title: myc-fast1a-wt-async-x16


title: hepaticTF-condition_PPAN_siRNA_Rep2

status: Public on Jun 24 2021

type: SRA

city: Seattle

first: Ryan

middle: Lehman

last: McCarthy

state: WA

address: 1900 9th Ave

department: Pediatrics

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Samples were demultiplexed to produce FASTQ files using cutadapt (v.1.15) with Python  (v.2.7.14)
Reads with low quality, adapter, high N rate or poly-A sequences were filtered out from the raw FASTQ data before alignment using SOAPnuke (v.2.0.2)
Clean reads were aligned to the hg38 reference and gene expression levels were quantified using RSEM (v.1.3.2)
Genome_build: hg38

molecule: polyA RNA

organism: Homo sapiens

source_name: Human BJ Fibroblast

growth_protocol: Human BJ foreskin fibroblasts were obtained from Stemgent (08-0027) at passage 6 and cultured in Eagle's Minimum Essential Medium (Sigma M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM L-glutamine (Gibco) at 37°C and 5% CO2

extract_protocol:
RNA was purified using the ZR-96 Quick-RNA kit (Zymo Research R1052) and was polyA-selected using Oligo(dT)25 Dynabeads (Thermo Fisher Scientific, #61002).
75-100 ng of isolated RNA was used to prepare RNA-seq libraries for sequencing. All custom primers used in cDNA synthesis are listed below. An oligo-dT primer was used to perform poly-A enrichment and was incubated with the sample for 5 minutes. First-stand cDNA synthesis was performed with Superscript II Reverse Transcriptase (Invitrogen 18064022) and a template switch oligo by incubating for 1.5 hours. Second-strand cDNA synthesis was performed with the KAPA HiFi HotStart Ready Mix (Roche 7958927001) and an IS primer with 3 cycles of PCR amplification. 5ng of cDNA was fragmented using the Tn5 enzyme-adaptor compound. 15 cycles of PCR were then carried out with barcoded primers compatible with the BGISEQ-500. The 300-500bp DNA fragments were selected and purified. The fragments were then heat-denatured and one of the single strands was circularized with DNA ligase to obtain a single strand circular DNA library. The remaining single strand was digested with the exonuclease. The sequencing process was conducted according to the BGISEQ-500 protocol

treatment_protocol: Cells were treated with two rounds of transfection with 10nM Silencer Silect siRNAs (Thermo Fisher Scientific) and 2.5 μl Lipofectamine RNAiMAX (Thermo Fisher #13778150), for 3 days per transfection. RNA was harvested at day 6 after the first transfection. For samples in the "hepatic TF" protocol, cells were first infected with lentiviruses delivering the human hepatic transcription factors FOXA3, HNF1A, and HNF4A (MOI 1.25 per virus) the day before the first siRNA transfection (day -1), or 7 days before RNA harvest.

tag: cell type

value: human BJ Fibroblast

tag: sirna


title: RB160-4

city: Pittsburgh

first: Sarah

last: Gaffen

state: PA

address: 200 lothrop street

institute: University of Pittsburgh

data_processing:
Raw data was processed and quality check was performed using CLC Genomics Workbench v11 QC tool with default parameters
Then the filtered reads were aligned against the mouse reference genome mm10 and also Ensembl annotations v86 using default parameters of “RNA-Seq Analysis” tool of CLC Genomics Workbench v12.
Differentially expressed genes (DEGs) were identified between treatment and control using “Differential Expressions in Two Groups” tool provided by CLC Genomics Workbench v11 (Qiagen Inc) . The tool uses a multifactorial statistic based on a negative binomial Generalized Linear Model.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include both raw read counts and normalized counts for each Sample
Supplementary_files_format_and_content: count matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator overnight

extract_protocol:
Cells were trypsinizedand RNA was harvested using Rneasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEFs were transfected with siRNA control or siRNA IMP2 . After 24 hours, media was changed and cells were left either unstimulated, or stimulated with IL-17 (200 ng/mL) for 8 hrs.

tag: strain

tag: tissue

value: Mouse embryonic fibroblasts

tag: age

value: E12.5–13.5 embryos

tag: genotype

value: wild type

tag: treatment

value: siControl + IL-17


title: hepaticTF-condition_PPAN_siRNA_Rep1


title: RB160-1

value: siControl


title: k56ac-fast1a-wt-async-x25

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64  with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out.txt file contains genome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: yeast cells were grown to saturation overnight in YPD  and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019

tag: antibody

tag: background

value: wt

value: async

tag: sensor

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: NA8

value: siIMP2 + IL-17


title: hepaticTF-condition_PIAS2_siRNA_Rep2


title: RB160-6


title: NA7


title: ha-slow1a-wt-async-x22

value: ha

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-Slow-MYC


title: hepaticTF-condition_PIAS2_siRNA_Rep1


title: hepaticTF-condition_PHB_siRNA_Rep2


title: NA6


title: NA5


title: hepaticTF-condition_PES1_siRNA_Rep2


title: ha-notag-wt-async-x21


title: hepaticTF-condition_PHB_siRNA_Rep1


title: RB160-3


title: hepaticTF-condition_PES1_siRNA_Rep1


title: hepaticTF-condition_NONO_siRNA_Rep2


title: hepaticTF-condition_NONO_siRNA_Rep1


title: ha-slow1b-wt-async-x22


title: hepaticTF-condition_NCOA7_siRNA_Rep2


title: NA4


title: hepaticTF-condition_NCOA5_siRNA_Rep2


title: NA3


title: hepaticTF-condition_POLDIP3_siRNA_Rep2


title: hepaticTF-condition_NCOA7_siRNA_Rep1


title: hepaticTF-condition_POLDIP3_siRNA_Rep1


title: ha-h4a-wt-async-x25

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: hepaticTF-condition_NCOA5_siRNA_Rep1


title: ha-h2b1a-wt-async-x25

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC


title: ha-h2b1b-wt-async-x25


title: hepaticTF-condition_MYEF2_siRNA_Rep2


title: NA2


title: NA1


title: hepaticTF-condition_MYEF2_siRNA_Rep1


title: ha-h2a1-wt-async-x19

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: hepaticTF-condition_MYBBP1A_siRNA_Rep2


title: hepaticTF-condition_MYBBP1A_siRNA_Rep1


title: ha-h4b-wt-async-x25


title: BRN-KO3

city: Scarborough

first: Arturo

last: Hernandez

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

data_processing:
FASTQC and multiQC v1.9 were used to determine the quality of sequencing data. The adaptor sequences were trimmed using cutadapt 3.1 with Phython 3.6.2 with -m 1 option. The STAR version 2.5.3a (Spliced Transcripts Alignment to a Reference was used to align the reads to the reference genome (GRCm38/mm10) using the default settings, and the genome index was built based on the GENCODE VM22 annotation (GRCm38/mm10). rRNA and tRNA were filtered using bedtools version 2.26.0, using the GTF files downloaded from the UCSC Table Browser (GRCm38/mm10). HTSeq was used to count the reads per transcript (HTseq counts) with a default setting over the union with -s no option. For differential gene expression analysis, DESeq2 version 1.30.1 was performed in the R environment (Version 4.0.3), using the HTseq counts and the significance cutoff set as adjusted p-values <0.05 . ComBat-seq was utilized to adjust the batch effects between the two batches of samples.
Genome_build: GRCm38/mm10

source_name: Fetal brain

extract_protocol:
Qiagen RNAeasy mini kit
Standard Illumina protocols

tag: background strain

value: fetal brain

tag: embryonic age

tag: Sex

value: male


title: hepaticTF-condition_MRTO4_siRNA_2_Rep2

value: human BJ Fibroblast


title: hepaticTF-condition_MRTO4_siRNA_2_Rep1


title: ha-fast2b-wt-async-x22


title: BRN-KO4


title: ha-fast2a-wt-async-x22


title: BRN-KO1


title: hepaticTF-condition_MRTO4_siRNA_1_Rep2


title: ha-fast2a-wt-async-x21


title: hepaticTF-condition_MBNL1_siRNA_Rep2


title: ha-fast1b-wt-async-x22


title: hepaticTF-condition_MPHOSPH10_siRNA_Rep2


title: hepaticTF-condition_MPHOSPH10_siRNA_Rep1


title: hepaticTF-condition_MRTO4_siRNA_1_Rep1


title: BRN-WT4

description: E18.5-Wild type


title: BRN-KO2


title: ha-fast1b-wt-async-x21


title: hepaticTF-condition_MBD3_siRNA_2_Rep2


title: hepaticTF-condition_MBD3_siRNA_2_Rep1


title: ha-fast1b-wt-async-x16


title: hepaticTF-condition_MBNL1_siRNA_Rep1


title: hepaticTF-condition_MBD3_siRNA_1_Rep2


title: ctrc-3

type: RNA

city: jinan

first: Bing

last: Li

address: Wenhua Xi Road 107

country: China

institute: Qilu Hospital

description: gene expression of colonic mucosa

hyb_protocol: 0.6 ug of cy3-labelled cRNA was fragmented at 60 ℃ for 30 minutes in a rection wolume of 22,5ul containing 1* Agilent fragmentation buffer and 2* Agilent blocking agent following the  manufacuturer's instructions. On completion of the fragmentation reaction, 22.5ul of 2* Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Scanner G5761A for 17 hours at 65 ℃ in a rotation Agilent hybridization oven.After hybridization, microarrays were washed 1 minute at roon temperature with GE wash buffer 1(Agilent) and 1 minute with 37 ℃ GE wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediatedly after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4*180k array slides (Scan area 61*21.6mm, scan resolution 3um, dye channel is set to green and green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction sofeware (version12.0.3.1,Agilent Technologies) using default paremeters to obtain background subtracted and spatially detrended processed signal intensities as the raw data. Raw data were nornalized in quantile algorithm with Genespring sofeware (version14.8,Agilent Technologies). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: colonic mucosa

label_protocol: Cyanine-3 (cy3) labeled cRNA was prepared from 0.2ug RNA using the one-color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencla, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from tissue samples using RNA Isolation Kit following the manufacturer's instructions

tag: subject status

value: Healthy control

tag: gender

value: female

value: colonic mucosa


title: ha-fast1a-wt-async-x25


title: BR-WT4

description: E13.5-Wild type


title: hepaticTF-condition_MATR3_siRNA_Rep1


title: hepaticTF-condition_MBD3_siRNA_1_Rep1


title: hepaticTF-condition_LTBP2_siRNA_Rep2


title: hepaticTF-condition_LTBP2_siRNA_Rep1


title: hepaticTF-condition_LOXL2_siRNA_Rep2


title: ha-fast1a-wt-async-x22


title: ha-fast1a-wt-async-x23


title: hepaticTF-condition_LLPH_siRNA_Rep2


title: ha-fast1a-wt-async-x21


title: BRN-WT2

description: E18.5-Wild type


title: DNMT3A W297Del LCLs-  RNA sequencing

city: Stanford

first: Yung-Hsin

last: Huang

state: CA

address: CCSR 2155, 269 Campus drive

institute: Stanford University

data_processing:
RNA-seq:
STAR v2.5.4a was used to map to the mouse genome GRCm38 and calculate the raw read counts using default parameter settings.
edgeR_3.26.8 was used to normalize the read count data and generate the gene expression matrix (Reads per Kilobase per Million).
WGBS (human):
Raw reads of whole genome bisulfite sequencing data were mapped to genome using BSMAP (v2.90) with default parameters.
Duplicated reads were removed and only properly paired reads that uniquely mapped to genome were used.
CpG methylation ratios on both strands were combined and CpG loci with sequencing depth less than 5 were excluded.
WGBS (mouse):
Raw reads of whole genome bisulfite sequencing data were mapped to genome using BSMAP (v2.90) with default parameters.
Duplicated reads were removed and only properly paired reads that uniquely mapped to genome were used.
CpG methylation ratios on both strands were combined and CpG loci with sequencing depth less than 5 were excluded.
Genome_build: GRCm38; hg19
Supplementary_files_format_and_content: raw read counts for each genes; CpG location and methylation ratio

source_name: Lymphoblastoid cell line

growth_protocol: DKO mESCs and their DNMT3A mutant-expressing derivatives were cultured in 12.5% Foundation ES serum, 1X Glutamax, 100 μM b-mercaptoethanol, 1X NEAA and 1000U/mL leukemia inhibitory factor (LIF) and Knockout DMEM. LCLs are cultured in RPMI 1640 medium (containing 10% fetal calf serum and 5% L -glutamine)

extract_protocol:
DNA is extracted using purelink genomic DNA extraction kit. RNA is extracted using Rneasy kit.
WGBS is generated using Truseq DNA methylation kit. RNAseq is generated using Truseq stranded mRNA kit.

treatment_protocol: 1uM MG132 and 2ug/ml doxycycline are treated for 30 days

tag: dnmt3a genotype

value: untreated


title: hepaticTF-condition_LOXL1_siRNA_Rep1


title: hepaticTF-condition_LOXL1_siRNA_Rep2


title: BR-WT1

description: E13.5-Wild type


title: hepaticTF-condition_KHDRBS1_siRNA_2_Rep2


title: hepaticTF-condition_LLPH_siRNA_Rep1


title: WT LCLs- RNA sequencing

value: WT


title: WT LCLs treated with 1uM MG132 -  RNA sequencing

value: 1 uM MG132


title: hepaticTF-condition_KHDRBS1_siRNA_1_Rep2


title: hepaticTF-condition_LOXL2_siRNA_Rep1


title: hepaticTF-condition_KHDRBS3_siRNA_Rep2


title: BR-KO2


title: DNMT3A W297Del LCLs treated with 1uM MG132-  RNA sequencing


title: hepaticTF-condition_KHDRBS3_siRNA_Rep1


title: ha-fast1a-wt-async-x16

value: wt

value: async


title: hepaticTF-condition_MATR3_siRNA_Rep2


title: DNMT3A W297Del LCLs treated with 1uM MG132- WGBS


title: hepaticTF-condition_KHDRBS1_siRNA_1_Rep1


title: hepaticTF-condition_KAP1_siRNA_2_Rep2


title: DNMT3A W297Del LCLs- WGBS


title: hepaticTF-condition_KHDRBS1_siRNA_2_Rep1


title: WT LCLs treated with 1uM MG132 - WGBS


title: hepaticTF-condition_KAP1_siRNA_1_Rep1


title: hepaticTF-condition_HP1BP3_siRNA_Rep1


title: SY2_TZ_1: RL tazemetostat

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Raw reads were mapped to hg19 using the STAR 2.7.3a two pass mode.
Gene counts were generated using "quantMode GeneCounts" from within STAR.
Genome_build: hg19

source_name: Diffuse large B-cell lymphoma

growth_protocol: SUDHL4 parental and engineered cell lines were grown at 37°C with 5% CO2 in RPMI 1640 supplemented with 2mM L-glutamine and 20% FBS. RL cells were cultured similarly in medium with 10% FBS.

extract_protocol:
RNeasy Mini Kit (Qiagen)
Illumina TruSeq Stranded mRNA Library Prep kit

treatment_protocol: The following model systems were used for RNA-seq: 1) RL cells treated with DMSO, 10μM lenalidomide, 5μM tazemetostat or combination; 2) SUDHL4 cells treated with DMSO, 10μM lenalidomide, 5μM tazemetostat or combination; and 3) SUDHL4 cells with either IKZF1 knockout or LacZ gRNA control treated with DMSO or 5μM tazemetostat. Two technical replicates of all samples and conditions were prepared. Cells were incubated with drug treatments for 6 days.

tag: cell line

value: RL

value: Diffuse large B-cell lymphoma

value: tazemetostat


title: SY2_LT_1: RL lenalidomide + tazemetostat

tag: cell type

value: lenalidomide + tazemetostat


title: hepaticTF-condition_HNRNPK_siRNA_Rep2

tag: sirna


title: SY2_TZ_2: RL tazemetostat


title: SY2_LN_2: RL lenalidomide

value: lenalidomide


title: hepaticTF-condition_HNRNPL_siRNA_Rep1


title: SY2_LN_1: RL lenalidomide


title: hepaticTF-condition_HMGA1_siRNA_Rep2


title: hepaticTF-condition_HDLBP_siRNA_Rep2


title: hepaticTF-condition_HNRNPL_siRNA_Rep2


title: hepaticTF-condition_HNRNPA2B1_siRNA_Rep1


title: hepaticTF-condition_GLTSCR2_siRNA_Rep1


title: hepaticTF-condition_GLTSCR2_siRNA_Rep2


title: hepaticTF-condition_HDLBP_siRNA_Rep1


title: SY2_DM_2: RL DMSO

value: DMSO


title: WT LCLs- WGBS


title: hepaticTF-condition_KAP1_siRNA_1_Rep2


title: hepaticTF-condition_GATAD2B_siRNA_Rep2


title: hepaticTF-condition_HP1BP3_siRNA_Rep2


title: hepaticTF-condition_GATAD2B_siRNA_Rep1


title: Jurkat RNA-seq

city: Shanghai

first: Jianing

last: Wang

address: Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
RNA-seq reads were trimmed using Trim Galore ,reads containing adapter were discarded,and HISAT2 software was used for mapping to hg38 genome,Then Stringtie (version 1.3.3) was used to assemble gene expression from aligned reads to quantify the number of reads mapped to each gene. The expression level of genes was assessed by Fragments per kilobase of exon per million reads mapped (FPKM)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

source_name: lymphocyte cells

growth_protocol: The cells were cultured with RPMI1640 medium (Biological Industries, Israel) containing 20% fetal bovine serum (Gibco BRL/Invitrogen, Carlsbad, CA, USA), 100μg/ml streptomycin, and 100IU/ml penicillin, and incubated with 37℃ and 5% CO2.

extract_protocol:
Total RNA was extracted from Jurkat cell and SW1353 samples by using TRIzol reagents (Invitrogen, Waltham, Massachusetts, USA) as recommended by the manufacturer.
One microgram of total RNA was used to construct the RNA-seq libraries by KAPA Stranded RNA-Seq Kit  following the manufacturer’s protocol. The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

value: Jurkat

value: Normal culture

tag: cell cycle

value: Interphase


title: SW1353 RNA-seq

source_name: Fibroblast Cells

growth_protocol: The cells were cultured with DMEM/F-12 medium (Biological Industries, Israel) containing 20% fetal bovine serum (Gibco BRL/Invitrogen, Carlsbad, CA, USA), 100μg/ml streptomycin, and 100IU/ml penicillin, and incubated with 37℃ and 5% CO2.


title: SY2_LT_2: RL lenalidomide + tazemetostat


title: MS1 [degradome]

city: Fu Yang

first: Min

last: Zhong

state: Hang Zhou

address: Rice research road NO.28

institute: China National Rice Research Institute

data_processing:
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low  quality reads
The extracted sequencing reads were then used to identify potentially cleaved  targets by the CleaveLand pipeline
The degradome reads were mapped to the mRNA.Only the perfect matching alignment(s) for the given read  would be kept for degradation analysis  downloaded from NCBI
All resulting reads (t-signature) were reversecomplemented and aligned to the miRNA identified in our study.No more than four alignment scores were allowed.
Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored.
All the identified targets were subjected to BlastX analysis to search for similarity, and then to GO analysis to uncover the miRNA-gene regulatory network on the basis of biological process ,cellular component and molecular function .
Supplementary_files_format_and_content: tab-delimited text files include Degradome Read Number

organism: Oryza sativa

growth_protocol: Germinating seedlings were removed to a hydroponics solution consisting of Hoagland’s solution (pH 5.5) in a climate chamber (relative humidity 80%, 30/28℃ day/night temperature)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.  The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit  (Agilent, CA, USA) with RIN number >7.0. Approximately 20 ug of total RNA were used to prepare  Degradome library. The method differed considerably from past efforts (Addo-Quaye et al., 2008, 2009b) and  followed as (Ma et al., 2010) with some modification. (1) Approximately 150 ng of poly(A)+ RNA was used as  input RNA and annealing with Biotinylated Random Primers. (2) Strapavidin capture of RNA fragments  through Biotinylated Random Primers. (3)5’ adaptor ligation to to only those RNAs containing 5’-  monophosphates. (4) Reverse transcription and PCR (5) Libraries were sequenced using the 5’ adapter only,  resulting in the sequencing of the first 36 nucleotides of the inserts that represented the 5’ ends of the original  RNAs. And then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO  (Hangzhou, China) following the vendor’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once the first leaf was fully expanded, seedlings were subjected to CdCl2•2.5H2O in different concentrations, including 0 µM (the control, MC) and 100 µM (MS) for 12 days, in triplicate.

tag: cultivar

value: Zhong Jiazao-17

tag: tissue

value: Shoot

tag: cadmium treatment

value: 100 μΜ cadmium treatment for 12 days (MS)

tag: development stage

value: rice at one leaf stage


title: hepaticTF-condition_HNRNPK_siRNA_Rep1

value: human BJ Fibroblast


title: hepaticTF-condition_HNRNPA2B1_siRNA_Rep2


title: MC1 [degradome]

value: 0 μΜ cadmium treatment for 12 days (control; MC)


title: hepaticTF-condition_HMGA1_siRNA_Rep1


title: hepaticTF-condition_GATAD2A_siRNA_Rep2


title: KT5_TZ_2: SUDHL4 IKZF1 KO + tazemetostat

value: SUDHL4 IKZF1 KO

tag: treatment


title: KT5_TZ_1: SUDHL4 IKZF1 KO + tazemetostat


title: KT4_TZ_2: SUDHL4 LacZ KO tazemetostat

value: SUDHL4 Lacz KO


title: KT4_TZ_1: SUDHL4 LacZ KO tazemetostat


title: MS2

data_processing:
Illumina Casava1.7 software used for basecalling.
ACGT101-miR (4.2) used to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Then sequence quality was verified using FastQC(v0.10.1).
Valid reads were aligned to the miRBase21.0 using Bowtie.Then StringTie(v1.3.0) and Ballgown were used to assemble and estimate the expression levels of all transcripts.
RNAfold software (3.7) used to predict novel miRNA and hairpin RNA structures.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: Excel file includes FPKM values for all Samples.
Sheet1 is the data about all identified miRNAs.
Sheet2 has the same data to the sheet1, but with more clearly displayed form.
Sheet3 is the data about miRNAs identified significantly altered.

source_name: Shoot

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacture’s protocol. The total RNA quantity and purity was analyzed using Bioanalyzer 2 100 and RNA 6 000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (50 bps) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

tag: stress

value: 100 μΜ cadmium treatment for 12 days


title: MS1


title: hepaticTF-condition_FYTTD1_siRNA_Rep2


title: hepaticTF-condition_FYTTD1_siRNA_Rep1


title: MS3


title: SY2_DM_1: RL DMSO

value: RL

value: Diffuse large B-cell lymphoma


title: MC3

value: 0 μΜ cadmium treatment for 12 days


title: hepaticTF-condition_ERH_siRNA_2_Rep1


title: hepaticTF-condition_FUS_siRNA_Rep2


title: hepaticTF-condition_EXOSC10_siRNA_Rep1


title: hepaticTF-condition_EXOSC10_siRNA_Rep2


title: KT5_DM_2: SUDHL4 IKZF1 KO DMSO


title: hepaticTF-condition_GATAD2A_siRNA_Rep1


title: MC2


title: hepaticTF-condition_FUS_siRNA_Rep1


title: KT5_DM_1: SUDHL4 IKZF1 KO DMSO


title: hepaticTF-condition_ERH_siRNA_2_Rep2


title: hepaticTF-condition_EBNA1BP2_siRNA_Rep2


title: hepaticTF-condition_ERH_siRNA_1_Rep2


title: hepaticTF-condition_ERH_siRNA_1_Rep1


title: KT4_DM_2: SUDHL4 LacZ KO DMSO


title: hepaticTF-condition_KAP1_siRNA_2_Rep1


title: hepaticTF-condition_EBNA1BP2_siRNA_Rep1


title: N3

city: Shantou

first: wenzhen

last: he

state: Guangdong

address: 57 Changping Road

institute: First Affiliated Hospital of Shantou University Medical College

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: healthy individuals

extract_protocol:
HiSeq LncRNA-Seq
RNA libraries were prepared for sequencing using standard illumina protocol

value: blood

tag: diagnosis

value: healthy

tag: age


title: hepaticTF-condition_DDX5_siRNA_Rep2


title: hepaticTF-condition_DDX5_siRNA_Rep1


title: KT4_DM_1: SUDHL4 LacZ KO DMSO

value: DMSO


title: N2


title: hepaticTF-condition_CUX1_siRNA_Rep2


title: N1


title: T3

source_name: ischemic stroke patients

value: ischemic stroke


title: SY1_TZ_2: SUDHL4 tazemetostat

value: tazemetostat


title: hepaticTF-condition_DDX17_siRNA_Rep2


title: T2


title: hepaticTF-condition_CUX1_siRNA_Rep1


title: SY1_LT_1: SUDHL4 lenalidomide + tazemetostat

value: lenalidomide + tazemetostat


title: hepaticTF-condition_DDX17_siRNA_Rep1


title: hepaticTF-condition_CHAF1A_siRNA_Rep2


title: T1


title: SY1_TZ_1: SUDHL4 tazemetostat


title: MC1

value: Zhong Jiazao-17

value: Shoot


title: SY1_LN_2: SUDHL4 lenalidomide

value: lenalidomide


title: hepaticTF-condition_CHTOP_siRNA_Rep1

value: human BJ Fibroblast


title: hepaticTF-condition_CHTOP_siRNA_Rep2


title: hepaticTF-condition_CEBPZ_siRNA_Rep2


title: hepaticTF-condition_CCDC86_siRNA_Rep1


title: hepaticTF-condition_CEBPZ_siRNA_Rep1


title: SY1_LN_1: SUDHL4 lenalidomide


title: hepaticTF-condition_CCDC86_siRNA_Rep2


title: hepaticTF-condition_CCDC59_siRNA_Rep1


title: SY1_DM_2: SUDHL4 DMSO


title: hepaticTF-condition_CCDC59_siRNA_Rep2


title: hepaticTF-condition_CCDC137_siRNA_Rep2


title: SY1_LT_2: SUDHL4 lenalidomide + tazemetostat


title: hepaticTF-condition_CHAF1A_siRNA_Rep1


title: hepaticTF-condition_CBX5_siRNA_Rep1


title: hepaticTF-condition_CBX5_siRNA_Rep2


title: hepaticTF-condition_CBX3_siRNA_Rep2


title: hepaticTF-condition_CBX3_siRNA_Rep1


title: hepaticTF-condition_CBX1_siRNA_Rep1


title: hepaticTF-condition_CBX1_siRNA_Rep2


title: datghter SKOV3 cells, clone 1

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
fastq files were preprocessed using fastp software to remove low quality reads
clean fastq files were mapped to human transcriptome (hg38) using salmon v0.14.1 to generate counts and TPM for each transcript
raw counts and TPM for each transcript were aggregated by gene symbols to generate a gene expression TPM table
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited txt file of TPM gene expression table

source_name: ATCC

growth_protocol: Hey and SKOV3 cell lines were cultured in MEM Eagle and RPMI-1640 media, respectively, supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit following the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with Paclitaxel (500 nM) for 16-18h, and recovered in regular medium for up to one month.

value: ovarian cancer cell line SKOV3

value: 500nM paclitaxel 16 hour, recover 30 days


title: parental SKOV3 cell line

value: untreated


title: PGCC SKOV3 cells at day 7

value: 500nM paclitaxel 16 hour, recover 3 days


title: hepaticTF-condition_C5orf41_siRNA_Rep2


title: PGCC HEY cells at day 3

value: ovarian cancer cell line Hey


title: hepaticTF-condition_C5orf41_siRNA_Rep1


title: parental HEY cell line


title: hepaticTF-condition_BCLAF1_siRNA_Rep1


title: hepaticTF-condition_BCLAF1_siRNA_Rep2


title: hepaticTF-condition_Control_siRNA_2_Rep2


title: daughter HEY cells, clone 1


title: SY1_DM_1: SUDHL4 DMSO

value: Diffuse large B-cell lymphoma


title: hepaticTF-condition_CCDC137_siRNA_Rep1


title: hepaticTF-condition_Control_siRNA_1_Rep1


title: hepaticTF-condition_Control_siRNA_2_Rep1


title: hepaticTF-condition_Control_siRNA_1_Rep2


title: CID4535

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: ***Raw Data Disclaimer: Raw human data files are deposited to the EGA (EGAS00001005173) to adhere to ethics.***

data_processing:
Raw bcl files were demultiplexed and mapped to the reference genome GRCh38 using the Cell Ranger Single Cell v2.0 software (10X Genomics). The EmptyDrops method from the DropletUtils package (v1.2.2) was applied for cell filtering with additional cutoffs for cells with a gene and unique molecular identifier (UMIs) count greater than 200 and 250, respectively, and a mitochondrial percentage less than 20%.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files in MM matrix format (*.mtx), genes and barcode IDs (*.tsv)

source_name: Mammary Tumor

extract_protocol:
Single-cell sequencing was performed using the Chromium Single-Cell v2 3’ and 5’ Chemistry Library, Gel Bead, Multiplex and Chip Kits (10X Genomics) according to the manufacturer's protocol. A total of 5,000 to 7,000 cells were targeted per well.
Libraries were sequenced on the NextSeq 500 platform (Illumina) with pair-ended sequencing and dual indexing. A total of 26, 8 and 98 cycles were run for Read 1, i7 index and Read 2, respectively.

value: ER+

value: female

value: Primary Breast Tumor


title: CID4523

value: TNBC


title: CID45171


title: BMC_12_DKO naïve (s36)

city: San Francisco

first: Julie

last: Zikherman

address: Koret Way

department: Medicine - Rheumatology

institute: University of California, San Francisco

description: DKO naïve CD4 (chimera 12)

data_processing:
Fastq files were trimmed for adapters and low quality base pairs using Fastp
Trimmed files were aligned to mm10 using STAR
FeatureCounts was used to obtain raw read count data from BAM files, and TPM calculations were performed in Python
Genome_build: mm10
Supplementary_files_format_and_content: xlsx contains raw read counts and TPM for each sample, as well as p-value and FDR output from EdgeR analysis to identify DEG between WT and DKO naïve, WT and DKO naïve stim, WT and DKO anergic, as well as between WT naive and WT anergic, and WT naive and WT naive stim

source_name: Spleen and lymph node

growth_protocol: n/a; cell sorted from bone marrow competitive chimeras as described above

extract_protocol:
Cells were sorted into RLT buffer or  lysed in RLT following 3hr in vitro stimulation as described above
Libraries were generated by Emory Genomics Core (EIGC) as follows: Cells were sorted directly into RLT + 1% BME buffer and RNA isolated using the Quick-RNA MicroPrep kit (Zymo,11-328M). 2000 cell equivalent of RNA was used as input to generate cDNA using the SMART-seq v4 Ultra Low Input cDNA Synthesis kit (Takara, 634888). cDNA was quantitated by Qubit (ThermoFisher Scientific) and 200 pg of cDNA was tagmented and PCR amplified using the NexteraXT kit (Illumina, FC-121-10300) to generate final sequencing libraries. Libraries were quantitated by Qubit, pooled at equimolar ratios, and sequenced using 75 bp paired-end Illumina chemistry.
RNA-seq performed as follows: Libraries were sequenced in an individual lane of an S1 flowcell on the NovaSeq6000 with a PE100 configuration using a NovaSeq 6000 SP Reagent Kit.

treatment_protocol: DKO and WT CD25-CD4+ T cells were sorted from competitive chimeras on the basis of CD62L/CD44/FR4/CD73 surface expression to identify either naïve (CD62LhiCD44loFR4loCD73lo) or anergic (CD62LloCD44hiFR4hiCD73hi) populations. Naïve and anergic cell populations were sorted directly into RLT buffer. In parallel, sorted naive CD4 samples were stimulated ex vivo withplate-bound anti-CD3 and anti-CD28 for 3 hrs.

value: Spleen and lymph node

tag: strain

tag: naïve or anergic

value: naïve CD25-CD4+CD62LhiCD44loFR4loCD73lo

tag: genotype

value: DKO

tag: stimulation

tag: chimera number

value: BMC 12


title: BMC_11_WT naïve + stimulation (s39)

description: WT naïve CD4 + 3h TCR stim (chimera 11)

value: WT

value: Anti-CD3 [8 ug/ml] + anti-CD28 [2 ug/ml], 3 h

value: BMC 11


title: BMC_10_DKO naïve + stimulation (s38)

description: DKO naïve CD4 + 3h TCR stim (chimera 10)

value: BMC 10


title: BMC_10_WT naïve + stimulation (s37)

description: WT naïve CD4 + 3h TCR stim (chimera 10)


title: BMC_12_WT naïve + stimulation (s41)

description: WT naïve CD4 + 3h TCR stim (chimera 12)


title: BMC_11_DKO naïve + stimulation (s40)

description: DKO naïve CD4 + 3h TCR stim (chimera 11)


title: BMC_12_DKO naïve + stimulation (s42)

description: DKO naïve CD4 + 3h TCR stim (chimera 12)


title: CID4515

tag: gender


title: RNA2: H.colon organoid#1 Inf(R) control 2

city: yushima bunnkyoku Tokyo

first: Sho

last: Watanabe

department: gastroenterology

country: Japan

institute: Tokyo medical and dental university

description: Gene expression of UC-model organoids #1

hyb_protocol: 0.6ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting (Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent)

source_name: UC-model organoids #1 treated with control treatment for 6 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human colonic organoids were maintained in DMEM-based culture medium (Advanced-DMEM, Invitrogen Corporation, Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated using an RNeasy Micro Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's instructions.

treatment_protocol: 1.0 μM of MST-312 or 100 μM of Madecassoside was added to media every other day and cultured for 3 weeks or 6 weeks, respectively.

value: Organoids derived from colonic mucosa

value: male

value: control treatment for 6 weeks


title: RNA4: H.colon organoid#1 Inf(R) MD 1

description: Gene expression of MD-treated UC-model organoids #1

source_name: UC-model organoids #1 treated with 100 μM of Madecassoside for 6 weeks

value: 100 μM of Madecassoside for 6 weeks


title: RNA1: H.colon organoid#1 Inf(R) control 1


title: RNA3: H.colon organoid#1 Inf(R) control 3


title: RNA5: H.colon organoid#1 Inf(R) MD 2


title: RNA6: H.colon organoid#1 Inf(R) MD 3


title: FVF high cells 3

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

data_processing:
The 10X Genomics core computational software Cellranger v.2.0 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment. (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
For QC, filtering and normalization, the scanpy python package v.1.4.5.2.dev6+gfa408dc7 and anndata==0.7.1 were used.
For RNA velocity estimation, velocyto v. 0.17.17 was used.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

source_name: whole embryo

extract_protocol:
Embryos were isolated and extra-embryonic compartments were removed mechanically. Embryonic compartments were washed with cold PBS. For single cell suspension embryos were incubated with TrypLE (Life technologies, #12605) for 10 min at 37°C. Cells were dissociated by pipetting up and down.
Single-cell libraries were generated using the Chromium Single Cell 3′ library and gel bead kit v2 (PN #120237) from 10x Genomics. Flow-sorted cells were loaded onto a channel of the 10x chip to produce Gel Bead-in-Emulsions (GEMs). This underwent reverse transcription to barcode RNA before cleanup and cDNA amplification followed by enzymatic fragmentation and 5′adaptor and sample index attachment. Libraries were sequenced on the HiSeq4000 (Illumina) with 150 bp paired-end sequencing of read2.

value: embryonic compartment

value: homozyous

tag: cell type

value: FVF high cells


title: FVF low cells 3

value: FVF low cells


title: CID4513

value: TNBC

value: female

value: Primary Breast Tumor


title: RNA8: H.colon organoid#1 MST

description: Gene expression of MST-312 treated organoids #1

source_name: normal organoids #1 treated with MST-312 for 3 weeks

value: MST-312 for 3 weeks


title: RNA7: H.colon organoid#1 control

description: Gene expression of normal organoids #1

source_name: normal organoids #1 treated with control treatment for 3 weeks

value: control treatment for 3 weeks


title: FVF high cells 2


title: BMC_12_WT anergy (s33)

description: WT anergic CD4 (chimera 12)

value: Spleen and lymph node

value: WT

value: BMC 12


title: CID4530N

value: ER+


title: BMC_11_DKO naïve (s32)

description: DKO naïve CD4 (chimera 11)

value: naïve CD25-CD4+CD62LhiCD44loFR4loCD73lo

value: DKO

value: BMC 11


title: CID44991


title: FVF low cells 2


title: BMC_11_DKO anergy (s31)

description: DKO anergic CD4 (chimera 11)


title: BMC_11_WT naïve (s30)

description: WT naïve CD4 (chimera 11)


title: BMC_12_DKO anergy (s35)

description: DKO anergic CD4 (chimera 12)


title: BMC_12_WT naïve (s34)

description: WT naïve CD4 (chimera 12)


title: CID4495


title: FVF negative cells 2

value: FVF negative cells


title: CID4471


title: BMC_11_WT anergy (s29)

description: WT anergic CD4 (chimera 11)


title: FVF high cells 1

value: embryonic compartment


title: BMC_10_DKO naïve (s28)

description: DKO naïve CD4 (chimera 10)

value: BMC 10


title: BMC_10_WT anergy (s25)

description: WT anergic CD4 (chimera 10)


title: FVF low cells 1

value: homozyous


title: CID4465


title: CID4463


title: FVF negative cells 1


title: CID4461


title: Naive_1

city: Melbourne

first: Luke

middle: C

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

institute: WEHI

description:
Naïve CD8+ T cell
Biological replicate 1

data_processing:
FASTQ files were output using standard Illumina protocols and software
Reads were aligned to the mouse genome by Rsubread 2.2.6
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Spleen

extract_protocol:
RNA was isolated from freshly sorted cells with the miRNeasy kit (Qiagen).
Total RNA was isolated from 18-36×10^3 sorted cells (Qiagen) and cDNA libraries were prepared using the SMARTer Stranded Total RNA-Seq kit for Pico Input (Takara)

tag: host strain background

value: gBT-I

tag: transgenic strain

value: Naïve


title: Skin_WT

description:
HSV skin OT-I T cell
Biological replicate 1

source_name: Skin

value: OT-I

value: HSV infection d14


title: Naive_3

description:
Naïve CD8+ T cell
Biological replicate 3


title: Liver_WT_2

description:
LmOVA liver OT-I Trm
Biological replicate 2

source_name: Liver

value: Lm Infection d14


title: CID44971

value: TNBC

value: female

value: Primary Breast Tumor


title: Naive_2

description:
Naïve CD8+ T cell
Biological replicate 2


title: Skeletal Muscle HFD SLC16A13 KO Animal 602

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Data was preprocessed as described in Sollner, J. F., G. Leparc, T. Hildebrandt, H. Klein, L. Thomas, E. Stupka and E. Simon (2017). "An RNA-Seq atlas of gene expression in mouse and rat normal tissues." Sci Data 4: 170185.
The limma package48 in the R programming environment was used to convert raw counts to log2-counts per million, normalized to account for the systematic mean-variance relationships often present in microarray and RNA-Seq data. A Wilcoxon Rank Sum-based gene set enrichment analysis was performed using the algorithm provided in the gage package49, which was designed for use on microarray and RNA-Seq data. All p-values were corrected for False Discovery Rate.
Genome_build: Mouse Genome (Ensembl Version 86)
Supplementary_files_format_and_content: read counts (tab-delimited)
Supplementary_files_format_and_content: normalized read counts (RPKM) (tab-delimited)

source_name: Skeletal Muscle HFD SLC16A13 KO

growth_protocol: Mice were sacrificed at an age of 20 weeks.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instructions.
mRNA_stranded library kit
Sequencing was performed as 85bp single-end reads and 7 bases index read on an Illumina HiSeq4000 instrument at a sequencing depth of approximately 30 million reads per sample

treatment_protocol: Mice were fed high-fat diet for 15 weeks.

value: Skeletal Muscle

value: SLC16A13 KO

tag: diet

value: HFD


title: Skeletal Muscle HFD SLC16A13 KO Animal 611

tag: tissue


title: CID44041


title: Liver_WT_1

description:
LmOVA liver OT-I Trm
Biological replicate 1


title: Skeletal Muscle HFD SLC16A13 KO Animal 598


title: Liver_KO_1

description:
LmOVA liver OT-I.Tgfbr2-/- Trm
Biological replicate 1


title: Liver_KO_2

description:
LmOVA liver OT-I.Tgfbr2-/- Trm
Biological replicate 2


title: CID4398

value: ER+


title: BMC_10_WT naïve (s26)

description: WT naïve CD4 (chimera 10)

value: Spleen and lymph node

value: naïve CD25-CD4+CD62LhiCD44loFR4loCD73lo

value: WT


title: BMC_10_DKO anergy (s27)

description: DKO anergic CD4 (chimera 10)

value: DKO

value: BMC 10


title: Pos_2_techRep2

description:
LmOVA SG OT-I CD69+CD103+
Biological replicate 2, technical replicate 2

source_name: Salivary Gland

extract_protocol:
RNA was isolated from freshly sorted cells with the miRNeasy kit (Qiagen).
Total RNA was extracted from 9-40×10^3 sorted cells (Qiagen) and cDNA libraries were prepared using the SMARTSeq protocol (Takara)


title: Pos_2_techRep1

description:
LmOVA SG OT-I CD69+CD103+
Biological replicate 2, technical replicate 1


title: CID4290A

description: ***Raw Data Disclaimer: Raw human data files are deposited to the EGA (EGAS00001005173) to adhere to ethics.***


title: Pos_1_techRep2

description:
LmOVA SG OT-I CD69+CD103+
Biological replicate 1, technical replicate 2


title: Skeletal Muscle HFD SLC16A13 KO Animal 597


title: Skeletal Muscle HFD SLC16A13 KO Animal 588


title: Pos_1_techRep1

description:
LmOVA SG OT-I CD69+CD103+
Biological replicate 1, technical replicate 1


title: Liver_WT_3

description:
LmOVA liver OT-I Trm
Biological replicate 3


title: Neg_3_techRep1

description:
LmOVA SG OT-I CD69+CD103-
Biological replicate 3, technical replicate 1


title: CID4066


title: Skeletal Muscle HFD SLC16A13 KO Animal 583


title: Neg_3_techRep2

description:
LmOVA SG OT-I CD69+CD103-
Biological replicate 3, technical replicate 2


title: Neg_1_techRep1

description:
LmOVA SG OT-I CD69+CD103-
Biological replicate 1, technical replicate 1


title: CID3963


title: Neg_1_techRep2

description:
LmOVA SG OT-I CD69+CD103-
Biological replicate 1, technical replicate 2


title: Neg_2_techRep1

description:
LmOVA SG OT-I CD69+CD103-
Biological replicate 2, technical replicate 1


title: Neg_2_techRep2

description:
LmOVA SG OT-I CD69+CD103-
Biological replicate 2, technical replicate 2


title: CID3948


title: Skeletal Muscle HFD SLC16A13 KO Animal 568


title: CID4040


title: Naive_3_techRep2

description:
Naïve CD8+ T cell
Biological replicate 3, technical replicate 2

value: Naive


title: Skeletal Muscle HFD SLC16A13 KO Animal 570


title: Naive_3_techRep1

description:
Naïve CD8+ T cell
Biological replicate 3, technical replicate 1


title: Naive_2_techRep1

description:
Naïve CD8+ T cell
Biological replicate 2, technical replicate 1


title: Naive_1_techRep2

description:
Naïve CD8+ T cell
Biological replicate 1, technical replicate 2


title: CID3946


title: Skeletal Muscle HFD SLC16A13 KO Animal 561


title: Naive_2_techRep2

description:
Naïve CD8+ T cell
Biological replicate 2, technical replicate 2


title: CID4067


title: Naive_1_techRep1

description:
Naïve CD8+ T cell
Biological replicate 1, technical replicate 1


title: CID3941


title: Skeletal Muscle HFD SLC16A13 KO Animal 587


title: Skeletal Muscle HFD SLC16A13 KO Animal 532


title: Skeletal Muscle HFD WT Animal 624

source_name: Skeletal Muscle HFD WT


title: CID3921


title: Skeletal Muscle HFD WT Animal 623


title: CID3838


title: CID3586


title: Skeletal Muscle HFD WT Animal 612


title: Skeletal Muscle HFD WT Animal 586


title: Skeletal Muscle HFD WT Animal 616


title: MH-serum

city: Nanjing

first: Ping

last: Xie

state: jiangsu

address: 300 Guangzhou Road

department: department of ophthalmology

institute: The First Affiliated Hospital of Nanjing Medical University

description: non-coding RNA (ncRNA)

data_processing:
Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: : TRAILING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25)
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levelswere presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression.
The statistically significant differentially Expressed gene were obtained by an adjusted P-value thresholdof 1 using the DEGseq software.
Genome_build: hg19

source_name: MH-serum exosomes

growth_protocol: Blood samples were collected at least 12 h after a meal, followed with standing for 2 h at 4℃, then centrifuging at 2000×g for 20 min at 4℃, discarding precipitation,and stored at -80°C.

extract_protocol:
Total RNA was isolated from exosomes using the Trizol (invitrogen) according to the manufacturer instruction. RNA purity was assessed by ND-1000Nanodrop required dA260/280≥1.8, A260/A230≥2.0. RNA integrity was evaluated by Agilent 2200 TapeStation (Agilent Technologies, USA) requiring RIN≥7.0. Briefly, rRNAs were removed from total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA), then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp.
Fragmented RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA). The libraries were paired-end sequenced (PE150, Sequencing reads were 150 bp) at Guangzhou RiboBio Co., Ltd. (Guangzhou, China)using IlluminaHiSeq 3000 platform

treatment_protocol: Serum  samples were mixed with RiboTM Exosome Isolation Reagent (Guangzhou, China) and exosomes isolation was performed according to the manufacturer’s instructions (RiboBio, Guangzhou, China)

value: serum exosomes

tag: disease state

value: macular hole


title: PDR-serum

description: non-coding RNA (ncRNA)

source_name: PDR-serum exosomes

value: proliferative diabetic retinopathy


title: ha-fast1a-wt-alpha2hr-x24

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out.txt file contains genome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

source_name: budding yeast

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019

treatment_protocol: For h2o2 samples: exponentially growing cultures were exposed to 0.3 mM H2O2 and samples taken at indicated timepoints (in minutes)

tag: antibody

value: ha

tag: background

value: wt

tag: sensor

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: RNASeq_CAD14_T0

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
RNASeq: Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
RNASeq: Reads were mapped using STAR_2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provide.

source_name: peripheral whole blood

growth_protocol: We analyzed a total of 4 patients including 2 control subjects (CTR group) and 2 patients with stable coronary artery disease (CAD group). A peripheral blood sample (9mL) has been collected within 24 hours from the coronary angiography. CTR group includes subjects without angiographically significant coronary artery stenosis. CAD group includes patients with chronic stable angiographically documented coronary artery disease, admitted to the hospital for provocative cardiac testing positive for inducible myocardial ischemia. Inclusion criteria were (a) gender (especially male); (b) age > 70 years; (c) dyslipidemia (total cholesterol ≥ 240 mg/dl, LDL-c ≥ 160 mg/dl, HDL-c < 40 mg/dl, Triglycerides ≥ 200 mg/dl); (d) hypertension, systolic blood pressure (BP) values ≥ 140 mmHg and/or di-astolic BP values ≥ 90 mmHg; (e) diabetes (only for one CAD patients), fasting plasma glucose ≥ 126 mg/dl (7.0 mmol/L) or 2-hour plasma glucose during 75 mg oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/L) or Hb1Ac ≥ 6,5% (48 mmol/mol); (f) smoking history for CAD patients.

extract_protocol:
RNA extraction from PBMCs was performed using Trizol reagent (Invitrogen™) according to manufacturer instructions. RNA concentration was evaluated using a NanoDrop DS-11 Spectrophotometer (DeNovix), whereas RNA quality was checked on agarose gel 1%. For sequencing, 500ng of fresh RNA input extracted from PBMCs have been used.
For library preparation, KAPA mRNA HyperPrep Kit for ILLUMINA has been used.
Sequencing has been performed using NextSeq 500 ILLUMINA platform. All samples passed quality control analysis.

treatment_protocol: PBMCs have been isolated by whole blood (9mL) using Ficoll® Paque Plus (GE Healthcare, Little Chalfont, UK) according to manufacturer instructions. Isolated PBMCs have been suspended in 1mL of Trizol® (Invitrogen™) and stored at -80°C until further analysis.

tag: clinical evaluation

value: patient with coronary artery diseases

tag: gender and age

value: male over 65

tag: recruitment time


title: RNASeq_CTR4

value: patient with healthy coronary arteries

value: A peripheral blood sample (9mL) has been collected within 24 hours from the coronary angiography


title: Skeletal Muscle HFD WT Animal 567

value: Skeletal Muscle

value: HFD


title: myc-h2a2a-spt6oe-async-x20

city: Rehovot

first: Naama

last: Barkai

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64  with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out file contains gneome coverage for all 12,157,105   bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

value: myc

tag: treatment

value: async

tag: strain

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , pTEF-SPT6::NAT


title: RNASeq_CTR2


title: myc-h2a2a-spt6damp-async-x20

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , DAmP-SPT6::NAT::NAT


title: Skeletal Muscle HFD WT Animal 537

value: WT


title: Skeletal Muscle HFD WT Animal 536


title: myc-h2a2a-htz1-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, htz1::NAT


title: RNASeq_CAD9_T0


title: myc-h2a2a-htz1-async-x19


title: Skeletal Muscle HFD WT Animal 531


title: myc-h2a1b-spt6oe-async-x20


title: myc-h42a-wt-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: myc-h2a1b-spt6damp-async-x20


title: Skeletal Muscle HFD WT Animal 528


title: 3D minox 1

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

description: Gene expression data from minox for 48 h

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

label: biotin

source_name: hair follicle dermal papilla cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: HFDPCs were purchaced from Cell application and were maintained in Papilla cell culture meduim

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour seeding  in 6-well-collagen-coated plates.  The medium was changed with 0 (Control) and 5 µg/ml APC 50% for 48 h.

value: minoxdil


title: 3D TCQA 2

description: Gene expression data from TCQA for 48 h

value: TCQA


title: 3D TCQA 1

description: Gene expression data from TCQA for 48 h


title: Skeletal Muscle HFD WT Animal 516


title: myc-h2a1b-htz1-async-x20

address: Herzl St 234


title: myc-h2a1b-htz1-async-x19


title: 2D TCQA 1

description: Gene expression data from TCQA for 48 h


title: 2D Control 1

description: Gene expression data from meduim treated for 48 h

value: meduim


title: 3D Control 2


title: 3D Control 1


title: 2D TCQA 2

description: Gene expression data from TCQA for 48 h


title: 2D minox 1


title: CHB_Liver_19

city: Amsterdam

first: Vladimir

last: Loukachov

state: Noord-Holland

address: Meibergdreef 9

department: Experimental Immunology

country: Netherlands

institute: Amsterdam UMC, location AMC

data_processing:
The library pool was sequenced using the Illumina NextSeq500 (Illumina, USA) sequencing instrument according to the manufacturer instructions. Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina). FASTQ data were checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Cutadapt (1.11) was used to extract information of adapter and UMI in raw reads, and output from cutadapt was used to remove adapter sequences and to collapse reads by UMI with in-house script. The reads were mapped to the reference genomes miRBase 20 and GRCh37 using Bowtie2 (2.2.2). The mapping criteria for aligning reads to abundant sequence and miRBase were that the reads have to have perfect match to the reference sequences. For mapping of the reads to the human genome one mismatch was allowed in the first 32 bases of the read. No indels were allowed in mapping.
After mapping, all miRNAs with less than 5 counts per million per group were excluded from further analysis.
A heatmap of expression profiles was generated and a two-way hierarchical clustering analysis was performed with RStudio using  trimmed mean of M-values (TMM) normalized quantifications from defined collections of samples as input. Differential expression analysis between CHB patients and controls was performed using the EdgeR statistical software package (Bioconductor, http://bioconductor.org/) in RStudio. For normalization, the TMM method based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalization) was used. Falls discovery rate (FDR) corrected p-values were calculated using the Benjamini-Hochberg method
Genome_build: miRBase 20 and GRCh37
Supplementary_files_format_and_content: tab-separated values files include miRNA counts and TPM values for each sample

extract_protocol:
Total RNA was isolated from 500μl plasma with proprietary RNA isolation protocol optimized for serum/plasma (no carrier added) (Exiqon Services, Denmark). Liver tissue (up to 5mg) was disrupted and homogenized for 4 x 1 minute at 30Hz using the TissueLyser II (Qiagen) and two 5mm stainless steel beads (Qiagen). Total RNA from liver samples was isolated using the miRNeasy Micro Kit, according to the manufacturer’s protocol.
A total of 5ul RNA from plasma was converted into microRNA NGS libraries using the QIAseq miRNA Library Kit (Qiagen). For liver samples, 100ng of total RNA was converted into microRNA NGS libraries. Adapters containing UMIs were ligated to the RNA and the RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles for plasma samples and 14 for liver samples) and during the PCR indices were added. The PCR samples were purified and library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using the qPCR ExiSEQ LNA™ Quant kit (Exiqon, Denmark).

value: Liver

value: Chronic Hepatitis B


title: myc-h2a1a-spt6oe-async-x20


title: CHB_Liver_18


title: Liver HFD SLC16A13 KO Animal 611

source_name: Liver HFD SLC16A13 KO

value: SLC16A13 KO


title: CHB_Liver_17


title: myc-h2a1a-htz1-async-x20


title: CHB_Liver_20


title: myc-h2a1a-spt6damp-async-x20


title: myc-h2a1a-htz1-async-x19


title: CHB_Liver_16


title: Liver HFD SLC16A13 KO Animal 602


title: CHB_Liver_15


title: myc-h2a1-wt-h202T68-x19

value: wt

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: myc-h2a1-wt-h202T63-x19


title: CHB_Liver_14


title: myc-h2a1-wt-h202T8-x19


title: Liver HFD SLC16A13 KO Animal 598


title: myc-h2a1-wt-h202T58-x19


title: Liver HFD SLC16A13 KO Animal 588


title: CHB_Liver_13


title: Liver HFD SLC16A13 KO Animal 597


title: myc-h2a1-wt-h202T43-x19


title: myc-h2a1-wt-h202T53-x19


title: myc-h2a1-wt-h202T38-x19


title: myc-h2a1-wt-h202T33-x19


title: Liver HFD SLC16A13 KO Animal 587


title: myc-h2a1-wt-h202T28-x19


title: Liver HFD SLC16A13 KO Animal 570


title: Liver HFD SLC16A13 KO Animal 583


title: myc-h2a1-wt-h202T3-x19


title: myc-h2a1-wt-h202T23-x19


title: myc-h2a1-wt-h202T18-x19


title: Healthy_Liver_9

value: Healthy


title: myc-h2a1-wt-h202T13-x19


title: Liver HFD SLC16A13 KO Animal 568

value: HFD


title: CHB_Liver_11


title: myc-h2a1-spt6-async-x19

value: myc


title: CHB_Liver_12


title: Healthy_Liver_8


title: Healthy_Liver_10


title: myc-h2a1-wt-h202T48-x19


title: Liver HFD SLC16A13 KO Animal 561


title: myc-fast2a-spt6oe-async-x20

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 ,  pTEF-SPT6::NAT


title: myc-fast2a-spt6damp-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , DAmP-SPT6::NAT


title: Liver HFD SLC16A13 KO Animal 532


title: myc-fast2b-asf-async-x16

value: asf

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , asf1::KANMX


title: Healthy_Liver_7


title: Healthy_Liver_6


title: myc-fast2a-htz1-async-x19

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , htz1::NAT


title: Liver HFD WT Animal 624

source_name: Liver HFD WT

value: WT


title: Healthy_Liver_5


title: myc-fast2a-asf-async-x16


title: myc-fast1b-spt6oe-async-x20


title: myc-fast1b-spt6damp-async-x20


title: Liver HFD WT Animal 623


title: myc-fast1b-htz1-async-x20


title: Healthy_Liver_4


title: myc-fast1b-htz1-async-x19


title: Healthy_Liver_2


title: Liver HFD WT Animal 616


title: myc-fast1b-asf-async-x16


title: myc-fast1a-wt-h202T68-x18

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: myc-fast1a-wt-h202T8-x18


title: Liver HFD WT Animal 586


title: myc-fast1a-wt-h202T58-x18


title: Liver HFD WT Animal 612


title: myc-fast2a-htz1-async-x20


title: myc-fast1a-wt-h202T63-x18


title: Liver HFD WT Animal 537


title: CHB_Plasma_20

source_name: Plasma

value: Plasma


title: myc-fast1a-wt-h202T48-x18


title: CHB_Plasma_19


title: Liver HFD WT Animal 567

value: Liver


title: Liver HFD WT Animal 536


title: CHB_Plasma_18

value: Chronic Hepatitis B


title: myc-fast1a-wt-h202T33-x18


title: myc-fast1a-wt-h202T3-x18


title: myc-fast1a-wt-h202T38-x18


title: Healthy_Liver_3


title: Liver HFD WT Animal 531


title: Healthy_Liver_1


title: CHB_Plasma_17


title: myc-fast1a-wt-h202T28-x18


title: Liver HFD WT Animal 528


title: myc-fast1a-wt-h202T18-x18


title: myc-fast1a-wt-h202T23-x18


title: myc-fast1a-wt-h202T53-x18


title: CHB_Plasma_16


title: Liver HFD WT Animal 516


title: myc-fast1a-wt-h202T13-x18


title: CHB_Plasma_15


title: myc-fast1a-wt-h202T43-x18


title: myc-fast1a-wt-h202T0-x18


title: myc-fast1a-htz1-async-x20


title: myc-fast1a-spt6oe-async-x20


title: myc-fast1a-spt6damp-async-x20


title: CHB_Plasma_14


title: myc-fast1a-htz1-async-x19


title: 10_sRNA_Oscmt3a/drm2_T1

city: shenzhen

first: yiming

last: yu

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Raw reads were removed adaptors using cutadapt version 1.18.
For BS-Seq, clean reads were mapped to MSU7.0 version reference genome using BSMAP v2.90 allowing 8% mismatches and methylation level was extracted using BSMAP v2.90. For mRNA-Seq, clean reads mapped to MSU7.0 version reference genome using HISAT2 v2.1.0 and quantified using StringTie v1.3.3b. For sRNA-Seq, clean reads were uniquely mapped to MSU7.0 reference genome using Bowtie v1.2.2 by allowing no mismatches.
Genome_build: MSU7.0
Supplementary_files_format_and_content: For BS-Seq, tab-delimited text files include sequencing results at each cytosine sites for each sample. Column 1 is the genomic coordinate of cytosines, and column 2 is methylation levels. For mRNA-Seq, tab-delimited text files include expression values for each sample. Columns 1-6 are the genomic coordinate of genes, column 7 is average coverage, column 8 is FPKM value, and column 9 is TPM value. For sRNA-Seq, tab-delimited text files include sRNA reads information for each sample. Column 1 is chromosome, column 2 is the genomic strand(+/-) the read mapped to, column 3 is the genomic coordinate the read mapped to, and column 4 is the length of the sRNA.

source_name: Oscmt3a/drm2 mutant

growth_protocol: The seeds of T0 mutants and callus culture-regenerated wild type were germinated and grown of hormone-free, 1/2 MS medium under 14/10h of light/dark at 28℃/25℃ in the light growth chamber during 14 days. Then the seedlings of homozygous T1 mutants were transplanted to greenhouse and grew in mud under 14/10h of light/dark at 34℃/25℃.

extract_protocol:
For BS-Seq, Genomic DNA was extracted from the mature leaves of 70-day-old wild type and mutant plants using the DNeasy plant mini kit (Qiagen). For mRNA-Seq and sRNA-Seq, total RNA of each genotype was extracted from the mature leaves of 70-day-old wild type and mutant plants using TRIzol reagent (Invitrogen)
The libraries were prepared and sequenced at the GENEWIZ Bioinformatics Institute on an Illumina Hiseq Xten platform.

tag: library strategy

value: Oscmt3a/drm2 mutant

tag: developmental stage

value: 70-day old

value: leaves

tag: generation


title: 24_BS_Osdrm2/drm3/cmt2/cmt3a_T1

data_processing:
Raw reads were removed adaptors using cutadapt version 1.18.
For BS-Seq, clean reads were mapped to MSU7.0 version reference genome using BSMAP v2.90 allowing 8% mismatches and methylation level was extracted using BSMAP v2.90. For mRNA-Seq, clean reads mapped to MSU7.0 version reference genome using HISAT2 v2.1.0 and quantified using StringTie v1.3.3b. For sRNA-Seq, clean reads were uniquely mapped to MSU7.0 reference genome using Bowtie v1.2.2 by allowing no mismatches.
Genome_build: MSU7.0
Supplementary_files_format_and_content: or BS-Seq, tab-delimited text files include sequencing results at each cytosine sites for each sample. Column 1 is the genomic coordinate of cytosines, and column 2 is methylation levels. For mRNA-Seq, tab-delimited text files include expression values for each sample. Columns 1-6 are the genomic coordinate of genes, column 7 is average coverage, column 8 is FPKM value, and column 9 is TPM value. For sRNA-Seq, tab-delimited text files include sRNA reads information for each sample. Column 1 is chromosome, column 2 is the genomic strand(+/-) the read mapped to, column 3 is the genomic coordinate the read mapped to, and column 4 is the length of the sRNA.

source_name: Osdrm2/drm3/cmt2/cmt3a mutant


title: CHB_Plasma_13


title: 9_sRNA_Oscmt2/drm2_T1

source_name: Oscmt2/drm2 mutant

value: Oscmt2/drm2 mutant


title: CHB_Plasma_12


title: myc-fast1a-asf-async-x16


title: 8_sRNA_Oscmt2/cmt3a_T1

source_name: Oscmt2/cmt3a mutant

value: Oscmt2/cmt3a mutant


title: myc-fast1-spt6-async-x19

value: myc


title: CHB_Plasma_11


title: k9ac-fast1b-asf-async-x24

value: async


title: 7_sRNA_Oscmt3a_T1

source_name: Oscmt3a mutant

value: Oscmt3a mutant


title: k9ac-fast1a-asf-async-x24


title: Healthy_Plasma_10

value: Healthy


title: k79m3-fast1b-asf-async-x24

value: asf


title: 6_sRNA_Oscmt2_T1

source_name: Oscmt2 mutant

value: Oscmt2 mutant


title: k4m3-fast1b-asf-async-x24

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , asf1::KANMX


title: k4m3-fast1a-asf-async-x24


title: 5_sRNA_Oscmt2/cmt3a/drm2_T1

source_name: Oscmt2/cmt3a/drm2 mutant

value: Oscmt2/cmt3a/drm2 mutant


title: ha-h42a-wt-async-x20

value: ha

value: wt

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: Healthy_Plasma_9

value: Plasma


title: myc-fast1a-hir2-async-x24

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , hir2::NAT


title: 4_sRNA_Oscmt2/cmt3a/drm2_T1

value: 70-day old


title: ha-h2a2a-spt6damp-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , DAmP-SPT6::NAT::NAT


title: myc-fast1a-hir1-async-x24

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , hir1::NAT


title: ha-h2a2a-spt6oe-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , pTEF-SPT6::NAT


title: 3_sRNA_Osdrm2_T1

source_name: Osdrm2 mutant

value: Osdrm2 mutant

value: leaves


title: Healthy_Plasma_6


title: ha-h2a2a-htz1-async-x19

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, htz1::NAT


title: Healthy_Plasma_7

value: Healthy


title: ha-h2a2a-htz1-async-x20


title: ha-h2a1b-spt6oe-async-x20


title: ha-h2a1b-spt6damp-async-x20


title: 2_sRNA_WT_T1

source_name: Wide type

value: Wide type


title: ha-h2a1b-htz1-async-x20


title: 1_sRNA_WT_T1


title: ha-h2a1b-htz1-async-x19


title: Healthy_Plasma_4


title: 30_mRNA_Oscmt3a/drm2_T1_r3

value: Oscmt3a/drm2 mutant


title: ha-h2a1a-spt6damp-async-x20


title: Healthy_Plasma_3


title: 29_mRNA_Oscmt3a/drm2_T1_r2


title: Healthy_Plasma_8


title: ha-h2a1a-htz1-async-x19


title: ha-h2a1-wt-h202T8-x19

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: Healthy_Plasma_2


title: 28_mRNA_Oscmt3a/drm2_T1_r1


title: ha-h2a1-wt-h202T68-x19

value: ha


title: ha-h2a1-wt-h202T63-x19

value: wt


title: Healthy_Plasma_1


title: Healthy_Plasma_5


title: ha-h2a1-wt-h202T58-x19


title: ha-h2a1-wt-h202T43-x19


title: ha-h2a1-wt-h202T48-x19


title: ha-h2a1-wt-h202T53-x19


title: srHC-seq_srHC_ERH_siRNA_rep1

city: Seattle

first: Ryan

last: McCarthy

address: 1900 9th Ave

institute: University of Washington

data_processing:
Library strategy: srHC-seq
Samples were demultiplexed (bcl2fastq using BaseSpace) to produce FASTQ files.
STAR output files were converted to .bam files using samtools (v.1.1), and then to .bed files using bedtools (v.2.20.1; bamtobed)
BED files were converted to BedGraph files using bedtools (v.2.20.1; genomeCoverageBed) and normalized to the number of millions of reads sequenced and then to bigWig using bedGraphToBigWig (v4).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: human BJ Fibroblast

growth_protocol: Human BJ foreskin fibroblasts were obtained from Stemgent (08-0027) at passage 6 and cultured in Eagle's Minimum Essential Medium (Sigma M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM L-glutamine (Gibco) at 37°C and 5% CO2

extract_protocol:
Nuclei were isolated and sonicated using a Covaris S220 sonicator, and the euchromatic fraction (short fragments) was isolated using SPRI beads (to create Euchromatic Libraries) . Large fragments were resonicated and prepped to create sonication resistant heterochromatin (srHC) Libraries.
Libraries were prepped using NEBNext Ultra II Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with two rounds of transfection with 10nM Silencer Silect siRNAs (Thermo Fisher Scientific) and 2.5 μl Lipofectamine RNAiMAX (Thermo Fisher #13778150), for 3 days per transfection.

tag: sirna

tag: fraction

value: srHC


title: 24_mRNA_Oscmt2/cmt3a_T1_r3

value: Oscmt2/cmt3a mutant


title: 25_mRNA_Oscmt2/drm2_T1_r1

value: Oscmt2/drm2 mutant


title: ha-h2a1-wt-h202T3-x19


title: ha-h2a1-wt-h202T38-x19


title: srHC-seq_Euchromatin_ERH_siRNA_rep2

value: Euchromatin


title: srHC-seq_srHC_ERH_siRNA_rep2


title: ha-h2a1-wt-h202T33-x19


title: ha-h2a1a-spt6oe-async-x20


title: ha-h2a1a-htz1-async-x20


title: ha-h2a1-wt-h202T28-x19


title: srHC-seq_Euchromatin_ERH_siRNA_rep1


title: ha-h2a1-wt-h202T23-x19


title: ha-h2a1-wt-h202T18-x19


title: 22_mRNA_Oscmt2/cmt3a_T1_r1

value: 70-day old


title: srHC-seq_srHC_NT_Control_siRNA_rep1


title: 27_mRNA_Oscmt2/drm2_T1_r3


title: ha-h2a1-wt-h202T13-x19


title: 26_mRNA_Oscmt2/drm2_T1_r2


title: 21_mRNA_Oscmt3a_T1_r3

value: Oscmt3a mutant


title: ha-fast2b-asf-async-x16

value: asf

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , asf1::KANMX


title: srHC-seq_Euchromatin_NT_Control_siRNA_rep2


title: ha-fast2a-spt6oe-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 ,  pTEF-SPT6::NAT


title: ha-fast2a-spt6damp-async-x20

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , DAmP-SPT6::NAT


title: ha-fast2a-htz1-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , htz1::NAT


title: ha-fast2a-htz1-async-x19


title: ha-fast1b-spt6oe-async-x20


title: 19_mRNA_Oscmt3a_T1_r1

value: leaves


title: ERH_ChIP_rep2

description: Sample did not contain Drosophila spike-in chromatin and as such was aligned to hg38 and no normalization to spike-in control was performed.

data_processing:
Samples were demultiplexed (bcl2fastq using BaseSpace) to produce FASTQ files.
For samples with a spike-in control sequenced read were aligned to the human hg38 genome assembly and to the Drosophila melanogaster dm6 genome assembly (to identify reads from the spike in) using STAR (v.2.3.0e)
STAR output files were converted to .bam files using samtools (v.1.1), and then to .bed files using bedtools (v.2.20.1; bamtobed)
BED files were converted to BedGraph files using bedtools (v.2.20.1; genomeCoverageBed) and normalized to the number of millions of reads sequenced.
BedGraphs from samples containing a spike in control were scaled based upon the change between corresponding input and IPs in dm6 to hg38 aligning reads realative to the non-targeting siControl treated samples.
Input subtracted BedGraph files were converted to  bigWig using bedGraphToBigWig (v4)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Human BJ Fibroblast

extract_protocol:
Nuclei were isolated and sonicated, lysates were clarified, for H3K9me3 and H3K27me3 ChIP experiments Drosophila spike-in chromatin (Active Motif cat 53083) was added in order to normalize for global changes in histone modification levels during computational analysis, and histone-DNA complexes were isolated with antibody.
Library constructed acording to NEBnext ULTRA II DNA Library Prep Kit for Illumina (#E7645S)

tag: chip antibody

value: ERH (Sigma-Millipore - HPA002567, Lot# A41692)


title: ha-fast2a-asf-async-x16

source_name: budding yeast


title: 18_mRNA_Oscmt2_T1_r3

value: Oscmt2 mutant

tag: tissue


title: ha-fast1b-spt6damp-async-x20

value: ha


title: ha-fast1b-htz1-async-x20


title: 23_mRNA_Oscmt2/cmt3a_T1_r2


title: ha-fast1b-htz1-async-x19


title: 16_mRNA_Oscmt2_T1_r1


title: 17_mRNA_Oscmt2_T1_r2


title: ERH_Input_rep2

description:
Input: ERH_ChIP_rep2
Sample did not contain Drosophila spike-in chromatin and as such was aligned to hg38 and no normalization to spike-in control was performed.


title: srHC-seq_srHC_NT_Control_siRNA_rep2


title: ERH_Input_rep1

description:
Input: ERH_ChIP_rep1
Sample did not contain Drosophila spike-in chromatin and as such was aligned to hg38 and no normalization to spike-in control was performed.


title: ha-fast1b-asf-async-x16


title: ha-h2a1-spt6-async-x19

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , DAmP-SPT6::NAT::NAT


title: ha-fast1a-wt-h202T68-x18

value: wt

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: H3K27me3_ChIP_NT_ERH_siRNA_rep2

tag: spike in

value: Drosophila

value: H3K27me3 (Active Motif -39155, Lot# 31618020)  & Drosophila H2AV (Active Motif - 104597, Lot # 00419007)


title: ha-fast1a-wt-h202T63-x18

tag: antibody


title: 15_mRNA_Oscmt2/cmt3a/drm2_T1_r3

value: Oscmt2/cmt3a/drm2 mutant

value: 70-day old


title: H3K27me3_ChIP_NT_ERH_siRNA_rep1


title: 14_mRNA_Oscmt2/cmt3a/drm2_T1_r2


title: ha-fast1a-wt-h202T58-x18

tag: background


title: ha-fast1a-wt-h202T53-x18

tag: sensor


title: 13_mRNA_Oscmt2/cmt3a/drm2_T1_r1


title: srHC-seq_Euchromatin_NT_Control_siRNA_rep1

value: Euchromatin


title: ChIP_NT_ERH_siRNA_input-H3K27me3_rep2

description: Input: H3K27me3_ChIP_NT_ERH_siRNA_rep2


title: ha-fast1a-wt-h202T43-x18


title: ChIP_NT_ERH_siRNA_input-H3K27me3_rep1

description: Input: H3K27me3_ChIP_NT_ERH_siRNA_rep1


title: 11_mRNA_Oscmt2/cmt3a/drm2_T1_r2


title: ha-fast1a-wt-h202T33-x18


title: ha-fast1a-wt-h202T3-x18


title: 20_mRNA_Oscmt3a_T1_r2

value: Oscmt3a mutant


title: H3K27me3_ChIP_NT_Control_siRNA_rep1


title: ha-fast1a-wt-h202T23-x18


title: H3K27me3_ChIP_NT_Control_siRNA_rep2


title: 10_mRNA_Oscmt2/cmt3a/drm2_T1_r1


title: ha-fast1a-wt-h202T28-x18


title: ha-fast1a-wt-h202T8-x18


title: 9_mRNA_Osdrm2_T1_r3

value: Osdrm2 mutant


title: ha-fast1a-wt-h202T13-x18


title: 8_mRNA_Osdrm2_T1_r2


title: ha-fast1a-wt-h202T0-x18


title: ChIP_NT_Control_siRNA_input-H3K27me3_rep2

description: Input: H3K27me3_ChIP_NT_Control_siRNA_rep2


title: ha-fast1a-wt-h202T48-x18


title: ChIP_NT_Control_siRNA_input-H3K27me3_rep1

description: Input: H3K27me3_ChIP_NT_Control_siRNA_rep1


title: ha-fast1a-spt6oe-async-x20

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 ,  pTEF-SPT6::NAT


title: 7_mRNA_Osdrm2_T1_r1


title: 12_mRNA_Oscmt2/cmt3a/drm2_T1_r3


title: H3K9me3_ChIP_NT_ERH_siRNA_rep2

value: H3K9me3 (Abcam ab8898, Lot #GR3291043 -1) & Drosophila H2AV (Active Motif - 104597, Lot #00419007)


title: ha-fast1a-wt-h202T38-x18


title: H3K9me3_ChIP_NT_ERH_siRNA_rep1


title: 6_mRNA_WT_T1_r3

value: Wide type

value: leaves


title: ha-fast1a-spt6damp-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , DAmP-SPT6::NAT


title: ha-fast1a-htz1-async-x20

value: ha

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , htz1::NAT


title: 5_mRNA_WT_T1_r2


title: ChIP_NT_ERH_siRNA_input-H3K9me3_rep2

description: Input: H3K9me3_ChIP_NT_ERH_siRNA_rep2


title: ChIP_NT_ERH_siRNA_input-H3K9me3_rep1

description: Input: H3K9me3_ChIP_NT_ERH_siRNA_rep1


title: ha-fast1a-htz1-async-x19


title: 4_mRNA_WT_T1_r1


title: 3_mRNA_WT_T1_r3


title: ha-fast1a-wt-h202T18-x18

value: wt


title: ha-fast1a-hir2-async-x24

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , hir2::NAT


title: H3K9me3_ChIP_NT_Control_siRNA_rep2

value: Drosophila


title: 2_mRNA_WT_T1_r2


title: T+/CD24-neg_Day4_Rep2

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: Gene expression data from FACS purified Foxa2-/T+/CD24 negative cells after four days of differentiation, biological replicate 2

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression data were RMA normalized using the oligo package (version 1.48.0)

label_protocol: Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: TGFP/+; Foxa2tagRFP/+ mouse ESCs were cultured on mitomycin c-treated mouse embryonic fibroblasts (feeders) in DMEM (Life Technologies, Cat#11965092) supplemented with 15  %  FCS (PAN Biotech) ,  0.1  mM  β-mercaptoethanol (Life Technologies, Cat#31350-10),  2 mM L-glutamine (Life Technologies, Cat#25030081), 1× non-essential amino acid (Sigma, Cat#M7145), 2 mM HEPES (Life Technologies, Cat#15630-056),   and 1000 U/ml leukemia inhibitory factor (LIF; Sigma, Cat#). Every 2-3 days cells were passaged by treatment with 0,05% Trypsin (Life Technologies, Cat#25300054) on new feeders and the medium was changed every day.

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol: Before differentiation, Wnt-3a feeders were seeded at a density of ~5 x 104 cells /24-well. TGFP/+; Foxa2tagRFP/+ mouse ESCs (ESCs) were passaged onto gelatine-coated plates for 30 min twice to remove remaining feeders from maintenance cultures. Next, ESCs were transferred to Wnt3a-expressing feeder plate with a seeding density of 2 x 105 cells /24-well. Endoderm differentiation medium (EDM), consisting of 500 ml Advanced DMEM/F-12 (Life Technologies, Cat#12634-10), 500 ml Advanced RPMI 1640 (Life Technologies, Cat#12633-012), 22 ml GlutaMAX (Life Technologies, Cat#12860-01), 200 µl AlbuMAX 100 mg/ml (Life Technologies, Cat#11021-029), 22 ml HEPES 1M, 70 µl Cytidine 150 mg/ml (SIGMA, Cat#C4654), 0,9 ml ß-Mercaptoethanol 50 mM, 12 ml Pen/Strep (10000U/ml) (Life Technologies, Cat#10378016), 1 ml Insulin-Transferrin-Selenium Ethanolamine (Life Technologies, Cat#51500-056) supplemented with 12 ng/ml Act A was used to induce the endoderm differentiation. For mesoderm differentiation, 3 ng/ml Act A and 7.5 ng/ml Bmp4 were added to EDM. The medium was changed every day.

tag: cell line

tag: background strain

tag: differentiation protocol

value: mesoderm differentiation

tag: differentiation stage

value: mesoderm

tag: days of differentiation

tag: facs

value: Foxa2-; T+; CD24 negative


title: T+/CD24-low_Day4_Rep2

description: Gene expression data from FACS purified Foxa2-/T+/CD24 low cells after four days of differentiation, biological replicate 2

scan_protocol: According to the Affymetrix expression protocol

value: Foxa2-; T+; CD24 low


title: T+/CD24-low_Day4_Rep1

description: Gene expression data from FACS purified Foxa2-/T+/CD24 low cells after four days of differentiation, biological replicate 1


title: H3K9me3_ChIP_NT_Control_siRNA_rep1


title: 1_mRNA_WT_T1_r1

tag: library strategy

value: 70-day old


title: ha-fast1a-asf-async-x16

growth_protocol: yeast cells were grown to saturation overnight in YPD  and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation

value: asf

tag: treatment

tag: strain

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , asf1::KANMX


title: T+/CD24-low_Day2_Rep2

description: Gene expression data from FACS purified Foxa2-/T+/CD24 low cells after two days of differentiation, biological replicate 2


title: T+/CD24-low_Day2_Rep1

description: Gene expression data from FACS purified Foxa2-/T+/CD24 low cells after two days of differentiation, biological replicate 1


title: T+/CD24-neg_Day4_Rep1

description: Gene expression data from FACS purified Foxa2-/T+/CD24 negative cells after four days of differentiation, biological replicate 1


title: ChIP_NT_Control_siRNA_input-H3K9me3_rep2

description: Input: H3K9me3_ChIP_NT_Control_siRNA_rep2

tag: sirna


title: 23_BS_Osmet1a_T0

source_name: Osmet1a mutant

value: Osmet1a mutant

tag: developmental stage

tag: generation


title: ha-fast1-spt6-async-x19

value: async


title: ChIP_NT_Control_siRNA_input-H3K9me3_rep1

description: Input: H3K9me3_ChIP_NT_Control_siRNA_rep1

tag: spike in

tag: chip antibody


title: 22_BS_Cr_WT_T0

value: Wide type

tag: tissue


title: myc-nc1a-wt-async-x20

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64  with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out.txt file contains genome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

tag: antibody

value: myc

tag: background

tag: sensor

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-NC-MYC


title: 21_BS_WT_T1

value: leaves


title: RL lenalidomide + tazemetostat - input_DNA_rep2

city: Toronto

first: Robert

last: Kridel

address: 101 College Street, Rm 12-311

institute: Princess Margaret Cancer Centre

data_processing:
The processed reads were then aligned using the BWA aligner (v0.7.15) in single-end mode to hg19 genome.
BAM files across multiple lanes were merged using picard v1.130 MergeSamFiles
Unmapped reads, multi-mapping reads, secondary alignments and PCR duplicates were removed post-alignment using Picard’s MarkDuplicates v1.126 and Bedtools v2.26
Single-end BAM files were used for peak calling using MACS2 v2.1.0. Peak-calling on replicates and pooled data was carried out with the parameters -B –broad –nomodels and –extsize 147 with all others set to default.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated using MACS2
Supplementary_files_format_and_content: Peaks files were generated using MACS2

growth_protocol: RL cell line routinely grown at 37°C with 5% CO2 and cultured in RPMI 1640 supplemented with 2mM L-glutamine and 10% FBS (Wisent)

extract_protocol:
ChIP samples were prepared using the SimpleChIP Enzymatic Chromatin IP Kit, based on the manufacturer’s instructions (Cell Signaling, #9003). Briefly, 4 million RL cells were incubated for 48 hours with either DMSO, 10μM lenalidomide, 5μM tazemetostat or combination, followed by cross-linking using 1% formaldehyde. Cells were lysed and chromatin was digested for 20 min using 0.5μl micrococcal nuclease. Nuclei were sonicated
After purification, DNA was used as an input for next-generation sequencing library construction using the SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina (Cell Signaling, #56795) following manufacturer’s protocol and sequenced on a NextSeq SR25 platform (Illumina) after standard library QC.

treatment_protocol: RL cells treated with DMSO, 10μM lenalidomide, 5μM tazemetostat or combination; Two technical replicates of all samples and conditions were prepared. Cells were incubated with drug treatments for 2 days.

tag: cell line

value: RL

tag: cell type

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: lenalidomide + tazemetostat

value: negative control rabbit IgG antibody (Cell Signaling, #2729)


title: RL lenalidomide + tazemetostat - input_DNA_rep1


title: 20_BS_Oscmt2/cmt3a/cmt3b/drm2/drm3_T1

source_name: Oscmt2/cmt3a/cmt3b/drm2/drm3 mutant

value: Oscmt2/cmt3a/cmt3b/drm2/drm3 mutant


title: myc-nc1a-wt-async-x14

value: wt


title: Foxa2+/CD24-low_Day4_Rep2

description: Gene expression data from FACS purified Foxa2+/T-/CD24 low cells after four days of differentiation, biological replicate 2

tag: background strain

tag: differentiation protocol

value: endoderm differentiation

tag: differentiation stage

value: definitive endoderm

tag: days of differentiation

value: Foxa2+; T-; CD24 low


title: ha-fast1a-hir1-async-x24

value: ha

tag: treatment

tag: strain

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , hir1::NAT


title: Foxa2+/CD24-low_Day4_Rep1

description: Gene expression data from FACS purified Foxa2+/T-/CD24 low cells after four days of differentiation, biological replicate 1

tag: facs


title: RL tazemetostat - input_DNA_rep2

source_name: RL tazemetostat - input_DNA

value: tazemetostat


title: myc-h41b-wt-async-x20

value: async

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: 19_BS_Oscmt2/cmt3a/cmt3b/drm2/drm3_T1

tag: library strategy

tag: developmental stage

value: 70-day old

tag: generation


title: RL tazemetostat - input_DNA_rep1

tag: chip antibody


title: Foxa2+/CD24-high_Day4_Rep1

description: Gene expression data from FACS purified Foxa2+/T-/CD24 high cells after four days of differentiation, biological replicate 1

value: Foxa2+; T-; CD24 high


title: Foxa2+/CD24-low_Day2_Rep2

description: Gene expression data from FACS purified Foxa2+/T-/CD24 low cells after two days of differentiation, biological replicate 2


title: 18_BS_Oscmt2/cmt3a/drm2_T1

value: Oscmt2/cmt3a/drm2 mutant

tag: tissue

value: leaves


title: RL lenalidomide -  input_DNA_rep2

source_name: RL lenalidomide -  input_DNA

value: RL

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: lenalidomide


title: myc-h41a-wt-async-x20

tag: antibody

value: myc

tag: background


title: myc-h2bNC1b-wt-async-x20

value: wt

tag: sensor

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-NC-MYC


title: myc-nc1b-wt-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-NC-MYC


title: Foxa2+/CD24-high_Day4_Rep2

description: Gene expression data from FACS purified Foxa2+/T-/CD24 high cells after four days of differentiation, biological replicate 2

tag: cell line

value: endoderm differentiation

value: definitive endoderm


title: 16_BS_Oscmt3a/drm2_T1

value: Oscmt3a/drm2 mutant


title: myc-h2bNC1a-wt-async-x20


title: WT_2_techRep2

description:
HSV skin OT-I T cells
Biological replicate 2, technical replicate 2

source_name: epidermis

extract_protocol:
Effector OT-I or OT-I/TGFbRII-/- cells were injected into HSV-infected mice and on day 14, skin was harvested from perfused mice and subject to a dispase digestion. This allowed the physical separation of the epidermis from the dermis skin. Epidermal skin was further digested in collagenase,  and the cell suspension was stained for sort purification on OT-I markers. A total of 500 cells were sorted into individual strip tubes containing buffer comprised of dNTPs and BSA.
Libraries were prepared with smartseq-nextera2 kit according to manufacturers instructions

tag: host strain background

tag: transgenic strain

value: OT-I

value: HSV Infection d14


title: Foxa2+/CD24-high_Day2_Rep1

description: Gene expression data from FACS purified Foxa2+/T-/CD24 high cells after two days of differentiation, biological replicate 1

tag: background strain

tag: differentiation protocol

tag: differentiation stage


title: Foxa2+/CD24-high_Day2_Rep2

description: Gene expression data from FACS purified Foxa2+/T-/CD24 high cells after two days of differentiation, biological replicate 2

tag: days of differentiation


title: 15_BS_Oscmt2/drm2_T1

value: Oscmt2/drm2 mutant


title: RL DMSO - input_DNA_rep2

source_name: RL DMSO - input_DNA

tag: cell type

tag: treatment

value: DMSO

value: negative control rabbit IgG antibody (Cell Signaling, #2729)


title: Foxa2+/CD24-low_Day2_Rep1

description: Gene expression data from FACS purified Foxa2+/T-/CD24 low cells after two days of differentiation, biological replicate 1

tag: facs

value: Foxa2+; T-; CD24 low


title: mESC_Rep2

description: Gene expression data from TGFP/+; Foxa2tagRFP/+ mouse ESCs, biological replicate 2

value: embryonic stem cell

value: no


title: myc-h2b2a-wt-async-x20

value: async

tag: strain

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC


title: WT_2_techRep1

description:
HSV skin OT-I T cells
Biological replicate 2, technical replicate 1


title: 14_BS_Osdrm2/drm3_T1

source_name: Osdrm2/drm3 mutant

tag: library strategy

value: Osdrm2/drm3 mutant

tag: developmental stage

value: 70-day old

value: leaves

tag: generation


title: myc-h2b1b-wt-async-x20

tag: antibody

value: myc

tag: background

value: wt


title: RL lenalidomide + tazemetostat - H3K27ac_rep2

tag: cell line

value: RL

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: lenalidomide + tazemetostat

tag: chip antibody

value: H3K27ac (clone D5E4, Cell Signaling, #8173)


title: RL DMSO - input_DNA_rep1


title: myc-h2b1a-wt-async-x20

tag: sensor


title: WT_1_techRep2

description:
HSV skin OT-I T cells
Biological replicate 1, technical replicate 2

tag: host strain background

tag: transgenic strain

value: OT-I

value: HSV Infection d14


title: WT_1_techRep1

description:
HSV skin OT-I T cells
Biological replicate 1, technical replicate 1


title: KO_2_techRep2

description:
HSV skin OT-I.Tgfbr2-/- T cells
Biological replicate 2, technical replicate 2


title: RL lenalidomide + tazemetostat - H3K27ac_rep1


title: 12_BS_Osdrm3_T1

source_name: Osdrm3 mutant

value: Osdrm3 mutant

tag: tissue


title: RL tazemetostat - H3K27ac_rep2

source_name: RL tazemetostat - H3K27ac

value: tazemetostat


title: myc-h2anc2a-wt-async-x17

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-NC-MYC


title: 11_BS_Osdrm2_T1

value: Osdrm2 mutant


title: 13_BS_Osdrm1a/drm1b_T1

source_name: Osdrm1a/drm1b mutant

value: Osdrm1a/drm1b mutant


title: RL tazemetostat - H3K27ac_rep1