title: Testes-Cd-2

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files include RPKM values for each Sample

source_name: Testes

extract_protocol:
Total RNAs were extracted from the purified sperm and testes samples using RNeasy® Plus Micro (Qiagen, Duesseldorf, Germany) according to the manufacturer’s instructions with some modifications. We added 1 ml of buffer RLT (a guanidine-thiocyanate lysis buffer supplemented with 10 mM DL-Dithiothreitol) to the sperm pellet and 10 mg testes tissues, and then homogenized the sample by passing the samples through a 20-G needle attached to a 1-ml syringe 10 to 15 times. After total RNA was bound to the membrane and other contaminants were efficiently washed away, on-column DNase digestion was performed to eliminate trace amounts DNA contamination. The concentration and integrity of the total RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and a 2100-Bioanalyzer with the RNA 6000 Nano Chip (Applied Biosystems, Carlsbad, CA, USA), respectively.
RNase H protocol was performed to removal rRNA as previously described (Adiconis et al. 2013). The DNase digested RNA was purified with AMPure Beads and then fragmented to about 140–160 nt. The RNA fragments were further converted into a DNA library through end repair, adaptor ligation, reverse transcription circularization, and PCR amplification. The library was further purified with AMPure Beads and validated using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., CA, USA) and ABI StepOnePlus Real-Time PCR System (Applied Biosystems, CA, USA). The qualified library was sequenced by Illumina Illumina HiSeqTM 4000.

treatment_protocol: Treatment group (n = 50) were administered with a single intraperitoneal injection of 3 mg of CdCl2 /kg body weight (bw). The control group (n = 50) was injected with saline (0.9% NaCl). Mice were sacrificed by cervical dislocation at 35 days after treatment. Testes, and mature sperm were quickly harvested until further study.

tag: strain

value: Testes

tag: age

value: 3-5 months

tag: agent

value: cadmium


title: ESP 1

status: Public on Oct 14 2019

type: SRA

city: Seoul

first: Eunmin

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description:
3-1
Liver
processed data file: Normalized_FPKM.txt

library_source: transcriptomic

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using Tophat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized_FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Bile duct epithelial cell

extract_protocol:
RNAs were extracted from the cells of Homo sapiens. Poly(A) mRNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit, according to the manufacturer’s protocol.

tag: cell line

tag: cell type

value: Bile duct epithelial cells

tag: treatment

value: ESP


title: Zfp281-ChIP_WT-ESC_I

city: Basel

first: Joerg

last: Betschinger

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

library_source: genomic

data_processing:
ChIP-seq reads were aligned to mouse GRCm38/mm10 genome using qAlign from the Bioconductor package QuasR (Gaidatzis et al., 2015) (package version 1.22.0) with default parameters.
We observed a non-linear relationship in Zfp281 ChIP-seq data when comparing read counts in Zfp281 peaks between ChIP-seq replicates in WT ESCs, and therefore performed loess regression using normalizeBetweenArrays function of the Bioconductor package limma (Ritchie et al., 2015) (package version 3.38.2) with method=cyclingloess.
In Bio-Ehmt1 ChIP-seq data we detected a variable dependency of read counts in genomic tiles on the tile’s GC composition (GC bias) which was most pronounced in input samples. In order to reduce this bias, we used a loess-based normalization method: First, reads were counted in each sample in 10kb windows. The counts were then scaled (divided by the total number of aligned reads (library size), multiplied with minimal library size, and added with a pseudocount of 8) and log2 transformed. A loess curve was fit to the log2-transformed counts as a function of the fraction of G+C bases in the window using the R function loess with span = 0.3. This fit robustly captures the global signal dependency on the underlying GC composition. GC-corrected log2 read counts were then obtained by subtracting the values predicted by the loess fit from the observed log2 read counts (residuals of the fit).
Peaks for Zfp281 or Zic2 were called on all replicates and in all conditions of Zfp281 or Zic2 ChIP-seq reads, respectively, using Macs2 (Zhang et al., 2008) (version 2.1.1.20160309) with default parameters. Peaks that were at least two-fold enriched (IP over respective inputs) in at least one ChIP samples were considered.
Peaks were assigned to genes by calculating the distances of peak midpoint to the nearest transcriptional start site (TSS) using a set of non-redundant TSSs with a single start site randomly selected for each gene.
Due to the broad chromatin distribution of Ehmt1 and H3K9me2, ChIP-seq reads were first quantified in genome-tiling windows of 10kb which were generated using tileGenome function from Bioconductor package GenomicRanges (Lawrence et al., 2013) (package version 1.34.0) with tilewidth=10000 and cut.last.tile.in.chrom=TRUE. To quantify Ehmt1 and H3K9me2 enrichment at Zfp281 binding sites, Zfp281 peak regions were extended to 10kb centered on the peak midpoint using the function resize from the Bioconductor package GenomicRanges. As a control set, DHS-seq peaks (peak annotation downloaded from ENCODE; accession number: ENCSR000CMW) were extended to 10kb centered on the peak midpoint and only regions non-overlapping with 10kb extended Zfp281 peaks were considered. The final set of control regions was obtained by randomly sampling one DHS 10kb peak per Zfp281 10kb peak, such that the distributions of DHS-seq signal (log2 RPM) and GC-content between Zfp281 10kb extended peaks and the selected control regions matched closely.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the Bioconductor package QuasR with default parameters using scaling=TRUE and binsize=100. The scores in the wig file therefore represent the number of alignments per 100bp window and scaled by the total number of aligned reads per sample.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells RGd2

growth_protocol: ESCs (female RGd2 cells containing a Rex1:GFPd2-IRES-Blasticidin (Wray et al., 2011)) were cultured on plastic coated with gelatin in N2B27 medium (DMEM/F12 (Life Technologies), Neurobasal (Gibco) supplemented with N2 (homemade) and B-27 Serum-Free Supplement (Gibco), 2mM L-glutamine (Gibco), and 0.1mM 2-mercaptoethanol (Sigma)) with 2i (3µM CHIR99021 and 1µM PD0325901 (Steward lab, Dresden)).

extract_protocol:
Cells were fixed with 1% formaldehyde and neutralized with glycine to a final concentration of 0.125 mM. After nuclei extraction, DNA for ChIPs of endogenous proteins and corresponding inputs was sonicated using Diagenode Bioruptor Plus in 15 ml Diagenode Falcon tubes, cell lysates incubated with corresponding antibody over night at 4°C and Dynabeads were added the next day. In case of Bio-Ehmt1 and corresponding inputs, DNA was digested with Micrococcal Nuclease (Cell Signaling) and incubated with M-280 Streptavidin coupled Dynabeads (Invitrogen) for 1h at 4°C. Beads were washed, eluted and the suspension was de-crosslinked over night at 65 °C. DNA of ChIPs from endogenous proteins and corresponding inputs was purified using MinElute PCR Purification Kit (QIAGEN) and of Bio-Ehmt1 ChIPs and corresponding inputs using AMPure XP beads (Beckman Coulter).
ChIP-seq libraries were prepared using NEBNext Ultra kit (New England BioLabs) following the manufacturer’s recommendations.

treatment_protocol: For differentiation, ESCs were seeded on gelatin-coated plates at 1.5 x 104 cells/cm2 in 2i and the following day 2i was withdrawn.

value: mouse embryonic stem cells

tag: chip antibody

value: Zfp281 (Bethyl Laboratories, A303-118A)

tag: genotype

value: WT

tag: time point

value: ESC


title: sigmoid biopsy, allogenic FMT, subject 013, baseline

type: RNA

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 Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.48.0).

label: biotin

source_name: sigmoid biopsy, uncleansed colon

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The study was conducted according to the principles of the Declaration of Helsinki and its revisions, and ethical approval was obtained from the Central Ethical Review Board of Uppsala, Sweden (registration number 2013/180). The study was performed at Örebro University Hospital in Örebro, Sweden, from May 2014 to April 2016. All participants were recruited in the greater area of Örebro and gave their written informed consent before participation. The trial has been registered at ClinicalTrials.gov (NCT02092402) on March 20, 2014. Adult IBS patients that fulfilled the Rome III diagnostic criteria for irritable bowel syndrome (IBS) were included in this study. All IBS subtypes, including postinfectious IBS, were eligible for the study. Reasons for exclusion were any other known organic gastrointestinal disease, previous complicated gastrointestinal surgery, nongastrointestinal malignancy, dementia, severe depression, major psychiatric disorder, severe endometriosis, recent diagnosis of lactose intolerance, celiac disease, pregnancy or breast-feeding, antimicrobial treatment within 4 weeks prior to first screening visit, regular consumption of probiotics within 4 weeks prior to randomization, abuse of alcohol and drugs, or any other clinically significant disease/condition which in the investigator’s opinion could interfere with the results of the trial. The patients were asked to keep their medication and diet stable  over the entire study period.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Two weeks before the FMT (baseline) as well as two and eight weeks after the FMT, the participants underwent a sigmoidoscopy, and biopsies were collected at a standardised location (20-25 cm from the anal verge at the crossing with the arteria iliaca communis) from an uncleansed sigmoid. Biopsies were transfered in RNAlater and immediately frozen at -80°C until further analysis.

tag: tissue

value: uncleansed colon

tag: sex (female=1, male=0)

tag: subjectid

tag: age (yrs)

tag: moment of sampling (pre/post intervention)

value: Baseline (app. 2w before intervention)

tag: time of sampling

value: Morning, after overnight fasting

tag: experimental condition

value: Allogenic FMT


title: Control2

description:
1-2
Liver
processed data file: Normalized_FPKM.txt

value: Control


title: sigmoid biopsy, allogenic FMT, subject 013, 2 weeks after intervention

value: 2 weeks after intervention


title: H3K9me2-ChIP_WT-32h_I

value: H3K9me2 (Abcam, ab1220)


title: Control1

description:
1-1
Liver
processed data file: Normalized_FPKM.txt


title: H3K9me2-ChIP_WT-ESC_I


title: Testes-Cd-1

country: China


title: sigmoid biopsy, autologous FMT, subject 012, 2 weeks after intervention

value: Autologous FMT


title: H3K27ac-ChIP_WT-ESC_I

value: H3K27ac (Active Motif, 39135)


title: H3K9me2-ChIP_WT-ESC_II


title: input_WT-32h_II

value: input


title: input_WT-32h_I


title: Sperm-Cd-1

source_name: Sperm

value: Sperm

value: 3-5 months

value: cadmium


title: Testes-Control-2

value: Testes

value: control


title: input_WT-ESC_I

value: mouse embryonic stem cells

value: WT


title: NDMA+ESP 1

description:
4-1
Liver
processed data file: Normalized_FPKM.txt

value: Bile duct epithelial cells

value: NDMA+ESP


title: sigmoid biopsy, autologous FMT, subject 012, baseline

value: uncleansed colon

value: Baseline (app. 2w before intervention)

value: Morning, after overnight fasting


title: sigmoid biopsy, allogenic FMT, subject 011, baseline

value: Allogenic FMT


title: sigmoid biopsy, autologous FMT, subject 008, 8 weeks after intervention

value: 8 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 011, 2 weeks after intervention

value: 2 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 008, baseline

value: Autologous FMT


title: sigmoid biopsy, autologous FMT, subject 008, 2 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 010, 8 weeks after intervention


title: Sperm-Cd-2


title: Testes-Control-1


title: sigmoid biopsy, allogenic FMT, subject 007, 8 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 010, 2 weeks after intervention


title: Sperm-Control-4


title: sigmoid biopsy, allogenic FMT, subject 011, 8 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 007, 2 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 010, baseline


title: input_WT-ESC_II

value: input

value: ESC


title: ST-HSC cells from Il27ra -/- mice treated with AngII, rep 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: short-term hematopoietic stem cell progenitors

extract_protocol:
A total of 5,000 LT-HSCs (Lin-Sca-1+c-Kit+CD150+CD48-) or ST-HSCs (Lin-Sca-1+c-Kit+CD150-CD48+) were FACS-sorted from the BM of Apoe-/-, Apoe-/-Il27ra+/- or Apoe-/-Il27ra-/- mice infused with Ang II or PBS for 2 weeks. RNA was extracted using RNA Isolation Kit (QIAGEN) according to manufacturer’s protocol.
Total RNA libraries were prepared by using Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara)

value: AngII

tag: genotype/variation

tag: replicate


title: ST-HSC cells from Il27ra -/- mice treated with AngII, rep 4

value: short-term hematopoietic stem cell progenitors


title: sigmoid biopsy, allogenic FMT, subject 007, baseline


title: sigmoid biopsy, autologous FMT, subject 006, 2 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 006, 8 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 006, baseline


title: Sperm-Control-3

tag: strain

value: Sperm

tag: age

value: 3-5 months


title: ST-HSC cells from Il27ra -/- mice treated with AngII, rep 2

tag: agent


title: Sperm-Control-2

tag: cell type

value: control


title: Sperm-Control-1


title: V-01M_IV-2

city: Beijing

first: Shiya

address: No. 2, Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

data_processing:
The raw reads were cleaned using FastQC software to remove the adaptors and poly-N-containing low-quality reads, as well as reads shorter than 40 bp. The transcriptome was assembled using Trinity software with the min_kmer_cov set to 2, and all other parameters set to their defaults. The assembled transcripts and unigenes were used for the subsequent annotation analysis.
The unigenes were functionally annotated by searching for homologs in a comparison against the public databases Swiss_Prot, Translated EMBL (TrEMBL), Non-redundant Proteins (NR), Protein Families Database (Pfam), Eukaryotic Orthologous Groups Database (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG)).
The number of fragments per kilobase of transcripts per million mapped reads (FPKM) was calculated for the quantification of the gene expression levels. The abundance of the gene transcripts was calculated using Cufflinks.
The cuffdiff command was used to filter out the differential genes with a mapping read sum greater than 10 in both samples, |log2 (fold change)| > 1, P-value ≤ 0.05, and Q-value ≤ 0.05. GO and KEGG significant enrichment analyses was performed, and a hypergeometric test (phyper) was used to identify any GO/KEGG terms that were significantly enriched in the differentially expressed genes (DEGs) compared with all of the expressed genes (P-value < 0.05).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Tagetes erecta

source_name: V-01M Petals

growth_protocol: The marigold (Tagetes erecta L.) inbred line ‘V-01’ (orange petals) and its natural mutant ‘V-01M’ (yellow petals) were grown in a climate chamber at 22°C with 70% relative humidity and a 16-h/8-h day/night photoperiod.

extract_protocol:
Total RNA was isolated from the petals using an RNAprep Pure kit (Tiangen Biotech Co.,Ltd., Beijing, China). The RNA concentration was determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA samples with an RNA integrity number (RIN) greater than 9 were used to construct the sequencing library using a NEB Next Ultra Directional RNA library prep kit, according to the manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Petals

tag: developmental stage

value: Stage IV


title: ST-HSC cells from Il27ra -/- mice treated with AngII, rep 1


title: ST-HSC cells from Il27ra +/- mice treated with AngII, rep 2


title: sigmoid biopsy, autologous FMT, subject 004, 8 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 005, baseline


title: sigmoid biopsy, allogenic FMT, subject 005, 2 weeks after intervention


title: sigmoid biopsy, autologous FMT, subject 004, 2 weeks after intervention


title: V-01M_IV-3


title: V-01M_III-3

value: Stage III


title: sigmoid biopsy, autologous FMT, subject 003, 8 weeks after intervention

value: uncleansed colon


title: sigmoid biopsy, autologous FMT, subject 003, baseline

value: Baseline (app. 2w before intervention)


title: sigmoid biopsy, autologous FMT, subject 003, 2 weeks after intervention

value: Morning, after overnight fasting


title: sigmoid biopsy, allogenic FMT, subject 002, 8 weeks after intervention

value: Allogenic FMT


title: sigmoid biopsy, autologous FMT, subject 004, baseline


title: V-01M_IV-1


title: sigmoid biopsy, allogenic FMT, subject 005, 8 weeks after intervention

value: 8 weeks after intervention


title: sigmoid biopsy, allogenic FMT, subject 002, 2 weeks after intervention

value: 2 weeks after intervention


title: ST-HSC cells from Il27ra +/- mice treated with AngII, rep 1


title: ST-HSC cells from Il27ra +/- mice treated with AngII, rep 4


title: sigmoid biopsy, allogenic FMT, subject 001, baseline


title: ST-HSC cells from Il27ra WT mice treated with AngII, rep 2

value: WT


title: sigmoid biopsy, allogenic FMT, subject 001, 2 weeks after intervention


title: V-01M_III-1


title: sigmoid biopsy, allogenic FMT, subject 002, baseline


title: ST-HSC cells from Il27ra WT mice treated with AngII, rep 3


title: V-01M_III-2


title: ST-HSC cells from Il27ra -/- mice treated with PBS, rep 2

value: PBS


title: ribosome footprinting rep6

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description: ribo.bigwig.tgz

data_processing:
Illumina OLB1.9 or CASAVA1.8 software used for basecalling.
Flexbar used for adapter trimming.
RSEM used to estimate the isoform expression level.
Tophat2 used to map reads against the reference genome.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample; or wig files contain +12nt position shifted tag density.

organism: Rattus norvegicus

source_name: brain

growth_protocol: Sprague Dawley rats were housed in standard cages and fed standard lab chow and water ad libitum

extract_protocol:
TRIzol or lysis buffer
Truseq

treatment_protocol: Four-week-old male animals were sacrificed.

value: brain

tag: subcellular compartment

tag: library strategy

value: ribosome footprinting


title: sigmoid biopsy, allogenic FMT, subject 001, 8 weeks after intervention


title: ribosome footprinting rep5

description: ribo.bigwig.tgz


title: ST-HSC cells from Il27ra WT mice treated with AngII, rep 1

value: short-term hematopoietic stem cell progenitors

value: AngII


title: V-01M_II-3

value: Stage II


title: ST-HSC cells from Il27ra -/- mice treated with PBS, rep 1


title: neuropil RNA-seq rep2

molecule: polyA RNA

source_name: hippocampal slices

value: hippocampus

value: neuropil

value: mRNA-seq


title: neuropil RNA-seq rep1


title: V-01M_I-2

value: Petals

value: Stage I


title: ribosome footprinting rep3

description: ribo.bigwig.tgz


title: ST-HSC cells from Il27ra -/- mice treated with PBS, rep 3


title: stem_isolated_secondary_xylem_rep1

city: Poznan

first: Katarzyna

last: Marzec-Schmidt

address: Umultowska 89

department: General Botany

country: Poland

institute: Adam Mickiewicz University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to an Affymetrix GeneChip Poplar Genome Array (A-AFFY-131) according to the provided Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Thermo Fisher Scientific, USA)

data_processing: The raw image data from a total of three A-AFFY-131 arrays were normalized with Robust Multi-Array Average (RMA). The normalized data were statistically analyzed using GeneSpringGX7 13.1 (Agilent Technologies Inc., USA) software. Data were subjected to a one-way ANOVA with a Benjamini Hochberg corrected p-value cut-off = 0.05. The analysis was limited to genes with statistically significant differences in expression level and a fold difference equal to or larger than 2 between PR1 and PR2/PR3 in the pioneer root samples and between PS1 and PS2/PS3 in stem samples.

organism: Populus trichocarpa

source_name: stem, 40-45cm – isolated secondary xylem

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Poplar Genome Array, A-AFFY-131).

growth_protocol: All experiments were performed on seed-grown Populus trichocarpa (Torr. & Gray). Seeds were germinated on 0.8% agar medium in a growth chamber. After developing of first roots, seedlings were transfered into multi-pot trays filled with sterile garden substrate mixed with perlite and kept in phytotron chamber (16h/8h, 18℃/14℃). After  1.5 months of growth, plants were planted into rhizotrons filled with natural soil with shoots extending from the top into the air. Plants were  grown in plastic tunel. Waterlogging was avoided by installing a drainage hole in the bottom of each rhizotron that permitted soil aeration and drainage of excess water.

extract_protocol: Total RNA was extracted from three biological replicates of each developmental stage of pioneer roots and stems using an RNeasy Plant Mini kit (Qiagen, USA).

treatment_protocol: After 2 months of growing in the rhizotrons in plastic tunel, fragments of pioneer roots and stem representing different stages of xylem development were collected. No special treatment was used in the experiment.

value: stem isolated secondary xylem


title: V-01M_I-1


title: V-01M_II-2


title: stem_isolated_secondary_xylem_rep3


title: ribosome footprinting rep2

description: ribo.bigwig.tgz


title: V-01M_II-1


title: V-01_IV-3

source_name: V-01 Petals

value: Stage IV


title: ST-HSC cells from Il27ra +/- mice treated with PBS, rep 1


title: somata RNA-seq rep1

value: somata


title: stem_secondary_development_rep2

source_name: stem, 20-25cm – secondary development

value: stem with secondary development


title: stem_isolated_secondary_xylem_rep2


title: ST-HSC cells from Il27ra +/- mice treated with PBS, rep 3


title: ribosome footprinting rep1

description: ribo.bigwig.tgz


title: ribosome footprinting rep4

description: ribo.bigwig.tgz


title: Cdk19 KO RasG12V Rep1

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

country: France

institute: CNRS

description:
Sample10_40.1
rRNA-depleted total RNA

data_processing:
Base calling was performed with Illumina RTA software. FastQC was used to perform quality control of the sequencing.
All the reads that passed the quality control were aligned to the mouse reference genome and the counts per gene were quantified using the tool STAR 2.6.0a.
The Ensembl mouse genome annotations (release 93) were used for establishing the coordinates of each gene and their corresponding transcripts.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *_ensembl_ReadsPerGene.out.tab: Standard STAR software output files. Tab-delimited text file with the raw read counts for each gene.

source_name: BMEL cells

growth_protocol: BMEL (Bipotential Mouse Embryonic Liver) cell line was isolated from CDK8F/F mouse. Cells were grown on collagen-coated plates in RPMI medium (Gibco/Life Technologies) supplemented with 10% fetal calf serum (Pan-Biotech), insulin 10 ug/mL (Sigma), IGFII 30 ng/mL (Peprotech), EGF 50 ng/mL (Peprotech), 100 units/ml penicillin, and 100 mg/ml streptomycin. Cells were grown under standard conditions at 37°C in a humidiﬁed incubator containing 5% CO2. All cells were routinely tested to confirm absence of mycoplasma contamination.

extract_protocol:
RNA was harvested using Qiagen RNeasy kit following manufacturer instructions. DNaseI treatment (Qiagen) was used to remove residual genomic DNA. RNA integrity was assessed by Agilent BioAnalyser. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NO

tag: cell line

value: BMEL

value: Bipotential mouse embryonic liver cells

tag: transformation

tag: condition

value: Exponentially growing on collagen coated plates


title: V-01M_I-3

tag: tissue


title: ST-HSC cells from Il27ra WT mice treated with PBS, rep 1

value: PBS

value: WT


title: hippocampus RNA-seq rep2

description: hippo.isoform.TPM.tsv.gz


title: ST-HSC cells from Il27ra +/- mice treated with PBS, rep 2

value: short-term hematopoietic stem cell progenitors


title: Cdk19 KO RasG12V Rep3

description:
Sample12_40.4
rRNA-depleted total RNA


title: hippocampus RNA-seq rep1

description: hippo.isoform.TPM.tsv.gz


title: somata RNA-seq rep2


title: ST-HSC cells from Il27ra WT mice treated with PBS, rep 2


title: LT-HSC cells from Il27ra -/- mice treated with AngII, rep 4

source_name: long-term hematopoietic stem cell progenitors

value: AngII


title: V-01_III-3

value: Stage III


title: stem_secondary_development_rep3


title: stem_secondary_development_rep1


title: V-01_IV-2


title: V-01_III-2


title: stem_primary_development_rep3

source_name: stem,  0-2cm – apical meristem with primary development

value: stem apical meristem with primary development


title: V-01_IV-1


title: LT-HSC cells from Il27ra -/- mice treated with AngII, rep 2

value: long-term hematopoietic stem cell progenitors


title: LT-HSC cells from Il27ra -/- mice treated with AngII, rep 3


title: LT-HSC cells from Il27ra +/- mice treated with AngII, rep 3


title: V-01_III-1


title: LT-HSC cells from Il27ra -/- mice treated with AngII, rep 1


title: LT-HSC cells from Il27ra +/- mice treated with AngII, rep 2


title: stem_primary_development_rep2


title: stem_primary_development_rep1


title: root_secondary_development_rep2

source_name: pioneer roots, 13-16cm – secondary development

value: pioneer roots with secondary development


title: lungs_normal 1_4d

first: Yifan

last: Rao

address: yuanmingyuanxi street

institute: Chinese academy of agricultural sciences

description:
Gene expression in normal cows at age 4d.
Replicate 1

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

organism: Bos taurus

source_name: lungs, normal, 4d

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

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: breed

value: Holstein

tag: cow group

value: naturally conceived

tag: disease status

value: healthy

value: lungs


title: lungs_normal 4_4d

description:
Gene expression in normal cows at age 4d.
Replicate 4


title: lungs_normal 2_4d

description:
Gene expression in normal cows at age 4d.
Replicate 2


title: lungs_normal 3_4d

description:
Gene expression in normal cows at age 4d.
Replicate 3


title: lungs_clone 4_4d

description:
Gene expression in cloned cows at age 4d.
Replicate 4

source_name: lungs, clone, 4d

value: cloned

value: respiratory failure


title: root_secondary_development_rep1


title: V-01_II-3

value: Petals

value: Stage II


title: root_secondary_development_rep3


title: root_primary_development_rep3

source_name: pioneer roots, 4-6cm – primary development

value: pioneer roots with primary development


title: LT-HSC cells from Il27ra +/- mice treated with AngII, rep 4


title: LT-HSC cells from Il27ra WT mice treated with AngII, rep 2


title: V-01_II-2


title: V-01_II-1


title: V-01_I-3

value: Stage I


title: V-01_I-1


title: LT-HSC cells from Il27ra +/- mice treated with AngII, rep 1


title: V-01_I-2


title: Dbus_Hi-C_for_assembly

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
We used our Hi-C data and PacBio data (SRR7029398, SRR7029397) in combination with published whole genome sequencing reads ((Zhou and Bachtrog 2015) and (Vicoso and Bachtrog 2015) accession codes SRR1795010, SRR1794619, SRR1794616, SRR1794617, SRR1794614 and SRR826809) for de novo genome assembly.
Genome assembly and hard-masked genome assembly of D. busckii

data_processing:
Hi-C: Paired-end reads were mapped using bwa mem with parameters -A1 -B4 -E50 -L0 (which promote a read to be split instead of adding a gap) and Hi-C matrices generated using `hicBuildMatrix`, Hi-C matrices of replicates were merged using `hicSumMatrices` and corrected at restriction enzyme resolution using `hicCorrectMatrix` tools from HiCExplorer v1.8.1. TAD boundaries were called using the `hicFindTADs` tool from HiCExplorer with settings `--minDepth 15000 --maxDepth 50000 --step 2000 --thresholdComparisons 0.01 --correctForMultipleTesting bonferroni`.
Supplementary_files_format_and_content: FASTA files of the D.busckii assembly are available on the series record.

organism: Drosophila busckii

source_name: fly embryos

growth_protocol: D. melanogaster and D. virilis flies were maintained  in standard Drosophila medium. D. busckii flies were additionally fed with instant Drosophila medium (Formula 4-24, Carolina Biological Supply Company, catalog number 173202) mixed with instant potato powder on top of the standard Drosophila medium.

extract_protocol:
In situ Hi-C experiments were performed using a modified version of the in situ Hi-C protocol (Rao et al. 2014) described in (Ramirez et al. 2018). Nuclei were extracted by resuspension in 1 mL ice-cold lysis buffer (10   mM Tris-HCl, pH 8, 10   mM NaCl, 0.2% IGEPAL CA-630) and sonication following the standardized nuclear extraction NEXON protocol (Arrigoni et al. 2015) (Covaris E220 sonicator, settings: 75   W peak power, 2 % duty factor, 200 cycles/burst, for 15-30   sec until about 70 % of intact nuclei were released). Samples were filtered through a 30 µm filter to remove bigger embryo fragments. From this step on we followed the protocol described in (Ramirez et al. 2018). Nuclei were digested using DpnII (NEB, R0543M, 150 U/ sample).
NEB Next Ultra II

value: San Diego stock center, stock number 13000-0081.31

value: late stage 16 embryos

value: embryos


title: Dvir_Hi-C

description:
SRR7029394, SRR7029393 (merge of 2 replicates); We used our Hi-C data (SRR7029394, SRR7029393) for Hi-C scaffolding of published D. virilis contigs (dvir_caf1 assembly, GCA_000005245.1, http://metazoa.ensembl.org/Drosophila_virilis/Info/Index) into a chromosome-length assembly, available on the series record.
processed Hi-C matrices and TAD boundaries.

data_processing:
Hi-C: Paired-end reads were mapped using bwa mem with parameters -A1 -B4 -E50 -L0 (which promote a read to be split instead of adding a gap) and Hi-C matrices generated using `hicBuildMatrix`, Hi-C matrices of replicates were merged using `hicSumMatrices` and corrected at restriction enzyme resolution using `hicCorrectMatrix` tools from HiCExplorer v1.8.1. TAD boundaries were called using the `hicFindTADs` tool from HiCExplorer with settings `--minDepth 15000 --maxDepth 50000 --step 2000 --thresholdComparisons 0.01 --correctForMultipleTesting bonferroni`.
Genome_build: Dvir_HiC, Dbus_HiC, Dm6
Supplementary_files_format_and_content: Hi-C: h5 files of corrected Hi-C matrices of merged two replicates and bed files of TAD boundaries.

organism: Drosophila virilis

source_name: stage 15-16 embryos

value: San Diego stock center,  stock number:15010-1051.0

value: stage 15-16 embryos


title: root_apical_meristem_rep2

source_name: pioneer roots, 0-2cm – root tips with apical meristem

value: pioneer root tips with apical meristem


title: Dbus_Hi-C

description:
SRR7029396, SRR7029395, SRR7029388, SRR7029387 (merge of 2 replicates, each sequenced two-times)
Reads for this sample were produced both with NextSeq 500 or HiSeq 3000 instruments
processed Hi-C matrices and TAD boundaries.

extract_protocol:
In situ Hi-C experiments were performed using a modified version of the in situ Hi-C protocol (Rao et al. 2014) described in (Ramirez et al. 2018). Nuclei were extracted by resuspension in 1 mL ice-cold lysis buffer (10   mM Tris-HCl, pH 8, 10   mM NaCl, 0.2% IGEPAL CA-630) and sonication following the standardized nuclear extraction NEXON protocol (Arrigoni et al. 2015) (Covaris E220 sonicator, settings: 75   W peak power, 2 % duty factor, 200 cycles/burst, for 15-30   sec until about 70 % of intact nuclei were released). Samples were filtered through a 30 µ m filter to remove bigger embryo fragments. From this step on we followed the protocol described in (Ramirez et al. 2018). Nuclei were digested using DpnII (NEB, R0543M, 150 U/ sample).
NEB Next Ultra II


title: LT-HSC cells from Il27ra -/- mice treated with PBS, rep 3

value: long-term hematopoietic stem cell progenitors

value: PBS


title: LT-HSC cells from Il27ra -/- mice treated with PBS, rep 2


title: lungs_clone 2_4d

description:
Gene expression in cloned cows at age 4d.
Replicate 2

value: Holstein


title: lungs_clone 3_4d

description:
Gene expression in cloned cows at age 4d.
Replicate 3


title: root_primary_development_rep1


title: polysome rep2

value: brain

value: polysome profiling


title: LT-HSC cells from Il27ra WT mice treated with AngII, rep 1

value: AngII

value: WT


title: root_apical_meristem_rep3


title: root_primary_development_rep2


title: LT-HSC cells from Il27ra -/- mice treated with PBS, rep 1


title: polysome rep1


title: root_apical_meristem_rep1


title: lungs_clone 1_4d

description:
Gene expression in cloned cows at age 4d.
Replicate 1

value: cloned

value: respiratory failure

value: lungs


title: ST-HSC cells from Il27ra +/- mice treated with AngII, rep 3

source_name: short-term hematopoietic stem cell progenitors


title: Input_Dvir_female

data_processing:
ChIP-seq: Data processing included sequencing quality and adaptor trimming of paired-end reads using trim_galore v0.4, mapping individual replicates using bwa v0.7.12 followed by sorting and indexing of bam files using samtools-1.2. The coverage of mapped reads was calculated using deeptools v2.0.1 with settings `-bs 10 --normalizeTo1x {EFFECTIVE_GENOME_SIZE}`. We defined the effective genome size as the total genome size minus the number of Ns which is 117 Mb and 188 Mb for D. busckii and D. virilis, respectively. Log2fold ratios of merged replicates over the input sample was calculated using bamCompare with settings `-bs 10 --scaleFactorsMethod SES`.
Genome_build: Dvir_HiC, Dbus_HiC, Dm6
Supplementary_files_format_and_content: ChIP-seq: bigWig files of mapped reads of individual replicates (SampleName.bw) and bigWig files of log2fold ratios of merged replicates over the input sample (SampleName-Input.bw).

source_name: Female 3rd instar larvae

extract_protocol:
ChIP-seq: Larvae were dissected and the front part fixed at RT for 15 min with 0.2% formaldehyde. Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II

tag: chip antibody

value: none (input)

value: anterior portion of third instar larvae

tag: Sex

value: female


title: free rep1

source_name: brain


title: monosome rep2


title: H4K16ac_ChIP-seq_Dvir_female

value: H4K16ac(Merck Milipore, 07-329)


title: H3_ChIP-seq_Dbus_female

value: San Diego stock center, stock number 13000-0081.31

value: H3(Active Motif, MABI 0301, 39763)


title: Input_Dbus_male

source_name: Male 3rd instar larvae

value: male


title: Input_Dbus_female


title: LT-HSC cells from Il27ra +/- mice treated with PBS, rep 3

value: long-term hematopoietic stem cell progenitors

tag: genotype/variation

tag: replicate


title: monosome rep1


title: Dbus_PacBio

data_processing:
PacBio reads were error-corrected using the FM-index Long Read Corrector FMLRC (Wang et al. 2018). Afterwards, the reads were aligned and overlapped to assembled short-read contigs using DBG2OLC (Ye et al. 2016) with parameters `LD 0 k 17 AdaptiveTh 0.01 KmerCov 2 MinOverlap 20 RemoveChimera 1 ChimeraTh 2`.'
Supplementary_files_format_and_content: FASTA files of the D.busckii assembly are available on the series record.

source_name: adult flies

extract_protocol: P6 chemistry

tag: strain

value: adult females

value: whole fly


title: H4K16ac_ChIP-seq_Dbus_male


title: H3_ChIP-seq_Dvir_female

value: San Diego stock center,  stock number:15010-1051.0


title: free rep2

value: brain

value: polysome profiling


title: H3_ChIP-seq_Dbus_male


title: iBAT ko2

status: Public on Oct 12 2019

city: Bunkyo-ku

first: Sho

last: Sugawara

state: Tokyo

department: Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Raw paired-end 150 bp reads were aligned to the reference genome (mm10) using HISAT2 (version 2.1.0).
The number of mapped reads to each gene was determined by featureCounts (version 1.6.2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 values for each sample.

source_name: Interscapular brown adipose tissue

extract_protocol:
Interscapular brown adipose tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Isogen (Wako). Total RNA (100 ng) were used for RNA-seq library preparation with a TruSeq Stranded mRNA Library Prep Kit for NeoPrep (Illumina, NP-202-1001) that allows polyA-oligo(dT)-based purification of mRNA, according to the manufacturer’s protocol with minor modification and optimization as follows. Custom dual index adaptors were ligated at the 5’ and 3’-ends of library, and PCR was performed for 11 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 10 week old

tag: genotype

value: PGAM5 KO

value: Interscapular brown adipose tissue


title: iBAT wt3

value: Wild-type


title: LT-HSC cells from Il27ra +/- mice treated with PBS, rep 2

tag: cell type

tag: agent

value: PBS


title: H3_ChIP-seq_Dvir_male

value: anterior portion of third instar larvae


title: Input_Dvir_male

value: none (input)


title: LT-HSC cells from Il27ra +/- mice treated with PBS, rep 1


title: iBAT wt1


title: D2 Mac1 -Dox rep2

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad St

department: Cell Biology

institute: Yale University

data_processing:
For RNA-Seq, sequencing reads were mapped to mouse mm10 using TopHat. Gene counts were quantified by Featurecounts.
For ATAC-Seq, sequencing reads were trimmed for adapter sequences using Cutadapt and aligned to mouse mm10 using Bowtie2. Duplicates from uniquely mapped reads were removed using Picard.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-Seq, processed data files are gene raw counts text files from featurecounts output.
Supplementary_files_format_and_content: For ATAC-Seq, processed data files are bigWig files generated from deepTools.

source_name: D2 Mac1 -Dox

growth_protocol: Cells were cultured in x-vivo15 supplemented with mIL3, Flt3L, mTPO, and mSCF.

extract_protocol:
RNA was extracted with TRIzol reagent.
For ATAC-Seq, libraries were prepared as previously described by Buenrostro et al. Nature Methods (2013).
RNA-Seq libraries were prepared using TruSeq Stranded mRNA Library Preparation Kit from Illumina.

treatment_protocol: Dox was used as 2ug/ml, palbociclib was used as 500nM.

tag: strain background

value: r/r iMLL-AF9+

value: Bone marrow

value: Mac1+ cells

tag: preparation

value: cultured in vitro for two days, untreated


title: D2 Mac1 +Dox rep2

source_name: D2 Mac1 +Dox

value: cultured in vitro with Dox for two days


title: D2 Mac1 +Dox rep1


title: Dmel_Hi-C

description:
SRR7029390,SRR7029389,SRR7029392,SRR7029391 (merge of 2 replicates, each sequenced two-times)
processed Hi-C matrices and TAD boundaries.

organism: Drosophila melanogaster

value: w1118 Oregon R

tag: developmental stage

value: stage 15-16 embryos

value: embryos


title: H4K16ac_ChIP-seq_Dvir_male

value: San Diego stock center,  stock number:15010-1051.0

value: H4K16ac(Merck Milipore, 07-329)

value: male


title: iBAT ko3

value: 10 week old

value: PGAM5 KO


title: LT-HSC cells from Il27ra WT mice treated with PBS, rep 1

source_name: long-term hematopoietic stem cell progenitors

value: WT


title: D2 GMP +Dox rep1

source_name: D2 GMP +Dox

value: granulocyte monocyte progenitors


title: iBAT ko4

value: Interscapular brown adipose tissue


title: D0 GMP rep1

source_name: D0 GMP

value: freshly isolated from bone marrow


title: iBAT wt2

value: Wild-type


title: D2 LKS +Dox rep1

source_name: D2 LKS +Dox

value: r/r iMLL-AF9+

value: Bone marrow

value: Lin- Kit+ Sca+ cells


title: H4K16ac_ChIP-seq_Dbus_female

value: San Diego stock center, stock number 13000-0081.31

value: anterior portion of third instar larvae

value: female


title: D2 Mac1 -Dox rep1

value: Mac1+ cells

value: cultured in vitro for two days, untreated


title: D2 GMP -Dox rep1

source_name: D2 GMP -Dox


title: D0 Mac1 rep1

source_name: D0 Mac1


title: D2 GMP +Dox rep2

value: cultured in vitro with Dox for two days


title: D2 GMP -Dox rep2


title: iBAT ko1

value: male


title: D0 Mac1 rep2


title: D2 LKS +Dox rep2


title: D0 GMP rep2


title: D2 LKS -Dox rep2

source_name: D2 LKS -Dox


title: D2 LKS -Dox rep1


title: astrocytoma_brain_27

city: Changsha

first: Chen-Xue

last: Mao

address: Xiangya road 110

department: Departments of Clinical Pharmacology

institute: Xiangya Hospital, Central South University

description:
T27
Human miRNA Microarray, Release 19.0, 8x60K

hyb_protocol: 200 ng of total RNA was labelled and hybridized with miRNA Complete Labeling and Hyb Kit (Agilent Technologies) following manufacturer’s instructions.

scan_protocol: microRNA expression profiles were performed using Human miRNA Microarray, Release 19.0, 8x60K (Agilent Technologies), which contains 2006 human miRNAs. Slides were scanned by Agilent G2565CA Microarray Scanner.

data_processing: Scanned images of microarray were processed with Agilent Feature Extraction Software v10.7 (Agilent Technologies).

source_name: Astrocytoma

extract_protocol: Total RNA was isolated from tissue specimens using the TRIzol Reagent (Invitrogen) and purified with NucleoSpin RNA clean-up (MACHEREY- NAGEL) according to the manufacturer’s instructions. The quality and integrity of the RNA were verified by gel electrophoresis. The total RNA was purified using mirVana miRNA Isolation Kit (Ambion) and quantified using NanoDrop ND-1000 spectrophotometer (NanoDrop).

treatment_protocol: All astrocytoma patients underwent surgical resection and histologically confirmed, and their clinical and pathologic data were collected.

value: Astrocytoma

tag: gender

value: Male


title: astrocytoma_brain_30

description:
T30
Human miRNA Microarray, Release 19.0, 8x60K

label_protocol: 200 ng of total RNA was labelled and hybridized with miRNA Complete Labeling and Hyb Kit (Agilent Technologies) following manufacturer’s instructions.

tag: tissue

value: Female


title: astrocytoma_brain_51

description:
T51
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_34

description:
T34
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_35

description:
T35
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_37

description:
T37
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_29

description:
T29
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_42

description:
T42
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_49

description:
T49
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_50

description:
T50
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_40

description:
T40
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_28

description:
T28
Human miRNA Microarray, Release 19.0, 8x60K


title: D0 LKS rep2

source_name: D0 LKS


title: astrocytoma_brain_41

description:
T41
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_43

description:
T43
Human miRNA Microarray, Release 19.0, 8x60K


title: D0 LKS rep1


title: astrocytoma_brain_39

description:
T39
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_31

description:
T31
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_38

description:
T38
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_26

description:
T26
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_14

description:
T14
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_22

description:
T22
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_24

description:
T24
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_17

description:
T17
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_15

description:
T15
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_16

description:
T16
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_19

description:
T19
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_23

description:
T23
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_3

description:
T3
Human miRNA Microarray, Release 19.0, 8x60K


title: non-tumor_brain_7

description:
N7
Human miRNA Microarray, Release 19.0, 8x60K

source_name: non-tumor brain tissues

value: non-tumor brain tissues


title: NSC siNOVA2_2

city: Strasbourg

first: Amélie

last: Piton

address: 1 rue Laurent Fries

institute: IGBMC

description: Librairies preparees a partir d'ARN total (300 ng) avec le kit KAPA mRNA HyperPrep Kit (Roche). 12 cycles de PCR. Selection de taille additionnelle (ratio billes / PCR : 0.6)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the hg19 assembly of the Homo sapiens genome using Tophat 2.0.14 and bowtie version 2-2.1.0
Quantification of gene expression has been performed using HTSeq-0.6.1 with annotations coming from Ensembl 75.
Read counts have then been normalized across libraries with the median-of-ratios method pro-  posed by Anders and Huber
Genome_build: hg19

source_name: human neural stem cells (hNSCs)

extract_protocol:
RNeasy mini kit (Qiagen, Valencia, CA, USA) including a DNase treatment
KAPA mRNA HyperPrep Kit (Roche)

value: human neural stem cells

tag: sirna


title: non-tumor_brain_9

description:
N9
Human miRNA Microarray, Release 19.0, 8x60K


title: non-tumor_brain_16

description:
N16
Human miRNA Microarray, Release 19.0, 8x60K


title: NSC siScr_2

value: siScr


title: non-tumor_brain_1

description:
N1
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_12

description:
T12
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_11

description:
T11
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_9

description:
T9
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_10

description:
T10
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_4

description:
T4
Human miRNA Microarray, Release 19.0, 8x60K


title: astrocytoma_brain_7

description:
T7
Human miRNA Microarray, Release 19.0, 8x60K


title: NSC INF_2

value: INTERFERin (transfection agent)


title: non-tumor_brain_17

description:
N17
Human miRNA Microarray, Release 19.0, 8x60K


title: non-tumor_brain_13

description:
N13
Human miRNA Microarray, Release 19.0, 8x60K


title: non-tumor_brain_4

description:
N4
Human miRNA Microarray, Release 19.0, 8x60K


title: 18_Pe_1

city: Lausanne

first: Michael

middle: Vincent

last: Frochaux

address: Route Cantonale

department: SV-IBI

institute: EPFL

data_processing:
Library strategy: BRB-seq
Fastq files were demultiplexed using BRB tools 1.2 with Demultiplex option.
Alignment was done using STAR 2.5.3a with the following parameters:   --outSAMtype BAM SortedByCoordinate   --twopassMode Basic   --outFilterMultimapNmax 1   --outSAMmapqUnique 60
Bam files were annotated using BRBtools 1.2 with the following parameter:  --UMI 15  --AnnotateBam
Removing duplicates using picard-tools 2.2.1 with parameters:  BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX  REMOVE_DUPLICATES=true  ASSUME_SORTED=false  CREATE_INDEX=true
Split N cigars read GATK 4.0.4.
Create realignment targets GATK 4.0.4.
Realigning GATK 4.0.4.
Reads were assigned to maternal or paternal genome using an in house script ASECounter.01.jar found at https://github.com/DeplanckeLab/Frochaux_BouSleiman_2020/tree/master/tool
Genome_build: BDGP 5.25
Supplementary_files_format_and_content: *txt: Tab-delimited text files include total gene counts and line-specific gene counts.

source_name: Drosophila gut

growth_protocol: Standard Drosophila rearing conditions.

extract_protocol:
Drosophila guts were dissected, then RNA was extracted using Trizol and Zymo RNA kit.
BRB-seq

treatment_protocol: Infection with 100 OD Pseudomonas entomophila and 1.5% sucrose or only sucrose.

value: gut

tag: maternal line

tag: paternal line

tag: condition

value: Pe

tag: zygosity

value: Homozygous


title: 10_Pe_1


title: 14_UC_2

value: UC


title: 18_Pe_2


title: 14_Pe_2


title: 10_UC_2


title: NSC siScr_1


title: NSC siNOVA2_1


title: 10_Pe_2


title: NSC INF_1


title: 7_UC_2


title: non-tumor_brain_3

description:
N3
Human miRNA Microarray, Release 19.0, 8x60K


title: non-tumor_brain_10

description:
N10
Human miRNA Microarray, Release 19.0, 8x60K


title: 18_UC_2


title: 14_UC_1


title: 2_Pe_2


title: 18_UC_1


title: Rec expression vector - sample 2

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

institute: Jena University Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Gene Array data was analyzed using Bioconductor version 2.12 and the R statistical programming language version 3.0.1. Thereby, RMA background adjustment was done using gcrma1 package version 2.32.0 and simpleaffy package version 2.36.1. For quality control we used the packages affyPLM version 1.36.0 and RColorBrewer version 1.0-5. Probe sets exhibiting little variation, or a consistently low signal, across samples were filtered by genefilter package version 1.42.0.
Differentially expressed genes were identified using Limma package version 3.16.6 and annotated by the use of the hgu133plus2.db package version 2.9.0 and the annotate package version 1.38.0.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 2 x 10^6 HEK-293 cells were cultured overnight in T25 flasks

extract_protocol: Total RNA from cell cultures was isolated using RNeasy Kits, according to manufacturer’s instructions (Qiagen, Hilden, Germany). Quality and quantity of RNA was analyzed by 1% agarose gel electrophoresis and photometry

treatment_protocol: Transfection was done using 10 µg of the expression vectors and 50 µl of LipofectamineTM 2000 according to manufacturer’s protocols (Invitrogen, Karlsruhe, Germany). Medium was renewed 16h after transfection. Samples for Affymetrix-Chip analysis were harvested 72 h after transfection

tag: cell line

value: human embryonic kidney cells

tag: transfected with

value: pCDNA3 vector expressing HERV-K(HML-2)-Rec protein

tag: time point

value: 72h post transfection


title: 2_Pe_1


title: 14_Pe_1


title: empty vector control - sample 2

value: pCDNA3 empty vector (control)


title: 10_UC_1


title: c18x19_UC_2

value: Heterozygous


title: c19x20_UC_1


title: c19x20_Pe_1


title: c18x19_UC_1


title: empty vector control - sample 1


title: 7_Pe_2


title: c17x18_Pe_1


title: 2_UC_2


title: c17x18_UC_2


title: 2_UC_1


title: c17x18_UC_1


title: c20x1_Pe_2


title: c20x1_UC_2


title: c20x1_UC_1


title: c19x20_Pe_2


title: c14x15_Pe_2


title: Rec expression vector - sample 1


title: c14x15_Pe_1


title: c19x20_UC_2


title: c18x19_Pe_2


title: c14x15_UC_1


title: GMP +Dox ATAC Seq rep2

source_name: GMP +Dox ATAC Seq

tag: genotype/variation

value: r/r iMLL-AF9+

value: Bone marrow

value: granulocyte monocyte progenitors

value: cultured in vitro for two days, Dox added after day one


title: c17x18_Pe_2


title: 7_Pe_1


title: c18x19_Pe_1


title: GMP +Dox ATAC Seq rep1


title: Collapsed Lungs

description: miRNA

data_processing:
The dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18-26 nucleotide were mapped to species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the ank 80 nt sequences using RNA fold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).
miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, and ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
Genome_build: bosTau8
Supplementary_files_format_and_content: xlsx files include fold_change(Collapsed/Normal),pvalue(chi_square_2x2) and pvalue(fisher_test) for each Sample

source_name: Lungs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer.s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: phenotype

value: Collapsed


title: Normal Lungs

description: miRNA

value: Normal


title: c20x1_Pe_1


title: GMP -Dox ATAC Seq rep2

source_name: GMP -Dox ATAC Seq

tag: cell type

value: cultured in vitro for two days, untreated


title: c12x13_Pe_2

value: gut


title: c13x14_UC_2


title: 10x Genomics GMP +Dox

description: scRNA_all_samples_expression_data.csv.gz

data_processing:
For single cell RNA-seq, the gene expression matrix was generated using CellRanger 2.1 with default parameters using the mm10 mouse genome indices from 10X genomics.
Genome_build: mm10
Supplementary_files_format_and_content: For single cell RNA-seq, the processed data file is a single matrix containing the filtered UMI counts from all three samples concatenated using scprep.

source_name: cultured in vitro for one day, -Dox

extract_protocol:
RNA was extracted with 10x Genomics Single Cell Chip
Single cell suspension in RT Master Mix is loaded on the Single Cell a Chip and partition with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Upon dissolution of the Gel Beads in a GEM, the primers with the unique cell barcodes are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA. Full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction.
10x Genomics

treatment_protocol: Dox was used as 2ug/ml.

tag: genotype

tag: strain


title: c14x15_UC_2


title: 10x Genomics GMP -Dox


title: Fresh GMP ATAC Seq rep1

source_name: Fresh GMP ATAC Seq

tag: strain background

tag: preparation

value: freshly isolated from bone marrow


title: c12x13_UC_1


title: c13x14_Pe_1

value: Pe


title: c12x13_UC_2

value: UC


title: c13x14_UC_1


title: GMP -Dox ATAC Seq rep1


title: c12x13_Pe_1


title: c11x12_Pe_1


title: c11x12_UC_2


title: c11x12_Pe_2


title: c11x12_UC_1


title: 10x Genomics Fresh GMP

source_name: freshly isolated from bone marrow


title: 3-B-25mM-DC

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

description: Cells treated with  metformin for 25 hours at the cumulate dose of 10mM- Biological replicate 3

data_processing:
Data generated with an Illumina HiSeq 2000 platform
Mapping with Tophat2 (2.0.8). The minimum and maximum intron lengths were also re-evaluated, respectively, to 30 and 1,200,000 to maximize the number of introns detected.
Alignment files in bam format were then filtered to removed poor mapping quality score (<10) and not primary alignments and read pairs with one single read mapped were filtered using Samtools (0.1.8)
For the differential gene expression analysis, reads mapping to genes were first quantified using the HTSeq-count script provided by the HTSeq python package (v0.5.4)
Splicing analysis with FARLINE pipeline (doi: 10.1038/s41598-018-21770-7) A filter was then applied on exon skipping events detected to select significant variants with an adjusted P value ≤0.05 and ΔΨ value ≥10%.
Gene expression analysis with package DESeq2 (v1.4.5). A filter was then applied to DESeq2 results to select genes with an adjusted P value ≤0.05 and the mean of normalized counts ≥10.
Genome_build: hg19, EnsEMBL r70
Supplementary_files_format_and_content: excel files containing splicing events differentially observed and genes differentially expressed ( xlsx)

source_name: Mesodermal Precursor Cells (MPC) from hES cells line

growth_protocol: cells were cultured on 0.1% gelatin-coated flasks and plates (Sigma-Aldrich) using Knockout Dulbecco’s Modified Eagle’s Medium (Invitrogen) supplemented with 20% fetal bovine serum (Eurobio, Les Ulis, France), 1 mmol/l Glutamax (Invitrogen), 1 mol/l nonessential amino acids (Invitrogen), and 0.1% β-mercaptoethanol (Invitrogen).

extract_protocol:
Total RNA was extracted from treated and none treated cells.
Sequencing libraries were prepared according to the Illumina TruSeq Stranded mRNA Sample Prep Kit (according to manufacturer’s protocol) (Illumina, San Diego, CA). A 2 × 101 bp pairedend sequencing was performed on the HiSeq2000 instrument, using half a lane per sample, to produce on average 80 million read pairs per sample (160 million sequences) with an average insert length of 130 bp. Trimmomatic,52 Tophat2,53 Picard suite (http://www.broadinstittute.github.io/picard), RNA-SeQC,54 and in-house metrics were used to evaluate data quality.

treatment_protocol: Cells were treated each day for 48 hours with 10mM and 25mM metformin.

value: VUB03 hES cell line

value: DM1 mutated


title: c13x14_Pe_2


title: Fresh GMP ATAC Seq rep2


title: c10x11_Pe_1


title: 2-B-25mM-DC

description: Cells treated with  metformin for 48 hours at the cumulate dose of 25mM- Biological replicate 2


title: c10x11_UC_1


title: 3-B-10mM-DC

description: Cells treated with  metformin for 48 hours at the cumulate dose of 10mM- Biological replicate 3


title: 1-B-10mM-DC

description: Cells treated with  metformin for 48 hours at the cumulate dose of 10mM- Biological replicate 1


title: c10x11_Pe_2


title: BMT untreated_1

city: Stanford

first: Panagiota

last: Iliopoulou

state: CA

address: 269 Campus Dr.

institute: Stanford University

description: Gene expression data from tissue samples from day9 post BMT

hyb_protocol: Labeled cRNSs were hybridized to (Affymetrix) according ot manufacturer's protocol

scan_protocol: The chips were scanned using a GeneChip Scanner 3000 GeneChip Mouse 2.0ST- this is a whole transcript desogn with probed as well as exon (Catalog number: 902118 (Affymetric)

data_processing: Background correction, normalization and estimation of gene expression was performed using the Robust Multiarray (RMA) method in R/Bioconductor (www.bioconductor.org). Following aggregation, the samples were re-normalized using quantile normalization.

source_name: Tissue samples from day9 post BMT_control

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using a proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 ug of total RNA was used

growth_protocol: Balb/c  were transplanted with T cell depleted BM (5x10^6 cell/mouse) and T cells (10^6 cells/mouse) of the B6  background. On day9 post bone marrow transplation the mice were euthanized and the tissues were harvested

extract_protocol: Total RNA was extraceted using an RNAeasy Micro Kit (Qiagen) and it's qulaity was assessed by an Agilent 2100 Bioanalyzer. Total RNA (from 500pg-2ng) was reverse transcribed into cDNA followed by in vitro transcription use GeneChip WT Pico (Affymetrix, Santta Clara, CA)

treatment_protocol: Whole gut and spleen tissues were collected on stored on RNA stabilization solution (RNAlater Solution) Invitrogen

value: Balb/c

value: spleen


title: 1-B-25mM-DC

description: Cells treated with  metformin for 48 hours at the cumulate dose of 25mM- Biological replicate 1


title: c10x11_UC_2

value: Heterozygous


title: 2-B-10mM-DC

description: Cells treated with  metformin for 48 hours at the cumulate dose of 10mM- Biological replicate 2


title: BMT untreated_2


title: c9x10_Pe_1


title: c9x10_Pe_2


title: 3-Ctrl-DC

description: None treated cells - Biological Replicate 3


title: 2-Ctrl-DC

description: None treated cells - Biological Replicate 2


title: c9x10_UC_2


title: 1-Ctrl-DC

description: None treated cells - Biological Replicate 1


title: c9x10_UC_1


title: no BMT

description: no BMT

source_name: no BMT


title: c8x9_Pe_2


title: c8x9_Pe_1


title: c8x9_UC_2


title: TGBC2TKB

city: Heidelberg

first: John

middle: M

last: Mariadason

state: Victoria

address: Austin Health, 145 Studyley Road

department: Gastrointestinal Cancers

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description:
Gallbladder tumour cells
processed data file: BTC_gene_counts.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic.
Sequenced reads were mapped to hg19 using tophat v2.0.8 with parameters -g 1.
Duplicate reads were marked using Picard 1.69 MarkDuplicates module.
Gene read counts were extracted using featureCounts (meta-features) using -t exon -g gene_name against Gencode release 15 annotations.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BTC_gene_counts.txt: Single tab-delimited text file containing read counts for all samples and gene refseq id.

source_name: Primary

growth_protocol: All cell lines were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% FBS, 1 mM HEPES buffer and penicillin/streptomycin (100 U/mL) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cell pellets using the High Pure RNA Isolation Kit (Roche, Basel, Switzerland) as per manufacturer’s protocol, which included a DNase I step.
Illumina TruSeq Stranded mRNA.

tag: line source

value: RIKEN

tag: subtype

value: Gallbladder


title: TGBC18TKB

description:
Ampullary tumour cells
processed data file: BTC_gene_counts.txt

value: Ampullary


title: c7x8_Pe_2

tag: tissue


title: TKKK

description:
Intrahepatic tumour cells
processed data file: BTC_gene_counts.txt

value: TKKK

value: Intrahepatic


title: TFK1

description:
Extrahepatic tumour cells
processed data file: BTC_gene_counts.txt

value: DSMZ

value: Extrahepatic


title: TGBC14TKB


title: c7x8_Pe_1

tag: maternal line


title: c7x8_UC_2

tag: paternal line


title: SNU869

value: KCLB


title: c8x9_UC_1

value: gut

tag: condition


title: c7x8_UC_1

tag: zygosity


title: BMT 3D10 treated_1

source_name: Tissue samples from day9 post BMT_3D10


title: SNU308

tag: cell line


title: SNU478


title: c6x7_Pe_2


title: SNU245


title: c6x7_Pe_1


title: SNU1196


title: c6x7_UC_2


title: SNU1079


title: c6x7_UC_1


title: SKCHA1

description:
Extrahepatic (ascites) tumour cells
processed data file: BTC_gene_counts.txt

source_name: Metastatic (Ascites)

value: Zurich Uni.


title: OZ

description:
Extra and Intrahepatic (ascites) tumour cells
processed data file: BTC_gene_counts.txt

value: OZ

value: HSRRB

value: Extra/Intrahepatic


title: 148KO

city: Montreal

first: Tomoko

last: Takano

state: Quebec

address: 1001 Decarie Boulevard

department: Department of Medicine

country: Canada

institute: McGill University Health Centre (MUHC)

data_processing:
Trim using fastp 0.19.5
Map using STAR 2.6.0 (2-pass method)
Count using HTSeq 0.11.1
Analysis using DESeq2
Genome_build: grch37
Supplementary_files_format_and_content: Gene expression table

source_name: Glomeruli

extract_protocol: Glomeruli were isolated and RNA was extracted using using RNeasy mini kit (QIAGEN).

tag: age

value: bPIX -/-


title: 146KO


title: c5x6_Pe_2

value: Pe


title: 147KO


title: Tbr2 conditional knockout _ embryonic cortex stage  E16_replicate 4

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

institute: INSERM U839

description: E16_Mutant_replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadArray Reader used to capture images with default setting.

data_processing: Illumina GenomeStudiov2011.1 were used to obtain raw signal intensities. Background substracted signal intensity for the detected probes (Detection p value<0.05) were used for analysis. Probes detected in one array and not in other were not considered during analysis. Further, outlier probes were removed and data were quantile normalized (Bolstad BM et al., 2003) along with our microarray gene expression data of E13 and E16 (GSE45450).

source_name: tissue: Brain cortex, cell type: basal Progenitors

label_protocol: Biotinylated cRNA were prepared by using Illumina TotalPrep-96 RNA amplification kit from Ambion # 4393543

extract_protocol: Total RNA was extracted from FACS isolated BPs by using  mirVana kit (ambion) following manufacturer's protocol

value: Embryonic day 16


title: 163CTRL

value: wild type


title: Tbr2 conditional knockout _ embryonic cortex stage  E16_replicate 3

description: E16_Mutant_replicate 3


title: OCUG1

description:
Gallbladder (ascites) tumour cells
processed data file: BTC_gene_counts.txt


title: Tbr2 conditional knockout _ embryonic cortex stage  E16_replicate 2

description: E16_Mutant_replicate 2


title: Tbr2 conditional knockout _ embryonic cortex stage  E13_replicate 4

description: E13_Mutant_replicate 4

value: Embryonic day 13


title: 162CTRL


title: c5x6_Pe_1

value: Heterozygous


title: Tbr2 conditional knockout _ embryonic cortex stage  E13_replicate 5

description: E13_Mutant_replicate 5


title: c5x6_UC_2

value: UC


title: Tbr2 conditional knockout _ embryonic cortex stage  E16_replicate 6

description: E16_Mutant_replicate 6


title: Tbr2 conditional knockout _embryonic cortex stage  E13_replicate 1

description: E13_Mutant_replicate 1


title: Tbr2 conditional knockout _ embryonic cortex stage  E13_replicate 3

description: E13_Mutant_replicate 3


title: Tbr2 conditional knockout _ embryonic cortex stage  E13_replicate 2

description: E13_Mutant_replicate 2


title: Tbr2 conditional knockout _ embryonic cortex stage  E16_replicate 5

description: E16_Mutant_replicate 5


title: Tbr2 conditional knockout _ embryonic cortex stage  E16_replicate 1

description: E16_Mutant_replicate 1


title: GMP +Dox +Pal rep2

source_name: GMP +Dox +Pal

value: r/r iMLL-AF9+

value: Bone marrow

value: granulocyte monocyte progenitors

value: cultured in vitro with palbociclib for two days, Dox added after day 1


title: GMP +Dox rep2

source_name: GMP +Dox

value: cultured in vitro for two days, Dox added after day 1


title: NOZ

value: NOZ

value: Gallbladder


title: MZCHA2

description:
Gallbladder (liver metastases) tumour cells
processed data file: BTC_gene_counts.txt

source_name: Metastatic (liver)

value: Zurich Uni.


title: c4x5_Pe_2

source_name: Drosophila gut

value: gut


title: GMP +Dox rep1


title: HUH28

value: HSRRB

value: Intrahepatic


title: GMP -Dox +Pal rep2

source_name: GMP -Dox +Pal

value: cultured in vitro with palbociclib for two days


title: c4x5_Pe_1

value: Pe


title: HUCCT1

description:
Intrahepatic (ascites) tumour cells
processed data file: BTC_gene_counts.txt

value: RIKEN


title: GMP -Dox +Pal rep1


title: 157CTRL

value: wild type


title: G415


title: GMP -Dox rep2

source_name: GMP -Dox

value: cultured in vitro for two days, untreated


title: Fresh GMP rep1

source_name: Fresh GMP

value: freshly isolated from bone marrow


title: 7_UC_1

value: UC

value: Homozygous


title: c4x5_UC_2

value: Heterozygous


title: GMP -Dox rep1

value: r/r iMLL-AF9+

value: Bone marrow

value: granulocyte monocyte progenitors


title: c5x6_UC_1


title: c3x4_Pe_1


title: Fresh GMP rep2


title: C4-2B-TaxR_Vehicle_48hrs

city: Sacramento

first: Hongwu

last: Chen

state: California

address: 2nd Ave, UCDMC Res III

department: Biochem & Mol Med

institute: UC Davis

data_processing:
Sequencing was perforemd on an Illumina HiSeq 2000 sequencer.
The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Sequence reads were mapped to GRCh37/hg19 assembly with BWA and Biotie software.
The Cufflinks package was used for transcripts assembly, quantification of normalized gene and isoform expression, and analysis of different expression.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

source_name: C4-2B-TaxR cells treated with vehicle for 48 hrs

growth_protocol: C4-2B-TaxR cells were cultured in RPMI supplemented with 10% FBS and 5 nM docetaxel. Cells were grown at 37℃ in 5% CO2 incubators.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen) from the treated cells.
RNA-seq libraries from 1 µg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacture's instruction.

treatment_protocol: C4-2B-TaxR cells were seeded into 6 well plate and, next day, cells were treated with vehicle, 10 nM docetaxel, and 2 microM SR2211  for 48 hours.

value: C4-2B-TaxR prostate cancer cell line with resistance to taxels

tag: treatment

value: vehicle


title: C4-2B-TaxR_2μMSR2211_10nMDocetaxel_48hrs

source_name: C4-2B-TaxR cells treated with 2 microM SR2211 and 10 nM docetaxel for 48 hrs

value: SR2211 and docetaxel


title: c2x3_Pe_1

value: gut


title: c4x5_UC_1


title: BMT 3D10 treated_2

value: Balb/c


title: sRNAseq-mouse-AKR-Testis-rep2

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

data_processing:
DNA sequencing raw reads were mapped to genome using BWA mem (version 0.7.12-r1044) allowing soft clipping. Mapped sam format results were transformed into sorted bam format via samtools (version 1.8). Then modified TEMP are used for new transposon insertion and transposon absence detecting.
RNA sequencing raw reads were mapped to genome using STAR (version 020201) after removing rRNA via bowtie2 with default parameters (version 2.2.5). Mapped sam format results were transformed into sorted and duplication removed bam format via samtools (version 1.8). Final mapped reads were assigned into protein-coding genes, non-coding RNAs and piRNA genes via HTSeq (version 0.9.1) and then reads per million unique mapped reads in per thousand nucleotide (RPKM) was calculated using custom bash scripts. rRNA removed RNA sequencing reads were also mapped to transposon consensus sequences directly using Hisat2 (version 2.1.0) with default parameters. Then transposon expression levels  were calculated via Bedtools (version 2.27.1).
The adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGT) of small RNA sequencing raw reads were first removed via cutadapt (version 1.15). Then reads with rRNA, miRNA, snoRNA, snRNA and tRNA filtered were mapped to genome and transposon consensus sequences independently via Bowtie (version 1.1.0). piRNA reads per million genome mapping reads (PPM) of piRNA clusters and transposons were calculated for unoxidized and oxidized samples.
Genome_build: phaCin_unsw_v4.1, mm10
Supplementary_files_format_and_content: TXT

source_name: Testis

extract_protocol:
Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
Small RNA sequencing libraries were prepared as previously described (Li et al., 2009a). Briefly, total RNA was isolated from flash frozen koala or mouse tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research).

value: Testis

value: AKR/J

tag: developmental stage

value: adult


title: c2x3_UC_1


title: c2x3_UC_2


title: GMP +Dox +Pal rep1

tag: genotype/variation

value: cultured in vitro with palbociclib for two days, Dox added after day 1


title: EGI1

value: DSMZ

value: Extrahepatic


title: IEC_Hdac3_wildtype_rep3

description:
Sample 6
Biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Bioconductor (limma) in R.

source_name: Intestinal epithelial cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: Total mRNA was isolated and DNase I treated using the High Pure RNA isolation kit from Roche Diagnostics (Roche, Indianapolis, IA) following the manufacturer instructions.

tag: strain/background

value: 4 weeks

tag: cell type

value: Intestinal epithelial cells


title: IEC_Hdac3_knockout_rep1

description:
Sample 1
Biological replicate 1


title: RNAseq-mouse-LP-Testis

extract_protocol:
Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
Strand-specific RNA sequencing libraries were prepared as previously described (Zhang et al., 2012). In brief, total RNA was isolated from frozen koala or mouse tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit for human, mouse, and rat (Illumina). Mouse total RNA samples were rRNA depleted as previously described (Adiconis et al., 2013; Morlan et al., 2012).

tag: strain

value: LP


title: IEC_Hdac3_knockout_rep4

description:
Sample 8
Biological replicate 4


title: c1x2_Pe_2

value: Pe

value: Heterozygous


title: c3x4_Pe_2


title: RNAseq-mouse-C57BL6NJ-Testis


title: c2x3_Pe_2


title: C4-2B-TaxR_2μMSR2211_48hrs

source_name: C4-2B-TaxR cells treated with 2 microM SR2211 for 48 hrs


title: c3x4_UC_2

value: UC


title: 2kop620160926

city: Shanghai

first: Sheng

middle: Bo

last: Zhang

address: No.1954. Huashan rode

institute: Shanghai Jiao Tong University

description: Include gene expression level and FPKM

data_processing:
For file (Treat_vs_control_diff)1.Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT 2.Quality filtered reads were then mapped to hg19 using STAR 3.Read counts were calculated by using htseq-count 4.Differential gene expression analysis was done using R package DESeq2
For file (2sample-genes.fpkm_tracking.info) 1 Illumina bcl2fastq v2.17.1.14 software used for basecalling. 2.Sequenced reads were removed adapter sequences and trimmed low-quality ends with Phred scores less than 20 from sequences, then mapped to hg38 whole genome using tophat v2.1.1 with parameters --solexa-quals -N 3 --read-edit-dist 3 -p 8 -G genes.gtf 3.Reads that could be uniquely mapped to a gene were assembled by Cufflinks 2.2.1 and used to calculate the expression level. The gene expression level was measured by fragments per kilobase of exon per million fragments mapped(FPKM)4.Cufflinks 2.2.1 was used to perform differential expression between case and control with threshold: p value≤0.05.
Genome_build: mm9/mm10
Supplementary_files_format_and_content: Excel file generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj   or tab-delimited text files include FPKM values for each Sample

source_name: primary tumor cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA LT V2 Sample Prep Kit(Illumina, Sandiego) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population

tag: tumor type

value: Colorectal cancer

value: BALB/C

tag: genotype

value: WT


title: sRNAseq-mouse-AKR-Testis-rep1


title: Treat1

description: Include gene expression level and raw count can be find at file (expression_level_all)


title: C4-2B-TaxR_10nMDocetaxel_48hrs

source_name: C4-2B-TaxR cells treated with 10 nM docetaxel for 48 hrs

value: C4-2B-TaxR prostate cancer cell line with resistance to taxels

value: docetaxel


title: c1x2_UC_2

value: gut


title: sRNAseq-mouse-AKR-Testis-rep3

value: Testis

value: AKR/J


title: c3x4_UC_1


title: IEC_Hdac3_wildtype_rep2

description:
Sample 3
Biological replicate 2


title: c1x2_UC_1


title: IEC_Hdac3_knockout_rep3

description:
Sample 5
Biological replicate 3


title: IEC_Hdac3_wildtype_rep1

description:
Sample 2
Biological replicate 1


title: c1x2_Pe_1


title: control2


title: DNAseq-K63464-Brain

data_processing:
DNA sequencing raw reads were mapped to genome using BWA mem (version 0.7.12-r1044) allowing soft clipping. Mapped sam format results were transformed into sorted bam format via samtools (version 1.8). Then modified TEMP are used for new transposon insertion and transposon absence detecting.
RNA sequencing raw reads were mapped to genome using STAR (version 020201) after removing rRNA via bowtie2 with default parameters (version 2.2.5). Mapped sam format results were transformed into sorted and duplication removed bam format via samtools (version 1.8). Final mapped reads were assigned into protein-coding genes, non-coding RNAs and piRNA genes via HTSeq (version 0.9.1) and then reads per million unique mapped reads in per thousand nucleotide (RPKM) was calculated using custom bash scripts. rRNA removed RNA sequencing reads were also mapped to transposon consensus sequences directly using Hisat2 (version 2.1.0) with default parameters. Then transposon expression levels  were calculated via Bedtools (version 2.27.1).
The adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGT) of small RNA sequencing raw reads were first removed via cutadapt (version 1.15). Then reads with rRNA, miRNA, snoRNA, snRNA and tRNA filtered were mapped to genome and transposon consensus sequences independently via Bowtie (version 1.1.0). piRNA reads per million genome mapping reads (PPM) of piRNA clusters and transposons were calculated for unoxidized and oxidized samples.
Genome_build: phaCin_unsw_v4.1
Supplementary_files_format_and_content: TXT

organism: Phascolarctos cinereus

source_name: Brain

extract_protocol:
Total DNA was isolated from koala (K63464 and K63855) tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen). Total RNA was isolated from brain, liver and testis from two koalas (K63464 and K63855) using the mirVana™ miRNA Isolation Kit (Life Technologies).
short fragment DNA-seq library was constructed in BGI China

value: Brain

tag: source

value: Gold Coast, Australia

tag: koala id

value: adult


title: 2wtp6220160926

description: Include gene expression level and FPKM


title: DNAseq-K63855-Brain

tag: tissue


title: RNAseq-mouse-AKR-Testis


title: DNAseq-K63464-Liver

source_name: Liver

value: Liver


title: control1


title: DNAseq-K63855-Liver


title: smallRNA-K63855-Testis-oxidized

extract_protocol:
Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen).


title: RNAseq-mouse-C57BL6J-Testis


title: DNAseq-K63464-Testis


title: RNAseq-mouse-C3H-Testis


title: smallRNA-K63464-Testis-oxidized


title: Treat2


title: U6(UVB 40mJ/cm2)

city: Chengdu

first: lidan

last: Xiong

address: No. 5, Gong Xing Road

institute: West China Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome whole genome using featureCounts 1.5.0-p3 with parameters -Q 10 -B -C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Garber M et al.,  Nature methods, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human genome
Supplementary_files_format_and_content: table-delimited text files include RPKM values for each Sample

source_name: Epidermis

extract_protocol:
RNA was extracted from tissues or cells by standard extraction method, followed by strict quality control of RNA samples, which mainly included the following three aspects. Agarose gel electrophoresis: analysis of RNA integrity and presence of DNA contamination. NanoPhotometer spectrophotometer: RNA purity was determined (OD260/280 and OD260/230 ratios). Agilent 2100 bioanalyzer: accurate detection of RNA integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HaCaT

value: Epidermis

tag: passages

value: Less than 30 passages


title: smallRNA-K63855-Liver-unoxidized


title: smallRNA-K63855-Brain-unoxidized


title: NI-T68-18

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch

description: NI+AI

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: Colonic Mucosa/Submucosa NI+AI

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: Total RNA containing miRNA was extracted from the pulverized colonic mucosa/submucosa using the miRNeasy Mini Kit (QIAGEN, Valencia, CA), according to the protocol provided by the manufacturer. RNA concentration was quantified in a Nanodrop. After quantification, RNA was stored in a -80 °C freezer.

treatment_protocol: The rats were divided into four treatment groups delivered intraluminally into the colon given a combination of vehicle (Ctl; normal saline) and/or trinitrobenzene sulfonic acid (TNBS) (NI/AI). The four groups as previously described were Ctl+Ctl, Ctl+AI, NI+Ctl, and NI+AI. To induce neonatal inflammation, TNBS (130 mg/kg dissolved in 200 µl saline containing 10% ethanol) was injected intraluminally 2 cm into the colon of male pups on post-natal day 10. The animals were kept in a head-down position while the anus was held closed for one minute to prevent leakage. Rats in the sham treatment groups received 200 µl of saline. Six to eight weeks later, animals were subjected to a secondary TNBS (65 mg/kg) insult, as AI. Under light anesthesia, 250 µl of TNBS in PBS containing 40% ethanol was injected intrarectally via a catheter, advanced to 8 cm into the colon. Control rats were given 250 μl of saline. Seven days after the second TNBS treatment, animals were decapitated under anesthesia. The colon was flushed clean with PBS and cut open longitudinally. The colonic mucosa and submucosa were isolated, snap-frozen in liquid nitrogen, pulverized, aliquoted, and stored in a -80 °C freezer.

value: Sprague Dawley

tag: gender

value: Male

value: 9 weeks old

value: TNBS given to rat as neonate and adult

value: Colonic Mucosa/Submucosa


title: smallRNA-K63855-Testis-unoxidized-rep1


title: NI-T68-6

description: NI+AI


title: U5(UVB 40mJ/cm2)


title: U4(UVB 40mJ/cm2)


title: U3(UVB 20mJ/cm2)


title: smallRNA-K63464-Liver-unoxidized


title: smallRNA-K63464-Testis-unoxidized-rep2


title: NI-2

description: NI+Ctl

source_name: Colonic Mucosa/Submucosa NI+Ctl

value: TNBS given to neonate rat and saline vehicle given as adult


title: NI-17

description: NI+Ctl


title: smallRNA-K63464-Brain-unoxidized


title: NI-16

description: NI+Ctl


title: smallRNA-K63464-Testis-unoxidized-rep1


title: RNAseq-K63855-Brain

extract_protocol:
Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
strand-specific RNA-seq library was constructed in BGI China


title: U2(UVB 20mJ/cm2)


title: C-T68-15

description: Ctl+AI

source_name: Colonic Mucosa/SubmucosaCtl+AI

value: saline vehicle given to neonate rat and TNBS given as adult


title: RNAseq-K63855-Liver


title: C-T68-4

description: Ctl+AI


title: RNAseq-K63855-Testis-Batch2-rep2

extract_protocol:
Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
Strand-specific RNA sequencing libraries for K63855 testis replicate 1, K63855 testis replicate 2 and K63464 testis replicate 2 were prepared as described in (Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012;3(1):9. Published 2012 Dec 28. doi:10.1186/1758-907X-3-90).  In brief, total RNA was isolated from frozen koala tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). RNAs greater than 200nt were selectively recovered using the RNA Clean & Concentrator-5 kit(Zymo Research).  RNA samples were fragmented and reverse transcribed. dUTP was incorportated during second strand synthesis for strand specificity. End repair and A-tailing was performed followed by adapter ligation and uracil-DNA glycosylase (UDG) treatment.  Finally, the library was PCR amplified.


title: C3(Control 3)


title: U1(UVB 20mJ/cm2)


title: smallRNA-K63855-Testis-unoxidized-rep2


title: RNAseq-K63464-Brain


title: NI-T68-1

description: NI+AI


title: C-T68-3

description: Ctl+AI


title: C-20

description: Ctl+Ctl

source_name: Colonic Mucosa/Submucosa Ctl+Ctl

value: saline vehicle given to rat as both neonate and adult


title: C2(Control 2)


title: RNAseq-K63464-Liver


title: RNAseq-K63464-Testis-Batch2

value: Testis


title: RNAseq-K63464-Testis


title: RNAseq-K63855-Testis-Batch2-rep1


title: C-14

description: Ctl+Ctl


title: C-7

description: Ctl+Ctl


title: JMICSM408_DC_NESAM

status: Public on Oct 11 2019

type: genomic

city: Houston

first: Neil

middle: A.

last: Hanchard

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450 BeadChip using the standard Illumina protocol.

scan_protocol: Arrays were imaged using iSan.

data_processing:
GenomeStudio Methylation Module (version 1.9.0) with background correction followed by color balancing and quantile normalization with the R package lumi (version 2.22.1). Probes meeting the following criteria were omitted from subsequent analyses: internal controls (N=65), detection P-value < 0.0001 in >10% of samples (N=860), bead counts <3 in 5% of samples (N=665), sex chromosomes (N=11,288), cross-reactive (N=29,895), and containing SNPs with a minor allele frequency (MAF) >0.01 in African populations at, or within 5bp of, the single base extension (SBE) site (N=16,918 and N=5,386, respectively).
matrix processed value definition: M-value (color balanced and quantile normalized)

label: Cy5 and Cy3

source_name: Buccal epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were collected and extracted with the help of the Oragene Discover (OGR-250) DNA collection kit.

value: Buccal epithelial cells

value: M

tag: sample timing

value: DC

tag: disease group

value: NESAM

tag: nationality

value: Jamaica

tag: sentrix id

tag: sentrix position

tag: diagnosis

value: child with SAM


title: JMICSM417_DC_NESAM

value: F

tag: age


title: JMICSM124_DL_NESAM

value: DL

value: health adult with history of SAM


title: JMICSM431_DC_NESAM


title: 51451_DC_NESAM

value: Malawi


title: 51450_DC_NESAM