title: Wild Type T30h_replicate A (RID-SMR1)

description: Biological replicate 1 of 3 of timepoint T30h of sexual reproduction time course

value: harvested after 126h at 28°C and 30 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

value: Wild type S mat-

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name of biosource 4


title: Wild Type T24h_replicate C (RID-SMR1)

status: Public on Sep 16 2019

type: RNA

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

description: Biological replicate 2 of 3 of timepoint T24h of sexual reproduction time course

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

molecule: total RNA

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: To facilitate biological materials collecting, S strains from mating type mat+ (female strain) were grown on cheesecloth (Sefar Nitex 03-48/31 Heiden) previously placed on Petri-dishes containing M2 medium. S mat- strain (Wild type or ∆SMR1) has been used as male gamete donor and S mat+ ((Wild type or ∆RID) as female. the S mat- male gamete donor strains were grown on M2 Petri-dishes.  For each points of the time course materials, number of Petri-dishes has been adjusted (5 were used for T12h, T24h, 4 for T30h, 2 for T42) to collect 20 to 100 mg of biological. All the time points were grown on cheesecloth. One to five Petri-dishes per time course experiment were thus inoculated simultaneously with a growing the male gamete donor strain and spermatia were collected by washing with 1.5 ml of H2O 6 days later. The collected spermatia (around 104 spermatia per ml) were pooled and then used to fertilize corresponding number of Petri-dishes of the S mat+ strain which was growing since 4 days. Time just prior the fertilization process was considered as the T0 (0h). The biological material was then collected 12h, 18h, 30h, 42h (for the mutant strains) after fertilization. The RNA pool used as a reference was assembled by combining equal amount of RNA issued from various growth and crosses conditions and has already been described (Bidard et al., BMC research notes, 2010).

extract_protocol: Strains were grown on cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

tag: female strain

value: Wild type S mat+

tag: growth condition

value: harvested after 120h at 28°C and 24 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

tag: male strain

source_name: Common reference

tag: biosource 1

tag: name of biosource 1


title: Untreated_control_rep2

type: SRA

city: Schlieren

first: Anna

last: Mallone

state: Zurich

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

description: Sample 2

library_source: transcriptomic

data_processing:
RNA quality control: The quality of RNA sequencing data was assessed using fastqc (v. 0.11.5) and RSeQC (v. 2.6.4 2).
Reads mapping: The reads were mapped to the reference genome using HiSat2 (v. 2.1.0).
Reads count: FeatureCounts (v. 1.6.0) was used to count the number of reads overlapping with each gene as specified in the genome annotation (Mus_musculus.GRCm38.91).
Differential gene expression between groups: the Bioconductor package DESeq2 was used to test for differential gene expression between the experimental groups. The log-fold change of each gene was adjusted to include the evidence based on which the log-fold change was estimated and to extrapolate the adjusted p-value (adjp). A false discovery rate correction was applied using DESeq2, based on the Benjamini-Hochberg procedure.
GO enrichment analysis: the gene ontology enrichment analysis was performed with TopGo and GOSeq. These tools were used to identify gene ontology terms and KEGG pathways containing unusual differentially expressed genes. Genes were ranked within a GO term using a two-fold approach including (1) the Fisher’s exact test, comparing the proportion of differentially expressed genes among all genes assigned to the GO term with all other genes, and (2) the Kolmogorov-Smirnov test, which orders all genes by p-value and tests if the genes assigned to a particular GO term are enriched at the top or the bottom of this table.
All analyses were run in R (version 3.4.4, 2018-03-15)
Genome_build: Mus_musculus.GRCm38.91
Supplementary_files_format_and_content: xlsx files describing the comparative quatitation of the different treatments. The files include the normalized abundance measurements  for each treatment (triplicate), the log2 of the Fold change, the p-value of the comparison and the adjusted p-value.

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone marrow-derived progenitor cells were isolated from femurs, tibiae and hip bones of non-transgenic C57BL/6 mice according to established protocols (Dubrot, Duraes et al. 2014). After 9 days of incubation at 37°C and 5% CO2 progenitor cells completely differentiated into immature bone marrow-derived dendritic cells (BM-DCs).

extract_protocol:
Total RNA was extracted using the GenElute Mammalian TotalRNA Kit (Sigma). The RNA concentration was measured using RNA HS Assay kit (Thermo Fisher Scientific) and RNA integrity was analyzed with the Qubit RNA IQ Assay (Thermo Fisher Scientific).
The library of mRNA sense transcripts was prepared using the TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Maturation of BM-DCs was achieved by an 18 h LPS-treatment at 100 ng/ml followed by an up-regulation of antigen-presentation markers such as MHC class II. During antigen presentation assays BM-DCs were treated with oligomeric Aβ1-42 (0.5 µM) on day 8 of the cultivation process prior maturation.

tag: strain

tag: genotype

value: wild type

tag: age

value: post-natal week 12

tag: cell type

value: Dendritic cells

tag: cell treatment

value: untreated


title: LPS_treatment_rep3

description: Sample 6

value: LPS treatment (18h)


title: Untreated_control_rep1

description: Sample 1


title: Neurospora csRNA-seq r3

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

description: csRNA-seq in Neurospora to identify TSS

data_processing:
Adapter sequences were first removed from the 3' end of reads for csRNA-seq and small RNA-seq libraries (AGATCGGAAGAGCACACGTCT). Reads were then aligned to the appropriate genome using HISAT2 (v2.1.0) with default settings. Normalized, single nucleotide resolution bigWig files and TSS cluster calls were generated using HOMER's makeUCSCfile and findcsRNATSS.pl tools, respectively (v4.11). findcsRNATSS.pl uses small RNA sequencing and total RNA-seq data as controls to remove non-TSS artifacts in the csRNA-seq data when identifying TSS clusters. http://homer.ucsd.edu/homer/ngs/csRNAseq/
Genome_build: hg38, mm10, ASM20922v1, NC12, IRGSP-1.0, C_owczarzaki_V2
Supplementary_files_format_and_content: BigWig files (.bigWig/.bw) were generated by constructing normalized, single-nucleotide resolution bedGraph files based on 5' read positions using HOMER and converted to bigWigs using UCSC's bedGraphToBigWig utility. TSS text files contain TSS cluster positions defined using HOMER's findcsRNATSS.pl command (tab-delimited text files).

organism: Neurospora crassa

source_name: whole organism (mixed stages)

extract_protocol:
K562 cells were grown in RPMI1640+L‐Glutamine with heat inactivated 10% FBS (Biowest Cat No.S1620, Lot 61N16) and 1x Pen/Strep (Gibco15140-163) and 1x L-Glutamine (Gibco25030164) in T75 flasks at 37°C with 5% CO2. HCT116 CMV-osTIR1 RAD21-mAC cells were obtained from Masato T. Kanemaki (Natsume et al., 2016) and cultured in McCoy’s 5A medium supplemented with 10% FBS. Cells were washed twice in 1x cold PBS (Gibco 10010023) and RNA isolated using Trizol LS. Human H9 cell RNA was provided by Yuanyuan Li and Mark H. Tuszynski (UC San Diego). H9 cells were grown as described in (Lu et al. 2017) and RNA isolated using the Qiagen RNA kit. Murine BMDMs were isolated, cultured and RNA extracted as described (Link et al. 2018). Nematostella vectensis (planula stage) was kindly provided by Drs. James Gahan and Fabian Rentzsch (University of Bergen). Neurospora crassa was provided by Dr. Jason Stajich (University of California, Riverside) and grown in Vogels media under constant light and gentle agitation (Wang et al. 2015). Rice was grown in the SALK greenhouse with 12 h light and leaves from adult plants provided by Dr. Joanne Chory (Salk Institute for Biological Studies). All non-mammalian samples were flash frozen in liquid N2, pulverized with a mortar and pestle and RNA extracted using Trizol LS as described by the manufacturer. Capsaspora owczarzaki RNA (Sebé-Pedrós et al. 2016) was gifted by Dr. Iñaki Ruiz-Trillo (Institut de Biologia Evolutiva; CSIC-Universitat Pompeu Fabra).
Small RNAs of ~20-60 nt were size selected form 2-15 µg of total RNA by denaturing gel electrophoresis.  A 10% input sample was taken aside and the remainder enriched for 5’Caped RNAs with 3’-OH. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequent 5’dephosporylation by CIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’adapter ligation by T4 RNA ligase 1 (NEB). The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) without prior 3’ repair to select against degraded RNA fragments.  Following cDNA synthesis, libraries were amplified for 12-14 cycles and sequenced SE75 on the Illumina NextSeq500. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina HiSeq 2500. A comprehensive description of the csRNA-seq method and analysis software can be found in the supplement as well as under http://homer.ucsd.edu/homer/ngs/csRNAseq/.

tag: tissue

value: whole organism (mixed stages)

tag: treatment

tag: assay

value: csRNA-seq

tag: genome build

tag: library id

tag: assayed molecule

value: capped short RNA (20-65nt)

tag: library strategy

value: capped short RNA-seq (csRNA-seq)


title: 0Bhet cortex

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ reads were quality checked and adaptor trimmed with FastQC (Andrews, S.. FastQC A Quality Control tool for High Throughput Sequence Data).
High quality trimmed reads were mapped to the mm10/GRCm38.p6 reference genome with Bowtie2 v2.3.4.3 (Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359).
Gene counts were calculated with featureCount using latest GENCODE main annotation file (Liao, Y., Smyth, G. K., & Shi, W. (2014). FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930).
Differential gene expression was calculated with DESeq2 (Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550).
Genome_build: mm10/GRCm38.p6

molecule: polyA RNA

source_name: Cerebral cortex

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

value: Cerebral cortex

tag: genotype/variation

value: Setd5 heterozygous


title: Wild Type T30h_replicate G (RID-SMR1)

description: Biological replicate 3 of 3 of timepoint T30h of sexual reproduction time course

tag: female strain

tag: growth condition

value: harvested after 126h at 28°C and 30 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

value: Wild type S mat-

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 2

tag: name of biosource 2

tag: biosource 3

tag: name of biosource 3

tag: biosource 4

tag: name of biosource 4


title: Wild Type T24h_replicate G (RID-SMR1)

description: Biological replicate 3 of 3 of timepoint T24h of sexual reproduction time course

tag: male strain

tag: biosource 1

tag: name of biosource 1

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: 1het cortex

tag: tissue


title: 30S_RPF_Wt

city: Guwahati

first: B

last: Anand

state: Assam

address: North guwahati

department: Biosciences and Bioengineering

country: India

institute: Indian institute of technology guwahati

data_processing:
Reads were filtered by removing reads with Phred score <20 using fastq_quality_trimmer
Trimming of 3’-end adapter sequences [5’-TGGAATTCTCGGGTGCCAAGGAACTC-3’] using Cutadapt-1.5
Alignment with E. coli reference genome NC_000913.3 using STAR 2.5.3 to remove reads mapping to genes for rRNA, tRNA, sRNA and other non-coding RNAs
Filtered reads aligned to E. coli reference genome using  STAR 2.5.3 with  spliced alignment turned off (--alignIntronMax 1), forced end to end alignment (--alignEndsType EndToEnd) and allowing 8 mismatches per 100 nt (--outFilterMismatchNoverLmax 0.08)
Sam to Bam conversion was accomplished using Samtools-1.4.1. Metagene analysis for mapping the reads to START and STOP codons was performed by employing custom written shell scripts utilizing Samtools-1.4.1.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: .txt files with  read counts in tabular format with geneIDs and counts per sample.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Wt or mutants were grown at 25 °C in 2 litres of LB medium. The culture was allowed to grow till OD600 reached 0.3.

extract_protocol:
Ribosomes bound to mRNA were relieved using MNase.The treated sample was again sepeated into 30S and 70S fractions using ultracentrifugation on a 10-40% sucrose gradient. The 30S and 70S fractions were decrosslinked and ribosome protected fragments were size selcted for 10-80 nucleotide on a denaturing Urea PAGE.
Libraries were prepared strictly according to the manufacturers recommendations using the TruSeq Small RNA Sample Preparation kit (Illumina, U.S.A)

treatment_protocol: Cells were snap chilled using ice and crosslinked with formaldehyde. Glycine was added to arrest the crosslinking after which the cells were pelleted and lysed by freeze thaw method followed by clarification of the lysate. Lysate was loaded on a 10-20 % sucrose gradient and the ribosome pellets were resuspeded in fresh lysis buffer

tag: strain background

value: wild type

tag: molecule subtype

value: 30S subunit ribosome protected fragment


title: Neurospora csRNAinput r2

description: small RNA-seq in Neurospora as a control for csRNA-seq

tag: treatment

tag: assay

value: small RNA input

tag: genome build

tag: library id

tag: assayed molecule

value: total short RNA (20-65nt)

value: small RNA-seq


title: Untreated_control_rep3

description: Sample 3

tag: strain

tag: genotype

tag: age

value: post-natal week 12

tag: cell type

value: Dendritic cells

tag: cell treatment

value: untreated


title: Neurospora csRNA-seq r2

description: csRNA-seq in Neurospora to identify TSS

value: whole organism (mixed stages)

value: csRNA-seq

value: capped short RNA (20-65nt)

tag: library strategy

value: capped short RNA-seq (csRNA-seq)


title: Wild Type T12h_replicate C (RID-SMR1)

description: Biological replicate 2 of 3 of timepoint T12h of sexual reproduction time course

tag: female strain

value: Wild type S mat+

tag: growth condition

value: harvested after 108h at 28°C and 12 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

tag: male strain

value: Wild type S mat-

tag: biosource 2

tag: name of biosource 2

tag: biosource 3

tag: name of biosource 3

tag: biosource 4

tag: name of biosource 4


title: 0Ahet cortex

tag: tissue

value: Cerebral cortex

tag: genotype/variation

value: Setd5 heterozygous


title: Wild Type T12h_replicate G (RID-SMR1)

description: Biological replicate 3 of 3 of timepoint T12h of sexual reproduction time course

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 1

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Neurospora csRNA-seq r1

description: csRNA-seq in Neurospora to identify TSS

tag: treatment

tag: assay

tag: genome build

tag: library id

tag: assayed molecule


title: sWAT-2

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

department: Biochemistry

country: China

institute: Wuhan University

data_processing:
Basecalls performed using  bcl2fastq
Single-end 50 bp read length Fastq files were checked for quality using fastqc and fastq_screen
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v1.127)
Read counts were generated using featureCounts (subread/1.4.6) for coding genes from gencode (vM4)
Normalized read counts generated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt file that includes normalized read counts for each sample per gene

source_name: Purified mature inguinal adipocytes

extract_protocol:
Mature dermal adipocytes and inguinal adipocytes were collected from P30 mice using Collagenase IV and DispaseII disgestion combined with the floating centrifuge method.  RNA was harvested using Trizol reagent, and purified with the Qiagen RNA purification kit. 1 µg of total DNAse treated RNA is then prepared for the library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Preparation Kit)
RNA-Seq-Whole transcriptome

tag: cell type

value: Primary purified inguinal adipocytes

tag: strain

tag: age


title: K562 total RNA-seq

description: total RNA-seq in K562 cells (ribozero)

organism: Homo sapiens

source_name: K562 cells

value: K562 cells

value: total RNA-seq (rRNA depleted)

value: total RNA

tag: library strategy

value: total RNA-seq


title: sWAT-1


title: Wild Type T12h_replicate A (RID-SMR1)

description: Biological replicate 1 of 3 of timepoint T12h of sexual reproduction time course

tag: female strain

tag: growth condition

tag: male strain

tag: biosource 2

tag: name of biosource 2

tag: biosource 3


title: JGE181008_NB_LIBRARY

city: Chapel Hill

first: Justin

middle: Gregory

last: English

state: NC

address: 120 Mason Farm Rd., 2113 Genetic Medicine Bldg

department: Pharmacology

institute: UNC Chapel Hill

description: barcoded amplicon

data_processing:
EGFP Data was trimmed to contain only paired reads with 100% matching sequences above a set length threshold
Trimmed reads were aligned to FASTA sequences (see supplement, JGE_EGFP.FASTA) using a Smith-Waterman alignment algorithm weighted m3, x1, o5, e1
Reads aligning to any part of the full length Sindbis genome were omitted, apart from those flanking the EGFP transgene
For EGFP alignments, individual base frequences per position were tabulated and mutations, insertions, and deletions were quantified per position and per read.
For NB alignments, data was aligned using a Smith-Waterman alignment algorith weighted m1, x5, o5, e5
Aligned NB reads was tabulated with score cut-offs at 25, 50, and 100. Individual base frequencies per position were tabulated.
Genome_build: Custom (see JGE_EGFP.FASTA)
Genome_build: Custom (see JGE_NB.FASTA)
Supplementary_files_format_and_content: Processed EGFP files (.csv) contain aggregate error frequencies at each position in the alignment (posstats) and error statistics for each individual read (readstats). Processed NB file (.xlsx) contain position and read length quantification.

organism: Sindbis virus

source_name: Transgenic Sindbis virus

extract_protocol:
Total RNA was isolated using MagMax RNA isolation kits
Amplicons of target region were PCR'd and used for libraries constructed with KAPA HyperPrep kit or Illumina TruSeq RNA library kit v2.

tag: library preparation kit

value: Illumina TruSeq RNA library kit v2

tag: culturing

value: no culturing, directly from in vitro mRNA

tag: barcode

value: GATCGG


title: JGE190320_EGFP_vector_R1

description: barcoded amplicon

source_name: pTSin-EGFP plasmid

value: KAPA HyperPlus (24 rxn) with SEQCAP Kit A & B

value: no culturing, direct from plasmid DNA

value: GTGGCC


title: JGE190320_EGFP_mRNA_R3

description: barcoded amplicon

source_name: pTSin-EGFP synthetic mRNA

value: GTGAAA


title: Neil2_Mo_rep2

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: stage 23 embryos injected at 1 cell stage with neil2 Morpholino, replicate 2

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina's bcl2fastq Conversion Software v1.8.4.
The raw sequence reads were quality assessed using FastQC and aligned to the Xenopus laevis 9.2 genome assembly with JGI gene annotation from Xenbase (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2) using STAR v.2.5.4b with option "--outFilterMismatchNmax 2".
The mapped reads were summarised on the gene level using Subread featureCounts v.1.5.1 with default parameters.
Differential gene expression analysis was performed with the Bioconductor package DESeq2 v.1.18.1 following the recommended analysis workflow with independent gene filtering.
Genome_build: Xenopus laevis 9.2
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from featureCounts

organism: Xenopus laevis

source_name: neil2 Morpholino injected embryos, replicate 2

growth_protocol: Xenopus laevis frogs were purchased from Xenopus 1 (http://xenopus1.com) and embryos were prepared by in vitro fertilization.

extract_protocol:
For each replicate sample a pool of 6 embryos at stage 23 was collected. Total RNA was extracted with Trizol according to the manufacturer’s instructions.
NGS libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s recommendations and amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). The NGS libraries were sequenced on a HiSeq 2000 Illumina sequencer, for 51 cycles plus seven cycles for the index read.

treatment_protocol: Each embryo at 1 cell stage was injected with 40 ng of either control or neil2 Morpholino into the animal hemisphere.

tag: tissue

value: stage 23 embryos

tag: treatment

value: neil2 Morpholino


title: JGE190320_EGFP_mRNA_R2

description: barcoded amplicon

value: GTCCGC


title: Neil2_Mo_rep1

description: stage 23 embryos injected at 1 cell stage with neil2 Morpholino, replicate 1

source_name: neil2 Morpholino injected embryos, replicate 1


title: JGE190320_EGFP_mRNA_R1

description: barcoded amplicon

value: CCGTCC


title: Control_Mo_rep3

description: stage 23 embryos injected at 1 cell stage with control Morpholino, replicate 3

source_name: control Morpholino injected embryos, replicate 3

value: control Morpholino


title: JGE190320_EGFP_vector_R3

description: barcoded amplicon

value: CGTACG


title: Control_Mo_rep2

description: stage 23 embryos injected at 1 cell stage with control Morpholino, replicate 2

source_name: control Morpholino injected embryos, replicate 2


title: Control_Mo_rep1

description: stage 23 embryos injected at 1 cell stage with control Morpholino, replicate 1

source_name: control Morpholino injected embryos, replicate 1


title: Neil2_Mo_rep3

description: stage 23 embryos injected at 1 cell stage with neil2 Morpholino, replicate 3

source_name: neil2 Morpholino injected embryos, replicate 3


title: H4K91E-2_1_RNASeq

city: Hong Kong

first: Jason

last: Wong

address: L1-51, Laboratory Block, 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong (HKU)

data_processing:
H4K91glu and input control ChIP-seq data (50bp sequence reads) were aligned to the human reference genome (hg19) using Burrows-Wheeler Aligner (BWA, version 0.7.17-r1188). To obtain an input-normalized BigWig files needed for the profile analysis, DeepTools (version 3.2.0) was applied.
Raw reads of RNA-seq data in FASTQ sequencing files were aligned by STAR (version 2.5.2b) aligner to the Saccharomyces cerevisiae reference genome (sacCer3). Read counts were generated by featureCounts (version 1.6.2).
Genome_build: ChIP-seq data: hg19
Genome_build: RNA-seq: sacCer3
Supplementary_files_format_and_content: For ChIP-seq data BigWig files were generated using deepTools
Supplementary_files_format_and_content: For RNA-seq data table with read counts were generated by featureCounts

organism: Saccharomyces cerevisiae

extract_protocol:
ChIP-seq data: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody; RNA-seq data: RNA was harvested using Trizol reagent
ChIP-seq data: (1) DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor.(2) PCR amplification and size selection (usually 100-300bp, including adaptor sequence). (3) Qualified library for sequencing. ; RNA-seq data: 1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.

tag: genotype/variation


title: H4K91E-1_1_RNASeq


title: Wild-type-2_1_RNASeq

value: Wild-type


title: JGE190320_EGFP_vector_R2

description: barcoded amplicon

value: GTTTCG


title: JGE190320_EGFP_36HR_R1

description: barcoded amplicon

tag: cell line

value: transfected with pCMV-SSG cultured in MEM-alpha supplemented media.

value: AGTCAA


title: JGE190320_EGFP_36HR_R2

description: barcoded amplicon

value: AGTTCC


title: Capsaspora total RNA-seq

description: total RNA-seq in Capsaspora (ribozero)

organism: Capsaspora owczarzaki

value: whole organism (mixed stages)

tag: assay

value: total RNA-seq (rRNA depleted)

tag: genome build

tag: library id

tag: assayed molecule

value: total RNA

value: total RNA-seq


title: Heads, 5mM paraquat in 2.5% Sucrose for 12h rep3

city: Tuscaloosa

first: Urmila

last: Maitra

state: Alabama

address: 1325 Science and Engineering Complex, Box 870344

department: DEPARTMENT OF BIOLOGICAL SCIENCES

institute: University of Alabama

description:
3124-JO-0013
PQ3 SL106360

data_processing:
Paired-end sequencing (25 million, 50-bp, paired-end reads) was performed using a 200 Cycle TruSeq SBS HS v4 Kit on an Illumina HiSeq2500 sequencer
TopHat v2.0 were used to map raw reads to the reference Drosophila melanogaster genome dm3
The transcript abundance was quantified for the final read list using Trimmed Means of M-values as the normalization method.
The p-value of the differentially expressed gene list were estimated by z-score calculations using Benjamini Hochberg corrections of 0.05 for false-discovery rate.
Genome_build: dm3
Supplementary_files_format_and_content: RNAseq_SR_2019.xls (RPKM values), Supplementary Table S1.xlsx (fold changes Sucrose Vs Paraquat (PQ))

organism: Drosophila melanogaster

source_name: Fly heads

growth_protocol: 3-5 days old adult Canton S male flies were used to study the differential gene expression in response to paraquat feeding.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific) from the fly heads following sucrose or PQ ingestion (thirty males/group).  The concentration and integrity of the extracted total RNA were estimated using the Qubit® 2.0 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively.
For paired-end library preparation, NEBNext mRNA Library Prep Reagent Set for Illumina was used and the library concentration was analyzed by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Paired-end sequencing (25 million, 50-bp, paired-end reads) was performed using a 200 Cycle TruSeq SBS HS v4 Kit on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA) at the HudsonAlpha Institute for Biotechnology, Huntsville, AL. TopHat v2.0 were used to map raw reads to the reference Drosophila melanogaster genome dm3

treatment_protocol: Age-matched adult Canton S male flies were fed either 2.5% sucrose (control) or 5 mM PQ in 2.5% sucrose for 12 h and the heads were collected for RNA extraction.

tag: age

value: 3-5 days old post-eclosion

value: heads

tag: strain

value: Canton S

tag: genotype

value: WT

tag: gender

value: male

value: PQ


title: Heads, 5mM paraquat in 2.5% Sucrose for 12h rep2

description:
3124-JO-0008
PQ2 SL106355


title: M_PP_2

city: Beijing

first: Yan

last: He

state: Beijing

address: 2 Yuanmingyuan West Road

department: Plant Genetics and Breeding

institute: China Agricultural University

data_processing:
Base calling  was performed following the standard Illumina protocol.
Raw paired-end reads of m6A-Seq and input RNA-Seq were filtered and adapter sequences were trimmed out by Trimmomatic (v0.35) with parameters ILLUMINACLIP TruSeq3-PE-2.fa MINLEN 30.
Cleaned reads from B73 samples were aligned to maize B73 reference genome (AGPv4.38) and cleaned reads from Mo17 samples were mapped to maize Mo17 reference genome (CAU-1.0) using Hisat2 with parameters -5 1 -3 1 --dta.
Reads matching to less than five places were retained for further analysis.
m6A peaks were identified using the MACS2 peak calling algorithm with the input as background and the parameter of effective genome size was adjusted to the transcriptome size (417272442) and q value was set to 0.01.
Genome_build: Zea mays B73 RefGen_v4, Zm-Mo17-REFERENCE-CAU-1.0
Supplementary_files_format_and_content: Tab-delimited text files include m6A peaks locus or FPKM values of genes for each Sample.

organism: Zea mays

source_name: Mo17_polysome profiling

growth_protocol: Plants were grown under normal condition with a photoperiod of 16 h light at 28°C and 8h dark at 25°C.

extract_protocol:
Total RNA was extracted using Trozol reagent (Ambion life technologies) according to manufacturer’s protocol. Polysome-bound RNA was extracted as described in Zhang et al., 2017.
m6A-seq ,RNA-seq and polysome profiling libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, NEB) following manufacturer’s instructions.

tag: ecotype

tag: developmental stage

value: seedings

tag: library sta

value: polysome profiling


title: M_PP_1


title: dWAT-2

source_name: Purified mature dermal adipocytes

tag: cell type

value: Primary purified dermal adipocytes


title: Titanium dioxide and estrogen 062619AFE18

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

description: Titanium dioxide and estrogen

hyb_protocol: Standard Affymatrix hybridization protocol

scan_protocol: Standard Affymatrix scan protocol

data_processing: RMA Express normalization and background

label: biotin

source_name: J774 macrophages exposed to titanium dioxide and estrogen

label_protocol: Standard Affymatrix label protocol

growth_protocol: Macrophages, murine cell line J774, were maintained in 100-mm Petri dishes in DMEM free of phenol red, supplemented with 10% FBS, 2mM L-glutamine, penicillin (100 U/mL), streptomycin (100 µg/mL) and 10 mM HEPES.

extract_protocol: RNA extraction was conducted through a RNeasy Mini Kit (Qiagen).

treatment_protocol: Macrophages were plated in 24 well-plate and exposed to 10 µg/well of particles and 2 µg/mL of estrogen for 24 hrs.


title: Heads, 5mM paraquat in 2.5% Sucrose for 12h rep1

description:
3124-JO-0002
PQ1 SL106350


title: dWAT-1


title: Wild-type-1_1_RNASeq

value: Wild-type


title: JGE190320_EGFP_24HR_R2

description: barcoded amplicon

tag: library preparation kit

value: KAPA HyperPlus (24 rxn) with SEQCAP Kit A & B

tag: culturing

value: transfected with pCMV-SSG cultured in MEM-alpha supplemented media.

tag: barcode

value: GGCTAC


title: B_PP_2

source_name: B73_polysome profiling

tag: tissue


title: JGE190320_EGFP_36HR_R3

description: barcoded amplicon

tag: cell line

value: ATGTCA


title: Heads, 2.5% Sucrose for 12h rep3

description:
3124-JO-0010
Suc3 SL106357

tag: treatment

value: control


title: Capsaspora csRNA-seq r1

description: csRNA-seq in Capsaspora to identify TSS

source_name: whole organism (mixed stages)

value: whole organism (mixed stages)

tag: assay

value: csRNA-seq

tag: genome build

value: capped short RNA (20-65nt)

tag: library strategy

value: capped short RNA-seq (csRNA-seq)


title: B_PP_1


title: JGE190320_EGFP_24HR_R1

description: barcoded amplicon

value: TAGCTT


title: Heads, 2.5% Sucrose for 12h rep2

description:
3124-JO-0007
Suc2 SL106354

tag: age

value: 3-5 days old post-eclosion

value: heads

value: Canton S

value: WT


title: Rice total RNA-seq

description: total RNA-seq in rice leaves (ribozero)

organism: Oryza sativa

source_name: rice leaves

value: rice leaves

value: total RNA-seq (rRNA depleted)

tag: library id

tag: assayed molecule

value: total RNA

value: total RNA-seq


title: Capsaspora csRNAinput r1

description: small RNA-seq in Capsaspora as a control for csRNA-seq

value: small RNA input

value: total short RNA (20-65nt)

value: small RNA-seq


title: JGE190320_EGFP_12HR_R3

description: barcoded amplicon

value: KAPA HyperPlus (24 rxn) with SEQCAP Kit A & B

value: transfected with pCMV-SSG cultured in MEM-alpha supplemented media.

value: GATCAG


title: JGE190320_EGFP_24HR_R3

description: barcoded amplicon

value: CTTGTA


title: M_CK_2

value: seedings

value: RNA-seq


title: Heads, 2.5% Sucrose for 12h rep1

description:
3124-JO-0001
Suc1 SL106349

value: 3-5 days old post-eclosion

tag: strain

tag: genotype

tag: gender

value: male

value: control


title: Nematostella csRNAinput r2

description: small RNA-seq in Nematostella as a control for csRNA-seq

organism: Nematostella vectensis

value: whole organism (mixed stages)


title: JGE190320_EGFP_12HR_R2

description: barcoded amplicon

value: ACTTGA


title: M_CK_1

tag: ecotype

tag: developmental stage

tag: library sta


title: JGE190320_EGFP_12HR_R1

description: barcoded amplicon

tag: library preparation kit

tag: culturing

value: CAGATC


title: Y37A1B_5_3: Y37A1B.5 RNAi rep 3

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
RNA-Seq reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4. The raw reads were quality-trimmed and filtered for low complexity with the tool preprocess from the SGA assembler (version 0.10.13, parameters -q 30 -m 50 --dust). The passed reads were mapped to the C. elegans genome (WBcel235, Ensembl release 90, http://aug2017.archive.ensembl.org/Caenorhabditis_elegans/Info/Annotation) with Ensembl gene annotation using TopHat2 (version 2.1.0; conservative settings, i.e --b2-sensitive --no-coverage-search --no-novel-juncs --no-novel-indels --transcriptome-max-hits=1). All reads mapping uniquely to an Ensembl gene were counted using FeatureCounts (version 1.5.0; multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 2”, Ensembl release 90 gene annotation).
Genome_build: WBcel235
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

organism: Caenorhabditis elegans

source_name: whole worm lysate of several hundred worms

growth_protocol: C. elegans strains were grown and maintained at 20 °C on standard nematode growth media (NGM) seeded with E. coli (OP50) until they reached young adulthood. They were then shifted to Y37A1B.5 RNAi or control vector RNAi bacteria.

extract_protocol:
Total RNA was extraceted from whole worm lysates of several hundred worms using acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol).
Approximately 1 µg of total RNA was used for library preparation using the TruSeq stranded mRNA library preparation kit (Illumina) following the manufacturer’s description.

treatment_protocol: Worms were treated with Y37A1B.5 or emtpy vector RNAi from young adulthood. RNAi treatment was performed for five days before worms were flash frozen in liquid nitrogen.

tag: tissue

value: day five post young adult

value: wild-type Bristol N2

tag: temperature

value: 20 °C

value: Y37A1B.5 RNAi


title: B_CK_2


title: B_CK_1


title: JGE190320_EGFP_6HR_R3

description: barcoded amplicon

source_name: Transgenic Sindbis virus

tag: cell line

tag: barcode

value: GCCAAT


title: Nematostella csRNA-seq r2

description: csRNA-seq in Nematostella to identify TSS

tag: treatment

tag: assay

value: csRNA-seq

tag: genome build

value: capped short RNA (20-65nt)

value: capped short RNA-seq (csRNA-seq)


title: Nematostella csRNAinput r1

value: small RNA input

tag: library id

value: total short RNA (20-65nt)

tag: library strategy

value: small RNA-seq


title: Y37A1B_5_2: Y37A1B.5 RNAi rep 2

value: whole worm lysate of several hundred worms

tag: age

tag: strain


title: JGE190320_EGFP_6HR_R2

description: barcoded amplicon

value: KAPA HyperPlus (24 rxn) with SEQCAP Kit A & B

value: transfected with pCMV-SSG cultured in MEM-alpha supplemented media.

value: ACAGTG


title: Nematostella csRNA-seq r1

value: whole organism (mixed stages)

tag: assayed molecule


title: Y37A1B_5_1: Y37A1B.5 RNAi rep 1


title: M_IP_2

tag: ecotype

value: seedings


title: M_IP_1

tag: developmental stage


title: input-2_ChIPSeq

library_source: genomic

molecule: genomic DNA


title: JGE190320_EGFP_6HR_R1

description: barcoded amplicon

value: TGACCA


title: L4440_2: L4440 control vector rep2

value: day five post young adult

value: wild-type Bristol N2

value: Control


title: B_IP_2

tag: library sta


title: L4440_1: L4440 control vector rep1

value: 20 °C


title: H4K91-2_ChIPSeq

tag: antibody


title: JGE190320_EGFP_3HR_R2

description: barcoded amplicon

tag: library preparation kit

tag: culturing

value: CGATGT


title: Neurospora total RNA-seq

description: total RNA-seq in Neurospora (ribozero)

tag: tissue

value: total RNA-seq (rRNA depleted)

value: total RNA

value: total RNA-seq


title: JGE190320_EGFP_3HR_R1

description: barcoded amplicon

tag: cell line

value: ATCACG


title: B_IP_1


title: H4K91-1_ChIPSeq


title: CRISPR inv cell clone C17 rep1

status: Public on Sep 15 2019

city: Shanghai

first: Jia

last: Shou

state: Shanghai

address: 800 Dongchuan Rd

department: Institute of Systems Biomedicine

institute: Shanghai Jiao Tong University

description: DNA interaction

data_processing:
The sequenced reads were mapped to the mouse (NCBI37/mm9) or human (GRCh37/hg19) reference genomes using Bowtie (version 1.0.0)
The r3Cseq program in the R/Bioconductor package was used to detect statistically significant long-range chromatin-looping interactions.
The sequencing data were visualized in the UCSC genome browser
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: processed data are bedGraph which can display DNA interaction between viewpoint and the surrounding region.

source_name: Human endometrial carcinoma cells

extract_protocol:
P0 mouse brain tissue was digested with 0.625 mg/ml collagenase in the DMEM supplemented with 10% FBS for 45 min at 37°C. Human cell lines were digested with trypsin to make single-cell suspension.
4C-seq library were prepared for sequencing using standard Illumina protocols

tag: genotype

value: pcdha CBS inversion

tag: cell type

value: endometrial carcinoma cells


title: CRISPR inv cell clone C20 rep1

description: DNA interaction


title: CRISPR inv cell clone E85 rep2

description: DNA interaction


title: CRISPR inv cell clone D67 rep2

description: DNA interaction


title: CRISPR inv cell clone D67 rep1

description: DNA interaction


title: CRISPR inv cell clone E85 rep1

description: DNA interaction


title: CRISPR inv cell clone A23 rep2

description: DNA interaction


title: CRISPR inv cell clone D8 rep2

description: DNA interaction


title: CRISPR inv cell clone A15 rep2

description: DNA interaction


title: input-1_ChIPSeq


title: CRISPR inv cell clone D8 rep1

description: DNA interaction


title: CRISPR inv cell clone C17 rep2

description: DNA interaction


title: L4440_3: L4440 control vector rep3

value: whole worm lysate of several hundred worms

tag: temperature

tag: treatment


title: HEC-1-B WT cell rep1

description: DNA interaction

value: wild type


title: JGE190320_EGFP_3HR_R3

description: barcoded amplicon

value: KAPA HyperPlus (24 rxn) with SEQCAP Kit A & B

value: transfected with pCMV-SSG cultured in MEM-alpha supplemented media.

tag: barcode

value: TTAGGC


title: CRISPR inv cell clone A23 rep1

description: DNA interaction


title: HEC-1-B WT cell rep2

description: DNA interaction


title: TH2BS11ph_ChIPSeq [P20]

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

description: TH2BS11ph occupancy in pachytene cells

data_processing:
Reads were aligned to mm10 genome using bowtie2
Discordant and unpaired reads were removed during alignment along with the PCR duplicates
After aligning replicates for each condition, the aligned files were merged into a single merged BAM file using samtools merge
Peaks were called for both P20 and P12 against publicly available TH2B (GSM1119611) ChIP-seq dataset using SICERpy
Genome_build: mm10
Supplementary_files_format_and_content: peak

source_name: Testicular cells

growth_protocol: This study involves experiments in mouse testicular cells and does not involve any cell culture model system

extract_protocol:
Mononucleosomes were isolated from mouse testicular cells (P12 and P20). Immunoprecipitation were carried out with the TH2BS11ph antibody. After washing of beads, DNA were extracted using phenol-choloroform method.
Libraries were prepared using Nebnext ultra DNA library preparation kit

treatment_protocol: Not Applicable

value: Pachytene spermatocytes

value: post natal day 20

tag: chip antibody

value: TH2BS11ph antibody


title: TH2BS11ph_ChIPSeq2 [P12]

description: TH2BS11ph occupancy in leptotene cells

value: Leptotene spermatocytes

tag: age

value: post natal day 12


title: TH2BS11ph_ChIPSeq2 [P20]

description: TH2BS11ph occupancy in pachytene cells

tag: strain


title: CRISPR inv cell clone A15 rep1

description: DNA interaction


title: TH2BS11ph_ChIPSeq [P12]

description: TH2BS11ph occupancy in leptotene cells


title: Mosaic_beta-catCA_GFP_pls_lot2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 (ver. 2.3.1).
UMI counts were extracted per HTSeq (ver. 0.6.1) from the CEL-Seq2 pipeline.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text file for expression data normalized by regularized logarithm.

organism: Danio rerio

extract_protocol:
Samples were prepared according to the CEL-Seq2 protocol described in Hashimshony et al. Geneome Biology 2016.
Libraries preparation was performed according to the published CEL-Seq2 protocol.

value: AB

value: early embryonic cell

value: 9 hpf (hour post fertilization)


title: Ubiquitous_beta-catCA_GFP_pls_lot1


title: Ubiquitous_beta-catCA_GFP_pls_lot2


title: Mosaic_beta-catCA_GFP_pls_lot1


title: Uninjected_lot1

source_name: Uninjected


title: Uninjected_lot2


title: CRISPR inv cell clone C20 rep2

description: DNA interaction


title: SC1 - mutant strant (SX1-25)

city: WuXi

first: Changhao

last: Sun

address: LI lake avenue 1900

institute: Jiangnan University

data_processing:
Bcl2fastq (v2.17.1.14) software used for basecalling.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1）
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Bowtie2 (v2.1.0) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2 (v2.1.0).
Genome_build: SMWW4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Serratia marcescens WW4

extract_protocol:
S. marcescens were frozen with liquid nitrogen, and total RNA was extracted using the Mini BEST Universal RNA extraction kit (TIANGEN, Beijing) and delivered in dry ice to GENEWIZ (GENEWIZ, Suzhou) for transcriptome resequencing analysis
RNA libraries were prepared for sequencing using standard Genewiz protocols

tag: genotype/variation

value: mutant strain (overexpression of xrpA)


title: SX1 - parent strain (JNB5-1)

value: wild type strain


title: n1-DoxoR-siSYF2-si1

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

data_processing:
Data generated with an Illumina HiSeq 2500 platform
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Splicing analysis with FARLINE pipeline ( doi: 10.1038/s41598-018-21770-7 )
Genome_build: hg19
Supplementary_files_format_and_content: excel files containing splicing events differentially observed (events : acceptor, donor, mutually exclusive, multi exon skipping), BigWig and bedGraphraph containing reads' coverage on hg19

growth_protocol: Cells were cultured in 4,5 g/L Glucose DMEM (Eurobio) supplemented with 10% (v/v) fetal bovine serum (Dutscher), and 2 mM L-Glutamine (Eurobio) in 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from total cells using TRIzol Reagent (ThermoFiscer Scientific).
Libraries were made using one µg of total RNA and the TruSeq Stranded mRNA Library Preparation Kit (Illumina) involving polyA+ RNA selection. Equimolar pool of libraries were sequenced on a Illumina HiSeq 2500 machine using paired-ends reads (PE, 2x101bp) and High Output run mode allowing to get 200 millions of raw reads per sample.

treatment_protocol: Cells were transfected with siRNAs at a final concentration of 100 nM with lipofectamine RNAimax from ThermoFischer Scientific.

value: Breast cancer cell line

tag: transfected sirna

value: SYF2 #1 siRNA

tag: extract

value: Total cells


title: n2-DoxoR-siSYF2-si1


title: n3-DoxoR-siZRANB2-si1

value: ZRANB2 #1 siRNA


title: NASH-CH 5

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against rattus norvegicus genome (Rnor.6) and the quantification of genes and transcripts were done with the RSEM program using ensembl annotation (Rattus_norvegicus.Rnor_6.0.91.chr.gtf)
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Rnor6
Supplementary_files_format_and_content: RSEM expected counts

organism: Rattus norvegicus

source_name: wistar rat hepatic tissue

extract_protocol:
RNAqueous-Micro kit (Ambion)
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E)

tag: group

value: NASH-CH


title: n2-DoxoR-siZRANB2-si1


title: NASH-CH 6


title: n1-MCF7-siCtl

value: Negative Control siRNA


title: n2-MCF7-siCtl


title: n1-DoxoR-siZRANB2-si1


title: n1-DoxoR-siSYF2-si2

value: SYF2 #2 siRNA


title: n3-DoxoR-siSYF2-si1


title: n3-MCF7-siCtl


title: NASH-CH 4


title: n2-DoxoR-siSYF2-si2


title: n2-DoxoR-siZRANB2-si2

value: ZRANB2 #2 siRNA


title: n1-DoxoR-siCtl


title: n3-DoxoR-siCtl


title: n1-DoxoR-siZRANB2-si2


title: NASH-CH 3


title: NASH-CH 2


title: NASH-CH 1


title: n3-DoxoR-siSYF2-si2


title: n3-DoxoR-siZRANB2-si2


title: n2-DoxoR-siCtl


title: NASH 5

value: NASH


title: NASH 4


title: wt_ACAGTG Setd5+/+ NSCs

data_processing:
Reads were mapped to the reference genome with TopHat2 2.1.1
Gene counts were calculated with HTSeq 0.6.1
Differential gene expression was performed with DESeq2 2.11.39
Genome_build: mm9
Supplementary_files_format_and_content: Coverage bigWig files were generated with bamCoverage 2.5 (deepTools2)

source_name: Cortex derived neural progenitors

extract_protocol:
RNA libraries were generated starting from 1 microgram of total RNA using TRIzol (Invitrogen, Life technologies). RNA quality was assessed by using a Tape Station instrument (Agilent).
RNA was processed according to the TruSeq Stranded mRNA Library Prep Kit protocol.

tag: development stage

value: Embryonic Cortex


title: wt_GCCAAT Setd5+/+ NSCs


title: D3 Setd5+/- NSCs


title: C5 Setd5+/- NSCs


title: wt_CGATGT Setd5+/+ NSCs


title: CT6

value: control


title: NASH 6


title: Pcdha deletion mice rep2-VP-ga3

description: DNA interaction

source_name: C57BL/6 P0 mouse brain tissue

value: pcdha CBS deletion

value: P0 mouse brain tissue


title: Pcdha deletion mice rep1-VP-ga3

description: DNA interaction


title: Pcdhab deletion mice rep2-VP-ga3

description: DNA interaction

value: pcdhab CBS deletion


title: NASH 1


title: Pcdhab deletion mice rep1-VP-ga3L

description: DNA interaction


title: Set001.G2

type: protein

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

hyb_protocol: Manufacturer's recommended

scan_protocol: Manufacturer's recommended

data_processing: SOMAscan raw data was processed following manufacturer’s recommendations. In brief, hybridization normalization was performed using control probes to remove intra-array hybridization variation. Calibrator control samples were run in replicates on all arrays along with clinical samples and the median values of calibrators were utilized to perform intensity scaling between plates. Normalized and scaled data were subjected to differential expression using Limma software14. In brief, intensity of each probe (i.e. protein) was compared between a pair of experimental groups using a linear model configured to compute moderated t-statistics via empirical Bayes moderation of standard errors. Protein fold changes (on log scale) were computed and differential expression p-values were corrected for multiple testing using Benjamini-Hochberg (FDR) method. Proteins with a corrected p-value ≤ 0.05 were considered as significantly differentially expressed between groups. All computations were performed in R statistical programming environment (version 3.4.1).

molecule: protein

source_name: Gastric Antrum

extract_protocol: The full-thickness gastric biopsy tissue was cryopulverized and protein extracted using T-Per tissue protein extraction agent. The Aptamer-based SomaLogic tissue scan that quantitatively identifies 1300 human proteins was used.

value: DG


title: Set001.D2


title: B4 Setd5+/- NSCs

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

institute: Ospedale San Raffaele


title: Set001.B2

value: Idiopathic


title: Set001.E4


title: Set001.D1


title: Set001.H2


title: WT mice rep2-VP_ga3

description: DNA interaction

value: wild type


title: NASH 2


title: CT5


title: WT mice rep1-VP_ga3

description: DNA interaction


title: Set001.B4


title: Set001.C1


title: Pcdhab deletion mice rep2-VP-HS5-1bL

description: DNA interaction


title: Set001.A1


title: NASH 3


title: Set001.H4


title: Pcdhab deletion mice rep1-VP-HS5-1bL

description: DNA interaction


title: Pcdha deletion mice rep1-VP-HS5-1bL

description: DNA interaction


title: CT3


title: CT1


title: Pcdha deletion mice rep2-VP-HS5-1

description: DNA interaction


title: CT2


title: WT mice rep1-VP_HS5-1

description: DNA interaction


title: WT mice rep1-VP_HS5-1bL

description: DNA interaction


title: Pcdha deletion mice rep2-VP-HS5-1bL

description: DNA interaction


title: WT mice rep2-VP_HS5-1

description: DNA interaction


title: WT mice rep2-VP_HS5-1bL

description: DNA interaction


title: Neuro2A WT cell rep2-VP_HS18-20

description: DNA interaction

source_name: Mouse neuroblastoma cells

value: neuroblastoma cells


title: Set001.E3


title: Set001.A2


title: Pcdha deletion mice rep1-VP-HS5-1

description: DNA interaction


title: Set001.E2


title: Neuro2A WT cell rep2-VP_HS7L

description: DNA interaction


title: Set001.D4

value: Control


title: Set001.H1


title: CT4


title: Set001.A4


title: Set001.A3


title: Neuro2A WT cell rep2-VP_HS5-1bL

description: DNA interaction


title: Set001.C2


title: Neuro2A WT cell rep1-VP_HS18-20

description: DNA interaction


title: Set001.F4


title: Neuro2A WT cell rep1-VP_HS7L

description: DNA interaction


title: Neuro2A WT cell rep1-VP_HS5-1bL

description: DNA interaction


title: 3D HTR8 C

city: Hamilton

first: Michael

state: Ontario

address: 1200 Main Street West, Health Sciences Building

country: Canada

institute: McMaster University

hyb_protocol: Samples were hybridized for 16 hr at 45°C using Affymetrix WT PLUS Kit.

scan_protocol: Affymetrix GeneChip™ 3000 instrument system

data_processing: Normalization and output file generation was performed with Affymetrix Gene Expression Console (Thermo) using the Robust Multi-Chip Analysis (RMA) algorithm [RMA-Gene-full].

label: Biotin

source_name: Immortalized human extravillous trophoblast cells

label_protocol: 200 ng of RNA was processed and labelled with Biotin Allonamide Triphosphate.

growth_protocol: HTR8/SVneo cells were cultured at 37°C in a humidified atmosphere of 5% CO2/95% atmospheric air in RPMI-1640 (Corning), supplemented with 5% heat-inactivated FBS (Gibco), 1% (v/v) penicillin-streptomycin (Corning) and 1% (v/v) L-glutamine (Corning). Media was replaced every two days, and at 70-80% confluency, HTR8/SVneo cells were sub-divided.

extract_protocol: Total RNA was extracted from cells using TRIzol Reagent (Invitrogen) and Direct-zol RNA MiniPrep Kit (Zymo Research), following the manufacturer’s protocol.

treatment_protocol: 96-well ultra-low attachment (ULA) plates (Corning) were used to promote the self-assembly of HTR8/SVneo cells into three-dimensional (3D) cellular spheroids. 2D monolayer samples were simply cultured on flat-bottom plates.

tag: culture condition

value: 3D spheroids

value: Placenta


title: Set001.B3


title: input RNA, parental cells

status: Public on Sep 14 2019

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: P.input

data_processing:
Library strategy: MeRIP-seq
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information. HOMER was used to generate bigwig files.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain raw counts for each gene and alignment tracks in bigwig format

source_name: PEO1 cells

growth_protocol: Parental and PARPi resistant PEO1 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C supplied with 5% CO2.

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and subsequently purified using RNeasy Midi Kit (QIAGEN). Purified total RNA was fragmented in freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2)
Library preparation and next generation sequencing were performed by the Genomics Facility at the Wistar Institute using ScriptSeq complete Gold kit (Epicentre) following the manufacturer’s instructions.

treatment_protocol: PARP inhibitor (PARPi) resistant BRCA2-mutated epithelial ovarian cancer PEO1 cells were developed by a continuous stepwise exposure to increasing concentrations of the PARPi (Olaparib).

value: parental PEO1 cells

tag: antibody

value: none, input


title: Set001.G1


title: 3D HTR8 B

tag: tissue


title: 3D HTR8 D


title: m6A pulldown, resistant cells

source_name: PARPi resistant PEO1 cells

value: PARPi resistant PEO1 cells


title: m6A pulldown, parental cells


title: High_emerged_fast_pool2

city: Leioa

first: Daniel

last: Prieto

address: Barrio Sarriena s/n

institute: University of the Basque Country

description: HEF pool 2

hyb_protocol: Samples were manually hybridized with SureHyb hybridization chambers (Agilent technologies). Hybridization was done in the oven of Agilent technologies following the Agilent protocol. Characteristics: 600 ng of marked cRNA; 40 µl volume; 65 ºC temperature; 20 hours duration at 10 rpm in the hybridization

scan_protocol: The scanning was carried out on the DNA microarrays G2565CA scanner with ozone –barrier slide covers with the Scan control Software version 8.5.1., using the default protocol AgilentG3_GX_1Color. The Scanning resolution was 3 µm and green channel

data_processing: We used Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies) to process the microarray images and to quantify the fluorescence of the probes

organism: Mytilus galloprovincialis

source_name: F mussels reared in BP diet. Experiment II treatment I

label_protocol: We used “One-Color Microarray-Based Exon Analysis” marking protocol from Agilent. Samples were marked using “Low Input Quick Amp WT Labeling kit, One-Color” (p/n 5190-2943) kit.

growth_protocol: Mussels were reared in laboratory under different nutritional conditions

extract_protocol: The RNA was extracted with Ribopure system (Ambion kit). The analysis of the quality and integrity of RNA was checked with Fragment AnalyzerTM Automated CE System equipment from advanced analytical with DNF-471 Standard Sensitivity RNA Analysis kit, (15 nt) and Fragment AnalyzerTM 1.1.0.11 software version. RNA quality was checked using PROSize 2.0.

treatment_protocol: Fast and slow growing individuals were obtained in each rearing condition. Mussels were dissected and gills were obtained to extract the RNA. Samples were stored immersed in RNA later at -80 ºC until the RNA was extracted

tag: growth

value: F

tag: diet

value: BP

tag: emersion

value: emerged

value: Gill sample


title: input RNA, resistant cells

description: R.input

tag: cell type


title: High_emerged_fast_pool4

description: HEF pool 4


title: High_emerged_fast_pool3

description: HEF pool 3


title: 3D HTR8 A


title: High_emerged_fast_pool1

description: HEF pool 1


title: High_emerged_slow_pool4

description: HES pool 4

source_name: S mussels reared in BP diet. Experiment II treatment I

value: S


title: 2D HTR8 D

value: 2D monolayers


title: 2D HTR8 C


title: 2D HTR8 B


title: Pancreas: KSR23 rep5

city: New York

first: Sergio

last: Lira

state: NY

address: 1425 Madison Ave room 12-20

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNAseq data was checked for quality using the Illumina FastQC algorithm on Basespace.
Single-end sequencing reads were aligned to the mouse genome (UCSC/mm10) using Tophat (version 2.1.0)
HTSeq (Version 0.6.1p1) was used to count the reads numbers mapped to each gene.
Raw count data were filtered to remove low expressed genes with less than five counts in any sample.
Differential gene expression analysis was performed by EdgeR (version 3.18.1)
Genome_build: UCSC/mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each samples

organism: Mus musculus

source_name: Pancreas

extract_protocol:
Pancreas were removed, homogenized in Trizol reagent. Total RNA was isolated from the homogenate following the Qiagen RNeasy Mini  kit protocol with an on-column DNAse digestion step included.
100 pg of total RNA was oligo-dT primed using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit and resulting the cDNA was amplified using 15 cycles of PCR. The double stranded cDNA (dscDNA) was purified using AMPure XP magnetic beads and assessed for quality using the Qubit dsDNA HS assay and an Agilent Bioanalyzer high sensitivity dscDNA chip (expected size ~600bp-9000bp). The Illumina Nextera XT kit was used for library preparation wherein 125 pg dscDNA was fragmented and adaptor sequences added to the ends of fragments following which 12 cycles of PCR amplification was performed. The DNA library was purified using AMPure XP magnetic beads and final library assessed using Qubit dsDNA HS assay for concentration and an Agilent Bioanalyzer high sensitivity DNA assay for size (expected range ~600-740bp). Library quantitation was also done using a NEBNext Library Quant kit for Illumina. Each library was then diluted to 4nM, pooled and denatured as per standard Illumina protocols to generate a denatured 20 pM pool. A single end 75bp sequencing was performed on the Illumina Nextseq 500 by loading 1.8 pM library with 5% PhiX on to a 75 cycle high output flow cell.

value: post natal day 5

tag: genotype


title: High_emerged_slow_pool3

description: HES pool 3


title: Pancreas: WT rep5

value: Wild type


title: Pancreas: WT rep3


title: High_emerged_slow_pool1

description: HES pool 1


title: Pancreas: WT rep1


title: Pancreas: WT rep2


title: High_emerged_slow_pool2

description: HES pool 2


title: 2D HTR8 A


title: Jejunum: KSR23 rep5

source_name: Jejunum

extract_protocol:
Jejunum were removed, homogenized in Trizol reagent. Total RNA was isolated from the homogenate following the Qiagen RNeasy Mini  kit protocol with an on-column DNAse digestion step included.
100 pg of total RNA was oligo-dT primed using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit and resulting the cDNA was amplified using 15 cycles of PCR. The double stranded cDNA (dscDNA) was purified using AMPure XP magnetic beads and assessed for quality using the Qubit dsDNA HS assay and an Agilent Bioanalyzer high sensitivity dscDNA chip (expected size ~600bp-9000bp). The Illumina Nextera XT kit was used for library preparation wherein 125 pg dscDNA was fragmented and adaptor sequences added to the ends of fragments following which 12 cycles of PCR amplification was performed. The DNA library was purified using AMPure XP magnetic beads and final library assessed using Qubit dsDNA HS assay for concentration and an Agilent Bioanalyzer high sensitivity DNA assay for size (expected range ~600-740bp). Library quantitation was also done using a NEBNext Library Quant kit for Illumina. Each library was then diluted to 4nM, pooled and denatured as per standard Illumina protocols to generate a denatured 20 pM pool. A single end 75bp sequencing was performed on the Illumina Nextseq 500 by loading 1.8 pM library with 5% PhiX on to a 75 cycle high output flow cell.


title: Pancreas: KSR23 rep4


title: Pancreas: KSR23 rep2


title: Pancreas: KSR23 rep1


title: Jejunum: WT rep3


title: Jejunum: WT rep4


title: Jejunum: KSR23 rep2


title: Jejunum: WT rep5


title: Jejunum: WT rep2


title: Pancreas: WT rep4


title: Jejunum: KSR23 rep1


title: 17EF018N seq [miRNA-Seq]

city: Guangzhou

first: kexing

last: Lyu

state: Guangdong

address: 58 Zhongzhan Road II, Yuexiu Distict

department: Otorhinolaryngology

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
high-quality clean reads were obtained by removing reads containing adapters, poly-N reads (with an N ratio greater than 10%) and low-quality reads (a proportion of bases with a Phred base quality score>20).
The transcriptome data were aligned to the reference genome using TopHat2 after removing the reads mapped to ribosomes
mapped reads were assembled by Cufflinks using reference annotation-based transcripts (RABTs)
Assembly data were merged using Cuffmerge, and potential assembly errors were removed for further differential analysis
To identify the new transcripts, all the reconstructed transcripts were aligned to the reference genome and were divided into twelve categories using Cuffcompare. Transcripts with one of the classcodes u, I, j, x, c, e, or o were defined as novel transcripts
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: Excel files include RPKM, p values,count,Symbol,  GO functions and KEGG pathways annotation for each Sample ...

source_name: adjecent normal tissue

extract_protocol:
Total RNA was extracted from the sample with the TRIzol reagent, and fragments that were 18-30 nucleotides in length were isolated by agarose gel electrophoresis. A 3? linker was ligated, and the ligation fractions that were 36-44 nt in length were extracted by 15% denaturing PAGE gel electrophoresis. The 5? linker was ligated followed by reverse transcription-polymerase chain reaction (RT-PCR). The reverse transcription product was separated by 3.5% agarose gel electrophoresis, and fragments that were 140-160 bp in length were selected. Finally, the quality of the library was evaluated on a StepOnePlus PCR system (Applied Biosystems Inc., CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal tissue

tag: organ

value: larynx

tag: tnm stage


title: 17EF031N seq [lncRNA and mRNA-seq]

extract_protocol:
Total RNA was extracted from the LSCC and adjacent nontumor tissue samples using the TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.A total of 10 µg of RNA per sample was used for RNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 17EF024T seq [miRNA-Seq]

source_name: laryngeal cancer tissue

value: tumor


title: 17EF018T seq [miRNA-Seq]


title: 17EF024N seq [lncRNA and mRNA-seq]


title: Jejunum: WT rep1

tag: age


title: 17EF031T seq [miRNA-Seq]


title: 17EF031T seq [lncRNA and mRNA-seq]


title: 17EF024N seq [miRNA-Seq]


title: 17EF031N seq [miRNA-Seq]


title: eIF2aS51A_15mins_3

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks)
Genome_build: mm10
Supplementary_files_format_and_content: csv files with differential expression

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF immortalized cell lines were grown in DMEM supplemented with 10% FBS and 5% Penicillin/Streptomycin

extract_protocol:
Total RNA from lysates was obtained using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: Cells were either untreated or treated with a final concentration of 500 uM hydrogen peroxide for either 15 mins or 120 mins

value: Mouse embryonic fibroblasts

tag: treatment

value: Oxidative Stress Induction

tag: treatment time (mins)

tag: stressor


title: eIF2aS51A_120mins_3


title: eIF2aS51A_15mins_2


title: eIF2aS51A_120mins_1


title: eIF2aS51A_120mins_2


title: Jejunum: KSR23 rep3

tag: strain


title: eIF2aS51A_15mins_1


title: 17EF018N seq [lncRNA and mRNA-seq]


title: 17EF024T seq [lncRNA and mRNA-seq]


title: 17EF018T seq [lncRNA and mRNA-seq]


title: Wild-Type_120mins_3

value: Wild-Type


title: eIF2aS51A_Untreated_3


title: eIF2aS51A_Untreated_2


title: Wild-Type_120mins_2


title: DP 4C-seq (Satb1)

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers. Read length starts at 50, but is reduced to 26 when removing bait sequence during demultiplexing

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2)
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata
Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm9
Supplementary_files_format_and_content: Cis files, containing a header and two columns (restriction fragment midpoint coordinate, counts), the input format for 4See

source_name: CD4+/CD8+ thymocytes

extract_protocol:
Cells were detached with trypsin, washed by centrifugation in PBS, and then fixed with 2% formaldehyde in mES culture medium for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40 and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation. 50 ng aliquots of this DNA were used as template for PCR with bait-specific primers containing Illumina adapter termini (primer sequences and optimal PCR conditions available on request)
PCR reactions were pooled, primers removed by washing with 1.8x AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).

treatment_protocol: 4 week old thymus was dissected, cells were washed and filtered in PBS, and then sorted by FACS with anti-CD4-PE and anti-CD8a-FITC antibodies (eBioScience)

value: Thymus

tag: restriction enzymes

value: DpnII - Csp6I


title: In vitro differentiated mES 4C-seq (Sox2 SCR)

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers. Read length starts at 50, but is reduced to 27 when removing bait sequence during demultiplexing

source_name: J1 embryonic stem cells

growth_protocol: J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells. In vitro differentiation was performed by culturing for six days in medium without LIF and 10% FCS, with supplementing of 5 μM final concentration retinoic acid for the final four days.

tag: cell line

value: mES J1


title: DP 4C-seq (Ikzf1)

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers. Read length starts at 50, but is reduced to 25 when removing bait sequence during demultiplexing


title: mES 4C-seq (Satb1)

growth_protocol: J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells.


title: Wild-Type_15mins_2


title: Wild-Type_15mins_3


title: Wild-Type_15mins_1


title: Wild-Type_Untreated_3


title: mES 4C-seq (Sox2 SCR, replicate 2)


title: Wild-Type_Untreated_2


title: eIF2aS51A_Untreated_1


title: A549 cells, MLN 0.5µM 24h  Replicate 2

city: Chongqing

first: Chuanming

last: Xie

state: Chongqing

address: 30 Gaotanyan Rd

department: Institute of Hepatobiliary Surgery

institute: Southwest Hospital

data_processing:
The sequencing data in the fastq files were first removed adapters using cutadapt (version 0.2.2)  with parameter setting: -q 30 -l 50 -Q 30 -k 5 -f sanger -m any -n -t 8
Reads in fastq.gz format were mapped to the human reference genome (hg19) using STAR (version 2.5.2b)  with the following parameter setting:  --twopassMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 24 --outSAMtype SAM --outSAMstrandField intronMotif
Mapped reads were assembled using StringTie (v1.3.1c) with parameter setting:  -p 16 -B -e -G
Differential expression analyses were performed using  DeSeq2 (v1.16.1). We used FDR < 0.05, Log2FC > 1.5 as cutoff
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file includes log2Foldchange value, Pvalue, FDR value and FPKM value for differentially expressed genes. txt file includes gene counts.

source_name: lung epithelial cells

growth_protocol: A549 cells were grown in DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).

extract_protocol:
Total RNA was isolated using TRIzol method and then depleted the ribosomal RNA, tRNA, etc using a "ribo-depletion" kit (Epicentre). All samples were run onto the same gel using HiSeq Rapid 50 Cycle Single-Read and 4 samples multiplexed into each lane with total of three lanes.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human lung cancer A549 cells were seeded into 60 mm dishes, treated with MLN4924 at two concentrations (0.25 or 0.5uM), plus one vehicle control (0.1% DMSO), for two time points (8 or 24 h) in duplicate. Overall, there are a total of 12 samples (0, 0.25, 0.5 uM for 8 h and 0, 0.25, 0.5 uM for 24 h treatment).

value: Lung cancer cells, epithelial

tag: time


title: Wild-Type_Untreated_1


title: A549 cells, MLN 0.25µM 24h Replicate 2


title: c_6.6_2

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

institute: Indian Institute of Science

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads
BEDTOOLS(2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using DESeq2 (genes with atleast 5 reads were selected for each comparative analysis)
Genome_build: Reference genome used : Mycobacterium tuberculosis H37Rv, accession number : NC_000962.3
Supplementary_files_format_and_content: tab delimited .txt files containing raw reads count (raw_data_counts.txt) and comparison of genes’ expression for sample pairs

organism: Mycobacterium tuberculosis H37Rv

source_name: whiB3 complemented strain of Mtb exposed to pH 6.6

growth_protocol: Mycobacterium tuberculosis H37Rv, whiB3 KO and whiB3 complemented strains were grown in 7H9-ADS till log phase at 37 degrees Celcius at 180 rpm.

extract_protocol:
Total RNA was extracted from bacteria and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for 15 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads and a 1% PhiX spike-in control.

treatment_protocol: Early log phase cultures of  Mycobacterium tuberculosis H37Rv (WT), whiB3KO and whiB3 complemented strains were exposed to buffered 7H9 media adjusted to pH 4.5 and pH 6.6 for 2 hours and then total RNA was extracted as per Mehta et al. (2016).

tag: genotype/variation

value: WhiB3 complemented strain

tag: culture condition

value: log phase bacteria grown in 7H9 media resuspended in pH 6.6 for 2 hrs

tag: sample type

value: In vitro grown bacteria


title: Wild-Type_120mins_1


title: A549 cells, MLN 0µM 24h Replicate 2

value: MLN4924 0µM


title: c_6.6_1


title: c_4.5_2

source_name: whiB3 complemented strain of Mtb exposed to pH 4.5

value: log phase bacteria grown in 7H9 media resuspended in pH 4.5 for 2 hrs


title: mES 4C-seq (Sox2 SCR, replicate 1)


title: c_4.5_1


title: 7ICV

city: Derio

first: MARTA

last: ALONSO-HEARN

state: Bizkaia

address: Berreaga 1

department: Animal Health

institute: NEIKER

data_processing:
Data filtering: The raw reads were filtered by their length (minimum size 60 bp long) and percentage of ambiguous base N less than 5 % using Prinseq-lite
Rad alignment: Trimmed reads were subsequently mapped to the Bos Taurus reference genome (Bos_taurus.UMD3.1. version 87) with TopHat mapper. Reads were assigned to a gene if they were not multi-hit reads. The resulting alignment files were provided to Cufflinks to generate a transcriptome assembly for each condition. These assemblies were then merged together using Cuffmerge, which is included in the Cufflinks package.
Abundance measurements: This merged assembly provided a uniform basis for calculating gene and transcript expression levels in each condition. The reads and merged assembly were fed to Cuffdiff which calculates expression levels and tested the statistical significance of each observed change in expression.The fold change (in log2 scale), P-values and false discovery rates (FDR) for each gene were obtained.
Genome_build: Bos_taurus.UMD3.1. version 87
Supplementary_files_format_and_content: files include FPKM values for each Sample

organism: Bos taurus

source_name: Ileocecal valve

extract_protocol:
At the time of slaughter, PB samples were collected from the coccygeal vein of all the cows included in the study in PAXgene Blood RNA tubes (2.5 ml) (Qiagen, Hilden, Germany). Total RNA was extracted from the PB samples using the PAXgene blood RNA kit according to the manufacturer´s instructions (Qiagen, Hilden, Germany). For RNA isolation, 150-200 mg of ICV of all the animals were harvested and immediately submerged in 2 ml of RNA later (Sigma, St. Louis, MO). Purification of RNA was performed using the Dynabeads mRNA DIRECT Micro Kit according to the manufacturer’s instructions (Invitrogen, Spain). Residual genomic DNA was removed using DNase digestion with RNase-free DNase I Amplification grade following the recommended protocol (Invitrogen, Spain). Concentration and quality of the total RNAs were measured using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). All samples had an RNA integrity value of 7 or greater.
Approximately 250 ng of RNA were used for each RNA-Seq library creation using the Illumina NEBNext® Ultra Directional RNA Library preparation kit following the manufacturer´s instructions (Illumina Inc, CA, US). All RNA-Seq libraries were quantified using a Qubit® Fluorometer and doubled stranded DNA high Sensitivity Assay Kit (Invitrogen). RNA-Seq libraries quality was assessed using an Agilent Bioanalyzer and Agilent high sensitivity DNA chip to confirm that the insert sizes were 200-250 bp for all the individual libraries.

tag: breed

value: Holstein

tag: tissue

value: ileocecal valve

tag: agent

value: Mycobacterium avium subsp. paratuberculosis

tag: lesion stage

value: focal


title: 11ICV

value: diffuse


title: 14ICV


title: 6ICV


title: 10ICV


title: 13ICV


title: A549 cells, MLN 0.25µM 8h Replicate 2

organism: Homo sapiens

tag: cell type


title: ko_6.6_1

source_name: whiB3 KO strain of  Mtb exposed to pH 6.6

value: WhiB3 knock out (KO)


title: ko_6.6_2


title: 5ICV


title: 12ICV


title: 9ICV


title: A549 cells, MLN 0µM 8h Replicate 2


title: wt_6.6_2

source_name: WT Mtb exposed to pH 6.6

value: wild type


title: 8ICV


title: wt_6.6_1


title: 4ICV


title: A549 cells, MLN 0.5µM 8h Replicate 2


title: wt_4.5_2

source_name: WT Mtb exposed to pH 4.5


title: ko_4.5_2

source_name: whiB3 KO strain of  Mtb exposed to pH 4.5


title: A549 cells, MLN 0.25µM 24h Replicate 1


title: 3ICV

value: control

value: no lesion


title: 2ICV


title: wt_4.5_1


title: 14PB

source_name: Peripheral blood

value: Peripheral blood


title: A549 cells, MLN 0.5µM 8h Replicate 1


title: A549 cells, MLN 0µM 24h  Replicate 1


title: 1ICV


title: A549 cells, MLN 0.25µM 8h  Replicate 1


title: Female pool #2

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Adapter sequences were removed from the output RNA-Seq sequence reads using cutadapt (http://code.google.com/p/cutadapt/)
Reads with low base quality (<13) were further trimmed and, if less than 25 base pairs, removed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The trimmed sequence reads were then aligned to the rat reference genome and gene annotation database (rn5) using TopHat2 (v2.1.1) with mammalian default parameters (PMID:23618408)
Transcripts in all of the sequencing libraries were assembled by Stringtie (PMID:25690850)
Differential expression analysis was performed by using Cufflinks (v2.2.1) (PMID: 20436464 )
The Benjamini-Hochberg procedure was used for controlling false discovery rates in multiple comparisons
Supplementary_files_format_and_content: Fold change cut-off in sorted data for pathway analysis was 1.5x (see processed data file "Female vs. male _>1.5 and <-1.5x change")
Supplementary_files_format_and_content: Final mRNA expression data by sex
Supplementary_files_format_and_content: Transcripts more than 1.5x higher and less than -1.5x fold lower in females than males, shown with p value, BH corrected q value and fold change
Supplementary_files_format_and_content: miRNA mapping rate

source_name: Kidney Inner Medulla Tissue

growth_protocol: Rats were purchased from Envigo Laboratories at 13-15 weeks of age and placed on 0.49% NaCl chow TD 96208 (Envigo) at  14-16 weeks of age for 2 weeks. Food and water were provided ad libitum

extract_protocol:
Kidney tissues were isolated and flash frozen in liquid nitrogen.  Total RNA was extracted using a Trizol-based method and quantified by Nanodrop. RNA deep sequencing and analysis was performed as previously described by the Human Molecular Genetic Center at the Medical College of Wisconsin (Chuppa et al., Kidney Int., 2018; PMID 28760335).
RNA libraries were constructed for pools of 4 rats, 2 pools per condition using an Illumina TruSeq Stranded Total RNA Kit
Samples were multiplexed on a 400 GB flow cell and pair-end sequenced using an Illumina HiSeq 2500.

treatment_protocol: No other treatment was administered.

value: Sprague Dawley

tag: diet

tag: Sex

value: Female


title: Female pool #1


title: Male pool #1

value: male


title: Male pool #2


title: 13PB


title: A549 cells, MLN 0µM 8h Replicate 1

value: Lung cancer cells, epithelial

tag: treatment


title: A549 cells, MLN 0.5µM 24h  Replicate 1


title: Pancreas: KSR23 rep3

source_name: Pancreas

tag: age

value: post natal day 5

tag: genotype


title: 12PB


title: WT2931

city: Lausanne

first: Jennifer

middle: Yihong

last: Tan

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

data_processing:
Hundred nucleotides long single-end stranded reads were mapped to mouse ribosomal RNA sequences with Hisat2 V 2.1.0 (Kim et al., 2019).
Reads not mapping to ribosomal RNA were then aligned to mouse genes using Hisat2 and quantified using HTseq (Anders et al, 2015).
Differential gene expression between KO and WT mice was identified using DEseq2 (Love et al, 2014).
Genome_build: mm10
Supplementary_files_format_and_content: The gene expression table contains the expression levels of genes (count).
Supplementary_files_format_and_content: The differential gene expression table contains differential gene expression called by DEseq2 (Love et al, 2014) between KO and WT mice while matching for littermate group.

source_name: islet

growth_protocol: Pancreatic islets were isolated from overnight fasted, 12 week-old WT and P0Rik7flox/flox mutant mice. After isolation, islets were incubated for 2h at 3 mM glucose to recover from the stress of the isolation prior to RNA extraction.

extract_protocol:
RNA was extracted using the miRNeasy kit (Qiagen), according to manufacturer guidelines.
Strand specific total RNA sequencing libraries were prepared using the NEB Ribo Zero protocol according to manufacturers’ instructions. Libraries were sequenced in an Illumina HiSeq 2000 to a depth of ~ 30 million 125 bp single-end reads.

tag: littermate group

tag: biological replicate

value: WT


title: KO2776

value: P0Rik7flox/flox mutant


title: KO2938


title: KO2775


title: WT2772


title: Colon epithelial tissue, day 7 after DSS/PhIP treatment

city: Piscataway

first: Hong

last: Wang

state: NJ

address: 164 Frelinghuysen

department: Chemical Biology

institute: Rutgers the State Univesrity of New Jersey

data_processing:
After having the raw FastQC data, first use (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) to do quality control on raw reads, check whether the data pass QC step. When raw reads pass QC, remove “dirty” reads in raw data, SOAP2 and then get the clean reads. Next step, use (http://soap.genomics.org.cn/soapaligner.html) to align the clean reads to the reference sequence, and then also do QC on the alignment result. This QC include: ‘sequencing saturation analysis’, ‘distribution of reads on reference genes’ and ‘coverage analysis’. We also use RPKM method to calculate the gene expression level, based on gene expression we select differentially expressed genes and do further functional analysis.
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs

source_name: Colon

extract_protocol:
RNA was extracted from mouse colon epithial tissues collected by scraping the epithelium from the muscle layer of the colon using Qiagen Rneasy kit.
After extracting the total RNA from the samples, mRNA of eukaryotes is enriched by using the oligo (dT) magnetic beads and mRNA of prokaryotes is enriched just by removing rRNA from the total RNA. By using the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via HiSeqTM Illumina 2000.

treatment_protocol: In this study, female hCYP1A mic at the age of 6 weeks old were separated into 3 groups, the control, the DSS-treated, and the PhIP/DSS-treated.  The control group was consisted of 3 mice without any treatment.  The DSS-treated group was consisted of 9 mice treated with 1.5% DSS in the drinking water for 5 days.  The PhIP/DSS-treated group was consisted of 9 mice treated with PhIP (2 doses of 100 mg/kg BW at 4 days apart) and then treated with 1.5% DSS drink water for 5 days at a week later.  The treated mice were sacrificed on Day 1, 3 and 7 after the DSS treatment for collecting the colon epithelial tissues.  Three mice were used at each time point.  RNA was then extracted.  Equally amount of RNA for each of 3 mice at each time point was combined as one sample for RNA-sequencing.

tag: strain

value: DSS/PhIP treated

value: day 7

value: Colon epithelial tissue

tag: pathology

value: Partial colitis


title: WT2777


title: Colon epithelial tissue, day 1 after DSS/PhIP treatment

tag: time

value: day 1

value: Colitis


title: 10PB

value: Holstein

value: Mycobacterium avium subsp. paratuberculosis

value: diffuse


title: rr11D53A 17h rep 1

city: Beijing

first: Juanjuan

address: Haidian Strict

department: Medical department

institute: Tsinghua University

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Tophat 2.1.1 and Bowtie 2.3.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated internally by Cufflink version 2.2.1 after aligning reads.
Genome_build: Streptococcus pneumoniae R6 (accession NC_003098.1, assembly GCA_000007045.1) was used directly in the analysis.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae cells cultured on TSA plate for 17 h

growth_protocol: S. pneumoniae strains of WT and TH9063 (∆rr11) knockout or TH11425 (rr11D53A) mutants were cultured on TSA plate with 6,000 units of catalase at 37ºC with 5% CO2 for about 12 hours or 17 hours.

extract_protocol:
Total RNA was extracted with the RNAprep pure Cell / Bacteria Kit from TIANGEN BIOTECH (BEIJING) COMPANY followed the instruction and then purified by using a RNeasy Mini Kit from QIAGEN COMPANY
The ribosomal RNA was removed from total RNA (~1.5 µg) using poly-T oligo-attached magnetic beads. Fragmentation of mRNAs and sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The cDNA molecules were ligated with the NEBNext Adaptor, and further processed for selected, purifed, and sequence amplification.

tag: antibiotic resistant

value: rpsL1 (StreptomycinR)

tag: culture time


title: rr11D53A 17h rep 2


title: ∆rr11 17h rep 2


title: 9PB

tag: breed

value: Peripheral blood

value: focal


title: Colon epithelial tissue, day 1 after DSS treatment

value: DSS treated

tag: tissue


title: 7PB

tag: agent


title: Colon epithelial tissue, Control

description: C

value: control

value: Normal


title: Colon epithelial tissue, day 3 after DSS treatment

value: day 3


title: ∆rr11 17h rep 1


title: Colon epithelial tissue, day 3 after DSS/PhIP treatment


title: WT 17h rep 2


title: WT 17h rep 1


title: 11PB

tag: lesion stage


title: 6PB


title: rr11D53A 12h rep 1

source_name: Streptococcus pneumoniae cells cultured on TSA plate for 12 h


title: 5PB


title: Colon epithelial tissue, day 7 after DSS treatment


title: 4PB


title: ko_4.5_1

tag: genotype/variation

value: WhiB3 knock out (KO)

tag: culture condition

value: log phase bacteria grown in 7H9 media resuspended in pH 4.5 for 2 hrs

tag: sample type

value: In vitro grown bacteria


title: 8PB


title: ∆rr11 12h rep 2


title: 3PB

value: no lesion


title: ∆rr11 12h rep 1


title: WT 12h rep 2


title: rr11D53A 12h rep 2


title: 42N Normal  lung tissues

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

institute: Hebei Medical University

description: Normal  lung tissues

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

source_name: Fresh frozen tissue

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)

extract_protocol: The total RNA was extracted from tissues using TRIzol® Reagent (Invitrogen life technologies)

value: normal


title: 1PB


title: WT 12h rep 1


title: 45N Normal  lung tissues

description: Normal  lung tissues

data_processing: Agilent Microarray Scanner (Agilent p/n G2565BA)


title: 42T Squamous cell carcinoma (SCC)

description: Squamous cell carcinoma (SCC)

value: tumor


title: Jejunum: KSR23 rep4

source_name: Jejunum

value: post natal day 5


title: 37T Squamous cell carcinoma (SCC)

description: Squamous cell carcinoma (SCC)


title: 45T Adenocarcinoma (AC)

description: Adenocarcinoma (AC)


title: 37N Normal  lung tissues

description: Normal  lung tissues