title: control (KD)

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Colorectal cancer

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer cell line

tag: genotype


title: CDU279 1

status: Public on Mar 25 2020

type: SRA

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

library_source: transcriptomic

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline
Reads were mapped using Salmon [reference Patroet al 2017] to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm38.cdna.all.fa file
Estimated transcript abundances from Salmon were imported into R using the tximeta package and analyzed for differential gene expression with edgeR

molecule: total RNA

organism: Homo sapiens

source_name: Fibroblasts

growth_protocol: Human cardiac fibroblasts medium (Cell Applications) + 10% Growth factor (Cell Applications)

extract_protocol:
Each sample was homogenized in TriPure Isolation Reagent (Roche, 11667165001) in lysing matrix tubes (Lysing Matrix D, MP Bio, 116913100). After guanidinium thiocyanate-phenol-chloroform extraction, RNA was further extracted on column (RNEasy, QuiaGEN, 74104) and treated with DNAse (DNAse-set, QuiaGEN, 79254) to reduce gDNA contamination. In total, RNA from each sample was quantified by Qubit RNA BR assay kit (Thermo Fisher Scientific, Q10211) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). RNA integrity was evaluated on the Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent, 5067-1511). All samples had RNA integrity number values ≥ 7.8. Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).
Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations. Libraries were equimolarly pooled and sequenced on a single lane on an Illumina NovaSeq 6000 platform.

treatment_protocol: transfection with a control siRNA or a siRNA targeting AMPKa1

tag: cell type

value: cultured cardiac fibroblasts

tag: treatment

value: transfected with a control siRNA 30nM


title: CDU279 3


title: SRD5A1 knockdown (Dox)

country: China

value: SRD5A1 knockdown

tag: cell line


title: CDU279 6

value: transfected with a siRNA targeting AMPKa1 30nM


title: MTCH2_KD-ChIP-R2

city: Toronto

first: Dilshad

middle: Hussain

last: Khan

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

library_source: genomic

data_processing:
Chip-seqdata has been aligned to the human genome using bowtie2.
Dipplicated reads and multiple loaci aligned reads have been discarded
Peaks were called using MACS2 peak caller.
Differentiallly binding peaks have been analyzed using edgeR package.
Genome coverage tracks have been created using the bamCoverage tool in the deeptools package.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are binary files that include the genome coverage tracks.  Bed files are 3 column text files that include the coordinates of the called peaks.

molecule: genomic DNA

growth_protocol: TEX cells were cultured in IMDM supplemented with 20% FCS, 100  units/mL streptomycin, 100 µg/mL penicillin,SCF (20 ng/mL), IL-3 (2 ng/mL), and L-glutamine (2 mM).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Samples were prepared as outlined by Takara Bio USA Inc’s ThruPLEX DNA-seq Kit user guide. Briefly, samples were normalized to 10ng of DNA input and topped up to 10ul with nuclease-free water. Samples were then mixed with 3ul of template preparation master mix and incubated at 22°C for 25 minutes, then 55°C for 20 minutes in a Veriti 96-well thermocycler (Thermo Fisher). Following template preparation, samples were mixed with 2ul of library synthesis master mix and incubated at 22°C for 40 minutes on the same cycler. Samples were prepared for library amplification as outlined in the user guide and indexed individually. From here, PCR cycles were optimized by adding 0.75ul of 10x SYBR green I nucleic acid gel stain (Thermo Fisher) to each sample. Once mixed, 10ul from each sample was removed and run on a CFX96 Touch Real-Time PCR cycler (Bio-Rad). Samples were normalized to 1/3 of their amplification curve and amplified on a Veriti 96-well thermocycler. Samples were topped up to 50ul with nuclease-free water prior to bead cleanup with AMPure XP beads (Beckman Coulter). Final library sizing and QC was evaluated on Agilent’s high sensitivity DNA kit run on the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: shRNA knockdown was performed with lentiviral infections. 2 mL of virus was added to 5 mL of media containing 5.0 x 106 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2). The following day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium with appropriate puromycin concentration (2.0 ug/ml) and subjected to selection for 3 days. After the selection period, knockdown cells were treated with or without with C646 (5 µM) for 3 days.

value: TEX

value: Acute Myeloid leukemia cell line

tag: genotype/variation

value: MTCH2 knockdown

tag: chip antibody


title: Ctrl-Input

value: control


title: H3K27me3 ChIP-seq in RCH-ACV cells

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: ChIP-seq performed using H3K27me3 antibody in RCH-ACV cells

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer v4.7

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

tag: tissue

value: Leukemia cell line (RCH-ACV)

value: Paediatric pre B-cell line derived from cALL with t(1;19)(q23;p13) translocation

value: Millipore 07-449


title: ChIP-seq Input for H3K27me3 in RCH-ACH cells


title: EZH2 ChIP-seq in RCH-ACV cells

description: ChIP-seq performed using EZH2 antibody in RCH-ACV cells

value: Cell Signalling Technology 5246/4


title: Ad-M3-mCherry+Ad-LacZ mCherry- A

city: Rehovot

first: Ofer

last: Elhanani

address: Herzl St 234

department: Dept. of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
M3_LacZ_Cherry_m_A
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted. All further steps were done using UTAP (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154)).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20 -m 30).
The remaining reads were mapped to the Mus musculus genome (mm10) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR . For further analysis genes were filtered out if their sum counts was less or equal to 5.
Normalization and differential expression analysis were performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value (BH) of less than 0.05 and at least 2-fold change.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RawUMIcounts.txt contains genes raw UMI counts.
Supplementary_files_format_and_content: Report-Deseq2.xlsx contains DESeq2 statistical data regarding 3921 differentially expressed genes in at least one of the contrasts between experimental groups: M3+LacZ (mcherry- vs. mCherry+); M3+REST (mCherry- vs. mCherry+); mCherry+ (M3+LacZ vs. M3+REST); M3+LacZ mCherry- vs. NGN3+LacZ GFP+; M3+REST mCherry- vs. NGN3+REST GFP+; GFP+ (NGN3+LacZ vs. NGN3+REST).

organism: Mus musculus

source_name: Primary pancreatic exocrine cells

growth_protocol: After isolation, exocrine cell clusters were infected with adenoviruses overnight in 6-well plates in Waymouth’s MB752/1 culture medium supplemented with 2.5% FBS, 2 mM glutamine 1%, 1% penicillin-streptomycin solution, 25 ng/ml murine EGF and 0.3 mg/ml trypsin inhibitor (Sigma, #T9128). After 24 hours, cell clusters were washed and plated on collagen coated plates. On day 5 after isolation, cells were dissociated and FACS sorted.

extract_protocol:
Cells were sorted into RLT lysis buffer and RNA was purified using RNeasy micro kit (QIAGEN #74004).
30 ng of purified RNA was used for library preparation with the bulk MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Infections with Ad-M3-mCherry, Ad-NGN3-GFP, Ad-LacZ and Ad-REST were carried overnight at a titer of 10*10^6 IFU/ml.

tag: strain

value: Primary pancreatic exocrine cells

tag: virus

tag: sorted population

value: mCherry-


title: ChIP seq Input for H3K4me1 in ML2 cells

description: ChIP-seq performed using H3K4me1 antibody in ML2 cells

value: Leukemia cell line (ML2)

value: Monocytic cell line derived from AML M4  after T-NHL/T-ALL with t(6;11)(q27;q23) translocation


title: Day 6 DSP-GFP

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

country: USA

institute: Boston Children's Hospital-Harvard Medical School

data_processing:
CellRanger 2.1.0 or CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 2.3  or Seurat 3.0.0.9000 was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
Seurat 3.0.0.9000 was used for integrative analysis of the day 6 and day 29 samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: gz file of filtered gene-barcode matrices

source_name: Skin Organoids

growth_protocol: Culture experiments were performed with the WA25 hESC line (passage 21-47), purchased from WiCell Research Institute, and the Desmoplakin-mEGFP (DSP-GFP) hiPSC line (passage 35-51), acquired from the Allen Institute for Cell Science and the Coriell Institute44. Cells were cultured on 6-well plates coated with Vitronectin Recombinant Human Protein (Invitrogen) at a concentration of 0.5 µg/cm2. Pluripotent stem cells were maintained in Essential 8 Flex (Gibco) medium with 100 µg/ml Normocin (hereafter, E8; Invivogen). The medium was replenished every other day. Cells were passaged at ~80% confluency (generally every 4-5 days) in medium containing 10 µM Y27632 (hereafter, Y; ROCK inhibitor that inhibits apoptosis, Stemgent). WA25 cells were passaged in clusters with 0.5 mM EDTA, and DSP-GFP cells were passaged as single cells with StemPro Accutase Cell Dissociation Reagent (hereafter, Accutase; Gibco). Fresh E8 medium was replenished twenty-four hours following passage. Detailed information concerning cell line specifics as well as validation and testing is available at: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/wa25.cmsx?closable=true and https://www.allencell.org/cell-catalog.html.

extract_protocol:
To dissociate WA25 and DSP-GFP into single cells, randomly selected day-6 organoids (n = 10) and day-29 organoids (n = 5) were pooled from each group. For day-48 WA25 cell aggregates, six representative skin organoids were collected, and the tail structure containing non-skin associated mesenchymal and neuronal cells was removed using two tungsten needles prior to dissociation in order to bias analysis toward skin tissue. Briefly, collected organoids were incubated with pre-warmed (37°C) TrypLE™ for total 8-30 min (depending on the organoid sizes and densities) in a 37°C incubator on a shaker at 65 rpm for a gentle swirl. During the incubation, the dissociation mixture was agitated every 3-10 min with gentle pipetting using wide-bore p1000 and p200 tips (Mettler-Toledo). By total 8-30 min of incubation, the tissue structure dissociated into a single cell suspension with no visible cell aggregation. Cold 3% BSA solution (Sigma-Aldrich) was added to the dissociated cell suspension in order to inactivate TrypLE enzymatic activity. The suspension was filtered through a 40 µm Flowmi™ cell strainer (Bel-Art™) in order to eliminate any debris. An additional three washes with cold 3% BSA solution were performed. Cells were resuspended in 3% BSA, and filtered through a 40 µm Flowmi™ cell strainer. Viability (live cell percentage) and live cell count was determined using Trypan Blue (used at 1:1 ratio) and Countess II. Final cell concentration was ~1,000 cells/µl and >90% viability.
Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and the NexSeq500 or NovaSeq 6000 sequencer (Illumina, Inc). Approximately 17,000 cells (targeting for 10, 000 cells) per sample were added to a single cell master mix, following the Chromium Single Cell 3’ Reagent Kits v2 User Guide, CG00052 Ver B (10x Genomics, Inc). Day-6 samples were processed using the Version 3 Chromium Single Cell 3’ Reagent Kits. Along with the single-cell gel beads and partitioning oil in separate wells of a Single Cell A Chip, the single cell reaction mixture was loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer. The resulting library was sequenced in a custom program for 26b plus 98b paired-end sequencing on an Illumina NextSeq500 or 28b plus 91b paired-end on Illumina NovaSeq 6000 to a read depth of >30,000 reads per cell.

treatment_protocol: For differentiation, pluripotent hPSC colonies were detached from the culture dish using Accutase. Once dissociated, hPSCs were collected as a single cell suspension in E8 medium containing 10 µM Y (hereafter, E8-10Y). Cell concentration was determined with an automated cell counter (Countess™ II Automated Cell Counter; Countess II, Life Technologies); Trypan blue (Gibco) was used at a ratio of 1:1 (Trypan blue:cell suspension) to distinguish dead vs. live cells. The appropriate number of live cells needed for an experiment was transferred into E8 medium containing 20 µM Y (hereafter, E8-20Y).  From the E8-20Y cell suspension, cells were distributed at a count of 3,500 cells in 100 µl per well into 96-well U-bottom plates (Thermo Scientific). Aggregation was aided by centrifugation at 110 rcf for 6 min. These cell aggregates were incubated in 37°C incubator under 5% CO2 for 48 hrs. Thus, we designated this timepoint as day -2. After 24 hrs incubation (at day -1), fresh 100 µl E8 medium was added to each well in order to dilute out Y and promote cell proliferation and aggregate growth. On day-0, to start differentiation, all cell aggregates were individually collected and transferred to new 96-well U-bottom plates in 100 µl of E6-based differentiation medium containing 2% Matrigel (Corning), 10 µM SB (Stemgent), 4 ng/ml basic-FGF (hereafter, FGF2; PeproTech), and 2.5 ng/ml BMP-4 (PeproTech) to initiate non-neural ectoderm formation. On day-3 of differentiation, to induce CNCC formation, 200 ng/ml LDN (BMP inhibitor, Stemgent), and 50 µg/ml of FGF2 were added in a volume of 25 µl per well, thus making the final volume 125 µl per well. On day-6 of differentiation, 75 µl of fresh E6 medium was added, bringing the final volume to 200 µl. Half of the media was changed (removal of 100 µl spent medium and addition of 100 µl fresh E6 medium) on days 8 and 10. On day-12, in order to induce self-assembly of epidermis, all aggregates were transferred into individual wells of 24-well low-attachment plates (Thermo Scientific) in 500 µl organoid maturation medium (OMM) containing 1% Matrigel. To maintain the aggregates in a floating culture for constant medium circulation, 24-well plates were placed on an orbital shaker shaking at a speed of 65 rpm in the 37°C incubator with 5% CO2. OMM is composed of Advanced DMEM/F12 (Gibco) and Neurobasal (Gibco) media at a 1:1 ratio, 1X GlutaMax™ (Gibco), 0.5X B-27 Minus Vitamin A (Gibco), and 0.5X N2 (Gibco) supplements, 0.1 mM 2-Mercaptoethanol (Gibco), and 100 µg/ml Normocin. On differentiation day-15, half of the spent medium was replenished (removal of 250 µl of spent medium and addition of 250 µl fresh medium) with OMM containing 1% Matrigel. Starting from day-18, half-medium was changed every three days (from day-18 to day-30) or every other day (from day-30 to day-150 or longer) with fresh OMM without Matrigel.

tag: tissue type

value: hiPSC-derived skin organoid

tag: passages


title: H3K4me1 ChIP-seq in ML2 cells


title: EZH2 ChIP-seq in THP1 cells

description: ChIP-seq performed using EZH2 antibody in THP1 cells

value: Leukemia cell line (THP1)

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: ChIP seq Input for EZH2 in THP1 cells


title: ChIP seq Input for H3K27me3 in SEM cells

description: ChIP-seq performed using H3K27me3 antibody in SEM cells

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: Day 6 WA25

value: hESC-derived skin organoid


title: Donor 2 Activated

first: David

last: Flores Santa Cruz

state: Oxfordshire

address: Roosevelt Drive

department: Diabetes and Inflammation Laboratory

institute: Wellcome Centre for Human Genetics

description: Sample 10

data_processing:
Mapping with minimap2 -x sr
Keep good quality reads with samtools view -h -u -q 30
Fix mate information with picard
Sort bam files with picard SortSam
Remove duplicates with picard MarkDuplicates and setting the param REMOVE_DUPLICATES=true
Use fseq to call peaks with params -b bff_35 -f 0
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq peaks in bed format

source_name: T-cells

growth_protocol: Purified CD4+ T cells were cultured for four hours in a humidifed incubator at 27 degrees centrigrde with 5% CO2 with and without stimulation with anti-CD3/Cd28 beads.

extract_protocol: Harvested cells were lysed and nuclei prepared for transposition with Tn5 enhanced transposase (Nextera Kit) at 37 degrees centrigrade for 30 minutes. Transposed purified DNA was amplified for 12 cycles of PCR incorporating dual indexes (Illumina)

tag: donor

tag: activation status

value: Activated

value: T-Cell


title: H3K27me3 ChIP-seq in SEM cells


title: Muscle_Bas_1044

type: RNA

city: Leeds

first: Pim

last: Knuiman

address: Clarendon Way

department: Biological Sciences

institute: University of Leeds

description:
Gene expression data from human muscle tissue
G314_H10_118_1044_B.CEL (B_A; p1044)

hyb_protocol: Total RNA was hybridized to human whole genome Genechip Human Gene 2 (Life Technologies, Bleiswijk, Netherlands)

scan_protocol: Sample labelling, hybdridization to chips, and image scanning were performed according manufacturer's instructions (Life technologies, Bleiswijk, Netherlands)

data_processing: The data were analyzed using limma R library

label: biotin

source_name: Vastus lateralus muscle, baseline

label_protocol: Total RNA was labelled using an Affymetrix WT plus reagent (Life Technologies, Bleiswijk, Netherlands)

extract_protocol: Total RNA was isolated from the skeletal muscle tissue by using Trizol reagent (Invitrogen, Breda, Netherlands)

treatment_protocol: Subjects consumed a 250-mL beverage containing either 29 casein protein or an isocaloric amount of carbohydrate immediately after cessation of each exercise session (3 per wk) and every day before sleep (7 per wk).

value: muscle

tag: Sex

value: male

tag: muscle name

value: Vastus lateralus

tag: time point

value: baseline


title: Muscle_Mid_1043

description:
Gene expression data from human muscle tissue
G314_H08_116_1043_M.CEL (M_P; p1043)

source_name: Vastus lateralus muscle, midterm

value: midterm


title: Donor 2 Not Activated

description: Sample 9

value: Not Activated


title: Donor 1 Activated

description: Sample 8


title: Muscle_Mid_1041

description:
Gene expression data from human muscle tissue
G314_H02_110_1041_M.CEL (M_P; p1041)


title: Muscle_Bas_1041

description:
Gene expression data from human muscle tissue
G314_H01_109_1041_B.CEL (B_P; p1041)


title: Muscle_Mid_1044

description:
Gene expression data from human muscle tissue
G314_H11_119_1044_M.CEL (M_A; p1044)


title: Muscle_Bas_1043

description:
Gene expression data from human muscle tissue
G314_H07_115_1043_B.CEL (B_P; p1043)


title: Day 48 WA25


title: Muscle_Mid_1042

description:
Gene expression data from human muscle tissue
G314_H05_113_1042_M.CEL (M_A; p1042)


title: Muscle_Mid_1040

description:
Gene expression data from human muscle tissue
G314_G11_107_1040_M.CEL (M_P; p1040)


title: Muscle_Bas_1038

description:
Gene expression data from human muscle tissue
G314_G04_100_1038_B.CEL (B_A; p1038)


title: Day 29 DSP-GFP


title: Muscle_Mid_1034

description:
Gene expression data from human muscle tissue
G314_F11_095_1034_M.CEL (M_A; p1034)


title: Muscle_Bas_1034

description:
Gene expression data from human muscle tissue
G314_F10_094_1034_B.CEL (B_A; p1034)


title: Muscle_Mid_1038

description:
Gene expression data from human muscle tissue
G314_G05_101_1038_M_2.CEL (M_A; p1038)


title: Muscle_Mid_1039

description:
Gene expression data from human muscle tissue
G314_G08_104_1039_M.CEL (M_A; p1039)


title: Muscle_Bas_1039

description:
Gene expression data from human muscle tissue
G314_G07_103_1039_B.CEL (B_A; p1039)


title: Muscle_Mid_1037

description:
Gene expression data from human muscle tissue
G314_G02_098_1037_M.CEL (M_P; p1037)


title: Muscle_Bas_1037

description:
Gene expression data from human muscle tissue
G314_G01_097_1037_B.CEL (B_P; p1037)


title: Muscle_Mid_1033

description:
Gene expression data from human muscle tissue
G314_F08_092_1033_M.CEL (M_A; p1033)


title: Muscle_Bas_1042

description:
Gene expression data from human muscle tissue
G314_H04_112_1042_B.CEL (B_A; p1042)


title: Muscle_Bas_1040

description:
Gene expression data from human muscle tissue
G314_G10_106_1040_B.CEL (B_P; p1040)


title: Muscle_Bas_1033

description:
Gene expression data from human muscle tissue
G314_F07_091_1033_B.CEL (B_A; p1033)


title: Donor 1 Not Activated

description: Sample 7


title: Day 29 WA25


title: Muscle_Mid_1032

description:
Gene expression data from human muscle tissue
G314_F05_089_1032_M.CEL (M_P; p1032)


title: Muscle_Bas_1032

description:
Gene expression data from human muscle tissue
G314_F04_088_1032_B.CEL (B_P; p1032)


title: MOLM-13 shMBNL1 #3

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
FASTQ sequence files were aligned to the human genome hg19 using STAR. AltAnalyze version 2.1.1 was used to derive gene expression and splicing profiles.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited-text

source_name: Leukemia cell line

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 supplemented with 10% FBS

extract_protocol:
After treatment, total RNA was isolated using the QIAGEN RNEasy Mini kit according to manufacturer's protocols.
Library construction was performed using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer's protocols. Purified and adapter-ligated cDNA was captured on a flowcell, and sequenced on an Illumina HiSeq 2500

treatment_protocol: MOLM-13 cells were transduced with lentiviral shRNA against MBNL1, and selected for 72h with puromycin

value: Acute myeloid leukemia

tag: translocation

tag: lentivirus


title: MOLM-13 shMBNL1 #2

tag: cell type


title: ATAC-seq in MLL-AF4 ALL patient blasts

description: ATAC-seq performed in MLL-AF4 ALL patient blasts

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer

source_name: MLL-AF4 ALL patient blasts

growth_protocol: Cells were continuously grown in RPMI with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)

value: MLL-AF4 ALL patient blasts

value: Bone marrow aspirate from a 15-year old MLL-AF4 ALL patient


title: ATAC-seq in THP1 cells

description: ATAC-seq performed in THP1 cells

source_name: Leukemia cell line (THP1)


title: MOLM-13 shMBNL1 #1


title: ChIP-seq Input in MLL-AF4 ALL patient blasts

description: ChIP-seq performed in MLL-AF4 patient blasts


title: MOLM-13 shNT #3

value: shNT


title: H3K27ac ChIP-seq in MLL-AF4 ALL patient blasts

description: ChIP-seq performed using H3K27ac antibody in MLL-AF4 patient blasts

value: Diagenode C15410196


title: H3K79me3 ChIP-seq in MLL-AF4 ALL patient blasts

description: ChIP-seq performed using H3K79me3 antibody in MLL-AF4 patient blasts

value: Diagenode C15410068


title: MOLM-13 shNT #2


title: Muscle_Mid_1031

description:
Gene expression data from human muscle tissue
G314_F02_086_1031_M.CEL (M_A; p1031)


title: MOLM-13 shNT #1


title: Muscle_Mid_1030

description:
Gene expression data from human muscle tissue
G314_E11_083_1030_M.CEL (M_A; p1030)


title: 8w_5

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on  [miRNA-4] Affymetrix Multispecies miRNA-4 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

organism: Rattus norvegicus

source_name: 8 weeks after vocal fold injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: All mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: For microarray profiling, the rat vocal fold total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, Canada) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using UV-Vis Spectrophotometer (Thermo, NanoDrop 2000, USA) at the absorbance of 260 nm. The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix GeneChip, Santa Clara CA, USA), which contains 65957 gene-level probe sets.

treatment_protocol: The vocal fold was injured by separating and removing the lamina propria from the thyroarytenoid muscle.

value: vocal fold

value: Sprague-Dawley

tag: treatment

value: 8 weeks after vocal fold injury


title: 8w_3


title: 8w_4


title: Muscle_Bas_1030

description:
Gene expression data from human muscle tissue
G314_E10_082_1030_B.CEL (B_A; p1030)


title: 8w_2


title: Muscle_Bas_1031

description:
Gene expression data from human muscle tissue
G314_F01_085_1031_B.CEL (B_A; p1031)


title: H3K4me3 ChIP-seq in MLL-AF4 ALL patient blasts

description: ChIP-seq performed using H3K4me3 antibody in MLL-AF4 patient blasts

value: Diagenode pAb-003-050


title: six_asthmatic_lead_24h

city: Nedlands

last: Iosifidis

state: Western Australia

address: 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

data_processing:
RNA-Seq libraries were sequenced on the Illumina® HiSeq 2500 platform using the RAPID mode
100bp single-end reads were sequenced at a depth of >3 million reads per sample, followed by bcl2fastq conversion and de-multiplexing
Single-end sequence reads were mapped to the reference genome (Homo sapiens GRCh38 v91 – Ensembl) using STAR (version 2.6.0c)
The count reads were then indexed to the metadata table using htseq-count (version 0.6.1p1)
To establish a signature gene expression profile from pAEC from children with or without asthma, DESeq2 (version 1.20.0) was used
Genome_build: Homo sapiens GRCh38 v91 – Ensembl
Supplementary_files_format_and_content: Excel spreadhseet includes gene counts for all samples

source_name: Primary airway epithelial cell

growth_protocol: Primary cell cultures were grown as per standard airway epithelial cell culture protocols.

extract_protocol:
Culture isolates were removed and RNA was harvested using QIAxol reagent. KAPA Stranded mRNA-Seq kit (KAPABiosystems (Roche)) was used for mRNA capture, with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard KAPABiosystems protocols

treatment_protocol: Cultures were starved overnight with bronchial epithelial growth medium minus epidermal growth factor. The next day, cultures were wounded in a single cross-hatch with a sterile p300 Gilson pipette tip. Cells were isolated from the leading edge of the wound (up to 3 rows of cells) or distal to the wound site, at times 0h and 24h post wounding.

value: tracheobronchial

value: Primary airway epithelial cell

tag: gender

tag: patient number

value: six

tag: diagnosis

value: asthmatic

tag: position

tag: time post wounding

value: lead

tag: lane

value: one


title: H3K4me1 ChIP-seq in MLL-AF4 ALL patient blasts

description: ChIP-seq performed using H3K4me1 antibody in MLL-AF4 patient blasts

tag: tissue

tag: chip antibody

value: Diagenode pAb-194-050


title: six_asthmatic_distal_24h

value: male

value: distal


title: six_asthmatic_lead_0h


title: H3K79me3 ChIP-seq in ALL primograft

description: ChIP-seq performed using H3K79me3 antibody in ALL primograft

value: Presentation ALL patient sample engrafted in mice and harvested from spleen


title: six_asthmatic_distal_0h


title: ChIP seq Input for H3K79me3 in THP1 cells

description: ChIP-seq performed using H3K79me3 antibody in THP1 cells

value: Leukemia cell line (THP1)

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: Muscle_Bas_1028

description:
Gene expression data from human muscle tissue
G314_E04_076_1028_B.CEL (B_P; p1028)

value: muscle

value: Vastus lateralus

value: baseline


title: five_asthmatic_lead_24h

value: five


title: 4w_5

source_name: 4 weeks after vocal fold injury

value: vocal fold

tag: strain

value: Sprague-Dawley

value: 4 weeks after vocal fold injury


title: 8w_1

value: 8 weeks after vocal fold injury


title: H3K79me3 ChIP-seq in THP1 cells

value: Diagenode C15410068


title: Muscle_Mid_1029

description:
Gene expression data from human muscle tissue
G314_E08_080_1029_M.CEL (M_A; p1029)

value: midterm


title: 4w_2


title: ChIP seq Input for H3K27me3 in THP1 cells

description: ChIP-seq performed using H3K27me3 antibody in THP1 cells


title: Muscle_Mid_1028

description:
Gene expression data from human muscle tissue
G314_E05_077_1028_M.CEL (M_P; p1028)


title: Muscle_Bas_1029

description:
Gene expression data from human muscle tissue
G314_E07_079_1029_B.CEL (B_A; p1029)


title: ChIP-seq Input for H3K79me3 in ALL primograft


title: five_asthmatic_distal_24h

value: tracheobronchial

value: Primary airway epithelial cell

value: asthmatic

value: one


title: 4w_3


title: Muscle_Mid_1027

description:
Gene expression data from human muscle tissue
G314_E02_074_1027_M.CEL (M_P; p1027)

value: male


title: 4w_4


title: 4w_1


title: Muscle_Mid_1026

description:
Gene expression data from human muscle tissue
G314_D11_071_1026_M.CEL (M_P; p1026)


title: 1w_5

source_name: 1 weeks after vocal fold injury

value: 1 weeks after vocal fold injury


title: H3K27me3 ChIP-seq in THP1 cells

value: Leukemia cell line (THP1)

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation

value: Millipore 07-449


title: Muscle_Bas_1026

description:
Gene expression data from human muscle tissue
G314_D10_070_1026_B.CEL (B_P; p1026)

value: muscle

value: Vastus lateralus

value: baseline


title: 1w_2

value: vocal fold

value: Sprague-Dawley


title: Muscle_Bas_1027

description:
Gene expression data from human muscle tissue
G314_E01_073_1027_B.CEL (B_P; p1027)


title: SEM_RNA_PROM1_shRNA_KD_replicate_3

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Genome_build: hg19

molecule: polyA RNA

source_name: Total RNA-seq in SEM cells with PROM1 shRNA KD

extract_protocol:
RNA was extracted from 10 million SEM cells using the Directzol RNA miniprep kit (Zymo R2050). Poly A purification was conducted using the NEB Poly(A) mRNA magnetic isolation module as per the manufacturer’s protocol.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7765).

treatment_protocol: Cells were untreated or shRNA expression was induced by treatment with 0.5 ug/ml doxycycline for 72h

value: Leukemia cell line (SEM)

value: SEM cells were transduced with lentiviral PROM1 shRNA and selected by puromycin. shRNA expression was induced with doxycycline at 0.5ug/ml for 72h.

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: 1w_4


title: five_asthmatic_distal_0h

value: tracheobronchial

value: five

value: distal


title: four_asthmatic_distal_24h

value: Primary airway epithelial cell

value: four

value: asthmatic

value: one


title: SEM_RNA_PROM1_shRNA_KD_replicate_2


title: five_asthmatic_lead_0h

value: male

value: lead


title: four_asthmatic_lead_24h


title: Muscle_Bas_1025

description:
Gene expression data from human muscle tissue
G314_D07_067_1025_B.CEL (B_A; p1025)

value: muscle


title: 1w_3

value: 1 weeks after vocal fold injury


title: four_asthmatic_distal_0h


title: Muscle_Mid_1023

description:
Gene expression data from human muscle tissue
G314_D02_062_1023_M.CEL (M_P; p1023)

value: Vastus lateralus

value: midterm


title: SEM_RNA_Control_replicate_3

source_name: Total RNA-seq in SEM cells

value: SEM cells were transduced with lentiviral PROM1 shRNA and selected by puromycin. Cells were not treated prior to harvest.


title: 1w_1

value: vocal fold

value: Sprague-Dawley


title: four_asthmatic_lead_0h


title: four_control_lead_24h

value: control


title: control_5

source_name: without treatment

value: without treatment


title: control_4


title: Muscle_Bas_1023

description:
Gene expression data from human muscle tissue
G314_D01_061_1023_B.CEL (B_P; p1023)

value: baseline


title: Muscle_Mid_1022

description:
Gene expression data from human muscle tissue
G314_C11_059_1022_M.CEL (M_P; p1022)


title: TIG-3 cells_vehicle_4d_DXR2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: DXR-induced senescent TIG-3 cells with vehicle for 4 days

data_processing:
Sequencing was performed on an Illumina HiSeq 2500/3000 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values

source_name: TIG-3 cells_vehicle_4d_DXR2

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: TIG-3 cells


title: four_control_lead_0h

value: tracheobronchial

value: Primary airway epithelial cell


title: four_control_distal_24h

value: four

value: distal


title: SEM_RNA_Control_replicate_1

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: Muscle_Bas_1022

description:
Gene expression data from human muscle tissue
G314_C10_058_1022_B.CEL (B_P; p1022)

value: muscle

value: male


title: D3_MF_Et

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

country: Germany

institute: Hans-Knoell-Institute Jena

data_processing:
Real Time Analysis Software (RTA) version 2.4.11 was used for base calling.
Sequenced reads were trimmed using trimmomatic v0.36. Trimmed reads were mapped to reference genome using Hisat2 v2.1.0.
Mapped reads were counted using featureCounts.
Genome_build: GRCh38.89
Supplementary_files_format_and_content: Comma-delimited text file include counts for each gene and sample

source_name: Macrophage

growth_protocol: Human monocytes were purified from PBMCs by magnetic cell sorting using CD14 microbeads and incubated at 37°C and 5 %CO2 atmosphere in RPMI-1640 supplemented with 10 % heat-inactivated FCS, 120 µg/ml Refobacin and 25 ng/ml GM-CSF. Macrophages for experiments were used at day 6.

extract_protocol:
RNA from MDM was extracted with RNeasy mini kit according to the manufacture's protocol.
Library construction was executed with the TruSeq® Stranded mRNA HT kit, according to the TruSeq® Stranded mRNA protocol.

treatment_protocol: Monocyte derived macrophages (MDM) were treated with etanercept (2µg/ml)  in presence or absence of A. fumigatus (MOI 0.5) for 6 h at 37°C under 5% CO2

tag: individual

value: donor 3

value: Macrophage

value: Etanercept 2 ug/mL


title: D3_MF_Et_AF

value: Etanercept 2 ug/mL; A. fumigatus ATCC 46645


title: D3_MF


title: SEM_RNA_Control_replicate_2

value: SEM cells were transduced with lentiviral PROM1 shRNA and selected by puromycin. Cells were not treated prior to harvest.


title: D3_MF_AF

value: A. fumigatus ATCC 46645


title: control_3

value: vocal fold

value: Sprague-Dawley

value: without treatment


title: Muscle_Mid_1024

description:
Gene expression data from human muscle tissue
G314_D05_065_1024_M.CEL (M_P; p1024)

tag: Sex

value: Vastus lateralus

value: midterm


title: three_control_lead_24h

value: tracheobronchial

value: Primary airway epithelial cell

value: female

value: three

value: control

value: lead

value: one


title: control_1


title: control_2


title: Muscle_Mid_1021

description:
Gene expression data from human muscle tissue
G314_C08_056_1021_M.CEL (M_P; p1021)

value: muscle

value: male

tag: muscle name


title: Muscle_Bas_1021

description:
Gene expression data from human muscle tissue
G314_C07_055_1021_B.CEL (B_P; p1021)

tag: time point

value: baseline


title: Muscle_Bas_1020

description:
Gene expression data from human muscle tissue
G314_C04_052_1020_B.CEL (B_P; p1020)


title: Muscle_Mid_1020

description:
Gene expression data from human muscle tissue
G314_C05_053_1020_M.CEL (M_P; p1020)


title: four_control_distal_0h

value: four

value: distal


title: Muscle_Mid_1019

description:
Gene expression data from human muscle tissue
G314_C02_050_1019_M.CEL (M_P; p1019)


title: three_control_distal_24h


title: TIG-3 cells_10 nM ARV82_4d_DXR2

description: DXR-induced senescent TIG-3 cells with 10 nM ARV82 for 4 days

source_name: TIG-3 cells_10 nM ARV82_4d_DXR2

value: TIG-3 cells


title: D2_MF_Et_AF

value: donor 2

value: Macrophage

value: Etanercept 2 ug/mL; A. fumigatus ATCC 46645


title: three_control_lead_0h


title: D2_MF_Et

value: Etanercept 2 ug/mL


title: three_control_distal_0h

value: tracheobronchial


title: Muscle_Bas_1019

description:
Gene expression data from human muscle tissue
G314_C01_049_1019_B.CEL (B_P; p1019)

value: Vastus lateralus


title: D2_MF_AF

value: A. fumigatus ATCC 46645


title: three_asthmatic_lead_24h

value: Primary airway epithelial cell

value: female

value: three

value: asthmatic


title: D2_MF


title: SEM_RNA_PROM1_shRNA_KD_replicate_1

value: Leukemia cell line (SEM)

value: SEM cells were transduced with lentiviral PROM1 shRNA and selected by puromycin. shRNA expression was induced with doxycycline at 0.5ug/ml for 72h.

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: three_asthmatic_distal_24h

value: one


title: Muscle_Mid_1025

description:
Gene expression data from human muscle tissue
G314_D08_068_1025_M.CEL (M_A; p1025)

value: muscle

value: male

value: midterm


title: Muscle_Mid_1016

description:
Gene expression data from human muscle tissue
G314_B11_047_1016_M.CEL (M_A; p1016)


title: D1_MF_Et_AF

value: donor 1

value: Macrophage


title: D1_MF_AF


title: D1_MF_Et

value: Etanercept 2 ug/mL


title: three_asthmatic_lead_0h

value: tracheobronchial

value: lead


title: three_asthmatic_distal_0h

value: distal


title: Muscle_Bas_1016

description:
Gene expression data from human muscle tissue
G314_B10_046_1016_B.CEL (B_A; p1016)

value: Vastus lateralus

value: baseline


title: two_control_lead_24h

value: Primary airway epithelial cell

value: two

value: control


title: D1_MF


title: two_control_distal_24h


title: Muscle_Mid_1014

description:
Gene expression data from human muscle tissue
G314_B05_041_1014_M.CEL (M_P; p1014)


title: two_control_lead_0h


title: Muscle_Mid_1015

description:
Gene expression data from human muscle tissue
G314_B08_044_1015_M.CEL (M_A; p1015)


title: e11.5_mouse_Hox13KO_Input

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

description: HI.5097.008.UDI0095_i7---UDI0095_i5.KMI-ID_input-A13-D13

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

extract_protocol:
HOXA11 ChIP was performed in forelimb buds of CD1 (wild type), Prx1Cre; RosaHoxa11/Hoxa11 (RA11KI) and Hox13-/- mice at E11.5 in the same conditions as previously described for HOX13 ChIP 7. Chromatin was cross-linked using a combination of disuccinimidyl glutarate (DSG) and formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4C with 5ug HOXA11 (SAB1304728, Sigma) antibody. The chromatin was coupled to the beads overnight at 4C. The immunoprecipitated samples were then sequentially washed in low salt (1% Triton, 0,1% SDS, 150 mM NaCl, 20 mM Tris (pH8), 2 mM EDTA), high salt (1% Triton, 0,1% SDS, 500 mM NaCl, 20 mM Tris pH8, 2 mM EDTA), LiCl (1% NP-40, 250 mM LiCl, 10 mM Tris (pH8), 1 mM EDTA) and TE buffer (50 mM NaCl, 10 mM Tris (pH8), 1 mM EDTA). The DNA was then purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

tag: strain background

value: mixed C57Bl/6 x 129

tag: genotype/variation

value: Hox13 KO

tag: developmental stage

value: forelimb bud

value: none (input)


title: Muscle_Bas_1015

description:
Gene expression data from human muscle tissue
G314_B07_043_1015_B.CEL (B_A; p1015)

value: muscle

value: male


title: two_asthmatic_lead_24h

tag: cell type

value: asthmatic

value: one


title: Muscle_Bas_1014

description:
Gene expression data from human muscle tissue
G314_B04_040_1014_B.CEL (B_P; p1014)


title: e11.5_mouse_distal_forelimb_HOX13KO_ATACseq_rep2

description:
ATAC_WT_vs_KO_diff_enrichment.txt
KO_rep2

data_processing:
ATAC-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads
Peak file for each replicates of WT distal and HOX13KO distal datasets were obtained using MACS v2.1.1.20160309
Peaks identified in at least one replicate of the four datasets were kept
Reads were count at the obtained position using analyzeRepeats.pl command from HOMER v4.9.1
Differential enrichment analysis was performed with getDiffExpression.pl from HOMER using Deseq2 settings
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files, Differential enrichment file

source_name: forelimb bud

extract_protocol:
Dissection of proximal and distal of forelimb buds from wild type embryos and distal forelimb buds of Hox13-/- embryos 7 were performed at E11.5. All samples for ATAC-seq were processed as previously described 15. Briefly, 50 000 cells were washed in PBS and incubated on ice for 30 minute in a hypotonic cell lysis buffer (0.1% w/v sodium citrate tribasic dehydrate and 0.1% v/v Triton X100) centrifugated (5 minutes at 2000g at 4°C). Cells were then incubated 30 minutes on ice in cell lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% v/v IGEPAL CA-630. After centrifugation (5 minutes at 2000g at 4°C) the resulting pellet of nuclei was re-suspended in transposase Master Mix (1.25 µl 10x TD buffer, 5 µl H2O and 6.5 µl of Tn5: Illumina Nextera Kit; FC-121-1031) and incubated for 30 minutes at 37°C. Samples were purified using MinElute PCR purification column (Qiagen). The eluted DNA was enriched and barcoded for multiplexing of samples using Nextera barcodes by PCR using Phusion kit.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2500 following the manufacturer's protocols to obtain 50bp paired end reads.

tag: age

value: mixed background C57Bl/6 x 129

tag: genotype

value: distal forelimb buds


title: two_asthmatic_distal_24h

value: tracheobronchial

tag: gender

tag: patient number

tag: diagnosis


title: iGFP-TFIISmut_b rep2

city: Gainesville

first: Kevin

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Arabidosis genome using bowtie v2.3.5
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al., Nature protocols, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plates were cultivated in the plant incubator (Percival Scientiﬁc) under long-day (LD) conditions (16 h light and 8 h dark) at 22 °C with light intensity 100 µmol m-2 s-1. Plants were grown on MS medium.

extract_protocol:
Using RNeasy R Mini Plant kit (Qiagen) according to the manufacturer’s manual.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Sample Preparation kit.

treatment_protocol: Exposure to 2 mM b-estradiol ("b") or EtOH (mock, "m") for 24 h prior to material harvesting.

tag: ecotype

value: Columbia

value: 10 DAS

tag: genetic background

tag: treatment (24 hours)

value: 2 mM b-estradiol

tag: inducibly expressed protein

value: GFP-TFIISmut (AT2G38560)


title: iGFP-TFIISmut_b rep1


title: Muscle_Mid_1013

description:
Gene expression data from human muscle tissue
G314_B02_038_1013_M.CEL (M_P; p1013)

tag: tissue

value: Vastus lateralus

value: midterm


title: e11.5_mouse_distal_forelimb_WT_ATACseq_rep1

description:
ATAC_WT_vs_KO_diff_enrichment.txt
WT_rep1

tag: strain

value: WT


title: Muscle_Bas_1013

description:
Gene expression data from human muscle tissue
G314_B01_037_1013_B.CEL (B_P; p1013)

source_name: Vastus lateralus muscle, baseline

tag: Sex

tag: muscle name

value: baseline


title: Muscle_Bas_1012

description:
Gene expression data from human muscle tissue
G314_A10_034_1012_B.CEL (B_A; p1012)

tag: time point


title: Muscle_Bas_1024

description:
Gene expression data from human muscle tissue
G314_D04_064_1024_B.CEL (B_P; p1024)


title: iGFP-TFIISmut_b rep3


title: iGFP-TFIISmut_m rep3

value: EtOH


title: two_asthmatic_distal_0h

value: Primary airway epithelial cell

value: two

tag: position

tag: time post wounding

value: distal

tag: lane


title: e11.5_mouse_Hox13KO_HOXA11_ChIPseq_rep1

description: HI.5097.008.UDI0094_i7---UDI0094_i5.KMI-ID_A11-A13-D13

tag: strain background

value: mixed C57Bl/6 x 129

tag: genotype/variation

value: Hox13 KO

tag: developmental stage

value: forelimb bud

tag: chip antibody

value: HOXA11 sigma:sab1304728


title: one_asthmatic_lead_24h

value: tracheobronchial

tag: cell type

tag: gender

value: male

tag: patient number

value: one

tag: diagnosis

value: asthmatic

value: lead


title: two_asthmatic_lead_0h


title: one_asthmatic_distal_24h


title: Muscle_Bas_1011

description:
Gene expression data from human muscle tissue
G314_A07_031_1011_B.CEL (B_A; p1011)

value: muscle

value: Vastus lateralus


title: iGFP-TFIISmut_m rep2

tag: ecotype

value: Columbia

tag: age

value: 10 DAS

tag: genetic background

tag: treatment (24 hours)


title: one_asthmatic_lead_0h

tag: tissue


title: e11.5_mouse_proximal_forelimb_WT_ATACseq_rep1

tag: strain

value: mixed background C57Bl/6 x 129

tag: genotype

value: Control RosaHoxa11/Hoxa11

value: proximal forelimb buds


title: e11.5_mouse_proximal_forelimb_WT_ATACseq_rep2


title: e11.5_mouse_forelimb_RA11KI_input

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

extract_protocol:
HOXA11 ChIP was performed in forelimb buds of CD1 (wild type) and Prx1Cre; RosaHoxa11/Hoxa11 (RA11KI) mice at E11.5 in the same conditions as previously described for HOX13 ChIP 7. Chromatin was cross-linked using a combination of disuccinimidyl glutarate (DSG) and formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4C with 5ug HOXA11 (SAB1304728, Sigma) antibody. The chromatin was coupled to the beads overnight at 4C. The immunoprecipitated samples were then sequentially washed in low salt (1% Triton, 0,1% SDS, 150 mM NaCl, 20 mM Tris (pH8), 2 mM EDTA), high salt (1% Triton, 0,1% SDS, 500 mM NaCl, 20 mM Tris pH8, 2 mM EDTA), LiCl (1% NP-40, 250 mM LiCl, 10 mM Tris (pH8), 1 mM EDTA) and TE buffer (50 mM NaCl, 10 mM Tris (pH8), 1 mM EDTA). The DNA was then purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

value: forelimb buds


title: Muscle_Mid_1010

description:
Gene expression data from human muscle tissue
G314_A05_029_1010_M.CEL (M_P; p1010)

source_name: Vastus lateralus muscle, midterm

tag: Sex

tag: muscle name

tag: time point

value: midterm


title: e11.5_mouse_distal_forelimb_WT_ATACseq_rep2

description:
ATAC_WT_vs_KO_diff_enrichment.txt
WT_rep2

value: WT

value: distal forelimb buds


title: Muscle_Bas_1010

description:
Gene expression data from human muscle tissue
G314_A04_028_1010_B.CEL (B_P; p1010)

value: baseline


title: Muscle_Mid_1011

description:
Gene expression data from human muscle tissue
G314_A08_032_1011_M.CEL (M_A; p1011)


title: e11.5_mouse_distal_forelimb_HOX13KO_ATACseq_rep1

description:
ATAC_WT_vs_KO_diff_enrichment.txt
KO_rep1


title: Muscle_Mid_1009

description:
Gene expression data from human muscle tissue
G314_A02_026_1009_M.CEL (M_A; p1009)


title: Muscle_Mid_1012

description:
Gene expression data from human muscle tissue
G314_A11_035_1012_M.CEL (M_A; p1012)


title: one_asthmatic_distal_0h

value: tracheobronchial

value: Primary airway epithelial cell

tag: position

tag: time post wounding

value: distal

tag: lane


title: iGFP-TFIIS_b rep3

value: 2 mM b-estradiol

tag: inducibly expressed protein

value: GFP-TFIIS (AT2G38560)


title: e11.5_mouse_forelimb_WT_input

tag: chip antibody


title: e11.5_mouse_forelimb_RA11KI_HOXA11_ChIPseq_rep1

value: HOXA11 sigma:sab1304728


title: one_control_distal_24h

tag: cell type

tag: gender

value: male

tag: patient number

value: one

value: control


title: one_control_lead_0h

tag: diagnosis

value: lead


title: one_control_lead_24h


title: one_control_distal_0h


title: iGFP-TFIISmut_m rep1

tag: ecotype

value: Columbia

tag: age

value: 10 DAS

tag: genetic background

value: EtOH


title: YY2: MCF7-EZH2

first: Yu

last: Yu

state: Hai Dian

institute: Peking University Health Science Center

hyb_protocol: According manufacturer's instructions, hybridization was carried out for the antisense RNA labeled with Cy5, including pre-hybridization, hybridization and hybridization washing.

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 Microarray Image Analysis Software for analysis. Expressed data were normalized using the Median normalization. Fold changes for differential expression were set as ≥ 2 and p ≤ 0.05. Finally, cluster analyses were used to classify lncRNAs based on their distinguishable expression in different samples.

source_name: breast cancer cell

label_protocol: The antisense RNA was generated using Amino Allyl messageAmp II kit (Life Technologies) and labeled with Cy5. Labeling efficiency can be calculated by the concentration of CyDye and RNA measured by K5500 micro-spectrophotometer. For good microarray result, labeling efficiency should be between 1.0~3.6.

growth_protocol: Breast cancer cells MCF7 were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco; Thermo Fisher Scientific, Waltham, MA USA) supplemented with 10% fetal bovine serum (FBS) at 37°C under 5% CO2 in a humidified incubator.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) according to manufacturer’s instructions.RNA quality and quantity was measured by using Agilent 2200 Bioanalyzer.

treatment_protocol: Empty vector and flag-EZH2 were transfected into breast cancer cell line MCF7 using Lipofectamine 2000 (Invitrogen).

tag: cell line

value: breast cancer

tag: genotype/variation

value: EZH2 high


title: iGFP-TFIIS_m rep2

tag: treatment (24 hours)


title: Muscle_Bas_1009

description:
Gene expression data from human muscle tissue
G314_A01_025_1009_B.CEL (B_A; p1009)

tag: tissue

value: muscle

tag: Sex

tag: muscle name

value: Vastus lateralus


title: iGFP-TFIIS_m rep1


title: Muscle_Mid_1008

description:
Gene expression data from human muscle tissue
G313_H07_023_1008_M_2.CEL (M_P; p1008)

tag: time point

value: midterm


title: iGFP-TFIIS_m rep3


title: YY1: MCF7-Control

value: EZH2 low


title: Muscle_Bas_1008

description:
Gene expression data from human muscle tissue
G313_H05_022_1008_B_3.CEL (B_P; p1008)

value: baseline


title: yfiQ-1

first: Zongmin

last: Du

address: No. 20, Fengtai Dongdajie Street

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Bowtie2-2.2.3. (Langmead, B. and S.L. Salzberg, 2012) was used to map clean reads to the  reference genome of Yersinia pestis biovar Microtus str. 91001 (NC_005810) to map clean reads to reference gene.
Genome_build: NC_005810
Supplementary_files_format_and_content: FPKM

organism: Yersinia pestis

source_name: bacterial culture

growth_protocol: The cobB and yfiQ mutants and the wild-type strain were individually inoculated in duplicate into fresh TMH medium from the overnight cultures and grown at 26°C to an OD620 of about 0.6. The cultures were pelleted, resuspended in equal amounts of fresh TMH medium and then cultivated at 26°C to mid-log phase (OD620 ≈ 1.2).

extract_protocol:
Total RNA was extracted using the Ambion PureLinkTM RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: yfiQ mutant of Yersinia pestis biovar Microtus str. 91001

tag: growth stage

value: mid-log phase


title: Muscle_Mid_1007

description:
Gene expression data from human muscle tissue
G313_G07_020_1007_M.CEL (M_A; p1007)


title: Muscle_Bas_1007

description:
Gene expression data from human muscle tissue
G313_G05_019_1007_B.CEL (B_A; p1007)


title: cobB-2

value: cobB mutant of Yersinia pestis biovar Microtus str. 91001


title: Muscle_Mid_1006

description:
Gene expression data from human muscle tissue
G313_F07_017_1006_M.CEL (M_A; p1006)

value: male


title: yfiQ-2


title: fsm3

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

institute: Shenyang Agricultural University

data_processing:
Illumina novaseq-PE150 sequencing platform used for sequencing cDNA libraries
All raw reads were filtered by removing reads with adaptors and low-quality reads. Clean reads were mapped to the reference database for the B. rapa genome (http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V3.0/) using HISAT2 software
Gene expression levels were calculated using the Fragments Per Kilo bases per Million fragments (FPKM) method in six libraries
The DESeq software was applied to analyze DEGs based on the FPKM-derived baseMean for each gene between samples. The screening criteria of DEGs were defined as |log2(FoldChange)| > 1 and P-value < 0.05
Genome_build: http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V3.0/
Supplementary_files_format_and_content: tab-delimited excel files include length, FPKM values,Chromosome,Start Site,End Site... for each gene

organism: Brassica rapa

source_name: the pistils

extract_protocol:
The pistils of Chinese cabbage were sampled, total RNA was extracted using Trizol reagent
cDNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Chinese cabbage

value: the pistils

tag: developmental stage

value: at the full-bloom stage

tag: genotype

value: mutant fsm1


title: iGFP-TFIIS_b rep2

value: Columbia

value: 10 DAS

value: 2 mM b-estradiol

tag: inducibly expressed protein

value: GFP-TFIIS (AT2G38560)


title: iGFP-TFIIS_b rep1


title: fsm2


title: cobB-1


title: fsm1


title: Muscle_Mid_1005

description:
Gene expression data from human muscle tissue
G313_E07_014_1005_M.CEL (M_P; p1005)

value: muscle


title: FT3

value: wild type 'FT'


title: Muscle_Bas_1005

description:
Gene expression data from human muscle tissue
G313_E05_013_1005_B.CEL (B_P; p1005)

value: Vastus lateralus


title: Experimental group 3

first: Yanyan

last: Zhao

address: 73 East Beijing Road, Nanjing 210008, P.R. China

institute: Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences

description: Gene expression in liver in mice exposed to 100 μg/L MC-LR for 12 months

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=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: liver 100 μg/L MC-LR 12 months

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: Mice were placed in a laboratory animal center and allowed to acclimate to the laboratory environment for 7 days before the experiment. Five mice were housed per cage. All cages were located in a temperature- and humidity-controlled room maintained under a 12:12 h light-dark cycle with temperatures ranging from 20 to 22 °C. Mice had free access to water and a standard rodent pellet diet.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus #9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mice in treatment were exposed to 100 μg/L microcystin-LR through drinking water for 12 months. The control mice were given normal sterile water for 12 months. At the end of exposure time, mice were weighed and anesthetized with 50 mg/kg BW sodium pentobarbital. The livers were immediately removed, weighed, and transferred into 2 mL tubes and stored in liquid nitrogen. The frozen tissue samples were then transferred into a -80 °C freezer until used for the following analyses.

tag: gender

value: liver


title: Experimental group 2


title: WT-2

value: Wild type strain Yersinia pestis biovar Microtus str. 91001


title: Muscle_Mid_1004

description:
Gene expression data from human muscle tissue
G313_D07_011_1004_M.CEL (M_A; p1004)

value: midterm


title: WT-1

value: mid-log phase


title: RNA-Seq-Col-Recovery-Rep1

first: Linhua

last: Sun

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
Adapter Sequences and poor-quality reads were removed by trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with flags --paired and --length 70 (minimum read length after trimming).
Then the clean reads were mapped to the Arabidopsis reference genome (TAIR10, https://www.arabidopsis.org) under the guide of annotation from Araport11 (https://www.araport.org) using TopHat2 with default parameters except options --min-intron-length 20 and --max-intron-length 5000.
Reads were then sorted, indexed and compressed by samtools.
Only uniquely mapped reads were kept for following analysis by samtools.
Here multi-mapped reads were disregarded because it is difficult to determine their real locations and uniquely mapped reads provide sufficient coverage and mappability.
Bigwig files were generated by bam2wig.py with options –u (skip non-unique hit reads) and --wigsum=10000000000 from RseQC.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig file and contain normalized reads coverage

source_name: Seedings

growth_protocol: All plants were grew on 1/2 Murashige and Skoog plates with 1% sucrose and 0.7% agar.

extract_protocol:
Total RNA was extracted from seedlings by using RNeasy Plant Mini Kit (Qiagen) with RNase-Free DNase (Qiagen)
Poly-A RNA-Seq library preparation and high-throughput sequencing were performed by Beijing Novogene Co. Ltd. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used to generate sequencing libraries following the manufacturer’s recommendations. The libraries were further sequenced by Illumina Hiseq 4000 platform and paired-end 150bp reads were generated.

treatment_protocol: Heat treatment: after 7 days growing under long photoperiod conditions at 22°C, the temperature rose to 37 °C in day and remained 22°C in night, last for (3 days+3 hours) 75 hours. Control treatment: 10 days + 3 hours growing under long photoperiod conditions at 22°C. Recovery condition: after heat treatment, grew 3 more days at 22°C.

tag: developmental stages

value: 13 days

tag: treatment

value: Recovery

tag: ecotype


title: Muscle_Bas_1004

description:
Gene expression data from human muscle tissue
G313_D05_010_1004_B.CEL (B_A; p1004)

data_processing: The data were analyzed using limma R library

extract_protocol: Total RNA was isolated from the skeletal muscle tissue by using Trizol reagent (Invitrogen, Breda, Netherlands)

value: male

value: baseline


title: FT1

value: Chinese cabbage

value: the pistils

value: at the full-bloom stage


title: RNA-Seq-Col-Recovery-Rep2


title: Experimental group 1


title: FT2


title: positive

city: Guangzhou

first: Chen

last: Zhipeng

address: Huangpu Avenue

institute: Jinan University

data_processing:
Basecalls performed using SOAPnuke v1.5.2
RNA-seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 genome using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts), version v2.1.0 with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）
Bowtie2 was used to compare clean reads to the reference gene sequence, and then RSEM was used to calculate the gene and transcript expression levels, version v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited csv files include RPKM values for Samples

source_name: epithelial

extract_protocol:
A549 cell total RNA was isolated from cells using Trizol reagent (TAKARA, Japan).
RNA libraries and RNA sequencing were performed by The Beijing Genomics Institute (BGI)

treatment_protocol: A549-TetOne-GATA6 cells were treated with(positive) or without DOX (negative)for 48 h. RNA libraries and RNA sequencing were performed by The Beijing Genomics Institute (BGI)

tag: cell type

value: lung cancer cells

value: lung


title: Control group 3

description: Gene expression in liver in mice fed with normal sterile water for 12 months

source_name: liver normal sterile water 12 months


title: Muscle_Bas_1003

description:
Gene expression data from human muscle tissue
G313_C05_007_1003_B.CEL (B_A; p1003)


title: Muscle_Bas_1006

description:
Gene expression data from human muscle tissue
G313_F05_016_1006_B.CEL (B_A; p1006)


title: RNA-Seq-Col-Heat-Rep1

value: 10 days

value: Heat


title: RNA-Seq-Col-Control-Rep2

value: Control


title: KPUM-YY1_BI-D1870

city: Kyoto

first: Junya

last: Kuroda

address: 465 Kajii-cho Kamigyo-ku

department: Division of Hematology and Oncology

institute: Kyoto Prefectural University of Medicine

description: KPUM-YY1 treated by BI-D1870

hyb_protocol: The biotynilated single stranded sense cDNA is then hybridized to GeneChip ClariomS Human (Affymetrix) using a GeneChip Hybridization Wash and Stain Kit, and Control Kit at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip Scanner 7G (Affymetrix).

data_processing: Data were analyzed using Affymetrix Transcriptome Analysis Console software ver. 4.0.0.25 and the SST-RMA method.

source_name: Mantle cell lymphoma-derived cell line

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Human mantle cell lymphoma cell lines were maintained in RPMI-1640 (Wako, Osaka, Japan) containing 10% fetal calf serum (Life Technologies, Carlsbad, CA), 2 mM L-glutamate, and penicillin/streptomycin at 37°C in humidified 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were treated with BI-D1870 (Cayman Chemical Company, Ann Arbor, MI) at IC80 for each cell line for 6 hours.

tag: cell line

tag: concentration


title: KPUM-YY1_Ctrl

description: KPUM-YY1 treated by DMSO

value: untreated


title: Muscle_Mid_1002

description:
Gene expression data from human muscle tissue
G313_B07_005_1002_M.CEL (M_A; p1002)

tag: tissue

value: muscle

value: Vastus lateralus


title: SiHa transfected with OV-Wnt11

first: XH

last: Li

state: Liaoning

address: No. 36, Sanhao Street

institute: China Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: SiHa transfected with OV-Wnt11

label_protocol: total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs  were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

value: SiHa

value: cervical cancer

tag: transfected with


title: Muscle_Mid_1003

description:
Gene expression data from human muscle tissue
G313_C07_008_1003_M.CEL (M_A; p1003)

tag: Sex

tag: muscle name

value: midterm


title: Muscle_Bas_1002

description:
Gene expression data from human muscle tissue
G313_B05_004_1002_B.CEL (B_A; p1002)

tag: time point


title: Control group 1

city: Nanjing

value: liver


title: Control group 2

value: male


title: RNA-Seq-Col-Control-Rep1


title: control


title: Human cervical cancer cell line SiHa

source_name: siha


title: RNA-Seq-Col-Heat-Rep2


title: Muscle_Mid_1001

description:
Gene expression data from human muscle tissue
G313_A07_002_1001_M.CEL (M_A; p1001)


title: Jeko-1_BI-D1870

description: Jeko-1 treated by BI-D1870


title: Hypoxia_rep1

status: Public on Mar 24 2020

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

description: YTHDF3 ab83716

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build mm9).
Bioinformatic and motif enrichment analysis was performed as described previously(Moore, M.J. et al. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 9, 263-293 (2014).)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files containing the peak number,the chromosomal location, depth and fold enrichment of the peaks obtained from the iCLIP experiments

growth_protocol: Cells were grown in RIPM-1640 media supplemented with 10% FBS

extract_protocol:
Cells were UV cross-linked and prepared as described previously (Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274-287 (2014)) and immunprecipitation of YTHDF3 using an anti-YTHDF3 antibody obtained from Abcam (ab83716).
RNA library constructed as described previously (Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274-287 (2014))

treatment_protocol: HTR8/Svneo cells were treated with or without 2% O2 for 12 h

tag: oxygen status

value: Hypoxia

tag: iclip antibody

value: anti-YTHDF3 antibody (ab83716).


title: Hypoxia_rep2

description: YTHDF3 ab83716


title: Human immortal cervical cell line H8


title: Normoxia_rep2

description: YTHDF3 ab83716

value: Normoxia


title: m1A Hypoxia IP - rep 2

data_processing:
Library strategy: m1A-Seq
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg38).
Bioinformatic and motif enrichment analysis was performed as described previously(Dominissini, D. et al. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441-446 (2016).)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files containing the peak associated genes,location and enrichment of the peaks obtained from the m1A-seq experiments

extract_protocol:
Total RNA was isolated from normoxia or hypoxia HTR8 cell lines. Polyadenylated RNA was further enriched from total RNA using a Dynabeads mRNA purification kit (Invitrogen).
RNA fragmentation, m1A-IP and library preparation were carried out according to previously published protocols(Dominissini, D. et al. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441-446 (2016).)

tag: m1a antibody

value: MBL life science D345-3


title: shYTHDF3 HTR8/Svneo

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files containing include RPKM values for each Sample

extract_protocol:
Total RNA was isolated from HTR8 cell lines infected with shControl or shYTHDF3 using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HTR8/Svneo cells infected with lentiviral shControl or shYTHDF3

tag: genotype/variation


title: Normoxia_rep1

description: YTHDF3 ab83716


title: shControl HTR8/Svneo

value: shControl


title: m1A Hypoxia IP - rep 1


title: Muscle_Bas_1001

last: Knuiman

institute: University of Leeds

description:
Gene expression data from human muscle tissue
G313_A05_001_1001_B.CEL (B_A; p1001)

value: baseline


title: m1A Normoxia input - rep2


title: m1A Normoxia IP - rep2


title: m1A Normoxia input - rep1


title: m1A Normoxia IP - rep1


title: Jeko-1_Ctrl

description: Jeko-1 treated by DMSO


title: SYSY_Normoxia_IP2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Library strategy: CLIP-exo sequencing
Sequencing reads were aligned to human hg19 reference genome by bowtie.
Bigwig files were generated using deepTools.
Peak calling was conducted using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: bed files for 6mA peaks

growth_protocol: Human HepG2 cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100× Pen Strep (Gibco, 15140).

extract_protocol:
Phenol/chloroform extraction and DNA precipitation with 1/10 volume of 5 M NaCl and 1 volume of isopropanol were performed. The obtained DNA pellet was dissolved with 3dH2O.
NEBNext® DNA Library Prep Master Mix Set for Illumina® E6040L was used to construct Illumina compatible DNA library.

value: normoxia

tag: molecule type

value: mtDNA


title: SYSY_Hypoxia_IP1

value: hypoxia


title: SYSY_Hypoxia_IP2


title: SYSY_Normoxia_IP1


title: NEB_Normoxia_IP


title: NEB_Hypoxia_IP


title: Input_Hypoxia2

value: input


title: Input_Hypoxia1


title: siMETTL4-2

data_processing:
Sequencing reads were aligned to human hg19 reference genome by HISAT.
RPKM values were generated by Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_table format for expression matrix

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

value: HepG2 Cell

tag: transfection


title: siCtrl-2

value: siCtrl


title: siCtrl-1


title: m1A Hypoxia input - rep 2


title: siMETTL4-1


title: vWAT, 20 weeks, control, rep 2

city: Lausanne

first: Richard

last: Coward

address: Dorothy Hodgkin Building, Whitson Street, Bristol

department: Bristol Medical School

institute: Bristol Royal hospital for Sick Children & University of Bristol

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads were filtered for low complexity with reaper (v. 15-065)
Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) using Mus musculus.GRCm38.86 gene annotation.
Genome_build: Mus musculus.GRCm38.86
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read counts

source_name: visceral (epididymal) adipose tissue

growth_protocol: C57/BL6 male, 4-wk-old (at time of sacrifice), mice were housed in  a 12 h light/12 h dark (LD) regimen  with water and food available ad libitum. All mice were fed  with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age they were either shifted to a high fat diet containing 60% in fat (D12492, Research Diet) or kept in control diet for 1, 8 and 20 weeks.  At each time time point, 20 mice were sacrified using CO2. Subcutaneous and viceral adipose tissue were immediately collected, snap-frozen in liquid nitrogen and kept at −80°C for RNA extraction and chromatin preparation. For chromatin preparation, aliquats of 4 grams of adipose tissue were homogenized on dry ice and immediately crosslinked in 45ml of PBS containing 0.5% formaldehyde. All animal care and handling was performed according to the Swiss law for animal protection

extract_protocol:
Trizol extraction of total RNA, followed by purification with Lipid RNeasy Mini Kit (Qiagen). After quality check,  total RNA from 4-10 individual mice of the same experimental group were pooled for RNA-seq.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: All mice were fed  with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age a total of 170 and 180 mice were put on HFD (D12492, Research Diet) and chow diet (D12450J, Research Diet, respectively. Mice were sacrified after 1, 8 or 20 week of diet.

tag: strain

tag: age

value: 26 weeks

tag: diet

value: Control chow diet (D12450J)

tag: time

value: 20 weeks

value: visceral (epididymal) adipose tissue


title: vWAT, 20 weeks, control, rep 1

value: male


title: m1A Hypoxia input - rep 1

tag: cell type


title: scWAT, 8 weeks, control, rep 5

source_name: subcutaneous (inguinal) adipose tissue

value: 14 weeks

value: 8 weeks

value: subcutaneous (inguinal) adipose tissue


title: scWAT, 8 weeks, high fat diet, rep 3

value: High fat diet (D12492)


title: scWAT, 8 weeks, control, rep 6


title: scWAT, 8 weeks, high fat diet, rep 5


title: scWAT, 8 weeks, high fat diet, rep 1


title: scWAT, 8 weeks, high fat diet, rep 6


title: scWAT, 8 weeks, control, rep 3


title: scWAT, 8 weeks, control, rep 2


title: Input_Normoxia1

tag: treatment


title: scWAT, 8 weeks, control, rep 1

tag: tissue


title: Input_Normoxia2


title: vWAT, 8 weeks, high fat diet, rep 6


title: vWAT, 8 weeks, high fat diet, rep 4


title: vWAT, 8 weeks, high fat diet, rep 3


title: vWAT, 8 weeks, high fat diet, rep 5


title: vWAT, 8 weeks, high fat diet, rep 2


title: vWAT, 8 weeks, control, rep 5


title: vWAT, 8 weeks, control, rep 6


title: vWAT, 8 weeks, control, rep 2


title: vWAT, 8 weeks, control, rep 3


title: vWAT, 8 weeks, high fat diet, rep 1


title: vWAT, 8 weeks, control, rep 4


title: vWAT, 8 weeks, control, rep 1


title: scWAT, 8 weeks, high fat diet, rep 4


title: scWAT, 8 weeks, high fat diet, rep 2


title: scWAT, 8 weeks, control, rep 4


title: scWAT, 1 week, high fat diet, rep 5

value: 7 weeks

value: 1 week


title: scWAT, 1 week, high fat diet, rep 3


title: scWAT, 1 week, control, rep 6


title: scWAT, 1 week, high fat diet, rep 4


title: scWAT, 1 week, high fat diet, rep 1


title: scWAT, 1 week, control, rep 4


title: scWAT, 1 week, control, rep 3


title: scWAT, 1 week, control, rep 2


title: scWAT, 1 week, control, rep 1


title: scWAT, 1 week, high fat diet, rep 2


title: vWAT, 1 week, high fat diet, rep 6


title: vWAT, 1 week, high fat diet, rep 5


title: vWAT, 1 week, high fat diet, rep 4


title: vWAT, 1 week, control, rep 6


title: vWAT, 1 week, high fat diet, rep 1


title: vWAT, 1 week, high fat diet, rep 2


title: vWAT, 1 week, control, rep 4


title: vWAT, 1 week, control, rep 3


title: vWAT, 1 week, control, rep 2


title: vWAT, 1 week, high fat diet, rep 3


title: vWAT, 1 week, control, rep 5


title: scWAT, 1 week, high fat diet, rep 6


title: vWAT, 1 week, control, rep 1


title: scWAT, 1 week, control, rep 5


title: L4

city: Santiago

first: Yessia

last: Hidalgo

state: Ñuñoa

address: Las Palmeras 3425

department: Sciences

country: Chile

institute: Universidad de Chile

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed  for adaptor sequence and  low-quality sequence, used CLC Genomics Workbench software version 7.0.4.
Mapped to Mus musculus GRCm38.p6 whole genome using salmon V0.8.0.
Deseq2 stadistical package was obtained for differential gene expression analysis.
Supplementary_files_format_and_content: Tab-delimited text files include total count values for each Sample.

source_name: BWF1 murine model of SLE_thymic B cells

extract_protocol:
Thymus are removed, cut and filtered, then B cells were selected with cell sorter BD FACSAriaII, and RNA was harvested using Trizol reagent. KAPA Stranded mRNA-Seq kit Illumina platform was used with 150 ng of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: New Zealand black/New Zealand white mice

value: 8 months

value: thymus

tag: cells type

value: B cells


title: L6

value: 7 months


title: L5


title: L1

source_name: control_thymic B cells

value: New Zealand white/BALB/c mice

value: non-lupus-susceptible control


title: L3


title: L2

value: 7.4 months


title: dKO sham 2

city: Tampa

first: Xuewei

last: Wang

state: FL

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

institute: University of South Florida

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads using Seqtk.
Hisat2 (version 2.0.4) was used to map the cleaned reads to the mouse GRCm38.p4 (mm10) reference genome with two mismatches.
Stringtie (version 1.3.0) was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: GRCm38.p4 (mm10)
Supplementary_files_format_and_content: Tab-delimited txt file containing FPKM for all samples

source_name: Lumbar 4 and 5 dorsal root ganglia

extract_protocol:
Total RNA of lumbar 4 and 5 dorsal root ganglia was isolated using RNeasy mini kit (Qiagen) following the manufacturer's manual.
Paired-end libraries were synthesized using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer's guide.

treatment_protocol: Sham surgery or sciatic nerve axotomy was performed on Myh9/10 double-floxed mice and Advillin-Cre:Myh9/10 double-floxed mice. Three days later, mice were sacrificed and lumbar 4 and 5 dorsal root ganglia were collected.

tag: genotype

value: Advillin-Cre:Myh9/10 double-floxed

value: Lumbar 4 and 5 dorsal root ganglia

value: Sham surgery


title: dKO SNI 2

value: Sciatic nerve axotomy


title: dKO SNI 1


title: WT SNI 1

value: Myh9/10 double-floxed


title: WT sham 2


title: dKO sham 1


title: WT SNI 2


title: WT sham 1


title: ChIP-seq-WT_Liver_STAT5_rep2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
The ChIP-seq analysis worklow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed by the application of bowtie aligner (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Homer software (Heinz et al., Mol. Cell, 2010) was applied  for the generation of bedGraph files.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of ChIP-seq

source_name: Liver

growth_protocol: Mouse mammary and kidney tissues were harvested at day one and ten of lactation (L1 and L10).

extract_protocol: Libraries for sequencing were prepared using standard Illumina protocols.

tag: developmental stage

value: Lactation day 10

value: wild-type

tag: antibody

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: ChIP-seq-WT_Liver_STAT5_rep1


title: ChIP-seq-Wap-Tbrg4het_Liver_H3K27ac_rep1

value: Wap-Tbrg4 fused

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq-E23-Tbrg4-L10-PolII-rep1

source_name: Mammary gland

value: RNA polymerase II (Abcam, ab5408)


title: ChIP-seq-SE-Tbrg4-Liver-H3K27ac_rep2


title: ChIP-seq-WT_Liver_H3K27ac_rep1


title: ChIP-seq-SE-Tbrg4-Liver-STAT5_rep1


title: ChIP-seq-E23-Tbrg4-L10-H3K27ac-rep1


title: ChIP-seq-SE-Tbrg4-Liver-STAT5_rep2


title: ChIP-seq-SE-Tbrg4-Liver-H3K27ac_rep1


title: ChIP-seq-E23-Tbrg4-L10-STAT5-rep1


title: ChIP-seq-Wap-Tbrg4het_Liver_STAT5_rep1


title: ChIP-seq-delCREB-L1-H3K4me3_rep2

value: Lactation day 1

value: H3K4me3 (Millipore, 07-473)


title: ChIP-seq-delCREB-L1-H3K4me3_rep1


title: ChIP-seq-delCREB-L1-H3K27ac_rep2


title: ChIP-seq-delCREB-L1-H3K27ac_rep1


title: ChIP-seq-delCREB-L1-CREB_rep1

value: phospho-CREB (Millipore, CS204400)


title: ChIP-seq-delCREB-L1-CREB_rep2


title: ChIP-seq-delCREB-L1-STAT5A_rep1


title: ChIP-seq-WT-L1-CREB_rep2


title: ChIP-seq-delCREB-L1-STAT5A_rep2


title: ChIP-seq-WT_Liver_H3K27ac_rep2


title: ChIP-seq-Wap-Tbrg4+/--L10-STAT5A_rep1


title: ChIP-seq-Wap-Tbrg4+/--L10-STAT5A_rep2


title: ChIP-seq-SE-Tbrg4-L10-STAT5A_rep2


title: ChIP-seq-WT-L1-CREB_rep1


title: ChIP-seq-WT-L10-PolII_rep2


title: ChIP-seq-SE-Tbrg4-L10-STAT5A_rep1


title: ChIP-seq-Wap-Tbrg4+/--L10-PolII_rep1


title: ChIP-seq-Wap-Tbrg4+/--L10-H3K27ac_rep1


title: scWAT, 20 weeks, high fat diet, rep 5

value: 26 weeks

tag: Sex

value: male

value: High fat diet (D12492)

value: 20 weeks

value: subcutaneous (inguinal) adipose tissue


title: ChIP-seq-SE-Tbrg4-L10-H3K27ac_rep2


title: scWAT, 20 weeks, high fat diet, rep 4


title: scWAT, 20 weeks, control, rep 5

value: Control chow diet (D12450J)


title: scWAT, 20 weeks, high fat diet, rep 1


title: scWAT, 20 weeks, high fat diet, rep 2


title: scWAT, 20 weeks, high fat diet, rep 3


title: scWAT, 20 weeks, control, rep 6


title: ChIP-seq-SE-Tbrg4-L10-PolII_rep1


title: scWAT, 20 weeks, control, rep 3


title: scWAT, 20 weeks, high fat diet, rep 6


title: scWAT, 20 weeks, control, rep 4


title: scWAT, 20 weeks, control, rep 2


title: scWAT, 20 weeks, control, rep 1


title: vWAT, 20 weeks, high fat diet, rep 5

value: visceral (epididymal) adipose tissue


title: vWAT, 20 weeks, high fat diet, rep 6


title: ChIP-seq-SE-Tbrg4-L10-PolII_rep2


title: vWAT, 20 weeks, high fat diet, rep 3


title: vWAT, 20 weeks, high fat diet, rep 4


title: vWAT, 20 weeks, high fat diet, rep 2


title: vWAT, 20 weeks, control, rep 6


title: vWAT, 20 weeks, high fat diet, rep 1


title: ChIP-seq-WT-L10-PolII_rep1


title: vWAT, 20 weeks, control, rep 4


title: vWAT, 20 weeks, control, rep 3


title: NCH644 Pb_H3K27ac ChIP

city: New York

first: Markus

last: Siegelin

institute: Columbia University Medical Center

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem
peaks were called using macs version 2.1.2 with the default setting
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using deepTools; Scores represent depth

growth_protocol: Glioblastoma cells were grown in 10% FBS/DMEM in 5% CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: NCH644 were treated with 0.5 uM for 24h harvested for ChIP.

tag: cell line

value: glioblastoma cells

tag: passages

tag: chip antibody


title: NCH644 Ctr_Input


title: LN229 PbR_Rpb1 ChIP2

treatment_protocol: U87 and LN229 were treated with 0.05 uM for 3 weeksand harvested for ChIP.


title: NCH644 Pb_Input


title: LPM_DMSO_Rep3

city: Hamilton

first: Brian

last: Coombes

state: ON

address: MDCL 2108, 1200 Main St W, McMaster University

department: Biochemistry

institute: McMaster University

data_processing:
Raw fastq files were trimmed with Cutadapt to remove Truseq adapter sequences
Trimmed reads were aligned against the Salmonella reference genome (NC_016810.1) using BWA (mem algorithm)
Read counts were quantified using featureCounts
DESeq2 was used for differential gene expression analysis
Genome_build: GCF_000210855.2
Supplementary_files_format_and_content: Fastq files contain raw unmapped reads for each sample, txt files contain read counts after alignment

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Bacterial culture

growth_protocol: Wild-type Salmonella was grown in LB until mid-log phase, then sub-cultured 1:100 into LPM for 5-6 h. 5 mL of each strain was pelleted by centrifugation before RNA extraction.

extract_protocol:
RNA was extracted with Trizol-chloroform separation, precipitated with isopropanol, washed with 75% ethanol, then treated with Dnase I.
Purified total RNA was treated with RiboZero for rRNA depletion and strand-specific dUTP sequencing was performed on an Illumina HiSeq 2000 platform to obtain single-end reads.

treatment_protocol: Samples were treated with DMSO (0.25%) or dephostatin (32 µg/mL) as indicated.

tag: growth media

value: LPM

tag: treatment group

value: DMSO

tag: replicate


title: LPM_Dephostatin_Rep1

value: Dephostatin


title: LPM_DMSO_Rep1


title: LPM_Dephostatin_Rep3


title: LPM_Dephostatin_Rep2


title: LPM_DMSO_Rep2


title: LN229 Ctr_Input2


title: LB_Dephostatin_Rep2

value: LB


title: LB_Dephostatin_Rep3


title: U87 PbR_Rpb1 ChIP2


title: LN229 Ctr_Rpb1 ChIP2


title: LB_Dephostatin_Rep1


title: LB_DMSO_Rep3


title: LB_DMSO_Rep1


title: LN229 PbR_Input


title: LB_DMSO_Rep2


title: U87 Ctr_Input2


title: U87 Ctr_Rpb1 ChIP2


title: NCH644 Ctr_H3K27ac ChIP