/trypsin, washed, resuspended in neurosphere culture medium (Merson et al., 2006), sieved, plated and cultured at 37oC and 5% CO2. Cells were passaged using Accutase (Sigma-Aldrich, A6964) for 5 min at 37oC to dissociate neurospheres and replated at 20,000 cells/cm2. Merson, T.D., Dixon, M.P., Collin, C., Rietze, R.L., Bartlett, P.F., Thomas, T., and Voss, A.K. (2006). The transcriptional coactivator Querkopf controls adult neurogenesis. J Neurosci 26, 11359-11370.

extract_protocol:
The antibodies used for ChIP were an anti-KAT7 antibody (13751-1-AP from Protein Tech) and an anti-H3K14ac antibodies (7627 from Cell Signaling). 10 million cells per sample were used. Chromatin immunoprecipitation (ChIP) was conducted as reported previously (Voss et al., 2012).
Sequencing libraries were generated using an Illumina TruSeq DNA library preparation kit and sequenced on an Illumina NextSeq sequencer.

treatment_protocol: The cells were either Kat7 intact or Kat7 deleted by cre-recombinase expression from the NesCre transgene.

tag: chip antibody


title: Vv1 (RNA-seq)


title: GFP_Crush-rep-1

value: Crush

value: wild-type


title: LS411N-BR/tet-MUC1shRNA_DOX+1

description:
LS411NBR_Gene_TPM.csv
LS411N-BR_DOXpositive_1


title: B5.fastq.gz


title: LS411N-BR/tet-MUC1shRNA_DOX-3

description:
LS411NBR_Gene_TPM.csv
LS411N-BR_DOXnegative_3

value: no DOX

value: Control


title: A9_Naive-rep-5

value: Naive


title: Anti-KAT7 (HBO1) ChIP-seq data of Kat7 (Hbo1) deleted mutant cells

value: Mouse neural stem and progenitor cells (NSPCs)


title: A9_Naive-rep-4


title: Anti-KAT7 (HBO1) ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 1


title: A9_Naive-rep-2


title: Anti-KAT7 (HBO1) ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 3


title: A9_Naive-rep-3


title: LS411N/tet-MUC1shRNA_DOX+3

description:
LS411N_Gene_TPM.csv
LS411N_DOXplus3

value: not resistant to BRAF inhibitors


title: LS411N-BR/tet-MUC1shRNA_DOX-1

description:
LS411NBR_Gene_TPM.csv
LS411N-BR_DOXnegative_1

value: resistant to BRAF inhibitors


title: Amino acid starvation_rep1

description: small RNA

value: Lung

value: fetal lung

value: untreated


title: B3.fastq.gz


title: A9_Naive-rep-1


title: LS411N/tet-MUC1shRNA_DOX+2

description:
LS411N_Gene_TPM.csv
LS411N_DOXplus2

value: Colon Cancer

value: resistant

value: MUC1 shRNA

value: DOX


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) deleted mutant cells, replicate 3


title: B4.fastq.gz

value: colon faeces

value: ICR

value: eriocitrin by gavage


title: A9_Crush-rep-4

value: Crush

value: a9k1 overexpression


title: LS411N-BR/tet-MUC1shRNA_DOX-2

description:
LS411NBR_Gene_TPM.csv
LS411N-BR_DOXnegative_2

value: no DOX

value: Control


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) deleted mutant cells, replicate 2

value: Mouse neural stem and progenitor cells (NSPCs)


title: A9_Crush-rep-3


title: IgG control ChIP-seq data of the H3K14ac ChIP-seq experiment


title: B1.fastq.gz


title: LS411N/tet-MUC1shRNA_DOX-3

description:
LS411N_Gene_TPM.csv
LS411N_DOX-3

value: not resistant to BRAF inhibitors


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) deleted mutant cells, replicate 1


title: LS411N/tet-MUC1shRNA_DOX-2

description:
LS411N_Gene_TPM.csv
LS411N_DOX-2


title: Anti-KAT7 (HBO1) ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 2


title: B2.fastq.gz


title: p28floxed-8, 10xRNA

city: Lyngby

first: Fredrik

last: Junghus

address: DTU Building 202

department: Experimental and Translational Immunology

country: Denmark

institute: Technical University of Denmark

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Small inestine lamina propria

extract_protocol:
SI-LP cell suspensions were generated as described previously (Luda et al., 2016). Briefly,   after removal of Peyer’s patches and fat, tissue was cut longitudinally into 1cm pieces and  incubated in RPMI 1640 (Gibco) containing HEPES (15mM, Gibco),  ethylenediaminetetraacetic acid (EDTA, 2mM) and fetal bovine serum (FBS, Sigma Aldrich,  2%) for 10 min at 37 C with agitation at 370rpm. This step was repeated 2 times with  incubation for 15 min at 37 C. Epithelial cells and debris were removed by filtering through a  nylon filter (250μm) after each wash. Remaining tissue was washed and incubated for 20-25  min in R10 media (RPMI 1640, FBS (10%), HEPES (10mM), sodium pyruvate (1mM),  penicillin (100U/mL), streptomycin (100μg/mL), Gibco) containing 2-ME (50μM, Gibco),  DNase I (30μg/mL, Sigma Aldrich) and Liberase TM (0.3 WuenschU/mL, Sigma Aldrich) on  a magnetic stirring plate at 37°C with 5% CO2. The resulting cell suspensions were filtered   through a cell strainer (100μm, Fischer Scientific) prior to density gradient centrifugation with  40-70% Percoll (GE Healthcare). CD4+ T cells were enriched from SI-LP cell suspensions using the EasySepTM Mouse CD4+ T cell isolation Kit (Stem Cell Technologies) according to the manufacturer’s instructions and CD4+TCRαβ+ T cells were sorted using a FACSAria™ II Cell Sorter (BD Bioscience)
Isolated CD4+ T cells were subjected to droplet-based scRNA-seq using the Chromium Single Cell 3′ Reagent Kit v3  following the manufacturer’s instructions (10x Genomics). The 10x Chromium Controller  generated Gel Bead-In Emulsions (GEMs), where each cell was labeled with a specific  barcode, and each transcript labeled with a unique molecular identifier (UMI). After RT, GEMs  were broken down, barcoded cDNA was purified with Dynabeads MyOne Silane beads  (Thermofisher) and amplified by Polymerase Chain Reaction (PCR). Amplified cDNA was  cleaned up with SPRIselect (Beckman Coulter). Indexed sequencing libraries were constructed  by enzymatic fragmentation, end-repair and A-tailing, before a second and final PCR  amplification using the Chromium i7 Sample Index (10x Genomics), introducing an Illumina  R2 sequence, a unique sample index (allowing multiplex sequencing) and P5/P7 Illumina  sequencing adaptors to each library. Muliplexed libraries were pooled and sequencing was  carried out at the National Genomic Infrastructure (NGI) SNP&SEQ Technology Platform,  Uppsala using an S1 flowcell, the NovaSeq 6000 system and v1.5 sequencing chemistry  (Illumina Inc.).

value: CD4+ T cells

value: Small inestine lamina propria

tag: age

value: 7-8 weeks old


title: p28floxed-6, 10xRNA

description: 10x Genomics


title: p28floxed-7, 10xRNA

description: 10x Genomics


title: A9_Crush-rep-1


title: p28wt-4, 10xRNA

description: 10x Genomics


title: p28floxed-5, 10xRNA

description: 10x Genomics


title: LS411N/tet-MUC1shRNA_DOX-1

description:
LS411N_Gene_TPM.csv
LS411N_DOX-1


title: LS411N/tet-MUC1shRNA_DOX+1

description:
LS411N_Gene_TPM.csv
LS411N_DOXplus1

value: MUC1-C knockdown


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 1


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 3


title: PTPN2 KO 4

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description:
B11_EXP_210813_C8
Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter, CRISPR mediated knockout of PTPN2 in exon 5-7

data_processing:
Adapter and quality trimming was performed with CutAdapt (v3.4) and TrimGalore! (v0.6.7).
STAR (v2.7.6a) and RSEM (v1.3.1) were used for alignment and quantification.
Quality control was checked with RSeQC (v3.0.1).
Assembly: GRCh38
Supplementary files format and content: Raw count matrix

source_name: MEL1 INS-GFP, CRISPR mediated knockout of PTPN2 in exon 5-7

extract_protocol:
Islets were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. QIAGEN RNEasy mini kit was used for purification of total RNA.
RNA libraries were constructed with TakaraBio SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian.

value: pancreas

value: islet cells

value: MEL1 INS-GFP


title: p28wt-3, 10xRNA

description: 10x Genomics


title: WT 4

description:
B9_EXP_210621_WT2
WT: Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter

source_name: MEL1 INS-GFP

value: Wild type


title: A9_Crush-rep-2


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 2


title: p28wt-2, 10xRNA

description: 10x Genomics


title: p28wt-1, 10xRNA

description: 10x Genomics


title: PTPN2 KO 2

description:
B8_EXP_220130_C8_2
Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter, CRISPR mediated knockout of PTPN2 in exon 5-7


title: Anti-H3K14ac ChIP-seq data of Kat7 (Hbo1) intact control cells, replicate 4


title: PTPN2 KO 3

description:
B10_EXP_220130_C8_3
Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter, CRISPR mediated knockout of PTPN2 in exon 5-7


title: Treg2 F1

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: Regulatory T cells WT

data_processing:
Adapters were removed with Trimmomatic-0.36
Reads were mapped to the reference genome mm10 using STAR_2.5.3 software with default parameters
Read counts were obtained using HTSeq-0.9.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: regular CD4+ T cells

extract_protocol:
We extracted RNA from 2x105 sorted CD4+ Foxp3- or CD4+ Foxp3+ populations in CD11c-  Cd70tg;CD27+/- Foxp3 reporter mice and CD27+/- mice (in duplicates), and RNA from 2x105  sorted CD4+ CD25+ in hCD2-Eomestg mice and wild-type C57Bl/6 mice (in triplicate) using  RNeasy Plus Mini kit according to manufacturer’sinstructions (Qiagen)
Libraries were prepared using Ovation SoLo RNA-Seq System (NuGEN Technologies) and  underwent paired-end sequencing

value: regular CD4+ T cells

value: WT


title: WT 3

description:
B8_EXP_210621_WT1
WT: Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter


title: PTPN2 KO 1

description:
B6_EXP_220126_C8_3
Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter, CRISPR mediated knockout of PTPN2 in exon 5-7


title: Young amino acid suplementation_rep4

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode. Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19. The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized Count and Normalized FPKM

source_name: young TIG-1 cells

extract_protocol:
Total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using TRIzol (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Library preparation was performed using TruSeq stranded mRNA sample prep kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: All replicates were incubated with amino acid free medium for 15h and two of them were suplemented with amino acids.

value: Lung

tag: genetics

value: fetal lung

value: treated with amino acids for 1h

value: TIG-1 cells


title: Differentiating, IgG control

description:
IgG.Differentiating
IgG control differentiating

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the mouse genome mm10 using Rsubread version 2.4.3.
Read counts were summarized by the transcriptional start site (TSS) + 1kb and by gene bodies using the Rsubread featureCounts function and mm10 RefSeq NCBI annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files for genomic region TSS + 1kb; columns represent Entrez Gene ID and the number of reads mapping to that region.
Supplementary files format and content: tab-delimited text files for gene body counts; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Neural stem and progenitor cells (NSPCs)

growth_protocol: E14.5 embryonic cortices and ganglionic eminences were dissected, washed in PBS, digested with pancreatin/trypsin, washed, resuspended in neurosphere culture medium (Merson et al., 2006), sieved, plated and cultured at 37oC and 5% CO2. Cells were passaged using Accutase (Sigma-Aldrich, A6964) for 5 min at 37oC to dissociate neurospheres and replated at 20,000 cells/cm2.Merson, T.D., Dixon, M.P., Collin, C., Rietze, R.L., Bartlett, P.F., Thomas, T., and Voss, A.K. (2006). The transcriptional coactivator Querkopf controls adult neurogenesis. J Neurosci 26, 11359-11370.

extract_protocol:
The antibodies used for ChIP were the anti-H3K14ac antibodies (Abcam ab52946). 10 million cells per sample were used. Chromatin immunoprecipitation (ChIP) was conducted as reported previously (Voss et al., 2012).
Sequencing libraries were generated using an Illumina TruSeq DNA library preparation kit and sequenced on an Illumina NextSeq sequencer.

treatment_protocol: To induce differentiation, neurospheres were dissociated and cultured on laminin substrate in cortical neuron culture medium (Voss et al., 2008). Voss, A.K., Britto, J.M., Dixon, M.P., Sheikh, B.N., Collin, C., Tan, S.S., and Thomas, T. (2008). C3G regulates cortical neuron migration, preplate splitting and radial glial cell attachment. Development 135, 2139-2149.

tag: Stage

value: Differentiating

value: anti-H3K14ac antibodies (Abcam ab52946)


title: Proliferating, IgG control

description:
IgG.Proliferating
IgG control proliferating

value: Neural stem and progenitor cells (NSPCs)

value: Proliferating


title: Proliferating, Hbo1 null cells

description:
Hbo1.null.Proliferating
Hbo1 null cells proliferating

value: Hbo1 null


title: Differentiating, Hbo1 null cells

description:
Hbo1.null.Differentiating
Hbo1 null cells differentiating


title: Treg1 CD70Tg

description: Regulatory T cells CD70Tg


title: WT 2

description:
B5_EXP_210415_WT
WT: Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter

tag: tissue


title: Treg1 F1

description: Regulatory T cells WT


title: Differentiating NSPCs, Input

description:
WT.Differentiating.1.Input
WT differentiating, Input


title: Proliferating NSPCs, Input

description:
WT.proliferating.1.Input
WT proliferating, Input


title: Young amino acid suplementation_rep2


title: Tconv2 F1

description: Conventional T cells WT

source_name: conventional CD4+ T cells

value: conventional CD4+ T cells


title: Treg2 CD70Tg

description: Regulatory T cells CD70Tg


title: Young amino acid suplementation_rep1


title: Tconv1 CD70Tg

description: Conventional T cells CD70Tg


title: Differentiating NSPCs, rep2

description:
WT.differentiating.2
WT differentiating NSPCs


title: Young_amino acid starvation_rep4

value: untreated


title: Tconv2 CD70Tg

description: Conventional T cells CD70Tg


title: Young_amino acid starvation_rep3


title: 18mo mouse, bulk retina, ATAC-Seq, replicate 6

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

state: California

address: 837 Health Sciences Rd, Gillespie Neuroscience Research Facility, Room#2226, Bench#8

department: Physiology & Biophysics

institute: UC Irvine

data_processing:
All clean-reads were mapped to Mus musculus reference genome mm10 by STAR v2.7.8a. Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.  The mitochondria DNA was removed from unique aligned reads by samtool (Version: 1.10, using htslib 1.10.2).
The open chromatin regions or significant reads coverage (q-value ≤ 0.05) of ATAC-Seq data were identified by peak calling using MACS2 (Model-based Analysis for ChIP-Seq, version 2.2.7.1) and annotated by annotatePeaks.pl. Bedgraph or BigWig files for genome browser viewing were generated by HOMER tools.
The chromatin accessibility of retina samples from each comparison pair were compared by using differential analysis tool edgeR in the count matrix built from the consensus list of detected open regions (excluded blacklist regions using bedtools2/2.29.2) from all samples with significance cutoff at 0.05 in FDR q-value.
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: bulk retina

extract_protocol:
Fresh retina tissue of each mouse eye was homogenized with 22Gx1’ BD Precision-glide syringe-needle and crosslinked by 1%(w/v) methanol-free formaldehyde (Cat no.28906, Thermo Scientific) in crosslinking buffer (10mM HEPES-NaOH pH7.5, 100mM NaCl, 1mM EDTA, 1mM EGTA) for 10min slow rotation at room temperature. Crosslinks were quenched by glycine with 125mM final concentration. Tissue samples were lysed into chromatin with 0.25% Triton X-100 and 0.5% NP40. 10mM sodium butyrate was added for deacetylation inhibition.Chromatin samples were sonicated (Pico Bioruptor, Diagenode) in polystyrene tubes on low power with 8 cycles of 30 sec "on", 45 sec"off". Anti-Histone H3acetylK27 antibody (Cat no. ab4729, Abcam) or IgG (Millipore #CS200581) was coupled with protein A Dynabeads (Life Technologies)
The eluted DNA fragments were then amplified by PCR with Nextera compatible indexed sequencing i5 and i7 adapters using NEBNext 2x PCR Master Mix PCR kit (M0541, NEB). The amplified DNA library was fragment size selected from 200bp to 800bp using Ampure XP beads (A63880, Beckman Coulter). The quality of the ATAC-Seq libraries was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Inc.). ATAC-Seq libraries was pooled and run on Illumina NovaSeq 6000 System (Flow Cell Type S4) sequencer with a paired-end read of 100 bp to harvest 25-50 million paired-end reads per sample.

treatment_protocol: The experimental group of animals was treated by intraperitoneal (IP) administration of dasatinib (Sigma, 5 mg/kg) after IOP elevation, and a control group of mice was sham-treated vehicle (PBS/DMSO). Each mouse underwent unilateral hydrostatic pressure- induced IOP elevation to 30 mm Hg, with the contralateral eye left as an untreated control. To ensure a sterile environment, compounds were prepared under the tissue culture hood using sterile PBS. The final solution was filtered through a 0.22-μm PES membrane just before injection. Tips, tubes, and syringes were sterile.

value: bulk retina

tag: date of tissue collection after treatment


title: Proliferating NSPCs, rep3

description:
WT.proliferating.3
WT proliferating NSPCs


title: Proliferating NSPCs, rep2

description:
WT.proliferating.2
WT proliferating NSPCs


title: Young_amino acid starvation_rep1

tag: treatment


title: Proliferating NSPCs, rep1

description:
WT.proliferating.1
WT proliferating NSPCs


title: 18mo mouse, bulk retina, ATAC-Seq, replicate 5


title: Young amino acid suplementation_rep3


title: SRP54 KD 3

city: Lubbock

first: Andrey

last: Karamyshev

state: TX

address: 3601 4th Street

department: Cell Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

data_processing:
FastQC (reads quality control)
Trim galore! Script (read quality filtering and trimming)
BWA (Mapping to the genome of reference)
SortSam (coordinate sorting .Bam files from mapping)
MarkDuplicates (remove PCR duplicates)
BamCoverage (mapping quality)
featureCounts (Counting matrix)
DESeq2 (Read count normalization and differential expression analysis)
Genome_build: GRCh38.p13 (Genome Reference Consortium Human Build 38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human cell ine HeLa Tet-On

growth_protocol: Cells were grown in 6-well plates at 37ºC with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), and penicillin and streptomycin mixture (100 units/ml and 100 µg/ml correspondingly).

extract_protocol:
Total RNA was purified using Trizol (Life technologies) and RNeasy Mini kit (Qiagen).
Libraries were prepared by the use of Illumina TruSeq Stranded mRNA Sample Preparation kit. Agilent 2100 Bioanalyzer System was used for total RNA and library quality check. Sequencing was conducted on Illumina HiSeq 2500 sequencer.

treatment_protocol: Cells were transfected with siRNA specific for SRP54 or with control siRNA by the use of Lipofectamine RNAiMAX Transfection Reagent (Life technologies) next day after plating. Three biological repeats were used for control and SRP54 knockdown. Samples were collected 55 hours after transfection.

value: Human cervical adenocarcinoma-derived cell line

value: Transfected with siRNA for SRP54


title: Hbo1 intact differentiating, rep4

description:
intact.Diff_4
Hbo1 intact differentiating NSPCs

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the mouse genome mm10 using Rsubread version 2.4.3.
Read counts were summarized using the Rsubread featureCounts function and RefSeq NCBI annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

growth_protocol: E14.5 embryonic cortices and ganglionic eminences were dissected, washed in PBS, digested with pancreatin/trypsin, washed, resuspended in neurosphere culture medium (Merson et al., 2006), sieved, plated and cultured at 37oC and 5% CO2. Cells were passaged using Accutase (Sigma-Aldrich, A6964) for 5 min at 37oC to dissociate neurospheres and replated at 20,000 cells/cm2.Merson, T.D., Dixon, M.P., Collin, C., Rietze, R.L., Bartlett, P.F., Thomas, T., and Voss, A.K. (2006). The transcriptional coactivator Querkopf controls adult neurogenesis. J Neurosci 26, 11359-11370. To induce differentiation, neurospheres were dissociated and cultured on laminin substrate in cortical neuron culture medium (Voss et al., 2008). Voss, A.K., Britto, J.M., Dixon, M.P., Sheikh, B.N., Collin, C., Tan, S.S., and Thomas, T. (2008). C3G regulates cortical neuron migration, preplate splitting and radial glial cell attachment. Development 135, 2139-2149.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy kit according to the manufacturer’s instructions from E14.5 neurospheres cultured in neural stem cell proliferation medium or differentiation medium.
Sequencing libraries were constructed using the Illumina TruSeq library construction kit according to the manufacturer’s instructions and sequenced on an Illumina NextSeq sequencer obtaining 75 bp paired-end reads.

treatment_protocol: NSPCs were either Kat7 intact or deleted by virtue of their germline genotypes, Kat7lox/loxNesCreT/+ and 4 Kat7+/+NesCreT/+.

value: Kat7 intact

value: Hbo1 Cre control


title: WT 1

description:
B3_EXP_210211_WT
WT: Human embryonic stem cell line “MEL1 INS-GFP” (Toronto) with a reporter GFP tag on the insulin promoter

value: pancreas

value: islet cells

value: Wild type

value: MEL1 INS-GFP


title: Hbo1 intact differentiating, rep3

description:
intact.Diff_3
Hbo1 intact differentiating NSPCs


title: PCIF1 KO m6A-exo-seq rep2 Input

city: San Diego

first: Lingling

last: Wang

address: 9500 Gilman Dr

institute: University of California San Diego

description:
m6Am.genes.rep2.csv
m6A-exo-seq of human lung cancer

data_processing:
library strategy: m6A-exo-seq
Paired-end sequencing data were trimmed by paired-end model of cutadapt software. Reads longer than 15bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 software using the default parameter for single or pair-end model
For RNA-seq, reads were counted by htseq, then gene expression was quantified by DESeq2. Read counts were saved as control.rep.counts.csv or PCIF1_KO.rep.counts.csv
For m6A-exo-seq, reads were counted by featureCount, then differential methylation sites at cap-region was detected by hypergeometric test through in-house scripts. The m6A marked genes are listed in m6Am.genes.rep.csv, with the gene names at first column, differential methylation FDR and p-value at second and third columns, change of enrichment fold in KO PCIF1 compared to KO control samples at the fourth column.
Assembly: hg38
Supplementary files format and content: m6Am.genes.rep.csv for m6Am marked genes in m6A-exo-seq
Supplementary files format and content: control.rep.counts.csv or PCIF1_KO.rep.counts.csv for raw gene counts in RNA-seq,

source_name: lung

extract_protocol:
After the extraction of total RNA, for RNA-seq, RNA was extracted from PCIF1-KO and control Calu-3 cells (three biological replicates for each) using a Quick-RNA Miniprep Kit. For m6A-exo-seq, mRNA was purified using Magnetic mRNA Isolation Kit (New England Biolabs, S1550S)
For m6A-exo-seq,  aliquots (100 μg) of mRNA were fragmented using a Fragmentation Reagents Kit (Invitrogen, AM8740) according to the manufacturer’s protocol. Fragmented mRNAs were phosphorylated with T4 PNK (NEB, M0201S) and then dephosphorylated with Terminator 5′-Phosphate-Dependent Exonuclease (Lucigen). Finally, Cap-Clip (CellScript) was added to remove capped transcripts. Of the final uncapped fragmented mRNA preparation, 10% was reserved as input material and the remaining 90% was subjected to immunoprecipitation with anti-m6A antibody (Abcam, ab151230). Immunoprecipitated RNA was eluted with RLT buffer (QIAGEN, 160051456), purified by ethanol precipitation, and prepared for library generation using a TruSeq mRNA library preparation kit (Illumina).
RNA-seq and m6A-exo-seq were sequenced at  Illumina NovaSeq 6000 platform with paired-end model

value: lung

value: lung cancer cell

value: PCIF1 knockout


title: Differentiating NSPCs, rep3

description:
WT.differentiating.3
WT differentiating NSPCs

value: WT

value: Neural stem and progenitor cells (NSPCs)

value: Differentiating

value: anti-H3K14ac antibodies (Abcam ab52946)


title: PCIF1 KO m6A-exo-seq rep2 IP


title: 3mo mouse, bulk retina, ATAC-Seq, replicate 6

value: untreated


title: 18mo mouse, bulk retina, ATAC-Seq, replicate 4

value: bulk retina


title: 3mo mouse, bulk retina, ATAC-Seq, replicate 5


title: SRP54 KD 1

value: Human cervical adenocarcinoma-derived cell line


title: Tconv1 F1

description: Conventional T cells WT

value: conventional CD4+ T cells


title: 3mo mouse, bulk retina, ATAC-Seq, replicate 4


title: Hbo1 intact differentiating, rep2

description:
intact.Diff_2
Hbo1 intact differentiating NSPCs

value: Kat7 intact


title: PCIF1 KO m6A-exo-seq rep1 IP

description:
m6Am.genes.rep1.csv
m6A-exo-seq of human lung cancer


title: PCIF1 KO m6A-exo-seq rep1 Input


title: Differentiating NSPCs, rep1

description:
WT.differentiating.1
WT differentiating NSPCs


title: Hbo1 intact differentiating, rep1

description:
intact.Diff_1
Hbo1 intact differentiating NSPCs

value: Hbo1 Cre control


title: Control 3

value: Transfected with control siRNA


title: Young_amino acid starvation_rep2

value: Lung

value: fetal lung

value: TIG-1 cells


title: 18mo mouse bulk retina, IOP, day2, ATAC-Seq, replicate 3

value: unilateral IOP (constant 30mmHg IOP for 1 hour)

value: day 2 from IOP


title: Control 2


title: Control 1


title: Hbo1 null differentiating, rep4

description:
null.Diff_4
Hbo1 null differentiating NSPCs

value: Kat7 deleted

value: Hbo1 null


title: SRP54 KD 2

value: Transfected with siRNA for SRP54


title: Control m6A-exo-seq rep2 Input

value: lung

value: lung cancer cell

value: Control


title: Control m6A-exo-seq rep2 IP


title: Hbo1 null differentiating, rep3

description:
null.Diff_3
Hbo1 null differentiating NSPCs

value: Neural stem and progenitor cells (NSPCs)

value: Differentiating


title: 18mo mouse bulk retina, contralateral control, day2, ATAC-Seq, replicate 3

value: bulk retina

value: WT

value: unilateral untreated control


title: 18mo mouse bulk retina, IOP, day2, ATAC-Seq, replicate 1


title: RALY_KD1

city: Gwang-ju

first: Kim

last: Donggun

address: 123 cheomdangawgi-ro, buk-gu

department: Life science

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
Trimmed reads were aligned to GRCh38 using Hisat2 version 2.0.4
Sam files were converted to bam files using samtools
Read counts were calculted using featureCounts function in subread.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

growth_protocol: HCT116 cells were maintained in RPMI-1640 medium (Hyclone) and were supplied with 10% fetal bovine serum (FBS, Hyclone), 100 U/ml penicillin and 100 μg/ml streptomycin and incubated at 37 ℃ and 5% CO2.

extract_protocol:
Total RNAs from cells were extracted using RiboEX reagent (GeneAll) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with Raly- or nonsilencing- targeting shRNA lentivirus and 10 µg/ml polyprene (sigma) for 72 h.


title: RALY_KD2


title: Hbo1 null differentiating, rep1

description:
null.Diff_1
Hbo1 null differentiating NSPCs


title: Hbo1 null differentiating, rep2

description:
null.Diff_2
Hbo1 null differentiating NSPCs


title: Control m6A-exo-seq rep1 IP


title: 18mo mouse bulk retina, contralateral control, day2, ATAC-Seq, replicate 2


title: 18mo mouse bulk retina, contralateral control, day2, ATAC-Seq, replicate 1


title: Hbo1 intact proliferating, rep4

description:
intact.Prolif_4
Hbo1 intact proliferating NSPCs

value: Proliferating

value: Kat7 intact

value: Hbo1 Cre control


title: Hbo1 intact proliferating, rep3

description:
intact.Prolif_3
Hbo1 intact proliferating NSPCs


title: WT1


title: MDA-MB-231 a6 biorep2

city: guangzhou

first: XinChen

last: Jiang

state: guangdong

address: 中国广州大学城外环东路132号

institute: school of pharmaceutical sciences, SUN YAT-SEN UNIVERSITY

data_processing:
After removing the adapter sequences and reads with poor quality by cutadapt, the qualified reads were mapped to the reference genome (hg38) and the expression level of genes was measured by DESeq2. Differentially expressed genes (DEGs) were defined as genes with fold change > 2 or < 0.5 and P value < 0.05.
G4 prediction in DEGs was analyzed by G4Hunter and G4 Annotation scripts written by Anaïs Vannutelli et al. The sequence of 2000 bp upstream of TSS used was obtained from Ensemble GRCh38. Scripts launched on the previously generated sequences using a sliding window approach with a window length of 60 nt and a step of 5 nt. Successive windows with G4H higher than 1.2 were grouped and returned as pG4 regions (pG4r) containing one or more pG4. Then two sets of detected pG4r were merged in order to detect and remove redundancy, and G4 score was counted according to the number of optimized pG4r. 100 genes were randomly selected from the human genome and were run the same protocol for the G4 background score. DEGs scored over the background in G4 score were defined as G4-related DEGs.
Genome_build: hg38
Supplementary_files_format_and_content: xls files DEGs of each group
Supplementary_files_format_and_content: comma-delimited csv files G4-related DEGs of each group

source_name: triple-negative breast cancer cells

growth_protocol: MDA-MB-231 cells (Procell, CL-0150, China) were and grown in DMEM medium (Cienry, CR12800, China) complemented with 10% fetal bovine serum (FBS) (ExCell Bio, FSP500, China) and 1% Penicillin-Streptomycin Solution (P/S) (Procell, PB180120, China) at a 37 °C constant-temperature incubator with 5% CO2.

extract_protocol:
The total RNA of each group was isolated by RNAiso Plus, separately.
1. Total RNA extraction. 2. Perform first strand cDNA synthesis. 2.Proceed immediately to second strand cDNA synthesis. 3. Purifiy double-stranded cDNA using DNA clean beads. 4. End prep of cDNA library. 5. Adaptor ligation. 6. Purifiy the Adaptor Ligated DNA Using Beads. 7. PCR Enrichment of Adaptor Ligated DNA. 8. Purification of the PCR reaction using beads.

treatment_protocol: MDA-MB-231 cells were treated with 2.5 µM compounds (SAHA, 1 or a6) or DMSO for 48 h.

value: triple-negative breast cancer cells

value: treated with a6 for 48 hours


title: Cell line nucleus species mixing experiment (Mixed_nuclei_0830_D200)

city: Houston

first: Chenghang

last: Zong

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Base-calling was performed with the standard Illumina NextSeq500 procedure.
The 3’ polyA tail of cDNA on Read 1 was trimmed with cutadapt v3.1, the Read 2 covering cell barcode sequences was assigned to a pre-defined barcode list.
Reads with successfully assigned cell barcodes were extracted with umi_tools extract (v1.0.1). Extracted Read 1 was mapped to the hg19 genome (or a combined genome of hg19 and mm10) with STAR v2.5.3a, and the uniquely mapped reads with mapping q score no smaller than 250 was used for downstream analysis.
The filtered reads were assigned to genes by featureCounts  v2.0.1 with appropriate Gencode annotation gtf files. (stradness parameter: -s 2)
For the reads with unambiguously assigned gene features, umi_tools “count” command was used to generate the transcript-based or exon-based digital gene expression matrix (parameter: --per-gene --gene-tag=XT --per-cell –method=directional).
Nuclei with mitochondrial UMI fraction higher than 5% were removed. Synapses with mitochondrial UMI fraction smaller than 5% were removed. Next, genes on chrMT and rRNA genes (based on Ensembl annotation) were removed from downstream analysis.
Assembly: hg19 and mm10
Supplementary files format and content: tab-delimited files include the transcript-based, intron-based, and exon-based UMI count matrix for each sample.

organism:
Homo sapiens
Mus musculus

source_name: HEK293T cell line and NIH/3T3 cell line

extract_protocol:
The frozen brain tissues were homogenized by Dounce Homogenizer, and the homogenate was fixed by incubating with 3% PFA at room temperature for 10 min. Hoechst-postive single nuclei and Hoechst-negative single synapses were sorted out by FANS.
Total-RNA based transcriptome library was generated with MATQ-Drop chemistry.

value: HEK293T cell line and NIH/3T3 cell line


title: 18mo mouse bulk retina, IOP, day2, ATAC-Seq, replicate 2

value: unilateral IOP (constant 30mmHg IOP for 1 hour)

value: day 2 from IOP


title: 3mo mouse bulk retina, IOP, day2, ATAC-Seq, replicate 3


title: 3mo mouse bulk retina, IOP, day2, ATAC-Seq, replicate 2


title: MDA-MB-231 1 biorep3

address: 中国广州大学城外环东路132号

value: treated with 1 for 48 hours


title: 3mo mouse bulk retina, IOP, day2, ATAC-Seq, replicate 1


title: MDA-MB-231 a6 biorep1

address: 中国广州大学城外环东路132号


title: 3mo mouse bulk retina, contralateral control, day2, ATAC-Seq, replicate 3


title: MDA-MB-231 1 biorep1

address: 中国广州大学城外环东路132号


title: Hbo1 null proliferating, rep4

description:
null.Prolif_4
Hbo1 null proliferating NSPCs

value: Kat7 deleted

value: Hbo1 null


title: Control m6A-exo-seq rep1 Input

value: lung

value: lung cancer cell

value: Control


title: MDA-MB-231 SAHA biorep3

address: 中国广州大学城外环东路132号

value: treated with SAHA for 48 hours


title: WT2


title: MDA-MB-231 a6 biorep3

address: 中国广州大学城外环东路132号


title: Hbo1 null proliferating, rep3

description:
null.Prolif_3
Hbo1 null proliferating NSPCs

value: Neural stem and progenitor cells (NSPCs)


title: MDA-MB-231 SAHA biorep2

address: 中国广州大学城外环东路132号


title: Hbo1 null proliferating, rep1

description:
null.Prolif_1
Hbo1 null proliferating NSPCs


title: MDA-MB-231 SAHA biorep1

address: 中国广州大学城外环东路132号


title: Hbo1 intact proliferating, rep2

description:
intact.Prolif_2
Hbo1 intact proliferating NSPCs


title: MDA-MB-231 Ctrl biorep3

address: 中国广州大学城外环东路132号

value: DMSO


title: 778_syn_5

description:
Synaptosome isolated by sucrose density gradientultra-centrifugation
Combined_778syn_transcript_counts_rRNA_MT_filtered.tsv

data_processing:
Base-calling was performed with the standard Illumina NextSeq500 procedure.
The 3’ polyA tail of cDNA on Read 1 was trimmed with cutadapt v3.1, the Read 2 covering cell barcode sequences was assigned to a pre-defined barcode list.
Reads with successfully assigned cell barcodes were extracted with umi_tools extract (v1.0.1). Extracted Read 1 was mapped to the mm10 genome with STAR v2.5.3a, and the uniquely mapped reads with mapping q score no smaller than 250 was used for downstream analysis.
The filtered reads were assigned to genes by featureCounts  v2.0.1 with appropriate Gencode annotation gtf files. (stradness parameter: -s 2)
For the reads with unambiguously assigned gene features, umi_tools “count” command was used to generate the transcript-based or exon-based digital gene expression matrix (parameter: --per-gene --gene-tag=XT --per-cell –method=directional).
Nuclei with mitochondrial UMI fraction higher than 5% were removed. Synapses with mitochondrial UMI fraction smaller than 5% were removed. Next, genes on chrMT and rRNA genes (based on Ensembl annotation) were removed from downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited files include the transcript-based, intron-based, and exon-based UMI count matrix for each sample.

value: WT

tag: gender

value: Male

value: hippocampus


title: MDA-MB-231 Ctrl biorep2

address: 中国广州大学城外环东路132号

value: triple-negative breast cancer cells


title: 3mo mouse bulk retina, recurring IOP, day2 from the 4th IOP, H3K27ac ChIP-Seq, replicate 3

data_processing:
All clean-reads were mapped to Mus musculus reference genome mm10 by STAR v2.7.8a. Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
The enriched chromatin regions or significant reads coverage (FDR q-value ≤ 0.05) of ChIP-Seq data were identified by peak calling using MACS2 (Model-based Analysis for ChIP-Seq, version 2.2.7.1) and annotated by annotatePeaks.pl. Bedgraph or BigWig files for genome browser viewing were generated by HOMER tools.
The genome-wide H3K27ac enrichment in retina samples between control and reccurent IOP were compared by using differential analysis tool edgeR in the count matrix built from the consensus list of detected H3K27ac enriched regions from all samples (excluded blacklist regions using bedtools2/2.29.2) with significance cutoff at 0.05 in FDR q-value.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
Fresh retina tissue of each mouse eye was homogenized with 22Gx1’ BD Precision-glide syringe-needle and crosslinked by 1%(w/v) methanol-free formaldehyde (Cat no.28906, Thermo Scientific) in crosslinking buffer (10mM HEPES-NaOH pH7.5, 100mM NaCl, 1mM EDTA, 1mM EGTA) for 10min slow rotation at room temperature. Crosslinks were quenched by glycine with 125mM final concentration. Tissue samples were lysed into chromatin with buffer 1 (0.25% Triton X-100, 0.5% NP40, 10% glycerol in crosslinking buffer). 10mM sodium butyrate was added for deacetylation inhibition.Lysed tissue were pelleted and washed once with buffer 2 (200mM NaCl in 10mM. Tris-HCl pH 8.0). Chromatin samples were sonicated (Pico Bioruptor, Diagenode) in polystyrene tubes on low power with 8 cycles of 30 sec ‘‘on’’, 45 sec ‘‘off’’ in buffer 3 (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine) and further cleared from debris by 16,000g centrifuge. Anti-Histone H3 acetyl K27 antibody (Cat no. ab4729, Abcam) was coupled with protein A Dynabeads (Life Technologies) in blocking buffer (0.1% BSA, 1% Triton X-100) before 16 hours incubation with beads precleared chromatin at 4℃. Dynabeads with antibody enriched chromatin were washed twice with low salt wash buffer (150mM NaCl, 2mM EDTA, 0.1%SDS, 1%Triton X-100 in 20mM Tris-HCl pH 8.0) and twice with lithium chloride wash buffer (1mM EDTA, 0.5% Sodium Deoxycholate, 0.25 M LiCl, 1% NP40 in 10 mM Tris-HCl pH 8.0). Beads were finally incubated at 65℃ in TE with 1% SDS at 65℃ for 16 hr with shaking for decrosslinking of the enriched chromatin. Chromatin DNA was isolated using Qiagen PCR Purification Kit (Cat.#.28304, Qiagen) and elute in 20 uL Elution Buffer.
The eluted DNA fragments were then amplified by PCR with Nextera compatible indexed sequencing i5 and i7 adapters using NEBNext 2x PCR Master Mix PCR kit (M0541, NEB). The amplified DNA library was fragment size selected from 200bp to 800bp using Ampure XP beads (A63880, Beckman Coulter). The quality of the ChIP-Seq libraries was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Inc.). ChIP-Seq libraries was pooled and run on Illumina NovaSeq 6000 System (Flow Cell Type S4) sequencer with a paired-end read of 100 bp to harvest about 50 million paired-end reads per sample.

value: bulk retina

tag: genotype

value: unilateral IOP (constant 30mmHg IOP for 1 hour, biweekly treatment, 4 times in total)

value: 3-month-old (at the 1st IOP)

value: day2 from the 4th IOP

value: anti-Histone H3 acetyl K27 antibody (Cat no. ab4729, Abcam)


title: 3mo mouse bulk retina, recurring IOP, day2 from the 4th IOP, H3K27ac ChIP-Seq, replicate 2


title: 3mo mouse bulk retina, recurring IOP, day2 from the 4th IOP, H3K27ac ChIP-Seq, replicate 1


title: Hbo1 intact proliferating, rep1

description:
intact.Prolif_1
Hbo1 intact proliferating NSPCs

value: Proliferating

value: Kat7 intact

value: Hbo1 Cre control


title: 778_syn_4


title: 778_syn_3


title: 778_syn_2


title: 3mo mouse bulk retina, contralateral control, day2, ATAC-Seq, replicate 1

value: unilateral untreated control

value: day 2 from IOP


title: MDA-MB-231 Ctrl biorep1

address: 中国广州大学城外环东路132号


title: 3mo mouse bulk retina, contralateral control to recurring IOP, day2 from the 4th IOP, H3K27ac ChIP-Seq, replicate 2


title: MDA-MB-231 1 biorep2

address: 中国广州大学城外环东路132号

value: treated with 1 for 48 hours


title: 3mo mouse bulk retina, contralateral control to recurring IOP, day2 from the 4th IOP, H3K27ac ChIP-Seq, replicate 1


title: OP35-normal

city: Rehovot

first: Itay

last: Tirosh

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
Base calling and bcl2fastq through Illumina BaseSpace sequence hub
Alignment to human and HPV genomes, followed by UMI quantification using cellranger v4.0
For each sample, cells with fewer than 1000 detected genes were removed as low-quality. Doublets were identified by combining the results of three alternative methods that were published recently and implemented in R packages – scdDblFinder (https://github.com/plger/scDblFinder), the hybrid score from scds (Bais and Kostka, 2020) and the doubletCells algorithm from scran (Lun et al., 2016). For each method, we set the expected doublet rate at 0.6%, per 500 cells per sample. Cells classified as doublets by at least two methods, totaling 2,744 of all 73,714 cells (3.7%), were removed as probable doublets.
Genome_build: hg38; human papillomavirus type 16 (NC_001526)
Supplementary_files_format_and_content: mtx file with raw UMI counts for every gene and cell. Does not have row or column names, these are found in the additional txt files
Supplementary_files_format_and_content: txt file with gene names
Supplementary_files_format_and_content: txt file with cell barcodes and sample names. The sample name is separated from the barcode by an underscore

source_name: Oropharynx

extract_protocol:
Fresh samples were minced, washed with PBS, and dissociated using a Human Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) per manufacturer guidelines. Red blood cell lysis was performed with ACK lysis buffer per manufacturer protocol (Thermo Fisher Scientific), followed by dead cell removal using a dead cell removal kit to improve the viability if needed (Miltenyi Biotec, Bergisch Gladbach, Germany). Viability was confirmed to be >80% in all samples based on trypan blue analysis (ThermoFisher Scientific). Cell suspensions were filtered using a 40 μm filter (ThermoFisher Scientific) and dissociated cells were pelleted and re-suspended in AutoMACS Rinsing Solution with 0.5% bovine serum albumin (BSA; Miltenyi Biotech). The single-cell suspension was sorted using human CD45 magnetic MicroBeads (Miltenyi Biotec) to enrich for CD45+ cells. Briefly, 20μl of CD45 MicroBeads per 107 total cells was added to the cell suspension and incubated for 15 minutes at 2-8°C. After incubation, CD45+ and CD45- cells were collected after the cells passed through the magnetic column. The CD45+ and CD45- cell pellets were then obtained after centrifuging at 450g for 5 minutes at 4°C.
Samples were processed using the Chromium Single Cell 3′ (v2 Chemistry), and in two cases 5’, platform with the target of ∼10,000 cells (10x Genomics, Pleasanton, CA) following manufacturer's instructions. Briefly, cells were added onto a chip to form Gel Bead-in-Emulsion (GEMs) in the Chromium instrument followed by cell lysis, barcoding, fragmentation, adaptor ligation and addition of sample index to the libraries before sequencing.

value: adjacent normal tissue

tag: hpv status

value: HPV+

tag: sequencing


title: Hbo1 null proliferating, rep2

description:
null.Prolif_2
Hbo1 null proliferating NSPCs

value: Neural stem and progenitor cells (NSPCs)

value: Kat7 deleted

value: Hbo1 null


title: 514_syn_5

value: WT

value: Female

value: hippocampus


title: 778_syn_1

value: Male


title: OP35-LN

value: metastatic lymph node


title: 3mo mouse bulk retina, contralateral control, day2, ATAC-Seq, replicate 2

value: bulk retina


title: OP35-tumor

value: tumor


title: 3mo mouse bulk retina, recurring IOP, day2 from the 4th IOP, polyA RNA-Seq, replicate 2

description:
FPKM_CTLvs4IOP.txt
Column name in processed data: IOP_2/

data_processing:
All clean-reads were mapped to Mus musculus reference genome mm10 by STAR v2.7.8a. Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification. The uniquely mapped tags in exons on minus strand (one isoform per locus) were quantified by analyzeRepeats.pl. Raw reads count was normalized to experiment totals and performed differential expression by DESeq v1.24.0 program.
For mRNA quantification, mm10 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
Differentially regulated RNA expression features were found via the homer tool - getDiffExpression.pl with the differential Expression Calculation program DESeq2. The significance cutoffs were log2fold>1, FDR<0.05 for up-regulated genes and log2fold<-1, FDR<0.05 for down-regulated genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Fresh bulk mouse retina tissue were collected and homogenized thoroughly in TRIzol Reagent (15596026, Invitrogen) followed by RNA isolation. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The poly-adenylated (poly-A) transcripts from the isolated total RNA sample were enriched and performed strand specific mRNA-Seq TruSeq libraries preparation for sequencing using standard Illumina protocols

treatment_protocol: Each mouse underwent unilateral hydrostatic pressure-induced IOP elevation to 30 mmHg, with the contralateral eye left as an untreated control. To ensure a sterile environment, compounds were prepared under the tissue culture hood using sterile PBS. The final solution was filtered through a 0.22-μm PES membrane just before injection. Tips, tubes, and syringes were sterile.

value: unilateral IOP (constant 30mmHg IOP for 1 hour, biweekly treatment, 4 times in total)

value: 3-month-old (at the 1st IOP)

value: day2 from the 4th IOP


title: 514_syn_4


title: 3mo mouse bulk retina, recurring IOP, day2 from the 4th IOP, polyA RNA-Seq, replicate 1

description:
FPKM_CTLvs4IOP.txt
Column name in processed data: IOP_1/


title: OP34-normal


title: 514_syn_3


title: 3mo mouse bulk retina, contralateral control to recurring IOP, day2 from the 4th IOP, H3K27ac ChIP-Seq, replicate 3

value: unilateral untreated control

value: anti-Histone H3 acetyl K27 antibody (Cat no. ab4729, Abcam)


title: OP34-tumor


title: 3mo mouse bulk retina, contralateral control to recurring IOP, day2 from the 4th IOP, polyA RNA-Seq, replicate 1

description:
FPKM_CTLvs4IOP.txt
Column name in processed data: CTL_1/


title: 3mo mouse bulk retina, contralateral control to recurring IOP, day2 from the 4th IOP, polyA RNA-Seq, replicate 2

description:
FPKM_CTLvs4IOP.txt
Column name in processed data: CTL_2/


title: OP33-normal

value: adjacent normal tissue


title: OP33-tumor

value: HPV+


title: T cells, HTO

city: Marseille

first: Rudy

last: AUSSEL

address: Parc Scientifique et Technologique de Luminy

country: France

institute: CIML

description: T cells, HTO

library_source: other

data_processing:
FASTQ raw files were processed using Cell Ranger software (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads   were aligned to the mouse mm10 genome.
Quality control (QC) was performed to remove poor quality cells thanks to in-house developed R scripts using Seurat v3 R package.
Expression data were normalized using the Seurat R package NormalizeData function (using logNormalize method and scale factor of 10000).
Expression data were centered and regressed from the number of UMI factor using the Seurat R package ScaleData function (centering true and scaling false).
Assembly: mm10
Supplementary files format and content: tsv and mtx files containing cell barcodes, features and count matrix for mRNA, HTO and ADT libraries, csv files containing expression matrix.

molecule: protein

source_name: Spleen

extract_protocol:
Lymphoid cells were extracted from spleens of WT, LatY136F, LatY136F x Stat6KO or LatY136F x Grap2KO mice. We isolate T cells using the EasySep Mouse T Cells Isolation Kit (StemCell). Each T cell sample was then labeled with a specific Hashtag (TotalSeq™ anti-mouse Hashtag antibody #A0301-A0310, Biolegend), a mix of 7 calibrated TotalSeq™-A anti-mouse specific antibodies (CD27, CD25, CD73, CD39, TCRb, PD-1, CD103) and a cocktail of 7 fluorescent-labeled anti-mouse antibodies (CD11b, IA/IEI, CD4, CD5, CD6, CD8a, CD90.2) plus a viability dye (Dapi) . Cells were then sorted as live singlets, CD11b– IA/IE–CD90.2+ CD6+, CD5 +. After sorting, cells were washed in PBS - 0.04% BSA as recommended in “10xGenomics sample preparation protocol” and kept on ice. Sorting of the 10 samples was performed in 3 days at 2-4 samples per day.
In order to eliminate duplicates and improve cell recovery, we pooled cells sorted from 2 time points. The cells were resuspended, counted and divided into 2 wells for GEMs production. We introduced 12,000 cells per well with the expectation of obtaining 5,000 to 6,000 cells in the GEMs. Single-cell RNA-Seq libraries, HTO libraries and ADT libraries were generated using the Chromium Single Cell 3′ V3 kit (10X Genomics) according to the manufacturer instructions.

value: T cells

tag: library type

value: ADT


title: T cells, ADT

description: T cells, ADT

value: HTO


title: OP20


title: T cells, mRNA

description: T cells

value: mRNA


title: OP17


title: 514_syn_2

value: WT

value: Female


title: 514_syn_1

value: hippocampus


title: 480_syn_2


title: OP19

value: HPV-


title: 480_syn_1


title: OP14-CD45-


title: 480_syn_5


title: OP16


title: 418_syn_6


title: OP14-CD45+


title: OP13


title: 418_syn_4


title: OP12


title: 418_syn_3


title: 418_syn_2


title: OP9-CD45-


title: 418_syn_1


title: 480_syn_4


title: XY8

first: Xiaojing

last: Yang

address: 9500 Gilman Drive, La Jolla

department: Pharmacology

data_processing:
Base calling was performed using bcl2fastq (v2.20; Illumina).
STAR (v2.7.9a) was used to align the RNA sequencing reads to the mouse genome (mm10) and to generate gene-level read counts from uniquely aligned reads.
Differentially expressed genes were calculated with DESeq2 (1.34.0).
Assembly: mm10
Supplementary files format and content: One excel file containing results from all samples.

source_name: Small intestine

extract_protocol:
Total RNA was extracted from approximately 100 mg of tissue samples using 1 mL TRIzol reagent (Thermo Fisher Scientific).
The sequencing library was prepared using the Illumina Stranded mRNA Sample Prep Kit (20040534; Illumina, San Diego, CA) with 1 µg of total RNA.

value: Small intestine

tag: strain

value: hUGT1 transgenic mice

value: 2 weeks

value: Arsenic (10 mg/kg)

tag: time


title: 480_syn_3


title: XY7


title: OP9-CD45+

value: tumor


title: 417_syn_6


title: OP8


title: XY6


title: 417_syn_5


title: OP6-CD45-


title: 417_syn_4


title: 417_syn_3


title: OP6-CD45+


title: XY4

value: Vehicle


title: XY5


title: 417_syn_2


title: XY3


title: OP4-CD45-


title: XY2


title: OP5


title: OP10


title: OP4-CD45+


title: 514_nucleus_3

source_name: Nuclei


title: XY1


title: 417_syn_1


title: 514_nucleus_2


title: MM patient stage3 rep5 [MM-III-5]

city: Chengdu

first: gong

last: bo

address: 四川省成都市青羊区一环路西二段32号

institute: Sichuan Provincial People’s Hospital

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat[1] (version 3.1.1). To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we apply a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers.
Differentially expressed genes(DEGs) were identified using the FindMarkers function of Seurat package. P value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: cell barcode files; gene files; gene-barcode counts

source_name: MM patient stage3_bone marrow

extract_protocol:
Bone marrow aspirates were placed in EDTA-containing tubes. Tubes were mixed, placed on ice and immediately transported to the lab.
Single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10×Genomics) to generate single cell gel beads in emulsions (GEMs).Single-cell RNA-seq libraries were prepared with Chromium Single cell 3'Reagent v3 Kits and according to the manufacturer’s protocol.

tag: subject status

value: MM patient

value: stage 3

value: BD

value: bone marrow


title: 514_nucleus_1


title: MM patient stage3 rep4 [MM-III-4]

address: 四川省成都市青羊区一环路西二段32号

value: BTD


title: 4-HPAA subcutaneous replicate 5

city: Cleveland

first: Lucas

last: Osborn

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic Foundation

data_processing:
Basecalls performed using Illumina RTA3
Paired-end 100 bp reads were controlled for quality with FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina adapters were trimmed from the 3’ ends using cutadapt  (Martin, 2011). STAR was used to align trimmed reads to the Mus musculus genome (NCBI GRCm38.93)  (Dobin et al., 2013). Read counts for each gene were calculated using HTseq  (Anders et al., 2015) and loaded into R (http://www.R-project.org/) (R Development Core Team, 2015) where DESeq2  (Love et al., 2014) (v.1.28.1, https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was used to perform differential expression analysis on genes with at least 1 count per sample with alpha set to 0.05. P-values were adjusted using the Benjamini-Hochberg correction procedure  (Benjamini and Hochberg, 1995) and genes with p < 0.05 were considered statistically significant.
Heatmaps were generated of the top 50 differentially expressed transcripts using pheatmap  (Kolde, 2019) and RColorBrewer  (Neuwirth, 2014). NMDS analysis was performed using the plotMDS function of edgeR  (Robinson et al., 2010) using the top 500 differentially expressed genes as sorted by adjusted P value and log2 fold change. Pathway analysis on the top 100 differentially expressed genes was performed using Metascape  (Zhou et al., 2019).
Genome_build: NCBI GRCm38.93
Supplementary_files_format_and_content: .txt file containing HTseq-assigned counts

source_name: Liver tissue

extract_protocol:
QIAGEN Rneasy
First, RNA quality was checked using a Bio-analyzer (Agilent). Then, libraries were prepared using the Illumina mRNA TruSEQ Directional library kit. Sequencing was performed using an Illumina NovaSeq 6000

treatment_protocol: Either scaffold control or 4-HPAA was administered subcutaneously for 6 weeks following induction of HFD obesity and hepatic steatosis. Liver flushed with salione and flash frozen at necropsy and subsequent RNA sequencing.

value: Liver


title: 4-HPAA subcutaneous replicate 6


title: 480_nucleus_2


title: 4-HPAA subcutaneous replicate 4


title: 480_nucleus_1


title: MM patient stage3 rep3 [MM-III-3]

address: 四川省成都市青羊区一环路西二段32号


title: 4-HPAA subcutaneous replicate 3


title: 52976_CGCTCATTCAGGACGT_rna_seq

city: Vienna

first: Rohit

middle: Anil

last: Dnyansagar

address: Althanstrasse 14 (UZA1) A-1090 Wien

department: Department of Molecular Evolution and Development

country: Austria

institute: University of Vienna

data_processing:
For RNA-seq reads were trimmed of adapter sequences ATTACTCGTATAGCCT, TCCGGAGAATAGAGGC, CGCTCATTCCTATCCT, GAGATTCCGGCTCTGA, ATTCAGAAAGGCGAAG, CTGAAGCTCAGGACGT, TAATGCGCGTACTGAC, CGGCTATGTATAGCCT,TCCGCGAAATAGAGGC, TCTCGCGCCCTATCCT, AGCGATAGGGCTCTGA, TCCGGAGATAATCTTA, CGCTCATTCAGGACGT, GAATTCGTATAGAGGC using cutadapt v1.8.1
Trimmed reads were aligned to N. vectensis genome (v1) using STAR aligner (v2.5.3a)
unaligned reads were then filtered
Transcripts per million (TPM) per transcript was calculated from reads that didn't align to RepBase were quasi-aligned to GENCODE v19 protein coding and lincRNA transcripts using Sailfish v0.6.3
Reads aligned to genomic features were counted with featureCounts (Subread v1.6.2)
The counts files generated were used as input to DESeq2 (v1.6.0)
Genes with Log2fold change of 1 and FDR corrected p-value (q-value) of 0.05 are considered as differentially expressed.
For ChIP-seq Trimmed reads were aligned to N.vectensis genome (v1) using BWA aligner using the BWA-MEM algorithm
ChIP-seq peaks were called using Peakzilla
Genome_build: https://mycocosm.jgi.doe.gov/Nemve1/Nemve1.home.html
Supplementary_files_format_and_content: tab separated values

organism: Nematostella vectensis

source_name: whole embryo

growth_protocol: Nematostella polyps were kept at 18°C and largely in the dark. Spawning was induced by a combination of light and elevated temperature. Embryos were raised at 21°C

extract_protocol: For Nematostella, we generated 6 biological replicates of each translational and splice morpholino and control. Libraries were multiplexed and sequenced on Illumina HiSeq2500 to generate 50bp SE reads.

treatment_protocol: Two non-overlapping antisense morpholinos against brachyury:  the translation-blocking morpholino BraATGMO TCGTCCGAGTGCATGTCCGACTATG, and the splice-blocking morpholino BraSpliceMO TCCCTGGTTGTCAACCATACCGTCC. 3-5 pl of both morpholinos were injected at the concentration of 500 µM. 50 µg/ml

tag: cell type

value: Embryo cells

tag: developmental stage

value: gastrula

tag: morpholino

value: translation  morpholino

tag: sample type

value: Bulk RNA-seq


title: 52980_GAATTCGTATAGAGGC_rna_seq

value: control  morpholino


title: MM patient stage3 rep2 [MM-III-2]

address: 四川省成都市青羊区一环路西二段32号

tag: age


title: 418_nucleus_3

value: Female

value: hippocampus


title: 4-HPAA subcutaneous replicate 2


title: 52975_TCCGGAGATAATCTTA_rna_seq


title: 418_nucleus_2


title: MM patient stage3 rep1 [MM-III-1]

address: 四川省成都市青羊区一环路西二段32号

tag: Stage

value: BCD


title: 4-HPAA subcutaneous replicate 1

tag: tissue


title: 418_nucleus_1


title: MM patient stage2 rep1 [MM-II-1]

address: 四川省成都市青羊区一环路西二段32号

source_name: MM patient stage2_bone marrow

value: stage 2


title: MM patient stage2 rep2 [MM-II-2]

address: 四川省成都市青羊区一环路西二段32号

value: PBD


title: 52973_AGCGATAGGGCTCTGA_rna_seq


title: MM patient stage1 rep2 [MM-I-2]

address: 四川省成都市青羊区一环路西二段32号

source_name: MM patient stage1_bone marrow

value: stage 1


title: 52972_TCTCGCGCCCTATCCT_rna_seq

value: splice  morpholino


title: Control replicate 6

value: Scaffold Control


title: Control replicate 5


title: 52971_TCCGCGAAATAGAGGC_rna_seq


title: 417_nucleus_4

value: WT


title: Control replicate 4


title: 417_nucleus_5


title: 52970_CGGCTATGTATAGCCT_rna_seq


title: normal control rep2 [CON2]

address: 四川省成都市青羊区一环路西二段32号

source_name: normal control_bone marrow

value: normal control

value: wild type

value: bone marrow


title: 417_nucleus_3


title: MM patient stage1 rep1 [MM-I-1]

address: 四川省成都市青羊区一环路西二段32号

value: MM patient

value: RBD


title: 52969_TAATGCGCGTACTGAC_rna_seq

value: Embryo cells

value: gastrula


title: Control replicate 3

value: Liver


title: 417_nucleus_2

value: Female


title: normal control rep1 [CON1]

address: 四川省成都市青羊区一环路西二段32号


title: 52968_CTGAAGCTCAGGACGT_rna_seq

value: traanslation  morpholino

value: Bulk RNA-seq


title: Control replicate 1


title: 417_nucleus_1

value: hippocampus


title: 52966_ATTCAGAAAGGCGAAG_rna_seq


title: WT6

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

description: 3 larynxes were collected in 150ul of Trizol and prepped for RNA and Dnase treated. 310ng total RNA; 155ng RNA taken into cDNA prep; RIN number of 9

data_processing:
Base calling was done using Illumina bcl2fasq version 1.37.0
Sequenced reads were mapped to mouse reference genome mm10 usinng HISAT2 v2.1.0.
Transcripts per million (TPM) were obtained usinng StringTie v1.3.6.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

source_name: mouse larynx

extract_protocol:
3 larynxes/sample were collected in 150ul of Trizol and prepped for RNA and Dnase treated. RNA was run on a BioAnalyzer to assess quality (all samples had RIN numbers > 7.5) and 100-150ng of RNA was taken into cDNA prep.
Libraries were enriched for PolyA by magnetic isolation and libraries were amplified for 10 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.  NEBNext Ultra II Directional RNA Library Prep Kit

value: Swiss Webster WT

value: 3-pooled larynx tissues (~60K cells)


title: 52965_GAGATTCCGGCTCTGA_rna_seq

value: translation  morpholino


title: WT4

description: 3 larynxes were collected in 150ul of Trizol and prepped for RNA and Dnase treated. 210ng total RNA; 110ng RNA taken in cDNA prep; RIN number of 7.7


title: TA_2

city: beijing

first: liang

middle: sheng

last: xian

address: shuangqing road

institute: chinese academy of science

data_processing:
Reads were filtered and then mapped to the reference genome sequence (GRCh38.p13) with HISAT
Sequences were aligned to reference genes with Bowtie2 tool
The gene expression level was determined by the RSEM software
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Txt files include FPKM values for each Sample

source_name: Hepatoblasts

growth_protocol: Undifferentiated H9 cells were maintained on vitronectin-coated tissue culture dishes in mTeSR1 medium.A previously reported hepatocyte-like cell differentiation protocol was performed to induce H9 cells into hepatocyte cells (Mathapati, et al., 2016)

extract_protocol:
Total RNA was extracted with the Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.1% DMSO as control, or10 μnM HFPO-TA.

value: day 19

value: liver

tag: derived cell line


title: 52964_CGCTCATTCCTATCCT_rna_seq

value: control  morpholino


title: TA_3


title: TA_1


title: Ctrl_3 (HFPO-TA control)


title: 52963_TCCGGAGAATAGAGGC_rna_seq

value: splice  morpholino


title: Shh2

description: 3 larynxes were collected in 150ul of Trizol and prepped for RNA and Dnase treated. 200ng total RNA; 100ng RNA taken into cDNA prep; RIN number of 7.7

value: Shhtm1amc Shh+/-


title: Ctrl_2 (HFPO-TA control)


title: Shh1

description: 3 larynxes were collected in 150ul of Trizol, and prepped for RNA and Dnase treated. 260ng total RNA; 130ng RNA taken into cDNA prep; RIN number of 8


title: Control replicate 2

tag: treatment

value: Scaffold Control


title: Ctrl_1 (HFPO-TA control)


title: 52962_ATTACTCGTATAGCCT_rna_seq

value: translation morpholino


title: IAV-GIL CD8 TCM_D0_2

type: RNA

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

description:
Biological replicate 2 of 2.  IAV-specific CD8 TCM cells
IAV_rep2

hyb_protocol: 750 ng of labeled sample probes mixed with equal amount of universal reference probes in 500 µl of hybridization solution onto Agilent SurePrint G3 Human Gene Expression 8x60 K microarrays chip (Agilent) at 60 °C for 17 hours according to manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2600D scanner

data_processing:
Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and LOWESS normalization. The data were further processed with ExAtlas. See https://lgsun.irp.nia.nih.gov/exatlas/ for details
Normalized as sum of log10 (Cy3/Cy5) and average of log10(cy5) over all  arrays

source_name: IAV-specific CD8 TCM cells

label_protocol: 400 ng of total RNA was used for cRNA synthesis using LowInput QuickAmp labeling kit (Agilent).

growth_protocol: Antigen-specific cells were sorted

extract_protocol: Total RNA extracted using RNeasy Mini kit (Qiagen) following manufacturer's instructions

tag: cell line

value: IAV-specific CD8 TCM cells

value: day 0

tag: antigen

value: IAV

source_name: Universal Human reference RNA

value: Reference RNA


title: IAV-GIL CD8 TCM_D0_1

description:
Biological replicate 1 of 2.  IAV-specific CD8 TCM cells
IAV_rep1


title: CMV-NLV CD8 TCM_D0_1

description:
Biological replicate 1 of 2. CMV-specific CD8 TCM cells
CMV_rep1

source_name: CMV-specific CD8 TCM cells

value: CMV-specific CD8 TCM cells

value: CMV


title: CMV-NLV CD8 TCM_D0_2

description:
Biological replicate 2 of 2. CMV-specific CD8 TCM cells
CMV_rep2


title: 23_Stroma

status: Public on Nov 29 2022

type: protein

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

institute: University of Queensland

hyb_protocol: DSP eluates were hybridised as per manufacturers instructions in nCounter Readout User Manual.

scan_protocol: Hybridised samples were loaded into Nanostring prep station and processed as per DSP Slide Prep User Manual. N counter was performed with default parameters, and counts from Ncounter uploaded back to DSP instrument

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

source_name: TNBC

label_protocol: DSP experiments were performed as per manufacturers DSP Slide Prep User Manual instructions. Slides were deparafinised, antigen retrieval by HIER, and overnight staining with antibody cocktail as per DSP Slide Prep User Manual. Slides were images and samples collected on DSP instrument

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: disease state

value: TNBC

tag: roi name

tag: segment name

value: Stroma

tag: surface area

tag: nuclei count

tag: qc flags

tag: patient

tag: grade

tag: t

tag: n

tag: mets post surgery (months)

tag: followup

tag: status

tag: reponse

value: CR

tag: metastasis


title: 24_Tumour

value: Tumour

tag: age


title: 24_Stroma


title: 23_Tumour


title: 22_Tumour


title: 21_Tumour


title: 20_Tumour


title: 21_Stroma


title: 17_Tumour

value: PD

value: liver, lung, skin


title: 20_Stroma


title: 22_Stroma


title: 25_Stroma

value: liver, lung


title: 19_Tumour


title: 19_Stroma


title: 16_Stroma


title: 14_Tumour


title: 25_Tumour


title: 15_Tumour


title: 17_Stroma


title: 15_Stroma


title: 14_Stroma


title: 11_Stroma


title: 11_Tumour


title: 10_Stroma

value: liver, lung, bone


title: 418_syn_5

tag: genotype

tag: gender

value: Female

tag: tissue

value: hippocampus


title: 13_Stroma

tag: disease state

tag: roi name

tag: segment name


title: 8_Stroma

tag: surface area

tag: nuclei count

tag: qc flags


title: 9_Tumour

tag: patient

tag: grade

tag: t

value: liver, lung, brain, bone


title: 2_Tumour

tag: n

tag: mets post surgery (months)

tag: followup


title: 18_Tumour

value: Low Surface Area,Low Nuclei Count

tag: status

tag: reponse

tag: metastasis


title: 1_Stroma

tag: age


title: 8_Tumour


title: 2_Stroma


title: 13_Tumour


title: 10_Tumour


title: 12_Stroma


title: 16_Tumour


title: 12_Tumour


title: 18_Stroma


title: 3_Tumour


title: Adult_Sperm_Bulk_WGBS

city: Dunedin

first: Donna

last: Bond

address: 270 Great King Street

department: Department of Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Raw reads were trimmed using Trim Galore! (v0.4.2) by removing 10 bp from the 5’ end of all reads and removing low-quality base calls (Phred score < 20). Bismark (v0.19.0), with the -pbat option, was used to map the trimmed reads to the possum genome reference (GCA_011100635), deduplicate and extract methylation calls in the CG dinucleotide context.
Assembly: Trichosurus vulpecula (GCA_011100635.1)
Supplementary files format and content: tab-delimited text file that includes Bismark mapping report for each sample

organism: Trichosurus vulpecula

source_name: Sperm

extract_protocol:
Sperm were isolated from the epididymis of an adult possum by allowing sperm to diffuse out into warm PBS (37 °C) for 1 hour. Plasma was removed twice with PBS using centrifugation at 1,500 rpm for 2 min. The resulting pellet was resuspended in PBS and passed through a 20 µm cell strainer and stored in PBS at -80 °C. DNA was extracted fromsperm using a Bio-On-Magnetic-Beads (BOMB) protocol that utilises solid-phase reversible immobilization (SPRI) carboxyl-coated magnetic beads to isolate DNA (Oberacker et al., 2019; PMID: 30629605), with the addtion of 10% v/v ß-mercaptoethanol added to the cell lysate as a reducing agent (Fujikura et al 2017; PMID: 31453223)
Bisulfite-converted genomic libraries from sperm DNA were prepared using a modified PBAT method outlined by Ortega-Recalde et al., 2021 (PMID:34009607)

tag: Sex

value: Male

tag: cell type

value: Sperm

tag: developmental stage

value: Adult

tag: treatment

tag: number of_cells


title: 090421_PY02_Somatic_WGBS

source_name: Somatic

extract_protocol:
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. GFP-negative cells (somatic cells) were sorted as negative controls into 0.2 % Triton-X and stored at -80 °C.
Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)

value: Somatic

value: 13 days postpartum

value: GFP (SSEA1) negative


title: 9_Stroma

tag: disease state

value: TNBC

tag: roi name

tag: segment name

value: Stroma

tag: surface area

tag: nuclei count


title: 7_Stroma

tag: qc flags

tag: patient

tag: grade

tag: t

tag: n


title: 3_Stroma

tag: mets post surgery (months)

tag: followup

tag: status

tag: reponse

value: CR

tag: metastasis


title: 1_Tumour

value: Tumour

tag: age


title: 6_Stroma


title: 5_Tumour

value: PD


title: 5_Stroma

value: liver, lung


title: 7_Tumour


title: 6_Tumour


title: 4_Stroma


title: 4_Tumour


title: 250521_PY01_liver

data_processing:
Raw reads were trimmed using Trim Galore! (v0.6.7) to remove adapters and low-quality base calls (Phred score < 20)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed reads were mapped to the possum reference genome (GCA_011100635.1) using HISAT2 (v2.2.1) with standard parameters
Read count extraction and normalization was performed using SeqMonk v1.48.0 (RNAseq quantitation pipeline)
Assembly: Trichosurus vulpecula (GCA_011100635.1)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
250 ng of DNase-treated RNA was used to construct poly(A) enriched, strand-specific RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Poly(A) mRNA Magnetic Isolation Module (¼ of the standard reaction volume) (NEB)
Total RNA was extracted from tissue samples (~50 mg) stored in RNAlater using TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines. RNA samples were treated to remove any contaminating DNA using the Turbo DNA-free kit (Invitrogen) according to the protocol.

tag: tissue

value: Liver

tag: developmental stage

value: Pouch young - 15 dpp

tag: Sex

tag: coat colour

tag: mother

tag: location

value: Pig Farm

tag: longtitude

tag: latitude


title: 250621_PY01_kidney

source_name: Kidney

value: Kidney

value: Pouch young - 46 dpp

value: Female

value: South Dale Rd


title: 090421_PY02_PGC_WGBS

source_name: PGC

extract_protocol:
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. Germ cells were identified as a small subpopulation that were very bright (GFP >10^4) with higher SSC (approx. 0.1 % of total cells). This population was gated conservatively, sorted into 0.2 % Triton-X and stored at -80 °C.
Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)

value: Male

tag: cell type

value: PGC

tag: treatment

value: GFP (SSEA1) sorted

tag: number of_cells


title: 250621_PY02_kidney

value: Pouch young - 62 dpp


title: 250621_PY02_brain

source_name: Brain

value: Brain


title: 090621_PY01_kidney

value: Pouch young - 85 dpp

value: Judy

value: Colony (Mother from Corstorphine)


title: 180621_PY01_liver

value: Pouch young - 72 dpp


title: 270521_PY01_liver

value: Pouch young - 10 dpp

value: Judith

value: Colony (Mother from South Dale Road)


title: 090621_PY01_liver

value: Liver


title: 250621_PY01_brain


title: 180621_PY01_kidney

value: Pig Farm


title: 270521_PY01_kidney

value: Kidney


title: 210521_PY01_brain

value: Pouch young - 41 dpp


title: 190521_PY04_kidney

value: Pouch young - 42 dpp

value: Coal place


title: 190521_PY03_brain

value: Pouch young - 17 dpp

value: Female


title: 190521_PY02_kidney

value: Pouch young - 14 dpp

value: Tilde


title: 270521_PY01_brain

value: Brain


title: 190521_PY02_brain


title: 140421_PY02_PGC_WGBS

value: Male

value: PGC

value: 16 days postpartum

value: GFP (SSEA1) sorted


title: 140421_PY02_Somatic_WGBS

value: Somatic

value: GFP (SSEA1) negative


title: 210721_PY02_liver

value: Liver

value: Pouch young - 104 dpp

value: Waverley


title: 120621_Becks_liver

value: Adult

value: Grey

value: Becks


title: 250521_PY01_kidney

value: Kidney

value: Pouch young - 15 dpp

value: Pig Farm


title: 210521_PY01_kidney

value: Pouch young - 41 dpp


title: 190521_PY02_liver

value: Pouch young - 14 dpp

value: Female

value: Tilde

value: Colony (Mother from South Dale Road)


title: 190521_PY01_liver

value: Pouch young - 9 dpp

value: Male

value: Raven

value: Colony (Mother from Ravensbourne)


title: 190521_PY04_liver

value: Liver

value: Pouch young - 42 dpp

value: Coal place


title: 250521_PY01_brain

value: Brain


title: 190521_PY03_liver

value: Pouch young - 17 dpp


title: 210521_PY01_liver


title: 210721_PY01_liver

value: Pouch young - 109 dpp

value: Waverley


title: 020721_PY01_liver

value: Pouch young - 64 dpp

value: South Dale Rd


title: 020721_PY02_liver

value: Pouch young - 76 dpp


title: 080721_PY01_liver

value: Female


title: 110721_MR_Cors_liver

value: Adult

value: Red

value: Corstorphine


title: 020721_PY03_liver

value: Pouch young - 99 dpp

value: Pig Farm


title: 300621_PY01_liver

value: Pouch young - 19 dpp

value: Male


title: 110721_M_Rav_liver

value: Liver

value: Grey

value: Ravensbourne


title: 240621_PY01_liver

value: Pouch young - 91 dpp

value: Brockville


title: 090621_MG_Cors_liver


title: 250521_MG_PF1_liver


title: 200521_MR_PF2_liver


title: 090621_MG_PF1_liver


title: 180521_MG_PF3_liver


title: 140421_MG_WSG1_liver

value: Woodside Glen


title: 180521_FG_PF2_liver


title: 040521_MB_SDR1_liver

value: Black


title: 050521_PY02_liver

value: Pouch young - 7 dpp

value: Mabel

value: Colony (Mother from Woodside Glen)


title: 070521_PY01_liver

value: Pouch young - 27 dpp

value: South Dale Rd


title: 140421_PY02_liver

value: Pouch young - 12 dpp

value: Tilde

value: Colony (Mother from South Dale Road)


title: 090421_MB_SDR1_liver

value: Adult


title: 140421_PY03_liver

value: Pouch young - 20 dpp

value: Male

value: Medusa


title: 090421_PY02_liver

value: Liver

value: Pouch young - 13 dpp


title: 150121_PY01_liver

value: Pouch young - 84 dpp

value: Female


title: 121020_PY01_liver

value: Pouch young - 30 dpp

value: Woodside Glen


title: 030621_MR_PF1_liver

value: Red

value: Pig Farm


title: 090421_PY01_liver

value: Pouch young - 8 dpp


title: 290920_PY01_liver

value: Pouch young - <2 dpp


title: 220920_PY01_liver

value: Juvenile

value: Grey

value: Raven

value: Ravensbourne


title: 100920_PY01_liver

value: Pouch young - 11 dpp


title: 180820_PY01_liver

value: Pouch young - 66 dpp

value: Male

value: South Dale Rd


title: 180820_FB_SDR1_liver

value: Liver

value: Adult

value: Black


title: 120820_PY01_liver


title: 120820_FG_WSG2_liver

value: Female


title: 180521_MG_PF1_liver


title: 200421_MB_SDR1_liver


title: 120820_MG_WSG1_liver

value: Woodside Glen


title: 040820_PY01_liver

value: Boulder Beach


title: 110820_FG_WSG1_liver


title: 280720_PY01_liver


title: 100720_MG_SDR2_liver


title: 040820_FG_BB1_liver


title: 280720_FG_SDR1_liver


title: 210720_MG_WSG1_liver


title: 180320_MG_WSG1_liver


title: 170920_FB_SDR1_liver


title: 100720_MG_SDR1_liver


title: 190820_MB_SDR1_liver


title: 130820_MG_WSG1_liver


title: 030920_MB_SDR1_liver