title: FOXA2 input TKO_PP

source_name: Triple-knockout pancreatic progenitors

extract_protocol:
Total RNA was isolated using the Trizol reagent following the manufacturer’s instructions. RNA integrity was determined using Agilent 2100 Bioanalyzer (Agilent Technologies). Subsequently, polyA tailed RNA were selected using the Dynabeads oligo(dT) (Thermo Fisher Scientific). Total gnomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen).
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep kit for Illumina (New England Biolabs). ATAC-seq libraries were prepared as previously described60. In brief, cells were enzymatically dissociated and lysed in lysis buffer (10 mM Tris-HCl, PH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Immediately after centrifugation, transposition reactions were carried out by adding Tn5 Transposes from the Illumina Nextera DNA library preparation kit to the isolated nuclei and incubated at 37 oC for 30 min. DNA fragments were purified using the MinElute PCR Purification kit (Qiagen) and amplified using the KAPA real-time library amplification kit. Libraries were purified using the PCRClean DXTM beads (Aline Biosciences). CMS-IP-seq libraries were performed as previously described with small modifications (Huang et al., 2012). Purified genomic DNA (with 5% of mouse DNA and 0.5% lambda DNA spike-in) was sheared to 200–500 bp fragments using the M220 Focused-ultrasonicator (Covaris). Bisulfite converted DNA libraries with methylated adapters were enriched using an in-house anti-CMS antibody bound to protein A/G dynabeads. Amplified libraries were purified by AmpuXP beads (Beckman Coulter) and then sequenced using the Illumina NextSeq (75 and 40 cycle, single-end) systems. Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen). WGBS library preparation and sequencing were conducted by BGI (Shengzhen, China). In brief, purified genomic DNA (with 1% of unmethylated lambda DNA spike-in, Promega) was sheared to a fragment size of 100–700 bp (main size 250bp) using Covaris focused ultrasonicator according to the manufacturer’s instructions. DNA fragments were subjected to bisulfited conversion using the EZ DNA Methylation-gold kit (Zymo Research). Bisulfite converted DNA was amplified and finally subjected to sequence on a MGISEQ-2000 system (100-cycle, paired-end) at BGI (Shengzhen, China). ChIP-seq was performed for TET1 (WT_PP cells), H3K4me1 (WT_PP and TKO_PP cells), and H3K27ac (WT_PP and TKO_PP cells). For TET1 ChIP-seq, approximately 5 x 107 cells were crosslinked, washed and snap frozen following the Cell Fixation protocol from Active Motif. TET1 ChIP-seq library preparation and sequencing were conducted by Active Motif. Chromatin immunoprecipitation of H3K4me1 and H3K27ac were performed as previously described28. WT_PP and TKO_PP cells were fixed, washed, and lysed in nuclear lysis buffer (50 mM Trish HCl, pH 8.0, 5mM EDTA, 1% SDS, and 1 protease inhibitor cocktail). Chromatin was sheared to 200-500 bp fragments using Bioruptor® (Diagenode), and the DNA fragments were precipitated with appropriate antibodies. ChIP-seq libraries were prepared using the NEBNext® Ultra IITM DNA Library Prep kit (New England Biolabs) following the manufacture’s instruction and subjected to high throughput sequencing on a Illumina HiSeq 2500 system (150 bp, paired-end) at Novogene (Tianjin, China).

value: Triple-knockout pancreatic progenitors

tag: antibody


title: FOXA2 input TKO_DE

status: Public on Apr 13 2022

type: SRA

city: Houston

first: Jianfang

last: Li

address: 2121 W. Holcombe Boulevard

country: USA

institute: Texas A&M University

library_source: genomic

data_processing:
For the 150 bp paired-end raw data of RNA-seq, low quality bases and adaptor were trimmed using TrimGalore v.0.5.0. Clean reads were aligned to hg38 reference genome using STAR v.2.5.354 with default parameters and only uniquely mapped reads were used for downstream analysis. Count matrix for each gene were generated using htseq-count (HTSeq package55). DESeq2 was used to identify significantly differentially expressed genes (DEGs) between groups (WT and TKO ; WT and TET1KO) at the ES, DE and PP stages (fold change ≥ 2; FDR < 0.05). Hierarchical cluster analysis of the union DEGs was used to determine the signature genes and groups. The ‘ClusterProfilter’ package in R was performed for the functional enrichment analysis of DEGs in KEGG pathways.
Adaptor trimming of raw reads were performed by TrimGalore v0.5.0, and high-quality reads were uniquely aligned to hg38 reference genome using Bowtie2 with ‘--very-sensitive’ option. Reads mapped to Mitochondrial DNA and PCR duplicate reads were removed and those uniquely mapped reads were finally extracted for downstream analysis. Genrich v.0.5 with ATAC-seq mode (option: -j, -q 0.01) was applied for each sample (with two biological replicates) to call ATAC peaks. Bedtools intersect was used to count the reads fall into peak regions, and the significantly differential accessible regions (DARs) were detected using DESeq2. Volcano plots were plotted using R package ggplot2. Motif annotation of DARs was performed using HOMER software.
The analysis of CMS-IP data was performed by in house software ‘CMSIP’ v0.1.1. Briefly, raw reads were mapped to hg38 and mm10 genome references using bsmap v.2.89 (options: -n 1 -q 3 -r 0). After removing the PCR duplicates and reads mapped to both human and spike-in mouse genome, species specific reads were used to do the normalization for each sample according to the spike-in size factors. The mean wigsum for every 200 bp windows of the whole human genome was used to call the hydroxymethylation enriched peak regions for each group agaist to input, respectively. Differentially hydroxymethylation regions (DHMRs) in between WT_PP and TKO_PP were identified (g-test; FDR < 0.05). GREAT analysis with single-nearest genes option was used to perform the functional annotation of hypo-DHMRs.
For WGBS data analysis, paired-end 100 bp reads were mapped against hg38 using bsmap v.2.89 with paired mode (options: -n 1 -q 3 -r 0), and only uniquely mapped reads were retained. More than 26.6 million CpG sites with coverage ≥ 5 reads were detected in both WT_PP and TKO_PP samples, which were used for downstream analyses. BSeQC and mcall module in MOABS30 was applied to do the quality control and calculate the methylation ratio for each CpG site (options: --trimWGBSEndRepairPE2Seq 40). Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. Mcomp module was used to call significantly differentially methylation CpG sites (DMCs) and differentially methylation regions (DMRs) (absolute credible difference of DNA methylation ratio of at least 20% and adjust p value of less than 0.05). The output bedGraph files from mcall include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization. Motif enrichment analysis of DMRs was performed using HOMER software and the functional annotation was performed by using GREAT with default settings.
The quality control and alignment for raw reads of ChIP-seq data were similar to ATAC-seq data analysis above, TrimGalore (options: --quality 20 and --length 50) was used to remove adaptor and only uniquely mapped reads were retained. Bam2wig.py was used to transform the bam file to normalized bigWig files (option: -t 2000000000). For the WT_PP TET1 ChIP-seq, Macs262 was used to call ChIP-seq enriched peak regions with default parameters.
Genome_build: hg38

molecule: genomic DNA

organism: Homo sapiens

source_name: Triple-knockout definitive endoderms

tag: cell type

value: Triple-knockout definitive endoderms


title: WT_Bicarb_3

city: Moscow

first: Daniil

middle: M.

last: Bobrovskiy

address: Leninskiye Gory, MSU, 1-73, Faculty of Bioengineering and Bioinformatics, office 433

country: Russia

institute: Lomonosov Moscow State University

library_source: transcriptomic

data_processing:
The RNA-seq reads were quality controlled and quantified using salmon v1.5.2 selective alignment with unstranded library type and parameters --validateMappings and --seqBias, using the entire Mus musculus reference genome (GRCm39, GENCODE M27) as the decoy sequence.
The resulting abundances were processed using edgeR package v3.34.0, the offsets being calculated with tximport v1.20.0.
Only protein-coding genes, according to BioMart (Ensembl release 104), were considered for analysis.
The transcripts expressed in less than 25% of samples or having less than 10 counts in each sample or total count less than 100 were filtered out. After all these filtration steps, our dataset contained 13430 genes.
The RPKM values were exported using edgeR.
Assembly: mm10
Supplementary files format and content: CSV file with the RPKM values, genes in rows. First row – Ensembl gene IDs, first column – sample names.

molecule: total RNA

organism: Mus musculus

source_name: Kidney

growth_protocol: Female mice C57Bl/6 strain, age 2-3 month, were obtained with a status of specific free-pathogens.

extract_protocol:
The kidney was removed from the abdominal cavity, washed in sterile PBS solution, and then, depending on the purpose of the experiment, was processed in two ways. For RNA sequencing, a segment of the kidney with a thickness of 3 mm was cut from the middle section along the horizontal plane; this part of the kidney was placed in RNAlater buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two genotypes were taken - wild type and IRR-/- knockout. Under normal conditions, the mice were given water as a drink, and under conditions of bicabonate loading, sodium bicarbonate NaHCO3 at a concentration of 250 mM (pH = 8.5) was added to the drinking water. Then four groups of animals were formed, n = 4, in total 16 animals. Bicarbonate loading was provided for 7 days.  Before experiment mice were fasting for 12 hours with free access of water or bicarbonate treated water.

tag: strain

tag: Sex

value: female

tag: genotype

value: Wild Type

tag: treatment

value: Bicarb


title: H10RNAT

city: Southampton

first: Rosanna

middle: C G

last: Smith

state: Hampshire

address: Centre for Cancer Immunology, University Hospital Southampton (MP 127), Tremona Road

department: Cancer Sciences Unit, Faculty of Medicine

country: United Kingdom

institute: University of Southampton

data_processing:
Illumina bcl2fastq v2.20.0 was used for converting bcl files to fastq.
Alignment: Sequenced reads from each sample and run were aligned to the human genome (primary assembly, GRCh38.p12, GCA_000001405.27) using the STAR alignment algorithm (version 2.5.2b, default parameters) and filtered for uniquely-mapped alignments using samtools (version 1.6, parameters: -q 255). Alignments were merged for sequencing runs from the same sample.
Counts: Uniquely-mapped alignments overlapping gene exons were counted using feature Counts from the Rsubread package (version 1.32.4). Counting was performed relative to Ensembl 97 (Jul 2019) gene annotation and counts summarized at the gene level. Rsubread parameters: countMultiMappingRead=FALSE, strandSpecific=2, isPairedEnd=TRUE, minFragLength=50, maxFragLength=700.
Gene expression: Gene expression filtering and normalization was carried out in R, using the edgeR package (version 3.24.2). Genes with below-threshold counts were filtered out (filterByExpr parameters: min.count=30, min.count.total=45) and between-sample normalization was performed using the trimmed mean of M-values method. Gene expression is reported as counts-per-million (CPM).
Genome_build: GRCh38.p12, GCA_000001405.27
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with between-sample normalised CPM expression values for every sample and those genes passing minimum counts threshold filter.

molecule: polyA RNA

source_name: Primary human monocytes - Donor H, 10hr, DMOG treated

growth_protocol: Anonymized leukocyte cones were sourced from healthy adult donors attending blood donation clinics at the National Blood Service (Southampton, UK). Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (Lymphoprep, Axis-Shield). Primary human monocytes were isolated from PBMCs using the Pan Monocyte Isolation Kit, human, (Miltenyi Biotech) from 1x108 PBMCs per isolation, according to the manufacturer’s protocol and cultured at low density (1 x 106/mL in a 24-well plate) in complete CTL medium at 37°C and 5% CO2.

extract_protocol:
Monocytes were lysed immediately (0hr) using QIAzol lysis reagent (Qiagen) or after culturing for 2, 10 or 24 hours. Total RNA was isolated using miRNeasy mini kit (Qiagen) as per manufacturer’s protocol.
Total RNA samples were enriched for mature, poly-A mRNA transcripts and prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. Two runs of 150 base pair paired-end sequencing were carried out per sample on the NovaSeq 6000 (Illumina) platform with v1.0 chemistry.

treatment_protocol: Samples were either cultured in the absence (untreated (U)) or presence (treated (T)) of 20μM Dimethyloxalylglycine (DMOG, EMD Millipore).

tag: donor

value: H

tag: timepoint

value: DMOG

value: Primary human monocytes


title: TP53-KO_Ctrl_RPF_rep2

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

country: Germany

institute: Heidelberg University

data_processing:
Adapters were removed with the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), retaining only sequences that are at least 28 nt long. The four random nucleotides at the beginning and the end of the reads were trimmed with an in-house developed perl script.
Alignment was performed with bowtie v1.2.2 (Langmead et al., Genome Biology 2009) allowing a maximum of two mismatches and reporting all alignments in the best stratum (settings: -a –best –stratum –v 2). Reads that did not map to tRNA or rRNA sequences (as downloaded from the UCSC Genome Browser) were aligned to a human transcriptome (Gencode V27 as downloaded from the UCSC Genome Browser wgEncodeGencodeBasicV27 table).
Reads were filtered with in-house developed perl scripts to retain only reads that are between 25 and 35 nt long and map to ORFs of isoforms arising from one specific gene (as defined by a common gene symbol). An offset of 12 nt upstream of the start codon and 15 nt upstream of the stop codon with respect to the 5’end of the read was assumed.
Normalization was performed using size factors obtained with the median ratio method of the DeSeq2 package, v1.18.1 (Love et al., Genome Biology 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts

molecule: cytoplasmic RNA

growth_protocol: HCT116 cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Biochrome), 2 mM L-Glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in a humidified atmosphere with 5% CO2. Every two to three days, cells were trypsinized and diluted 1:10. Two days before experiments, HCT116 cells were seeded at a density of 2 x 106 cells per 10 cm dish (Sarstedt, 83.3902).

extract_protocol:
Cells grown in 10-cm dishes were washed once with ice-cold PBS containing 100 µg/ml cycloheximide (CHX) and directly lysed using 290 µl of Ribo-Seq lysis buffer (20 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 200 mM KCl, 2 mM DTT, 100 µg/ml CHX, 1% NP-40, 40 U/ml RNasin (Promega), EDTA-free complete protease inhibitors (Roche)). The total RNA concentrations between samples were adjusted by measuring absorbance at 260 nm. From the adjusted cellular lysates, 50 µl was taken and diluted with in 250 µl of Ribo-Seq lysis buffer for preparing input samples to be analyzed by RNA-Seq. The remaining lysate (approximate volume of 250 µl) was treated with 240 U/1 A260 of RNase I (Ambion) for 5 min at 4°C on a rotator, and then loaded on top of 3.95 ml 17.5–50% sucrose density gradients  for which sucrose was dissolved in a buffer containing 20 mM Tris-HCl, pH 7.5, 5 mM MgCl2, and 150 mM NaCl. Centrifugation and profile recording were carried out as in the above section, and fractions of 300 µl each were collected with the fraction collector as part of the Teledyne ISCO Foxy RI system. Fractions corresponding to monosomes and disomes were used for preparation of ribosome protected fragments (RPF). Input samples and the monsome/disome fractions were first mixed with 300 µl of urea buffer (10 mM Tris-pH 7.5, 350 mM NaCl, 10 mM EDTA, 1% SDS, 7% urea), incubated with 300 µl phenol:chloroform:isamylalcohol (25:24:1) for 10 min at 65°C, and the RNA was extracted upon centrifugation by recovery of the aqueous phase followed by precipitation using 600 µl isopropanol and 1 µl of GlycoBlue (Invitrogen) at -20°C over night. After washing with 70% ethanol, the RNA was dissolved in 10 µl H2O. To prepare monosome footpints, cell lysates were first separated on 17.5-50% sucrose gradients and monosome fractions were collected manually. Monosome containing fraction was treated with 24 U/1 A260 (according to input sample) of RNase I as indicated above and RNA was purified with the same method with total foot prints.
From both input and ribosome protected fragments, ribosomal RNA was depleted from the RFP samples using the Ribo-Zero Gold Kit (Illumina).  Input RNA was randomly fragmented by alkaline hydrolysis at pH 10.0 for 12 min at 95°C. Fragmented RNA and RPFs were then size-selected (25–35 nt) on a 15% polyacrylamide Tris-borate-EDTA-urea gel. The gel pieces were crashed and RNAs were extracted by incubating overnight in 300 µl buffer containing (0.3 M NaCl and 80 u RNase OUT (invitrogen)) at 4oC. Gels were removed by centrifugation at 14.000 x g for 5 min at 4oC with a 0.45 µm NanoSep MF tubes (PALL) and RNAs were precipitated with 300 µl isopropanol and 1 µl GlycoBlue (Ambion). After washing with 70% Ethanol, RNA were dissolved in 14 µl H2O and subjected to end-repair with T4 polynucleotide kinase (NEB) for 1 h at 37°C. Following an additional round of purification and precipitation using isopropanol, upto 20 ng RNA were used for library preparation using the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer) according to the manufacturer’s manual. Libraries were multiplexed and sequenced with a NextSeq500 sequencer (Illumina).

treatment_protocol: HCT116 cells were treated with PBS or neocarizinostatin (0.2 µg/ml, Sigma-Aldrich, N0162) for 4 h.

tag: material

value: ribosome-protected fragments

value: PBS


title: TP53-KO_Ctrl_IN_rep2

value: Input


title: FOXA2 input WT_PP

source_name: Normal pancreatic progenitor

value: Normal pancreatic progenitor


title: H2RNAU

source_name: Primary human monocytes - Donor H, 2hr, untreated

value: Untreated


title: FOXA2 input WT_GT

source_name: Normal primitive gut tube

value: Normal primitive gut tube


title: H2RNAT

source_name: Primary human monocytes - Donor H, 2hr, DMOG treated


title: WT_NCS_RPF_rep2

value: neocarzinostatin (4 h)

value: wild type


title: WT_NCS_IN_rep2


title: WT_Water_3

department: Faculty of Bioengineering and Bioinformatics

value: Water


title: WT_Water_4


title: WT_Bicarb_4


title: FOXA2 ChIP TKO_PP 2

value: Triple-knockout pancreatic progenitors


title: WT_Water_2


title: FOXA2 input WT_DE

source_name: Normal definitive endoderm

value: Normal definitive endoderm


title: G24RNAU

source_name: Primary human monocytes - Donor G, 24hr, untreated

value: G


title: FOXA2 ChIP TKO_PP 1


title: H0RNAU

source_name: Primary human monocytes - Donor H, 0hr, untreated


title: WT_Ctrl_IN_rep2


title: WT_Ctrl_RPF_rep2


title: WT_Water_1

value: female

value: Wild Type


title: WT_Bicarb_2

value: Bicarb


title: G24RNAT

source_name: Primary human monocytes - Donor G, 24hr, DMOG treated

value: DMOG


title: G10RNAU

source_name: Primary human monocytes - Donor G, 10hr, untreated

value: Primary human monocytes


title: TP53-KO_NCS_RPF_rep1

value: ribosome-protected fragments


title: WT_Bicarb_1


title: FOXA2 ChIP WT_PP 2


title: G10RNAT

source_name: Primary human monocytes - Donor G, 10hr, DMOG treated


title: TP53-KO_NCS_IN_rep1


title: TP53-KO_Ctrl_RPF_rep1

value: PBS


title: FOXA2 ChIP TKO_DE 1

value: Triple-knockout definitive endoderms


title: G2RNAU

source_name: Primary human monocytes - Donor G, 2hr, untreated


title: FOXA2 ChIP WT_PP 1

value: Normal pancreatic progenitor


title: G0RNAU

source_name: Primary human monocytes - Donor G, 0hr, untreated

value: Untreated


title: TP53-KO_Ctrl_IN_rep1

value: Input


title: FOXA2 ChIP WT_GT 2

value: Normal primitive gut tube


title: WT_NCS_IN_rep1

value: neocarzinostatin (4 h)

value: wild type


title: G2RNAT

source_name: Primary human monocytes - Donor G, 2hr, DMOG treated


title: FOXA2 ChIP WT_GT 1


title: FOXA2 ChIP WT_DE 2


title: WT_Ctrl_RPF_rep1


title: 1898_S273

city: Minneapolis

first: Megan

last: Paulsen

state: MN

address: 2450 Riverside Avenue, S AO-401

department: Pediatrics

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the mouse (mm10 as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Assembly: mm10
Supplementary files format and content: counts

source_name: CON Male

extract_protocol:
Invitrogen RNAqueous total RNA isolation kit extration protocol followed. RNA was isolated from the hypothalamus.
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: C57Bl/6J dams were fed a control of high-fat-high-sugar (OB) diet during pregnancy and lactatation. Offspring from respective dams were weaned at PN21 and placed on standard chow diet. At 3 months of age all offspring were fed an OB diet for 4 weeks. Offspring were studied at 4-months of age.

tag: maternal diet

value: control

value: Male

tag: tissue

value: Hypothalamus

tag: age

value: 4 months


title: FOXA2 ChIP WT_DE 1

value: Normal definitive endoderm


title: FOXA2 ChIP TKO_DE 2

source_name: Triple-knockout definitive endoderms


title: WT_Ctrl_IN_rep1


title: F10RNAU

source_name: Primary human monocytes - Donor F, 10hr, untreated

value: F


title: F24RNAT

source_name: Primary human monocytes - Donor F, 24hr, DMOG treated

value: DMOG


title: ChIP-seq input TKO_PP 2

source_name: Triple-knockout pancreatic progenitors

extract_protocol:
Total RNA was isolated using the Trizol reagent following the manufacturer’s instructions. RNA integrity was determined using Agilent 2100 Bioanalyzer (Agilent Technologies). Subsequently, polyA tailed RNA were selected using the Dynabeads oligo(dT) (Thermo Fisher Scientific). Total gnomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen).
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep kit for Illumina (New England Biolabs). ATAC-seq libraries were prepared as previously described60. In brief, cells were enzymatically dissociated and lysed in lysis buffer (10 mM Tris-HCl, PH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Immediately after centrifugation, transposition reactions were carried out by adding Tn5 Transposes from the Illumina Nextera DNA library preparation kit to the isolated nuclei and incubated at 37 oC for 30 min. DNA fragments were purified using the MinElute PCR Purification kit (Qiagen) and amplified using the KAPA real-time library amplification kit. Libraries were purified using the PCRClean DXTM beads (Aline Biosciences).  CMS-IP-seq libraries were performed as previously described with small modifications (Huang et al., 2012). Purified genomic DNA (with 5% of mouse DNA and 0.5% lambda DNA spike-in) was sheared to 200–500 bp fragments using the M220 Focused-ultrasonicator (Covaris). Bisulfite converted DNA libraries with methylated adapters were enriched using an in-house anti-CMS antibody bound to protein A/G dynabeads. Amplified libraries were purified by AmpuXP beads (Beckman Coulter) and then sequenced using the Illumina NextSeq (75 and 40 cycle, single-end) systems. Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen). WGBS library preparation and sequencing were conducted by BGI (Shengzhen, China). In brief, purified genomic DNA (with 1% of unmethylated lambda DNA spike-in, Promega) was sheared to a fragment size of 100–700 bp (main size 250bp) using Covaris focused ultrasonicator according to the manufacturer’s instructions. DNA fragments were subjected to bisulfited conversion using the EZ DNA Methylation-gold kit (Zymo Research). Bisulfite converted DNA was amplified and finally subjected to sequence on a MGISEQ-2000 system (100-cycle, paired-end) at BGI (Shengzhen, China).  ChIP-seq was performed for TET1 (WT_PP cells), H3K4me1 (WT_PP and TKO_PP cells), and H3K27ac (WT_PP and TKO_PP cells). For TET1 ChIP-seq, approximately 5 x 107 cells were crosslinked, washed and snap frozen following the Cell Fixation protocol from Active Motif. TET1 ChIP-seq library preparation and sequencing were conducted by Active Motif. Chromatin immunoprecipitation of H3K4me1 and H3K27ac were performed as previously described28. WT_PP and TKO_PP cells were fixed, washed, and lysed in nuclear lysis buffer (50 mM Trish HCl, pH 8.0, 5mM EDTA, 1% SDS, and 1 protease inhibitor cocktail). Chromatin was sheared to 200-500 bp fragments using Bioruptor® (Diagenode), and the DNA fragments were precipitated with appropriate antibodies. ChIP-seq libraries were prepared using the NEBNext® Ultra IITM DNA Library Prep kit (New England Biolabs) following the manufacture’s instruction and subjected to high throughput sequencing on a Illumina HiSeq 2500 system (150 bp, paired-end) at Novogene (Tianjin, China).

value: Triple-knockout pancreatic progenitors

value: input


title: ChIP-seq input TKO_PP 1


title: F10RNAT

source_name: Primary human monocytes - Donor F, 10hr, DMOG treated

value: Primary human monocytes


title: TET1 input

source_name: Normal pancreatic progenitor


title: 1890_S246


title: TET1 ChIP WT_PP


title: CMSIP input 2

data_processing:
Library strategy: CMS-IP
For the 150 bp paired-end raw data of RNA-seq, low quality bases and adaptor were trimmed using TrimGalore v.0.5.0. Clean reads were aligned to hg38 reference genome using STAR v.2.5.354 with default parameters and only uniquely mapped reads were used for downstream analysis. Count matrix for each gene were generated using htseq-count (HTSeq package55). DESeq2 was used to identify significantly differentially expressed genes (DEGs) between groups (WT and TKO ; WT and TET1KO) at the ES, DE and PP stages (fold change ≥ 2; FDR < 0.05). Hierarchical cluster analysis of the union DEGs was used to determine the signature genes and groups. The ‘ClusterProfilter’ package in R was performed for the functional enrichment analysis of DEGs in KEGG pathways.
Adaptor trimming of raw reads were performed by TrimGalore v0.5.0, and high-quality reads were uniquely aligned to hg38 reference genome using Bowtie2 with ‘--very-sensitive’ option. Reads mapped to Mitochondrial DNA and PCR duplicate reads were removed and those uniquely mapped reads were finally extracted for downstream analysis. Genrich v.0.5 with ATAC-seq mode (option: -j, -q 0.01) was applied for each sample (with two biological replicates) to call ATAC peaks. Bedtools intersect was used to count the reads fall into peak regions, and the significantly differential accessible regions (DARs) were detected using DESeq2. Volcano plots were plotted using R package ggplot2. Motif annotation of DARs was performed using HOMER software.
The analysis of CMS-IP data was performed by in house software ‘CMSIP’ v0.1.1. Briefly, raw reads were mapped to hg38 and mm10 genome references using bsmap v.2.89 (options: -n 1 -q 3 -r 0). After removing the PCR duplicates and reads mapped to both human and spike-in mouse genome, species specific reads were used to do the normalization for each sample according to the spike-in size factors. The mean wigsum for every 200 bp windows of the whole human genome was used to call the hydroxymethylation enriched peak regions for each group agaist to input, respectively. Differentially hydroxymethylation regions (DHMRs) in between WT_PP and TKO_PP were identified (g-test; FDR < 0.05). GREAT analysis with single-nearest genes option was used to perform the functional annotation of hypo-DHMRs.
For WGBS data analysis, paired-end 100 bp reads were mapped against hg38 using bsmap v.2.89 with paired mode (options: -n 1 -q 3 -r 0), and only uniquely mapped reads were retained. More than 26.6 million CpG sites with coverage ≥ 5 reads were detected in both WT_PP and TKO_PP samples, which were used for downstream analyses. BSeQC and mcall module in MOABS30 was applied to do the quality control and calculate the methylation ratio for each CpG site (options: --trimWGBSEndRepairPE2Seq 40). Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. Mcomp module was used to call significantly differentially methylation CpG sites (DMCs) and differentially methylation regions (DMRs) (absolute credible difference of DNA methylation ratio of at least 20% and adjust p value of less than 0.05). The output bedGraph files from mcall include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization. Motif enrichment analysis of DMRs was performed using HOMER software and the functional annotation was performed by using GREAT with default settings.
The quality control and alignment for raw reads of ChIP-seq data were similar to ATAC-seq data analysis above, TrimGalore (options: --quality 20 and --length 50) was used to remove adaptor and only uniquely mapped reads were retained. Bam2wig.py was used to transform the bam file to normalized bigWig files (option: -t 2000000000). For the WT_PP TET1 ChIP-seq, Macs262 was used to call ChIP-seq enriched peak regions with default parameters.
Genome_build: hg38


title: 1887_S271

source_name: CONFemale

value: Female


title: F2RNAU

source_name: Primary human monocytes - Donor F, 2hr, untreated


title: F2RNAT

source_name: Primary human monocytes - Donor F, 2hr, DMOG treated


title: 1885_S270


title: F24RNAU

source_name: Primary human monocytes - Donor F, 24hr, untreated


title: WT_NCS_RPF_rep1

value: ribosome-protected fragments


title: ChIP-seq input WT_PP 1

value: Normal pancreatic progenitor


title: F0RNAU

source_name: Primary human monocytes - Donor F, 0hr, untreated

value: Untreated


title: H3K27ac TKO_PP 2


title: E24RNAU

source_name: Primary human monocytes - Donor E, 24hr, untreated

value: E


title: CMSIP input 1


title: CMSIP TKO_PP 2


title: 1893_S272


title: 1878_S268


title: 1876_S267

source_name: CON Female


title: H3K27ac TKO_PP 1


title: CMSIP TKO_PP 1


title: ChIP-seq input WT_PP 2


title: E10RNAU

source_name: Primary human monocytes - Donor E, 10hr, untreated


title: E24RNAT

source_name: Primary human monocytes - Donor E, 24hr, DMOG treated


title: CMSIP WT_PP 2


title: H3K27ac WT_PP 2


title: E10RNAT

source_name: Primary human monocytes - Donor E, 10hr, DMOG treated


title: 1871_S266

source_name: CON Male


title: CMSIP WT_PP 1


title: H3K27ac WT_PP 1


title: 1870_S265


title: 1882_S269


title: E2RNAU

source_name: Primary human monocytes - Donor E, 2hr, untreated


title: H3K4me1 TKO_PP 2


title: 1867_S264


title: H3K4me1 TKO_PP 1


title: ATAC TKO_PP 2


title: ATAC TKO_PP 1


title: 1861_S262


title: 1864_S263


title: H3K4me1 WT_PP 2


title: ATAC WT_PP 2


title: D24RNAU

source_name: Primary human monocytes - Donor D, 24hr, untreated

value: D


title: ATAC WT_PP 1


title: H3K4me1 WT_PP 1


title: D24RNAT

source_name: Primary human monocytes - Donor D, 24hr, DMOG treated


title: E0RNAU

source_name: Primary human monocytes - Donor E, 0hr, untreated


title: D10RNAU

source_name: Primary human monocytes - Donor D, 10hr, untreated


title: 1851_S260


title: E2RNAT

source_name: Primary human monocytes - Donor E, 2hr, DMOG treated


title: 1857_S261


title: RNA TET1KO_PP 2

source_name: TET1-knockout pancreatic progenitors

value: TET1-knockout pancreatic progenitors


title: D2RNAU

source_name: Primary human monocytes - Donor D, 2hr, untreated


title: RNA TKO6_PP 2

source_name: Triple-knockout pancreatic progenitors clone6


title: RNA TKO2_PP 2

source_name: Triple-knockout pancreatic progenitors clone2


title: D2RNAT

source_name: Primary human monocytes - Donor D, 2hr, DMOG treated


title: D10RNAT

source_name: Primary human monocytes - Donor D, 10hr, DMOG treated


title: D0RNAU

source_name: Primary human monocytes - Donor D, 0hr, untreated


title: 1838_S255

source_name: OB Female

value: obesogenic


title: bladder tumour 2188

type: RNA

city: Leeds

first: Margaret

last: Knowles

address: Beckett Street

institute: University of Leeds

hyb_protocol: Microarrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip 7G microarray scanner.

data_processing: Data QC was analysed using Affymetrix Expression Console Software and samples were normalised using RMA.

label: biotin

source_name: fresh frozen bladder tumour tissue

label_protocol: Total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to manufacturer's instructions. The resulting cDNA was quantified using OD (NanoDrop). The cDNA was normalised and hybridised onto Affymetrix Human Transcriptome 2.0 microarrays for 16 hours at 45 degrees C.

extract_protocol: Total RNA was extracted from fresh frozen tissue samples comprising at least 70% tumour using an RNeasy  Plus Micro Kit (Qiagen). The protocol for fibrous tissue was followed with the inclusion of an on-column DNase digestion step

tag: tumour stage

value: Pure SCC

value: bladder tumour


title: 1848_S258

source_name: OB Male

value: Male

value: Hypothalamus

value: 4 months


title: RNA WT_PP 2

source_name: Normal pancreatic progenitor


title: RNA TKO6_PP 1

value: Triple-knockout pancreatic progenitors clone6


title: RNA TKO2_PP 1

value: Triple-knockout pancreatic progenitors clone2


title: 1845_S256


title: 1846_S257


title: 1834_S275


title: C24RNAU

source_name: Primary human monocytes - Donor C, 24hr, untreated

value: C


title: bladder tumour 2159


title: 1829_S253


title: 1849_S259

source_name: CON Female

value: control


title: RNA TET1KO_PP 1


title: 1836_S254


title: C24RNAT

source_name: Primary human monocytes - Donor C, 24hr, DMOG treated

value: DMOG

value: Primary human monocytes


title: C10RNAU

source_name: Primary human monocytes - Donor C, 10hr, untreated


title: RNA TKO6_DE 2

source_name: Triple-knockout definitive endoderms clone6


title: C2RNAU

source_name: Primary human monocytes - Donor C, 2hr, untreated


title: RNA WT_PP 1

value: Normal pancreatic progenitor


title: bladder tumour 2124


title: C2RNAT

source_name: Primary human monocytes - Donor C, 2hr, DMOG treated


title: bladder tumour 1462


title: 1827_S274

value: Female


title: bladder tumour 1789


title: RNA TKO6_DE 1

value: Triple-knockout definitive endoderms clone6


title: bladder tumour 2067


title: C10RNAT

source_name: Primary human monocytes - Donor C, 10hr, DMOG treated


title: bladder tumour 1907


title: bladder tumour 1271


title: bladder tumour 1552


title: RNA TKO2_DE 2

source_name: Triple-knockout definitive endoderms clone2


title: C0RNAU

source_name: Primary human monocytes - Donor C, 0hr, untreated

value: Untreated


title: RNA WT_DE 2

source_name: Normal definitive endoderm

value: Normal definitive endoderm


title: RNA TKO2_DE 1

value: Triple-knockout definitive endoderms clone2


title: 1813_S249

value: obesogenic


title: B24RNAU

source_name: Primary human monocytes - Donor B, 24hr, untreated

value: B


title: 1821_S251


title: RNA TKO6_ES 2

source_name: Triple-knockout hESCs clone6

value: Triple-knockout hESCs clone6


title: bladder tumour 1241

value: Pure SCC

value: bladder tumour


title: B24RNAT

source_name: Primary human monocytes - Donor B, 24hr, DMOG treated


title: 1815_S250

value: Male

value: Hypothalamus

value: 4 months


title: RNA WT_DE 1


title: 1809_S248


title: RNA TKO6_ES 1


title: RNA TKO2_ES 2

source_name: Triple-knockout hESCs clone2

value: Triple-knockout hESCs clone2


title: 1803to1911_S244

source_name: OB Female


title: B10RNAT

source_name: Primary human monocytes - Donor B, 10hr, DMOG treated

value: DMOG


title: B2RNAU

source_name: Primary human monocytes - Donor B, 2hr, untreated

value: Primary human monocytes


title: RNA WT_ES 2

source_name: Normal hESC

value: Normal hESC


title: B10RNAU

source_name: Primary human monocytes - Donor B, 10hr, untreated


title: bladder tumour 1207

source_name: fresh frozen bladder tumour tissue


title: 1823_S252

source_name: OB Male


title: RNA TKO2_ES 1


title: bladder tumour 697


title: 1806to1921_S245


title: bladder tumour 1202


title: bladder tumour 1014


title: RNA WT_ES 1


title: B0RNAU

source_name: Primary human monocytes - Donor B, 0hr, untreated


title: SLE3

city: Nashville

first: David

last: Patrick

state: TN

address: 2213 Garland Avenue

institute: Vanderbilt University Medical Center

data_processing:
QC was performed using FastQC package from Babraham Institute
Reads with poor quality were trimmed and adapter sequences were removed by cutadapt.
Reads were aligned using STAR and quantified by featureCounts.
Significantly differential expressed genes with FDR-adjusted p-value < 0.05 and absolute fold change > 2.0 were detected by DESeq2
Assembly: mm10
Supplementary files format and content: Matrix file includes columns for each sample.

source_name: Primary

growth_protocol: Cells were sorted from 7 week old mouse spleens.

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen). 0.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Stranded mRNA (NEB) mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
n/a
n/a

tag: cell line

value: Primary

value: Dendritic Cells

value: 7 weeks old


title: SLE4


title: B2RNAT

source_name: Primary human monocytes - Donor B, 2hr, DMOG treated


title: AML01 negative control well 2 [AML01_neg_H01_181120_scRNAseq_S154]

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

description: processed data file: AML01_scRNAseq_TEtranscripts_counts.txt.gz

data_processing:
scRNA-seq data was trimmed using Trim Galore (v0.6.5), with default setting in paired-end mode.
Hisat2 (v2.1.0) and Samtools (v1.1.0) were used to convert, map and align unique and ambiguous reads to the human reference genome build GRCh38 from raw fastq reads into bam format.
TEtranscripts [Jin, Y., et al., TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 2015] was used to obtain raw gene and transposable element counts from the unique and ambiguously aligned reads using the GTF files for 1) TEs (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/) and 2) genes (https://asia.ensembl.org/info/data/index.html; release 101 from the FTP server) in GRCh38 ensembl format. TEtranscripts was run in a Conda (Inc., A., Anaconda Software Distribution. 2020, Anaconda Inc.) environment setup with Python (v3.7.7), Pysam (v0.16.0.1), R-base (v4.0.3) and Bioconductor-Deseq2 (v1.28.0).
Genome_build: GRCh38 ensembl format
Supplementary_files_format_and_content: The read count table are in tab-deliminated format with the first column containing the gene ensembl ID and TE name, followed by each column containing an individual named sample and associated counts.

organism: blank sample

source_name: negative control

growth_protocol:
AML01: Enriched mononuclear cells were purified from peripheral blood using Lymphoprep density gradient medium (StemCell, catalog # 7851) and SepMate tubes (StemCell, catalog # 85450), and cryopreserved. Cryopreserved primary human cells were resuspended in thawing media (IMDM, 20% FBS), washed twice and resuspended in thawing media. The cells were then rested for 1h at 37°C before preparation for flow cytometry. Cells (1x106/100ul) were stained with 1.5μg/mL propidium iodide (PI, Sigma-Aldrich), 1:20 CD45-PECy7 (2D1, Invitrogen), 1:20 CD33-FITC (WM-53, Invitrogen) and 1:20 CD19-BV711 (SJ25C1, BD Biosciences). Single blasts (PI-CD45dim) were collected in 2.5μL RLT Plus Lysis Buffer containing 1U/μL SUPERase-In (Invitrogen) in 96 well plates.
KG1a: KG1a cells were resuspended in binding buffer before staining with annexin V and 7-AAD. Live cells (Annexin V - /7-AAD -) were sorted into individual wells of a 96 well plate containing lysis buffer 2.5μL RLT Plus Lysis Buffer (QIAGEN, catalog # 1053393) containing 1U/μL SUPERase-In (ThermoFisher, catalog # AM2696) in 96 well plates. Before sorting, bulk samples of 1000000 cells were collected from both the untreated and treated populations.

extract_protocol:
We utilised the G&T-seq protocol to separate genomic DNA and RNA from the single-cell samples. [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015]
Matched single cell RNA sequencing (scRNA-seq) libraries were prepared as per the scM&T-seq protocol. [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015]

treatment_protocol: Cell lines were treated with 100nM decitabine every 24 hours (0, 24 and 48 hours) and harvested at 72 hours

tag: sample type

value: negative control


title: SLE2


title: 29R5I2

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

country: Canada

institute: Université de Sherbrooke

data_processing:
FASTQ files were generated using bcl2fastq version v2.20.0.422
FASTQ files were filtered using Trimmomatic 0.36 (PE ILLUMINACLIP:adapters.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:45).
The quality was assessed with FastQC 0.11.8.
The transcriptome was generated with gffread, using the GRCh38.p13 genome and the latest Ensembl annotation (Homo sapiens version 98).
Complete read pairs were aligned and quantified on a human transcriptome using Kallisto 0.44.0 (index built with –kmer-size=31).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Kallisto output tsv file with transcripts abundance (raw counts and tpm).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with tpm values for every gene and every sample

source_name: Colorectal cancer cell line

growth_protocol: 250000 resistant and sensitive DLD-1, HCT-116 and HT-29 cells were grown in 100-mm petri dish for 72 hours.

extract_protocol:
The cells were washed three times in cold PBS 1X, harvested in cold PBS 1X and centrifuged at 500 x g at 4°C for 5 minutes. The pellets were lysed in 8M urea 10 mM HEPES pH 8.0 and centrifuged at 16000 x g at 4°C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: They were treated with either 10 μM uracil (condition 1) or 10 μM 5-FU (condition 2) for 24 hours. Medium was changed and cells were irradiated with corresponding DL50 using an X-ray irradiator (X-RAD 225 XL, Precision X-Ray) (condition 3).

value: Resistant

value: 5FU 10 uM 24h + Irradiation (DL50)


title: bladder tumour 1366

value: MIBC non-SD


title: 29R5I3


title: bladder tumour 780


title: AML01 negative control well 1 [AML01_neg_A01_181120_scRNAseq_S97]


title: bladder tumour 1338


title: bladder tumour 491


title: bladder tumour 1322


title: bladder tumour 1321


title: WT3


title: KG1a negative control well 1 [KG1a_neg_D06_180808_scRNAseq_S42]

description: processed data file: KG1a_scRNAseq_TEtranscripts_counts.txt.gz

value: blank sample


title: 29R53

value: 5FU 10 uM 24h


title: WT4


title: 29R5I1


title: KG1a negative control well 4 [KG1a_neg_E07_180808_scRNAseq_S55]


title: KG1a negative control well 3 [KG1a_neg_E06_180808_scRNAseq_S54]


title: bladder tumour 1148

value: bladder tumour


title: bladder tumour 1157


title: E14.5 dermal SmoM2YFP mutant

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

data_processing:
Raw sequencing data was aligned using Cellranger (3.0)
Seurat v3 was used to perform data preprocessing and downstream analysis
Assembly: mm10
Supplementary files format and content: Gzipped text file which includes cell barcodes and gene names; Gzipped gene-by-cell count matrix

source_name: skin

growth_protocol: Standard mouse housing conditions, freshly isolated cells

extract_protocol:
Trypsin (no EDTA) at 37 degrees celsius for 20 minutes to obtain single-cell suspensions for all samples
10x single cell RNA-seq protocol

treatment_protocol: Tamoxifen at 50 ug/gm weight was administered by gavage to pregant mom at E11.5 for E14.5 SmoM2 samples. No treatment of mice for all other experiments. No treatement of cells.

value: skin

value: Axin2CreER;RosaLSLSmom2YFP on CD1

tag: developmental stage

value: SmoM2 MUT


title: KG1a negative control well 2 [KG1a_neg_D07_180808_scRNAseq_S43]


title: WT2


title: 29R52


title: SLE1


title: bladder tumour 944


title: 29R51


title: WT1


title: 29RU2

value: Uracil 10 uM 24h


title: E15.5 epidermal SHH knockout

value: K14Cre;SHH fl/fl on CD1

value: SHH KO


title: bladder tumour 1049


title: Sample160.Yellow-bellied marmot.203877620053_R06C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Blood species=Yellow-bellied marmot

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Marmota flaviventris

source_name: Blood

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

value: Blood


title: E14.5 control (SmoM2YFP)

value: SmoM2 WT


title: 29RU1


title: 29RU3


title: bladder tumour 848


title: E14.5 epidermal SHH knockout


title: 116R5I3


title: 116R5I2


title: 116R5I1


title: 116R53


title: E14.5 control (SHH)

value: SHH WT


title: E14.5 epidermal bcatenin knockout

value: K14Cre;bcatenin fl/fl on CD1

value: bcat KO


title: E15.5 control (SHH)


title: E14.5 control (bcatenin)

value: bcat WT


title: 116R52

value: Resistant


title: Sample159.Yellow-bellied marmot.203877620053_R05C02


title: bladder tumour 826

value: MIBC non-SD


title: bladder tumour 701


title: E13.5 epidermal bcatenin knockout


title: bladder tumour 778


title: bladder tumour 498


title: Sample158.Yellow-bellied marmot.203877620053_R04C02


title: bladder tumour 360


title: Sample156.Yellow-bellied marmot.203877620053_R02C02


title: bladder tumour 433


title: Sample154.Yellow-bellied marmot.203877620053_R06C01


title: E13.5 control (bcatenin)


title: 116RU3


title: 116RU2


title: RNA-seq Idax-Rinf Double Knockout

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Trim Galore (version 0.6.5) was used to trim adapters from sequencing reads. Clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.9a). Mapped reads were assigned to genes using featureCounts (Liao et al., 2014) with --largestOverlap option. edgeR (Robinson et al., 2010) was used for differential expression analysis.
Samtools was used to convert SAM to BAM files (version 1.9). Bigwig files were generated from mapped bam files using deepTools (version 3.1.0) function bamCoverage.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Mouse ESCs

growth_protocol: ESC were differentiated to embryoid boidies (EBs) by hanging drop protocol in the absence of LIF for 6 days

extract_protocol:
RNA extraction was performed using Omega E.Z.N.A Total RNA kit.
Sequencing libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina by Novogene (en.novogene.com).
Libraries were subjected to 150-bp paired-end sequencing on Illumina Novoseq 6000 platform by Novogene (en.novogene.com).

treatment_protocol: Culture in media without LIF for 6 days.

value: Embryonic stem cells

value: V6.5 Male mixed 129/C57BL/6

value: Idax-Rinf Double Knockout


title: RNA-seq Rinf Knockout

value: Rinf Knockout


title: bladder tumour 291

value: bladder tumour


title: 116R51

value: 5FU 10 uM 24h


title: Sample157.Yellow-bellied marmot.203877620053_R03C02


title: 116RU1

value: Uracil 10 uM 24h


title: bladder tumour 500


title: Sample155.Yellow-bellied marmot.203877620053_R01C02


title: RNA-seq Wildtype

value: Wildtype


title: DR5I3

value: 5FU 10 uM 24h + Irradiation (DL50)


title: Sample153.Yellow-bellied marmot.203877620053_R05C01

value: Blood


title: KO_MSU_rep3

city: La Jolla

first: Isidoro

last: Cobo

address: Dept. of Cellular & Molecular Medicine, GPL210 9500 Gilman Drive, MC 0651

department: Cellular and Molecular Medicine

institute: University California San Diego

data_processing:
FASTQ sequencing files were mapped to the mm10 or hg38 reference genomes for mouse samples or human samples, respectively using STAR with default parameters. Biological replicates were used in all experiments.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: Raw expression (TPM) files

source_name: BMDM

growth_protocol: Flushed bone marrow from both femurs and tibias of C57BL/6 mice were cultured in DMEM medium supplemented with 10% de-complemented FBS, 100 units/ml penicillin and 100 ug/ml streptomycin, 2mM L-glutamine, and 20% of L929 conditioned media for for six days at 37ºC and 5% CO2. On day six, BMDM were trypsinized and plated in DMEM medium supplemented with 10% de-complemented FBS, 2mM L-glutamine, 100 units/ml penicillin and 100 ug/ml streptomycin, and 10 ng/mL recombinant murine M-CSF (Peprotech, #315-02) for one day prior being stimulated for five hours with 100ng/mL of LPS or 250 μg/mL of MSUc

extract_protocol:
BMDM or mDM were lysed in TRIzol (ThermoFisher, #15596026). RNA isolation and DNase treatment was carried out using Direct-zol RNA MicroPrep kit (Zymoresearch, #11-33MB)
500ng-1 μg total RNA was enriched in poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 min at 94ºC in 2X Superscript III first-strand buffer containing 10mM DTT (Invitrogen, #P2325). The 10 μl of fragmented RNA was added to 0.5 μl of Random primers (Invitrogen, #48190011), 0.5 μl of Oligo d(T) primer (Invitrogen, #18418020), 0.5 μl of SUPERase inhibitor (Ambion, #AM2696), 1 μl of 10mM dNTPs and incubated at 50ºC for three minutes. Then, 5.8 μl of water, 1 μl of 10mM DTT, 0.1 μl of 2 μg/μl Actinomycin D (Sigma, #A1410), 0.2 μl of 1% Tween-20 (Sigma) and 0.5 μl of SuperScript III (Invitrogen, #ThermoFisher 18080044) was added to the mix. Reverse-transcription (RT) reaction was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and eluted in 10 μl in 0.01% Tween-20. The RNA-cDNA complex was then added to 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5U/μl RNAseH (Enzymatics, #Y9220L), 1 μl of 10U/μl DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween-20 and 1.05 μl of nuclease free water; and incubated at 16ºC for 2.5h or overnight. The resulting dsDNA product was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Healthcare, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration, washed twice with 80% etOH, air dry and eluted in 40 μl of 0.05% Tween-20. The purified 40 μl of dsDNA was end-repaired by blunting followed by A-tailing and adapter ligation as described elsewhere (69) using BIOO Barcodes (BIOO Scientific, #514104), IDT TruSeq Unique Dual Indexes or Kapa Unique Dual-Indexed Adapters using 15 μl Rapid Ligation Buffer (Enzymatics, #L603-LC-L), 0.33 μl 1% Tween-20 and 0.5 μl T4 DNA ligase HC (Enzymatics, #L6030-HC-L). Libraries were amplified by PCR for 11-15 cycles using Solexa IGA and Solexa IGB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate in 15.2 μl of 20%PEG8000:2.5M NaCl, washed with 80% etOH and eluted in 0.05% Tween-20. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on a NextSeq 500 or Hi-Seq 4000 (Illumina, San Diego, California).

treatment_protocol: 20 μM of JNK inhibitor SP600125 (Tocris, #1496), 10 μM of BHA (Sigma, B1253), 20nM of BAY-876 (Selleckchem,#S8452), 3 μM of p38 MAPK inhibitor SB203580 (Tocris, #1202) or NLRP3 inflammasome inhibitor MCC950 (1uM, Selleckchem, #S7809) were added to the media one hour prior to stimulation with LPS or MSUc.

tag: agent

value: MSU

tag: time point


title: Sample151.Yellow-bellied marmot.203877620053_R03C01


title: AEEC_3 TGFbeta: atrial endocardial endothelial cells_3 TGFbeta

city: TauYau

first: Yun-Shien

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: AEEC_3 TGFbeta

hyb_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol

scan_protocol: Standard Applied Biosystems protocol

data_processing: Normalize with SST-RMA by Applied Biosystems Transcriptome Analysis Console Ver 4.0

source_name: Human heart tissue

growth_protocol: The AEECs were growth on gelatin-coated culture dishes with EGM™-2 medium

extract_protocol: Total RNA was isolated from Human atrial endothelial cells with the TRIzol reagent and was further purified and concentrated by using the WelPrep tissue RNA array . The quality and quantity of total RNA were analyzed by using a Bioanalyzer 2100

treatment_protocol: The AEECs were treated with TGFbeta(5ng/mL) for 24hr

tag: cell type

value: atrial endocardial endothelial cells

tag: gender

value: Male


title: Sample152.Yellow-bellied marmot.203877620053_R04C01


title: DR5I2


title: bladder tumour 95


title: AEEC_2 TGFbeta: atrial endocardial endothelial cells_2 TGFbeta

description: AEEC_2 TGFbeta

label_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol


title: Sample150.Yellow-bellied marmot.203877620053_R02C01


title: AEEC_1 TGFbeta: atrial endocardial endothelial cells_1 TGFbeta

description: AEEC_1 TGFbeta

value: Female


title: KO_MSU_rep2


title: mouse08, bmdm cell, AC [P5482_SR_15]

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

data_processing:
CLC Genomics Workbench v 11.0.1
Raw fastq files were mapped to reference genomes (GRCm38) with STAR software.
Gene reads count were calculated with FeatureCounts in R.
Gene by sample matrix were integrated and performed the differential gene expression analysis workflow using DESeq2 package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include reads count values for each Sample

source_name: Annexin V+/PI- Cal27 cell

growth_protocol: Cal27 cell line aliquots were obtained from ATCC, and were cultured with RPMI-1640 medium, with 10% FBS, 1% penicillin/streptomycin, 1% HEPES, 1% Glutamax, and 0.1% beta-mercaptoethanol.

extract_protocol:
For generation of mouse macrophages, bone marrow from femur and tibia of mice was flushed with ice-cold PBS using a 25-gauge 30cc needle. Red blood cells (RBC) were removed using erythrocyte lysis buffer. Cells were resuspended in complete media and differentiated using either 50ng/ml GM-CSF or 100ng/ml M-CSF for 7days. Fresh media supplemented with appropriate concentration of GM-CSF or M-CSF was added every alternate day. Where mentioned, to generate M2 macrophages, on day 7, cells were treated with 20ng/ml IL-4 for 24hrs. For M1 macrophages, on day 7, cells were treated with 1ug/ml LPS and 20ng/ml IFN- for 24hrs. Apoptosis was induced in Cal27 cells by treating cells with 2uM Staurosporine for 15hrs. To induce apoptosis in MOC2 cells, they were incubated with 75uM AZD5582 for 20hrs.   Cells were harvested and washed in PBS and resuspended in 100ul 1X Annexin V staining buffer. Cells were stained with 5ul Annexin V (APC) for 15mins in the dark at RT. Cells were washed once in Annexin V buffer, stained with PI and analyzed by flow cytometry. This process regularly yielded 70-80% early apoptotic cells (Annexin V+PI-).
RNA was isolated using Trizol and used for sequencing at VANTAGE next generation sequencing facility at VU.

treatment_protocol: Mouse BMDM were incubated with Annexin V+/PI- Cal27 cells stained with PKH26+ dye for 1hr. After this, macrophages were washed with ice cold DPBS to remove apoptotic tumor cells that were not engulfed by the BMDM. After additional 6hr, macrophages were harvested and processed for flow sorting to obtain BMDM that had engulfed AC (PKH26+).

tag: strain

value: Annexin V+/PI- Cal27 cell

value: macrophage

value: AC


title: RNA-seq Idax Knockout

value: Embryonic stem cells

tag: genotype

value: Idax Knockout


title: mouse08, bmdm cell [P5482_SR_14]

tag: treatment

value: untreated


title: DR53

value: Resistant


title: AEEC_3: atrial endocardial endothelial cells_3


title: KO_MSU_rep1


title: DR52


title: mouse07, bmdm cell, AC [P5482_SR_13]


title: Sample148.Yellow-bellied marmot.203877620024_R06C02


title: Sample147.Yellow-bellied marmot.203877620024_R05C02


title: KO_LPS_rep3

value: LPS


title: DR5I1


title: DR51

value: 5FU 10 uM 24h


title: AEEC_1: atrial endocardial endothelial cells_1


title: KO_LPS_rep2


title: mouse07, bmdm cell [P5482_SR_12]


title: DRU3

value: Uracil 10 uM 24h


title: Sample145.Yellow-bellied marmot.203877620024_R03C02


title: mouse06, bmdm cell, AC [P5482_SR_11]


title: KO_LPS_rep1


title: Sample144.Yellow-bellied marmot.203531420082_R06C02


title: Sample149.Yellow-bellied marmot.203877620053_R01C01


title: Sample146.Yellow-bellied marmot.203877620024_R04C02


title: AEEC_2: atrial endocardial endothelial cells_2


title: mouse06, bmdm cell [P5482_SR_10]


title: mouse05, bmdm cell, AC [P5482_SR_09]


title: DRU2


title: KO_PBS_rep2

value: PBS


title: DRU1


title: 29S5I2

value: Sensitive

value: 5FU 10 uM 24h + Irradiation (DL50)


title: Sample141.Yellow-bellied marmot.203531420082_R03C02

value: Blood


title: WT_MSU_rep3

value: MSU


title: KO_PBS_rep1


title: Sample142.Yellow-bellied marmot.203531420082_R04C02


title: Sample140.Yellow-bellied marmot.203531420082_R02C02


title: mouse05, bmdm cell [P5482_SR_08]


title: 29S5I1


title: Sample143.Yellow-bellied marmot.203531420082_R05C02


title: mouse03, bmdm cell [P5482_SR_05]


title: Sample139.Yellow-bellied marmot.203531420082_R01C02


title: KO_PBS_rep3


title: 29S52


title: mouse01, bmdm cell, AC [P5482_SR_02]


title: WT_MSU_rep1


title: mouse01, bmdm cell [P5482_SR_01]


title: 29S5I3


title: WT_LPS_rep3


title: Sample138.Yellow-bellied marmot.203531420082_R06C01


title: Sample137.Yellow-bellied marmot.203531420082_R05C01


title: mouse03, bmdm cell, AC [P5482_SR_06]


title: Lv_AI662270

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

country: China

institute: Nanjing University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
RNA-seq reads were aligned to the mm10 genome assembly using TopHat2
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: kidney

growth_protocol: The cells maintained in DMEM(Invitrogen) containing 10% fetal calf serum, penicillin (100 units/ml) and streptomycin (100 μg/ml). All cells were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted fromSV40 MES13 subline cells with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate the SV40 MES13 cells that stably express lncRNA AI662270, SV40 MES13 cells were infected with the recombinant lentivirus expressing SV40 MES13 (Lv_AI662270) or the control virus (Lv_NC) respectively. After lentivirus infection, the stable cell lines were selected using 0.5 mg/ml of puromycin. The stable lines were maintained in DMEM supplemented with 10% FBS and 0.25 mg/ml of puromycin. The stable expression of Sox9 was confirmed by qRT-PCR.

value: kidney

value: SV40 MES13

value: mesangial cell

value: lncRNA AI662270 overexpression


title: 29S51


title: WT_LPS_rep2


title: WT_MSU_rep2


title: Sample135.Yellow-bellied marmot.203531420082_R03C01


title: WT_LPS_rep1


title: Lv_NC

source_name: Kidney

value: Kidney

value: WT


title: 29SU2


title: Sample136.Yellow-bellied marmot.203531420082_R04C01


title: WT_PBS_rep2


title: WT_PBS_rep1


title: 29SU1


title: SRF rep3

city: Changsha

first: Caijiao

last: Yi

state: Hunan

address: Tianxin District

department: Aier School of Ophthalmology

institute: Central South University

data_processing:
Low-quality reads or reads containing adapter and ploy-N were filtered by using the FASTP (Version 0.18.0, Haplox, Shenzhen, China)
StringTie was used to count the numbers of reads mapped to each gene.
Gene expression was calculated and expressed as fragments per kilobase of transcript per million mapped reads (FPKM)
DESeq2 was used to determine the differentially expressed genes (DEGs)
Genome_build: Ensembl_release98
Supplementary_files_format_and_content: text files include count and FPKM values for each Sample

growth_protocol: The mice used in the experiment were raised in specific pathogen-free (SPF) conditions on a 12-hour day/night cycle with free access to food and water.

extract_protocol:
Twenty days after the second laser, total RNAs were extracted from RPE-choroid using miRNeasy Micro Kit
The RNA purity was determined by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA), RNA quantity was measured using Qubit2.0 Fluorometer (Invitrogen, Carlsbad, CA) and the RNA integrity was determined by Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). The cDNA libraries from 3 subretinal fibrosis mice and 3 healthy control mice were sequenced using the Illumina sequencing platform by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

treatment_protocol: Laser-induced choroidal neovascularization (CNV) was conducted using photocoagulator (Topcon, Tokyo, Japan) (200 mv power, 100ms duration and 60 μm spot size). Four laser burns were conducted around the optic head (at least two optic disc diameter away from the optic nerve head) in each eye. 10 days later, a second laser burn was applied to each lesion.

value: two-stage laser treatment

value: RPE-choroid


title: 116S5I3


title: 29S53


title: SRF rep1


title: Sample133.Yellow-bellied marmot.203531420082_R01C01


title: Sample132.Yellow-bellied marmot.203524370003_R06C02


title: 116S5I2


title: Sample131.Yellow-bellied marmot.203524370003_R05C02


title: siFosl1_LPS_rep2


title: control rep2

value: untreated


title: Sample130.Yellow-bellied marmot.203524370003_R04C02


title: control rep1


title: control rep3


title: siFosl1_LPS_rep1


title: 116S53


title: 29SU3


title: 116S5I1


title: siFosl1_PBS_rep2


title: MCHCF 17

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Library strategy: 16S rDNA
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: cecum

extract_protocol:
CECUM were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

value: ICR

value: cecum

value: 10 weeks

value: High fat diet +control-FMT


title: 116S51

value: Sensitive

value: 5FU 10 uM 24h


title: Sample128.Yellow-bellied marmot.203524370003_R02C02

value: Blood


title: 116S52


title: siFosl1_MSU_rep2

value: MSU


title: SRF rep2


title: siFosl1_PBS_rep1

value: PBS


title: Sample127.Yellow-bellied marmot.203524370003_R01C02


title: Sample134.Yellow-bellied marmot.203531420082_R02C01


title: MCHCF 13


title: siFosl1_MSU_rep1

value: LPS


title: 116SU3

value: Uracil 10 uM 24h


title: Sample129.Yellow-bellied marmot.203524370003_R03C02


title: siJun_MSU_rep2

value: siJun


title: Sample125.Yellow-bellied marmot.203524370003_R05C01


title: Sample126.Yellow-bellied marmot.203524370003_R06C01


title: MCHCF 12


title: MCHCF 11


title: 116SU2


title: siJun_MSU_rep1


title: Sample124.Yellow-bellied marmot.203524370003_R04C01


title: siJun_LPS_rep3


title: MCHCF 10


title: 116SU1


title: siJun_LPS_rep2


title: Sample123.Yellow-bellied marmot.203524370003_R03C01


title: DS5I2

value: 5FU 10 uM 24h + Irradiation (DL50)


title: DS5I3


title: DS5I1


title: siJun_PBS_rep2


title: siJun_LPS_rep1


title: siJun_PBS_rep1


title: DS52


title: DS53


title: MCHCF 1


title: MCHCF 6


title: MCHCF 5


title: Sample122.Yellow-bellied marmot.203524370003_R02C01


title: MCHAF 23

value: High fat diet +AOS10mg/kg-FMT


title: MCHCF 2


title: Sample121.Yellow-bellied marmot.203524370003_R01C01


title: DS51


title: siControl_MSU_rep2

value: siControl


title: Sample119.Yellow-bellied marmot.203524370006_R05C02


title: DSU3


title: Sample117.Yellow-bellied marmot.203524370006_R03C02


title: siControl_MSU_rep1


title: siControl_LPS_rep3


title: MCHAF 18


title: Sample114.Yellow-bellied marmot.203524370006_R06C01


title: DSU2


title: Sample118.Yellow-bellied marmot.203524370006_R04C02


title: Sample115.Yellow-bellied marmot.203524370006_R01C02


title: MCHAF 17


title: DSU1


title: Sample120.Yellow-bellied marmot.203524370006_R06C02


title: siControl_LPS_rep2


title: siControl_MSU_rep3


title: Sample113.Yellow-bellied marmot.203524370006_R05C01


title: MCHAF 14


title: siControl_LPS_rep1


title: MCHAF 19


title: Trisomy 18 syndrome-3

city: Xiamen

first: Jing

last: Wang

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

institute: Huaqiao University

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: human amniotic fluid cells

extract_protocol: For scRNA-seq, the PBMC were dissociated into single cells suspensions using Ficoll-Paque buffer (Sigma), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: amniotic fluid cells


title: MCHAF 15


title: Sample112.Yellow-bellied marmot.203524370006_R04C01


title: Trisomy 18 syndrome-1


title: Trisomy 18 syndrome-2


title: siControl_PBS_rep3


title: siControl_PBS_rep1


title: siControl_PBS_rep2


title: Sample110.Yellow-bellied marmot.203524370006_R02C01


title: MCHAF 4


title: Normal-1


title: Sample109.Yellow-bellied marmot.203524370006_R01C01


title: Ashi 25DPA Fiber rep3

city: Beijing

address: China Agricultural University Yuanmingyuan West Road 2#,Haidian District Beijing

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to 3-79 whole genome using HISAT v2.0.4 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: assembly 3-79

organism: Gossypium barbadense

source_name: fiber

extract_protocol:
Total RNA was extracted from the fibers of the boll samples with an EASYspin RNA Plant Mini Kit (Cat # RN0902, Aidlab Biotechnologies., Ltd).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fiber


title: MCHA10 12

value: ICR

value: High fat diet +AOS10mg/kg


title: Sertoli-WT_IgG_1

city: Xi'an

first: Bo

last: Liu

address: No.169 Changle West Road

institute: the Fourth Military Medical University

data_processing:
Data from Cut-tag experiments were mapped to mm39 genome with Bowtie 2 using default settings, with all duplicates removed by samtools.
MACS2 was used to identify peaks with default parameters.
For visualization, the aligned reads files (Binary Alignment Map [BAM]) were converted to normalized coverage files (bigWig) using bamCoverage from deepTools.
Normalization was performed using bamCoverage from deepTools.
Genome_build: mm39
Supplementary_files_format_and_content: Snapshots of the data were constructed using the Integrative Genomics Viewer (IGV). Heatmaps and Meltplots were generated with ComputeMatrix from deepTools. The motif analysis was performed using the MEME software (https://meme-suite.org/meme/doc/meme.html).

source_name: mouse Sertoli cell

growth_protocol: Primary sertoli cells were cultured at 37˚C in a shumidified atmosphere with 5% CO2.

extract_protocol:
Sertoli cells were harvested, counted, and centrifuged for 5 min at 600×g at room temperature. Aliquots of cells (60–500,000 cells), were washed twice in 1 mL Wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. Concanavalin A coated magnetic beads (Vector, AL-1003-100) were prepared as described and 5 μl of activated beads were added per sample and incubated at RT for 15 min. The unbound supernatant was removed and bead-bound cells were resuspended in 50 μl Dig-wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) including 1mg/ml BSA and a 1:50 dilution of the appropriate primary antibody. After incubation on a rotating platform for 2 h at room temperature (RT), the primary antibody was removed by placing the tube on the magnet stand to clear and pulling off all the liquid. The secondary antibody (Guinea Pig anti-Rabbit IgG antibody, ABIN101961) was diluted 1:50 in 50 μl of Dig-Wash buffer and cells were incubated at RT for 1 h. Cells were washed using the magnet stand 2-3× for 5 min in 200 μl Dig-Wash buffer to remove unbound antibodies. A 1:50 dilution of pA-Tn5 adapter complex (151017, EpiCypher) was prepared in Tag Buffer (0.01% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail). After removing the liquid on the magnet stand, 50 μl was added to the cells with gentle vortex, which was incubated with pA-Tn5 at RT for 1 h. Cells were washed 3 times for 5 min in 200 μl Tag Buffer to remove unbound pA-Tn5 protein. Next, cells were resuspended in 30 μl Activation buffer (10mM MgCl2 in Tag Buffer) and incubated at 37 °C for 1 h. To stop tagmentation, 1.5 μl of 0.5M EDTA, 0.3 μl of 10% SDS and 3 μl of 20 mg/mL Proteinase K was added to 30 μl of sample, which was incubated at 55 °C for 1 hour, and then at 65 °C for 1 hour to inactivate Proteinase K. To extract the DNA, 40 μl SPRIselect® Reagent Kit (Beckman Coulter, Inc. #B23317) were added to each tube with vortex, quickly spun and held 5 min. Tubes were placed on a magnet stand to clear, then the liquid was carefully withdrawn. Without disturbing the beads, beads were washed twice in 1mL 80% ethanol. After allowing to dry ~5 min, 25 μl of 10mM Tris pH 8 was added, the tubes were vortexed, quickly spun and allowed to sit for 5 min. Tubes were placed on a magnet stand and the liquid was withdrawn to a fresh tube.  To amplify libraries, 23 μl DNA was mixed with 1 μl of a universal i5 and 1μl of a uniquely barcoded i7 primer, using a different barcode for each sample. A volume of 25 μL Ultima Amplification Mix (Hieff NGS® Fast Tagment DNA Library Prep Kit for Illumina®, 12207-E, Yeasen) was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min (gap filling); 95 °C for 30 s; 14 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 30 s; final extension at 72 °C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.2× volume of SPRIselect® Reagent Kit (Beckman Coulter, Inc. #B23317), and libraries were incubated with beads for 15 min at RT, washed twice gently in 80% ethanol, and eluted in 30 μL 10mM Tris pH 8.0. Paired-end Illumina sequencing on the barcoded libraries using an NovaSeq 6000 System.
Sequencing libraries were generated with NEBNext® UltraTM II DNA Library Prep Kit for Illumina (E7645S), according to the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA were used for library preparation. NEBNext Multiplex Oligos for Illumina (Set 1, NEB #E7600) were used for PCR amplification of adaptor-ligated DNA. Libraries were purified with SPRIselect® Reagent Kit (Beckman Coulter, Inc. #B23317). Sequencing was performed on Illumina NovaSeq 6000 System.

treatment_protocol: untreated

value: mouse Sertoli cell

tag: chip antibody

value: moue IgG (Abmart, B30011)

value: untreated

value: wild type


title: MCHAF 5

value: cecum

value: 10 weeks


title: Sertoli-WT_IgG_2


title: MCHAF 3


title: Ashi 25DPA Fiber rep2


title: Normal-2


title: Sertoli-WT_PA1_2

value: anti-PA1 (Merck, ABE1863)


title: Ashi 25DPA Fiber rep1


title: MCHA10 10


title: MCHCF 7

value: High fat diet +control-FMT


title: MCHA10 11


title: Sample111.Yellow-bellied marmot.203524370006_R03C01

value: Blood


title: Ashi 20DPA Fiber rep3


title: Sample108.Yellow-bellied marmot.203531420023_R06C02


title: Ashi 20DPA Fiber rep2


title: Sample107.Yellow-bellied marmot.203531420023_R05C02


title: Sample103.Yellow-bellied marmot.203531420023_R01C02


title: Sample105.Yellow-bellied marmot.203531420023_R03C02


title: Sample106.Yellow-bellied marmot.203531420023_R04C02


title: Tumor NHS-rmIL12 2

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

data_processing:
Basecalling was performed using RTA 3.4.4
Demultiplexing was performed using Bcl2fastq 2.20. Demultiplexing was done allowing 1 mismatch in the barcodes
Downstream analysis was performed with the Cell Ranger v6.0.2 software using the default parameters
Genome_build: mm10 - 2020-A

source_name: Tumor

growth_protocol: 5e6 MOC22 cells were transplanted into WT B6 mice. Treatment starting on tumor day 12 consisted of three intratumor doses (every other day) of PBS or 0.4 ug NHS-rmIL12. 48 hours after the final treatment, tumors were harvested for analysis.

extract_protocol:
Single cells were captured on the 10X Chromic Controller from 10X Genomics per manufacturer recommendations.
cDNA libraries were constructed using the 3' chemistry v3.1 and library contruction kits from 10X Genomics per manufacturer recommendations.

treatment_protocol: Tumors were digested into a single cell suspension using the Mouse Tumor Dissociation Kit from Miltenyi per manufacturer recommendations.

value: Tumor

value: NHS-rmIL12 treated

tag: timepoint

value: post-treatment


title: Tumor NHS-rmIL12 1


title: Ashi 20DPA Fiber rep1


title: Sertoli-WT_PA1_1


title: Tumor Control 2

value: PBS treated


title: MCHA10 9


title: MCHAF 2

value: High fat diet +AOS10mg/kg-FMT


title: Ashi 15DPA Fiber rep2

value: fiber


title: Ashi 15DPA Fiber rep3


title: wt_m

city: Basel

first: Duygu

last: Karademir Sigurdsson

address: Klybeckstrasse 200

country: Switzerland

institute: Institute of Molecular and Clinical Ophthalmology Basel

description: Barcodes originating from this sample end with the tag "_3" in aggr_filtered_counts_matrix.h5

data_processing:
Demultiplexing was performed with cellranger mkfastq (v3.0.1).
cellranger count (v3.0.1) was used on the sequencing data of each sample to align to reference and generate feature counts for single cells.
cellranger aggr (v3.0.1) was used to combine the four samples into a single feature-barcode matrix and normalize sequencing depth between the four samples.
Seurat v3.2 was used for downstream data analysis.
Genome_build: GRCm38.p5 Release_91-2018-02-26
Supplementary_files_format_and_content: Filtered sparse matrix output from cellranger aggr that contains the counts for each gene in a column, where each row is a barcoded cell.

source_name: Retina

extract_protocol:
Retinas were removed and the vitreous and other tissues were cleared with forceps. Retinas were digested with the Worthington Tissue Dissociation kit to yield single-cell preparations. Preps were then fixed with methanol and kept at -80ºC until sequencing. On day of sequencing, samples were rehydrated and loaded onto an individual lane of a 10X Genomics droplet sequencing chip each to generate cell-bead suspensions, using the Single Cell 3' v3 chemistry.
Library construction was performed according to 10X Genomics standard protocols.
Single Cell 3ʹ v3

value: Retina

value: Postnatal day 21


title: Tumor Control 1


title: Ashi 15DPA Fiber rep1


title: MCHA10 2

value: ICR

value: High fat diet +AOS10mg/kg


title: wt_f

description: Barcodes originating from this sample end with the tag "_4" in aggr_filtered_counts_matrix.h5


title: Sample104.Yellow-bellied marmot.203531420023_R02C02


title: MCHA10 6


title: MCHA10 5


title: MCHA10 3


title: rd10_f

description: Barcodes originating from this sample end with the tag "_2" in aggr_filtered_counts_matrix.h5


title: Sample102.Yellow-bellied marmot.203531420023_R06C01


title: MCHA10 1


title: Ashi 10DPA Fiber rep3


title: rd10_m

description: Barcodes originating from this sample end with the tag "_1" in aggr_filtered_counts_matrix.h5


title: Sample101.Yellow-bellied marmot.203531420023_R05C01


title: MCHA10 4


title: Sample99.Yellow-bellied marmot.203531420023_R03C01


title: MCHFD 20

value: High fat diet


title: Ashi 10DPA Fiber rep1


title: Sample98.Yellow-bellied marmot.203531420023_R02C01


title: Sample100.Yellow-bellied marmot.203531420023_R04C01


title: Sample96.Yellow-bellied marmot.203531420078_R06C02


title: MCHFD 19


title: Dapl1-KO

city: Houstion

first: Xiaofei

last: Zhou

state: Texas

address: 7455 Fannin Street

department: Immunology

institute: UT MD Anderson Cancer Center

description: Single Cell 3' v3

data_processing:
Single cell libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility.
The raw reads of FASTQ files were aligned to the Mouse reference genome build mm10 to perform read alignment, UMI counting and secondary analysis, using cellranger 5.0.0 software.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: immune cell from TILs

extract_protocol:
CD45+CD90.2+ immune cells were sorted from tumor by FACS.
Single cell libraries were prepared for sequencing using standard 10x Genomics protocols.

value: CD45+CD90.2+ immune cells from TILs


title: Ashi 5DPA Fiber rep3


title: WT

description: Single Cell 3' v3

value: WT


title: Sample95.Yellow-bellied marmot.203531420078_R05C02


title: Sample97.Yellow-bellied marmot.203531420023_R01C01


title: Ashi 5DPA Fiber rep1


title: Ashi 5DPA Fiber rep2


title: MCHFD 17

value: cecum

value: 10 weeks


title: MCHFD 18


title: Ashi 10DPA Fiber rep2


title: N2a siEwsr1 rep3

city: Barcelona

first: Riccardo

last: Aiese Cigliano

address: Calle Comte D'Urgell 240

country: Spain

institute: Sequentia Biotech SL

data_processing:
Sequenced reads were trimmed and clipped using Bbduk v35.85, minimum quality was set to 25 and minimum read lenght to 35 bp
Reads were mapped against the Mus musculus genome (GRCm38) using STAR v2.5.2b with double pass mode
Read summarization was performed with FeatureCounts v1.5.1 enabling the paired-end mode, considering only reads with MAPQ > 30
Lowly expressed genes were removed with HTSFilter and differential expression analysis was performed with edgeR using the TMM normalization
Differential splicing analysis was performed with rMATS v4.4.1
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: N2a cells

extract_protocol:
RNA from sicontrol and siEwsr1 N2a cells was isolated and DNase digested using the RNAeasy Mini Kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA); TruSeq RNA technology with Ribo-Zero ribosomal RNA reduction chemistry

treatment_protocol: 50,000 N2a cells were subjected to double pulse of transfection by using Lipofectamine RNAiMAX, and cells were collected 24 hours after the last pulse of transfection. N2a cells were transfected with control siRNA and siRNA for Ewsr1 at the final concentration of 100 µM.


title: Ashi 0DPA Fiber rep2


title: N2a siEwsr1 rep2


title: MCHFD 11


title: Ashi 0DPA Fiber rep3


title: N2a siEwsr1 rep1


title: Sample93.Yellow-bellied marmot.203531420078_R03C02


title: MCHFD 10


title: Sample94.Yellow-bellied marmot.203531420078_R04C02


title: N2a sictrl rep2

value: siCtrl


title: Ashi 0DPA Fiber rep1


title: LuoSaiNa 25DPA Fiber rep3


title: N2a sictrl rep1


title: MCHFD 7


title: Sample92.Yellow-bellied marmot.203531420078_R02C02

value: Blood


title: Sample90.Yellow-bellied marmot.203531420078_R06C01


title: MCHFD 8


title: Sample89.Yellow-bellied marmot.203531420078_R05C01


title: LuoSaiNa 25DPA Fiber rep2


title: lncRNA Mature_1

city: Shenzhen

first: Saineng

last: Hu

address: Lianhua Road Futian District

department: Biomedical Research Institute

institute: Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center

description:
lncRNA.expression.xls
mRNA.expression.xls
circRNA.expression.xls
GHR191286_order_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: Bone marow B cells

extract_protocol:
Total RNA was purified from sorted populations of cells by using Trizol Reagent kit and Spin Column & Collection Tube.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

tag: development stage

value: Mature B cells

value: wild type


title: lncRNA Immature_1

value: Immature B cells


title: lncRNA Pre_1

value: Pre-B cells


title: MCHFD 1


title: Sample88.Yellow-bellied marmot.203531420078_R04C01


title: LuoSaiNa 25DPA Fiber rep1

value: fiber


title: LuoSaiNa 20DPA Fiber rep3


title: lncRNA Pro_1

value: Pro-B cells


title: MCcon 12

value: control


title: Sample91.Yellow-bellied marmot.203531420078_R01C02


title: Sample87.Yellow-bellied marmot.203531420078_R03C01


title: LuoSaiNa 20DPA Fiber rep1


title: LuoSaiNa 20DPA Fiber rep2


title: MCcon 11

value: ICR


title: AML01_Alu_pool_cell_96 [i508_H12_i712_201027_AML01_Alu_pool_S4_L001]

city: Newcastle

first: Heather

last: Lee

address: University Drive, Callaghan

institute: The University of Newcastle

data_processing:
library strategy: single-cell transposable element methylation sequencing (scTEM-seq)
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis. We excluded cells with coverage of less than 1000 annotated TE sites.
Downstream analysis was performed using Seqmonk and custom R scripts
Genome_build: GRCh38
Supplementary_files_format_and_content: The genome-wide CpG methylation reports (.cov files) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>

source_name: negative control

growth_protocol: Enriched mononuclear cells were purified from peripheral blood using Lymphoprep density gradient medium (StemCell, catalog # 7851) and SepMate tubes (StemCell, catalog # 85450), and cryopreserved. Cryopreserved primary human cells were resuspended in thawing media (IMDM, 20% FBS), washed twice and resuspended in thawing media. The cells were then rested for 1h at 37°C before preparation for flow cytometry. Cells (1x106/100ul) were stained with 1.5μg/mL propidium iodide (PI, Sigma-Aldrich), 1:20 CD45-PECy7 (2D1, Invitrogen), 1:20 CD33-FITC (WM-53, Invitrogen) and 1:20 CD19-BV711 (SJ25C1, BD Biosciences). Single blasts (PI-CD45dim) were collected in 2.5μL RLT Plus Lysis Buffer containing 1U/μL SUPERase-In (Invitrogen) in 96 well plates.

extract_protocol:
We utilised the G&T-seq protocol to separate genomic DNA and RNA from the single-cell samples [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015.]. Genomic DNA from each cell was purified and bisulphite conversion was performed as described [Angermueller, C., et al., Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nature methods, 2016], with minor modifications.
Bisulphite conversion was carried out using the EZ-96 DNA Methylation-Direct MagPrep Kit (Integrated Sciences, catalog # D5054) with half volumes of the manufacturer’s instructions. Bisulphite converted DNA was eluted directly from MagBeads into PCR-mix, and amplification of TEs was performed with MagBeads still in the well. PCR cycling conditions used were 95°C for 5 min (1 cycle), 98°C for 20 sec, 53°C for 15 sec, 72°C for 1 min (35 cycles), and 72°C for 10min (1 cycle). PCR mix used 7.5µl 1x KAPA HiFi hotStart Uracil + ReadyMix (Millennium, catalog # ROC-07959079001) and 0.3µM primer mix. Primers were designed against SINE Alu and LINE-1 consensus sequences (Supplementary Figure S2A) and are contained in Supplementary Tables S1 and S2. After amplification, plates of 96 single cell libraries purified using a 1.2x volume of AMPure XP beads (Beckman Coulter, catalog # A63881). All libraries were then quantified using the Qubit dsDNA HS kit (Life Technologies), normalised and pooled to a single tube. Pools where then added to 0.8µM NEBNext dual index oligo sets (Genesearch, catalog # E7780S) and 14.5µl 1x KAPA HiFi HotStart ReadyMix (Millennium, catalog # ROC-07958935001) for indexing and adaptor addition. PCR cycling conditions used were 98°C for 45 sec (1 cycle), 98°C for 15 sec, 65°C for 30 sec, 72°C for 30 sec (5 cycles), and 72°C for 5 min (1 cycle). Pools were then purified using 0.9x volume of Ampure XP beads, normalised and combined for sequencing.

value: NC

value: genomic DNA, bisulfate treated

tag: molecule subtype

value: negative control


title: MCHFD 5

tag: tissue

value: High fat diet


title: Sample86.Yellow-bellied marmot.203531420078_R02C01

address: 695 Charles E. Young Drive South, Box 708822

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

source_name: Blood

extract_protocol: genomic DNA was extracted


title: AML01_Alu_pool_cell_85 [i508_H1_i701_201027_AML01_Alu_pool_S4_L001]


title: LuoSaiNa 15DPA Fiber rep3


title: MCcon 10

value: cecum

tag: age


title: MCcon 9

value: 10 weeks


title: Sample84.Yellow-bellied marmot.203531420073_R06C02


title: Sample85.Yellow-bellied marmot.203531420078_R01C01


title: AML01_Alu_pool_cell_12 [i501_A12_i712_201027_AML01_Alu_pool_S4_L001]


title: Sample83.Yellow-bellied marmot.203531420073_R05C02


title: LuoSaiNa 15DPA Fiber rep2


title: AML01_Alu_pool_cell_1 [i501_A1_i701_201027_AML01_Alu_pool_S4_L001]


title: MCcon 8


title: MCcon 5


title: KG1a_Alu_pool_cell_55 [i505_E7_i707_KG1a_Alu]

growth_protocol: KG1a cells were resuspended in binding buffer before staining with annexin V and 7-AAD. Live cells (Annexin V - /7-AAD -) were sorted into individual wells of a 96 well plate containing lysis buffer 2.5μL RLT Plus Lysis Buffer (QIAGEN, catalog # 1053393) containing 1U/μL SUPERase-In (ThermoFisher, catalog # AM2696) in 96 well plates. Before sorting, bulk samples of 1000000 cells were collected from both the untreated and treated populations.

tag: cancer type

tag: Sex


title: LuoSaiNa 10DPA Fiber rep3


title: KG1a_Alu_pool_cell_54 [i505_E6_i706_KG1a_Alu]

tag: sample type


title: Sample81.Yellow-bellied marmot.203531420073_R03C02


title: Sample79.Yellow-bellied marmot.203531420073_R01C02


title: KG1a_Alu_pool_cell_43 [i504_D7_i707_KG1a_Alu]


title: Sample82.Yellow-bellied marmot.203531420073_R04C02


title: MCcon 4


title: MCcon 3


title: LuoSaiNa 10DPA Fiber rep2

tag: developmental stage


title: LuoSaiNa 10DPA Fiber rep1


title: MCcon 2


title: KG1a_Alu_pool_cell_42 [i504_D6_i706_KG1a_Alu]


title: LuoSaiNa 5DPA Fiber rep3


title: LuoSaiNa 15DPA Fiber rep1


title: MCcon 1


title: LuoSaiNa 5DPA Fiber rep2


title: MCA10 10


title: MCA10 9


title: LuoSaiNa 5DPA Fiber rep1


title: Sample78.Yellow-bellied marmot.203531420073_R06C01


title: Ethyl carbamate 1

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

institute: University of Saskatchewan

data_processing:
HISAT2 v2.0.5 used for mapping to the C. elegans reference genome
FeatureCounts v1.5.0-p3 used for Quantification
StringTie v1.3.3 used for novel gene prediction.
DESeq2 v1.20.0 used for differential expression analysis
Genome_build: wbcel235
Supplementary_files_format_and_content: Wu_2021_ifg1_processed_data.xls (Abundance count for FPKM for gene expression and DEG analysis)

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Total RNA extracted using the RNAqueous Total RNA Isolation Kit
Standard Illumina protocols with oligo-dT beads

value: whole animal

value: 100mM ethyl carbamate (24h)

value: wildtype

value: young adult


title: Ethyl carbamate 2


title: Ethyl carbamate 3


title: LuoSaiNa 0DPA Fiber rep3


title: MCA10 8


title: EV control 3


title: Sample77.Yellow-bellied marmot.203531420073_R05C01

city: Los Angeles

first: Steve

institute: University of California, Los Angeles

value: Blood


title: Sample80.Yellow-bellied marmot.203531420073_R02C02


title: Sample76.Yellow-bellied marmot.203531420073_R04C01


title: Sample74.Yellow-bellied marmot.203531420073_R02C01


title: LuoSaiNa 0DPA Fiber rep1


title: Sample73.Yellow-bellied marmot.203531420073_R01C01


title: LuoSaiNa 0DPA Fiber rep2


title: EV control 2


title: Sample75.Yellow-bellied marmot.203531420073_R03C01


title: EV control 1


title: MCA10 7


title: XH33 25DPA Fiber rep3


title: MCA10 6


title: Sample71.Yellow-bellied marmot.203531420042_R05C02


title: MCA10 5


title: XH33 25DPA Fiber rep2


title: MCA10 3

value: AOS 10mg/kg


title: MCA10 4


title: WB

first: Kelang

last: Kang

address: No.1 Nongda Road, Furong District, Changsha, China

institute: Hunan Agriculture University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Gallus-gallus-6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Gallus gallus

source_name: pectoralis muscle

extract_protocol:
Samples were dissociated with enzymatic digestion with collagenase I for 30 minutes at a concentration of 0.15 g per 100 mL. Then single-cell suspension were obtained by passing the dissociated cell suspensions through a 40 μm cell strainer. All isolated cells were applied to magnetic bead separation method to remove dead cells. Then trypan blue (Thermo Fisher Scientific, waltham, MA, USA) and Automated Cell Counter (TC 20TM, BIO-RED Inc., CA, USA) were used to evaluate the viability of filtrated single cells. Noteworthy, the lipid cells were excluded. Following counting, the appropriate volume was calculated for a target capture of 8000 cells.
RNA libraries were prepared with Chromium Single cell 3'Reagent v3 Kits according to the manufacturer's protocol.

value: pectoralis muscle

tag: disease state

value: wooden breast birds

value: commercial breeds


title: XH33 25DPA Fiber rep1

value: fiber


title: NORM

value: healthy birds


title: XH33 20DPA Fiber rep3


title: XH33 20DPA Fiber rep2


title: M_S_KD_3

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Breast cancer cell-line MCF7

growth_protocol: MCF7 control-shRNA and SETDB1-shRNA cells were cultured in RPMI medium with 5% DCC for 48hrs prior to estrogen (E2) treatment.

extract_protocol:
Total RNA from MCF7 control-shRNA and SETDB1-shRNA cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: MCF7 control-shRNA and SETDB1-shRNA cells were incubated with estrogen (E2) for 12hrs and the RNA was isolated for RNA-seq analysis.

tag: cell-line

tag: shRNA

value: SETDB1 shRNA

value: Stable tranfection were generated using puromycin selection


title: MCA10 2

value: ICR


title: Sample72.Yellow-bellied marmot.203531420042_R06C02

last: Horvath


title: Sample68.Yellow-bellied marmot.203531420042_R02C02


title: Sample70.Yellow-bellied marmot.203531420042_R04C02


title: XH33 20DPA Fiber rep1


title: M_S_KD_1


title: Sample67.Yellow-bellied marmot.203531420042_R01C02


title: Sample69.Yellow-bellied marmot.203531420042_R03C02


title: MCA10 1


title: MIHCF 17

source_name: small intestinal

extract_protocol:
small intestinal were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

value: small intestinal

value: High fat diet +control-FMT


title: MIHCF 12

value: 10 weeks


title: XH33 15DPA Fiber rep1


title: M_Con_1

value: control non-targeted shRNA


title: M_Con_3


title: M_S_KD_2


title: XH33 10DPA Fiber rep3


title: M_Con_2


title: MIHCF 10