title: ependymoma_1_region_C

value: C


title: long_term_HSC_CD150+CD48-cKit+Sca1+ cells [SLAM_KSL_p27low_3]

status: Public on Dec 20 2019

type: SRA

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.6.0) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow from femurs and tibias

extract_protocol:
BM hematopoietic cells was isolated from femurs and tibias by flushing and depleted of red blood cells by ACK Lysing Buffer (Thermo Fisher Scientific).
CD150+CD48-cKit+Sca1+ cells were FACS-purified.
Single-cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer.
Libraries were prepared using the Illumina Nextera XT DNA preparation kit.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 2500.
Samples were used to construct Nextera XT libraries (Illumina) from 125 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems).

tag: treatment

value: Ctrl


title: RNAseq_RT4_Ni_exposed_Dup

city: Charlottesville

first: Zhenjia

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

country: USA

institute: University of Virginia

data_processing:
ChIP-Seq reads were aligned to the human reference genome (GRCH38/hg38) using BWA. SAM files were then converted into BAM format using samtools. Bedtools was used to convert BAM files into BED format. Only 1 copy of the redundant reads that were mapped to the exact same location in the genome was retained. All non-redundant reads from H3K4me3 ChIP-Seq datasets were included for downstream analyses without peak calling.
RNA-Seq raw sequence were mapped to human genome using STAR ; multi hits removed. Gene expression levels were quantified as count, TPM and FPKM. Differential gene expression was calculated using DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: ChIP-seq: promoter (TSS +/-2kb) RPKM, RNA-seq: gene level count, TPM, FPKM

organism: Homo sapiens

growth_protocol: Human lung epithelial BEAS-2B cells (ATCC, CRL-9609) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Cellgro) supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum (FBS, Atlanta Biologicals) at 37°C and 5 % CO2. Human urinary bladder epithelial RT4 cells were cultured in McCoy's 5A Modified Medium (Life Technologies, Carlsbad, CA), supplemented with 10% FBS (Atlanta Biologicals) and 0.5% Penicillin‐Streptomycin at 37°C and 5% CO2. Human urinary bladder epithelial RT4 cells (a generous gift from Dr. Tang, New York University School of Medicine, NY) were cultured in McCoy's 5A Modified Medium (Life Technologies, Carlsbad, CA), supplemented with 10% FBS (Atlanta Biologicals) and 0.5% Penicillin‐Streptomycin at 37°C and 5% CO2. The cells were exposed to 100 μM NiCl2 for 6 weeks. Following exposure, the cells were washed and cultured in Ni‐free medium for 2 weeks to obtain Ni‐washed‐out cells.

extract_protocol:
Total RNA was isolated using RNeasy Kit (Qiagen 74104). ChIP was performed using samples isolated from two biological replicates. The cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500bp fragments. ChIP was performed as described earlier using ChIP grade antibodies against H3K4me3 (Millipore, 07-473).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002) according to manufacturer’s protocol. ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP -202-1024), according to manufacturer’s protocol.

treatment_protocol: Both BEAS-2B and RT4 cells cells were exposed to  100 μM NiCl2  for 6 weeks. Following exposure, the cells were washed and cultured in Ni‐free medium for 2 weeks to obtain Ni‐washed‐out cells. For BEAS-2B cells, following 6-week exposure, a homogenous populations of Ni-exposed cells was isolated as described. Briefly, the Ni-exposed cells were then plated in 15 cm plates at the rate of 1000, 500, 100 and 50 cells per plate in Ni-free medium. Nicely separated single colonies were randomly isolated and the populations were expanded in Ni-free medium. A randomly selected homogenous population of Ni-washed-out cells (Ni-W)  in culture for >6 months post Ni exposure was used for a detailed examination.

tag: cell line

tag: tissue

value: Human urinary bladder


title: RNAseq_RT4_Ni_washout


title: CRC ≤ 45 years. Sample 147

type: genomic

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

hyb_protocol: Hybridization was carried out in a Roche NimbleGen Hybridisation Chamber (Roche NimbleGen, Inc.) for 48 h.

scan_protocol: Slides were washed and scanned using a NimbleGenMS 200 Microarray Scanner (Roche NimbleGen, Inc.).

data_processing: Array image ﬁles produced by the MS 200 Data Collection Software were imported into DEVA v1.2.1(Roche NimbleGen Inc.) for analysis. In addition,segmentation analysis was performed in all cases byusing circular binary segmentation (CBS) available in waviCGH software (http://wavi.bioinfo.cnio.es/).

molecule: genomic DNA

source_name: Rectum

label_protocol: One microgram of genomic DNA(gDNA) from each test and reference sample(Human Genomic DNA [Male G1471/FemaleG1521] from Promega Corporation, Madison, WI) was labeled using the NimbleGen Dual-C olor DNALabeling Kit.

extract_protocol: DNA was extracted using proteinase K digestion, phenol/chloroform extraction, Phase Lock Gel Light (Eppendorf AG, Hamburg, Germany), and ethanol precipitation.

tag: Sex

value: Male

tag: age

tag: molecular classification

value: MSS y CIMP-Low/0

tag: sample type

value: reference


title: CRC ≤ 45 years. Sample 146

source_name: Left colon

source_name: Human Genomic DNA [Male G1471/FemaleG1521] from Promega Corporation


title: long_term_HSC_CD150+CD48-cKit+Sca1+ cells [SLAM_KSL_p27high_4]


title: long_term_HSC_CD150+CD48-cKit+Sca1+ cells [SLAM_KSL_p27low_1]


title: genomic DNA from HBMVECs in EBM plus EVs isolated from GBM8 neurosphere culture_C3

city: Houston

first: Aleksandar

last: Milosavljevic

state: Texas

address: 1 Baylor Plaza

department: Genetics and Genomics

institute: Baylor College of Medicine

description: Cell pellet from medium (floating cells) and Matrigel (dispase treated and resuspended)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: Illumina Human 450K Infinium Methylation BeadChip beta values from GenomeStudio were input to RnBeads [version 2.0.1] with annotations from RnBeads.hg19 [version 1.14.0] (Assenov et. al., 2014) in R [version 3.5.1]. Filtering removed probes annotated as non-CpG, cross-reactive, snp-containing, or on sex chromosomes. Probes with variance of less than .05 across all samples were excluded.

label: Cy5 and Cy3

label_protocol: Illumina Cy3 and Cy5

extract_protocol: Genomic DNAs for methylation analysis were purified (Qiagen QIAamp® DNA Micro Kit, Qiagen,Stanford, CA, USA)

tag: disease state

value: normal

tag: cell type

value: HBMVECS

tag: protocol

value: 16 hours on Matrigel with GBM8 EVs in Basal medium


title: CRC ≤ 45 years. Sample 143


title: genomic DNA from HBMVECs in EBM plus angiogenic growth factors_B3

value: 16 hours on Matrigel with angiogenic growth factors in Basal medium


title: genomic DNA from HBMVECs in EBM plus EVs isolated from GBM8 neurosphere culture_C1


title: CRC ≤ 45 years. Sample 142


title: Chimpanzee_PrefrontalCortex_NeuNpositive_ATAC_5

city: Utrecht

first: Menno

middle: P

last: Creyghton

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
ATAC-seq: Illumina sequencing reads were trimmed to remove Nextera adapters using cutadapt (1.13). Reads were mapped using bowtie version 1.1.2 (http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length 36 base pairs) or with multiple aligment. Duplicate reads were discarded using Samtools verions 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq and ATAC-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac and ATAC bigwig files are in .bw

organism: Pan troglodytes

source_name: Chimpanzee Prefrontal Cortex

extract_protocol: NEBNext High-Fidelity PCR (NEB)

value: Chimpanzee Prefrontal Cortex


title: RNAseq_RT4_Ni_exposed


title: genomic DNA from HBMVECs in EBM plus angiogenic growth factors_B2


title: CRC ≤ 45 years. Sample 141

source_name: Righ colon

value: MSS y CIMP-High


title: RNAseq_RT4_Untreated_Dup


title: CRC ≤ 45 years. Sample 140

value: Female


title: RNAseq_RT4_Untreated


title: Chimpanzee_PrefrontalCortex_NeuNpositive_ATAC_4


title: CRC ≤ 45 years. Sample 145


title: long_term_HSC_CD150+CD48-cKit+Sca1+ cells [SLAM_KSL_p27high_3]


title: ChIPseq_B2B_Ni_washout_H3K4me3

value: Human lung epithelial cell line


title: Chimpanzee_WhiteMatter_H3K27ac_3

source_name: Chimpanzee White Matter

extract_protocol: TruSeq DNA sample preparation kit (Illumina)

tag: antibody

value: Chimpanzee White Matter


title: long_term_HSC_CD150+CD48-cKit+Sca1+ cells [SLAM_KSL_p27high_1]


title: long_term_HSC_CD150+CD48-cKit+Sca1+ cells [SLAM_KSL_p27high_2]


title: Chimpanzee_PrefrontalCortex_NeuNnegative_ATAC_4


title: ChIPseq_B2B_Ni_washout_input


title: Chimpanzee_WhiteMatter_H3K27ac_2


title: Chimpanzee_WhiteMatter_H3K27ac_1


title: Sample_TH3_NEG

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

description: Thyroid3 Nkx2-1 negative

data_processing:
Fastq files were aligned to the GRCm38 reference genome using STAR and default parameters
Ensembl Mus_musculus.GRCm38.92.gtf gene annotations were used for gene count summarization, gene counts were obtained using STAR
Limma voom was used to perform differential expression analysis, using false discovery rate (FDR) < 0.05 as threshold for statistical significance
Genome_build: GRCm38
Supplementary_files_format_and_content: tab separated values containing expression count matrix

molecule: polyA RNA

source_name: embryonic progenitors

growth_protocol: All embryonic progenitor populations were isolated from mouse embryos using the Nkx2-1GFP reporter mouse. Briefly, breeding cages were set up with one male and three female mice and the morning of the day a vaginal plug was detected was defined as embryonic day E0.5. Foregut endoderm and ectoderm cells were isolated from E8.25 embryos, forebrain and lung cells were isolated from E9.0 embryos and thyroid cells were isolated from E13.5 embryos

extract_protocol:
For each replicate (3 replicates per population) to be used in RNA-Seq, samples from several sorts were pooled. The mRNA was isolated using magnetic beads-based poly(A) selection, fragmented, and randomly primed for reverse transcription
These cDNA fragments were then end-repaired, added with a single ‘A’ base, and ligated to Illumina® Paired-End sequencing adapters. The products were purified and PCR-amplified to create the final cDNA library. The libraries from individual samples were pooled in groups of four for cluster generation on the Illumina® cBot using Illumina® TruSeq® Paired-End Cluster Kit

tag: developmental stage

value: Thyroid


title: ChIPseq_B2B_Ni_exposed_H3K4me3


title: ChIPseq_B2B_Untreated_input


title: Sample_TH3+

description: Thyroid3 Nkx2-1 positive


title: ChIPseq_B2B_Untreated_H3K4me3


title: Chimpanzee_WhiteMatter_RNAseq_2

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
RNA-seq:  Sequencing reads were aligned using HISAT2 version 2.0.5. Reads that mapped to multiple locations and duplicate reads were removed using Samtools version 1.3.1. Reads in genes were counted using the featureCount function of the Rsubread package in R.  The GTF file of Marmoset genes was obtained here: ftp://ftp.ensembl.org/pub/release-91/gtf/callithrix_jacchus.
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw; RNA-seq count values are in _RNAseq.txt;

extract_protocol: TruSeq Stranded mRNA Library Preparation (Illumina)

value: White Matter


title: Chimpanzee_WhiteMatter_RNAseq_1


title: genomic DNA from HBMVECs in EBM_A3

value: 16 hours on Matrigel with Basal medium


title: Sample_TH2_NEG

description: Thyroid2 Nkx2-1 negative


title: genomic DNA from HBMVECs in EBM_A2


title: RNA-seq T11F80L_8 rep2

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description:
CRISPR/Cas9 engineered stable mutant cell-line
HS18_T11F80L_8_37_2

data_processing:
Single reads were mapped onto the Hg19 human genome using STAR_2.5.2b  (Bioinformatics. 2013 Jan 1;29(1):15–21), with the following options : --outSAMmultNmax 50, --outFilterMatchNminOverLread 0.4, --quantMode TranscriptomeSAM
Per gene read counts and normalized RPKM (Reads Per Kilobase of transcript per Million mapped reads) were calculated using RSEM-1.3.0 (BMC Bioinformatics. 2011 Aug 4;12:323). Only genes with an RPKM value above 1.2 in at least one sample were considered as transcribed and kept for further analysis.
Differential transcription was calculated using DESeq2 (Genome Biol. 2014 Dec 5;15(12):550.) Genes with an absolute fold-change value above 0.5 and an adjusted p-value below 0.05 were submitted to Gene Ontology (GO) analysis.
Genome_build: UCSC Hg19

source_name: Embryonic kidney cell line

growth_protocol: 0.15 x 106 cells per well were seeded in 6-well plates and incubated at 37°C for 72 hours.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit (Qiagen 74104) according to the manufacturer protocol. The RNA was eluted in water and quantified.
Samples quality control and sequencing was done by the UNIL Genomic Technology Facility (GTF). Ribosomal RNA was removed using the Ribo-zero rRNA removal kit (Illumina MRZH11124). Libraries were prepared using the truSEQ stranded RNA LT kit (Illumina) and 80-nucleotides single-read high-throughput sequencing was performed with 6 samples per line (multiplexing).

treatment_protocol: no treatment

tag: experiment

value: RNA-seq

tag: cell-line

value: HEK 293

tag: mutation

value: THAP11-F80L homozygous

tag: chip antibody


title: Sample_TH2+

description: Thyroid2 Nkx2-1 positive


title: CRC ≤ 45 years. Sample 139

value: Male

value: MSS y CIMP-Low/0


title: RNA-seq T11F80L_8 rep1

description:
CRISPR/Cas9 engineered stable mutant cell-line
HS17_T11F80L_8_37_1


title: Marmoset_PrefrontalCortex_Input

organism: Callithrix jacchus

source_name: Marmoset Prefrontal Cortex

value: Prefrontal Cortex


title: Sample_TH1+

description: Thyroid1 Nkx2-1 positive


title: Sample_TH1_NEG

description: Thyroid1 Nkx2-1 negative


title: CRC ≤ 45 years. Sample 138

value: reference


title: CRC ≤ 45 years. Sample 137


title: CRC ≤ 45 years. Sample 136


title: CRC ≤ 45 years. Sample 135


title: genomic DNA from HBMVECs in EBM plus angiogenic growth factors_B1

value: normal

value: HBMVECS


title: CRC ≤ 45 years. Sample 134


title: RNA-seq WT rep 2

description:
Wild-type HEK 293
HS14_WT_37_2

value: Parental


title: Marmoset_Cerebellum_Input

source_name: Marmoset Cerebellum

value: Cerebellum


title: Marmoset_PrefrontalCortex_H3K4me3_2

value: anti-H3K4me3 (Abcam, catalog#:ab8580)


title: Marmoset_PrefrontalCortex_H3K4me3_1


title: Marmoset_Cerebellum_H3K4me3_2


title: ChIP-seq THAP11 IP T11F80L

description: CRISPR/Cas9 engineered stable mutant cell-line

data_processing:
Paired reads were mapped individually onto the Hg19 human genome using STAR_2.5.2b  (Bioinformatics. 2013 Jan 1;29(1):15–21), with the following options : --outSAMmultNmax 50, --outFilterMatchNminOverLread 0.4, --quantMode TranscriptomeSAM. The STAR output was parsed using in-house scripts to extract paired-reads with up to 10 muliple matches on the genome and with a maximum redundancy of 3
Peaks were detected using the Model-based Analysis of ChIP-Seq (MACS2) tool (Genome Biol. 2008;9(9):R137)  (format = BEDPE, q-value cut-off = 10-3, duplicates allowed = 3, Broad region calling = off). MACS peaks were further filtered using the bins-based method described in Genome Res 24: 37–51. Only MACS-identified peaks intersecting with the selected bins were kept.
Peak scores were calculated as follows: (i) peak fragments of the IP sample were summed on the whole peak region, and normalized to total fragments in the sample and peak width (bringing all peaks width at an arbitrary 1 kb size); (ii) the same procedure was done for the input sample; (iii) for each sample, the peak score was calculated as the log2 of the normalized IP counts (done in (i)) minus the input normalized counts (done in (ii)).
Genome_build: UCSC Hg19

growth_protocol: Cells were expanded at 37°C and approximately 150 millions of cells were used per IP.

extract_protocol:
Cells were on-plate crosslinked with 1% of formaldehyde (Sigma F1635-500ml) during precisely 8 minutes, then 0.125 M of Glycine (Axonlab A1067.5000) was added to terminate the crosslinking reaction. Cells were washed twice with cold PBS 1X and lyzed for 10 min on ice in 0.5% NP40 lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40, supplemented with one tablet of complete EDTA-free Protease Inhibitor Cocktail (Roche 04693132001) per 50 mL; 950 uL per 10 million of cells). The nuclei were recovered by high-speed centrifugation (5 minutes at 3200 x g, at 4 C), resuspended in nuclei lysis buffer (NLB, 50 mM Tris-HCl pH 8.1, 10 mM EDTA pH 8.0, 1% SDS, supplemented with one tablet of complete EDTA-free Protease Inhibitor Cocktail) and incubated for 20 minutes at 4°C.  Chromatin was sonicated using a Bioruptor Pico (Diagenode) to obtain fragments of around 200 base pairs. Sonicated chromatin was clarified by centrifugation and subsequently 1:2 diluted in 2X IP buffer (33.4 mM Tris pH 8.1, 167 mM NaCl, 167 mM LiCl, 2.4 mM EDTA pH 8.0, 2.2% Triton X-100, 0.02% SDS, supplemented with one tablet of complete EDTA-free Protease Inhibitor Cocktail) before being snap frozen in liquid nitrogen. A 50 uL aliquot was kept to analyze the chromatin quality and concentration. The frozen sonicated chromatin was stored at - 80°C.
The day prior to the chromatin immunoprecipitation, protein G agarose beads (Roche 1243233) were washed with NLB:IP buffer (a mix of equal amounts of NLB and 2X IP buffer) and further incubated overnight under rotation at 4°C) in NLB:IP buffer supplemented with 100 ug/mL of Bovine Serum Albumine (BSA, Sigma A8022-100).  The sonicated chromatin was thawed. A 60 uL aliquot was kept for the input sample, while, for each IP, 9 ug of chromatin (in a total volume of 1200 uL of NLB:IP buffer) was overnight incubated under rotation at 4°C with 2 ug of anti-THAP11 antibody. Samples were further incubated under rotation at room temperature with 60 uL of the above washed and BSA-blocked protein G agarose beads. Immunoprecipitated samples were washed twice with IPWB1 buffer (IP wash buffer 1: 20 mM Tris pH 8.1, 50 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100 and 0.1% SDS). Each IP was performed 5 times in parallel as described and subsequently pooled to form a single IP sample at this step, after the washes with IPWB1 buffer. Pooled IP samples were then washed once with IPWB2 bffuer (IP wash buffer 2: 10 mM Tris pH 8.1, 250 mM LiCl, 1 mM EDTA pH 8.0, 1% NP40 and 1% Na-deoxycholate) and finally twice with TE buffer (10 mM Tris pH 8.1, 1 mM EDTA pH 8.0). Two elutions with IPEB buffer (elution buffer: 100 mM NaHCO3, 1% SDS) were sequentially done (5 minutes at 37°C under agitation) and pooled.  The input sample was thawed and supplemented with 190 uL of IPEB buffer. Eluates (IP) and input samples were decrosslinked by overnight incubation at 65°C in presence of 20 ug/mL of RNAse A (DNAse-free RNAse A, Roche 1119915) and 300 mM of NaCl. The samples were further incubated during 90 minutes at 45°C with 350 ug/mL of proteinase K (Promega V3021). Samples were finally purified using the Nucleospin Gel and PCR clean-up kit (Macherey-Nagel 740609) using the NTB buffer for SDS-containing samples. Samples were eluted with 50 uL of the pre-warmed (72°C) buffer NE (from the kit), and subsequently re-eluted using the previous eluate. DNA yield was quantified using a Qubit spectrophotometer.
For each IP sample, two separate libraries were prepared and sequenced, using the same immunoprecipitated-DNA material. For this, 5 ng of purified DNA was used to prepare paired-end sequencing libraries using the MicroPlex Library Preparation kit (Diagenode C05010014) following the manufacturer instructions. Here, 8 PCR cycles were done for DNA amplication and the DNA fragments were not size selected. Then, libraries were purified using AMPure XP magnetic beads (Diagenode) and entrusted to the UNIL Genomic Technology Facility (GTF) for 100-nucleotide paired-end high-throughput sequencing (Illumina, HiSeq 2100) with 3 samples per line (multiplexing).

treatment_protocol: No treatment

value: ChIP-seq

value: anti-THAP11 (sheep, R & D Systems AF5727)


title: Sample_LU3NEG

description: Lung3 Nkx2-1 negative

value: Lung


title: Sample_LU3+

description: Lung3 Nkx2-1 positive


title: Sample_LU2_NEG

description: Lung2 Nkx2-1 negative


title: ChIP-seq THAP11 IP T11F80L a


title: ChIP-seq Input T11F80L


title: Sample_LU2+

description: Lung2 Nkx2-1 positive


title: Sample_LU1_NEG

description: Lung1 Nkx2-1 negative


title: Marmoset_PrefrontalCortex_H3K27ac_3

value: anti-H3K27ac (Abcam, catalog#:ab4729)


title: ChIP-seq THAP11 IP WT b

description: Wild-type HEK 293


title: CRC ≤ 45 years. Sample 133

value: Female

value: MSS y CIMP-High


title: genomic DNA from HBMVECs in EBM_A1

source_name: EBM1 _zappulliMGH1_A1

value: 16 hours on Matrigel with Basal medium


title: genomic DNA from HBMVECs in EBM plus EVs isolated from GBM8 neurosphere culture_C2

value: 16 hours on Matrigel with GBM8 EVs in Basal medium


title: Marmoset_PrefrontalCortex_H3K27ac_2


title: CRC ≤ 45 years. Sample 127

value: Male


title: CRC ≤ 45 years. Sample 131

value: MSI y CIMP-Low/0


title: Sample_LU1+

description: Lung1 Nkx2-1 positive


title: CRC ≤ 45 years. Sample 130

value: MSS y CIMP-Low/0


title: ChIP-seq THAP11 IP WT a

description: Wild-type HEK 293

value: HEK 293


title: CRC ≤ 45 years. Sample 132

value: reference


title: ChIP-seq Input WT

description: Wild-type HEK 293


title: CRC ≤ 45 years. Sample 129

value: MSI y CIMP-High


title: CRC ≤ 45 years. Sample 128


title: Chimpanzee_PrefrontalCortex_NeuNnegative_ATAC_5

value: Chimpanzee Prefrontal Cortex


title: Sample_FG3

value: Foregut


title: Marmoset_Cerebellum_H3K27ac_3

value: Cerebellum


title: Marmoset_Cerebellum_H3K4me3_1

value: anti-H3K4me3 (Abcam, catalog#:ab8580)


title: Sample_FG2


title: B2B_HCl3_Dup

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

description:
H_Cl3_Dup_S24
Expt 4: BEAS2B cells treated with NiCl2-100µM for 6 Weeks,  following 6-week Ni exposure,  single cells clone were isolated and expanded  the populations to obtain homogenous clones of Ni-washed-out cells.

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample

growth_protocol: Human lung epithelial BEAS-2B cells (ATCC, CRL-9609) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Cellgro) supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum (FBS, Atlanta Biologicals) at 37°C and 5 % CO2. Human urinary bladder epithelial RT4 cells were cultured in McCoy's 5A Modified Medium (Life Technologies, Carlsbad, CA), supplemented with 10% FBS (Atlanta Biologicals) and 0.5% Penicillin‐Streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Kit (Qiagen 74104).  For ChIP the cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500bp fragments. ChIP was performed using ChIP grade antibodies.
RNA-Seq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002) according to manufacturer’s protocol. ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP -202-1024), according to manufacturer’s protocol.

value: Human lung epithelial cell line


title: B2B_HCl3

description:
H_Cl3_S23
Expt 3: BEAS2B cells treated with NiCl2-100µM for 6 Weeks,  following 6-week Ni exposure,  single cells clone were isolated and expanded  the populations to obtain homogenous clones of Ni-washed-out cells.


title: Marmoset_Cerebellum_H3K27ac_2


title: Sample_FG1


title: Marmoset_PrefrontalCortex_H3K27ac_1

value: Prefrontal Cortex


title: Sample_ECT3

value: Ectoderm


title: Marmoset_Cerebellum_H3K27ac_1

value: anti-H3K27ac (Abcam, catalog#:ab4729)


title: RNAseq_B2B_Ni_washout_Dup

description:
RNAseq_B2B_Ni_washout_Dup
BEAS-2B cells treated with NiCl2-100µM for 6 Weeks,  following 6-week Ni exposure,  single cells clone were isolated and expanded  the populations to obtain homogenous clones of Ni-washed-out cells.


title: CRC ≤ 45 years. Sample 126

value: Female

value: MSS y CIMP-High


title: Sample_ECT2


title: RNAseq_B2B_Ni_washout

description:
RNAseq_B2B_Ni_washout
BEAS-2B cells treated with NiCl2-100µM for 6 Weeks,  following 6-week Ni exposure,  single cells clone were isolated and expanded  the populations to obtain homogenous clones of Ni-washed-out cells.

source_name: Nickel-washed-out cells (Ni-W)


title: CRC ≤ 45 years. Sample 125


title: CRC ≤ 45 years. Sample 123


title: CRC ≤ 45 years. Sample 124


title: RNAseq_B2B_Ni_exposed _Dup

description:
RNAseq_B2B_Ni_exposed _Dup
Expt 2: BEAS2B cells treated with NiCl2-100µM for 6 Weeks.

source_name: Nickel-exposed cells (Ni-E)

value: NiCl2-100µM for 6 Weeks


title: CRC ≤ 45 years. Sample 122

value: Male


title: Sample_ECT1


title: CRC ≤ 45 years. Sample 121


title: RNAseq_B2B_Ni_exposed

description:
RNAseq_B2B_Ni_exposed
Expt 2: BEAS-2B cells treated with NiCl2-100µM for 6 Weeks.


title: RNAseq_B2B_Untreated_Dup

source_name: Untreated BEAS-2B cells

value: none (control)


title: RNAseq_B2B_Untreated

source_name: Untreated_BEAS-2B cells


title: Sample_BR3_NEG

description: Brain3 Nkx2-1 negative

value: Brain


title: Sample_BR2_NEG

description: Brain2 Nkx2-1 negative


title: OBHS-MCF7_RNAseq_12hrs_rep2

city: Wuhan

first: Kaiwei

last: Liang

state: Hubei

address: # 185 Dong Hu Road

institute: Wuhan University

data_processing:
ChIP-seq was done according to a previously published protocol (Liang et al., 2015). Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultrasonicator for 6 minutes and immunoprecipitated with the indicated antibody. Libraries were prepared with the HTP Library Preparation Kit for Illumina (KAPA Biosystems) and sequenced on a NextSeq 500. ChIP-seq reads were aligned to the human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm). Peaks were called using MACS (model based analysis of ChIP-Seq) (Zhang et al., 2008) version 1.4.2 using default parameters. Heatmaps tables were made for the indicated windows around the TSS or TES using the average coverage (r.p.m) in 25bp & 50bp bins (50bp bins for 50kb downstream of the TSS). Meta gene tables were made by approximating the coverage across all genes to the same length. All ChIP-seq heatmaps were sorted by the decreasing coverage in indicated windows by the control sample a. Average profile plots were made by averaging the coverage for all genes using NGSPLOT V2.41.
Total RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33 (Bolger et al., 2014) and then aligned to the human genome (UCSC hg19, using Tophat version 2.1.0) with the following options -no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 10 --max-multihits 20 then post filtering for uniquely mapped reads using the NH flag. Protein coding genes from Ensembl version 75 that also had a refseq identifier were only considered for analysis. Raw read counts were normalized to r.p.m. per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks.  Reads were assigned to specific genes from Ensembl release 75 using HTseq-count. We used the R Bioconductor package DEseq2 to fit the data to a negative binomial generalized log–linear model and estimate a dispersion parameter. GO term analysis was done using Metascape
Genome_build: hg19
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

source_name: MCF7_20 uM OBHS

growth_protocol: MCF7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Total RNA Preparation Kit with  oligo(dT) selection. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Treatment with 20 uM OBHS or 10 nM estrogen was administrated for 1 hours in ChIP-seq experiment and 12 hours in RNA-seq

tag: tissue source

value: Mammary gland, breast

value: derived from metastatic site; pleural effusion

value: 20 uM OBHS

tag: treatment time

value: for 12 hour


title: Sample_BR2+

description: Brain2 Nkx2-1 positive


title: Sample_BR3+

description: Brain3 Nkx2-1 positive


title: CRC ≤ 45 years. Sample 120

value: MSS y CIMP-Low/0

value: reference


title: Paraffin embedded tissue of ESCC patient 122

type: RNA

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-122T

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

label: biotin

source_name: Paraffin embedded tissue of ESCC patients

label_protocol: Total RNA were amplified, labeled and purified by using Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) and FL-Ovation™ cDNA Biotin Module V2(Cat#4200，NuGEN, San Carlos, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted and purified using RecoverAllTM  Total Nucleic Acid Isolation (Cat#AM1975, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: patient diagnosis

value: Esophageal squamous cell carcinoma (ESCC)

value: Esophagus


title: Paraffin embedded tissue of ESCC patient 123

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-123T

tag: tissue


title: Sample_BR1__NEG

description: Brain1 Nkx2-1 negative


title: Paraffin embedded tissue of ESCC patient 125

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-125T


title: Estrogen-MCF7_RNAseq_12hrs_rep2

source_name: MCF7_10 nM estrogen

tag: cell line

tag: treatment

value: 10 nM estrogen


title: CRC ≤ 45 years. Sample 118

tag: Sex

tag: age

tag: molecular classification


title: Sample_BR1+

description: Brain1 Nkx2-1 positive


title: CRC ≤ 45 years. Sample 116

value: MSI y CIMP-High

tag: sample type


title: Paraffin embedded tissue of ESCC patient 126

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-126T


title: CRC ≤ 45 years. Sample 114

source_name: Left colon


title: Paraffin embedded tissue of ESCC patient 124

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-124T


title: CRC ≤ 45 years. Sample 115

source_name: Human Genomic DNA [Male G1471/FemaleG1521] from Promega Corporation


title: Paraffin embedded tissue of ESCC patient 121

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-121T


title: DMSO-MCF7_RNAseq_12hrs_rep2

tag: cell type

value: DMSO


title: CRC ≤ 45 years. Sample 117


title: CRC ≤ 45 years. Sample 113


title: OBHS-MCF7_RNAseq_12hrs_rep1


title: DMSO-MCF7_RNAseq_24hrs_rep1


title: Estrogen-MCF7_RNAseq_12hrs_rep1


title: HFD_THCA_1

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

data_processing:
Pre-processing: Sequences were pre-processed with Trimmomatic v0.36
Alignment: Pre-processed sequences were algined to mouse genome assembly mm10 using HISAT2 v2.1.0
Counts per gene were obtained with featureCounts v1.6.1 using the in-built RefSeq annotation for mm10 genome assembly
The raw counts were then analyzed with DESeq2 v1.20.0 excluding those genes with less than 15 counts across samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include raw counts obtained from featureCounts

source_name: HFD_THCA_adipose tissue

extract_protocol:
Total RNA was isolated from mice frozen skin tissue using QIAzol lysis reagent (Qiagen, Hilden, Germany) and purified with RNeasy mini kit (Qiagen).
Transcriptome libraries were constructed with TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero Human/Mouse/Rat, #RS-122-2201). In brief, 300 ng of total RNA from each Sample was used to construct a cDNA library, followed by sequencing on the Illumina Hiseq 2500 with single end 50 bp reads and ~30 millions of reads per sample.

tag: strain

value: Eight weeks

value: HFD+THCA

value: Adipose tissue


title: Paraffin embedded tissue of ESCC patient 120

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-120T


title: single-cell RNA-seq

city: Minneapolis

first: Sunny

last: Chan

state: MN

address: 2231 6th St SE

department: Pediatrics

institute: University of Minnesota

data_processing:
cellranger mkfastq
cellranger count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing filtered barcodes and genes, MetaStream ASCII file containing the filitered matrix

source_name: Pluripotent stem cell derivative

growth_protocol: Doxcycline-inducible Mesp1-expressing mouse embryonic stem cells were differentiated as embryoid bodies for 5 days, upon which were dissociated and plated as a monolayer. On day 12 cells were harvested for single-cell sequencing.

extract_protocol: As recommended by 10X Genomics protocol

treatment_protocol: Doxycycline (500 ng/ml) was added from day 3 to day 8 to induce Mesp1.

value: Mesp1-induced mesoderm

value: Doxcycline treatment from day 3-8 to induce Mesp1


title: HFD_2

source_name: HFD_adipose tissue

value: HFD


title: CRC ≤ 45 years. Sample 111

value: Male


title: Paraffin embedded tissue of ESCC patient 119

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-119T


title: Paraffin embedded tissue of ESCC patient 118

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-118T


title: Paraffin embedded tissue of ESCC patient 116

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-116T


title: CBD_2

data_processing:
Pre-processing: Sequences were pre-processed with Trimmomatic v0.36
Alignment: Pre-processed sequences were algined to human genome assembly hg38 using HISAT2 v2.1.0
Counts per gene were obtained with featureCounts v1.6.1 using the in-built RefSeq annotation for hg38 genome assembly
The raw counts were then analyzed with DESeq2 v1.20.0 excluding those genes with less than 15 counts across samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file include raw counts obtained from featureCounts

source_name: Primary keratinocytes

extract_protocol:
Total RNA was isolated from Human Epidermal Keratinocytes by Qiazol lysis reagent (Qiagen, Hilden, Germany) and purified with miRNeasy mini kit (Qiagen, Hilden, Germany) following manufacturer´s instructions. RNA quantification was performed using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Transcriptome libraries were then constructed using poly-A selection with the TruSeq Stranded mRNA Library Prep Kit (Cat. No. RS-122-2101, Illumina, San Diego, CA, USA). In brief, 300 ng of total RNA from each sample was used to construct a cDNA library, followed by sequencing on the Illumina HiSeq 2500 with single end 50 bp reads and ~30 millions of reads per sample.

tag: group

value: CBD


title: HFD_1


title: CBD_1


title: CBD_3


title: CRC ≤ 45 years. Sample 112

value: MSI y CIMP-Low/0


title: THCA_T007_2

source_name: THCA_T007_adipose tissue


title: CRC ≤ 45 years. Sample 109

source_name: Rectum

value: Female


title: CRC ≤ 45 years. Sample 110

value: MSS y CIMP-Low/0


title: Control_3

value: Control


title: Control_2


title: Paraffin embedded tissue of ESCC patient 117

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-117T

value: Esophageal squamous cell carcinoma (ESCC)


title: RNA-seq WT rep 1

description:
Wild-type HEK 293
HS13_WT_37_1

source_name: Embryonic kidney cell line

tag: experiment

value: RNA-seq

value: HEK 293

value: Parental


title: THCA_2

source_name: THCA_adipose tissue

value: THCA


title: Control_1


title: THCA_1

value: Eight weeks


title: THCA_T007_1


title: Paraffin embedded tissue of ESCC patient 113

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-113T

value: Esophagus


title: Paraffin embedded tissue of ESCC patient 114

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-114T


title: Control 2

source_name: Control_adipose tissue

value: control

value: Adipose tissue


title: Control 1


title: Paraffin embedded tissue of ESCC patient 111

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-111T


title: Paraffin embedded tissue of ESCC patient 115

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-115T


title: CRC ≤ 45 years. Sample 106

value: reference


title: CRC ≤ 45 years. Sample 104

source_name: Righ colon


title: CRC ≤ 45 years. Sample 108


title: CRC ≤ 45 years. Sample 103

value: MSS y CIMP-High


title: CRC ≤ 45 years. Sample 107


title: Paraffin embedded tissue of ESCC patient 110

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-110T


title: CRC ≤ 45 years. Sample 102

value: Male


title: Paraffin embedded tissue of ESCC patient 112

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-112T


title: CRC ≤ 45 years. Sample 105


title: Th1 Foxp3 ChIP

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Basecalls performed using CASAVA
Reads were filtered to remove adapters using fastq-mcf and for quality using seqkt
Reads were then aligned to the mouse genome (mm9) with Bowtie2 (default settings)
Regions of significant enrichment (10^-7) were identified using MACS version 1.4 (Zhang et al., 2008) using input as background, with the setting –keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks derived from analyses

source_name: iTreg

growth_protocol: CD4+ T cells from spleens and lymph nodes of 4- to 10-wk-old Balb/c mice were purified by CD4 positive selection (Miltenyi Biotec) followed by sorting of naive CD4+CD25-CD62LhighCD44low cells using a FACSAria II (BD Biosciences).

extract_protocol:
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent.  Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 5 µg each of 2 Foxp3 antibodies, Santa Cruz S-31738 and eBioscience FJK-16. Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNase A, proteinase K and phenol:chloroform extraction followed by ethanol precipitation.
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 35 or 50 bp single-end read sequencing with an Illumina GAIIx or HiSeq 2000 sequencer

treatment_protocol: Cells were activated for 72 hours by plate-bound anti-CD3 and anti-CD28 (both 10 ug/ml; clones 145-2C11 and 37.51, respectively; Bio X Cell). iTreg cells were generated by culturing in recombinant human TGF-β1 (33 ng/ml) and IL-2 (20 ng/ml; R & D Systems) for 7 days. Th1 cells were polarized with 20 ng/ml IL-2 (Biolegend) and polarized with 20 ng/ml IL-12 (eBioscience) and 10 μg/ml anti-IL-4 (BioXCell).

value: iTreg

value: Balb/c

value: anti-Foxp3 (Santa Cruz S-31738 and eBioscience FJK-16)


title: CRC ≤ 45 years. Sample 101

value: MSI y CIMP-Low/0


title: Paraffin embedded tissue of ESCC patient 109

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-109T


title: Paraffin embedded tissue of ESCC patient 107

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-107T


title: Paraffin embedded tissue of ESCC patient 108

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-108T


title: CRC ≤ 45 years. Sample 100

value: Female

value: MSS y CIMP-Low/0


title: CRC ≤ 45 years. Sample 97


title: CRC ≤ 45 years. Sample 98


title: Paraffin embedded tissue of ESCC patient 104

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-104T

value: Esophageal squamous cell carcinoma (ESCC)


title: Brain_interleukin-18 knockout_12w-biological rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: whole brain derived from 12 week-old IL-18KO strain

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for data processing.

source_name: whole brain derived from 12w IL-18KO strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from whole brains stored in RNA later (Ambion), derived from wild type and interleukin-18 knockout mice using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

value: BALB/c

tag: organ

value: Brain

tag: genotype

value: interleukin-18 knockout

value: 12 week-old


title: Paraffin embedded tissue of ESCC patient 106

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-106T

value: Esophagus


title: CRC ≤ 45 years. Sample 96


title: Paraffin embedded tissue of ESCC patient 103

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-103T


title: Brain_interleukin-18 knockout_12w-biological rep2


title: Brain_interleukin-18 knockout_6w-biological rep3

description: whole brain derived from 6 week-old IL-18KO strain

source_name: whole brain derived from 6w IL-18KO strain

value: 6 week-old


title: CRC ≤ 45 years. Sample 95

value: MSI y CIMP-High


title: Paraffin embedded tissue of ESCC patient 102

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-102T

source_name: Paraffin embedded tissue of ESCC patients


title: Paraffin embedded tissue of ESCC patient 101

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-101T


title: Brain_wild type_12w-biological rep2

description: whole brain derived from 12 week-old wild type strain

source_name: whole brain derived from 12w wild type strain

value: wild type


title: CRC ≤ 45 years. Sample 93

value: reference


title: Paraffin embedded tissue of ESCC patient 98

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-098T


title: CRC ≥ 70 years. Sample 89


title: Brain_interleukin-18 knockout_6w-biological rep2


title: Paraffin embedded tissue of ESCC patient 99

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-099T


title: Brain_interleukin-18 knockout_12w-biological rep1


title: Paraffin embedded tissue of ESCC patient 100

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-100T


title: Paraffin embedded tissue of ESCC patient 105

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-105T


title: CRC ≤ 45 years. Sample 94

source_name: Left colon

value: Male


title: Brain_wild type_12w-biological rep3


title: Brain_interleukin-18 knockout_6w-biological rep1


title: Paraffin embedded tissue of ESCC patient 97

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-097T


title: Brain_wild type_12w-biological rep1


title: Paraffin embedded tissue of ESCC patient 95

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-095T


title: Brain_wild type_6w-biological rep3

description: whole brain derived from 6 week-old wild type strain

source_name: whole brain derived from 6w wild type strain


title: CRC ≥ 70 years. Sample 87

source_name: Human Genomic DNA [Male G1471/FemaleG1521] from Promega Corporation


title: CRC ≥ 70 years. Sample 86


title: CRC ≥ 70 years. Sample 85


title: Paraffin embedded tissue of ESCC patient 94

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-094T


title: Brain_wild type_6w-biological rep1


title: Paraffin embedded tissue of ESCC patient 96

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-096T


title: the_callus_of_rice_mRNA-SEQ-pOE-rep3

city: Beijing

first: Kun

last: Zhang

address: Haidian district Yuanmingyuanxilu2

institute: Chins Agricultural University

description: pOE versus Teqing mRNA-Seq.xls

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads analyzed using Bcl2Fastq
Raw data can be filtered according to NEBNext Ultra RNA Library Prep Kit. The RNA 5' Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; the RNA 3' Adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Clean data were mapped to the Os-Nipponbare-Refrence-IRGSP-1.0 (MSU7) by TopHat2
The Cufflinks package was used to assemble transcripts, compare and merge assembles, and identify differentially expressed genes (DEGs).
Genome_build: Os-Nipponbare-Refrence-IRGSP-1.0 (MSU7)
Supplementary_files_format_and_content: FPKM

organism: Oryza sativa

source_name: the callus of subcultured 21d

extract_protocol:
Total RNA was extracted from various samples using TRIzol reagent (Life Technologies) and purified using the RNeasy mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tiissue

value: callus of subcultured 21d

tag: cultivar

value: pOE


title: the_callus_of_rice_mRNA-SEQ-pOE-rep1

description: pOE versus Teqing mRNA-Seq.xls


title: the_callus_of_rice_mRNA-SEQ-Teqing3-rep3

description: pOE versus Teqing mRNA-Seq.xls

value: Teqing


title: the_callus_of_rice_mRNA-SEQ-pOE-rep2

description: pOE versus Teqing mRNA-Seq.xls


title: Brain_wild type_6w-biological rep2


title: Paraffin embedded tissue of ESCC patient 93

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-093T


title: the_callus_of_rice_mRNA-SEQ-Teqing3-rep2

description: pOE versus Teqing mRNA-Seq.xls


title: CRC ≥ 70 years. Sample 84

extract_protocol: DNA was extracted using proteinase K digestion, phenol/chloroform extraction, Phase Lock Gel Light (Eppendorf AG, Hamburg, Germany), and ethanol precipitation.


title: C2C12 myoblasts transfected with scramble rep4 [re-analysis]

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
C2C12_Myob_scramble_rep4
C2C12 cells were seeded in same numbers and cultured in same condition.

hyb_protocol: 800 ng of labeled sample target were mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl of mix was dispensed onto the array. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C US22502723 (ChipScan software version A.8.5.1), scan region 61 x 21.6 mm, scan resolution 3 micron single pass, Green PTM 100%, no extended dynamic range (NO XDR).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_1200_Jun14). Quantile inter-arrays normalization was performed on the gProcessedSignal column of the result table and normalized data is reported in the VALUE column. lincRNAs (marked as “lincRNAs” in the “Description” field of platform) were not used in the normalization process and marked as “null”. Probes with Found or Well Above Background value of zero were disregarded and labeled as “null”. Mean values were calculated for multiple probes with the same Agilent Probe ID.

label_protocol: RNA obtained from cells was amplified and labeled starting from 150 ng using the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) as described by the proprietary protocol. Labeled cRNA was purified with miRNeasy Mini Kit (Qiagen) and quantified using NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). On average, cRNA yield was about 10 µg and the specific activity was of 35 pmol Cy3 per µg cRNA.

growth_protocol: C2C12 cells were cultured using standard protocols provided by the ATCC.

extract_protocol: RNA from transfected cells was isolated using the standard phenol-chloroform extraction with TRIzol Reagent (Thermo Fisher Scientific) followed by ethanol precipitation.

treatment_protocol: C2C12 myoblasts were cultured in Dulbecco's Modified Eagle Medium with high glucose (Life Technologies) + 10% Fetal Bovine Serum (Life Technologies) in 10 cm dishes and split every 2 or 3 days before they reached 70% of confluence. Cells were transfected using Lipofectamine 2000 (Life Technologies) following the manufacturer’s instructions with 150 nM of mirVana miRNA mimics or scrambled sequence, purchased from Life Technologies.

value: myoblasts

tag: transfected with

value: Scrambled sequence


title: the_callus_of_rice_mRNA-SEQ-Teqing3-rep1

description: pOE versus Teqing mRNA-Seq.xls


title: CRC ≥ 70 years. Sample 83

value: MSS y CIMP-Low/0


title: CRC ≥ 70 years. Sample 82


title: Paraffin embedded tissue of ESCC patient 92

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-092T

tag: patient diagnosis

value: Esophageal squamous cell carcinoma (ESCC)


title: the_callus_of_rice_mRNA-SEQ-pCPL-rep3

description: pCPL versus Teqing mRNA-Seq.xls

value: pCPL


title: C2C12 myoblasts transfected with scramble rep3 [re-analysis]

description:
C2C12_Myob_scramble_rep3
C2C12 cells were seeded in same numbers and cultured in same condition.


title: C2C12 myoblasts transfected with scramble rep2 [re-analysis]

description:
C2C12_Myob_scramble_rep2
C2C12 cells were seeded in same numbers and cultured in same condition.


title: Paraffin embedded tissue of ESCC patient 91

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-091T

tag: tissue


title: C2C12 myoblasts transfected with scramble rep1 [re-analysis]

description:
C2C12_Myob_scramble_rep1
C2C12 cells were seeded in same numbers and cultured in same condition.

tag: cell line


title: HFD_THCA_2

source_name: HFD_THCA_adipose tissue

value: Eight weeks

tag: treatment

value: HFD+THCA

value: Adipose tissue


title: Paraffin embedded tissue of ESCC patient 90

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-090T

value: Esophagus


title: C2C12 myoblasts transfected with miR-142-3p rep6

description:
C2C12_Myob_miR-142-3p_rep6
C2C12 cells were seeded in same numbers and cultured in same condition.

value: miR-142-3p mimic


title: CRC ≥ 70 years. Sample 80

tag: Sex

value: Female


title: CRC ≥ 70 years. Sample 81

tag: age

value: MSI y CIMP-High


title: CRC ≥ 70 years. Sample 79

tag: molecular classification

value: MSI y CIMP-Low/0

value: reference


title: the_callus_of_rice_mRNA-SEQ-pCPL-rep2

description: pCPL versus Teqing mRNA-Seq.xls

value: callus of subcultured 21d


title: the_callus_of_rice_mRNA-SEQ-pCPL-rep1

description: pCPL versus Teqing mRNA-Seq.xls


title: the_callus_of_rice_mRNA-SEQ-Teqing2-rep3

description: pCPL versus Teqing mRNA-Seq.xls


title: the_callus_of_rice_mRNA-SEQ-Teqing2-rep2

description: pCPL versus Teqing mRNA-Seq.xls


title: the_callus_of_rice_mRNA-SEQ-Teqing2-rep1

description: pCPL versus Teqing mRNA-Seq.xls


title: C2C12 myoblasts transfected with miR-142-3p rep5

description:
C2C12_Myob_miR-142-3p_rep5
C2C12 cells were seeded in same numbers and cultured in same condition.


title: Paraffin embedded tissue of ESCC patient 87

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-087T


title: Paraffin embedded tissue of ESCC patient 89

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-089T


title: Paraffin embedded tissue of ESCC patient 85

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-085T


title: CRC ≥ 70 years. Sample 78

tag: sample type


title: Paraffin embedded tissue of ESCC patient 86

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-086T


title: C2C12 myoblasts transfected with miR-142-3p rep4

description:
C2C12_Myob_miR-142-3p_rep4
C2C12 cells were seeded in same numbers and cultured in same condition.

tag: cell type


title: C2C12 myoblasts transfected with scramble rep4

description: C2C12 cells were seeded in same numbers and cultured in same condition.


title: Paraffin embedded tissue of ESCC patient 88

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-088T


title: CRC ≥ 70 years. Sample 77

value: Male


title: Paraffin embedded tissue of ESCC patient 84

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-084T


title: C2C12 myoblasts transfected with miR-142-3p rep1

description:
C2C12_Myob_miR-142-3p_rep1
C2C12 cells were seeded in same numbers and cultured in same condition.


title: C2C12 myoblasts transfected with miR-142-3p rep3

description:
C2C12_Myob_miR-142-3p_rep3
C2C12 cells were seeded in same numbers and cultured in same condition.


title: the_callus_of_rice_mRNA-SEQ-YIL25-rep2

description: YIL25 versus Teqing mRNA-Seq.xls


title: CRC ≥ 70 years. Sample 76


title: C2C12 myoblasts transfected with miR-142-3p rep2

description:
C2C12_Myob_miR-142-3p_rep2
C2C12 cells were seeded in same numbers and cultured in same condition.


title: C2C12 myoblasts transfected with scramble rep3


title: the_callus_of_rice_mRNA-SEQ-YIL25-rep3

description: YIL25 versus Teqing mRNA-Seq.xls


title: Paraffin embedded tissue of ESCC patient 83

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-083T


title: CRC ≥ 70 years. Sample 75

value: MSS y CIMP-High


title: C2C12 myoblasts transfected with scramble rep2

value: myoblasts


title: the_callus_of_rice_mRNA-SEQ-YIL25-rep1

description: YIL25 versus Teqing mRNA-Seq.xls


title: Paraffin embedded tissue of ESCC patient 82

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-082T


title: CRC ≥ 70 years. Sample 73


title: CRC ≥ 70 years. Sample 72


title: CRC ≥ 70 years. Sample 74


title: CRC ≥ 70 years. Sample 71


title: the_callus_of_rice_mRNA-SEQ-Teqing1-rep3

description: YIL25 versus Teqing mRNA-Seq.xls

value: Teqing


title: CRC ≤ 45 years. Sample 92

value: MSS y CIMP-Low/0


title: the_callus_of_rice_mRNA-SEQ-Teqing1-rep1

description: YIL25 versus Teqing mRNA-Seq.xls


title: the_callus_of_rice_mRNA-SEQ-Teqing1-rep2

description: YIL25 versus Teqing mRNA-Seq.xls


title: C2C12 myoblasts transfected with scramble rep1

value: Scrambled sequence


title: Mock infected, DM-tRNA-seq, rep 4

city: Berkeley

first: Jessica

middle: Mitchell

last: Tucker

state: CA

address: 565 Li Ka Shing Center

department: Plant and Microbial Biology

institute: University of California, Berkeley

description:
small RNA
S15

data_processing:
Adaptor removal, trimming with BBDuk
Aligned to mature tRNA reference using end-to-end mapping in Bowtie2 version 2.3.4.1
Aligned to masked mm10 genome with appended premature tRNA reference using Bowtie2 (Uniquely mapping reads only)
Aligned to masked mm10 genome with appended premature tRNA reference using Salmon
RUVSeq to normalize raw counts using spike-ins
Differential Gene expression analysis using edgeR
Genome_build: mm10, tRNA reference is from tRNAscan-SE
Supplementary_files_format_and_content: counts

source_name: fibroblasts

growth_protocol: MC57Gs were maintained in DMEM+10% FBS.

extract_protocol:
Total RNA was isolated with Trizol. IVT tRNAs were spiked in at 0.01 pmol per ug RNA. RNA was deacylated and dephosphorylated, and then small RNA was isolated with a mirVANA kit (ThermoFisher AM1560). Small RNA was demethylated with WT/D135S AlkB demethylases prior to reverse transcription.
Library was contructed with TGIRT™ Improved Modular Template-Switching RNA-seq Kit (InGex) following manufacturer's instructions.

treatment_protocol: For infection, 4.5E6 cells were plated into 15 cm dishes. 24 hours later, media or media containing virus (MOI=5) was added to the cells and allowed to adhere for 1 hour. Media was replaced and infection was allowed to proceed for 24 hours.


title: MHV68 infected, DM-tRNA-seq, rep 4

description:
small RNA
S16


title: Paraffin embedded tissue of ESCC patient 80

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-080T

value: Esophageal squamous cell carcinoma (ESCC)


title: CRC ≥ 70 years. Sample 70

data_processing: Array image ﬁles produced by the MS 200 Data Collection Software were imported into DEVA v1.2.1(Roche NimbleGen Inc.) for analysis. In addition,segmentation analysis was performed in all cases byusing circular binary segmentation (CBS) available in waviCGH software (http://wavi.bioinfo.cnio.es/).


title: Mock infected, DM-tRNA-seq, rep 3

description:
small RNA
S13


title: C2C12 myoblasts transfected with miR-27a-3p rep5

value: miR-27a-3p mimic


title: CRC ≥ 70 years. Sample 67


title: C2C12 myoblasts transfected with miR-27a-3p rep6


title: Paraffin embedded tissue of ESCC patient 81

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-081T


title: Paraffin embedded tissue of ESCC patient 79

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-079T


title: Paraffin embedded tissue of ESCC patient 75

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-075T


title: Paraffin embedded tissue of ESCC patient 76

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-076T


title: C2C12 myoblasts transfected with miR-27a-3p rep3


title: Paraffin embedded tissue of ESCC patient 78

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-078T


title: CRC ≥ 70 years. Sample 68


title: CRC ≥ 70 years. Sample 66


title: C2C12 myoblasts transfected with miR-27a-3p rep4


title: Paraffin embedded tissue of ESCC patient 74

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-074T


title: MHV68 infected, DM-tRNA-seq, rep 2

description:
small RNA
S12


title: C2C12 myoblasts transfected with miR-27a-3p rep1


title: CRC ≥ 70 years. Sample 69


title: C2C12 myoblasts transfected with miR-27a-3p rep2


title: Myofiber MyHC-2B_10(E22)

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.

hyb_protocol: 800 ng of labeled cDNA were mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl of mix was dispensed onto one array of the SurePrint G3 Mouse Gene Expression 8x60K microarray. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_107_Sep09). Quantile inter-arrays normalization was performed with the Expander software (Bioinformatics 2003; 19:1787-99) on the gProcessedSignal column of the result table and normalized data is reported in the VALUE column. Only characterized lincRNAs (with the “accession string” field of platform defined with a symbol) was used in the normalization process. The other lincRNAs (with the “accession string” field of platform defined with the chromosomal location) was not used in the normalization process and marked as “null”. Probes with Found or Well Above Background value of zero were disregarded and labeled as “null”. Mean values were calculated for multiple probes with the same Agilent Probe ID.

source_name: Individual pure type 2B myofiber from EDL muscle.

label_protocol: RNA was exponentially amplified using the TransPlex WholeTranscriptome Amplification 2 Kit (Sigma-Aldrich) in accordance with the manufacturer’s instructions, using 18 cycles of amplification. Amplification product was purified with the GenElute PCR Clean-up columns (Sigma-Aldrich). Resulting cDNA was quantified with Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific). 2 µg of amplified-purified cDNA were labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies), as suggested by manufacturer, and purified using the Amicon 30kDa filters (Millipore). On average, cDNA yield was about 4 µg and the specific activity of 30 pmol Cy3 per µg cDNA.

growth_protocol: CD1 male mice were housed in a normal environment provided with ad libitum food and water and were killed by rapid cervical dislocation to minimize suffering.

extract_protocol: A single myofiber was lysed in 250 µl of TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s instructions. After phases separation the upper aqueous phase containing RNA was added with 70% ethanol before column purification with RNeasy Micro Kit (Qiagen). Total RNA quality was monitored using the RNA Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Muscles from both hind limbs of the same mouse were immediately removed by microdissection, taking care to handle them only by their tendons to minimize mechanical damage to the fibers. Digestion proceeded for 40 - 45 min. at 37°C in 1 ml high-glucose DMEM (Thermo Fisher Scientific) containing 10 mg type I collagenase (220 U mg-1, Sigma-Aldrich). The collagenase-treated muscles were sequentially rinsed for 2 min. in 3 ml of DMEM, 3 ml DMEM supplemented with 10% fetal bovine serum (FBS) and 3 ml of DMEM and finally transferred into 50 mm x 18 mm well containing 3 ml of DMEM with 10% FBS. Single myofibers were liberated by gentle physical trituration with a wide-mouth plastic Pasteur pipette (about 4 mm diameter). Quickly, intact, not contracted, and well-isolated fibers were picked under stereomicroscope and washed first in DMEM and then in phosphate buffered saline. About one-third of each fiber was clipped and placed in Laemmli buffer for fiber typing by SDS-PAGE; the remaining part of the fiber was dissolved TRIzol Reagent (Thermo Fisher Scientific) for RNA extraction. All samples were collected within 45 min. from the last trituration step.

tag: strain

value: 3 months

tag: gender

value: EDL muscle

tag: myofiber type

value: Individual pure type 2B myofiber


title: Myofiber MyHC-2B_9(E21)


title: Paraffin embedded tissue of ESCC patient 73

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-073T

value: Esophagus


title: Paraffin embedded tissue of ESCC patient 77

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-077T


title: CRC ≥ 70 years. Sample 65

source_name: Rectum


title: Mock infected, DM-tRNA-seq, rep 2

description:
small RNA
S11


title: CRC ≥ 70 years. Sample 64

value: Female


title: H3: Cattle3

city: nanning

first: kongwei

last: huang

address: 100, Daxue Road Nanning,Guangxi P.R.CHINA

institute: Guangxi University

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14).
Select transcripts with length ≥ 200 bp and Exon ≥ 2; calculate reads ≥ 3 by cufflinks.
Coding potential screening: CPC analysis, CNCI analysis, pfam protein domain analysis and phyloCSF analysis take the intersection to screen for unencoding lncRNA.
Then screening lncRNA-mRNA relationship pairs to construct lncRNA-mRNA co-expression network.
LncRNAs were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Supplementary_files_format_and_content: Additional file 1: Primers designed for quantitative real time PCR.
Supplementary_files_format_and_content: Additional file 2: Four predictive software(CNCI,CPAT,CPC,Pfam) prediction results to plot the result list file of Venn diagram in bovine muscle tissues.
Supplementary_files_format_and_content: Additional file 3: All sample lncRNA expression distribution box line graph
Supplementary_files_format_and_content: Additional file 4: LncRNA cis target gene prediction result in skeletal muscle, using LncTar soft the prediction results based on the principle of sequence complementation.
Supplementary_files_format_and_content: Additional file 5: LncRNA trans target gene prediction result file, using LncTar soft the prediction results based on the principle of sequence complementation.
Supplementary_files_format_and_content: Additional file 6: Comparative analysis of lncRNA and mRNA expression.
Supplementary_files_format_and_content: Additional file 7: Differential expression lncRNA target gene protein interaction on the list of details, based on the STRING database

organism: Bos taurus

source_name: adult longissimus muscle

growth_protocol: Six longissimus muscle samples from Guangxi native cattles and swamp buffalo ( adult, 12 M old) were collected from nanning meat factory abattoir, a local slaughterhouse of Nanning, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries. For RNase R treatment, ribosome-depleted RNA was incubated for 15 min at 37°C with 5 units μg−1 of RNase R (Epicentre Technologies, Madison, WI).
Then the rRNA depleted RNA samples or circRNAs samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with an Agilent 2100 Bioanalyzer and sequenced by HiSeq 2500 (Illumina, San Diego, CA) on a 150 bp paired-end (PE) run.

value: longissimus muscle

tag: developmental stage

value: Adult

value: 12 M old

tag: molecule subtype

value: lncRNA


title: H2: Cattle2


title: Myofiber MyHC-2B_8(E20)

value: Male


title: MHV68 infected, DM-tRNA-seq, rep 1

description:
small RNA
S10


title: H1: Cattle1


title: Myofiber MyHC-2B_7(E19)


title: Paraffin embedded tissue of ESCC patient 72

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-072T


title: Mock infected, DM-tRNA-seq, rep 1

description:
small RNA
S9


title: Paraffin embedded tissue of ESCC patient 71

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-071T


title: CRC ≥ 70 years. Sample 63

value: reference


title: CRC ≥ 70 years. Sample 60


title: CRC ≥ 70 years. Sample 62


title: CRC ≥ 70 years. Sample 59


title: Myofiber MyHC-2B_6(E18)


title: Myofiber MyHC-2B_5(E17)


title: Paraffin embedded tissue of ESCC patient 69

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-069T


title: Paraffin embedded tissue of ESCC patient 68

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-068T


title: Paraffin embedded tissue of ESCC patient 66

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-066T


title: Paraffin embedded tissue of ESCC patient 70

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-070T


title: CRC ≥ 70 years. Sample 58

value: MSS y CIMP-High


title: Myofiber MyHC-2B_3(E16)


title: CRC ≥ 70 years. Sample 57


title: siNC-1.Input

first: Lin-jian

last: Wang

address: No.119 South 4th Ring West Road

institute: Beijing Tiantan Hospital, Capital Medical University

description:
Total RNA
Methylated_RNA_sites.mRNA, mRNA Expression Profiling

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer
High quality clean reads were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
Cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA
Genome_build: hg19
Supplementary_files_format_and_content: excel format
Supplementary_files_format_and_content: Number of raw junction read

source_name: Human Umbilical Vein Endothelial Cells

extract_protocol:
Total RNAs were extracted and purified using TRIzol reagent according to the manufacturer’s instructions
m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit.

tag: passages

tag: genotype

value: wild type

tag: rip antibody


title: siNC-2.Input


title: siWT-2.Input

value: Knockdown WTAP (WT1 associated protein)


title: CRC ≥ 70 years. Sample 56

first: Juan Luis

last: Garcia

address: Campus Miguel de Unamuno

institute: Centro de Investigación del Cáncer IBMCC-CIC

value: MSS y CIMP-Low/0


title: Myofiber MyHC-2B_2(E15)


title: CRC ≥ 70 years. Sample 61


title: siWT-1.Input


title: Myofiber MyHC-2B_4(E16)


title: siME-2.Input

value: Knockdown METTL3 (methyltransferase like 3)


title: CRC ≥ 70 years. Sample 55


title: Myofiber MyHC-2B_1(E14)


title: Paraffin embedded tissue of ESCC patient 67

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-067T

tag: patient diagnosis

value: Esophageal squamous cell carcinoma (ESCC)


title: Myofiber Hyb-2X/2B_10(E23)

source_name: Individual hybrid type 2X/2B myofiber from EDL muscle.

value: 3 months

tag: tissue

value: Individual hybrid type 2X/2B myofiber


title: Paraffin embedded tissue of ESCC patient 64

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-064T


title: MHV68 infected, DM-tRNA-seq, rep 3

description:
small RNA
S14

tag: cell line


title: CRC ≥ 70 years. Sample 54


title: Paraffin embedded tissue of ESCC patient 63

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-063T


title: siNC-2.IP

description:
m6A IP RNA
Methylated_RNA_sites.mRNA, siNC-2.mRNA.m6A

value: m6A antibody (Synaptic Systems,202003)


title: Paraffin embedded tissue of ESCC patient 62

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-062T

value: Esophagus


title: CRC ≥ 70 years. Sample 53


title: Paraffin embedded tissue of ESCC patient 65

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-065T


title: Myofiber Hyb-2X/2B_9(E23)

value: EDL muscle


title: Paraffin embedded tissue of ESCC patient 61

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-061T


title: siNC-1.IP

description:
m6A IP RNA
Methylated_RNA_sites.mRNA, siNC-1.mRNA.m6A


title: siME-1.Input


title: Myofiber Hyb-2X/2B_8(E22)

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.


title: siWT-2.IP

description:
m6A IP RNA
Methylated_RNA_sites.mRNA, siWT-2.mRNA.m6A


title: CRC ≥ 70 years. Sample 52

source_name: Righ colon

value: Female


title: Paraffin embedded tissue of ESCC patient 60

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-060T


title: CRC ≥ 70 years. Sample 51


title: CRC ≥ 70 years. Sample 88


title: CRC ≥ 70 years. Sample 49


title: siWT-1.IP

description:
m6A IP RNA
Methylated_RNA_sites.mRNA, siWT-1.mRNA.m6A


title: Myofiber Hyb-2X/2B_5(E18)


title: Myofiber Hyb-2X/2B_6(E20)


title: CRC ≥ 70 years. Sample 50


title: Myofiber Hyb-2X/2B_7(E22)


title: Myofiber Hyb-2X/2B_4(E18)


title: siME-2.IP

description:
m6A IP RNA
Methylated_RNA_sites.mRNA, siME-2.mRNA.m6A


title: CRC ≥ 70 years. Sample 48


title: 17: EXP1-GBM8-EV_smallRNA

first: Aleksandar

last: Milosavljevic

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
base-calling: The size selected libraries were sequenced on a HiSeq 4000 sequencing system.
read quality filtering: Condition2 Replicate1 was removed from analysis due to a markedly lower total miRNA count (273,468) compared to the other 8 samples (nearly 5x fewer counts than the sample with the next fewest counts). In the remaining samples, the samples with the fewest total miRNA counts (which was Condition3 Replicate2) had a total miRNA count of 1,338,649. Therefore, the scaled data for the remaining samples were filtered to remove miRNAs with fewer than 7.5 scaled counts (corresponding to a cutoff of 10 raw counts/1,338,649 total miRNA counts) in at least 2 samples; after this filtering, 430 miRNAs remained.
alignment: Paired-reads were mapped simultaneously to the GRCh37.83 cDNA and ncRNA transcriptomes (Kinsella et.al., 2011) using Kallisto[v0.44.0] (Bray et. al., 2016). Kallistos were imported to R with tximport. All reads mapping to ncRNA were excluded from the analysis, then transcript abundances were aggregated by Ensembl Gene ID. Genes with less than 10 reads across all samples were excluded from further analysis.
The data were further filtered using the Qlucore data analysis and visualization software package (www.qlucore.com) by selecting for miRNAs that displayed a variance across the dataset of 0.01, leaving 29 miRNAs. Differential expression analysis was then performed among the three conditions, and using a p-value <0.03/q-value <0.75, obtained 15 miRNAs.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab delimited, transcript abundance fold change, p-value

growth_protocol: HBMVECs (500,000/well) were cultured on Matrigel™-coated (BD Matrigel™ 10mg/mL, BD Biosciences, Franklin Lakes, NJ, USA) wells in a 6-well plate in endothelial basal medium (EBM-2)

extract_protocol:
Total RNA for this study was isolated from samples using the Qiagen (Exiqon) miRCURY RNA isolation kit.
Small RNAseq libraries were generated using the NEB Next SmallRNA library preparation kit according to the manufacturer’s protocol, with some minor modifications. The reaction volumes were reduced to 1/5thof the recommended volume. Due to the low amounts of RNA input, the 3’ SR adaptor, SR RT primer and the 5’ SR adaptors were diluted 1:6 to avoid excessive amounts of free adaptors and the formation of adaptor dimers. The final libraries were purified using the Zymo DNA clean and concentrator-5 kit and subjected to size selection on the Pippin Prep with a cut off between 117 and 135 bp to deplete adaptor dimers and most of larger RNA species such as tRNA fragments.

treatment_protocol: EV pellet from GBM8-cell-conditioned medium

value: Brain Microvascular Endothelial Cell


title: CRC ≥ 70 years. Sample 47


title: Paraffin embedded tissue of ESCC patient 57

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-057T


title: Paraffin embedded tissue of ESCC patient 58

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-058T


title: Paraffin embedded tissue of ESCC patient 59

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-059T


title: Myofiber Hyb-2X/2B_3(E15)


title: 16: EXP1-EGM_smallRNA

treatment_protocol: angiogenic growth factors; EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza, Basel, Switzerland) supplemented with 5% EV-depleted FBS according to manufacturer protocol.


title: 15: EXP1-EBM2_smallRNA


title: siME-1.IP

description:
m6A IP RNA
Methylated_RNA_sites.mRNA, siME-1.mRNA.m6A


title: Paraffin embedded tissue of ESCC patient 56

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-056T


title: Myofiber Hyb-2X/2B_2(E14)


title: 10: EXP1-GBM8-EV_smallRNA


title: Paraffin embedded tissue of ESCC patient 54

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-054T


title: CRC ≥ 70 years. Sample 46


title: CRC ≥ 70 years. Sample 45


title: Myofiber Hyb-2X/2B_1(E14)


title: Myofiber MyHC-2X_10(S9)

source_name: Individual pure type 2X myofiber from soleus muscle.

value: Soleus muscle

value: Individual pure type 2X myofiber


title: Myofiber MyHC-2X_9(S9)

value: Male


title: Paraffin embedded tissue of ESCC patient 55

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-055T


title: 8: EXP1-EBM2_smallRNA


title: 9: EXP1-EGM_smallRNA


title: Myofiber MyHC-2X_7(S7)


title: CRC ≥ 70 years. Sample 44

value: reference


title: Paraffin embedded tissue of ESCC patient 53

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-053T


title: CRC ≥ 70 years. Sample 42


title: Myofiber MyHC-2X_8(S8)


title: Paraffin embedded tissue of ESCC patient 52

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-052T


title: 3: EXP1-GBM8-EV_smallRNA


title: Myofiber MyHC-2X_5(S6)


title: Myofiber MyHC-2X_6(S7)


title: CRC ≥ 70 years. Sample 40

value: MSS y CIMP-High


title: Paraffin embedded tissue of ESCC patient 50

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-050T


title: Paraffin embedded tissue of ESCC patient 49

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-049T


title: CRC ≥ 70 years. Sample 41


title: Paraffin embedded tissue of ESCC patient 51

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-051T


title: CRC ≥ 70 years. Sample 43


title: 2: EXP1-EGM_smallRNA


title: no12

first: Bernard

last: Roelen

state: The Netherlands

address: Uppsalalaan 8

department: Department of Farm Animal Health

institute: Utrecht University

data_processing:
Sequencing data were processed as described previously (Grün, D. et al.,Cell Stem Cell, 2016).In brief, after demultiplexing, sequencing reads were mapped to a cDNA library, reads mapping to the same gene with identical UMI were counted as a single read.
Genome_build:  UMD3.1, 2017
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: oocyte

growth_protocol: oocytes were cultured in the presence of a cyclin-dependent kinase (CDK) inhibitor (roscovitine) for 16 h to delay meiotic resumption followed by culture in maturation medium for 22 h.

extract_protocol:
A total of 24 oocytes (12 oocytes from the injection group, 12 oocytes for non-injection group) were collected to isolate of total RNA using an RNeasy Micro Kit (Qiagen, city, state, USA) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the CEL-seq2 protocol.

treatment_protocol: 12 oocytes injected with scrambled siRNA

value: MII stage oocyte

value: wild type


title: 1: EXP1-EBM2_smallRNA


title: no9


title: Myofiber MyHC-2X_2(S3)

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.


title: no11


title: CRC ≥ 70 years. Sample 38

value: MSS y CIMP-Low/0


title: Myofiber MyHC-2X_3(S6)


title: Myofiber MyHC-2X_4(S6)


title: Paraffin embedded tissue of ESCC patient 46

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-046T


title: Paraffin embedded tissue of ESCC patient 48

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-048T


title: no8


title: no10


title: Paraffin embedded tissue of ESCC patient 44

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-044T


title: Paraffin embedded tissue of ESCC patient 45

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-045T


title: Paraffin embedded tissue of ESCC patient 47

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-047T


title: Myofiber Hyb-2A/2X_10(S11)

source_name: Individual hybrid type 2A/2X myofiber from soleus muscle.

value: Individual hybrid type 2A/2X myofiber


title: Myofiber MyHC-2X_1(S2)


title: Paraffin embedded tissue of ESCC patient 43

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-043T

source_name: Paraffin embedded tissue of ESCC patients

value: Esophageal squamous cell carcinoma (ESCC)


title: CRC ≥ 70 years. Sample 31


title: CRC ≥ 70 years. Sample 32


title: Myofiber Hyb-2A/2X_8(S9)

value: 3 months


title: CRC ≥ 70 years. Sample 33


title: Paraffin embedded tissue of ESCC patient 42

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-042T


title: no7


title: Myofiber Hyb-2A/2X_7(S9)


title: CRC ≥ 70 years. Sample 36


title: CRC ≥ 70 years. Sample 34


title: CRC ≥ 70 years. Sample 30


title: CRC ≥ 70 years. Sample 37


title: CRC ≥ 70 years. Sample 35


title: no5


title: no4


title: Myofiber Hyb-2A/2X_6(S8)


title: no6


title: no3


title: Paraffin embedded tissue of ESCC patient 39

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-039T


title: Paraffin embedded tissue of ESCC patient 38

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-038T


title: Paraffin embedded tissue of ESCC patient 37

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-037T


title: Paraffin embedded tissue of ESCC patient 40

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-040T


title: Myofiber Hyb-2A/2X_5(S6)


title: Myofiber Hyb-2A/2X_4(S5)


title: CRC ≥ 70 years. Sample 29


title: Myofiber Hyb-2A/2X_2(S5)


title: Paraffin embedded tissue of ESCC patient 41

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-041T


title: CRC ≥ 70 years. Sample 28


title: Myofiber Hyb-2A/2X_9(S10)


title: CRC ≥ 70 years. Sample 26


title: CRC ≥ 70 years. Sample 27


title: Myofiber Hyb-2A/2X_1(S3)


title: Myofiber Hyb-2A/2X_3(S5)


title: no2


title: CRC ≥ 70 years. Sample 25


title: NegsiRNA11

value: scrambled siRNA injected


title: no1


title: NegsiRNA12


title: NegsiRNA10


title: NegsiRNA9


title: Paraffin embedded tissue of ESCC patient 36

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-036T


title: CRC ≥ 70 years. Sample 23


title: Paraffin embedded tissue of ESCC patient 35

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-035T


title: NegsiRNA8


title: Myofiber MyHC-2A_9(S12)

source_name: Individual pure type 2A myofiber from soleus muscle.

value: Individual pure type 2A myofiber


title: Myofiber MyHC-2A_10(S13)


title: Paraffin embedded tissue of ESCC patient 33

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-033T

value: Esophagus


title: Paraffin embedded tissue of ESCC patient 32

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-032T


title: Paraffin embedded tissue of ESCC patient 30

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-030T


title: CRC ≥ 70 years. Sample 18


title: CRC ≥ 70 years. Sample 22


title: Myofiber MyHC-2A_5(S8)

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.


title: Myofiber MyHC-2A_7(S10)


title: Myofiber MyHC-2A_8(S12)


title: Paraffin embedded tissue of ESCC patient 31

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-031T


title: NegsiRNA7


title: CRC ≥ 70 years. Sample 24


title: CRC ≥ 70 years. Sample 17


title: NegsiRNA5


title: NegsiRNA4


title: NegsiRNA6


title: Myofiber MyHC-2A_6(S8)


title: CRC ≥ 70 years. Sample 16


title: Myofiber MyHC-2A_3(S3)


title: Paraffin embedded tissue of ESCC patient 34

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-034T


title: Paraffin embedded tissue of ESCC patient 26

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-026T


title: Myofiber MyHC-2A_1(S1)


title: Paraffin embedded tissue of ESCC patient 23

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-023T


title: CRC ≥ 70 years. Sample 19


title: CRC ≥ 70 years. Sample 15


title: Paraffin embedded tissue of ESCC patient 28

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-028T


title: CRC ≥ 70 years. Sample 21


title: NegsiRNA2


title: Paraffin embedded tissue of ESCC patient 25

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-025T


title: CRC ≥ 70 years. Sample 20

source_name: Left colon


title: Myofiber MyHC-2A_2(S3)


title: Myofiber MyHC-1_10(S12)

source_name: Individual pure type 1 myofiber from soleus muscle.

value: Individual pure type 1 myofiber


title: CRC ≥ 70 years. Sample 13

source_name: Human Genomic DNA [Male G1471/FemaleG1521] from Promega Corporation


title: NegsiRNA1


title: Paraffin embedded tissue of ESCC patient 24

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-024T


title: NegsiRNA3


title: CRC ≥ 70 years. Sample 14


title: CRC ≥ 70 years. Sample 12


title: Paraffin embedded tissue of ESCC patient 22

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-022T


title: CRC ≥ 70 years. Sample 11

value: Female


title: M_108

city: Kunming

first: Zunxi

last: Huang

state: Yunnan

address: 768 Ju Xian Street

institute: Yunnan Normal University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GS115 whole genome using Hisat2 v2.0.5
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010.The effect of sequencing depth and gene length on fragments count was also considered.
Genome_build: GS115
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Komagataella phaffii

source_name: Fermentation mixture

growth_protocol: High-cell-density fed-batch cultivation encompassing four stages, namely, bench-scale batch fermentation, glycerol feed, GM phase, and methanol induction phases is used for Pichia pastoris to analysis the synthesis of recombinant proteins and investigating responses to various carbon sources

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Komagataella phaffii GS124

tag: fermentation stage

value: Methanol growth at 108 h


title: M_120

value: Komagataella phaffii GS125

value: Methanol growth at 120 h


title: M_96

value: Komagataella phaffii GS123

value: Methanol growth at 96 h


title: M_84

value: Komagataella phaffii GS122

value: Methanol growth at 84 h


title: M_72

value: Komagataella phaffii GS121

value: Methanol growth at 72 h


title: M_60

value: Komagataella phaffii GS120

value: Methanol growth at 60 h


title: Paraffin embedded tissue of ESCC patient 21

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-021T

value: Esophageal squamous cell carcinoma (ESCC)


title: CRC ≥ 70 years. Sample 10

city: Salamanca

tag: Sex

value: Male

value: MSS y CIMP-Low/0

value: reference


title: CRC ≥ 70 years. Sample 9

tag: age


title: Paraffin embedded tissue of ESCC patient 19

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-019T

value: Esophagus


title: Myofiber MyHC-1_7(S8)

value: 3 months

value: Soleus muscle

value: Individual pure type 1 myofiber


title: Paraffin embedded tissue of ESCC patient 20

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-020T


title: Myofiber MyHC-1_6(S7)


title: Myofiber MyHC-1_4(S6)


title: Myofiber MyHC-1_3(S4)


title: CRC ≥ 70 years. Sample 8

tag: molecular classification

value: MSS y CIMP-High


title: CRC ≥ 70 years. Sample 6

value: Female

tag: sample type


title: CRC ≥ 70 years. Sample 4


title: Myofiber MyHC-1_5(S7)


title: Paraffin embedded tissue of ESCC patient 16

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-016T


title: M_48

value: Komagataella phaffii GS119

value: Methanol growth at 48 h


title: CRC ≥ 70 years. Sample 5


title: CRC ≥ 70 years. Sample 3


title: Th1 input

source_name: iTreg

tag: cell type

value: iTreg

value: Balb/c