title: Dox_24hr_rep2

city: Manchester

first: Andrew

middle: Joshua

last: Lilly

address: Wilmslow Road

department: Stem Cell Haematopoiesis

country: United Kingdom

institute: CRUK Manchester Institute

description:
NoDox24h_vs_Dox24h
DE genes relative to no dox

data_processing:
bcl2fastq (v2.16.0.10) was used for basecalling and demultiplexing. bcl2fastq parameter: -r 14 -d 14 -p 14 -w 1
Lane-wise alignment was performed by bowtie2 v2.21 to GRCm38 (Ensembl v76) Mus musculus reference genome with default parameters
Generated SAM files from bowtie2 alignment were converted to BAM files by samtools v0.1.19. Parameters for samtools SAM to BAM conversion: -q 10 -F 260.
Resulting lane-wise BAM files from the same sequence library was merged into one BAM. Further, BAM files from the two different batch was merged into one final BAM to be used for downstream analysis.
Read counts from BAM files were extracted under the R environment (R v3.1.0) with the package Rsubread v1.16.1. Count table was loaded to edgeR v3.8.5 and differentially expressed genes between groups were identified by exact test function
Genome_build: GRCm38
Supplementary_files_format_and_content: rawReadCount, RPKM

source_name: hemogenic endothelium (HE)

growth_protocol: ES cell–derived HE cells were routinely generated by isolating FLK1+ cells from d3.5 embryonic body differentiations. FLK1+ cells where maintained on gelatin coated plates in liquid blast medium (IMDM supplemented with 10% FCS, P/S, 2mM L-Glutamine, 20μg/ml transferrin, 0.45mM MTG, 25μg/ml AA, 15% D4T conditioned medium, 5ng/ml VEGF and 10ng/ml IL6). After 48hous of liquid blast culture cells were treated with and without doxycyline

extract_protocol:
RNA was isolated using an Rneasy mini kit according to the manufacturers instructions.
libraries were prepared using 200ng of Total RNA and 14 cycles of amplification in the  Agilent Sure Select Automated Strand Specific RNA library prep for Illumina Multiplexed sequencing  (G9691-90030) on an Agilent Bravo-BenchCel-MiniHub  Automated Liquid Handling Platform. Libraries were sized on an Agilent Bioanalyzer (G2940CA) using a High Sensitivity DNA Kit (5067-4626) and quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (KK4835).
Pooled libraries were sequenced at 1 x 75bp on an Illumina NextSeq500 system (SY-415-1001).

treatment_protocol: Cells were treated with and without 1µg/ml doxycyline for 6, 12 and 24 hours before cells were harvested

value: Dox

tag: time point

value: FLK1+ cells from ESCs differentiated for 48hours

tag: derivative


title: 52806sacCer3_KY1419_11867431001_3HA-Rtf1_rep2

status: Public on Nov 07 2016

type: SRA

city: University Park

first: Alain

middle: Roger

last: Bataille

state: PA

address: 453 North Frear

department: BMB

country: USA

institute: Penn State University

description:
Biological replicate 2 of 2, Rtf1 IP with anti-HA antibody in 3HA-RTF1 strain
52805-06sacCer3_KY1419_11867431001_3HA-Rtf1_comb_READ1_shift6.tab

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads. Read1 tags were shift 6 bp (to better reflect the crosslinking coordinates).
Genome_build: sacCer3/R64
Supplementary_files_format_and_content: tab files of shifted merge datasets used for mapping. Format: chr/index/forwardTag#/reverseTag#. The tab file of each combined dataset contains the coordinates of the shifted (6bp in the 3' direction) exo digested end (5') corresponding to the Read 1 of the sequencer.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: All yeast cells were grown to an OD600 of 0.6-0.8 at 30 °C following standard procedures in indicated media.

extract_protocol:
ChIP-exo experiments were carried out essentially as described (Rhee and Pugh, 2012). Briefly, crosslinked cells were lysed, and chromatin pellets were isolated and then fragmented by sonication. Chromatin was then immunoprecipitated using antibody-conjugated magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and on beads digestion by lambda and recJ exonuclease. After elution of the single-stranded DNA, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina sequencing adaptor was ligated to exonuclease treated ends, and the products PCR-amplified and gel-purified.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
ChIP-exo-Seq

treatment_protocol: Cell were crosslink with 1% formaldehyde final concentration for 15 min.

tag: media

value: YPD

tag: antibody

tag: antibody lot#

tag: genotype

value: MATalpha 3xHA-RTF1 lys2-128delta his3delta200 leu2delta1 ura3-52 trp1delta63

tag: tag

value: HA

tag: protocol

value: ChIP-exo


title: NoDox_24hr_rep2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment

tag: cell type


title: 52832sacCer3_KY404-pKB1140_H6030_3HSV-HMD_rtf1D_pHMD_rep2

description:
Biological replicate 2 of 2, HMD IP with anti-HSV antibody in rtf1D plasmid(HSV-HMD) strain
52831-32sacCer3_KY404-pKB1140_H6030_3HSV-HDM_rtf1D_pHDM_comb_READ1_shift6.tab

value: Sc-Trp

value: Sigma H6030

value: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63

value: HSV


title: 52808sacCer3_KY1529_11867431001_3HA-Rtf1-E104K_rep2

description:
Biological replicate 2 of 2, Rtf1-E104K IP with anti-HA antibody in 3HA-rtf1-E104K (rtf1 mutant) strain
52807-08sacCer3_KY1529_11867431001_3HA-Rtf1-E104K_comb_READ1_shift6.tab

value: MATalpha 3xHA-rtf1-E104K lys2-128delta leu2delta1 ura3-52 trp1delta63


title: Dox_12hr_rep2

description:
NoDox12h_vs_Dox12h
DE genes relative to no dox


title: Dox_6hr_rep2

description:
NoDox6h_vs_Dox6h
DE genes relative to no dox


title: 52804sacCer3_KY1221_11867431001_3HA-Paf1_rep2

description:
Biological replicate 2 of 2, Paf1 IP with anti-HA antibody in 3HA-PAF1 strain
52803-04sacCer3_KY1221_11867431001_3HA-Paf1_comb_READ1_shift6.tab

value: MATa 3xHA-PAF1 his3delta200 leu2delta1 ura3-52 trp1delta63


title: 52805sacCer3_KY1419_11867431001_3HA-Rtf1_rep1

description:
Biological replicate 1 of 2, Rtf1 IP with anti-HA antibody in 3HA-RTF1 strain
52805-06sacCer3_KY1419_11867431001_3HA-Rtf1_comb_READ1_shift6.tab


title: NoDox_12hr_rep2


title: 52803sacCer3_KY1221_11867431001_3HA-Paf1_rep1

description:
Biological replicate 1 of 2, Paf1 IP with anti-HA antibody in 3HA-PAF1 strain
52803-04sacCer3_KY1221_11867431001_3HA-Paf1_comb_READ1_shift6.tab


title: 581 IP

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM and CPM) and differential expression analysis using limmavoom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

molecule: polyA RNA

extract_protocol:
HA samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by nanodrop.
Paired-end libraries for multiplexed sequencing were generated from 100ng of IP or input RNA using the KAPA Stranded RNA-Seq Kit with mRNA enrichment.

tag: developmental stage

tag: tissue

value: brain

value: Aldh1l1-creERT2 hemi; Ribotag het

tag: rna sample type

value: HA IP


title: 52802sacCer3_KY784_ab9132_Ctr9-6Myc_rep2

description:
Biological replicate 2 of 2, Ctr9 IP with anti-Myc antibody in CTR9-6Myc strain
52801-02sacCer3_KY784_ab9132_Ctr9-6Myc_comb_READ1_shift6.tab

value: MATalpha CTR9-6xMyc::LEU2 lys2-128delta his3delta200 leu2delta0 ura3delta0 trp1delta63

value: MYC


title: 52801sacCer3_KY784_ab9132_Ctr9-6Myc_rep1

description:
Biological replicate 1 of 2, Ctr9 IP with anti-Myc antibody in CTR9-6Myc strain
52801-02sacCer3_KY784_ab9132_Ctr9-6Myc_comb_READ1_shift6.tab


title: NoDox_6hr_rep2


title: NoDox_24hr_rep1


title: Dox_24hr_rep1

value: Dox


title: 52814sacCer3_GHY1092_11867431001_Leo1-3HA_rep2

description:
Biological replicate 2 of 2, Leo1 IP with anti-HA antibody in LEO1-3HA strain
52813-14sacCer3_GHY1092_11867431001_Leo1-3HA_comb_READ1_shift6.tab

value: MATa LEO1-3xHA::HIS3MX6 lys2-128delta his3delta200 leu2delta1 ura3-52 trp1delta63


title: Dox_12hr_rep1

value: FLK1+ cells from ESCs differentiated for 48hours


title: Dox_6hr_rep1


title: NoDox_12hr_rep1


title: NoDox_6hr_rep1


title: Mitotic Input 3

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description:
processed data file:
peaks_Mitotic_ChIP_vs_Input_3rep_qval005_notInBlacklist.bed

data_processing:
Each individual sample/replicate were mapped to the mouse genome (mm10 assembly) using the mapping module of HTSstation [David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/] (based on Bowtie2) with option discard PCR duplicates.
Mapping calls bowtie2 (v. 2.2.1) with parameters -k 20 --end-to-end --sensitive -p 5
Peaks were called using MACS2 with option --bw 200 -m 10 100 -q 0.05 (or 0.01 for Mitotic) --call-summits, using the Input as control (-c input.bam). Only peaks with a fold enrichment greater than 2 and not present in blacklist regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were kept.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage densities (.bw files) were calculated for each strand separately. They represent the genomic position-specific reads counts normalized by total number of reads (in units of 10 millions), where each multiple mapping read is counted as 1/total count.

source_name: Mitotic Input

growth_protocol: Cells were cultured on dishes coated with 0.1% gelatin type B, in GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, L-glutamine, sodium pyruvate, 100μM 2-mercaptoethanol, penicillin and streptomycin, leukemia inhibitory factor, CHIR99021 at 3μM and PD184352 at 0.8μM.

extract_protocol:
Sonicated DNA from formaldehyde-fixed cells was pulled down with anti-Sox2 antibody.
Libraries were prepared with NEBNext ChIP-seq Library Prep Master Mix kit.

treatment_protocol: Mitotic cells were obtained by overnight nocodazole synchronization followed by fixation, staining, and sorting for H3S10p-positive cells

tag: cell line

value: Embryonic stem cells (ESCs)

tag: cell subtype

value: mitotically purified ESCs


title: ddm1C24_RNA_rep2

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
For bisulfite sequencing data processing, adapter and low quality reads (q < 20) were trimmed first. Then the remaining clean reads were mapped to the Col-0 TAIR10 Arabidopsis thaliana genome by BSMAP aligner (whole genome bisulfite sequence MAPping program) allowing up to 4 mismatches (Xi and Li, 2009). Unique mapped reads were extracted to determine the cytosine methylation level as previously described (Lister et al., 2008).Only the cytosines with >4 reads in all samples were used for subsequent analyses.
High-throughput sequencing generated sequences for each  sample and the raw reads passed quality filtering (Q > 17 and length >= 25 bp). Raw reads were first subject to 3’ adapter removal. Clean reads of fastq file were transferred into fasta file. Clean reads were mapped to the  Col-0 TAIR10 Arabidopsis thaliana genome using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (reads per million) in at least three samples were kept for further analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq WIG files represent methylation level (from 0 to 1) of each cytosine that are covered ≥4 times in all 4 samples.Tab-delimited text file include RPM(Reads per Million) values for 24 Samples .

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Seeds were stratified for 7 days at 4 °C and grown on 1/2 Murashige and Skoog (MS) nutrient medium supplemented with 1.2% agar under long day conditions (16h light, 8h dark cycle at 22 °C) for two weeks before harvested.

extract_protocol:
Paired-end (90bp) BS-seq and RNA-seq data were generated with an Illumina HiSeq 2000 using standard protocols.
Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.

tag: age

value: whole seedling


title: ddm1C24_RNA_rep3


title: ddm1ColXddm1C24_DNA


title: ddm1Col_DNA


title: Mitotic Input 2


title: ddm1C24_DNA


title: ddm1C24Xddm1Col_RNA_rep3


title: ddm1C24_RNA_rep1


title: ddm1C24Xddm1Col_DNA


title: ddm1ColXddm1C24_RNA_rep3


title: ddm1C24Xddm1Col_RNA_rep2


title: 52410sacCer3_BY4741_ab1790_H2B

description:
Biological replicate 1 of 2, H2B IP with anti-H2B antibody in wildtype strain
52410-56727sacCer3_BY4741_ab1790_H2B_comb_READ1_shift6.tab

value: YPD

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0

value: ChIP-exo


title: ddm1ColXddm1C24_RNA_rep2


title: Asynchronous ChIP 1

description:
processed data file:
peaks_Asynchronous_ChIP_vs_Input_3rep_qval001_notInBlacklist.bed

source_name: Asynchronous ChIP

value: asynchronous ESCs

tag: chip antibody

value: Sox2 Y-17 (sc-17320, Santa Cruz)


title: ddm1Col_RNA_rep3


title: ddm1Col_RNA_rep2


title: ddm1ColXddm1C24_RNA_rep1


title: Asynchronous Input 3

source_name: Asynchronous Input


title: Asynchronous Input 1


title: Asynchronous ChIP 2


title: Mitotic ChIP 1

source_name: Mitotic ChIP


title: Asynchronous ChIP 3


title: Asynchronous Input 2


title: Mitotic ChIP 2


title: ddm1Col_RNA_rep1


title: Mitotic ChIP 3


title: Mitotic Input 1


title: C24_RNA_rep1


title: ddm1C24Xddm1Col_RNA_rep1


title: C24_RNA_rep2


title: C24XCol_RNA_rep3


title: mock 293T-hDcr-KO Total

city: Riverside

first: Jinfeng

last: Lu

address: 900 University Ave

institute: UC Riverside

data_processing:
Adaptors were removed by in-house perl script searching for the first 6-nts of the adaptor sequence (TGGAAT) from the 3'-end of the sequenced reads
Reads no shorter than 15-nt and without any 'N's were collapsed and converted to fasta files
18- to 28-nt reads were aligned to the relative virus genome using Bowtie 1.0.0 (allowing no mismatches) for further normalization and analysis
Genome_build: The genomes of mutant viruses were modified on the original wildtype virus genomes downloaded from NCBI
Supplementary_files_format_and_content: Each line represents one small RNA species aligned to virus genome, shown by its sequence and copy number

organism: Homo sapiens

source_name: Cultured somatic cells

growth_protocol: Cells were seeded in a 6-cm plate at a density of 2.5 × 106/plate one day before infection

extract_protocol:
RNA extraction using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol
Libraries of small RNAs were constructed from total RNA extracted 24 hours after infection by the method that depends on the 5' monophosphate of small RNAs with the TruSeq Small RNA Sample Preparation Kit of Illumina (San Diego, CA)

treatment_protocol: Cells were inoculated with serum-free DMEM (mock), PR8/delNS1 or WSN/delNS1 (moi=1) and harvested after 24 hours

tag: virus

value: mock

tag: co-ip antibody

value: no antibody

tag: cell genotype

value: Dcr-knockout cells


title: PR8/delNS1 293T-hDcr-KO +dDcr-2+Loqs-PD+R2D2 Total

value: Dcr-knockout cells, expressing Drosophila Dcr-2+Loqs-PD+R2D2


title: PR8/delNS1 293T-hDcr-KO Total


title: mock 293T Total

value: wildtype cells


title: C24XCol_RNA_rep1


title: C24_RNA_rep3


title: C24XCol_RNA_rep2


title: PR8/delNS1 A549 Total


title: ColXC24_RNA_rep3


title: ColXC24_RNA_rep2


title: ColXC24_RNA_rep1


title: Sample_GSNO_231114

status: Public on Nov 06 2016

city: Haifa

first: Serge

last: Ankri

address: 1 Efron street

department: Microbiology

country: Israel

institute: Technion

data_processing:
The quality of the sequenced data was checked using FASTQC v0.10.1 software. The number and percentage of reads that passed filter, the control mapping, error rate and the per-base quality scores demonstrate that the run was of high quality (phred scores≥30).
After quality assessment, the high-quality reads were aligned to the Entamoeba reference genome (http://amoebadb.org/amoeba/) by TopHat version 2.0.11, allowing up to 3 mismatches per read.
Only uniquely mapped reads were counted in the analysis, using HTSeq-count package version 0.6.1 with 'union' mode (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Normalization and differential gene expression analysis were performed  using the DESeq2 package version 1.6.2. DESeq2 performs statistical tests to determine whether genes are differentially expressed between pairs of conditions.
We used ‘FDR (false discovery rate) ≤ 0.001 and the absolute value of log2 fold change  ≥ 1’ as the threshold to judge the significance of gene expression difference.
Genome_build: Entamoeba reference genome (http://amoebadb.org/amoeba/)
Supplementary_files_format_and_content: DESeq output with columns of normalized counts for each sample

organism: Entamoeba histolytica HM-1:IMSS

source_name: NAT

growth_protocol: E. histolytica trophozoites strain HM-1 IMSS  were grown under axenic conditions in Diamond's TYI S-33 medium  at 37°C.

extract_protocol:
Total RNA was extracted from control trophozoites (two biological replicates) and from NAT (three biological replicates) using the TRI Reagent kit following the manufacturer’s instructions (Sigma-Aldrich).
RNA-Seq libraries have been prepared using the TruSeq RNA library preparation kit V2 (Illumina Inc. San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Trophozoites were exposed to 30 μM GSNO for one week before further increase in GSNO concentration was made. The concentration of GSNO was increased by 30 μM until it reached 120 μM. A strain growing at 120 μM GSNO was obtained approximately after 4 weeks, and was used in all experiments.

tag: strain

value: HM-1 IMSS

tag: adaptation status

value: NO adapted

value: trophozoites


title: Sample_GSNO_211114


title: Col_RNA_rep3

tag: genotype

value: Col


title: Sample_GSNO_181114


title: PR8/delNS1 293T-hDcr-KO +dDcr-2 Total

value: Dcr-knockout cells, expressing Drosophila Dcr-2


title: Sample_1109_211014

source_name: control trophozoites

value: non-adapted (control)


title: PR8/delNS1 293T AGO-IP

value: Anti-pan Ago (Millipore, Billerica, MA)


title: Col_RNA_rep1

value: whole seedling


title: PR8/delNS1 293T-hDcr-KO +hDcr Total

value: Dcr-knockout cells, expressing human Dcr


title: Col_RNA_rep2


title: WSN/delNS1 293T AGO-IP


title: Sample_1109_231014


title: TG2

status: Public on Nov 05 2016

city: La Jolla

first: Li-Fan

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

description:
Total RNA (including small RNAs).
Processed data file: Foxp3cre_het_miR-27Tg_RPKM.txt

data_processing:
Reads from all libraries were mapped to the mouse genome (mm10) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts were calculated using HOMER.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Foxp3cre_het_miR-27Tg_RPKM.txt: Tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq transcripts.

source_name: CD4+Foxp3+ Treg cells, miR-27 Tg

extract_protocol:
Total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted CD4+Foxp3+ Treg cells isolated from indicated mice.
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

tag: strain/background

tag: genotype/variation

value: miR-27 Tg

tag: gender

value: female

tag: disease state

value: healthy

value: CD4+Foxp3+ Treg cells


title: shTMEM258_3

city: Cambridge

first: Daniel

middle: Bartholomew

last: Graham

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

data_processing:
Alignment with Tophat 2.0.14 + Bowtie 1.1.2 + Samtools 0.0.19
Counting of genes with htseq-count
QC with RSeqC read_distribution.py + custom scripts, alignment file needs to have header reformatted to run with RSeqC (chromosome names
Differential gene expression with EdgeR + limma

source_name: HeLa

growth_protocol: DMEM 10% FBS

extract_protocol:
dynabead mRNA extraction protocol
(smartseq2) equal amounts of RNA from each sample into RT. NEBNext Second Strand. 0.5ng tagmentation in half the standard reaction size.
whole transcriptome. paired end. 30 and 29 cycles. 2 indices each 8 cycles

treatment_protocol: lentiviral shRNA

tag: cell type

value: Human derived cell line

tag: treatment


title: TG3


title: shTMEM258_4


title: WSN/delNS1 293T Total

description: Including cells from 2 different sources

value: no antibody


title: TG1


title: PR8/delNS1 293T Total


title: WT3

source_name: CD4+Foxp3+ Treg cells, WT Tg

value: WT Tg


title: shCtl_2

value: shCtl


title: PR8/delNS1 293T FLAGtag-AGO2-IP

value: Anti Flag M2 (Sigma-Aldrich, St Louis, MO)

value: wildtype cells, expressing FLAG-tagged human AGO2


title: WT2


title: Tr3_WT

description:
Total RNA (including small RNAs).
Processed data file: CD4cre_miR-23_clusterTg_Tr_RPKM.txt

data_processing:
Reads from all libraries were mapped to the mouse genome (mm10) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts were calculated using HOMER.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CD4cre_miR-23_clusterTg_Tr_RPKM.txt: Tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq transcripts.

source_name: CD4+CD25hi Treg cells, WT Tg

extract_protocol:
Total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted CD4+CD25hi Treg cells isolated from indicated mice.
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

value: CD4+CD25hi Treg cells


title: Tr2_WT


title: Brassica napus

city: Nanjing

first: Pu

last: Chu

address: No.1 Weigang street

country: China

institute: Nanjing Agriculture University

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads with adaptors only, those with more than 5% unknown nucleotides and reads with more than 20% low-quality bases (quality value ≤10) were filtered out before data analysis.
The short reads assembling program “Trinity” (release 2013-02-25) was used to assembly the transcriptome de novo using the clean reads.
Gene expression levels were normalized and calculated using the Reads Per Kilobase per Million reads (RPKM) method from Mortazavi et al., Nature Methods, 2008.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Brassica napus

source_name: floral buds

extract_protocol:
RNA was extracted using Trizol reagent, followed by RNase-free DNase I (Takara, Dalian, China)  treatment according to the manufacturer’s protocol. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Zhongshuang 11

tag: development stage

value: initial flowering stage

tag: tissue

value: floral buds


title: G.gallus E8-E8.5 rep 3

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

data_processing:
Read mapping was done using Tophat2/Bowtie2
Transcript abundances were calculated using cuffdiff from cufflinks package
Genome_build: WASHUC2 (chicken)
Genome_build: genome and transcript annotation reference files (assemblies from 2014-02-18) for pigeon were from (Giga)n database at gigadb.org
Supplementary_files_format_and_content: Two tab-delimited output files from cufflinks containing FPKM values for all transcripts in pigeon and chicken

organism: Gallus gallus

source_name: retina

growth_protocol: Pigeon and chicken fertilized eggs were placed in a 37°C humidified incubator for the embryos to grow. Retinas were dissected in PBS, 1 to 6 whole retinas were collected in the proper volume of Trizol Reagent.

extract_protocol:
RNA was extracted using Trizol Reagent (Life Technologies), following the manufacturer’s instructions
Stranded-mRNA libraries were prepared from 1 μg of total RNA using the The TruSeq Stranded mRNA Library Preparation Kit (Illumina), following the manufacturer’s instructions

value: retina

tag: developmental stage


title: Tr3_DKO

source_name: CD4+CD25hi Treg cells, DKO Tg

value: DKO Tg


title: G.gallus E8-E8.5 rep 1


title: Tr2_DKO


title: G.gallus E5-E5.5 rep 3


title: WT1


title: Tr3_cluster

source_name: CD4+CD25hi Treg cells, cluster Tg

value: cluster Tg


title: shTMEM258_1


title: Tr2_cluster


title: G.gallus E5-E5.5 rep 1


title: Tr1_cluster


title: G.gallus E8-E8.5 rep 2


title: shCtl_1


title: G.gallus E5-E5.5 rep 2


title: Tr2_27

source_name: CD4+CD25hi Treg cells, miR-27 Tg

value: miR-27 Tg


title: G.gallus E3-E3.5 rep 2


title: G.gallus E3-E3.5 rep 3


title: Tr2_24

source_name: CD4+CD25hi Treg cells, miR-24 Tg

value: miR-24 Tg


title: Tr3_27


title: Tr3_23

source_name: CD4+CD25hi Treg cells, miR-23 Tg

value: miR-23 Tg


title: Tr1_24


title: Tr2_23


title: Tr1_23


title: Tr1_DKO


title: G.gallus E3-E3.5 rep 1


title: 4C_GTMm_d11

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
4C of the genital tubercle of a mouse using the Hoxd11 viewpoint
library strategy: 4C-seq

data_processing:
The reads obtained were then demultiplexed, mapped and analyzed using the HTSstation pipeline (http://htsstation.epfl.ch) (David et al., 2014).
Genome_build: mm9, CornSnake_HoxD_Scaffold (KU866087)
Supplementary_files_format_and_content: bedgraph of aligned 4C-seq reads

source_name: genital tubercle

extract_protocol:
One E11.5 whole mouse embryo, one 2.5 dpo (days post oviposition) whole snake embryo, ca. 30 mouse and corn snake genital buds as well as mouse and snake trunk tissue dissected from comparable anterior-posterior levels were processed as previously described (Noordermeer et al., 2011).
Mouse libraries were constructed by using NlaIII as the first restriction enzyme and DpnII (New England Biolabs) as the second restriction enzyme and the baits and inverse primers used for the Hoxd4, Hoxd9, Hoxd11 and Hoxd13 viewpoints were described in Noordermeer et al. (2011). Snake libraries were constructed using DpnII as primary enzyme and NlaIII as secondary enzyme. For the Hoxd4, Hoxd9, Hoxd11 and Hoxd13 baits, the primers are listed in Supplementary table S2.

value: genital tubercle

tag: viewpoint


title: Tr1_WT


title: 4C_WEMm_d4

description:
4C of the embryo of a mouse using the Hoxd4 viewpoint
library strategy: 4C-seq

source_name: whole embryo

value: whole embryo


title: Tr1_27


title: 4C_GTMm_d13

description:
4C of the genital tubercle of a mouse using the Hoxd13 viewpoint
library strategy: 4C-seq


title: 4C_GTMmcont_d13

description:
4C of the trunk region with the same anterior-posterior position as the genital tubercle of a mouse embryo using the Hoxd13 viewpoint
library strategy: 4C-seq

source_name: control trunk region

value: control trunk region


title: 4C_WEMm_d11

description:
4C of the embryo of a mouse using the Hoxd11 viewpoint
library strategy: 4C-seq


title: 4C_GTMmcont_d11

description:
4C of the trunk region with the same anterior-posterior position as the genital tubercle of a mouse embryo using the Hoxd11 viewpoint
library strategy: 4C-seq


title: H3K27ac_AT_Mm

description: H3K27ac ChIP of the mouse anterior trunk. bedGraph processed data was normalized to input.  Peak calling of H3K27ac ChIP of the mouse anterior trunk in the bed file.

data_processing:
The reads obtained from the sequencing were mapped to ENSEMBL Mouse assembly NCBIM37 (mm9) or to the corn snake scaffold using the HTSstation mapping pipeline (http://htsstation.epfl.ch)(David et al., 2014).
Peak calling for H3K27 acetylation was done using MACS (Zhang et al., 2008)
All ChIP-seq mappings were normalized to total input chromatin using the bamCompare software from the deepTools Galaxy web server (http://deeptools.ie-freiburg.mpg.de) (Ramirez et al., 2014).
Genome_build: mm9, CornSnake_HoxD_Scaffold (KU866087)
Supplementary_files_format_and_content: bedGraph of subtraction between ChIP and input signal or bed of H3K27ac called peaks

source_name: anterior trunk

extract_protocol:
Snake forebrain, anterior trunk and posterior trunk samples as well as mouse anterior trunk samples were dissected and fixed in 1% formaldehyde for 10 minutes. For each ChIP-seq experiment approximately 100 ng of tissue were used and processed according to (Lee et al., 2006) or the ChIP-IT® High Sensitivity (Active motif) specifications.
Sequencing was performed using 100 bp single-end reads in the Illumina HiSeq 2500 system according to manufacturer’s instructions.

value: anterior trunk

tag: antibody

value: H3K27ac (Abcam, catalog# ab4729, lot# GR184558-1)


title: AT_Pg_Input

description: Input chromatin of snake anterior trunk

organism: Pantherophis guttatus

value: 5.5 dpo


title: PT_Pg_Input

description: Input chromatin of corn snake posterior trunk

source_name: posterior trunk

value: 2.5 dpo

value: posterior trunk


title: Tr3_24

value: CD4+CD25hi Treg cells


title: 1275C9

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

data_processing:
Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: text file including FPKM for each sample

source_name: neuron cell line

extract_protocol:
RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.
Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation.

tag: sample group

value: patients

value: iPSC-derived neuron


title: FB_Pg_Input

description: Input chromatin of corn snake embryonic brain

source_name: brain

value: brain


title: H3K27ac_AT_Pg

description: H3K27ac ChIP of the corn snake anterior trunk. bedGraph processed data was normalized to input.  Peak calling H3K27ac ChIP of the corn snake anterior trunk in the bed file.


title: 22q1130_dup


title: 22q1110C5


title: 4C_WEMm_d13

description:
4C of the embryo of a mouse using the Hoxd13 viewpoint
library strategy: 4C-seq


title: 22q1160


title: 1220C2


title: 4C_WEMm_d9

description:
4C of the embryo of a mouse using the Hoxd9 viewpoint
library strategy: 4C-seq


title: iPSC2_dup

value: control


title: H3K9me3_FB_Pg

description: H3K9me3 ChIP of the corn snake embryonic brain. Processed data was normalized to input

value: H3K9me3 (Abcam, catalog# ab8898, lot# 1407388)


title: H3K27me3_PT_Pg

description: H3K27me3 ChIP of the corn snake embryonic posterior trunk. Processed data was normalized to input

value: H3K27me3 (Millipore, catalog# 17-622, lot# JBC1870087)


title: AT_Mm_Input

description: Input chromatin of mouse anterior trunk


title: iPS1_dup


title: Brassica carinata

organism: Brassica carinata

value: initial flowering stage

value: floral buds


title: iPS1


title: 22q1115_dup


title: 553C2


title: 3113C4


title: H3K27me3_FB_Pg

description: H3K27me3 ChIP of the corn snake embryonic brain. Processed data was normalized to input


title: 690C5


title: C.livia E8-E8.5 rep 2

organism: Columba livia

value: retina


title: C.livia E8-E8.5 rep 3


title: 4C_HPPg_d13

description:
4C of the hemipenes of a corn snake using the Hoxd13 viewpoint
library strategy: 4C-seq

source_name: hemipenes

value: 8.5 dpo

value: hemipenes


title: 4C_HPPgcont_d11

description:
4C of the trunk region with the same anterior-posterior position as the hemipenes of a corn snake using the Hoxd11 viewpoint
library strategy: 4C-seq

value: control trunk region


title: C.livia E5-E5.5 rep 3


title: C.livia E5-E5.5 rep 2


title: 4C_WEPg_d9

description:
4C of the embryo of a corn snake using the Hoxd9 viewpoint
library strategy: 4C-seq

value: whole embryo


title: C.livia E8-E8.5 rep 1


title: 4C_HPPgcont_d13

description:
4C of the trunk region with the same anterior-posterior position as the hemipenes of a corn snake using the Hoxd13 viewpoint
library strategy: 4C-seq


title: C.livia E3-E3.5 rep 2


title: C.livia E5-E5.5 rep 1


title: 4C_WEPg_d13

description:
4C of the embryo of a corn snake using the Hoxd13 viewpoint
library strategy: 4C-seq


title: interspecific Brassica hybrid

description: interspecific hybrid between B. carinata and B. napus

organism: Brassica carinata x Brassica napus


title: 4C_WEPg_d11

description:
4C of the embryo of a corn snake using the Hoxd11 viewpoint
library strategy: 4C-seq


title: 4C_WEPg_d4

description:
4C of the embryo of a corn snake using the Hoxd4 viewpoint
library strategy: 4C-seq


title: C.livia E3-E3.5 rep 1


title: 4C_HPPg_d11

description:
4C of the hemipenes of a corn snake using the Hoxd11 viewpoint
library strategy: 4C-seq


title: H2A S121A mutant 10 min 39°C [Sample_18_13479_GAGTGG]

status: Public on Nov 04 2016

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

description: replicate 3

data_processing:
Raw sequencing reads were mapped to the sacCer3 genome using TopHat2 v2.0.1.
Quantification was performed with featureCounts v1.4.6-p5 using the Ensembl R64-1-1 annotation.
Differential expression testing was performed using DESeq2 v1.10.1
Genome_build: sacCer3
Supplementary_files_format_and_content: DESeq2_raw_counts.txt  contains raw read counts obtained via featureCounts after alignment. Each column represents one sample in lexicographical order.

source_name: whole cell

growth_protocol: Wild-type and HTA1-S121A mutant strains were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to osmotic stress (15 min 0.4M NaCl) or heat stress (10 min 39ºC).

extract_protocol:
Total RNA was extracted with standard hot-phenol protocol.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (ref. RS-122-2101) according to the manufacturer's protocol starting with 1 µg of total RNA for poly(A)-mRNA selection. Libraries were analyzed with the Agilent Bioanalyzer using a DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to sequencing with 50 bp paired-end reads on Illumina's HiSeq 2500 with v4 sequencing chemistry.

treatment_protocol: Untreated (no stress) / osmotic stress (15 min 0.4M NaCl) / heat stress (10 min 39ºC)

value: FY406 MATa (hta1-htb1)::LEU2 (hta2-htb2)::TRP1 his3delta200 leu2delta1 ura3-52 trp1delta63 lys2-128delta plasmid (HTA1-HTB1)S121A-HIS5


title: wild type 10 min 39°C [Sample_15_13476_CAGATC]

description: replicate 3

value: FY406 MATa (hta1-htb1)::LEU2 (hta2-htb2)::TRP1 his3delta200 leu2delta1 ura3-52 trp1delta63 lys2-128delta plasmid (HTA1-HTB1)wt-HIS5


title: H2A S121A mutant 10 min 39°C [Sample_17_13478_CGTACG]

description: replicate 2

value: FY406 MATa (hta1-htb1)::LEU2 (hta2-htb2)::TRP1 his3delta200 leu2delta1 ura3-52 trp1delta63 lys2-128delta plasmid (HTA1-HTB1)S121A-HIS4


title: wild type 10 min 39°C [Sample_14_13475_ACAGTG]

description: replicate 2

value: FY406 MATa (hta1-htb1)::LEU2 (hta2-htb2)::TRP1 his3delta200 leu2delta1 ura3-52 trp1delta63 lys2-128delta plasmid (HTA1-HTB1)wt-HIS4


title: C.livia E3-E3.5 rep 3


title: H2A S121A mutant 15 min 0.4 M NaCl [Sample_11_13472_GGCTAC]

description: replicate 2


title: H2A S121A mutant 15 min 0.4 M NaCl [Sample_10_13471_TAGCTT]

description: replicate 1

value: FY406 MATa (hta1-htb1)::LEU2 (hta2-htb2)::TRP1 his3delta200 leu2delta1 ura3-52 trp1delta63 lys2-128delta plasmid (HTA1-HTB1)S121A-HIS3


title: H2A S121A mutant 15 min 0.4 M NaCl [Sample_12_13473_ATGTCA]

description: replicate 3


title: wild type 15 min 0.4 M NaCl [Sample_8_13469_GCCAAT]

description: replicate 2


title: wild type 15 min 0.4 M NaCl [Sample_9_13470_ACTTGA]

description: replicate 3


title: H2A S121A mutant no stress [Sample_6_13467_ATTCCT]

description: replicate 3


title: wild type 15 min 0.4 M NaCl [Sample_7_13468_ATCACG]

description: replicate 1

value: FY406 MATa (hta1-htb1)::LEU2 (hta2-htb2)::TRP1 his3delta200 leu2delta1 ura3-52 trp1delta63 lys2-128delta plasmid (HTA1-HTB1)wt-HIS3


title: H2A S121A mutant no stress [Sample_4_13465_CCGTCC]

description: replicate 1


title: wild type no stress [Sample_2_13463_TTAGGC]

description: replicate 2


title: wild type no stress [Sample_3_13464_GATCAG]

description: replicate 3


title: wild type no stress [Sample_1_13462_CGATGT]

description: replicate 1


title: H2A S121A mutant no stress [Sample_5_13466_GTCCGC]

description: replicate 2


title: H2A S121A mutant 10 min 39°C [Sample_16_13477_GTGGCC]

description: replicate 1


title: G4B_cOrgPR62d

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description: processed data file: data_chimpOrg_344cells_log2FPKM_annotated.txt

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38, panTro4
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

organism: Pan troglodytes

source_name: iPSC PR818-5

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Whole cerebral organoids and microdisseccted ventricles were dissociated in 2 ml of Accutase (StemPro) containing 2.0 U/µl Dnase I (Roche) for approximately 45 minutes. Dissociated cells were filtered through 30, and 20 μm diameter strainers to create a single cell suspension.

tag: Stage

value: 62 days

value: Dissociated dissected ventricle


title: H6B_cOrgPR62d


title: F9B_cOrgPR62d


title: G5B_cOrgPR62d


title: H11B_cOrgPR62d


title: H3B_cOrgPR62d


title: F1B_cOrgPR62d


title: H12B_cOrgPR62d


title: G1B_cOrgPR62d


title: F4B_cOrgPR62d


title: H7B_cOrgPR62d


title: G12B_cOrgPR62d


title: H4B_cOrgPR62d


title: wild type 10 min 39°C [Sample_13_13474_TGACCA]

description: replicate 1


title: E9B_cOrgPR62d


title: G3B_cOrgPR62d


title: F8B_cOrgPR62d


title: F6B_cOrgPR62d


title: E12B_cOrgPR62d


title: E10B_cOrgPR62d


title: D9B_cOrgPR62d


title: D12B_cOrgPR62d


title: F11B_cOrgPR62d


title: F10B_cOrgPR62d


title: E4B_cOrgPR62d


title: C9B_cOrgPR62d


title: B7B_cOrgPR62d


title: C4B_cOrgPR62d


title: C12B_cOrgPR62d


title: B8B_cOrgPR62d


title: C8B_cOrgPR62d


title: E2B_cOrgPR62d


title: C2B_cOrgPR62d


title: A9B_cOrgPR62d


title: B4B_cOrgPR62d


title: B3B_cOrgPR62d


title: A5B_cOrgPR62d


title: D8B_cOrgPR62d


title: D6B_cOrgPR62d


title: D4B_cOrgPR62d


title: A1B_cOrgPR62d


title: C11B_cOrgPR62d


title: H5B_cOrgPR51d

value: 51 days


title: B12B_cOrgPR62d


title: E11B_cOrgPR62d


title: A8B_cOrgPR62d


title: G3B_cOrgPR51d


title: A2B_cOrgPR62d


title: F8B_cOrgPR51d


title: G6B_cOrgPR51d


title: G2B_cOrgPR51d


title: G9B_cOrgPR51d


title: A3B_cOrgPR62d


title: G1B_cOrgPR51d


title: F5B_cOrgPR51d


title: F4B_cOrgPR51d


title: F9B_cOrgPR51d


title: F7B_cOrgPR51d


title: F3B_cOrgPR51d


title: A10B_cOrgPR62d


title: H6B_cOrgPR51d


title: D10B_cOrgPR62d


title: H10B_cOrgPR51d


title: H4B_cOrgPR51d


title: F2B_cOrgPR51d


title: F1B_cOrgPR51d


title: A4B_cOrgPR62d


title: H9B_cOrgPR51d


title: F12B_cOrgPR51d


title: F10B_cOrgPR51d


title: F11B_cOrgPR51d


title: G7B_cOrgPR51d


title: F6B_cOrgPR51d


title: E9B_cOrgPR51d


title: E8B_cOrgPR51d


title: E7B_cOrgPR51d


title: E5B_cOrgPR51d


title: E11B_cOrgPR51d


title: D5B_cOrgPR51d


title: D7B_cOrgPR51d


title: D4B_cOrgPR51d


title: E3B_cOrgPR51d


title: C8B_cOrgPR51d


title: C9B_cOrgPR51d


title: D3B_cOrgPR51d


title: D2B_cOrgPR51d


title: C7B_cOrgPR51d


title: C6B_cOrgPR51d


title: C5B_cOrgPR51d


title: C4B_cOrgPR51d


title: C2B_cOrgPR51d


title: C11B_cOrgPR51d


title: C10B_cOrgPR51d


title: B9B_cOrgPR51d


title: B5B_cOrgPR51d


title: B7B_cOrgPR51d


title: B6B_cOrgPR51d


title: D9B_cOrgPR51d


title: E12B_cOrgPR51d


title: B11B_cOrgPR51d


title: A7B_cOrgPR51d


title: B1B_cOrgPR51d


title: E10B_cOrgPR51d


title: B2B_cOrgPR51d


title: B4B_cOrgPR51d


title: A6B_cOrgPR51d


title: C3B_cOrgPR51d


title: A3B_cOrgPR51d


title: A5B_cOrgPR51d


title: A4B_cOrgPR51d


title: B10B_cOrgPR51d


title: B3B_cOrgPR51d


title: A2B_cOrgPR51d


title: H9A_cOrg4PR80d

value: 80 days

value: Dissociated whole cerebral organoid


title: A9B_cOrgPR51d


title: A10B_cOrgPR51d


title: H8A_cOrg4PR80d


title: H5A_cOrg4PR80d


title: H2A_cOrg4PR80d


title: A11B_cOrgPR51d


title: H6A_cOrg4PR80d


title: B8B_cOrgPR51d


title: G8A_cOrg4PR80d


title: G5A_cOrg4PR80d


title: H10A_cOrg4PR80d


title: G6A_cOrg4PR80d


title: G4A_cOrg4PR80d


title: G3A_cOrg4PR80d


title: G2A_cOrg4PR80d


title: E4A_cOrg4PR80d


title: G10A_cOrg4PR80d


title: E5A_cOrg4PR80d


title: E6A_cOrg4PR80d


title: F11A_cOrg4PR80d


title: E12A_cOrg4PR80d


title: D12A_cOrg4PR80d


title: C7A_cOrg4PR80d


title: C8A_cOrg4PR80d


title: D8A_cOrg4PR80d


title: D9A_cOrg4PR80d


title: C6A_cOrg4PR80d


title: C12A_cOrg4PR80d


title: B4A_cOrg4PR80d


title: B9A_cOrg4PR80d


title: B11A_cOrg4PR80d


title: C2A_cOrg4PR80d


title: B5A_cOrg4PR80d


title: A8A_cOrg4PR80d


title: A9A_cOrg4PR80d


title: A12A_cOrg4PR80d


title: A2A_cOrg4PR80d


title: H7A_cOrg3PR61d

value: 61 days


title: A3A_cOrg4PR80d


title: A7A_cOrg4PR80d


title: E11A_cOrg4PR80d


title: H3A_cOrg3PR61d


title: D4A_cOrg4PR80d


title: G7A_cOrg3PR61d


title: H11A_cOrg3PR61d


title: H12A_cOrg3PR61d


title: G12A_cOrg3PR61d


title: G11A_cOrg3PR61d


title: F9A_cOrg3PR61d


title: F8A_cOrg3PR61d


title: F6A_cOrg3PR61d


title: F3A_cOrg3PR61d


title: F12A_cOrg3PR61d


title: F2A_cOrg3PR61d


title: F5A_cOrg3PR61d


title: F4A_cOrg3PR61d


title: E2A_cOrg3PR61d


title: E7A_cOrg3PR61d


title: F10A_cOrg3PR61d


title: H4A_cOrg3PR61d


title: E9A_cOrg3PR61d


title: E10A_cOrg3PR61d


title: E1A_cOrg3PR61d


title: D7A_cOrg3PR61d


title: D6A_cOrg3PR61d


title: D5A_cOrg3PR61d


title: D2A_cOrg3PR61d


title: D1A_cOrg3PR61d


title: D10A_cOrg3PR61d


title: C9A_cOrg3PR61d


title: C5A_cOrg3PR61d


title: C1A_cOrg3PR61d


title: D11A_cOrg3PR61d


title: C10A_cOrg3PR61d


title: C4A_cOrg3PR61d


title: B7A_cOrg3PR61d


title: C3A_cOrg3PR61d


title: C11A_cOrg3PR61d


title: D3A_cOrg3PR61d


title: E8A_cOrg3PR61d


title: B12A_cOrg3PR61d


title: B10A_cOrg3PR61d


title: B2A_cOrg3PR61d


title: G9A_cOrg3PR61d


title: A5A_cOrg3PR61d


title: A6A_cOrg3PR61d


title: B3A_cOrg3PR61d


title: A4A_cOrg3PR61d


title: H8B_cOrg2PR55d

value: 55 days


title: H9B_cOrg2PR55d


title: A11A_cOrg3PR61d


title: A10A_cOrg3PR61d


title: H1B_cOrg2PR55d


title: H11B_cOrg2PR55d


title: H10B_cOrg2PR55d


title: G5B_cOrg2PR55d


title: G9B_cOrg2PR55d


title: B8A_cOrg3PR61d


title: B6A_cOrg3PR61d


title: B1A_cOrg3PR61d


title: G1B_cOrg2PR55d


title: G11B_cOrg2PR55d


title: F7B_cOrg2PR55d


title: G6B_cOrg2PR55d


title: G10B_cOrg2PR55d


title: F4B_cOrg2PR55d


title: E5B_cOrg2PR55d


title: F10B_cOrg2PR55d


title: E4B_cOrg2PR55d


title: D9B_cOrg2PR55d


title: E11B_cOrg2PR55d


title: E1B_cOrg2PR55d


title: F5B_cOrg2PR55d


title: E8B_cOrg2PR55d


title: A1A_cOrg3PR61d


title: D2B_cOrg2PR55d


title: C1B_cOrg2PR55d


title: D12B_cOrg2PR55d


title: C2B_cOrg2PR55d


title: C5B_cOrg2PR55d


title: C9B_cOrg2PR55d


title: C12B_cOrg2PR55d


title: C11B_cOrg2PR55d


title: B9B_cOrg2PR55d


title: B2B_cOrg2PR55d


title: B8B_cOrg2PR55d


title: B1B_cOrg2PR55d


title: A9B_cOrg2PR55d


title: E2B_cOrg2PR55d


title: B12B_cOrg2PR55d


title: A1B_cOrg2PR55d


title: A3B_cOrg2PR55d


title: H7B_cOrg1PR50d

value: 50 days


title: A10B_cOrg2PR55d


title: H6B_cOrg1PR50d


title: H5B_cOrg1PR50d


title: D6B_cOrg2PR55d


title: D4B_cOrg2PR55d


title: H3B_cOrg1PR50d


title: G7B_cOrg1PR50d


title: G4B_cOrg1PR50d


title: G3B_cOrg1PR50d


title: F6B_cOrg1PR50d


title: F2B_cOrg1PR50d


title: F1B_cOrg1PR50d


title: G2B_cOrg1PR50d


title: E3B_cOrg1PR50d


title: B11B_cOrg2PR55d


title: D3B_cOrg1PR50d


title: C7B_cOrg1PR50d


title: D1B_cOrg1PR50d


title: C6B_cOrg1PR50d


title: B7B_cOrg1PR50d


title: C4B_cOrg1PR50d


title: C3B_cOrg1PR50d


title: H4B_cOrg1PR50d


title: H2B_cOrg1PR50d


title: A8B_cOrg1PR50d


title: B5B_cOrg1PR50d


title: B3B_cOrg1PR50d


title: B6B_cOrg1PR50d


title: A6B_cOrg1PR50d


title: A5B_cOrg1PR50d


title: A4B_cOrg1PR50d


title: A7B_cOrg1PR50d


title: A2B_cOrg1PR50d


title: H7_cOrg1Sandra45d

source_name: iPSC SandraA

value: 45 days


title: H8_cOrg1Sandra45d


title: F3B_cOrg1PR50d


title: E7B_cOrg1PR50d


title: H4_cOrg1Sandra45d


title: D7B_cOrg1PR50d


title: H3_cOrg1Sandra45d


title: H11_cOrg1Sandra45d


title: H12_cOrg1Sandra45d


title: G8_cOrg1Sandra45d


title: Control animal 8 timepoint 2 (one week post infection)

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
basecalling by Illumina Real Time Analysis (RTA) v1.18.64
output of RTA was de-multiplexed and converted to FastQ format with Illumina Bcl2Fasta v1.8.4
aligned to Oar3.1 using STAR 2.3.0e_r291
raw gene counts calculated using featureCounts from Subread v1.3.5-p4.
differentially expressed genes detected using limma voom with normalization factors calculated using edgeR
Genome_build: Oar3.1
Supplementary_files_format_and_content: Raw gene counts generated by FeatureCounts software using the Ensembl GTF annotation Oar3.1 Ensembl release 79

organism: Ovis aries

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMCs were isolated from heparinized blood by centrifugation over Ficoll-Histopaque (Sigma). PBMCs were frozen at -80 ℃ immediately after isolation.

extract_protocol:
E.Z.N.A total RNA kit (Omega) was used for total RNA extraction.
RS-122-2101-TruSeq® Stranded mRNA LT(Set A) was used for library Preparation.

treatment_protocol: As described in Overall design, PBMCs were isolated from 4 vaccinated and 5 control animals. For vaccination group, animals were injected with 200 µg rmFhCL1 protein in 2ml of adjuvant of Montanide 70 for three times with 2 weeks interval. For control group animals were injected with 2ml saline solution instead. All animals were orally infected with 90 metacercariae of F. hepatica at two weeks post the third vaccination.

tag: time

tag: group

value: Control

tag: animal

value: Peripheral blood mononuclear cells


title: Vaccinated animal 3 timepoint 3 (14 weeks post infection)

value: Vaccinated


title: Control animal 6 timepoint 3 (14 weeks post infection)


title: G2_cOrg1Sandra45d


title: G1_cOrg1Sandra45d


title: Vaccinated animal 5 timepoint 1 (pre-infection)


title: Control animal 5 timepoint 3 (14 weeks post infection)


title: G12_cOrg1Sandra45d


title: G5_cOrg1Sandra45d


title: F8_cOrg1Sandra45d


title: F6_cOrg1Sandra45d


title: F9_cOrg1Sandra45d


title: F7_cOrg1Sandra45d


title: Control animal 6 timepoint 2 (one week post infection)


title: Vaccinated animal 4 timepoint 1 (pre-infection)


title: F2_cOrg1Sandra45d


title: F1_cOrg1Sandra45d


title: F3_cOrg1Sandra45d


title: Vaccinated animal 6 timepoint 0 (pre-vaccination)


title: F12_cOrg1Sandra45d


title: dhh1∆_mRNA_YPD_rep3

city: Münster

first: Danny

middle: D.

last: Nedialkova

address: Von-Esmarch-Str. 54

department: Max Planck Research Group for RNA Biology

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
Basecalls were performed with Illumina Casava 1.8.
3' adapter sequences were removed with FastX-toolkit
Reads were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of CDS sequences containing 18 nt of genomic flanking regions. Only reads with unique matches to the sense strand were retained for further analysis.
Raw read counts were determined using custom scripts. Yeast footprint reads mapping within the first 15 codons of coding sequences were omitted to avoid effects of growth conditions and translation inhibitor treatement on ribosome density in the beginning of ORFs.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab-delimited text files containing gene annotations and raw read count data.

source_name: Whole cells

growth_protocol: Cells were grown from OD600 of 0.02 to OD600=0.4, collected by rapid vacuum filtration, and immediately frozen in liquid nitrogen.

extract_protocol:
Frozen cells were were resuspended in 50 mM NaOAc (pH=5.5), 10 mM EDTA, 1% SDS to 1% and homogenized in a Precellys 24 bead beater. Clarified ysates were treated with Proteinase Kand total RNA was extracted with acid phenol. Following DNase treatment,d poly(A) RNA was purified by two rounds of selection with Poly(A)Purist MAG Kit. Purified RNA was fragmented by alkaline hydrolysis and fragments of 50-80 nt were used for library preparation.
Fragmented poly(A) RNA was dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was cirularized and amplified by PCR.

treatment_protocol: YPD medium; cycloheximide (1 min)

tag: strain

value: wild-type (BY4741)

tag: replicate

tag: molecule

value: total RNA


title: F11_cOrg1Sandra45d


title: Vaccinated animal 6 timepoint 3 (14 weeks post infection)


title: dhh1∆_mRNA_YPD_rep2


title: Vaccinated animal 4 timepoint 3 (14 weeks post infection)


title: dhh1∆_mRNA_YPD_rep1


title: F10_cOrg1Sandra45d


title: E9_cOrg1Sandra45d


title: E8_cOrg1Sandra45d


title: Control animal 8 timepoint 3 (14 weeks post infection)


title: Control animal 7 timepoint 1 (pre-infection)


title: dhh1∆_ribo_YPD_rep3

data_processing:
Library strategy: Ribo-seq
Basecalls were performed with Illumina Casava 1.8.
3' adapter sequences were removed with FastX-toolkit
Reads were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of CDS sequences containing 18 nt of genomic flanking regions. Only reads with unique matches to the sense strand were retained for further analysis.
Raw read counts were determined using custom scripts. Yeast footprint reads mapping within the first 15 codons of coding sequences were omitted to avoid effects of growth conditions and translation inhibitor treatement on ribosome density in the beginning of ORFs.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab-delimited text files containing gene annotations and raw read count data.

extract_protocol:
Frozen cells were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.5 mM DTT, 100 µg/ml CHX. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction. Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was cirularized and amplified by PCR.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was cirularized and amplified by PCR.

value: ribosome-protected footprint


title: E6_cOrg1Sandra45d


title: Control animal 7 timepoint 3 (14 weeks post infection)


title: dhh1∆_ribo_YPD_rep2


title: E5_cOrg1Sandra45d


title: E4_cOrg1Sandra45d


title: dhh1∆_ribo_YPD_rep1

extract_protocol:
Frozen cells were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.5 mM DTT, 100 µg/ml CHX. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was cirularized and amplified by PCR.


title: E2_cOrg1Sandra45d


title: E11_cOrg1Sandra45d


title: D7_cOrg1Sandra45d


title: E1_cOrg1Sandra45d


title: Vaccinated animal 5 timepoint 0 (pre-vaccination)


title: Vaccinated animal 6 timepoint 2 (one week post infection)


title: Vaccinated animal 3 timepoint 1 (pre-infection)


title: D3_cOrg1Sandra45d


title: E12_cOrg1Sandra45d


title: Control animal 8 timepoint 0 (pre-vaccination)


title: Control animal 3 timepoint 0 (pre-vaccination)


title: D5_cOrg1Sandra45d


title: D1_cOrg1Sandra45d


title: Vaccinated animal 5 timepoint 3 (14 weeks post infection)


title: D10_cOrg1Sandra45d


title: D11_cOrg1Sandra45d


title: C8_cOrg1Sandra45d


title: Vaccinated animal 5 timepoint 2 (one week post infection)


title: C7_cOrg1Sandra45d


title: C6_cOrg1Sandra45d


title: Vaccinated animal 4 timepoint 2 (one week post infection)


title: C5_cOrg1Sandra45d


title: C3_cOrg1Sandra45d


title: C4_cOrg1Sandra45d


title: Vaccinated animal 3 timepoint 2 (one week post infection)


title: C2_cOrg1Sandra45d


title: C12_cOrg1Sandra45d


title: Vaccinated animal 6 timepoint 1 (pre-infection)


title: C11_cOrg1Sandra45d


title: C10_cOrg1Sandra45d


title: D2_cOrg1Sandra45d


title: Control animal 3 timepoint 1 (pre-infection)


title: B7_cOrg1Sandra45d


title: B6_cOrg1Sandra45d


title: Vaccinated animal 3 timepoint 0 (pre-vaccination)


title: Control animal 8 timepoint 1 (pre-infection)


title: Control animal 7 timepoint 0 (pre-vaccination)


title: B2_cOrg1Sandra45d


title: B10_cOrg1Sandra45d


title: B1_cOrg1Sandra45d


title: Control animal 3 timepoint 3 (14 weeks post infection)


title: A8_cOrg1Sandra45d


title: A9_cOrg1Sandra45d


title: Control animal 7 timepoint 2 (one week post infection)


title: A7_cOrg1Sandra45d


title: A4_cOrg1Sandra45d


title: Control animal 5 timepoint 2 (one week post infection)


title: A1_cOrg1Sandra45d


title: A10_cOrg1Sandra45d


title: Vaccinated animal 4 timepoint 0 (pre-vaccination)


title: Control animal 6 timepoint 1 (pre-infection)


title: Control animal 5 timepoint 1 (pre-infection)


title: Control animal 6 timepoint 0 (pre-vaccination)


title: B9_cOrg1Sandra45d


title: Control animal 5 timepoint 0 (pre-vaccination)


title: Nucleosome_occupancy_meiosis_NGS

city: Tampa

first: John

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

data_processing:
Fastq files from 5 sample runs were merged using Unix cat command and then mapped to mm9 mouse genome using Bowtie version 0.12.7.
A combined sam file was converted to bam file, sorted and indexed using samtools version 0.1.9. The sorted bam file and the bai index file were imported into Integrative Genomic Viewer (IGV 2.3) tools to create the tdf file using count function.
Genome_build: mm9
Supplementary_files_format_and_content: The sorted bam file and the bai index file were imported into Integrative Genomic Viewer (IGV 2.3) tools to create the tdf file using count function.The tdf file was visualized using IGV browser.

source_name: Testis

extract_protocol:
Mono-nucleosomal DNA was isolated from total meiotic populations of 10-week old B6 mouse male testes (1.3 x 106  cells) by MNase digestion of native chromatin. Final mono-nucleosomal DNA was purified using phenol/chloroform extraction followed by ethanol precipitation, run on 2 % agarose gel and isolated using Qiagen gel extract kit. Gel-purified mono-nucleosomal DNA was then used as a template for sequencing library construction.
Library was prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. The library was sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: age

value: 10 weeks


title: B3_cOrg1Sandra45d


title: riboseq_root_bufferA

city: Durham

first: Polly

middle: Yingshan

last: Hsu

state: NC

address: Duke University

department: Biology

institute: Duke University

description: ribosome footprint

data_processing:
quality filtering by FASTX_toolkit (Pearson et al., 1997)(parameter: –q 20 –p 85)
the adaptor sequence (AGATCGGAAGAGCACACGTCT) was removed using FASTX_clipper (included in FASTX_toolkit)
the riboseq reads were mapped to expected contaminant RNA sequences in Arabidopsis, including rRNA, tRNA and snoRNA sequences using bowtie2 (Langmead and Salzberg, 2012)(parameter: -L 20, -p 4).
The unaligned reads above were then mapped to Arabidopsis genome using TAIR10.29 reference using split-aware aligner STAR (v2.5.1b)(Dobin et al., 2013) allowing up to 3 mismatches and a maximum of 20 multi-mapping positions. For the multi-mapped reads, the best alignment position was selected.
Riboseq read counts on the coding sequence of each gene were determined using several Bioconductor packages including genomation (Akalin et al., 2015), GenomicRanges, GenomicFeatures and GenomicAlignments (Lawrence et al., 2013).
Genome_build: TAIR10.29
Supplementary_files_format_and_content: txt file containing riboseq read counts on the coding sequence of each gene

source_name: Arabidopsis root

growth_protocol: Arabidopsis Col seeds were surface sterilized and grown hydroponically on fine nylon mesh supported by a customized rack in Magenta vessel GA-7-3 with filtered sterile liquid media (2.15 g/L Murashige and Skoog salt, 1 % sucrose, 0.5g/L MES (2-(N-morpholino) ethanesulfonic), pH 5.7), shaking at 85 rpm under 16 hours light and 8 hours dark at 22°C.

extract_protocol:
About 0.1 g of pulvernized root or shoot tissue was resuspended in 600 or 800 µl of polysome extraction buffer. The lysate was treated with RNase to obtain ribosome footprints. Ribosomes were isolated with size exclusion columns (illustra MicroSpin S-400 HR Columns, GE Healthcare, Cat. # 27-5140-01). Purified ribosome footprints were then subjected to rRNA depletion.
Libraries were constructed according to ARTseq/TruSeq Ribo Profile Library Preparation Kit manual

treatment_protocol: Shoots and roots of 4-day old seedlings (post-imbibition) were harvested at ZT 3 (3 hours after light on).

value: 4 days old

tag: ecotype

value: Col

tag: buffer

value: buffer A


title: riboseq_shoot_bufferD

description: ribosome footprint

source_name: Arabidopsis shoot

value: buffer D


title: riboseq_shoot_bufferA

description: ribosome footprint


title: riboseq_shoot_bufferC

description: ribosome footprint

value: buffer C


title: riboseq_root_bufferD

description: ribosome footprint


title: riboseq_root_bufferC

description: ribosome footprint


title: riboseq_root_bufferB

description: ribosome footprint

value: buffer B


title: A6_cOrg1Sandra45d

value: Dissociated whole cerebral organoid


title: RNAseq_shoot_3

description: rRNA depleted RNA

data_processing:
quality filtering by FASTX_toolkit (Pearson et al., 1997)(parameter: –q 20 –p 85)
the adaptor sequence (AGATCGGAAGAGCACACGTCT) was removed using FASTX_clipper (included in FASTX_toolkit)
the riboseq reads were mapped to expected contaminant RNA sequences in Arabidopsis, including rRNA, tRNA and snoRNA sequences using bowtie2 (Langmead and Salzberg, 2012)(parameter: -L 20, -p 4).
The unaligned reads above were then mapped to Arabidopsis genome using TAIR10.29 reference using split-aware aligner STAR (v2.5.1b)(Dobin et al., 2013) allowing up to 3 mismatches and a maximum of 20 multi-mapping positions. For the multi-mapped reads, the best alignment position was selected.
The translated ORFs were identified using RiboTaper v1.3 (Calviello et al., 2015).
Genome_build: TAIR10.29
Supplementary_files_format_and_content: Translated ORF ranges in BED files (ORFs that have riboseq coverage >30% resulted from multi-mapping reads were removed ; suitable to browse in IGV.

extract_protocol:
About 0.1 g of pulvernized root or shoot tissue was resuspended in 300 or 400 µl of polysome extraction buffer. The lysate was either treated with RNase to obtain ribosome footprints or used to isolate total RNA using Zymo RNA Clean and Concentrator kit. Ribosomes were isolated with size exclusion columns (illustra MicroSpin S-400 HR Columns, GE Healthcare, Cat. # 27-5140-01). Purified ribosome footprints and total RNA were then subjected to rRNA depletion.
Libraries were constructed according to ARTseq/TruSeq Ribo Profile Library Preparation Kit manual

treatment_protocol: Shoots and roots of four-day old seedlings (post-imbibition) were harvested at ZT 3 (3 hours after light on)

value: shoot


title: LXD_TL_3_3

city: Guangzhou

first: andyslee

address: Wushan 483

institute: South China Agricultural University

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18-25 nt were mapped to rice precursors in miRBase 20.0 (ftp://mirbase.org/pub/mirbase/CURRENT/) by BLAST search to identify known miRNAs
The unmapped sequences were BLASTed against the rice genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).
Data normalization followed the procedures. (1) Find a common set of sequences among all samples. (2) Construct a reference data set. Each data in the reference set is the copy number median value of a corresponding common sequence of all samples. (3) Perform 2-based logarithm transformation on copy numbers (Log2 (copy#)) of all samples and reference data set. (4) Calculate the Log2 (copy#) difference (ΔLog2 (copy#)) between individual sample and the reference data set. (5) Form a subset of sequences by selecting │ΔLog2 (copy#)│<2, which means less than (22 =) 4 fold change from the reference set. (6) Perform linear regressions between individual samples and the reference set on the subset sequences to derive linear equations y = aix + bi, where ai and bi are the slop and interception, respectively, of the derived line, x is Log2 (copy#) of the reference set, and y is the expected Log2 (copy#) of sample i on a corresponding sequence. (7) Calculate the mid value xmid = (max(x) - min(x)) / 2 of the reference set. Calculate the corresponding expected Log2 (copy#) of sample i, yi,mid = aixmid + bi. Let yr,mid=xmid, let Δyi = yr,mid-yi,mid, which is the logarithmic correction factor of sample i. We then derive the arithmetic correction factor fi = 2Δyi sample i. (8) Correct copy numbers of individual samples by multiplying corresponding arithmetic correction factor to original copy numbers.
To find out the siRNAs associated with the transposable elements, we filtered reads that did not match tRNA, rRNA, miRNA, snRNA, or snoRNA, and mapped them against the rice reference genome (ftp://ftp.plantbiology.msu.edu) to select the genome sequences annotated as transposable elements. These subsequent of siRNAs associated with transposable elements were used for further analysis.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: rice anther

extract_protocol:
Total RNA was extracted from the anthers using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.
The total RNA quantity and purity were analysis by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 μg of total RNA were used to prepare small RNA library according to the protocol of TruSeq small RNA sample preparation Kits (Illumina, San Diego, USA). Then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) according to the manufacturer’s protocol. After the Illumina sequencing, the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to detected the known and novel miRNA.

treatment_protocol: Autotetraploid rice (Taichung65-4x) was developed from the chromosome doubling of Taichung65-2x by colchicine treatment and self-crossed for more than 20 generations. Anthers during three stages of pollen development, including pre-meiotic interphase (PMA), meiosis (MA) and single microspore stage (SCP), were collected from Taichung65-4x and Taichung65-2x. All samples were stored at -80 °C for RNA isolation.

tag: ploidy

value: diploid rice

tag: floret length/mm

tag: anther length/mm

tag: pollen stage

value: single microspore stage (SCP)


title: LXD_TL_2_3

value: meiosis (MA)


title: LXD_T4_3

value: autotetraploid rice


title: LXD_T4_2


title: LXD_T4_1

value: pre-meiotic interphase (PMA)


title: LXD_TL_1_3


title: Control animal 3 timepoint 2 (one week post infection)

value: Control

tag: cell type

value: Peripheral blood mononuclear cells


title: RNAseq_shoot_2

description: rRNA depleted RNA

tag: tissue


title: RNAseq_root_3

description: rRNA depleted RNA

value: root


title: RNAseq_shoot_1

description: rRNA depleted RNA


title: RNAseq_root_1

description: rRNA depleted RNA


title: 6.555mg/l chronic nitrite exposure

city: Shanghai

first: Xu

last: Zhixin

address: 500 Dongchuan Rd.,Shanghai 200241

institute: East China Normal University

description:
28d after acute nitrite exposure
MT

data_processing:
The clean reads were then aligned to Macrobrachium nipponense genome (RNA denovo) using the bwa_mem (Version: 0.7.8-r455). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied HTseq to calculate the mRNA counts based on the mapping result
Genome_build: All-Unigene.final.fa is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: All_Counts.txt

organism: Macrobrachium nipponense

source_name: Hepatopancreas, 6.555mg/l nitrite

growth_protocol: 12 tanks of Macrobrachium nipponense (initial weight 1.12±0.06g g) were reared in freshwater, with 50 prawns in each tank. During the experiment, 1/3 of the water was replaced every day with aerated fresh water or saline water. Prawns were fed twice per day, at 08:00 h and 16:00 h, Daily rations were adjusted to a feeding level that was slightly over satiation, and feed that was not consumed was removed every day with a siphon tube.

extract_protocol:
Total RNA was extracted from Hepatopancreas by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two sets of three tanks were acclimated to the nitrite of 26mg/l and 6.555mg/l, the test cycle of acute  nitrite exposure （26mg/l）is 24h，anther  test cycle chronic nitrite exposure is 4 weeks

value: Hepatopancreas

value: Histiocytes of hepatopancreas

tag: developmental stage

value: juvenile

tag: sample size

value: 9 healthy M. nipponense

tag: treatment

value: 6.555mg/l chronic nitrite exposure


title: control for acute nitrite exposure

description:
24h after acute nitrite exposure
CL

source_name: Hepatopancreas, 0 mg/l nitrite

value: control for acute nitrite exposure


title: riboseq_shoot_bufferB

description: ribosome footprint

value: 4 days old

value: Col

value: buffer B


title: control for chronic nitrite exposure

description:
28d after acute nitrite exposure
ML

value: control for chronic nitrite exposure


title: riboseq_shoot_2

description: ribosome footprint

data_processing:
Library strategy: Ribo-Seq
quality filtering by FASTX_toolkit (Pearson et al., 1997)(parameter: –q 20 –p 85)
the adaptor sequence (AGATCGGAAGAGCACACGTCT) was removed using FASTX_clipper (included in FASTX_toolkit)
the riboseq reads were mapped to expected contaminant RNA sequences in Arabidopsis, including rRNA, tRNA and snoRNA sequences using bowtie2 (Langmead and Salzberg, 2012)(parameter: -L 20, -p 4).
The unaligned reads above were then mapped to Arabidopsis genome using TAIR10.29 reference using split-aware aligner STAR (v2.5.1b)(Dobin et al., 2013) allowing up to 3 mismatches and a maximum of 20 multi-mapping positions. For the multi-mapped reads, the best alignment position was selected.
The translated ORFs were identified using RiboTaper v1.3 (Calviello et al., 2015).
Genome_build: TAIR10.29
Supplementary_files_format_and_content: Translated ORF ranges in BED files (ORFs that have riboseq coverage >30% resulted from multi-mapping reads were removed ; suitable to browse in IGV.

value: shoot


title: Lgr5_T5_Ctl_13

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

description: T0 after Tgfb

data_processing:
Approximately 8 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38.p4/mm10) using STAR software to generate read alignments for each sample.
Annotations Mus_musculus.GRCm38.84.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq and normalized to 20 millions of aligned reads.
Fold of changes (FC) were computed on these values between the conditions.
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab delimited text files include count data normalized to 20 millions of aligned reads and gene informations for each sample

source_name: skin squamous cell carcinoma

growth_protocol: Epcam+ tumors epithelial Cells were FACS cells sorted from tumours.

extract_protocol:
qiagen kit
For RNA extracted, indexed cDNA libraries were obtained using the Ovation Solo RNA-Seq Systems (NuGen) following manufacturer recommendation.

treatment_protocol: Epcam+ cells were plated and treated or not with TGFb during 48 hours and then FACS sorted

value: epithelial tumor cell

tag: genotype


title: Dhh1_2

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the S.cerevisiae genome by Bowtie2 (version 2.2.4).
Peak calling was performed by Ivan Dotu using pyicoclip (http://regulatorygenomics.upf.edu/Software/Pyicoteo/pyicoclip.html).
Peaks that were identified in both Dhh1 samples that did not overlap with peaks found in the Wt samples were used to generate a list of Dhh1-crosslinked mRNAs.
Genome_build: S. cerevisiae genome S288C (EF2.59.1.0)
Supplementary_files_format_and_content: bedpk (see http://regulatorygenomics.upf.edu/Software/Pyicoteo/intro.html#the-bedpk-format)

source_name: BY4741 yeast strain

growth_protocol: Wild-type BY4741 yeast cells or yeast cells expressing Dhh1-His-Tev-ProtA from the genomic Dhh1 locus were grown in exponential phase in YPD.

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-ProtA-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Cells were crosslinked using UV (254 nm) in culturo as previously described (Bohnsack et al., 2012)

tag: tag


title: riboseq_shoot_1

description: ribosome footprint


title: H5A_hOrgSC60d

description: processed data file: data_humanOrg_SC60_52cells_log2FPKM.txt

source_name: iPSC SC102-A1

tag: Stage

value: 60 days

value: Dissociated dissected ventricle


title: riboseq_root_3

description: ribosome footprint


title: H4A_hOrgSC60d


title: Dhh1_1


title: Wt_1

value: no tag


title: Lgr5_T5_48h_TGF_14

description: T48h after TGFb

value: TGFb for 48h


title: H12A_hOrgSC60d


title: A2_cOrg1Sandra45d

value: 45 days

value: Dissociated whole cerebral organoid


title: riboseq_root_1

description: ribosome footprint

value: root


title: RNAseq_root_2

description: rRNA depleted RNA


title: H3A_hOrgSC60d


title: H1A_hOrgSC60d


title: Wt_2


title: 26mg/l acute nitrite exposure

description:
24h after acute nitrite exposure
CT

source_name: Hepatopancreas, 26mg/l nitrite

value: Hepatopancreas

value: Histiocytes of hepatopancreas

value: juvenile

value: 26mg/l acute nitrite exposure


title: G5A_hOrgSC60d


title: G9A_hOrgSC60d


title: G3A_hOrgSC60d


title: riboseq_shoot_3

description: ribosome footprint

value: 4 days old


title: G4A_hOrgSC60d


title: G2A_hOrgSC60d


title: G12A_hOrgSC60d


title: G1A_hOrgSC60d


title: G8A_hOrgSC60d


title: G11A_hOrgSC60d


title: F9A_hOrgSC60d


title: riboseq_root_2

description: ribosome footprint

value: Col


title: F7A_hOrgSC60d


title: F5A_hOrgSC60d


title: H11A_hOrgSC60d


title: F12A_hOrgSC60d


title: F11A_hOrgSC60d


title: E5A_hOrgSC60d


title: E8A_hOrgSC60d


title: F4A_hOrgSC60d


title: D9A_hOrgSC60d


title: E4A_hOrgSC60d


title: E1A_hOrgSC60d


title: D5A_hOrgSC60d


title: F3A_hOrgSC60d


title: D2A_hOrgSC60d


title: D8A_hOrgSC60d


title: D3A_hOrgSC60d


title: D11A_hOrgSC60d


title: C8A_hOrgSC60d


title: C2A_hOrgSC60d


title: C12A_hOrgSC60d


title: C10A_hOrgSC60d


title: C6A_hOrgSC60d


title: B5A_hOrgSC60d


title: B3A_hOrgSC60d


title: C9A_hOrgSC60d


title: B6A_hOrgSC60d


title: B11A_hOrgSC60d


title: B2A_hOrgSC60d


title: C3A_hOrgSC60d


title: E3A_hOrgSC60d


title: A8A_hOrgSC60d


title: A5A_hOrgSC60d


title: A4A_hOrgSC60d


title: A2A_hOrgSC60d


title: A3A_hOrgSC60d


title: Total_R1_RZ

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

data_processing:
Reads were first mapped to rRNA sequences using bowtie v1.0.1 (https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1/bowtie-1.0.1-linux-x86_64.zip/download) (Langmead et al., 2009). Reads that did not map to rRNA were subject to downstream analysis.
To quantify primary and mature transcript expression we used using RSEM v 1.2.11 (http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.11.tar.gz) (Li and Dewey, 2011). To calculate primary transcript expression we included an additional isoform corresponding to the sequence of the full gene locus. Specifically, we modified the GENCODEv19 gtf and used this as the input for the ‘rsem-prepare-reference’ function to generate a modified index used for quantification.
For each gene, we calculated the “mature” RNA expression as the sum of all isoforms for that gene excluding the “primary” transcript. For intronless genes, “primary” and “mature” expression values were summed.
Code and interactive-data visualization available a https://ohlerlab.mdc-berlin.de/software/Classification_of_human_genes_by_RNA_metabolism_profiles_130/
Genome_build: hg19
Supplementary_files_format_and_content: text matrix of TPM

growth_protocol: HEK293 cells were cultured in DMEM high glucose (Thermofisher, 41965039) supplemented with 10% fetal bovine serum (Thermofisher, 16000044) and 1% Pen/Strep (Thermofisher, #15070063).

extract_protocol:
RNA was extracted with TRIzol. For samples treated with 4-thiouridine, labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6).
RNA-seq libraries were prepared for paired end sequencing on illumina using

treatment_protocol: Cells were treated with 500 uM 4 thiouridine for 0, 7.5, 15, 30, 45, and 60 minutes.

tag: cell line

tag: molecule subtype

value: depeletion of rRNA with ribozero


title: Total_R1_RH

value: depletion of rRNA with RNAse H and oligos


title: A11A_hOrgSC60d


title: D10A_hOrgSC60d


title: Lab60_R1_C

tag: 4-thiouridine labeling time

value: 60 minutes labeling

value: 4-thiouridine labeled RNA


title: Total_R1_PA

value: Enrichment of polyA RNA with one round oligoDT selection


title: Lab60_R1_B


title: Lab60_R1_A


title: ATCC 17978 rep2

city: Winnipeg

first: Manu

middle: Kumar

last: Singh

state: Manitoba

address: 45 Chancellors circle, 412 Buller

country: Canada

institute: University of Manitoba

data_processing:
Data was analyzed using the Galaxy online tool kit
Sequences obtained were illumina adapter trimmed with TrimGalore 0.4.1  and were subjected to quality check using FastQC 0.64
Trimmed sequences were alligned using Bowtie2  2.2.6 aligner using a already published A. baumannii ATCC 17978 genome (NC_009085.1).
Sorted and indexed aligned files from both biological replicates were used to calculate the differential expression between wild type (ATCC 17978) and mutant (AB141) via Cufflink 2.2.1 pipeline
Gene annotation and chromosomal location was done using already published annotation file from the same organism.
Final filtered gene differential expression file made was using log 1.5 value as a cut-off value.
Genome_build: A. baumannii ATCC 17978 genome (NC_009085.1)
Supplementary_files_format_and_content: .tabular, Filtered Gene Diff.txt

organism: Acinetobacter baumannii ATCC 17978

source_name: ATCC

growth_protocol: All samples were grown in LB and supplemented with triclosan, when required.

extract_protocol:
Cells were pelleted at OD600 between 0.6 to 0.8 and total RNA were extracted using Rneasy mini kit from QIAGEN.
Illumina standard protocols were used.

value: Wild type


title: AB141 rep1

source_name: KumarLab collection

value: AdeN KO mutant


title: ATCC 17978 rep1


title: Lab45_R1_C

value: 45 minutes labeling


title: Lab45_R1_B


title: Lab45_R1_A


title: Lab30_R1_C

value: 30 minutes labeling


title: Lab30_R1_A


title: Lab15_R1_C

value: 15 minutes labeling


title: Lab30_R1_B


title: Lab15_R1_B


title: Lab7_R1_C

value: 7.5 minutes labeling


title: PM_T3

city: Wuhan

first: Wei

last: Zhang

state: Hubei Province

address: Luoyu

institute: Central China Normal University

data_processing:
Illumina CASVA 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence through in-house perl scripts, then mapped to the assembled Unigene sequences using RSEM 1.2.0 with Bowtie allowing  mismatchs of no more than two bases (Bowtie default parameter).
The left files (read1 file) from all samples were pooled into one big left.fq file, and right files (read2 file) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (r2012-10-05) with min_kmer_cov set to 2 by default and all other parameters set defalut.Unigenes was selected from the longest transcript copy of each gene clusters using in-house Perl scripts to avoid redundant transcripts.
Gene expression level for each sample were estimated using the software package RSEM (v 1.2.0) based on the expectation-maximization (EM) algorithm. Firstly, clean reads of each sample were mapped back onto the assembled transcripts. Then, the read count for each gene was obtained from the mapping results. The gene expression level was estimated by calculating the fragments per kb per million reads (FPKM).
Genome_build: Assembly Unigene.fasta
Supplementary_files_format_and_content: xls files include Readcount and FPKM values for each Sample,and fasta file is the assembled Unigene sequence.

organism: Leptobrachium boringii

extract_protocol:
Tissues of brain, testis and upper jaw skin were removed, and RNA was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: wild type

value: Testis

value: Post breeding period


title: Lab15_R1_A


title: PM_T1


title: Lab7_R1_B


title: M_T2

value: Breeding period


title: Lab7_R1_A


title: M_T1


title: AB141 rep2


title: MM-HS_R-2

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

description: pollen of tomato cultivar 39° replicate 2

data_processing:
FastQC preprocessing
First and last 8 nucleotides were cropped from all reads as ligation adapter
RNA-seq reads were aligned using TopHat2 via the NGS pipeline Pfand
Only best scoring hits with up to two mismatches were reported (-g 1and --read-mismatches 2)
Genome_build: ITAG2.4
Supplementary_files_format_and_content: text files (.txt) representing the fragment counts for annotated mRNAs

organism: Solanum lycopersicum

growth_protocol: Tomato plants (cv. Moneymaker and cv. Red Setter) were grown under controlled greenhouse conditions (24°C / 18°C, day / night temperature; 60% humidity). Flower buds containing pollen of different developmental stages were harvested directly after stress treatment or after recovery. Untreated/control plants were kept at 24oC for the same time.

extract_protocol:
After isolation of pollen, all developmental pollen stages (microspore mother cell, tetrads, microspores and mature pollen) were pooled together for each of the four conditions: cv. Moneymaker-CO, cv. Moneymaker-HS, cv. Red Setter-CO and cv. Red Setter-HS. For each condition, two biological replicates were used. Total RNA was extracted from pollen of all eight samples using the E.Z.N.A. Plant RNA Kit (Omega Bio-Tek, Norcross, GA, USA).
Total RNA was used for the preparation of mRNA-seq libraries by GenXPro performing rRNA depletion and enrichment of mRNA via polyadenylation (polyA) selection and purification
mRNA-seq with IlluminaTruSeq adapter and paired-end libraries

treatment_protocol: Flowering plants approximately 8 weeks old were transferred to a climate chamber and exposed to a 39°C HS treatment for 1 hour and then allowed to recover for 1.5 hour at 24°C.

value: pollen

tag: stress

value: Heat stress

tag: cultivar

value: Moneymaker


title: RS-C-2

description: pollen of tomato cultivar 25° replicate 2

value: Control

value: Red Setter


title: RS-HS_R-2


title: RS-C-1

description: pollen of tomato cultivar 25° replicate 1


title: 30min plus ciprofloxacin

city: Copenhagen

first: Rasmus

middle: Nielsen

last: Klitgaard

address: Ole Maaløes vej 5, Building 4 2nd floor

department: Department of biology

country: Denmark

institute: University of Copenhagen

description:
E. coli ST131 UR40
UR40 is the unique isolate number from: Cerquetti, M., et al. "Ciprofloxacin-resistant, CTX-M-15-producing Escherichia coli ST131 clone in extraintestinal infections in Italy." Clinical Microbiology and Infection 16(10): 1555-1558.
Processed data files: ST2_30min_NA114.txt, ST2_30min_NA114.xml

data_processing:
All data was processed using Rockhopper Ver.2.03. Rockhopper is an "automatic" bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). "Computational analysis of bacterial RNA-Seq data." Nucleic Acids Res 41(14): e140. The default general parameters were used with the "verbose output" tab ticked and the "orientation of mate-pair reads" changed to "rf".
Genome_build: NC_017644.1 (Escherichia coli NA114)
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint.

organism: Escherichia coli O25b:H4-ST131

source_name: Clinical isolate, plus ciprofloxacin, 30min

growth_protocol: The cultures were balanced and grown in CAMHB media at 37 degrees Celsius.

extract_protocol:
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit.
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min.

tag: isolate

value: ciprofloxacin

tag: time point


title: MM-HS_R-1

description: pollen of tomato cultivar 39° replicate 1


title: 90min minus ciprofloxacin

description:
E. coli ST131 UR40
UR40 is the unique isolate number from: Cerquetti, M., et al. "Ciprofloxacin-resistant, CTX-M-15-producing Escherichia coli ST131 clone in extraintestinal infections in Italy." Clinical Microbiology and Infection 16(10): 1555-1558.
Processed data files: ST2_90min_NA114.txt, ST2_90min_NA114.xml

source_name: Clinical isolate, minus ciprofloxacin, 90min


title: 30min minus ciprofloxacin

source_name: Clinical isolate, minus ciprofloxacin, 30min


title: 0min plus ciprofloxacin

description:
E. coli ST131 UR40
UR40 is the unique isolate number from: Cerquetti, M., et al. "Ciprofloxacin-resistant, CTX-M-15-producing Escherichia coli ST131 clone in extraintestinal infections in Italy." Clinical Microbiology and Infection 16(10): 1555-1558.
Processed data files: ST2_0min_NA114.txt, ST2_0min_NA114.xml

source_name: Clinical isolate, plus ciprofloxacin, 0min


title: 90min plus ciprofloxacin

source_name: Clinical isolate, plus ciprofloxacin, 90min


title: MM-C-1


title: 0min minus ciprofloxacin

source_name: Clinical isolate, minus ciprofloxacin, 0min


title: Zscan4c-Positive Replicate 1

status: Public on Nov 03 2016

city: Pasadena

first: Michael

last: Elowitz

state: Ca

address: 1200 E California Blvd MC 114-96

department: Bioengineering

institute: Caltech

data_processing:
Base calls were performed with RTA 1.13.48.0 and converted to FASTQ with bcl2fastq 1.8.4
Sequenced reads were mapped to mm10 using tophat v2.0.14 using default parameters
Transcript abundance and differential expression were quantified using Cufflinks and Cuffdiff v2.2.1, respectively, using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Counts.txt reports FPKMs

organism: Mus musculus

source_name: PiggbyBac Zscan4c Promoter Fragment Reporter

extract_protocol:
RNA was extracted using Qiagen RNEasy kit
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) following manufacturer’s instructions

value: E14Tg2a.4 mouse ES cells

tag: genotype/variation


title: Zscan4c-Negative Replicate 2

tag: cell type


title: Esrrb-Positive Tbx3-Positive Replicate 2

source_name: Esrrb/Tbx3 Double Knockin Reporter

value: Esrrb-Positive Tbx3-Positive


title: Esrrb-Positive Tbx3-Positive Replicate 1


title: Esrrb-Positive Tbx3-Negative Replicate 2

description: EsrrbOn

value: Esrrb-Positive Tbx3-Negative


title: Esrrb-Positive Tbx3-Negative Replicate 1

description: EsrrbOn


title: Esrrb-Negative Tbx3-Negative Replicate 2

value: Esrrb-Negative Tbx3-Negative


title: Esrrb-Negative Tbx3-Negative Replicate 1


title: RS-HS_R-1

tag: tissue


title: rs2382817_locus_DLD

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGGACAGTGTATCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATACGCTGCTAACCAACTGT

data_processing:
Library strategy: 4C-seq
he raw sequencing reads were de-multiplexed based on viewpoint specific primer sequences. Reads were then trimmed to 16 bases and mapped to an in silico generated library of fragends (fragment ends) neighboring all DpnII sites in human genome (NCBI37/hg19), using the custom Perl scripts. No mismatches were allowed during the mapping and the reads mapping to only one possible fragend were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: wig files contain information abut fragend sequencing coverage (0 - not covered, 1 covered)

organism: Homo sapiens

source_name: DLD

growth_protocol: DLD-1 cells were cultured in RPMI-1640 with 10% FCS and standard supplements. Cells were harvested for 4C template preparation by trypsinisation at 60-80% confluence.

extract_protocol:
4C-chromatin preparation, primer design and library preparation were described previously (van de Werken, H. J. G. et al. 4C technology: protocols and data analysis. Methods in enzymology 513, (Elsevier Inc., 2012).)
10x106 cells were used per cell type. Cells were crosslinked in 2% formaldehyde. After chromatin isolation, the chromatin was digested with DpnII (NEB, # R0543L). Digestion was stopped through heat inactivation of the restriction enzyme. Samples were diluted and ligated by T4 DNA ligase. The second digestion was carried out with CviQI (NEB, #R069S) and inactivated by phenol:chloroform extraction. The chromatin was diluted, for the final T4 ligation and the chromatin was purified. The quality of digestion and ligation was assessed on agarose gels. the PCR of 4C template was performed with 600 ng - 1,6 µg of 4C template per reaction. 8 to 10 primer pairs were multiplexed in the initial PCR reaction. Primers pairs were pooled according to primer efficiency (based on intensity on gel electrophoresis signal after PCR on test template). PCR products were purified after an initial PCR reaction of 6 cycles (reaction volume = 200 µL) and divided among 8-10 PCR reactions containing single primer pairs for another 26 cycles (reaction volume = 25 µL). Thereafter, PCR products derived from the same cells were pooled in equimolar amounts and a final 6 cycle PCR reaction containing 20 ng of pooled PCR product (reaction volume = 100 µL) was performed with primers that contained sequencing adaptor sequences. All fragments >700bp were removed using size selection on a 1% agarose gel follow by gel extraction of the selected products (Qiagen, #28704).

value: DLD-1 cell line


title: MM-C-2


title: rs11230563_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAGGCATTCCATGGATC
Rv primer: CAAGCAGAAGACGGCATACGATCTTCCTGATATGGGCTAAA


title: rs2823286_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATACAAGGGCAATGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCAAGTCATAAGGCAGTTTT


title: rs6545800_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAACATTCTCTCTTTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTCTTCTTTGTAGTGACG


title: rs6426833_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGGGGTCTCTGCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATCTAAGGGAAGATGTGCA


title: metastasis #1 from PTEN-deficient hSS1 primary tumor #4

city: Salt Lake City

first: Kevin

middle: B

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

institute: University of Utah

description:
11819X2
11819R.txt

data_processing:
Reference fasta files generated by combining mm10 chromosome sequences with splice junction sequences generated by Useq (v8.8.8) MakeTranscriptome using Ensembl transcript models (build 74)
aligned with Novoalign (v2.08.01) allowing up to 50 alignments per read.
Best alignments selected by Useq SamTranscrimptomeParser and converted coordinates of reads aligning to splices back to genomic space.
Differential gene expression was measured using USeq DefinedRegionDifferentialSeq, which counts the number of reads aligned to each gene and then call DESeq2 (v1.4.5) using default settings.
Genome_build: mm10 Ensembl build 74
Supplementary_files_format_and_content: tab-delimited files containing FPKM values, log2 Fold Changes and FDR for all tested genes

source_name: metastatic tumor in lung parenchyma

growth_protocol: Spontaneous tumors, primary in the limb or metastatic to the lung parenchyma

extract_protocol:
Qiagen RN-easy
Illumina TruSeq
RiboZero method

tag: ss fusion type

tag: pten genotype

value: fl/fl


title: Zscan4c-Positive Replicate 2


title: metastasis #3 from PTEN-deficient hSS1 primary tumor #4

description:
11819X4
11819R.txt


title: PTEN-deficient hSS1 primary tumor #4

description:
11819X1
11819R.txt

source_name: primary tumor from hind limb


title: PTEN-deficient hSS2 primary tumor #3

description:
11819X7
11819R.txt


title: metastasis from PTEN-deficient hSS2 primary tumor #3

description:
11819X8
11819R.txt


title: PTEN-deficient hSS1 primary tumor #5

description:
11819X5
11819R.txt


title: metastasis #2 from PTEN-deficient hSS1 primary tumor #4

description:
11819X3
11819R.txt


title: metastasis from PTEN-deficient hSS1 primary tumor #5

description:
11819X6
11819R.txt


title: Zscan4c-Negative Replicate 1


title: PTEN-proficient hSS2 primary tumor #3

description:
11361X13
11361R.txt

value: wt/wt


title: PTEN-deficient hSS2 primary tumor #2

description:
11361X16
11361R.txt


title: rs6679677_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCGAGTCCAGGTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGTGCTCCACTTTCTAACC


title: rs12568930_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCTTGCAACTCCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTACATTCAGTGTGCAATGG


title: rs17085007_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCAACCAGGAAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAATAACAGTAGCAGCCACA


title: PTEN-deficient hSS2 primary tumor #1

description:
11361X15
11361R.txt


title: rs12663356_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCACTCTGCATGACCGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTCTGGCCCCTGAGGTAC


title: rs4899554_locus2_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTTTTTAGAGGGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTCTTTATTCTCCAGCCCT


title: PTEN-proficient hSS2 primary tumor #1

description:
11361X11
11361R.txt


title: PTEN-proficient hSS2 primary tumor #2

description:
11361X12
11361R.txt


title: PTEN-deficient hSS1 primary tumor #3

description:
11361X6
11361R.txt


title: rs13204742_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCGGAGGCTCAGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCACACACACATACACCAC


title: rs6920220_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCAACCTTCACTTGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGCACTCATTTTCTCAGCT


title: rs2266959_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCCACCATGGGCTTAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCAGAGGTTGTGTGTAGGAC


title: rs4246215_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGAGTTTCAGTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGGATTGAGACTGTGGTTTA


title: PTEN-deficient hSS1 primary tumor #2

description:
11361X5
11361R.txt


title: PTEN-proficient hSS1 primary tumor #3

description:
11361X3
11361R.txt


title: rs11564258_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGTTTGGGTAACTAATGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGCTCAGGAAGTGTTTGTAC


title: rs7134599_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCATTTTCCCCTATGATC
Rv primer: CAAGCAGAAGACGGCATACGACCACTGTTAACAATTTGGGT


title: PTEN-proficient hSS1 primary tumor #1

description:
11361X1
11361R.txt


title: rs1250546_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATCATTTGTCTGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGTAATACGCATTCTTCCCT


title: rs11010067_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATTGGGGCTAATGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAAAGAGCAAGCACCATACT