title: 202_Wang_HiC_BWX3270_30m_rif

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: text files contain 10kb bins of B. subtilis genome and normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files contain genome position and number of reads at each genome position

treatment_protocol:
Cells were growing in CH medium at 37˚C, rifampicin was added to 25ug/ml final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 25 ug/ml rifampicin for 30 min

value: parS-delta-9 no a.b., -94^ring parS no a.b.


title: CTCF_KD_ChIP-seq

status: Public on Sep 23 2019

type: SRA

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description:
CTCF_KD_peaks.bed pvalue = p<0.0025
RM_CTCF_CT_peaks.bed pvalue = p<0.001

library_source: genomic

data_processing:
Filtering: Unpaired sequencing reads were trimmed and subjected to proprietary quality filtration for the Ion Torrent platform (minimum quality threshold 20). Reads with sequence length ranging from 80 to 300 base were used for further analysis.
Alignment: Reads were mapped using bowtie2 against repeat-masked (hg38.fa.masked) and repeat-unmasked (hg38.fa) human genome. Reads were mapped end-to-end with default option.
RM Filtering: Reads were mapped to repeat-masked genome. All reads with ambiguous nucleotide (N) were removed and subjected to peak-calling to get RM CTCF peaks.
Peak calling: MACS2 (single sample peak calling).
Genome_build: hg38
Supplementary_files_format_and_content: bed files with MACS2 called peaks (*peaks.bed) on sample records or overlapping peaks from different conditions made by bedtools intersect -v found on series record.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10 % FBS at 37C and 5%CO2.

extract_protocol:
Lysates were clarified from sonicated nuclear lysates and protein-DNA complexes were isolated using specific antibodies.
The Ion Xpress(TM) Plus Fragment Library Kit (Cat. no. 4471269) was used for library preparation. All the steps were performed as per manufacturer’s instructions for sequencing on Ion Torrent S5 platform without any barcoding.

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) and CGGBP1-overexpressing (OE). For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin.

tag: antibody

value: SC-28198 and SC-271514 (Santa Cruz Biotechnology)

tag: cell line

tag: cggbp1 status

value: knockdown


title: PSPAO1_Rep2

city: VALENCIA

first: LOMAS LOPEZ

last: RODRIGO

address: C/ Eduardo Primo Yúfera, 3 (junto Oceanogràfic)

country: Spain

institute: CIPF

library_source: transcriptomic

data_processing:
Illumina reads were mapped to the Pseudomonas genome PA14 (NCBI reference sequence, NC_008463.1) and PAO1 (GeneBank, version AE004091.2) by TopHat (version TopHat v1.0.12)
Gene expression was done by the Htseq package, after removing rRNA mapping reads
Data was normalized using the RPKM conversion
Differential expression analysis was done using the Bioconductor package NOISeqBIO version 2.6.0.
Genome_build: PA14 (NCBI reference sequence, NC_008463.1) and PAO1 (GeneBank, version AE004091.2)
Supplementary_files_format_and_content: All processed txt data are single text tables with gene coverage (HTSeq-count).

molecule: total RNA

organism: Pseudomonas aeruginosa PA14

source_name: P. aeruginosa PA14

growth_protocol: Cultures were inoculated at an optical density at 600 nm (OD600) of 0.1 with overnight cultures, and strains were grown at 37°C with aeration in rich media (LB) to early stationary phase.

extract_protocol:
Total RNA was isolated from cell pellets equivalent to 2 OD600 units of bacterial culture using SV total RNA isolation system (Promega) folowing the manufacturer's instructions. Once isolated and prior to the library preparation, the integrity of RNA samples was assessed with Bioanalyzer system.
Libraries were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit from Illumina. 50 base pair single end sequence reads were generated using the Illumina HiSeq 2000 platform at the Vienna BioCenter Core Facility (http://www.csf.ac.at)

tag: sample type

value: cell pellets


title: MZ_RT0

city: atlanta

first: Jeffery

last: Streelman

address: 950 atlantic drive

country: USA

institute: georgia institute of technology

data_processing:
Raw sequence reads from RT and TB samples were quality controlled using the NGS QC Toolkit (Patel and Jain 2012). Raw reads with an average PHRED quality score below 20 were filtered out. The remaining reads were further trimmed of low-quality bases at the 3’ end.
Quality controlled reads for each sample were aligned to the Metriaclima zebra genome v1.1 (Brawand et al. 2014) using TopHat v2.0.9 (Kim et al. 2013).
The resulting TopHat2 output bam files were sorted and converted to sam files using samtools v0.19 (Li et al. 2009). Sorted sam files were used as input for the HTSeq-count v0.6.1 program to obtain fragment counts for each locus (Anders et al. 2014).
Fragment counts were scale-normalized across all samples using the calcNormFactors function in the edgeR package v3.6.8 (Robinson et al. 2010). Multidimensional scaling (MDS) plots were also produced via the edgeR package v.3.6.8 to determine the relative consistency among the replicates and samples. Scale-normalized fragment counts were converted into log2 counts per million reads mapped (cpm) with precision weights using voom and fit to a linear model using the limma package v3.20.9 (Smyth 2005; Law et al. 2014). Pairwise contrasts were constructed between RT and TB samples.
Genome_build: MZ_UMD1
Supplementary_files_format_and_content: raw read counts

organism: Maylandia zebra

source_name: M. zebra_Replacement Tooth

extract_protocol:
Animals were sacrificed and immediately dissected for RNA extraction. A ribbon approximately 1mm x 10mm of epithelium was removed labial to the outer row of teeth from the dentary of experimental animals using a #12 scalpel blade. The extra-osseous soft tissue was removed from the entire jaw to reduce the risk of TB containing epithelium carryover. The bone was then shaved down using a scalpel to expose the bony crypts and intraosseous RT were extracted with fine forceps.
Extracted tissue was quickly placed in RNAlater RNA Stabilization Reagent (Qiagen). Tissues were frozen in liquid nitrogen, homogenized using a mortar and pestle and placed in trizol. Following standard chloroform extraction RNeasy mini columns (Qiagen) were utilized to purify RNA for storage at -80ᴼC. Total RNA was quantified using Qubit (Molecular probes) and quality analyzed using the Agilent 2100 Bioanalyzer System for RNA library preparation. RNA input was normalized to 1µg and libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina- Kit A). Libraries were again quantified, quality assessed, and normalized for sequencing on the HiSeq 2500 Illumina Sequencing System.

tag: tissue

value: Replacement Tooth


title: 201_Wang_HiC_BWX3270_10m_rif

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq 500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, rifampicin was added to 25ug/ml final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature
None

tag: developmental stage

value: CH, 37 C, 25 ug/ml rifampicin for 10 min

tag: genotype

tag: restriction enzyme

value: HindIII


title: canine mammary tumour tissue [D1]

city: Guangzhou

first: Kun

last: Jia

address: Wushan Street

department: College of Veterinary Medicine

country: China

institute: South China Agricultural University

data_processing:
paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software.
Raw junction reads for all samples were normalized by total mapped reads and log2 transformed.
Differentially expressed circRNAs were identified by ttest between two groups, and fold change between two samples.
Genome_build: cm6
Supplementary_files_format_and_content: excel format

organism: Canis lupus familiaris

source_name: mammary

extract_protocol:
Canine mammary tumour tissues and their adjacent normal tissues were immediately flash frozen with liquid nitrogen and the total RNA was extracted from the samples using Trizol reagent (TaKaRa, Japan), following the manufacturer's instructions.
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: tumour


title: canine mammary tumour tissue's adjacent normal tissue [B2]

value: adjacent normal tissue


title: CTCF_CT_ChIP-seq

description:
CTCF_CT_peaks.bed pvalue = p<0.0025
RM_CTCF_CT_peaks.bed pvalue = p<0.001

value: endogenous


title: canine mammary tumour tissue [B1]


title: PSPAO1_Rep1


title: hela-siH2A.Z-RNA-seq_rep1

status: Public on Sep 22 2019

city: Beijing

first: Liwei

last: Zhang

address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

department: National Laboratory of Biomacromoluclues

institute: Institute of Biophysics

data_processing:
ChIP-seq: clean reads were mapped to hg38 and mm10 reference genomes using bowtie2 with default parameters. Unique aligments were then retained for further analysis.ChIP-seq and NS-seq peaks were called using MACS (version 1.4.2, p-value ≤ 1e-5) and PeakSeq (version 1.3.1, false discovery rate ≤ 0.005) against their corresponding native genomic input data with a shift size of 75 bp. Peaks of ORC1, with distances between which were less than 500 bp, were further merged using bed-tools.
RNA-seq: clean reads were mapped to hg38 and mm10 reference genomes using TopHat (version 2.2.0) with default parameters. Differential expression analysis were performed using cufflinks (version 2.2.0). Genes with |log2(ratio)|≥ 1 and FDR less than 0.05 were selected as differentially expressed genes.
NS-seq: clean reads were mapped to hg38 and mm10 reference genomes using bowtie2 with default parameters. Unique alignments were then retained. RNase-untreated sample was initially used to call peak as described for ChIP-seq. Then RNase treated sample was used to remove non-NS derived noise using Fisher's exact test, peaks with low signals after RNase digestion were remained as true NS peaks (FDR≤0.05, log2(untreated/treated)≥log2(1.5)).
Genome_build: hg38, mm10
Supplementary_files_format_and_content: bed file with at least three tab-delimited fields,representing chromsome name, start  and end.

source_name: Hela cell

growth_protocol: Hela cells were cultured in medium with 90% DMEM, 10%FBS, 1% Pen/Strep in standard incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP-seq: Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For native ChIP-seq, cells were collected and digested by MNase to get the mono-nucleosome. For BrdU-IP-seq, genomic ChIP-seq: DNA were extracted from cells and then sonicated to 200-500bp.
Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.
NS-seq: The genomic DNA was extracted by DNAzol. Then the DNA was denatured by boiling 10 mins at 100 °C and loaded onto 30ml neutral 5%-30% sucrose gradients. The mixture was centrifuged in SW28 rotor at 25000rpm for 20 hours. 1 ml-fraction was withdrawn from the top of the gradients. DNA fragments ranged from 0.5-2.5Kb were collected and purified. Half of the total purified DNA was treated with RNAase A.
NS-seq: The single strand DNA was converted to double strand DNA by BioPrime Array CGH Genomic Labeling System (life technology). DNA library for Immunila was prepared using a NEBNext Ultra DNA Library Prep Kit (NEB) according to the manufactory’s instruction.
RNA-seq: RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction.
RNA-seq: For RNA-seq, libraries were prepared according to the Illumina TruSeq protocol.

treatment_protocol:
ChIP-seq: Cells were transfected with siRNA oligos by lipo2000. Active CD4+ T cells were induced by by anti-CD3 and anti-CD28 for 72h from naïve CD4+ T cells of H2A.Zf/f and CD4creH2A.Zf/f mice
NS-seq: Cells were transfected with siRNA oligos by lipo2000. Active CD4+ T cells were induced by by anti-CD3 and anti-CD28 for 72h from naïve CD4+ T cells of H2A.Zf/f and CD4creH2A.Zf/f mice
RNA-seq: Cells were transfected with siRNA oligos by lipo2000.  Active CD4+ T cells were induced by by anti-CD3 and anti-CD28 for 72h from naïve CD4+ T cells of H2A.Zf/f and CD4creH2A.Zf/f mice

value: Hela cell

tag: transfection

tag: genotype/variation


title: hela-siNC-RNA-seq_rep2

value: siNC

value: wild type


title: hela-WT-input

description: genomic input

data_processing:
Library strategy: NS-seq
ChIP-seq: clean reads were mapped to hg38 and mm10 reference genomes using bowtie2 with default parameters. Unique aligments were then retained for further analysis.ChIP-seq and NS-seq peaks were called using MACS (version 1.4.2, p-value ≤ 1e-5) and PeakSeq (version 1.3.1, false discovery rate ≤ 0.005) against their corresponding native genomic input data with a shift size of 75 bp. Peaks of ORC1, with distances between which were less than 500 bp, were further merged using bed-tools.
RNA-seq: clean reads were mapped to hg38 and mm10 reference genomes using TopHat (version 2.2.0) with default parameters. Differential expression analysis were performed using cufflinks (version 2.2.0). Genes with |log2(ratio)|≥ 1 and FDR less than 0.05 were selected as differentially expressed genes.
NS-seq: clean reads were mapped to hg38 and mm10 reference genomes using bowtie2 with default parameters. Unique alignments were then retained. RNase-untreated sample was initially used to call peak as described for ChIP-seq. Then RNase treated sample was used to remove non-NS derived noise using Fisher's exact test, peaks with low signals after RNase digestion were remained as true NS peaks (FDR≤0.05, log2(untreated/treated)≥log2(1.5)).
Genome_build: hg38, mm10
Supplementary_files_format_and_content: bed file with at least three tab-delimited fields,representing chromsome name, start  and end.


title: hela-siH2A.Z-10min_rep1

tag: time point

value: 10 minutes

value: BrdU

tag: antibody (vendor, catalog)

value: BD, BD44


title: hela-siH2A.Z-RNA-seq_rep2


title: hela-siNC-BrdU-3h

value: 3 hour


title: hela-siNC-BrdU-6h

value: 6 hour


title: hela-siH2A.Z-1h

value: 1 hour


title: hela-siH2A.Z-6h


title: hela-siH2A.Z-3h


title: hela-siH2A.Z-genome

description:
native genomic input
siNC_NS_peaks.bed


title: hela-siNC-BrdU-10min_rep1


title: hela-siNC-BrdU-1h


title: hela-siNC-genome

description:
native genomic input
siNC_NS_peaks.bed


title: hela-siH2A.Z-NS

description:
nascent strand DNA
siNC_NS_peaks.bed


title: hela-siH2A.Z-Rnase-treated-NS

description:
nascent strand DNA
siNC_NS_peaks.bed


title: CTCF_OE_ChIP-seq

description:
CTCF_OE_peaks.bed pvalue = p<0.005
RM_CTCF_CT_peaks.bed pvalue = p<0.001

value: SC-28198 and SC-271514 (Santa Cruz Biotechnology)

value: overexpression


title: hela-siNC-NS_rep2

description:
nascent strand DNA
siNC_NS_peaks.bed


title: hela-siNC-NS_rep1

description:
nascent strand DNA
siNC_NS_peaks.bed


title: hela-siNC-Rnase-treated-NS_rep1

description:
nascent strand DNA
siNC_NS_peaks.bed


title: CL6_24h

city: Aurora

first: Olivia

middle: S

last: Rissland

state: CO

address: 12801 E 17th Avenue

department: Department of Biochemistry and Molecular Genetics

institute: RNA Bioscience Initiative, University of Colorado Denver School of Medicine

data_processing:
Basecalling was performed using Illumina Real-Time Analysis v1.18.54 or later, and bcl2fastq2 v2.17 was used to convert to fastq format (by The Center for Applied Genetics (SickKids)).
Library quality was assessed using FastQC v0.11.5
Reads were trimmed and clipped for Illumina adapters using Trimmomatic v0.36 with the following settings: -phred33 ILLUMINACLIP: TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were aligned to the indexed hg38+dm6+sacCer3 genome using STAR version 2.5.2 with the following non-default settings: --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.85 --alignIntronMax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts.
HTSeq version 0.6.1 was used to quantify gene counts from aligned BAM files using the following settings: --order=pos --stranded=reverse --minaqual=10 --mode=intersection-strict.
Genome_build: hg38 + dm6 + sacCer3
Supplementary_files_format_and_content: comma separated values files containing read counts for human, fly, or yeast genes in each sample

molecule: polyA RNA

source_name: HEK293T Cells

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Media (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution. Cell lines were cultured at 37°C in a humidified incubator with 5% CO2. Cell lines were maintained under ~80% confluence by regular trypsinization and re-plating.

extract_protocol:
Cells were harvested at 1, 2, 4, 8, 12, and 24 hours after addition of 4SU. Harvesting was performed by dislodging cells off the plate during two washes with cold PBS followed by spinning at 1,000G for 5 minutes at 4°C. Cell pellets were resuspended in 1mL TRI-Reagent and extracted according to manufacturer instructions. Extracted samples were spiked with Drosophila melanogaster and Saccharomyces Cerevisiae RNA. For timepoints, 4SU labeled RNA was purified as described in detail in the published methods. In addition, an unpurified subset of the 24 hour RNA was taken as the “Steady State” sample.
Purified 4SU labeled RNA or unpurified total RNA from the 24-hour time point was used to prepare sequencing libraries using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina), according to manufacturer’s instructions. Adapter-ligated fragments were enriched with 14x PCR cycles. ~16-22 samples were multiplexed on a single lane in an Illumina HiSeq 2500.

treatment_protocol: Freshly thawed HEK293T hORFeome cell lines were seeded into DMEM + FBS culture media such that they attained ~50% confluence on the day of the time course. Media was replaced with DMEM + 10% FBS + 100µM 4SU reconstituted in DMSO. Cells were harvested at 1, 2, 4, 8, 12, and 24 hours after addition of 4SU.

tag: treatment

value: Untreated

tag: horfeome cell line

value: 24 hour


title: hela-siH2A.Z-ORC1_rep2

value: streptavidin (Invitrogent, M280)


title: CL6_SteadyState

value: Steady State


title: hela-siNC-Rnase-treated-NS_rep2

description:
nascent strand DNA
siNC_NS_peaks.bed


title: hela-siNC-RNA-seq_rep1


title: hela-siNC-BrdU-10min_rep2


title: hela-siNC-ORC1_rep2


title: hela-siH2A.Z-10min_rep2


title: CL6_12h

value: 12 hour


title: hela-siNC-ORC1_rep1


title: CL6_4h

value: 4 hour


title: CL6_2h

value: 2 hour


title: hela-siH2A.Z-H4K20me3_rep2

value: Hela cell


title: hela-siH2A.Z-ORC1_rep1


title: CL6_1h


title: hela-siH2A.Z-H4K20me2_rep2


title: CL5_24h


title: CL5_SteadyState


title: hela-siH2A.Z-H4K20me1_rep2


title: CL5_4h


title: hela-siH2A.Z-H4K20me2_rep1


title: CL5_12h


title: hela-siH2A.Z-H4K20me1_rep1


title: CL5_2h


title: hela-siNC-native-input

value: siNC

value: wild type


title: CL5_1h


title: CL3_SteadyState


title: hela-siH2A.Z-native-input


title: hela-siNC-H4K20me3_rep2


title: hela-siNC-H4K20me3_rep1


title: hela-siNC-H4K20me2_rep1

description: siNC H4K20me2_peaks.bed


title: CL3_4h


title: CL3_12h


title: hela-siNC-H4K20me1_rep2


title: hela-siNC-H4K20me2_rep2

description: siNC H4K20me2_peaks.bed


title: CL3_1h


title: hela-siNC-H4K20me1_rep1


title: hela-siH2A.Z-H2A.Z_rep2


title: hela-siH2A.Z-H2A.Z_rep1


title: hela-siH2A.Z-H4K20me3_rep1


title: CL2_24h


title: CL2_SteadyState


title: CL2_4h


title: hela-siNC-H2A.Z_rep1


title: CL1_12h


title: CL2_2h


title: CL2_1h


title: hela-siNC-H2A.Z_rep2


title: E18.5-T1 (Wt1)

city: Ramat Gan

first: Achia

last: Urbach

address: Ramat Gan

department: Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

data_processing:
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Sequenced reads were mapped to the Mus Musculus genome version GRCm38 using STAR (v2.4.2a) (using alignEndsType EndToEnd option).
Counting reads on genes annotated in ensembl release 92, was done with HTSeq-count (version 0.6.1p1)
Normalization of read counts and differential analysis were computed using Deseq2 (version 1.10.1)
Genome_build: GRC38
Supplementary_files_format_and_content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: Excel file includes the normalized counts (DESeq2 normalization)

organism: Mus musculus

source_name: E18.5 embryonic lung

growth_protocol: Mice were hold in a SPF units. Crossing were preformed as described above. The day of finding plug was designated as E0.5. Pregant females were sacrified by CO2 at different time points as described and the lungs were harvested.

extract_protocol:
Embryonic lungs were harvested from the embryos and were subjected to RNA extraction using regular Trizol protocol
Inhouse poly A based RNA seq

treatment_protocol: Doxcycyclin was added to the driniking water at a concentration of 1g/L from E0.5

tag: lin28a expression

value: expression in the mesenchymal cells

tag: embryonic day


title: E18.5-T3 (Nkx2.1)

value: expression in the lung epithelial cells


title: Pl4.4EGI1.SS

treatment_protocol: Freshly thawed HEK293T hORFeome cell lines were seeded into DMEM + FBS culture media such that they attained ~50% confluence on the day of the time course. Media was replaced with DMEM + 10% FBS + 100µM 4SU reconstituted in DMSO. Cells were harvested at 1, 2, 4, 8, 12, and 24 hours after addition of 4SU. For translation inhibition experiments, hORF cell line 1 or cell line 4 cells growing in 10mL DMEM + FBS were pre-treated with either 0.1% DMSO or 100µM 4EGI-1 dissolved in DMSO for 1 hour. Following this, 100µM 4SU was added to media for all plates and the time course was performed as described above.

value: HEK293T Cells


title: CL3_24h


title: E18.5-T1 (Nkx2.1)


title: Pl4.4EGI1.12h


title: E18.5-T2 (Nkx2.1)


title: CL3_2h


title: E18.5-T2 (Wt1)


title: E18.5-T5 (Vasa)

value: Global expression


title: Pl4.4EGI1.8h

value: 8 hour


title: Pl4.4EGI1.4h


title: E18.5-T3 (Vasa)


title: Pl4.4EGI1.2h


title: E18.5-T4 (Vasa)


title: E18.5-T2 (Vasa)


title: Pl4.4EGI1.1h

value: 1 hour


title: Pl1.4EGI1.24h


title: Pl1.4EGI1.SS


title: E18.5-T1 (Vasa)


title: Pl4.4EGI1.24h


title: E18.5-C4

value: None (control)


title: siCon rep3

city: Daejeon

first: Jimyung

last: Seo

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology (KAIST)

data_processing:
The raw sequencing data were quality-checked by FastQC and filtered using Trimmomatic (version 0.36) tool.
The trimmed data were subsequently aligned to human reference genome (GRCh37) using Tophat2 (ver 2.1.1).
The aligned read counts for each gene were calculated by HTSeq (version 0.9.1).
The read count data were filtered, resulting in remaining transcripts with ENTREZ gene IDs and at least 1 count-per-million reads (CPM) in at least one sample.
Genome_build: Alignment was to human reference genome (GRCh37).
Supplementary_files_format_and_content: Tab-delimited text file includes count-per-million reads (CPM) for each sample.

source_name: LATS1/2-null RPE1_control siRNA

growth_protocol: LATS1/2-null RPE1 cells were cultured in DMEM/F12 (Welgene) supplemented with 10 % FBS and 1 % penicillin/streptomycin.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control or MK5 siRNAs were transfected with Lipofectamine RNAiMAX (Invitrogen).

tag: cell type

value: non-transformed epithelial cells

tag: editing

value: LATS1 and LATS2 inactivation by the CRISPR-Cas9 system


title: siCon rep2

tag: cell line


title: siMK5 rep1

source_name: LATS1/2-null RPE1_MK5 siRNA


title: Pl1.4EGI1.8h


title: E18.5-C5


title: siMK5 rep2


title: mouse-active-T-cell-siH2A.Z-NS

description: nascent strand DNA

source_name: active T cell

value: mose active T cell


title: mouse-active-T-cell-siH2A.Z-Rnase-treated-NS

description: nascent strand DNA


title: Pl1.4EGI1.4h


title: mouse-active-T-cell-siNC-Rnase-treated-NS

description: nascent strand DNA


title: mouse-active-T-cell-siNC-NS

description: nascent strand DNA


title: E18.5-C2


title: mouse-active-T-cell-siH2A.Z-input

tag: antibody


title: Pl1.4EGI1.2h


title: mouse-active-T-cell-siNC-input


title: E18.5-C3


title: E18.5-C1


title: mouse-active-T-cell-siH2A.Z-H4K20me2


title: siMK5 rep3


title: Pl1.4EGI1.1h


title: mouse-active-T-cell-siNC-H4K20me2


title: E16.5-T3 (Vasa)

source_name: E16.5 embryonic lung


title: Pl1.4EGI1.12h


title: Pl4.DMSO.SS

value: Steady State


title: siCon rep1


title: SmallRNA WildType Replicate8

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: count files

source_name: Hippocampus

extract_protocol: Hippocampi were isolated, snap frozen in liquid nitrogen and total RNA was isolated using Qiagen miRNeasy mini kit as per the manufacturer's protocol. Libraries were constructed with the standard Illumina small RNA seq protocol.

tag: strain

value: Hippocampus

tag: age

value: 6 weeks

value: Wild Type


title: SmallRNA WildType Replicate9

tag: tissue


title: E16.5-T2 (Vasa)


title: SmallRNA WildType Replicate7

tag: genotype


title: E16.5-T1 (Vasa)


title: Pl4.DMSO.24h

value: 24 hour


title: Pl4.DMSO.12h

value: 12 hour


title: SmallRNA WildType Replicate4


title: E16.5-C3


title: SmallRNA WildType Replicate5


title: SmallRNA WildType Replicate3


title: SmallRNA WildType Replicate6


title: Pl4.DMSO.4h

value: 4 hour


title: SmallRNA Foxg1Cre/+ Replicate9

value: Foxg1 cre/+


title: SmallRNA WildType Replicate2


title: Pl4.DMSO.8h


title: SmallRNA WildType Replicate1


title: Pl4.DMSO.2h

value: 2 hour


title: E16.5-C2


title: E16.5-C1


title: SmallRNA Foxg1Cre/+ Replicate7


title: Pl4.DMSO.1h

value: HEK293T Cells


title: E14.5-T4 (Vasa)

source_name: E14.5 embryonic lung

value: Global expression


title: SmallRNA Foxg1Cre/+ Replicate5


title: E14.5-T3 (Vasa)


title: SmallRNA Foxg1Cre/+ Replicate6


title: Pl1.DMSO.SS


title: SmallRNA Foxg1Cre/+ Replicate4


title: Pl1.DMSO.24h


title: E14.5-T2 (Vasa)


title: SmallRNA Foxg1Cre/+ Replicate3


title: Pl1.DMSO.12h


title: E14.5-C3


title: SmallRNA Foxg1Cre/+ Replicate2


title: Pl1.DMSO.8h

value: 8 hour


title: SmallRNA Foxg1Cre/+ Replicate1


title: E14.5-C2


title: CL_P18 of pregnancy_4

type: RNA

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression in CL pregnant p18

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Pregnant CL p18

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the corpus luteum using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: breed

value: Japanese-Black

value: Corpus luteum

tag: experiment

value: In vivo

tag: group

value: Pregnancy p18

tag: phase


title: E14.5-C1

value: None (control)


title: CL_P18 of pregnancy_3

description: Gene expression in CL pregnant p18


title: Pl1.DMSO.2h

tag: time point


title: Inhibited_C3_Treated_tumor

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

description:
generated tumors
rRNA depleted RNA

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: Tabular text file with cufflinks output.

source_name: MDA-MB-231 tumors

growth_protocol: Tumors were generated by subcutaneous injection of MDA-MB-231 cells in Balb/c nude mice.

extract_protocol:
Total RNA was extracted from tumors with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or mRNA purified thanks to NEB kit
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Mice were treated wih docetaxel 15 mg/kg, when the tumors were at 12 mm². The Caspase-3 inhibition for the MDA-MB-231 tumors was achieved by cell culture of MDA-MB-231 with the Caspase-3 inhibitor Z-DEVD-FMK, Caspase-3 Inhibitor from BD Pharmingen, Ref: 550378.

tag: host mouse strain

value: Balb/c nude mice

value: MDA-MB-231 tumors

tag: treatment

value: Docetaxel


title: Pl1.DMSO.4h

tag: horfeome cell line


title: E12.5-T3 (Vasa)

source_name: E12.5 embronic lung

tag: lin28a expression

tag: embryonic day


title: CL_P18 of pregnancy_2

description: Gene expression in CL pregnant p18


title: E12.5-T2 (Vasa)


title: Efficient_C3_Treated_tumor

description:
generated tumors
rRNA depleted RNA

treatment_protocol: Mice were treated wih docetaxel 15 mg/kg, when the tumors were at 12 mm².


title: Pl1.DMSO.1h

value: 1 hour


title: Efficient_C3_tumor

description:
generated tumors
rRNA depleted RNA

value: No treatment


title: E14.5-T1 (Vasa)


title: CL_P18 of pregnancy_1

description: Gene expression in CL pregnant p18


title: E12.5-T1 (Vasa)


title: Pl4.24h

value: Untreated

value: 24 hour


title: C3_proficient_Treated_MCF-7

description:
rRNA depleted RNA
cancer cell line

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on hg19 reference genome
Cufflink was applied
Genome_build: hg19
Supplementary_files_format_and_content: Tabular text file with cufflinks output.

source_name: MCF-7 cells

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FBS and 1% antibiotics

extract_protocol:
Total RNA was extracted from 300,000 cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or mRNA purified thanks to NEB kit
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Cells were treated 24 hours with 10 nM docetaxel. Then, the medium was replaced by fresh docetaxel free medium during 24 hours.

tag: modification

value: Stably transfected with Caspase-3 cDNA

value: Breast


title: CL_P15 of pregnancy_3

description: Gene expression in CL pregnant p15

source_name: Pregnant CL p15

value: Pregnant p15


title: CL_P15 of pregnancy_4

description: Gene expression in CL pregnant p15


title: C3_proficient_MCF-7

description:
rRNA depleted RNA
cancer cell line

tag: cell line


title: CL_P15 of pregnancy_2

description: Gene expression in CL pregnant p15


title: CL_P15 of pregnancy_1

description: Gene expression in CL pregnant p15


title: CL_D15 of the estrous cycle_4

description: Gene expression in CL cyclic d15

source_name: Cyclic CL d15

value: Non pregnant d15


title: E12.5-C2


title: C3_deficient_Treated_MCF-7

description:
rRNA depleted RNA
cancer cell line

value: Stably transfected with empty vector


title: CL_D15 of the estrous cycle_3

description: Gene expression in CL cyclic d15

value: Japanese-Black


title: C3_deficient_MCF-7

description:
rRNA depleted RNA
cancer cell line


title: Pl4.8h

value: HEK293T Cells

value: 8 hour


title: E12.5-C1


title: Pl4.4h

value: 4 hour


title: Pl4.12h

value: 12 hour


title: Pl4.1h


title: Pl4.2h

value: 2 hour


title: CL_D15 of the estrous cycle_1

description: Gene expression in CL cyclic d15

value: Corpus luteum

value: In vivo


title: CL_D15 of the estrous cycle_2

description: Gene expression in CL cyclic d15


title: Pl4.SS

value: Steady State


title: 37l: liver wt_37

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: genetics

institute: Children's National

hyb_protocol: Clariom S mouse per protocol

scan_protocol: GeneChip 3000

data_processing: Data processing information not provided

label: biotin

source_name: flash frozen liver from littermate control

label_protocol: WT terminal labeling with Reverse transcription initiated at the poly-A tail as well  as throughout the entire length of RNA to capture both coding and multiple forms of non-coding RNA, then converted to biotinidated dsDNA target for unbiased hybridization

growth_protocol: Mice maintained in standard manner on standard diet, not fasted prior to sacrifice

extract_protocol: MirVana whole RNA per protocol

treatment_protocol: Sacrificed using carbon dioxide, liver and heart removed and flash frozen to time of the RNA isolation.

value: flash frozen liver

value: littermate control


title: 39l: liver wt_39


title: C3_proficient_ChIP-seq

description: cancer cell line

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with Bowtie2 on hg19 reference genome
BAM files were visualized with the Golden Helix software
Genome_build: hg19
Supplementary_files_format_and_content: bed file with peaks called by MACS.

extract_protocol:
Crosslinking, extraction and shearing of chromatin was performed by using the Truchip chromatin shearing reagent kit from 1,500,000 cells by following manufacturer protocol. Then, sheared chromatin was immunoprecipitated with different antibodies (anti-active Caspase-3 or control Immunoglobulin) by using the Active Motif's ChIP IT Kit by following manufacturer's instructions
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina. After library validation on a fragment analyzer, the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

value: No treatment

tag: antibody

value: Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb from Cell Signaling, Ref:#9664, Batch:0019


title: E12.5-C3

value: None (control)


title: Pl1.SS

value: Untreated


title: 38l_mut: liver Mut k0/ki_38

source_name: flash frozen liver from MUT ko/ki (MUT p.M700K)

value: MUT p.M700K described in Forny et al JBC 2016


title: C3_deficient_Treated_ChIP-seq

description: cancer cell line

value: Stably transfected with empty vector

value: Breast

value: Docetaxel


title: C3_deficient_ChIP-seq

description: cancer cell line


title: 43h: heart wt_43

source_name: flash frozen heart from littermate control

value: flash frozen heart


title: 43l: liver wt_43


title: Hdac1/2_cKD rep2

city: Hangzhou

first: Yanna

last: Dang

email: yannadang@126.com, yannadang@zju.edu.cn

state: Zhejiang

address: 866 Yuhangtang Rd

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normolized by Salmon
Differentially expressed genes between NC and cKD group were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >2 or <0.5
Genome_build: GRCm38
Supplementary_files_format_and_content: Text files include normalized counts by DESeq2 for each sample

extract_protocol:
At E2.75, embryos were collected (60 embryos per sample, n=3). Total RNA was isolated from embryos using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) according to the manufacturer's instruction. Before RNA extraction, 2 × 106 copies of RFP and GFP mRNA was added.
mRNAs were separated with oligo(dT)25 beads, and was used to prepare sequencing libraries with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, mRNA was fragmented and reverse transcribed. The cDNA library was subject to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

tag: strain background

tag: genotype/variation

value: Hdac1/2 co-knockdown

value: embryo


title: Pl1.24h

source_name: HEK293T Cells

tag: tissue

value: HEK293T Cells

value: 24 hour


title: Pl1.8h

value: 8 hour


title: Sin3a_KD rep2

tag: age

value: Sin3a knockdown


title: 36l_mut: liver Mut k0/ki_36

value: flash frozen liver

tag: genotype


title: Hdac1/2_cKD rep1


title: Sin3a_KD rep1


title: Pl1.12h

value: 12 hour


title: 39h: heart wt_39

value: littermate control


title: NC rep3

value: wild type


title: 38h_mut: heart Mut ko/ki_38

source_name: flash frozen heart from MUT ko/ki (MUTp.M700K)


title: Pl1.4h

value: 4 hour


title: Pl1.2h

value: Untreated

value: 2 hour


title: 36h_mut: heart Mut ko/ki_36

value: MUT p.M700K described in Forny et al JBC 2016


title: NC rep2


title: Hdac1/2_cKD rep3


title: NC rep1


title: Pl1.1h

value: 1 hour


title: Female.D10UUO.PT.3

status: Public on Sep 21 2019

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description: TRAP-seq

data_processing:
Sequencing reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was accessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: Ensembl release 76 assembly
Supplementary_files_format_and_content: Raw counts, RPKMs.

source_name: Proximal tubule

extract_protocol: [TRAP-seq protocol]  Kidneys were removed and decapsulated after perfusion with iced-cold PBS. Renal cortex was rapidly dissected and minced on ice. Samples were then transferred to 1 ml of ice-cold extraction buffer for homogenization. Streptavidin Dyanbeads, which were freshly coated with monoclonal anti-GFP antibodies (clone 19C8 and clone 19F7) through biotinylated Protein L, were added to the kidney postmitochondrial supernatants and incubated at 4°C under end-over-end rotation for 4 hours for immunoprecipitation. After that, beads were collected on a magnetic rack, and the unbound fraction of samples were taken. Collected beads were then washed 4 times by high-salt washing buffer. Bound fractions of samples were then extracted by Qiagen RNeasy lysis buffer. All of the bound and unbound fractions of RNA were then purified by RNeasy MinElute Cleanup Kit  with in-column DNase digestion

tag: gender

value: Female

tag: disease state

value: day 10 after unilateral ureteral obstruction (UUO) surgery (severe kidney injury model)

value: Proximal tubule


title: UM-UC-3 4th spheres differentiation 10 hours cells

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

description: Bladder cancer cell line UM-UC-3 4th spheres are digested into single cell and re-adhered on complete medium for 10 hour

hyb_protocol: Hybridization was performed at 45℃ with rotation for 16 h (Agilent Hybridization Oven G2545A). The GeneChip arrays were washed on an CapitalBio Slide Washer8.

scan_protocol: GeneChips were scanned using Agilent G2565CA Microarray Scanner.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V11.5 (Agilent). The data were normalized by percentile 75 normalization.

label_protocol: An aliquot of 0.1 µg of total RNA was used to synthesize double-stranded cDNA,then cRNA was produced by T7 Enzyme Mix.Then cDNA was produced by reverse transcription using CbcScriptⅡ enzyme.The resulting cDNA were fragmented and labled with cy3/cy5 according to the protocols from Affymetrix.

growth_protocol: UM-UC-3 cells were cultured in DMEM containing 10% FBS. UM-UC-3 4th sphere cells were cultured in DMEM/F12 medium (Life Technologies) supplemented with 20 ng/ml epidermal growth factor (EGF, PeproTech), 5 μg/ml insulin, 0.4% bovine serum albumin (Sigma), and 2% B27 (Life Technologies).

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: Sphere culture. 1000/ml cells were seeded into ultra low attachment plates and incubated in DMEM/F12 medium (Life Technologies) supplemented with 20 ng/ml epidermal growth factor (EGF, PeproTech), 5 μg/ml insulin, 0.4% bovine serum albumin (Sigma), and 2% B27 (Life Technologies).Differentiation.Cells dissociated from spheres were plated at on 6-well plates precoated with Collagen IV (BD BioScience) in DMEM supplemented with 10% FCS without growth factors and passaged when they reached ~95% confluence.

value: differentiated bladder cancer cell line UM-UC-3 4th spheres

tag: cell status

value: differentiation 10 hours

tag: supplemented with 10% fbs medium

value: Yes


title: Sin3a_KD rep3

value: embryo


title: UM-UC-3 4th spheres

source_name: Bladder cancer cell line UM-UC-3 4th spheres

value: bladder CSCs

value: No


title: C3_proficient_Treated_ChIP-seq

description: cancer cell line

value: Stably transfected with Caspase-3 cDNA

value: Breast

value: Docetaxel

value: Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb from Cell Signaling, Ref:#9664, Batch:0019


title: Female.CLK.PT.3

description: TRAP-seq

value: contralateral kidney (healthy control)


title: Female.CLK.PT.2

description: TRAP-seq


title: Female.D5UUO.PT.3

description: TRAP-seq

value: day 5 after unilateral ureteral obstruction (UUO) surgery (moderate kidney injury model)


title: Female.D10UUO.PT.1

description: TRAP-seq


title: Female.D5UUO.PT.1

description: TRAP-seq


title: Female.D5UUO.PT.2

description: TRAP-seq


title: Female.D10UUO.Total.1

description: TRAP-seq

source_name: Total kidney

value: Total kidney


title: Female.D5UUO.Total.3

description: TRAP-seq


title: Female.D10UUO.PT.2

description: TRAP-seq


title: Female.D5UUO.Total.1

description: TRAP-seq


title: Female.CLK.PT.1

description: TRAP-seq


title: Male.D10UUO.PT.4

description: TRAP-seq

value: Male


title: Female.CLK.Total.1

description: TRAP-seq

value: Female


title: Female.D5UUO.Total.2

description: TRAP-seq


title: WT_B_Dox24h RNA-Seq

city: Tianjin

first: Kuangyu

last: Yen

address: Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Reads were aligned to mm10 mouse genome assembly by STAR Viersion 2.5.1 with ENCODE recommended parameters.
Data were filtered using Samtools Version 1.3 with parameters view -q 4-f 2
Counts number were called using HTSeq Version 0.10.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene raw count number for each Sample

source_name: bone marrow

growth_protocol: MLL-AF9-induced AML cells were maintained in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/ml mIL-3 and 50 ng/ml mSCF (PeproTech). Mouse HSPCs were cultured in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/mL mIL-3, 50 ng/ml SCF, 20 ng/ml thrombopoietin (TPO, PeproTech) and 10 ng/ml Flt3 ligand (Flt3-L, PeproTech).

extract_protocol: RNA samples were prepared using rRNA depletion and strand-specific library construction method. RNA was extracted using TRlzolTM (invitrogen) and followed by rRNA removal (Ribo-ZeroTM rRNA Removal Kits) before library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® Kit).

treatment_protocol: Dox (1 mg/ml, Sigma) was used at a concentration of 2 μg/ml

tag: strain

tag: cell type

value: Normal HSPCs

tag: group

value: treatment


title: UM-UC-3 4th spheres differentiation 1 day cells

description: Bladder cancer cell line UM-UC-3 4th spheres are digested into single cell and re-adhered on complete medium for 1 day

value: differentiated bladder cancer cell line UM-UC-3 4th spheres

value: differentiation 1 day


title: Male.D10UUO.PT.3

description: TRAP-seq

value: day 10 after unilateral ureteral obstruction (UUO) surgery (severe kidney injury model)

value: Proximal tubule


title: WT_B_Dox12h RNA-Seq


title: UM-UC-3 adherent cells

source_name: Bladder cancer cell line UM-UC-3

value: Bladder cancer cell line UM-UC-3

value: bladder non-CSCs

value: Yes


title: Female.D10UUO.Total.3

description: TRAP-seq


title: Inhibited_C3_tumor

description:
generated tumors
rRNA depleted RNA

tag: host mouse strain

value: Balb/c nude mice

value: MDA-MB-231 tumors

tag: treatment

value: No treatment


title: Male.D10UUO.PT.1

description: TRAP-seq


title: Female.CLK.Total.3

description: TRAP-seq

value: contralateral kidney (healthy control)


title: Male.D5UUO.PT.4

description: TRAP-seq

value: day 5 after unilateral ureteral obstruction (UUO) surgery (moderate kidney injury model)


title: Male.D10UUO.PT.2

description: TRAP-seq


title: WT_B_Con12h RNA-Seq

value: control


title: WT_B_Con24h RNA-Seq


title: Male.D5UUO.PT.2

description: TRAP-seq

value: Male


title: Male.D5UUO.PT.1

description: TRAP-seq


title: Female.D10UUO.Total.2

description: TRAP-seq

value: Female

value: Total kidney


title: WT_A_Dox24h RNA-Seq

value: Normal HSPCs

value: treatment


title: WT_B_Dox3h RNA-Seq


title: Male.CLK.PT.2

description: TRAP-seq


title: WT_B_Con3h RNA-Seq


title: Male.D10UUO.Total.4

description: TRAP-seq


title: Male.CLK.PT.1

description: TRAP-seq


title: SmallRNA Foxg1Cre/+ Replicate8

source_name: Hippocampus

value: Hippocampus

value: 6 weeks

value: Foxg1 cre/+


title: Male.D10UUO.Total.3

description: TRAP-seq

value: day 10 after unilateral ureteral obstruction (UUO) surgery (severe kidney injury model)


title: WT_A_Dox6h RNA-Seq


title: WT_A_Dox12h RNA-Seq


title: Male.D10UUO.Total.2

description: TRAP-seq


title: WT_A_Dox3h RNA-Seq


title: Male.D10UUO.Total.1

description: TRAP-seq


title: WT_A_Con24h RNA-Seq


title: WT_B_Dox6h RNA-Seq


title: WT_A_Con12h RNA-Seq


title: Male.D5UUO.PT.3

description: TRAP-seq

value: Proximal tubule


title: Male.CLK.PT.4

description: TRAP-seq


title: Male.D5UUO.Total.4

description: TRAP-seq


title: WT_B_Con0h RNA-Seq


title: WT_B_Con6h RNA-Seq


title: Male.CLK.PT.3

description: TRAP-seq


title: WT_A_Con6h RNA-Seq


title: WT_A_Con3h RNA-Seq


title: MA9_B_Dox24h RNA-Seq

value: leukemia cells


title: WT_A_Con0h RNA-Seq


title: Male.CLK.Total.3

description: TRAP-seq


title: Male.D5UUO.Total.1

description: TRAP-seq


title: Male.D5UUO.Total.2

description: TRAP-seq


title: Male.D5UUO.Total.3

description: TRAP-seq


title: MA9_B_Dox12h RNA-Seq


title: MA9_B_Dox3h RNA-Seq


title: Male.CLK.Total.4

description: TRAP-seq


title: Male.CLK.Total.1

description: TRAP-seq


title: Male.CLK.Total.2

description: TRAP-seq


title: Fibroblast CRIST-seq IgG control

city: Palo Alto

first: Jifan

last: Hu

state: CA

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

description:
CRIST-seq IgG control
FIB IgG CTL

data_processing:
Library strategy: CRIST-seq
filter raw data with fastx(version:0.0.13)
clean reads were mapped by mouse genome with Bowtie (version: 0.12.8)
peak calling with MACS(version:1.4.2)

source_name: Fibroblasts (BC180594)

extract_protocol:
Oct4 promoter-interacting lncRNA libraries were prepared using Illumines Kit (Part# 0801-0303).
Fibroblasts were treated with formaldehyde to fix the lncRNA-chromatin structure. LncRNAs were reverse transcribed in situ using biotin-dCTP. The promoter lncDNAs were immunoprecipitated and pulled down with streptavidin beads. The purified lncDNAs were eluted for Illumina library sequencing. As the control, a Cas9 randomn gRNA was used in the CRIST assay. In additon, a IgG control was performed in parallel with Oct4  promoter specific Cas9 gRNAs.

value: Fibroblasts

tag: project

value: Reprogramming


title: Fibroblast CRIST-seq Cas9 random gRNA (gCT) control

description:
CRIST-seq Cas9 random gRNA (gCT) control
FIB Oct4 CRIST-seq


title: Fibroblast Oct4 CRIST-seq

description:
Oct4 promoter-interacting lncRNA identified by CRIST-Seq
FIB gCT CTL


title: MA9_B_Con24h RNA-Seq


title: OB_295

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

data_processing:
bcl2fastq-1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm9 whole genome using Hisat2 (Hisat2-2.1.0) software.
Read count was obtained using featureCount software (subread-1.6.2).
Raw counts were processed using DESeq2 package (v1.20.0) to obtain normalized counts (median of ratio method).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample.

source_name: brain tumor cells

extract_protocol:
RNA was harvested from cells using Sepazol reagent. Illumina TruSeq Strand HT kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: olfactory bulb (OB) tumor cells

value: Foxr2 overexpression, p53 cko


title: MA9_B_Con12h RNA-Seq


title: OB_287


title: KKU-213NG

city: Muang Khon Kaen

first: Charupong

last: Saengboonmee

state: Khon Kaen

address: 123 Moo 16, Mittraphap Highway

department: Department of Biochemistry, Faculty of Medicine

country: Thailand

institute: Khon Kaen University

data_processing:
Initial sequence analysis was performed using the HGSC Mercury analysis pipeline (https://www.hgsc.bcm.edu/software/mercury).
Reads were mapped to the GRCh37 Human reference genome (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/) using the Burrows-Wheeler aligner (BWA, http://biobwa.sourceforge.net/) and a BAM (binary alignment/map) file was generated
RNA BAMs were analyzed using TOPHAT and CUFFLINKS . The expression of transcript species was reported as Fragments Per Kilobase of transcript per Million mapped reads (FPKMs).
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files include FPKM values of all transcripts for each Sample

source_name: Cholangiocarcinoma cell line

growth_protocol: KKU-213 were cultured in DMEM with 5.6 mM glucose (NG) or 25 mM glucose (HG) at least 5 passages and lebel as KKU-213NG or KKU-213HG. KKU-213L5 was cultured in DMEM with 25 mM glucose. The culture medium was supplemented with 10% fetal bovine serum and 1% antibiotics-antimycotics.

extract_protocol:
Confluent cells were trypsinized and preserve in RNAlater® and keep in -80 degree Celcius until use. The extraction was follow the TRIzol® protocol combine with the instruction of RNeasy® kit.
Strand-specific, poly-A+ RNA-seq libraries were prepared and whole-transcriptome RNA sequencing (RNA-seq) was performed on the Illumina HiSeq 2000 platform. Briefly, poly-A+ mRNA was purified using Oligo(dT)25 Dynabeads (Life Technologies) followed by fragmentation . The first strand cDNA was synthesized using NEBNext RNA First Strand Synthesis Module (New England BioLabs) and purified using Agencourt RNA Clean XP beads (Beckman Coulter). A dNTP mix containing dUTP was used for the second strand cDNA synthesis, to introduce strand-specificity (NEBNext Ultra Directional RNA Second Strand Synthesis Module, NEB). The resultant cDNA was processed through end-repair and A-tailing, ligated with Illumina PE adapters, and then digested with Uracil-DNA Glycosylase (NEB). The libraries were amplified and barcoded (13 PCR cycles) using the Phusion High-Fidelity PCR Master Mix (NEB). They were purified, pooled in equimolar amounts, and loaded onto a HiSeq flow cell lane. Sequencing runs were performed in paired-end mode (2 x 100-bp reads) following amplification with Illumina’s cBot cluster generation system.

value: Intrahepatic cholangiocarcinoma

tag: passage

tag: culture medium

value: DMEM low glucose (5.6 mM)


title: KKU-213HG

value: DMEM high glucose (25 mM)


title: OB_257


title: MA9_B_Con6h RNA-Seq

value: control


title: MA9_B_Con3h RNA-Seq


title: MA9_B_Dox6h RNA-Seq


title: BS_296

value: brainstem (BS) tumor cells


title: MA9_A_Dox24h RNA-Seq


title: BS_295


title: MA9_B_Con0h RNA-Seq


title: FoxA1_ChIPseq 1

city: Boston

first: Justin

last: Hwang

state: MA

address: 450 Brookline Ave Dana Bldg

department: Medical Oncology

institute: Dana farber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
RNA-seq: aligned with Tophat 2.0.2
Gene expression is quantitated with Cufflinks for unsupervised analysis
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline
Supplementary_files_format_and_content: Cuff_Gene_Counts.csv

source_name: metastatic lymph node lesion of human prostate cancer

growth_protocol: LNCaP cells were maintained in phenol red free RPMI with glutamine and 10% FBS and, subcultured soon after reach 80% confluence.

extract_protocol:
For ChIPseq, Lysates were sonicated,enriched with antibody for ChIP, decrosslinked, purified and prepped as library for the subsequent sequencing. For ATACseq, the purified intact nuclei were treated Transposase, extracted and prepped as library for further sequencing. For RNAseq, extracted RNA using collected from the cells using RNeasy plus kit (74104, Qiagen)  was prepped as library for RNA sequencing.
For ChIP seq, samples were prepared as library using using the ThruPLEX-FD Prep Kit (Rubicon Genomics, Ann Arbor, MI) with Illumina indexes. For ATACseq, TN5 (Nextera DNA Library Prep Kit) treated samples were amplified with index_primers and prepped as library.

treatment_protocol: LNCaP cells expressing either luciferase or CREB5 were cultured in either 2.5uM enzalutamide or DMSO control for 4 days

value: metastatic human prostate cancer cell

tag: chip antibody

value: FoxA1 (Abcam, ab23738)

tag: cell line

value: LNCaP

value: DMSO for 4 days

tag: expression

value: LNCaP expressing Luciferase


title: ATACseq 2

value: LNCaP expressing CREB5


title: FoxA1_ChIPseq 4

value: 2.5 uM enzalutamide for  4 days


title: FoxA1_ChIPseq 2


title: BS_287

tag: tissue

tag: genotype/variation


title: ATACseq 4


title: MA9_A_Dox12h RNA-Seq

value: leukemia cells

value: treatment


title: H3K27Ac_ChIPseq 4

description: LNCaP_CREB5_Enzalutamide_H3K27Ac_ChIPseq

value: H3K27Ac ( Diagenode, C15410196 )


title: FoxA1_ChIPseq 3


title: KKU-213L5


title: AG_3

source_name: brain cells

value: astroglia (AG)

value: p53 DN, Nf1 shRNA


title: MA9_A_Dox6h RNA-Seq


title: H3K27Ac_ChIPseq 3


title: H3K27Ac_ChIPseq 1


title: AG_2


title: CREB5_V5_ChIPseq 4

description: LNCaP_CREB5_Enzalutamide_CREB5_V5_ChIPseq

value: CREB5_V5 (Cell signaling, #13202, lot2 )


title: CREB5_V5_ChIPseq 3


title: ATACseq 1


title: MA9_A_Dox3h RNA-Seq


title: AG_1


title: CREB5_V5_ChIPseq 2


title: CREB5_V5_ChIPseq 1


title: MA9_A_Con24h RNA-Seq


title: MA9_A_Con12h RNA-Seq


title: AR_ChIPseq 4

value: Androgen Receptor ( Santa Cruz , sc-816x, lot J216)


title: AR_ChIPseq 3


title: H3K27Ac_ChIPseq 2


title: MA9_A_Con3h RNA-Seq


title: MA9_A_Con6h RNA-Seq


title: AR_ChIPseq 2


title: MA9_A_Con0h RNA-Seq


title: AR_ChIPseq 1


title: WT_B_Dox24h ATAC-Seq

data_processing:
Reads were aligned to mm10 mouse genome assembly by BWA Version: 0.7.5a-r405 with bwa mem default setting
Data were filtered using Samtools Version 1.3 with parameters view -q 1 -f 2 -F 256
Peaks were called using macs2 Version 2.1.1.20160309
Genome_build: mm10
Supplementary_files_format_and_content: Peak files were generated using macs2

extract_protocol: Briefly, 50,000 cells were lysed in lysis buffer (10mM Tirs-HCl, PH7.4, 10mM NaCl, 3mM MgCl2, 0.1%(v/v) IGPAL CA-630) for 10min on ice before centrifuged at 500g for 5min. The nuclei were added with 50ul transposition reaction buffer (5μL TruePrep Tagment Enzyme,10μL TruePrep Tagment Buffer L and 35μL ddH2O from Vazyme TD501-01) and followed with incubation at 37oC for 30min. After tagmentation, VAHTS DNA Clean Beads were used to stop the reaction and DNA was purified for final library construction (TruePrepTM DNA Library Prep Kit V2 for Illumina) before paired-end high-throughput sequencing using HiSeq XTen.

value: Normal HSPCs


title: WT_B_Dox12h ATAC-Seq


title: ATACseq 3


title: Macula retina 3 Microfluidics

city: New Haven

first: Brian

last: Hafler

state: Connecticut

address: 300 George Street

institute: Yale School of Medicine

description:
counts.mtx
gene_names.txt
sample_annotations.tsv

data_processing:
Sample demultiplexing, read alignment to the NCBI reference genome, quantification and initial quality control (QC) of the microfluidics-based sequencing dataset was performed using the Cell Ranger Software (version 3.0.2; 10X Genomics) for each sample separately.
We used the command “-forcecells 4000” in Cell Ranger count to extract a larger number of cell barcodes in the data, as the automatic estimate by Cell Ranger was too conservative.
Genome_build: hg19
Supplementary_files_format_and_content: text files contain the count matrix, gene names and the sample annotations for the dataset

source_name: Retina

extract_protocol:
Trephine punches (6mm) were used to isolate samples from (1) the macula in the central retina and (2) a region of mid-peripheral retina. Retinal samples were processed using a single-use papain dissociation system (Worthington, Catalog No. LK003150).
Libraries were constructed using the protocol from 10X Genomics (Chromium Single Cel 3' kit).

value: Macula retina

tag: cell types

value: neuronal, glial and vascular cells


title: Peripheral retina 2 Microfluidics

value: Peripheral retina


title: Peripheral retina 3 Microfluidics


title: Macula retina 1 Microfluidics


title: Peripheral retina 1 Microfluidics


title: GSC528-SRSF3-KO

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Reads were aligned to the human genome hg19 using HISAT2 (Galaxy Version 2.1.0+galaxy4).
Quantification was performed using HTSeq-count (Galaxy Version 0.9.1).
Differential expression of genes was calculated by DESeq2 (Galaxy Version 2.11.40.2).
The mapped reads were processed through the MISO (version 0.5.4) pipeline to estimate expression of alternatively spliced isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: tabular files include raw counts for each transcript of each sample generated from HTSeq-count; txt files include Percent Spliced In (PSI) values for each AS events of each sample calculated by MISO.

growth_protocol: Patient-derived GSCs that were cultured in DMEM/F12 medium (Thermo Fisher Scientific, 11320-033) containing 2% B27 supplement (Thermo Fisher Scientific, 17504-044), 1% penicillin and 1% streptomycin (Thermo Fisher Scientific, 11860-038), 5 μg/ml heparin (Sigma-Aldrich, 9041-08-1), 20 ng/ml EGF (Peprotech, 100-15R0, and 20 ng/ml bFGF (Peprotech, 100-18B).

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit according to the manufacturer's instruction.
Libraries were prepared using the Illumina stranded Total RNA TruSEQ kit according to the manufacturer's instruction.

treatment_protocol: GSCs were infected with CRISPR/Cas9 lentivirus that targeting SRSF3 for KO or control. After 5-8 days,  cells were harvested to extract RNA.

value: Patient-derived glioma stem-like cells (GSCs)


title: GSC528-WT

value: wild-type


title: GSC83-SRSF3-KO


title: GSC83-WT


title: WT_B_Dox3h ATAC-Seq


title: Macula retina 2 Microfluidics


title: MSCs, Ezh2 Het 12M, sample S9, technical replicate 2

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were mapped to mouse genome build mm10 (NCBI annotation) using Subread
Genewise counts were obtained using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts in tab delimited format

source_name: Ezh2 Het 12M, sample S9

growth_protocol: Mesenchymal stromal cells were isolated from the long-bones of Ezh2fl/+:Prxx-1-Cre  heterozygous mice or Ezh2+/+:Prrx-1-Cre control mice at 3 and 12 months of age. The mesenchymal stromal cells were prepared and cultured in regular growth media as previously described (Hemming et al. FASEB J, 2017).

extract_protocol:
Primary mesenchymal stromal cells cultures were liberated by trypsin digest and used to prepare total RNA RNA using Directzol RNA miniprep kit with approximately 1 million cells per sample. 500ng was analyzed for RNA quality control and RNA sequencing was performed by the David Gunn Genomics Facility, SAHMRI, Adelaide, South Australia.
TruSeq RNA Library Preparation Kit v2, illumina

treatment_protocol: Ezht_Het KO mice and control mice were kept

tag: gender

value: Female

tag: genotype

value: Ezh2 Het

tag: age

value: mesenchymal stromal cells (MSCs)


title: WT_B_Con24h ATAC-Seq

tag: strain

value: control


title: mammary gland, restricted nutrient intake during preweaning, replicate 5

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Bovine Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.44.0).

source_name: mammary gland parenchyma, restricted level of nutrient intake during preweaning

label_protocol: Purified total RNA (100ng per sample) was labeled with the Ambion WT Expression Kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: The experimental protocols describing the management and animal care have previously been reported [PMID: 28390726; DOI: 10.3168/jds.2016-11826]. In brief, Holstein heifers were randomly assigned at birth to 1 of 2 treatments in which they were offered either an elevated level of nutrient intake (ELE, n = 6), whereby metabolizable energy (ME) was provided at 0.3 Mcal ME/kg BW0.75 in milk replacer (MR), or a restricted level of nutrient intake (RES, n = 6) that was designed to replicate standard industry MR feeding strategies. Heifers consuming RES were fed twice per day (2.8 ± 0.2 Mcal of ME intake in 4 L of MR/d), whereas ELE heifers consumed their ME allotment in three feedings per day (4.2 to 8.4 Mcal ME intake in 6 to 12 L of MR/d, 5.9 ± 0.2 (mean ± SE) Mcal ME intake in 8.4 L of MR/d). Milk replacer composition was 28% protein and 15% fat (Excelerate, Milk Specialties, Inc., Eden Prairie, MN, USA). Both ELE and RES heifers were offered starter grain (22% CP, Cargill Inc., Minneapolis, MN, USA) ad libitum from d 18 postnatal. Treatments were fed for 54 d, adjusting weekly for changes in BW, until calves were slaughtered. Calves were housed in individual hutches bedded with sawdust throughout the study. Body weights and hip heights of each calf were measured weekly 1 h after the morning feeding. All protocols were reviewed and approved by the Cornell University Animal Care and Use Committee, Ithaca, USA, (Protocol number 2009–0120).

extract_protocol: Total RNA was prepared from frozen parenchymal samples using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 7.0).

treatment_protocol: At 54 ± 2 d, calves were fed at 0700h, weighed, and transported to the Cornell University abattoir (Ithaca, NY, USA) for slaughter and tissue collection. Calves were killed by stunning with a captive bolt, followed directly by exsanguination. Immediately after exsanguination, the mammary gland was removed from the body and skinned. After the mammary gland was isolated and total weight recorded, the fat pad was removed from the parenchyma. Tissue samples of the mammary parenchyma were then collected, placed in foil bags, snap-frozen in liquid N2, and stored at -80°C until RNA isolation. Though six ELE and six RES heifers were killed and had their mammary glands harvested, the parenchyma of a heifer from the RES was too small and could not be separated from the fat pad; therefore, it was not available to be sampled due to minimal development of the mammary gland. Thus, data from the RES treatment calves is representative of five as opposed to six heifers in the ELE group.

tag: Sex

value: female

tag: breed

value: Holstein heifer

tag: energy group

value: RES (restricted)

tag: sampleID


title: MSCs, Ezh2 Het 12M, sample S9, technical replicate 1

tag: cell type


title: mammary gland, elevated nutrient intake during preweaning, replicate 6

source_name: mammary gland parenchyma, elevated level of nutrient intake during preweaning

value: ELE (elevated)


title: mammary gland, elevated nutrient intake during preweaning, replicate 5


title: mammary gland, restricted nutrient intake during preweaning, replicate 4


title: mammary gland, elevated nutrient intake during preweaning, replicate 3


title: mammary gland, elevated nutrient intake during preweaning, replicate 4


title: mammary gland, restricted nutrient intake during preweaning, replicate 3


title: WT_B_Dox6h ATAC-Seq

tag: group

value: treatment


title: MSCs, Ezh2 Het 12M, sample S9, technical replicate 4


title: MSCs, Ezh2 Het 12M, sample S15, technical replicate 4

source_name: Ezh2 Het 12M, sample S15


title: MSCs, Ezh2 Het 12M, sample S9, technical replicate 3


title: MSCs, Ezh2 Het 12M, sample S15, technical replicate 3


title: WT_B_Con6h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S15, technical replicate 1


title: WT_B_Con3h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S16, technical replicate 4

source_name: Ezh2 Het 12M, sample S16


title: WT_B_Con12h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S15, technical replicate 2


title: mammary gland, restricted nutrient intake during preweaning, replicate 2


title: MSCs, Ezh2 Het 12M, sample S16, technical replicate 3


title: MSCs, Ezh2 Het 12M, sample S16, technical replicate 2


title: WT_B_Con0h ATAC-Seq


title: Stress zmnf-ya1 mutant-2

city: qingdao

first: wang

last: baomei

state: shandong

address: school of life science，shandong university，72 binhai road， aoshanwei town， jimo city

department: school of  life science

institute: zea maize

data_processing:
Primary sequencing data that produced by Illumina HiSeq 2000, called as raw reads, is subjected to quality control (QC) that determine if a re-sequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on).
Further, we also can perform deep analysis based on DEGs (We use 'FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1' as the threshold to judge the significance of gene expression difference), including Gene Ontology (GO) enrichment analysis, pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Genome_build: B73 inbred line V3; https://www.maizegdb.org/genome/genome_assembly/B73%20RefGen_v3
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Zea mays

source_name: W22_zmnf-ya1 mutant_Drought stress_leaf

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

tag: background

value: W22 maize inbred line

tag: development stage

value: V4 stage

value: zmnf-ya1 mutant

tag: condition

value: Drought stress

value: Leaf


title: MSCs, Ezh2 Het 12M, sample S16, technical replicate 1


title: Stress zmnf-ya1 mutant-1


title: mammary gland, elevated nutrient intake during preweaning, replicate 2


title: WT_A_Dox24h ATAC-Seq

value: Normal HSPCs


title: Stress W22-2

source_name: W22_wild type_Drought stress_leaf

value: wild type


title: MSCs, Ezh2 Het 3M, sample S10, technical replicate 4

source_name: Ezh2 Het 3M, sample S10

value: Male


title: Stress W22-1


title: MSCs, Ezh2 Het 3M, sample S10, technical replicate 2


title: MSCs, Ezh2 Het 3M, sample S10, technical replicate 1


title: WT_A_Dox12h ATAC-Seq

source_name: bone marrow


title: Stress ZmNF-YA1OE-2

source_name: DH4866_ZmNF-YA1OE_Drought stress_leaf

value: DH4866 maize inbred line


title: mammary gland, restricted nutrient intake during preweaning, replicate 1


title: WT_A_Dox6h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S17, technical replicate 4

source_name: Ezh2 Het 12M, sample S17

value: Ezh2 Het


title: MSCs, Ezh2 Het 12M, sample S17, technical replicate 2

value: mesenchymal stromal cells (MSCs)


title: WT_A_Dox3h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S17, technical replicate 1


title: Female.CLK.Total.2

description: TRAP-seq

source_name: Total kidney

value: Female

tag: disease state

value: contralateral kidney (healthy control)

value: Total kidney


title: MSCs, Ezh2 Het 12M, sample S17, technical replicate 3


title: MSCs, Ezh2 Het 3M, sample S8, technical replicate 4

source_name: Ezh2 Het 3M, sample S8


title: Stress DH4866-2

source_name: DH4866_wild type_Drought stress_leaf

tag: tissue


title: Stress ZmNF-YA1OE-1

tag: genotype/variation


title: WT_A_Con12h ATAC-Seq

value: control


title: MSCs, Ezh2 Het 3M, sample S8, technical replicate 2


title: MSCs, Ezh2 Het 3M, sample S10, technical replicate 3


title: WT_A_Con24h ATAC-Seq


title: MSCs, Ezh2 Het 3M, sample S8, technical replicate 3


title: Stress DH4866-1


title: MSCs, Ezh2 Het 3M, sample S8, technical replicate 1


title: Stress ZmNF-YB16 OE-2

source_name: B104_ZmNF-YB16 OE_Drought stress_leaf

value: B104 maize inbred line

value: ZmNF-YB16 OE


title: MSCs, Ezh2 Het 12M, sample S11, technical replicate 4

source_name: Ezh2 Het 12M, sample S11


title: MSCs, Ezh2 Het 12M, sample S11, technical replicate 2


title: MSCs, Ezh2 Het 12M, sample S11, technical replicate 3


title: MSCs, Ezh2 Het 12M, sample S11, technical replicate 1


title: WT_A_Con6h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S1, technical replicate 4

source_name: Ezh2 Het 12M, sample S1


title: WT_A_Con3h ATAC-Seq


title: Stress ZmNF-YB16 OE-1


title: WT_A_Con0h ATAC-Seq


title: MSCs, Ezh2 Het 12M, sample S1, technical replicate 3


title: Stress B104-2

source_name: B104_wild type_Drought stress_leaf


title: MSCs, Ezh2 Het 12M, sample S1, technical replicate 2


title: MSCs, Ezh2 Het 12M, sample S1, technical replicate 1


title: MA9_B_Dox24h ATAC-Seq

value: leukemia cells

value: treatment


title: MA9_B_Dox12h ATAC-Seq


title: Control zmnf-ya1 mutant-2

source_name: W22_zmnf-ya1 mutant_normal control_leaf

value: W22 maize inbred line

value: V4 stage

value: zmnf-ya1 mutant

value: normal control


title: Control zmnf-ya1 mutant-1

value: Leaf


title: MSCs, Ezh2 Het 3M, sample S14, technical replicate 4

source_name: Ezh2 Het 3M, sample S14


title: MSCs, Ezh2 Het 3M, sample S14, technical replicate 3


title: MSCs, Ezh2 Het 3M, sample S14, technical replicate 2


title: MA9_B_Dox6h ATAC-Seq


title: Control W22-2

source_name: W22_wild type_normal control_leaf

value: wild type


title: MSCs, Ezh2 Het 3M, sample S14, technical replicate 1


title: Control W22-1


title: MSCs, Ezh2 WT 3M, sample S5, technical replicate 4

source_name: Ezh2 WT 3M, sample S5

value: Male

value: Ezh2 WT


title: MA9_B_Dox3h ATAC-Seq


title: MSCs, Ezh2 WT 3M, sample S5, technical replicate 3

value: mesenchymal stromal cells (MSCs)


title: MA9_B_Con24h ATAC-Seq


title: MSCs, Ezh2 WT 3M, sample S5, technical replicate 2


title: MSCs, Ezh2 WT 3M, sample S3, technical replicate 4

source_name: Ezh2 WT 3M, sample S3

value: Female


title: Control ZmNF-YA1OE-2

source_name: DH4866_ZmNF-YA1OE_normal control_leaf

value: DH4866 maize inbred line


title: MSCs, Ezh2 WT 3M, sample S3, technical replicate 2


title: Stress B104-1

value: Drought stress


title: mammary gland, elevated nutrient intake during preweaning, replicate 1

source_name: mammary gland parenchyma, elevated level of nutrient intake during preweaning

value: female

value: Holstein heifer

value: ELE (elevated)


title: Control ZmNF-YA1OE-1


title: MA9_B_Con12h ATAC-Seq

source_name: bone marrow

value: leukemia cells

value: control


title: MSCs, Ezh2 WT 3M, sample S5, technical replicate 1


title: MSCs, Ezh2 WT 3M, sample S3, technical replicate 1


title: MA9_B_Con6h ATAC-Seq


title: Control DH4866-2

source_name: DH4866_wild type_normal control_leaf


title: MA9_B_Con3h ATAC-Seq


title: MSCs, Ezh2 WT 3M, sample S12, technical replicate 4

source_name: Ezh2 WT 3M, sample S12


title: MSCs, Ezh2 WT 3M, sample S12, technical replicate 3


title: Control DH4866-1


title: MA9_B_Con0h ATAC-Seq


title: Control ZmNF-YB16 OE-2

source_name: B104_ZmNF-YB16 OE_normal control_leaf

value: B104 maize inbred line

value: ZmNF-YB16 OE


title: MSCs, Ezh2 WT 3M, sample S12, technical replicate 2


title: siCtrl-3

city: Wuhan

first: Qifan

last: Yang

state: Hubei

address: 13,Hangkong Road

department: Cancer Center

institute: Huazhong University of Science and Technology

data_processing:
Analysis description: Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated  by using the Stringtie-1.3.3b software. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with FPKM

source_name: Human Lung cancer cell line

growth_protocol: All the cells were cultured in PRMI-1640 medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Invitrogen), and concentration was determined using Nanodrop spectrophotometer (Thermo Scientific).
Paired-end libraries sequencing with Illumina HiSeq2500 were prepared with the mRNA-seq sample prep kit (Illumina) according to the manufacturer’s specifications. The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: H1299 cells were transfected with control or IQGAP3-targeting siRNAs for 48 h. Total RNA was isolated using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

tag: cell line

value: Lung cancer cell line

value: siCtrl


title: MSCs, Ezh2 WT 3M, sample S12, technical replicate 1

tag: gender


title: MA9_A_Dox24h ATAC-Seq

value: treatment


title: siCtrl-2

tag: genotype


title: siCtrl-1


title: MSCs, Ezh2 WT 3M, sample S4, technical replicate 4

source_name: Ezh2 WT 3M, sample S4

tag: age


title: MSCs, Ezh2 WT 3M, sample S3, technical replicate 3


title: siIQGAP3-3


title: MSCs, Ezh2 WT 3M, sample S4, technical replicate 3


title: MA9_A_Dox12h ATAC-Seq

tag: strain


title: Control B104-2

source_name: B104_wild type_normal control_leaf

value: V4 stage

value: wild type

value: normal control

value: Leaf


title: Control B104-1


title: Control ZmNF-YB16 OE-1


title: MA9_A_Dox6h ATAC-Seq


title: MA9_A_Dox3h ATAC-Seq


title: siIQGAP3-1


title: MA9_A_Con24h ATAC-Seq


title: siIQGAP3-2


title: MSCs, Ezh2 WT 3M, sample S4, technical replicate 1

value: Female

value: Ezh2 WT

value: mesenchymal stromal cells (MSCs)


title: CD4+CD25neg_4

city: Philadelphia

first: Ying

state: Pennsylvania

address: 3900 Spruce Street

institute: University of Pennsylvania

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A12]

data_processing:
Sequence reads were trimmed using Skewer v0.1.125 to remove adaptor and achor sequences, then mapped to canine genome, CanFam3.1, using HISAT2 v2.0.0-beta.
The mapped read pairs were quantified using featureCounts v1.5.0, and annotated using the same canine genomic data.
Mapping matrics were generated using Picard Tools v1.92. The metrics and variants for assessing read distribution, biotype distribution and mapped transcripts were generated using R v3.4.2.
Read counts were all converted to transcripts per milllion (TPM).
Genome_build: CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Canis lupus

source_name: peripheral blood

extract_protocol:
CD4+CD25high and CD4+CD25neg cells were sorted from peripheral blood mononuclear cells and sorted by FACS. Total RNA was extracted from cells using RNA Bee and Direct-zol RNA MicroPrep Kit.
RNA libraries were generated following standard Illumina protocols.

tag: sorted cell

tag: animal

value: healthy dog_4


title: CD4+CD25neg_5

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A13]

value: healthy dog_5


title: MSCs, Ezh2 WT 3M, sample S4, technical replicate 2


title: RNAseq_rep2 4

source_name: metastatic lymph node lesion of human prostate cancer

value: metastatic human prostate cancer cell

value: LNCaP

tag: treatment

value: 2.5 uM enzalutamide for  4 days

tag: expression

value: LNCaP expressing CREB5


title: MSCs, Ezh2 WT 12M, sample S6, technical replicate 4

source_name: Ezh2 WT 12M, sample S6

tag: cell type


title: CD4+CD25neg_3

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A11]

value: healthy dog_3


title: MA9_A_Con12h ATAC-Seq

value: leukemia cells

tag: group

value: control


title: RNAseq_rep2 3

value: LNCaP expressing Luciferase


title: RNAseq_rep2 2

value: DMSO for 4 days


title: CD4+CD25neg_2

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A10]

value: healthy dog_2


title: MSCs, Ezh2 WT 12M, sample S6, technical replicate 2


title: MA9_A_Con3h ATAC-Seq


title: MA9_A_Con6h ATAC-Seq


title: CD4+CD25neg_1

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A9]

value: healthy dog_1


title: MSCs, Ezh2 WT 12M, sample S6, technical replicate 3


title: MA9_A_Con0h ATAC-Seq


title: CD4+CD25high_5

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A5]


title: RNAseq_rep1 4


title: MSCs, Ezh2 WT 12M, sample S6, technical replicate 1


title: RNAseq_rep2 1


title: CD4+CD25high_4

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A4]


title: CD4+CD25high_3

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A3]


title: RNAseq_rep1 2


title: MSCs, Ezh2 WT 12M, sample S7, technical replicate 2

source_name: Ezh2 WT 12M, sample S7


title: CD4+CD25high_2

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A2]


title: RNAseq_rep1 3


title: MSCs, Ezh2 WT 12M, sample S7, technical replicate 3


title: MSCs, Ezh2 WT 12M, sample S7, technical replicate 1


title: CD4+CD25high_1

description: GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A1]


title: MDA-MB-231 cells, shPDE3A_2_3

last: Hao

address: 94, Weijin Road

institute: Nankai University

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

source_name: Breast cancer

extract_protocol:
Cells were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using  oligo -dT beads


title: MSCs, Ezh2 WT 12M, sample S13, technical replicate 4

source_name: Ezh2 WT 12M, sample S13

value: Male


title: MDA-MB-231 cells, shPDE3A_2_2


title: Sample_A8_zjl

city: Haining

first: Jian

last: Liu

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

data_processing:
Raw reads of 150 nucleotides, paired-end filtered for quality score > 20.
Reads were mapped to the human genome (UCSC hg19) using hisat2
Genome_build: hg19

source_name: healthy control-3

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood mononuclear cells

value: healthy control


title: Sample_A9_xt

source_name: healthy control-4


title: Sample_A10_jyq

source_name: healthy control-5


title: MSCs, Ezh2 WT 12M, sample S13, technical replicate 3

value: Ezh2 WT

value: mesenchymal stromal cells (MSCs)


title: MSCs, Ezh2 WT 12M, sample S7, technical replicate 4

value: Female


title: Pca tumor, CTBP1 control, rep2

city: Buenos Aires

first: Adriana

last: De Siervi

state: Buenos Aires

address: Vuelta de Obligado 2490

department: Instituto de Biología y Medicina Experimental

country: Argentina

institute: CONICET

description: miRNA expression data from PC3 xenograft with CTBP1 control expression generated in metabolic syndrome mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C

scan_protocol: microarray were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Affymetrix Expression Console Software  using Affymetrix default analysis settings
affymetrix-algorithm-name = rma : dabg

source_name: PC3 xenograft with CTBP1 control expression from Metabolic Syndrome mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: nu/nu mice after 12 weeks fed with high fat diet were injected subcutaneously with PC3.pGIPZ (CTBP1 control expression) or PC3.shCtBP1 (CTBP1 depleted expression).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RNA from xenograft were obteined

value: human prostate cancer cell line PC3

tag: cell line genotype/variation

value: CTBP1 control

tag: xenograft host

value: metabolic syndrome mice

tag: tissue (rna extracted)

value: PC3 xenograft


title: MDA-MB-231 cells, shPDE3A_2_1


title: Pca tumor, CTBP1 depleted rep2

description: miRNA expression data from PC3 xenograft with CTBP1 depleted expression generated in metabolic syndrome mice

source_name: PC3 xenograft with CTBP1 depleted expression from Metabolic Syndrome mouse

value: CTBP1 depleted


title: MSCs, Ezh2 WT 12M, sample S13, technical replicate 2


title: Intrahepatic CD8 T, ASGM1 positive, rep1

city: Taipei

first: ChiChang

last: Sung

state: Taiwan

address: No.1 Ren Ai Rd.

department: Graduate Institute of Immunology

country: Taiwan

institute: College of Medicine, National Taiwan University

description: Gene expression data from intrahepatic ASGM1 positive CD8 T of naïve NFIL3 knockout mice

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Mouse Clariom D. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips image were collected by NCFPB High-throughput Genome Analysis Core Facility

data_processing: The image analysis was done using Affymetrix Transcriptome Analysis Suite (TAS) by default analysis settings and global scaling as normalization method.

label: WT PLUS

source_name: Intrahepatic ASGM1 positive CD8T, naïve

label_protocol: CRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix WT Plus Expression Sense Target Protocol).

growth_protocol: 6 week old male NFIL3 KO mice were bred in SPF facility.

treatment_protocol: Intrahepatic IHL were harvested, stained and sorted with a FACSAria cell sorter

value: NFIL3 KO


title: Intrahepatic CD8 T, ASGM1 negative, rep1

description: Gene expression data from intrahepatic ASGM1 negative CD8 T of naïve NFIL3 knockout mice

source_name: Intrahepatic ASGM1 negative CD8T, naive


title: Sample_A7_jh

institute: Zhejiang University

source_name: healthy control-2

tag: disease state


title: Pca tumor, CTBP1 control, rep1


title: MDA-MB-231 cells, shPDE3A_1_3


title: BT16

city: Aurora

first: Jean

last: Mulcahy Levy

state: CO

institute: University of Colorado - Anschutz

data_processing:
Quality trimming using trimmomatic with a  min length of 130 bp and phred score of 33
Alignment using gnsap to hg38 max mismatch of 0.06
Generation of normalized expression counts using cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: Sorted file, details fpkm lists

source_name: Brain tumor cell line

growth_protocol: Standard mammalian tissue culture

extract_protocol:
Zymo RNA extraction kit
Illumina TrueSeq

treatment_protocol: No treatments administered

tag: tumor type

value: AT/RT tumor

tag: origin

value: Pediatric

tag: passage


title: RNAseq_rep1 1

value: metastatic human prostate cancer cell

tag: cell line

value: LNCaP

value: DMSO for 4 days

value: LNCaP expressing Luciferase


title: MSCs, Ezh2 WT 12M, sample S13, technical replicate 1

tag: gender

value: Male

tag: genotype


title: BT12


title: MDA-MB-231 cells, shPDE3A_1_2


title: 1337X_PCL

source_name: Brain tumor


title: Sample_A6_smz

source_name: healthy control-1

tag: tissue

value: peripheral blood mononuclear cells

value: healthy control


title: Sample_A5_yl

source_name: LADA Patient-4

value: Latent Autoimmune Diabetes (LADA)


title: MSCs, Ezh2 WT 12M, sample S2, technical replicate 4

source_name: Ezh2 WT 12M, sample S2

value: Ezh2 WT

tag: age

value: mesenchymal stromal cells (MSCs)


title: MDA-MB-231 cells, shPDE3A_1_1


title: 1337


title: MSCs, Ezh2 WT 12M, sample S2, technical replicate 3


title: MDA-MB-231 cells, shNC_3

value: sh Negative Control


title: Pca tumor, CTBP1 depleted rep1

value: human prostate cancer cell line PC3

value: metabolic syndrome mice


title: MDA-MB-231 cells, shNC_2


title: 737


title: Sample_A3_wxy

source_name: LADA Patient-2


title: MDA-MB-231 cells, shNC_1


title: Sample_A2_cyx

source_name: LADA Patient-1


title: MSCs, Ezh2 WT 12M, sample S2, technical replicate 2


title: MSCs, Ezh2 WT 12M, sample S2, technical replicate 1


title: Tree_18_Benz_T2

status: Public on Sep 20 2019

city: Gainesville

first: Leandro

middle: Octavio

last: Balzano

state: FL

address: 1275 Center Drive

department: Pathology, Immunology, and Laboratory Medicine

institute: University of Florida

data_processing:
Alignment of reads  to the Clementina genome with TopHat2 (Kim et al. 2013)
Count of gene expression with HTSEQ-count (Anders et al. 2015)
Genes with less than 10 reads collectively for all samples were discarded
Gene expression values were normalized using the TMM method (Robinson and Oshlack, 2010)
Batch effects were removed witrh ARSyNseq (Tarazona et al. 2011).
Genome_build: ncbi_gca_000493195_1_citrus_clementina_v1_0
Supplementary_files_format_and_content: csv, gene expression counts

organism: Citrus sinensis

source_name: RNA-seq

growth_protocol: ‘Valencia’ sweet orange trees (Citrus sinensis [L.] Osbeck), ranging in age from twenty to thirty years old. Standard grove care and maintenance was performed in each grove throughout the field trials, which included irrigation, fertilization and pest management.

extract_protocol:
Fifty leaves were collected randomly from the canopy of each tree. Following collection, the midrib and petiole of each leaf was excised and immediately submerged in RNAlater. Prior to RNA extraction, the tissue samples were freeze (-80°C), dried and homogenized.  25 mg of each powdered leaf was used. Total RNA was extracted with Isolate II RNA Plant Kit (Bioline, Taunton, MA). RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
TruSeq Stranded total RNA with Ribo-Zero Plan Kit (Illumina)

treatment_protocol: Three group of infected trees each were established: control plants, plants treated with benzbromarone and plants treated with tolfenamic acid. RNA was obtained two months before treatment (T0) and 2 weeks after treatment (T2).

tag: cultivar

value: Valencia

tag: infected with

value: Liberibacter asiaticus

value: leaf midrib and petiole

tag: tree number

value: Benzbromarone

tag: treatment time


title: Tree_24_Control_T2

tag: treatment

value: Control


title: Tree_17_Control_T2


title: Tree_19_Tolf_T2

value: Tolfenamic acid


title: Tree_23_Benz_T2


title: Tree_25_benztoff_T2


title: Tree_10_Control_T2


title: Tree_26_benztoff_T2


title: Tree_20_Tolf_T2


title: Tree_09_Benz_T2


title: Tree_13_Control_T2


title: Tree_12_Tolf_T2


title: Tree_21_Control_T2


title: Tree_11_Benz_T2


title: Tree_06_Benz_T2


title: Sample_A4_cyl

state: Zhejiang

source_name: LADA Patient-3


title: 1298

value: AT/RT tumor

value: Pediatric


title: Tree_07_Control_T2


title: Tree_16_Benz_T2


title: Tree_14_Benz_T2


title: Tree_22_Tolf_T2


title: Tree_04_Tolf_T2


title: Tree_02_Control_T2


title: Tree_01_Tolf_T2


title: Tree_25_benztoff_T0


title: Tree_15_Tolf_T2


title: Tree_08_Tolf_T2


title: Tree_18_Benz_T0


title: Tree_21_Control_T0


title: Tree_23_Benz_T0


title: Tree_24_Control_T0


title: Tree_17_Control_T0


title: Tree_16_Benz_T0


title: Tree_14_Benz_T0


title: Tree_13_Control_T0


title: Tree_12_Tolf_T0


title: Tree_09_Benz_T0


title: Tree_22_Tolf_T0


title: Tree_15_Tolf_T0


title: Tree_07_Control_T0


title: Tree_08_Tolf_T0


title: Tree_11_Benz_T0


title: Tree_10_Control_T0


title: Tree_05_Control_T0


title: Tree_04_Tolf_T0


title: Tree_05_Control_T2


title: Tree_03_Benz_T2


title: Tree_02_Control_T0


title: Tree_26_benztoff_T0


title: Tree_03_Benz_T0