title: single-cell RNA seq data of the cerebrospinal fluid from rat [CSF]

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

description:
processed data file:
rat_barcodes.tsv.gz
rat_features.tsv.gz
rat_matrix.mtx.gz
rat_annotation_tissue.csv
rat_annotation_cluster.csv

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.1.0)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count and the cellranger vdj pipelines with standard parameters
 The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples without normalization.
Genome_build: mm10 or Rattus_norvegicus.Rnor_6.0.dna.topleve
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CSF

extract_protocol:
Cells from CNS, SDM, dura, and CP were extracted as described before and sorted for  CD45+CD45iv- cells. CSF cells were not sorted. Blood cells were not sorted, but purified by  gradient centrifugation on Lymphoprep (Stemcell) in accordance with manufacturer's  instructions. After centrifugation, peripheral blood mononuclear cells enriched in the interface  were taken off and washed in 10 ml of PBS with 2% FCS media. Single cell suspensions  from all tissues (5 μl each) were manually counted in a Fuchs-Rosenthal chamber and the  cell concentration was adjusted to achieve a cell recovery of approx. 6’000-10’000 cells.  In total, 25 naive Lewis rats were used to generate single cell RNA sequencing data from rat  tissues. Per tissue, an average of 4,384 ± 736 SEM cells were used for analysis. 51,278 ±  2,859 SEM reads per cell were sequenced and this resulted in 733 ± 100 SEM median  genes detected per cell. In addition, we did single cell RNA sequencing on the cells isolated  from the skull dura of 3 pooled C57BL/6 mice at the peak of active EAE and 4 pooled  unimmunized C57BL/6 mice as ctrl. On average, 3,900 ± 1,100 SEM cells per sample were  used for analysis. 60,541 ± 4,644 SEM reads per cell were sequenced and resulted in 1,736  ± 852 SEM median genes detected per cell.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit (both from 10X Genomics). Rat experiments were done with v2 chemistry. The mouse experiments were done with v3 chemistry because of the manufacturer's reagent update. For BCR sequencing, we developed a method to sequence antigen receptor information from the 3’ scRNA-seq libraries by removing the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. In summary, the method involves self-circulating the cDNA library, enriching the VDJ region and re-linearizing. Sample processing and library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup and Novaseq 150-8-0-150 read setup (NextSeq: read1-26bp, read2-57bp. Novaseq: PE150bp).

value: CSF-derived leukocytes

value: Lewis

tag: condition

value: Naive

value: CSF

tag: type of library

value: RNA expression


title: NT-rep1

status: Public on May 01 2021

type: SRA

city: Seoul

first: Yunhyeong

last: Kim

address: kyunghee daero 23

country: South Korea

institute: KYH

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Tooth and periodontal ligament

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: tissue

value: Tooth and periodontal ligament

tag: age

value: post natal day 21

tag: treatment

value: control

tag: time


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 255

city: Berkeley

first: David

last: DeTomaso

state: CA

address: Stanley Hall

department: Computational Biology

country: USA

institute: UC Berkeley

data_processing:
Sequencing reads were initially filtered with Trimmomatic 0.32 to remove low quality ends and adapter sequences
Bowtie2 v2.2.9  was used to align reads to a reference transcriptome derived from the GRCm38 Mus musculus genome (NCBI Refseq).
RSEM 1.2.31 was used to compile the transcriptome and estimate transcript abundance following read alignment.
Prior to alignment, the GRCm38 reference was augmented to include the modified eGFP+IL23R functional knockout transcript.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_expression_tpm.txt.gz: tab-delimited text table (genes x cells) of TPM-normalized gene expression values.  cell_metadata.txt: tab-delimited table which contains GFP label, genotype, and stimulation for each cell.

molecule: polyA RNA

organism: Mus musculus

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

extract_protocol:
Spleen and lymph nodes were extracted and then a single-cell suspension was prepared by homogenization with a syringe plunger and debris was filtered with a 70um filter. Red blood cells were lysed with ACK lysis buffer from Lonza. CD4+ T cells were enriched using a bead protocol from Miltenyi Biotech (cat #. 130-117-043) and then stained with anti-CD44 (clone IM7), anti-CD62L (clone Mel14), anti-CD4 (clone RM4-5) and anti-CD25 (clone PC61) in preparation for FACS. Naive T cells were sorted based on CD44lowCD62LhiCD4+CD25-.
T cells were sorted into 96-well plates containing 5 μl TCL Buffer (QIAGEN) with 1% 2-mercaptoethanol, centrifuged and frozen at −80 °C.  Single-cell sequencing libraries were then created using the Smart-seq2 protocol (Picelli et al., Nature Methods 2014) and carried out as described in Singer et. al, Cell 2016.

treatment_protocol: 1x106/ml naive T cells were plated in 6 well dishes and incubated for 4 days with (1) IL-12+IL-21+IL-23 (Th1 cell condition) and (2) IL-1b+IL-6+IL-23 (pathogenic Th17 cell condition). Viable CD4+ T cells were sorted with FACS into eGFP+ (i.e. IL-23R+) and eGFP- (i.e. IL-23R-) population as single cells into 96 well plates pre-loaded with 5ul TCL buffer (containing b-mercaptoethanol according to the manufacturer's instructions, Qiagen). cDNA libraries were prepared as outlined in Pawlak M., DeTomaso, D. et al. 2021 and sequenced.

tag: differentiation

tag: gfp

tag: genotype

value: IL23R Knockout

tag: cell type

value: CD4 T Cells


title: single-cell RNA seq data of blood from rat [PBMC]

source_name: Blood

value: Blood-derived leukocytes

tag: strain

value: Blood


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 256


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 984mkd # 053372

type: RNA

city: West Point

first: Keith

last: Tanis

address: 770 Sumnetown Pike

institute: Merck & Co, Inc

hyb_protocol: Purified Cy3 or Cy5 complementary RNA was hybridized to two microarrays with fluor reversal for 24 hr in a hybridization chamber, washed, and scanned. Sample studies utilized GPL15569 and others GPL3631 as indicated in the sample annotations. Each GEO sample represents the mean of the 2 fluor-reversed hybridizations.

scan_protocol: Arrays were scanned using a laser confocal scanner.

data_processing:
Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels using the Rosetta Resolver error model as described in PMID: 16522673.
The submitted raw data files include the mean intensity values from the Cy3,Cy5 fluor-reversed hybridizations.

source_name: Heart Day 14 Angiotensin II Control pool

label_protocol: Total RNA was reverse transcribed using an oligo-dT primer containing a T7 RNA polymerase promoter site, followed by complementary strand synthesis using random hexamers. In vitro transcription (IVT) was then performed using RNA polymerase and the RNA was then labeled with one of two fluorescent dyes, Cy3 and Cy5.

extract_protocol: Trizol reagent (1 ml per 100 mg of tissue) was added to the tissue, and samples homogenized immediately. An aliquot of the homogenate was then transferred to a separate vial and chloroform extracted to remove proteins. The remaining tissue homogenate was stored at –70C for future use. The supernatant was then transferred to a separate vial, and RNA isolated using Qiagen RNeasy columns or 96-well plates as described by the manufacturer. Following RNA isolation, samples were treated with DNase to remove contaminating DNA, and quantified.

treatment_protocol: The compounds, vehicles, frequency of administration, dose levels and time points collected are presented in the sample annotations. In general, the study details were consistent between protocols and were as follows: male and/or female Sprague-Dawley CD (SD) or rats were obtained from Charles River Laboratories, Inc. (Raleigh, North Carolina). The rats were approximately seven to eight weeks of age and weighed from 125 to 325 grams at the start of the study. The animals were acclimated for approximately one week and randomized into the treatment and control groups. In general, five rats were included in each treatment group. Doses were calculated based on animal body weight, and the last dose was given 24 hours prior to necropsy in studies with daily dosing. All animals were fasted overnight prior to necropsy. Tissue samples (liver, kidney, heart, and skeletal muscle) were collected from each animal at necropsy. Tissue sections were removed and processed for histopathology assessment, and an additional adjacent tissue section removed and placed immediately on dry ice for genomic analyses, allowing for direct comparison of the gene expression response to histopathology outcome. For the skeletal muscle, the quadriceps muscle group was selected as a representative muscle, consisting of 3 muscles (vastus lateralis, vastus medialis, and rectus femoris) comprised of predominantly Type II (glycolytic) muscle fibers, and 1 muscle (vastus intermedius) comprised of predominantly Type I (oxidative) muscle fibers. Tissue samples were stored at –70C until RNA extraction.

tag: sample type

value: Study Compound Control Pool

tag: study

source_name: Heart

value: Heart

tag: compound

value: Angiotensin II

tag: necropsy day

tag: dose

tag: dose unit

value: mkd

tag: animal number


title: single-cell RNA seq data of the pia from rat [Pia]

source_name: Pia

value: Pia-derived leukocytes

tag: condition

value: Pia

tag: type of library


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 949mkd # 053394

tag: tissue


title: single-cell RNA seq data of the dura from rat [Dura]

source_name: Dura

value: Dura-derived leukocytes

value: Lewis

value: Dura


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 259


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 949mkd # 053388


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 0mkd # 053274


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 949mkd # 053386


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 254


title: single-cell RNA seq data of the central nervous system from rat [CNS]

source_name: CNS

value: CNS-derived leukocytes

value: Naive

value: CNS

value: RNA expression


title: goosepimples mutant

city: Mumbai

first: Mahendra

last: Sonawane

state: Maharashtra

address: Homi bhabha road, navy nagar

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description: GM

data_processing:
Illumina Casava1.7 software used for basecalling.
AVADIS NGS v1.2 was used for alignment and RPKM calculation and normalization forllowed by differential expression analysis
Genome_build: ZV9 (danRer7)
Supplementary_files_format_and_content: Complete_Data_and_Differential.xlsx  (Excel file containing RPKM values for detected transcripts and fold change)

organism: Danio rerio

source_name: zebrafish larvae

growth_protocol: heterozygote parents carrying either romeharsha or goosepimplesmutation were crossed, the clutches were grown in E3 buffer. Homozygous mutant larvae were identified and segregated from siblings at 43 hpf followed by dechorionation. 20 each of each group were subsequently fixed in RNAlater and used for RNA seq.

extract_protocol:
RNAlater extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 48 hpf

value: goosepimples/Myovb(-/-)

value: larvae


title: romeharsha sibling

description: RS

value: romeharsha siblings  (heterozygous+homozygous wt)


title: romeharsha mutant

description: RM

value: romeharsha(-/-)


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 949mkd # 053392

value: Study Compound Control Pool

value: Heart


title: goosepimples sibling

description: GS

value: goosepimples/Myovb siblings (heterozygous+homozygous wt)


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 251

value: IL23R Knockout

value: CD4 T Cells


title: single-cell RNA seq data of the choroid plexus from rat [CP]

source_name: CP

value: CP-derived leukocytes

value: CP


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 249


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 250


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 253


title: SP-delta 0579

city: Daegu

first: Md.

middle: Maidul

last: Islam

address: 680 Gukchaebosang-Ro, Jung-gu

department: Department of Microbiology

institute: Kyungpook National University

data_processing:
Illumina HiSeq 4000
For quality check used FastQC v0.10.1
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data (Trimmomatic 0.32)
Data assessment (Error rate, AT and GC content distribution, daat filtration)Mapping to reference genome (Bowtie1.1.2 software)
Expression quantification (HTSeq version 0.6.1p1 software)
Genome_build: GCF_000015425.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Acinetobacter baumannii

source_name: Liqiud bacterial culture

growth_protocol: Bacteria were cultured in LB under shaking conditions at 200 rpm at 37ºC for overnight. Fresh culture by 1/100 dilution with LB and culture upto early stationary phage

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (QIAGEN) following the manufacturer instructions. Sequencing libraries were generated using Ribo-Zero rRNA Removal Kit (Bacteria), TruSeq RNA Sample Prep Kit v2 following manufacturer’s recommendations. Ribo-Zero User Guide, TruSeq RNA sample prep v2 Guide, Part # 15026495 Rev. F was used for making library protocol. mRNA was purified from total RNA using ribo-zero rRNA removal kit. Fragmentation was carried out using divalent cations under elevated temperature.Reverse transcribe  onto cDNA. Nat Rev Genet. 2011 Sep 7;12(10):671-82
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNAprotect (Qiagen) before RNA extraction

tag: strain background

tag: genotype/variation

tag: growth stage

value: Early stationary phage

tag: treatment


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 0mkd # 053270

value: Angiotensin II

value: mkd


title: episomal_MPRA_DNA_rep2

city: St. Louis

first: Barak

middle: A

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Department of Genetics

institute: Washington University in St. Louis

library_source: genomic

data_processing:
patchMPRA and episomal MPRA: Fastq reads were first filtered to only include reads that contain barcodes in the correct sequence context. Promoter barcodes were then decoded using the FREE barcodes software (Hawkins et al., 2018).
TRIP expression: Fastq reads were first filtered to only include reads that contain barcodes in the correct sequence context. TRIP random barcodes were further filtered such that they are at least 3 hamming distance apart.
TRIP mapping: The reads were aligned to the human hg38 genome using bwa (v0.7.17) with default parameters. The barcodes were then matched to the aligned reads. Only reads that were confidently aligned to one location was kept for subsequent analyses.
Genome_build: hg38
Supplementary_files_format_and_content: txt files are tab-separated files containing barcodes and the corresponding raw counts of each barcode. Bed files contain barcodes and the corrsponding location of the transposon integration.

molecule: other

organism: Escherichia coli DH5[alpha]

source_name: Bacterial culture

growth_protocol: K562 cells were grown in IMDM (Isocove's Modified Dulbecco's Medium) supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids (NEAA) and 1% penicillin/streptomycin (pen/strep).

extract_protocol:
The plasmid library was extracted from electroporated E. coli using the the ZymoPure II Plasmid Maxiprep Kit.
RNA samples was first converted to cDNA by reverse transcription with the SuperScript IV First Strand Synthesis Systems (Invitrogen) using oligo dT primers. Barcodes were amplified from the respective plasmid/genomic DNA/cDNA samples using custom primers. Illumina sequencing adapters were then further added on 2 rounds of PCR with custom primers.

tag: cell line

tag: library

value: plasmid core promoter library


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 252

tag: differentiation

tag: gfp

tag: genotype

tag: cell type


title: episomal_MPRA_DNA_rep1


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 248


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 0mkd # 053272

tag: sample type

tag: study

tag: compound

tag: necropsy day

tag: dose


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 841mkd # 053356

source_name: Heart Day 3 Angiotensin II Control pool

tag: tissue

tag: dose unit

tag: animal number


title: GE1_oviducts of Yun7Ge

city: Ankang

first: Anli

last: Chen

address: Yucai Road

country: China

institute: The Key Sericultural Laboratory of Shaanxi

description: Ge 1

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts, and clean reads were aligned with reference genome sequences using Tophat software.
Gene expression levels were calculated using the reads per kb per million reads (RPKM) method.
P value<0.05, false discovery rate (FDR) ≤ 0.001 and RPKM>5 were thresholds for gene expression. Differential expression analysis of Yun7 and Yun7Ge was performed using the DEGseq (2010)  R package.
Q value<0.005 & ∣log 2 (foldchange)∣>1 was set as the threshold for significantly differential expression. The DEG sequences were BLAST-searched, mapped, annotated, and analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolism pathways and Blast2GO software (version 2.7.2) according to the Blast2GO Tutorial.
Genome_build: PRJDA20217
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and differentially expressed genes

organism: Bombyx mori

source_name: oviduct

extract_protocol:
Total RNA was prepared using TRIzol (Invitrogen) from the mixture of three whole oviduct of Yun7 and Yun7Ge before mating, and two replicates were set for each sample. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard illumina protocols

value: oviduct

tag: strain

tag: developmental period

value: Female moth before mating


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 247


title: SP-WT

tag: strain background

tag: genotype/variation

value: wild-type

tag: growth stage

tag: treatment

value: RNAprotect (Qiagen) before RNA extraction


title: GE2_oviducts of Yun7Ge

description: Ge 2


title: SE2_oviducts of Yun7

description: Se 2


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 0mkd # 053268


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 841mkd # 053350


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 841mkd # 053354


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 246

tag: differentiation

tag: gfp


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 417mkd # 053310


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 245

tag: genotype

tag: cell type


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 244


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 417mkd # 053308

tag: sample type

tag: study


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 841mkd # 053352

tag: compound

tag: necropsy day


title: SE1_oviducts of Yun7

description: Se 1

tag: tissue


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 243


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 241


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 417mkd # 053306

tag: dose

tag: dose unit


title: PT8-D15: Patient 8 PBMC-15 days post reovirus

city: Bronx

first: RADHASHREE

last: MAITRA

state: NY

address: 1300 Morris Park Ave

department: Medicine (Oncology)

institute: Albert Einstein College of Medicine of Yeshiva University

description: Gene Expression Data From Patient 8 PBMC-15 days post reovirus

hyb_protocol: The ss-cDNA generated from cRNA was chemically fragmented, biotin-labeled and made into a hybridization cocktail using hybridization kit (Catalog Number 900454) according to the Affymetrix Genechip protocol, which was then hybridized to Clariom D Gene Chip human probe array.

scan_protocol: The array image is generated by a high-resolution Gene Array Scanner 3000 7G (Thermo Fisher Scientific, Santa Clara, CA,) and the Cq value for each gene expression of a patient at a given time point was recorded.

data_processing: Individual sample signals for each patient at each time point were extracted from the TAC 4.0 software

label: biotin

organism: Homo sapiens

source_name: Patient 8 PBMC-15 days post reovirus

label_protocol: TAC Thermo fisher

extract_protocol: PBMC and RNA Isolation

treatment_protocol: Reovirus was administered as a 60-min intravenous infusion for 5 consecutive days every 28 days, at tissue culture infective dose (TCID50) of 3X1010. Peripheral blood mononuclear cells (PBMC) were isolated from whole blood pre and post reovirus administration at 48hr, Day-8, and Day-15. Clariom_D_Human_Assay was used to determine the overall gene expression compared to pre-reovirus treatment by RNA sequencing.

tag: disease state

value: colorectal cancer

value: peripheral blood mononuclear cells


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 417mkd # 053304

value: Study Compound Control Pool

tag: animal number


title: S7_NS

city: Shanghai

first: Xiang

last: Wang

address: 399 Wanyuan Road, Minhang District, Shanghai

department: Children’s Hospital and Institute of Biomedical Sciences

institute: Fudan University

description: LncRNA expression in PBMCs from asthma patients

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: PBMCs, asthma patient, replicate 4

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Freshly drawn peripheral blood from healthy volunteers and asthma patients was sent to suffer from microarray analysis.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: peripheral blood mononuclear cells (PBMCs)

tag: diagnosis

value: asthma

tag: gender

value: female

tag: age

value: 5 y


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 0mkd # 053258

value: Heart


title: S6_NS

source_name: PBMCs, asthma patient, replicate 3

value: male


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 0mkd # 053260


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 242

value: IL23R Knockout

value: CD4 T Cells


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 0mkd # 053256

value: Angiotensin II

value: mkd


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 984mkd # 053374


title: PT8-Pre: Patient 8 PBMC-pre reovirus

description: Gene Expression Data From Patient 8 PBMC-pre reovirus

source_name: Patient 8 PBMC-pre reovirus


title: patients_8_NS

source_name: PBMCs, asthma patient, replicate 1

value: 3 y


title: PT7-D15: Patient 7 PBMC-15 days post reovirus

description: Gene Expression Data From Patient 7 PBMC-15 days post reovirus

source_name: Patient 7 PBMC-15 days post reovirus


title: S5_NS

source_name: PBMCs, asthma patient, replicate 2


title: PT8-48: Patient 8 PBMC-48 hours post reovirus

description: Gene Expression Data From Patient 8 PBMC-48 hours post reovirus

source_name: Patient 8 PBMC-48 hours post reovirus


title: PT8-D8: Patient 8 PBMC-8 days post reovirus

description: Gene Expression Data From Patient 8 PBMC-8 days post reovirus

source_name: Patient 8 PBMC-8 days post reovirus


title: US-1098242 vs. Heart; Day 3; Angiotensin II; 0mkd # 053254

source_name: Heart


title: SC with low extent of elongation

city: Cincinnati

first: zhenyuan

last: xu

state: OH

address: 2378 Montana Ave, AptE

department: Chemical Engineering

institute: University of Cincinnati

description: Gene expression data for round SCs

hyb_protocol: 2.3 µg of fragmented cDNA was hybridized to Rat Clariom S Arrays (902934, Thermo Fisher) by incubating at 45°C for 17 hours before washing and staining with the GeneChip™ Hybridization, Wash, and Stain kit (900720, Thermo Fisher).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The raw data files were generated by Command Console (Affymetrix). The data were analyzed using the Transcriptome Analysis Console (TAC) Software in combination with Rstudio.

source_name: Not elongated

label_protocol: GeneChip™ WT PLUS Reagent Kit (902280, Thermo Fisher) was used to generate biotin labeled single-stranded complementary DNA

growth_protocol: SCs were cultured under standard cell culture condition (37°C, 5% CO2) for 2 days before RNA isolation.

extract_protocol: RNeasy mini kit (Qiagen) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: PDMS cell culture substrates were coated with laminin to increase cell adhesion. PDMS and micropatterned cell culture substrates were sterilized with 70% ethanol for 30 minutes before seeding cells.

tag: passage number


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 240

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

tag: differentiation


title: PT7-D8: Patient 7 PBMC-8 days post reovirus

description: Gene Expression Data From Patient 7 PBMC-8 days post reovirus

source_name: Patient 7 PBMC-8 days post reovirus


title: S2_NS

description: LncRNA expression in PBMCs from healthy volunteer

source_name: PBMCs, healthy volunteer, replicate 4

value: healthy

value: 7 y


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 239

tag: gfp


title: DR-7 rep5

source_name: Tooth and periodontal ligament

value: Tooth and periodontal ligament

value: post natal day 21

tag: treatment

value: DR

tag: time

value: 7 days


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 238

tag: genotype

tag: cell type


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 237


title: S1_NS

source_name: PBMCs, healthy volunteer, replicate 3

value: peripheral blood mononuclear cells (PBMCs)


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 236


title: normal_6_NS

source_name: PBMCs, healthy volunteer, replicate 2


title: SC with high extent of elongation

description: Gene expression data for elongated SCs

source_name: Elongated


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 050mkd # 1126-005:1032

source_name: Heart Day 15 Allylamine Control pool

tag: sample type

value: Study Compound Control Pool

tag: study

tag: compound

value: Allylamine


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 235


title: normal_5_NS

source_name: PBMCs, healthy volunteer, replicate 1

tag: tissue

value: female

value: 5 y


title: Prostate-MDAPCa2B-HiC-2

city: Knoxville

first: Rebeca

last: SanMartin

state: TN

address: 1311 Cumberland Avenue

institute: University of Tennessee Knoxville

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github
Iterative correction was performed using method described by Imakaev et al.
Genome_build: hg19
Supplementary_files_format_and_content: Each .tar file contains the iteratively corrected and raw matrix.gz files for 20 kb, 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 2.5 Mb bin size

molecule: genomic DNA

source_name: MDAPCa2b cells (Navone. MD Anderson, Houston TX). Bone metastatic prostate cancer

growth_protocol: All cell lines maintained and split according to ATCC SOPs. MDA Cells grown on FCN Coting Mix (Athena), used according to the manufacturer's instructions

extract_protocol:
Hi-C was performed using the Arima Hi-C (Arima Genomics) kit, or according to established protocols (Goloshi. et.al doi: 10.1016/j.ymeth.2018.04.033)
Manufacturer’s protocol A160141 v01 for library amplification from Arima was used along the NEBNext Ultra II kit (NEB E7645S).

treatment_protocol: Cells were collected from T75 flasks at 80% confluency, under normal growth conditions.

tag: cell line

tag: source tissue/cell type

value: Bone metastatic prostate cancer

tag: condition

value: Cells grown under control conditions

tag: media

value: HPC1 Media, 10%FBS, 100 g/ml penicillin-streptomycin.


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 050mkd # 1126-005:1029

value: Heart

tag: necropsy day

tag: dose

tag: dose unit

tag: animal number


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 050mkd # 1126-005:1030

value: mkd


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 050mkd # 1126-005:1031


title: SC with small spreading area

description: Gene expression data for SCs with small spreading area

source_name: Small spreading area

tag: passage number


title: SC with large spreading area

description: Gene expression data for SCs with large spreading area

source_name: Large spreading area


title: Prostate-MDAPCa2B-HiC-1


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 984mkd # 053378

source_name: Heart Day 14 Angiotensin II Control pool

value: Angiotensin II


title: PT7-48: Patient 7 PBMC-48 hours post reovirus

description: Gene Expression Data From Patient 7 PBMC-48 hours post reovirus

source_name: Patient 7 PBMC-48 hours post reovirus

tag: disease state

value: colorectal cancer

value: peripheral blood mononuclear cells


title: SC with stiff ECM

description: Gene expression data for SCs with stiff ECM

source_name: High ECM stiffness


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 000mkd # 1126-005:1079

source_name: Heart


title: SC with soft ECM

description: Gene expression data for SCs with soft ECM

source_name: Low ECM stiffness


title: PT6-D15: Patient 6 PBMC-15 days post reovirus

description: Gene Expression Data From Patient 6 PBMC-15 days post reovirus

source_name: Patient 6 PBMC-15 days post reovirus


title: PT6-48: Patient 6 PBMC-48 hours post reovirus

description: Gene Expression Data From Patient 6 PBMC-48 hours post reovirus

source_name: Patient 6 PBMC-48 hours post reovirus


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 234

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

tag: differentiation

tag: gfp

value: IL23R Knockout

value: CD4 T Cells


title: Prostate-MDAPCA2a-HiC-2

source_name: MDAPCa2a cells (Navone. MD Anderson, Houston TX). Bone metastatic prostate cancer


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 233

tag: genotype

tag: cell type


title: PT7-Pre: Patient 7 PBMC-pre reovirus

description: Gene Expression Data From Patient 7 PBMC-pre reovirus

source_name: Patient 7 PBMC-pre reovirus


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 232


title: Prostate-MDAPCA2a-HiC-1


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 000mkd # 1126-005:1077

tag: sample type

tag: study


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 000mkd # 1126-005:1078

tag: tissue

tag: compound


title: PT6-D8: Patient 6 PBMC-8 days post reovirus

description: Gene Expression Data From Patient 6 PBMC-8 days post reovirus

source_name: Patient 6 PBMC-8 days post reovirus


title: Prostate-VCaP-HiC-3

source_name: VCaP cells (ATCC CRL-2876). Vertebral metastastatic prostate cancer

tag: cell line

value: VCaP

tag: source tissue/cell type

value: Vertebral metastastatic prostate cancer

value: DMEM-F12 Ham 1:1, 10%FBS, 100 g/ml penicillin-streptomycin.


title: PT5-D15: Patient 5 PBMC-15 days post reovirus

description: Gene Expression Data From Patient 5 PBMC-15 days post reovirus

source_name: Patient 5 PBMC-15 days post reovirus


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 230


title: Prostate-VCaP-HiC-1

tag: condition

tag: media


title: Heart Day 15 Allylamine Control pool vs. Heart; Day 15; Allylamine 000mkd # 1126-005:1080

source_name: Heart Day 15 Allylamine Control pool

value: Study Compound Control Pool

tag: necropsy day

tag: dose


title: PT6-Pre: Patient 6 PBMC-pre reovirus

description: Gene Expression Data From Patient 6 PBMC-pre reovirus

source_name: Patient 6 PBMC-pre reovirus


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 228


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 227


title: Prostate-PC3-HiC-1

source_name: PC-3 cells (ATCC CRL-1435). Bone metastatic prostate cancer

value: ATCC RPMI, 10%FBS, 100 g/ml penicillin-streptomycin.


title: Prostate PC3-HiC-2


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 050mkd # 1126-005:1025

source_name: Heart Day 08 Allylamine Control pool

value: Allylamine

tag: dose unit

tag: animal number


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 050mkd # 1126-005:1026


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 050mkd # 1126-005:1027


title: PT5-48: Patient 5 PBMC-48 hours post reovirus

description: Gene Expression Data From Patient 5 PBMC-48 hours post reovirus

source_name: Patient 5 PBMC-48 hours post reovirus

tag: disease state


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 231

tag: differentiation


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 226

tag: gfp


title: PT5-D8: Patient 5 PBMC-8 days post reovirus

description: Gene Expression Data From Patient 5 PBMC-8 days post reovirus

source_name: Patient 5 PBMC-8 days post reovirus


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 000mkd # 1126-005:1075


title: PT4-D8: Patient 4 PBMC-8 days post reovirus

description: Gene Expression Data From Patient 4 PBMC-8 days post reovirus

source_name: Patient 4 PBMC-8 days post reovirus


title: PT5-Pre: Patient 5 PBMC-pre reovirus

description: Gene Expression Data From Patient 5 PBMC-pre reovirus

source_name: Patient 5 PBMC-pre reovirus


title: PT4-48: Patient 4 PBMC-48 hours post reovirus

description: Gene Expression Data From Patient 4 PBMC-48 hours post reovirus

source_name: Patient 4 PBMC-48 hours post reovirus


title: PT4-D15: Patient 4 PBMC-15 days post reovirus

description: Gene Expression Data From Patient 4 PBMC-15 days post reovirus

source_name: Patient 4 PBMC-15 days post reovirus


title: Prostate-VCaP-HiC-2


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 000mkd # 1126-005:1076

source_name: Heart


title: Prostate-DU145-HiC-2

source_name: DU145 cells (ATCC HTB-81). Brain metastatic prostate cancer

value: Brain metastatic prostate cancer

value: DMEM, 10%FBS, 100 g/ml penicillin-streptomycin.


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 225

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

tag: genotype


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 224

tag: cell type


title: Prostate-LNCaP-HiC

source_name: LNCaP cells clone FGC (ATCC CRL-1740) lymph node metastatic prostate cancer

value: LNCaP clone FGC

value: lymph node metastatic prostate cancer

value: Cells grown under control conditions


title: PT4-Pre: Patient 4 PBMC-pre reovirus

description: Gene Expression Data From Patient 4 PBMC-pre reovirus

source_name: Patient 4 PBMC-pre reovirus


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 229


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 223


title: LTAD_No.10-3_rep2_PSF-RIP

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
To remove rRNA sequence, we used bowtie 2 version 2.2.6. Mapping to human genome (hg19) was perforemd using tophat 2.1.0.with bowtie.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq mRNA database for RIP-seq data.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to faciliate comparison among different samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FKPM values for each Sample

source_name: prostate cancer cells

growth_protocol: LTAD cells were treated with phenol-red free RPMI1640 containing 10% charcoal/dextran treated FBS.

extract_protocol:
For RIP, cell lysates were immunoprecipitated using EZ-magna RIP RNA binding protein immunoprecipitation kit (Millipore 17-701).
Illumina TruSeq Stranded kit was used for library construction according to the manufacuture's protocol.

treatment_protocol: Cells were treated with vehicle (DMSO) or No.10-3 (5 µM)

value: LTAD

value: prostate cancer

tag: treatment

tag: antibody

value: PSF


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 222


title: LTAD_No.10-3_PSF-RIP


title: Heart Day 03 Allylamine control pool vs. Heart; Day 03; Allylamine 100mkd # 1126-005:1039

source_name: Heart Day 03 Allylamine control pool

tag: sample type

tag: study

tag: tissue

value: Heart

value: mkd


title: Prostate-DU145-HiC-1

tag: cell line

tag: source tissue/cell type


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 221

value: IL23R Knockout

value: CD4 T Cells


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 000mkd # 1126-005:1074

tag: compound


title: Heart Day 08 Allylamine Control pool vs. Heart; Day 08; Allylamine 000mkd # 1126-005:1073

tag: necropsy day


title: Heart Day 03 Allylamine control pool vs. Heart; Day 03; Allylamine 100mkd # 1126-005:1038

tag: dose


title: LTAD_Control_PSF-RIP

value: vehicle


title: PT3-48: Patient 3 PBMC-48 hours Control

description: Gene Expression Data From Patient 3 PBMC-48 hours Control

source_name: Patient 3 PBMC-48 hours Control

value: colorectal cancer

value: peripheral blood mononuclear cells


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 220


title: LTAD_No.10-3_input

value: input


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 219


title: PT3-D15: Patient 3 PBMC-15 days Control

description: Gene Expression Data From Patient 3 PBMC-15 days post Control

source_name: Patient 3 PBMC-15 days Control


title: Rapamycin_Gut_Day50_rep3

city: Cologne

first: Yu-Xuan

address: Joseph-Stelzmann-Str. 9b

department: Biological Mechanisms of Ageing

institute: Max-Planck-Institute for Biology of Ageing

description:
Gene_expression_Analysis_results_Day50_Gut_Rapa-vs-Control.txt
Differential_Gene_expression_Analysis_results_Day50_Gut_Rapa-vs-Control.txt
htseq.counts.summary.tsv

data_processing:
Raw sequence reads were quality-trimmed using Flexbar (v2.5.0) and aligned using HiSat (v2.0.14) against the Dm6 reference genome (Dodt et al., 2012; Kim et al., 2015).
Mapped reads were filtered using SAMtools (v1.2) (Li et al., 2009), and guided transcriptome assembly was done using StringTie (v1.04) (Pertea et al., 2015).
Merging of assembled transcriptomes was performed using Cufflinks v2.2.1 (Trapnell et al., 2013).
The number of reads per gene was assessed using HTSeq v0.6.1 and differential gene expression was done by DESeq2 with ERCC normalization (Anders et al., 2015; Love et al., 2014).
Genome_build: Dm6
Supplementary_files_format_and_content: Macintosh Formatted text file for results of differential gene expression analysis. htseq.counts.summary.tsv.

organism: Drosophila melanogaster

source_name: Gut

growth_protocol: flies were maintained and experiments conducted at 25°C on a 12 hr:12 hr light/dark cycle at 60% humidity, on food containing 10 % (w/v) brewer’s yeast, 5% (w/v) sucrose, and 1.5% (w/v) agar unless otherwise noted.

extract_protocol:
Total RNA was extracted from 25 guts using Trizol following standard protocols. DNA concentration were evaluated using a Qubit 2.0 fluorometer before DNase I treatment. After adjusting final RNA concentration to 100 ng/µl, 2-3 µl ERCC ExFold RNA Spike-In Mixes was added for normalization to the DNA content of the sample.
Ribosomal RNA depletion libraries were generated at the Max Planck Genome Centre Cologne (MPGCC)

treatment_protocol: Rapamycin dissolved in ethanol was added to food at 200 µM final concentration, for control food ethanol alone was added.

tag: strain

value: wDahomy

value: gut

value: wild type

tag: developmental stage

value: adult

tag: age

value: 50 days

tag: agent

value: Rapamycin


title: CHIP Seq-C17 His-tagged

city: Singapore

first: Azhar

middle: B

last: Ali

address: 14 Medical Drive MD6 #11-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

description:
CHIP-Seq C17 His
C17 His

data_processing:
Mapping to the reference genome was done by using BWA.
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
The resulting bam files are converted to bigWig format by bedGraphToBigWig from bedGraph generated by bedtools.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig format

source_name: PC-9 lung cancer cell line

growth_protocol: Vector and macroH2A1.2 overexpressed PC-9 cells were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passage every 3 to 4 days.

extract_protocol:
Cells were fixed with 1% formaldehyde and insoluble chromatin fraction was isolated. Chromatin was sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antibodies.
CHIP-seq library were prepared by sequencing provider, Novogene IT.  100-350bp insert DNA library (CHIP Seq) was used for sequencing.

treatment_protocol: 200µg/ml Hygromycin selection antibody

value: Lung cancer cell line

tag: mutation

value: EGFR mutant, macroH2A1.2 transfected

tag: passage


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 218

tag: differentiation

tag: gfp

tag: genotype

tag: cell type


title: Heart Day 03 Allylamine control pool vs. Heart; Day 03; Allylamine 100mkd # 1126-005:1037

tag: sample type

value: Study Compound Control Pool

tag: study

value: Allylamine

tag: dose unit

tag: animal number


title: Heart Day 03 Allylamine control pool vs. Heart; Day 03; Allylamine 000mkd # 1126-005:1071

tag: tissue

value: Heart

tag: compound

value: mkd


title: PT2-D15: Patient 2 PBMC-15 days Control

description: Gene Expression Data From Patient 2 PBMC-15 days Control

source_name: Patient 2 PBMC-15 days Control

tag: disease state


title: Heart Day 03 Allylamine control pool vs. Heart; Day 03; Allylamine 000mkd # 1126-005:1070

tag: necropsy day

tag: dose


title: PT3-Pre: Patient 3 PBMC-pre Control

description: Gene Expression Data From Patient 3 PBMC-pre Control

source_name: Patient 3 PBMC-pre Control


title: PT3-D8: Patient 3 PBMC-8 days Control

description: Gene Expression Data From Patient 3 PBMC-8 days post Control

source_name: Patient 3 PBMC-8 days Control


title: Heart Day 03 Allylamine control pool vs. Heart; Day 03; Allylamine 000mkd # 1126-005:1072


title: Rapamycin_Gut_Day50_rep2

tag: strain

tag: developmental stage

tag: age


title: PT2-48: Patient 2 PBMC-48 hours Control

description: Gene Expression Data From Patient 2 PBMC-48 hours Control

source_name: Patient 2 PBMC-48 hours Control


title: PT2-Pre: Patient 2 PBMC-pre Control

description: Gene Expression Data From Patient 2 PBMC-pre Control

source_name: Patient 2 PBMC-pre Control


title: CHIP Seq-C17 H3K27ME3

description:
CHIP-Seq C17 K27
C17 K27

tag: mutation

tag: passage


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 216

tag: differentiation

tag: gfp

value: IL23R Knockout

value: CD4 T Cells


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 217

tag: genotype

tag: cell type


title: CHIP Seq-C17 H3K4ME3

description:
CHIP-Seq C17 K4
C17 K4


title: Rapamycin_Gut_Day50_rep1

tag: agent


title: LTAD_Control_input

tag: cell line

value: LTAD

value: prostate cancer

tag: treatment

value: vehicle

tag: antibody


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 215


title: Control_Gut_Day50_rep3

value: wDahomy

tag: tissue

value: Control


title: CHIP Seq-C17 Rabbit IgG

description:
CHIP-Seq C17 RbIgG
C17 RbIgG


title: CHIP Seq-C1 His-tagged

description:
CHIP-Seq C1 His
C1 His


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 214


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 213


title: Control_Gut_Day50_rep1

value: gut

value: wild type


title: CHIP Seq-C1 H3K27ME3

description:
CHIP-Seq C1 K27
C1 K27

value: EGFR mutant, pCMV3 transfected


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 212


title: PT2-D8: Patient 2 PBMC-8 days Control

description: Gene Expression Patient 2 PBMC-8 days post Control

source_name: Patient 2 PBMC-8 days Control

tag: disease state

value: colorectal cancer

value: peripheral blood mononuclear cells


title: PT1-D8: Patient 1 PBMC-8 days Control

description: Gene Expression Data From Patient 1 PBMC-8 days Control

source_name: Patient 1 PBMC-8 days Control


title: CHIP Seq-C1 H3K4ME3

description:
CHIP-Seq C1 K4
C1 K4

value: Lung cancer cell line


title: PT1-D15: Patient 1 PBMC-15 days Control

description: Gene Expression Data From Patient 1 PBMC-15 days Control

source_name: Patient 1 PBMC-15 days Control


title: PT1-Pre: Patient 1 PBMC-pre Control

description: Gene Expression Data From Patient 1 PBMC-pre Control

source_name: Patient 1 PBMC-pre Control


title: Rapamycin_Gut_Day30_rep2

description:
Gene_expression_Analysis_results_Day30_Gut_Rapa-vs-Control.txt
Differential_Gene_expression_Analysis_results_Day30_Gut_Rapa-vs-Control.txt
htseq.counts.summary.tsv

value: adult

value: 30 days

value: Rapamycin


title: Rapamycin_Gut_Day30_rep1


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 210

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout


title: Rapamycin_Gut_Day30_rep3


title: Control_Gut_Day30_rep2


title: Control_Gut_Day30_rep3


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 209


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 208


title: PRO-seq dTAG47 4hr rep2

city: Nashville

first: Jing

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
Library strategy: PRO-seq
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Differential binding peaks were identified using DiffBind.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
ATAC-seq reads were aligned to the human genome hg19 using Bowtie2 (bowtie2 -p 8 -X 2000 --no-mixed --no-discordant).
Peaks were called using MACS2 with q-value of 0.05.
Differential enriched peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content:
RNA-seq: tab-delimited text file include raw counts for each Sample
ChIP-seq: one peak file per Sample
ATAC-seq: one peak file per Sample
PRO-seq: tab-delimited text file include raw counts for proximal-promoter and gene body region, and density for gene body

molecule: nuclear RNA

source_name: Malignant rhabdoid tumor of kidney cell line

growth_protocol: G401 cells were maintained in DMEM supplemented with 10% FBS and 1%Penicillin/Streptomycin. This maintenance media was also the same media that DMSO or dTAG47 was diluted in for all experiments.

extract_protocol:
For ChIP-seq experiments, chromatin was extracted from nuclear pellets and frozen until ready for immunoprecipitation with antibodies. Immunoprecipitated DNA was extracted using a PCR purification kit. For ATAC-seq, nuclei were treated with transposase, followed by PCR purification to extract DNA. For RNA-seq, RNA was extracted using Trizol and the Direct-zol RNA mini prep kit by Zymol. For PRO-seq, run-on biotinylated RNA from nuclei were extracted using trizol and streptavidin Dynabeads, and then processed and continually purified through multiple rounds of streptavidin Dynabead addition.
For ChIP-seq, libraries were made with the NEBnext Ultra II DNA library Prep and NEBNext Multiplex Oligos for Illumina with the addition of an AMPure clean up prior to beginning the end repair. For ATAC-seq libraries were made using the NEBNext High-Fidelity 2x PCR Master Mix, and Nextera based primers ordered from IDT to allow for dual indexing. For RNA-seq, libraries were made at Vanderbilt University Medical Center VANTAGE core using their standard methods with ribosomal RNA depletion. For PRO-Seq, biotinylated-RNA was extracted by trizol, underwent base hydrolysis, and purified using Streptavidin Dynabeads. Adaptors were ligated to 3’ ends and 5' caps were removed and ends repaired prior to adding 5'-adaptors. Purified biotinylated RNA containing adaptors was used in a reverse transcriptase reaction to create cDNA which was subsequently used to generate libraries using NEB High Fidelity Phusion polymerase.

treatment_protocol: Parental or engineered G401 cells were treated with DMSO or 500 nM dTAG47 for the following time periods: ChIP-seq and PRO-Seq were 4 hour timepoints, ATAC-seq and RNA-seq were 24 hour timepoints.

value: DTMYC G401 cells

value: 500 nM dTAG47

value: ten-thirty


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 207

value: IL23R Knockout

value: CD4 T Cells


title: PRO-seq DMSO rep2

value: DMSO


title: PRO-seq DMSO rep1


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 211


title: CHIP Seq-C1 Rabbit IgG

description:
CHIP-seq C1 RbIgG
C1 RbIgG


title: MDS4 - Slan+ monocytes

city: Utrecht

first: Nathalie

last: van Leeuwen-Kerkhoff

state: The Netherlands

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 2 minutes, then 45° for 5 minutes. Centrifuge at max speed for 1 minute and then transfer 200μl on to the array. Hybridize 18 hours at 45° at 60rpm. Fluidics washing using the program FS450_0001.

scan_protocol: Signals were scanned by Affymetrix GeneChip Scanner 3000 7G

data_processing: Microarray signals were normalized using the RMA algorithm in the Affymetrix® Expression Console software (Affymetrix®).

label: Biotin

source_name: Bone marrow

label_protocol: Labeled with the Encore Biotin Module Kit (NuGEN) according to manufacturer’s protocols

growth_protocol: not applicable

extract_protocol: Total RNA isolated from FACS-sorted cells was amplified using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA)

treatment_protocol: not applicable

tag: disease

value: myelodysplastic syndromes (MDS)

value: Slan+ monocytes


title: Rapamycin_Gut_Day10_rep3

description:
Gene_expression_Analysis_results_Day10_Gut_Rapa-vs-Control.txt
Differential_Gene_expression_Analysis_results_Day10_Gut_Rapa-vs-Control.txt
htseq.counts.summary.tsv

value: wDahomy

value: gut

value: 10 days


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 206


title: Rapamycin_Gut_Day10_rep2

value: wild type


title: PRO-seq dTAG47 4hr rep1


title: Control_Gut_Day50_rep2

value: 50 days

value: Control


title: MDS3 - Slan+ monocytes


title: Control_Gut_Day30_rep1

value: adult


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 205


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 204


title: Rapamycin_Gut_Day10_rep1


title: Control_Gut_Day10_rep3


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 203


title: RNAseq DTMYC dTAG47 rep1

description: RNAseq-proteincoding-count.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Differential binding peaks were identified using DiffBind.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
ATAC-seq reads were aligned to the human genome hg19 using Bowtie2 (bowtie2 -p 8 -X 2000 --no-mixed --no-discordant).
Peaks were called using MACS2 with q-value of 0.05.
Differential enriched peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content:
RNA-seq: tab-delimited text file include raw counts for each Sample
ChIP-seq: one peak file per Sample
ATAC-seq: one peak file per Sample
PRO-seq: tab-delimited text file include raw counts for proximal-promoter and gene body region, and density for gene body


title: Control_Gut_Day10_rep2


title: RNAseq DTMYC dTAG47 rep2

description: RNAseq-proteincoding-count.txt


title: RNAseq DTMYC dTAG47 rep3

description: RNAseq-proteincoding-count.txt


title: RNAseq DTMYC DMSO rep3

description: RNAseq-proteincoding-count.txt


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 202


title: Control_Gut_Day10_rep1


title: Mut3: dmd1 rep3

city: Beijing

first: lijun

last: Ren

address: No. 1 West Beichen Road, Chaoyang District

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: Oryza sativa Japonica Group IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: anthers

extract_protocol:
Total RNA was extracted from the sample using Plant RNA Purification Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: anther

value: dmd1 mutant

value: 3 months

tag: loc


title: Mut2: dmd1 rep2


title: Mut1: dmd1 rep1


title: TRIP_mapping_DNA_pool4_rep1

source_name: Chronic myelogenous leukemia (CML)

extract_protocol:
DNA and RNA was harvested simultaneously using the TRIzol reagent (Life Technologies) following the manufacturer's protocol.
Genomic DNA was digested overnight with XbaI, SpeI, NheI and AvrII (New England Biolabs). The digested DNA was then ligated overnight with T4 DNA ligase (New England Biolabs). Custom primers were used to perform inverse PCR on the ligated molecules to amplify the barcodes and genomic region where the transposon is integrated. Illumina sequencing adapters were then added on with 2 rounds of PCR with custom primers.

treatment_protocol: Wild-type K562 cells were cotransfected with PiggyBac transposase and six core promoters that were randomly barcoded. Cells were sorted for GFP signal after 24 hours to enrich for cells that contained transgene integrations. After culturing for a week, the cells were sorted into pools of 7000 cells each and allowed to grow until there were sufficient cells for DNA and RNA extraction.

tag: library

value: randomly barcoded core promoters integrated


title: TRIP_mapping_DNA_pool3_rep2


title: TRIP_mapping_DNA_pool4_rep2


title: MDS2 - Slan+ monocytes


title: MDS1 - Slan+ monocytes


title: MDS2 - cDC2


title: MDS4 - cDC2


title: PT1-48: Patient 1 PBMC-48 hours Control

description: Gene Expression Data From Patient 1 PBMC-48 hours Control

source_name: Patient 1 PBMC-48 hours Control

value: colorectal cancer

value: peripheral blood mononuclear cells


title: MDS3 - cDC2


title: TRIP_mapping_DNA_pool3_rep1


title: WT2: wild-type rep2

value: dmd1 wild-type


title: WT3: wild-type rep3


title: TRIP_mapping_DNA_pool2_rep2


title: RNAseq parental DMSO rep3

description: RNAseq-proteincoding-count.txt

value: G401 cells

value: DMSO

value: ten-thirty


title: WT1: wild-type rep1


title: TRIP_mapping_DNA_pool2_rep1


title: RNAseq parental DMSO rep2

description: RNAseq-proteincoding-count.txt


title: TRIP_mapping_DNA_pool1_rep2


title: RNAseq parental DMSO rep1

description: RNAseq-proteincoding-count.txt


title: TRIP_mapping_DNA_pool1_rep1


title: RNAseq parental dTAG47 rep3

description: RNAseq-proteincoding-count.txt

value: 500 nM dTAG47


title: RNAseq DTMYC DMSO rep1

description: RNAseq-proteincoding-count.txt

value: DTMYC G401 cells


title: RNAseq parental dTAG47 rep2

description: RNAseq-proteincoding-count.txt


title: MKO_Tac_H3K27ac_ChIPseq_Rep1

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

description:
H3K27ac  ChIP-Seq of myod ko differentiating myocytes at 12h treated with Tacedinaline
MKO_Tac_K27ac.bw

data_processing:
RNA-seq reads were aligned to the mm9 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ChIP-Seq reads were mapped to mm9  genome with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 3kb, 5 kb and 10 kb resolutions with modified parameters for pooled Hi-C matrices of each  condition.
Genome_build: mm9
Supplementary_files_format_and_content: .hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count for each sample

source_name: Differentiating myocytes for 12h

extract_protocol:
Primary myoblasts were isolated from the hindlimb skeletal muscle of WT and KO mice at 2~3 weeks, minced and digested in a mixture of type II collagenase and Dispase B (Roche Applied Science). Cells were filtered from debris, centrifuged and cultured in growth medium (F-10 Ham’s medium supplemented with 20% FBS, 10 ng/ml basic fibroblast growth factor, 1% penicillin– streptomycin and 1% glutamine) on collagen-coated cell culture plates at 37 °C in 5% CO2. At 60-70% confluence, cells can be switched to differentiation medium (DMEM with 2% horse serum).
Hi-C were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). Briefly, cells were cross-linked with formaldehyde and nucleuses were isolated by lysis buffers. The chromain was then randomly fragmented by 4-bp enzymes (HaeIII) and then two proximal fragments were connected by 20 bp biotinylated bridge linker in nucleus. A whole genome chromatin was extracted and sheared into 400 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads. After amplification, the DNA were ready for library construction. RNA for NRA-seq was harvested using Trizol reagent. For ChIP-seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with related antibody.
Hi-C libaries were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645)

tag: chip antibody

value: skeletal muscle

value: myod KO


title: RNAseq DTMYC DMSO rep2

description: RNAseq-proteincoding-count.txt


title: RNAseq parental dTAG47 rep1

description: RNAseq-proteincoding-count.txt


title: MKO_Tac_H3K27ac_ChIPseq_Rep2


title: DU145_siOCT4

description:
DU145_siOCT4
Gene expression data from DU145 cells trasfected with siOCT4

hyb_protocol: The samples were hybridized to Human Clariom S-arrays or D-arrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: DU145, LNCaP, DU145-CR, PC3-CR, and 22Rv1 cells were cultured in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: LNCaP and 22Rv1 cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or dihydrotestosterone (DHT) (10 nM) for 24 h. DU145, DU145-CR, and PC3-CR cells were treated with siRNA for 72 h before RNA extraction. DU145 and DU145-CR cells were treated with vehicle or riba 10 μM for 48 h.

value: AR-negative Castration-resistant prostate cancer (CRPC) cell line

tag: sirna

tag: ligand/treatment


title: MKO_DMSO_H3K27ac_ChIPseq_Rep2

description:
H3K27ac  ChIP-Seq of myod ko differentiating myocytes at 12h treated with DMSO
MKO_DMSO_K27ac.bw

tag: passage


title: ATAC-seq dTAG47 rep3


title: TRIP_expression_RNA_pool4

extract_protocol:
DNA and RNA was harvested simultaneously using the TRIzol reagent (Life Technologies) following the manufacturer's protocol.
RNA samples was first converted to cDNA by reverse transcription with the SuperScript IV First Strand Synthesis Systems (Invitrogen) using oligo dT primers. Barcodes were amplified from the respective plasmid/genomic DNA/cDNA samples using custom primers. Illumina sequencing adapters were then further added on 2 rounds of PCR with custom primers.


title: HD1 - Slan+ monocytes

value: Healthy donor

value: Slan+ monocytes


title: HD1 - cDC2


title: MKO_DMSO_H3K27ac_ChIPseq_Rep1


title: S14_GBM

city: Houston

first: Zhongming

last: Zhao

state: Texas

address: 7000 fannine St

institute: University of Texas Health Science Center at Houston

data_processing:
For RNA-seq analysis, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p11 annotation using HISAT2 (version 2.1.0) .The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) value of the  transcripts was calculated based on StringTie (version 1.3.4) with default parameters.
Expression of individual miRNA was measured by quantitative real-time PCR with TaqMan miRNA Expression kit (Applied Biosystems, Thermo Fisher Scientific, USA).
Genome_build: RNA-seq: GRCh38.p11
Supplementary_files_format_and_content: Merged file: tab-delimited text files include FPKM values for RNAseq and read counts for small RNA-seq for each Sample.

source_name: Brain

extract_protocol:
Total RNAs were extracted from snap-frozen GBM tissue samples using Trizol (Ambion, Thermo Fisher, USA) by following the manufacturer’s protocol.
Total RNA sequencing was carried out for the extracted total RNA by Illumina HiSeq-4000 at the Advanced Technology Genomics Core (ATGC) in the University of Texas MD Anderson Cancer Center.

value: Brain

tag: diagnosis

value: GBM


title: DU145_riba

description:
DU145_R
Gene expression data from DU145 cells treated with riba

value: riba 10 μM


title: TRIP_expression_RNA_pool3_rep2

value: randomly barcoded core promoters integrated


title: MDS1 - cDC2

value: myelodysplastic syndromes (MDS)


title: DU145_siControl

description:
DU145_siControl
Gene expression data from DU145 cells trasfected with siControl

value: siControl


title: S12_GBM


title: ATAC-seq dTAG47 rep1


title: ATAC-seq dTAG47 rep2


title: WT_c646_H3K27ac_ChIPseq_Rep1

description:
H3K27ac  ChIP-Seq of wildtype differentiating myocytes at 27h treated with c646
WT_c646_K27ac.bw

source_name: Differentiating myocytes for 27h

value: wild type


title: TRIP_expression_RNA_pool3_rep1


title: ATAC-seq DMSO rep3


title: TRIP_expression_RNA_pool2


title: DU145_Control

description:
DU145_Control_veh
Gene expression data from DU145 cells treated with vehicle (water)

value: Vehicle


title: HD3 - Slan+ monocytes


title: HD2 - Slan+ monocytes


title: S19_GBM


title: S10_GBM


title: WT_c646_H3K27ac_ChIPseq_Rep2


title: HD3 - cDC2


title: ATAC-seq DMSO rep2

value: DMSO


title: WT_DMSO_H3K27ac_ChIPseq_Rep2

description:
H3K27ac  ChIP-Seq of wildtype differentiating myocytes at 27h treated with DMSO
WT_DMSO_K27ac.bw


title: HD2 - cDC2


title: TRIP_expression_RNA_pool1


title: S9_GBM


title: TRIP_expression_DNA_pool4


title: S7_GBM


title: WT_DMSO_H3K27ac_ChIPseq_Rep1


title: ChIP-seq MYC dTAG47 rep3

value: ten-thirty

value: MYC


title: MKO_DM_H3K27me3_ChIPseq_Rep2

description:
H3K27me3  ChIP-Seq of myod ko differentiating myocytes at 24h
MKO_DM_K27me3.bw

source_name: Differentiating myocytes for 24h

value: millipore 07-449


title: TRIP_expression_DNA_pool3_rep2


title: S5_GBM


title: MKO_DM_H3K27me3_ChIPseq_Rep1

value: skeletal muscle


title: ChIP-seq MYC dTAG47 rep2

value: DTMYC G401 cells

value: 500 nM dTAG47


title: TRIP_expression_DNA_pool3_rep1


title: ChIP-seq MYC dTAG47 rep1


title: S21_Control

value: Normal


title: MKO_GM_H3K27me3_ChIPseq_Rep2

description:
H3K27me3  ChIP-Seq of myod ko proliferating myoblasts
MKO_GM_K27me3.bw

source_name: Proliferating myoblasts

value: myod KO


title: TRIP_expression_DNA_pool2


title: ChIP-seq MYC DMSO rep3


title: S18_Control

value: Brain


title: ATAC-seq DMSO rep1


title: TRIP_expression_DNA_pool1


title: S17_Control


title: MKO_GM_H3K27me3_ChIPseq_Rep1


title: ChIP-seq IgG rep3

value: IgG


title: WT_DM_H3K27me3_ChIPseq_Rep2

description:
H3K27me3  ChIP-Seq of wildtype differentiating myocytes at 24h
WT_DM_K27me3.bw


title: ChIP-seq MYC DMSO rep1


title: WT_DM_H3K27me3_ChIPseq_Rep1


title: episomal_MPRA_RNA_rep1

extract_protocol:
RNA was harvested from transfected cells using the Purelink RNA Mini Kit (Invitrogen) according to the manufacturor's instructions.
RNA samples was first converted to cDNA by reverse transcription with the SuperScript IV First Strand Synthesis Systems (Invitrogen) using oligo dT primers. Barcodes were amplified from the respective plasmid/genomic DNA/cDNA samples using custom primers. Illumina sequencing adapters were then further added on 2 rounds of PCR with custom primers.

treatment_protocol: Wild-type K562 cells were transfected with a library of core promoters and RNA was harvested from the cells after 24 hours.

value: episomal core promoter library


title: S16_Control


title: ChIP-seq IgG rep2


title: patchMPRA_no_enhancer_RNA_rep3_2

treatment_protocol: K562 'landing pad' cell lines were cotransfected with CRE recombinase and a library of core promoters containing Lox sites for recombination into the 'landing pads'. After 3 days, the transfected cells were treated with 2mM Ganciclovir for 4 days. The live cells were then selected using MACS Dead Cell Removal Kit (Miltenyi Biotech) and allowed to grow until there were sufficient cells for DNA/RNA extraction.

value: core promoter library without enhancer integrated


title: ChIP-seq IgG rep1


title: WT_GM_H3K27me3_ChIPseq_Rep1

description:
H3K27me3  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_K27me3.bw


title: WT_GM_H3K27me3_ChIPseq_Rep2


title: SHSC30

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

data_processing:
Fastq files obtained from paired-end sequencing were aligned to the Rattus Norvegicus 6.0 ENSEMBL genome using standard parameters in STAR version 2.5.4a. Raw counts files were generated next using Htseq version 0.9.1 with -t exon option enabled to ensure transcript specificity. Differential gene expression was performed using DESeq2 version 1.26.0 using standard parameters. Counts were normalized using a negative binomial distribution as is standard with DESeq2. Experimental and control groups were compared using a Wald test in a pairwise comparison. Only genes with a multiple comparisons adjusted p value less than 0.05 were considered significant in the comparison. Gene Ontology analysis was performed using the PANTHER classification system and a statistical overrepresentation test on significantly changed genes.
Genome_build: mm10

source_name: Rat right ventricle

extract_protocol: The right ventricular free wall was dissected and snap frozen in liquid nitrogen. RNA extraction, quantification and sample integrity was performed by Novogene using Nanodrop spectrophotometer and Agilent 2100 bioanalyzer respectively.  Library preparation and sequencing were performed using an Illumina Platform PE150 by Novogene.

value: heart

value: Sugen Hypoxia (pulmonary hypertension)


title: SHSC29


title: MKO_DM_H3K4me1_ChIPseq_Rep2

description:
H3K4me1  ChIP-Seq of myod ko differentiating myocytes at 24h
MKO_DM_K4me1.bw


title: patchMPRA_no_enhancer_RNA_rep3_1

data_processing:
patchMPRA and episomal MPRA: Fastq reads were first filtered to only include reads that contain barcodes in the correct sequence context. Promoter barcodes were then decoded using the FREE barcodes software (Hawkins et al., 2018).
TRIP expression: Fastq reads were first filtered to only include reads that contain barcodes in the correct sequence context. TRIP random barcodes were further filtered such that they are at least 3 hamming distance apart.
TRIP mapping: The reads were aligned to the human hg38 genome using bwa (v0.7.17) with default parameters. The barcodes were then matched to the aligned reads. Only reads that were confidently aligned to one location was kept for subsequent analyses.
Genome_build: hg38
Supplementary_files_format_and_content: txt files are tab-separated files containing barcodes and the corresponding raw counts of each barcode. Bed files contain barcodes and the corrsponding location of the transposon integration.


title: S22_GBM

value: GBM


title: S11_GBM


title: SHSC25


title: episomal_MPRA_RNA_rep2


title: MKO_DM_H3K4me1_ChIPseq_Rep1


title: patchMPRA_no_enhancer_RNA_rep1


title: SHSC23


title: MKO_GM_H3K4me1_ChIPseq_Rep2

description:
H3K4me1  ChIP-Seq of myod ko proliferating myoblasts
MKO_GM_K4me1.bw


title: patchMPRA_no_enhancer_RNA_rep2


title: SHSC24


title: NC53

value: normal


title: MKO_GM_H3K4me1_ChIPseq_Rep1


title: patchMPRA_no_enhancer_DNA_rep3_1


title: NC54


title: liverTissue_RNA-seq_sample_SJLB794

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
rawCount-and-TPM_table_liver_RNA-seq.txt.gz
DESeqDatasets-GCcorrection-withRIN-onlyMedianTPMFilter_RNA_liver-SaintJude-20samples.RData

data_processing:
RNA-seq reads were adapter-trimmed using Trimmomatic
RNA-seq reads were aligned to the hg19 genome assembly using STAR v2.53 with default parameters
Using verifyBamID v1.1.1, we found no evidence of library contamination or sample swaps
Expression levels of GENCODE v19 genes were quantified using QoRTs v1.2.42. We classified genes as expressed if the median transcripts per million (TPM) across the 20 individuals was at least 1.
Genome_build: hg19
Supplementary_files_format_and_content: .bam files contain RNA sequence alignments to the hg19 genome (genomic coordinates) in a compressed format
Supplementary_files_format_and_content: The rawCount-and-TPM_table_liver_RNA-seq.txt.gz file contains gene expression values for 13,782 expressed genes (median transcripts per million>=1) for all 20 samples. The first 8 columns list information about the gene. Columns 9-28 contain the number of reads (rawCount) mapping to the gene in each of the 20 samples determined using QoRTs. Columns 29-48 contain the gene-level transcripts per million (TPM) across the 20 samples determined using QoRTs.
Supplementary_files_format_and_content: The .Rdata file 'DESeqDatasets-GCcorrection-withRIN-onlyMedianTPMFilter_RNA_liver-SaintJude-20samples.RData' contains R objects produced by DESeq2, known as DESeq datasets. The file contains two DESeq2 datasets: genes.dds containing the raw gene counts across the 20 samples, and genes.rlog containing the variance-stabilized gene counts. The raw gene counts can be extracted with the R command 'counts(genes.dds,normalized=F)'. The normalization factors used are the combination of RASQUAL GC offsets per gene and DESeq2 size factors. Sample covariates can be obtained with 'colData(genes.dds)'.

source_name: liver tissue

extract_protocol:
Total RNA was extracted from 20 frozen liver tissue samples using Trizol.
Strand-specific Illumina True-Seq protocol; Paired-end, strand-specific, poly-A RNA sequencing (RNA-seq) was performed on an Illumina NovaSeq 6000 with 2x151 bp cycles

tag: Sex

value: Male

tag: age

value: liver


title: liverTissue_RNA-seq_sample_SJLB786


title: liverTissue_RNA-seq_sample_SJLB797

value: Female


title: patchMPRA_no_enhancer_DNA_rep3_2


title: WT_DM_H3K4me1_ChIPseq_Rep2

description:
H3K4me1  ChIP-Seq of wildtype differentiating myocytes at 24h
WT_DM_K4me1.bw

tag: genotype

value: wild type


title: liverTissue_RNA-seq_sample_SJLB795


title: liverTissue_RNA-seq_sample_SJLB793


title: NC52


title: WT_DM_H3K4me1_ChIPseq_Rep1

value: skeletal muscle


title: patchMPRA_no_enhancer_DNA_rep2


title: NC36


title: liverTissue_RNA-seq_sample_SJLB753


title: patchMPRA_no_enhancer_DNA_rep1


title: liverTissue_RNA-seq_sample_SJLB715


title: NC34


title: patchMPRA_RNA_rep3

value: core promoter library integrated


title: liverTissue_RNA-seq_sample_SJLB713


title: patchMPRA_RNA_rep2


title: MKO_DM_H3K27ac_ChIPseq_Rep2

description:
H3K27ac  ChIP-Seq of myod ko differentiating myocytes at 24h
MKO_DM_K27ac.bw


title: WT_GM_H3K4me1_ChIPseq_Rep1

description:
H3K4me1  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_K4me1.bw


title: MKO_DM_H3K27ac_ChIPseq_Rep1


title: patchMPRA_RNA_rep1_2


title: liverTissue_RNA-seq_sample_SJLB684


title: liverTissue_RNA-seq_sample_SJLB767


title: patchMPRA_RNA_rep1_1


title: liverTissue_RNA-seq_sample_SJLB683


title: MKO_GM_H3K27ac_ChIPseq_Rep2

description:
H3K27ac  ChIP-Seq of myod ko proliferating myoblasts
MKO_GM_K27ac.bw


title: liverTissue_RNA-seq_sample_SJLB662


title: patchMPRA_DNA_rep3


title: patchMPRA_DNA_rep2


title: MKO_GM_H3K27ac_ChIPseq_Rep1


title: patchMPRA_DNA_rep1_2


title: WT_GM_H3K4me1_ChIPseq_Rep2


title: WT_DM_H3K27ac_ChIPseq_Rep1

description:
H3K27ac  ChIP-Seq of wildtype differentiating myocytes at 24h
WT_DM_K27ac.bw


title: liverTissue_RNA-seq_sample_SJLB651


title: patchMPRA_DNA_rep1_1


title: WT_GM_H3K27ac_ChIPseq_Rep2

description:
H3K27ac  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_K27ac.bw


title: AIOLOS_G159R_input

city: Bunkyo

first: Motoi

last: Yamashita

state: Tokyo

address: 1-5-45, Yushima

institute: Tokyo Medical and Dental University

data_processing:
Basecalls were performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using BWA (Burrows-Wheeler Aligner, version 0.7.17)  with default parameters.
Peaks were called using MACS2 (version 2.1.1) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: BED6+3 format file for each ChIP-seq sample.

growth_protocol: NALM-6 cells were maintained in RPMI 1640 medium supplemented with 10 % FBS and 1 % Penicillin-Streptomycin.

extract_protocol:
Lysates were purified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs)

treatment_protocol: NALM-6 cells were treated with 1 ng/ml doxycycline for 48 hours for the induction of AIOLOS proteins.


title: liverTissue_RNA-seq_sample_SJLB469


title: liverTissue_RNA-seq_sample_SJLB459


title: AIOLOS_WT_input


title: WT_GM_H3K27ac_ChIPseq_Rep1


title: MKO_DM_H3K4me3_ChIPseq_Rep2

description:
H3K4me3  ChIP-Seq of myod ko differentiating myocytes at 24h
MKO_DM_K4me3.bw


title: liverTissue_RNA-seq_sample_SJLB670


title: liverTissue_RNA-seq_sample_SJLB438


title: MKO_DM_H3K4me3_ChIPseq_Rep1


title: WT_DM_H3K27ac_ChIPseq_Rep2


title: A21T

city: chiba

first: sachi

last: oshima

state: chiba

address: 1-8-1 inohana chuo-ku

department: Grad. Sch. Med

institute: Chiba Univ

hyb_protocol: Agilent one-color Gene Expression Wash Pack (5188-5327 : Agilent) hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G4900DA Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were Images were quantified using Agilent Feature Extraction software version  12.1.1.1

source_name: HNSCC tissues

label_protocol: Agilent one-color Low Input Quick Amp Labeling Kit(5190-2305 :Agilent), protocol

growth_protocol: Normal cell culture medium DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

value: tongue


title: AIOLOS_G159R_NALM6_rep4

value: anti-FLAG antibody (M2, Sigma-Aldrich)


title: A19T


title: CAF1

source_name: CAF

value: oral floor


title: A14T


title: CAF2


title: liverTissue_RNA-seq_sample_SJLB365


title: A21N

source_name: normal oral epithelial tissues


title: MKO_GM_H3K4me3_ChIPseq_Rep2

description:
H3K4me3  ChIP-Seq of myod ko proliferating myoblasts
MKO_GM_K4me3.bw

value: myod KO


title: liverTissue_RNA-seq_sample_SJLB485


title: AIOLOS_G159R_NALM6_rep3


title: AIOLOS_G159R_NALM6_rep2


title: 37A

city: Shenyang

first: Pai

last: Pang

state: Liaoning

address: No. 117 Nanjing Bei Jie, Heping, Shenyang, Liaoning 110002, P.R. China

institute: China Medical University

description: MicroRNA expression in 37A

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: head and neck squamous cell carcinoma cell line

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: HNSCC cell lines PCI-4A/4B and PCI-37A/37B were cultured at 37 °C in a humidified atmosphere of 5% CO2 in the medium of Dulbecco's modified Eagle's medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Carlsbad, CA, USA), 100U/ml penicillin G and 100U/ml streptomycin.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: No treatment

tag: source

value: primary focus


title: AIOLOS_G159R_NALM6_rep1

tag: cell line


title: 37B

description: MicroRNA expression in 37B

value: metastasis


title: liverTissue_ATAC-seq_sample797

description:
The first three digits of raw and processed filenames represent the sample IDs. For each tissue sample, nuclei was extracted and divided into three portions prior to library preparation. This resulted in triplicate libraries for each tissue sample. If a library did not receive high enough sequencing depth, the same library was resequenced. Consequently, some libraries have two sets of raw fastq files, designated by RG1 and RG2. The fastq files are named as follows: 3 digits sample ID followed by a ., number indicating one of the three triplicate libraries followed by _, and RG1 or RG2 indicating the first round of sequencing (all samples) or second round of sequencing (only samples that didn't reach sufficient read depth on first sequencing run).
consensusNarrowPeaksWithPeakIDs-1bpOverlap-min3samples_liver-firstPass-20samples.bed
DESeq2Datasets_GC-correct_consensusNarrowPeaks-1bpOverlap-min3samples_liver-secondPass-20samples.RData

data_processing:
We trimmed ATAC-seq reads to a uniform length of 126 bp using cutadapt and trimmed sequencing adapters using CTA (https://github.com/ParkerLab/cta)
We merged readgroups for the same library, aligned reads to the hg19 human genome using BWA-MEM, selected properly paired autosomal alignments with high mapping quality (mapq>30) with samtools, and removed duplicate alignments using Picard.
We merged the replicate bam files for each individual and used ataqv to generate ATAC-seq quality metrics and confirmed ATAC-seq libraries corresponded to the correct genotypes using verifyBamID.
To identify consensus peaks, we converted the merged .bam files for each individual to .bed files using BEDTools, called narrow peaks for each individual using MACS2 with parameters –nomodel –shift -100 –extsize 200 –keep-dup all, and removed peaks overlapping blacklisted regions (Duke-excluded and Dac-blacklist from ENCODE). We then merged peaks across individuals using BEDTools and defined consensus peaks as merged peaks that shared at least 1 base with a peak present in samples from at least 3 individuals.
Genome_build: hg19
Supplementary_files_format_and_content: .bam files contain ATAC-seq high-quality autosomal alignments (HQAA) to the hg19 genome in a compressed format
Supplementary_files_format_and_content: .narrowPeak files contain peaks called on individual ATAC-seq samples (after merging across replicates) using MACS2. The columns of the file are: peak_chromosome, peak_start, peak_stop, peak_name, score, strand, fold enrichment, -log10(p_value), -log10(q_value), and peak summit location relative to peak_start.
Supplementary_files_format_and_content: .bw files contain ATAC-seq signal values produced by MACS2 and can be loaded into the UCSC genome browser for visualization.
Supplementary_files_format_and_content: The .Rdata file 'DESeq2Datasets_GC-correct_consensusNarrowPeaks-1bpOverlap-min3samples_liver-secondPass-20samples.RData' contains R objects produced by DESeq2, known as DESeq datasets. The file contains two DESeq2 datasets: peaks.dds containing the raw peak counts across the 20 samples, and peaks.rlog containing the variance-stabilized peak counts. The raw peak counts can be extracted with the R command 'counts(peaks.dds,normalized=F)'. The normalization factors used are the combination of RASQUAL GC offsets per peak and DESeq2 size factors. Sample covariates can be obtained with 'colData(peaks.dds)'.
Supplementary_files_format_and_content: The .bed file 'consensusNarrowPeaksWithPeakIDs-1bpOverlap-min3samples_liver-firstPass-20samples.bed' contains the consensus peaks present in at least 3 samples. The file contains a header describing each column.

extract_protocol:
Omni-ATAC-seq protocol. We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher, Cork Island), homogenized the tissue powder in ice cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol, pH 7.5) using a 1-mL dounce for 40 strokes, and rotated for 5 minutes at 4oC. We filtered the solution through a Miracloth (Calbiochem, San Diego, Ca USA), centrifuged at 1100g for 10 minutes at 4oC, washed the pellet with 250-uL NIB containing 0.5% Triton-X, centrifuged at 500g for 5 minutes at 4oC, and resuspended the pellet in 250-uL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4). After counting isolated nuclei, we pelleted 50,000 nuclei at 500g for 5 minutes at 4oC for each of three replicate ATAC-seq libraries per sample.
Libraries were prepared using Nextera kits (Illumina)


title: MKO_GM_H3K4me3_ChIPseq_Rep1


title: WT_DM_H3K4me3_ChIPseq_Rep2

description:
H3K4me3  ChIP-Seq of wildtype differentiating myocytes at 24h
WT_DM_K4me3.bw


title: liverTissue_RNA-seq_sample_SJLB348


title: AIOLOS_WT_NALM6_rep4


title: A19N


title: WT_DM_H3K4me3_ChIPseq_Rep1


title: A14N


title: 4B

description: MicroRNA expression in 4B


title: Total_mRNA_puf-8(ok302)_rep3

city: Hefei

first: Zheng

last: Xu

state: Anhui

address: Huangshan road

department: Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Genome_build: WS269
Supplementary_files_format_and_content: number of reads targeting each transcript

organism: Caenorhabditis elegans

source_name: young adult stage

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).

extract_protocol:
Total RNAs were isolated from young adult stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: temperature

value: 20oC on OP50

tag: developmental stage

value: young adult


title: Total_mRNA_puf-8(ok302)_rep2


title: 4A

description: MicroRNA expression in 4A


title: AIOLOS_WT_NALM6_rep2


title: AIOLOS_WT_NALM6_rep3


title: liverTissue_ATAC-seq_sample715

tag: tissue


title: Total_mRNA_puf-8(ok302)_rep1


title: WT_GM_H3K4me3_ChIPseq_Rep1

description:
H3K4me3  ChIP-Seq of wildtype proliferating myoblasts
WT_GM_K4me3.bw


title: AIOLOS_WT_NALM6_rep1


title: Total_mRNA_puf-8(ust223)_rep2


title: Total_mRNA_puf-8(ust223)_rep3


title: Cell line MT-CHC01

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Fastq files were subjected to quality control by means of FastQC.
Reads were trimmed using Cutadapt and then mapped to the human GRCh38 reference genome using Star (v2.0.8b). Gene expression levels have been evaluated using the FeatureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts

source_name: Human cell line

growth_protocol: DMEM/Knockout/F-12 culture medium with 10% FBS, penicillin and streptomycin (P/S), 37°C 5% CO2; MT-CHC01R1.5 was cultured in presence of 1.5 uM of Gemcitabine

extract_protocol:
Absolutely RNA miRNA kit (Agilent Technologies).
TruSeq Stranded Total RNA Library Prep Gold

tag: cell type

value: cholangiocarcinoma

tag: resistance to

value: sensible to chemotherapy


title: MKO_DM_CTCF_ChIPseq_Rep2

description:
CTCF  ChIP-Seq of myod ko differentiating myocytes at 24h
MKO_DM_CTCF.bw


title: liverTissue_ATAC-seq_sample485


title: liverTissue_ATAC-seq_sample459


title: Cell line MT-CHC01R1.5

value: gemcitabine and 5FU resistant


title: liverTissue_ATAC-seq_sample793


title: MKO_GM_CTCF_ChIPseq_Rep2

description:
CTCF  ChIP-Seq of myod ko proliferating myoblasts
MKO_GM_CTCF.bw


title: MKO_DM_CTCF_ChIPseq_Rep1


title: Cell line 82.3

value: multidrug resistance


title: Total_mRNA_puf-8(ust222)_rep3


title: liverTissue_ATAC-seq_sample348

value: Male

value: liver


title: liverTissue_ATAC-seq_sample438

value: Female


title: Total_mRNA_puf-8(ust222)_rep1


title: Total_mRNA_puf-8(ust222)_rep2