title: ABCB5+_Low_Passage_Replicate5

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

data_processing:
Basecalls performed using CASAVA version 1.4
the fastq files were used to align to human genome reference (GRCh38) using Hisat2, followed by transcripts assembly, abundances estimation and differential expression were performed by cufflinks and cuffdiff, respectively. The visualization of RNASeq data analyses were performed by R packages, cummeRbund, gplots, ggplot2 using customized scripts.
Genome_build: human genome reference (GRCh38)
Supplementary_files_format_and_content: FPKM values of each replicates

source_name: Human dermal/mesenchymal cells

growth_protocol: ABCB5+ dermal MSCs were cultured in Ham´s F10 supplemented with 15% heat-inactivated high quality fetal bovine serum, 6mM HEPES, 2.8µg/ml hydrocortisone, 100U/ml penicillin/streptomycin, 2mM L-glutamine, 10µg/ml insulin, 0.2mg/ml glucose, 6.16ng/ml PMA (Sigma-Aldrich) and 0.6ng/ml recombinant human basic fibroblast growth factor (Prospecbio), at 37°C and 3% CO2. Versene (Gibco) was used to detach ABCB5+ dermal cells from the culture plastic. ABCB5- HDFs were maintained in DMEM with 10% high quality fetal bovine serum, 100U/ml penicillin/streptomycin and 2mM L-glutamine (Biochrom), at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cells using Rneasy micro kit (Qiagen)
To prepare the total RNA-Seq library, 500 ng of total RNA was used as input. 500 ng of total RNA first was used to deplete the rRNA using a commercially available kit (Low Input Ribominus Eukaryotic System v2, Thermo) as described in the manual with slight modifications. In brief, after the rRNA was depleted using RiboMinus™ Eukaryote Probe Mix, the supernatant containing rRNA depleted RNA was collected and incubated with 3x Agencourt RNAClean XP beads for 20 min on ice, followed removal of supernatant and washing of RNAClean XP beads two times with 80% ethanol and finally the rRNA depleted RNA was eluted from the beads in 10 µl of nuclease free water. This rRNA depleted RNA was used to prepare RNASeq library for Illumina platform using NEBNext Ultra II Directional RNA library prep kit (NEB) with some modifications.

value: skin derived mesenchymal cells

tag: passage

value: low


title: ABCB5+_Low_Passage_Replicate3

status: Public on Jan 30 2019

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: ABCB5+_High_Passage_Replicate2

value: high


title: ABCB5+_Low_Passage_Replicate4


title: ABCB5+_Low_Passage_Replicate2


title: ABCB5+_Low_Passage_Replicate6


title: B6_28wks_HFD_18wks_3

city: Freiburg

first: Steffen

last: Heyne

address: Stübeweg 51

department: Epigenetic Focus

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
barcodes 1-96
scRNA_counts_mouse.tar.gz
celseq_barcodes.192.txt

data_processing:
Please note: the detailed description of processing steps here is correct and differs in some details/parameters from the original generalized description in the publication!  Beta cells from 14 week old mice (WT/EED KO) as well as from 28 week old mice (NCD/HFD) were processed similar as described in Grün et al. (Cell Stem Cell 2016 http://dx.doi.org/10.1016/j.stem.2016.05.010) Read 2 was aligned to the transcriptome using bwa v0.7.12 (Li and Durbin, 2010). The transcriptome index is based on gencode version M9 for mouse (http://www.gencodegenes.org). Pseudogenes and all smallRNA genes were removed. The most common of  isoforms (“basic” subset) of the same gene were merged to a single gene locus. Cell demultiplexing was done using the cell barcode (6nt) and the unique molecular identifier (UMI, 6nt) present in the first 12 nt of Read 1 of the read pair. Reads mapping to multiple loci were discarded. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Grün et al., 2014).
For min6-B1 cell data, read 2 was mapped against mouse genome version mm9 (UCSC) using tophat (Kim et al., 2013) and RefSeq gene models. Cell demultiplexing was done using the cell barcode (6nt) and the unique molecular identifier (UMI, 6nt) present in the first 12 nt of Read 1 of the read pair. Reads mapping to multiple loci were discarded. Reads were counted with featureCounts (subread-1.4.6) against RefSeq gene models. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene.
Genome_build: GRCm38 (data from 14 week old mice (WT/EED KO) and 28 week old mice (NCD/HFD)); mm9 (data from min6-B1 cells)
Supplementary_files_format_and_content: scRNA_counts_mouse.tar.gz contains the count matrices with the cells used in RACEID after applying intial filtering steps, ie. as shown in the Figures.  Cell names contain either the used barcode or the barcode index.
Supplementary_files_format_and_content: celseq_barcodes.192.txt contains the index of all cell barcodes

organism: Mus musculus

source_name: pancreatic islets

extract_protocol:
Adult pancreata were perfused through the common bile duct using a 27/30-gauge needle with Collegenase XI (Sigma) solution. Perfused pancreata were digested and purified by centrifugation in Histopaque gradient (Sigma). Isolated islets were hand picked and cultured in complete media (RMPI-1640 containing 11 mM glucose, 10% FBS, 0.1% Penicillin/Streptomycin) and maintained at 37°C in 5% CO2 environment
Single cell RNA sequencing was performed using CEL-Seq2 method (Hashimshony et al., 2016) with several modifications. Importantly, a fivefold volume reduction was achieved using a nanoliter-scale pipetting robot, Mosquito HTS (TTP Labtech). Sorted plates were centrifuged at 2200 g for 10 min at 4°C, snap-froze in liquid nitrogen and stored at -80°C until processed. 160 nL of reverse transcription reaction mix and 2.2 μL of second strand reaction mix was used to convert RNA into cDNA. cDNA from 96-cells was pooled together before clean up and in vitro transcription, generating 4 libraries from one 384-well plate. 0.8 μL of AMPure/RNAClean XP beads (Beckman Coulter GmbH, Germany) per 1 μL of sample were used during all the purification steps including library cleanup.

tag: cell type

value: pancreatic islets

tag: genotype

value: WT

tag: strain

tag: treatment


title: ABCB5+_High_Passage_Replicate3


title: ABCB5+_High_Passage_Replicate1


title: Day5_Control

city: HsinChu

first: Chih-Hung

last: Chou

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

data_processing:
Reads of RNA-seq were quality pre-processed using FASTX-Toolkit.
The reads with Phred quality score ≥ 20 and longer were retained.
Reads were then mapped to the UCSC Mouse genome mm10 using TopHat2
Genome_build: mm10
Supplementary_files_format_and_content: raw count sample matrix file

source_name: whole layer 5-day non-stretched skin

extract_protocol:
RNAZol kit (Sigma-Aldrich).
TruSeq RNA Preparation Kit v2

treatment_protocol: with 33% strain (Day5_Tension) or without strain (Day5_Control) for 5 days

value: wild type

value: skin

value: Control


title: Day5_Tension

source_name: whole layer 5-day stretched skin

value: Tension


title: ABCB5+_Low_Passage_Replicate1


title: B6_28wks_HFD_18wks_2

description:
barcodes 97-192
scRNA_counts_mouse.tar.gz
celseq_barcodes.192.txt


title: B6_28wks_HFD_18wks_1


title: TAK_1836-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_RNaseHII

city: Durham

first: Zhi-Xiong

last: Zhou

address: 111 TW Alexander Dr.

country: USA

institute: National Institute of Envinromental Health Sciences

library_source: genomic

data_processing:
Library strategy: HydEn-seq
Base calling and generation of FASTQ files performed by Illumina Hiseq standard pipeline
Reads trimmed for adapter sequence using cutadapt 1.12, discarding pairs with one or both reads shorter than 15 nt
Align end 1 to index of oligos used during library prep, exclude successful pairs from further analysis (bowtie 1.2 -k1 -v2, see supplementary file oligos.fa)
Align remaining pairs to reference genome, trim single nt from 3' end of reads to allow mapping of 100% overlapping pairs (bowtie 1.2 -m1 -v2 -X10000 -3 1)
Align end 1 of unmapped pairs to reference genome (bowtie 1.2 -m1 -v2)
Retain 5' end only for all single- and paired-end unique alignments, combine
Determine counts of ends mapped to SbfI-HF restriction sites, calculate size factors using method applied in DESeq, Anders et al., 2010
Filter ends mapping within 2 nt of an SbfI-HF restrition site or site with 1 bp mismatch relative to SbfI-HF motif, divide by previously determined size factors
Genome_build: L03 background S. cerevisiae assembly (see supplementary files L03_ref_v2.fa), S. pombe assembly 2.23
Supplementary_files_format_and_content: bigWig, count of HydEn-seq 5' ends per position

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Log phase cell culture

growth_protocol: Yeast strains were grown to mid log phase (OD600=0.5-1) at 30°C in YPDA medium supplemented with 0.25 mg/ml adenine

extract_protocol:
DNA was isolated using the MasterPure™ Yeast DNA Purification Kit (Epicentre) without RNase A treatment.
HydEn-seq libraries are constructed as previously described (Clausen, et al. 2015 NSMB) with modifications by the following steps. Briefly, extract yeast genomic DNA (gDNA) using Epicenter MasterPure Yeast DNA Purification Kit. Treat 200 ng gDNA with Shrimp Alkaline Phosphatase (rSAP, New England Biolabs). Denature rSAP and restriction digest with SbfI-HF at 37 °C for 1 hour. Split the DNA into two fractions. Treat one fraction with RNase HII (NEB) at 37 °C for 2 hours and designate the other fraction as non-treatment control. Denature the DNA by incubation at 90 °C for 2 min and ligate to adaptor ARC140 by T4 RNA ligase 1 (NEB) overnight at 25 °C. Denature DNA and anneal to the duplex adaptor ARC76/77. Synthesize the second strand using T7 DNA polymerase (NEB). Amplify the library for 20 cycles by primer ARC49 and an indexing primer using KAPA HiFi HotStart Ready Mix (KAPA Biosystems). 0.8 volumes of MagBio HighPrep PCR beads were used to purify DNA between steps that require changing buffers and/or removal of oligo adaptors and in the final library cleanup. The library was sequenced on an Illumina Illumina HiSeq 4000 machine for paired end 50 bp reads. The rSAP, SfbI-HF and RNase HII treatments are the main modifications to the original protocol to improve on signal-to-noise ratio, quantitation and specificity.

value: pol3-L612G rnh201delta

value: RNaseHII


title: TAK_1835-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_RNaseHII

value: pol2-M644G rnh201delta


title: TAK_1838-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_RNaseHII


title: TAK_1834-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_RNaseHII


title: DMSO_Replicate 3

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

description:
DL_DMSO_C_S3
Sample_3_DMSO C

data_processing:
Reads were mapped to GRCh38 genome assembly with the HISAT2 followed by using UCSC reference annotation and HTSeq to estimate gene abundance.
Per sample read counts were calculated with htseq-count, mode: union, feature type: exon, id attribute: gene_id, and all other defaults.
Normalized read count abundance was estimated and differential expression was calculated with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: polyA RNA

extract_protocol:
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol. Cardiac spheres were generated from cells at differentiation day 5 and subjected to maturation factors or DMSO treatment from day 21 to day 28. RNA samples from cells at differentiation day 28 were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq protocol and next-generation sequencing was done through an Illumina HiSeq 2500, 75bp paired end sequencing.

value: IMR90 iPSC derived cardiomyocytes

tag: developmental stage

value: Day 28 differentiated cells

tag: condition

value: 3D cardiac spheres


title: B6_28wks_2

value: NCD


title: B6_28wks_HFD_18wks_4


title: TAK_1832-S_cerevisiae_HydEn-seq_pol1-Y869A_rnh201_RNaseHII

value: pol1-Y869A rnh201delta


title: TAK_1833-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_RNaseHII


title: TAK_1827-S_cerevisiae_HydEn-seq_rnh201_RNaseHII


title: Treat_Replicate 1

description:
DL_Treat_A_S7
Sample_7_Treat A


title: TAK_1831-S_cerevisiae_HydEn-seq_pol1-Y869A_rnh201_RNaseHII


title: 5c

source_name: min6-B1 cells

growth_protocol: Cells were cultured in DMEM supplemented with 15% fetal calf serum, 25 mM glucose, 71 μM 2-mercaptoethanol, 2 mM glutamine and 100 U/mL penicillin and 100 mg/mL streptomycin, in 5% CO2 atmosphere incubator at 37°C.

extract_protocol:
4 days after electroporation, cells were harvested, trypsinized and single cells were sorted in 384-well plates containing 240 nL of primer mix and 1.2 μL of PCR encapsulation barrier, Vapor-Lock (Qiagen GmbH, Germany)
Single cell RNA sequencing was performed using CEL-Seq2 method (Hashimshony et al., 2016) with several modifications. Importantly, a fivefold volume reduction was achieved using a nanoliter-scale pipetting robot, Mosquito HTS (TTP Labtech). Sorted plates were centrifuged at 2200 g for 10 min at 4°C, snap-froze in liquid nitrogen and stored at -80°C until processed. 160 nL of reverse transcription reaction mix and 2.2 μL of second strand reaction mix was used to convert RNA into cDNA. cDNA from 96-cells was pooled together before clean up and in vitro transcription, generating 4 libraries from one 384-well plate. 0.8 μL of AMPure/RNAClean XP beads (Beckman Coulter GmbH, Germany) per 1 μL of sample were used during all the purification steps including library cleanup.

treatment_protocol: Min6-B1 cell line were electroporated using Nucleofector II device (Lonza, Kit T, Program O-017) with pMAXGFP (Lonza) or mouse cDNA ORF clones of the 6 different transcription factors (Origene).

value: min6-B1 cells

value: transfected with 6 TFs (1mg)


title: 5d


title: 5b


title: B6_28wks_1


title: 4d

value: transfected with 6 TFs (500ng)


title: 5a


title: TAK_1819-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_NT

value: NT (non-treatment control)


title: TAK_1820-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_NT


title: 2d

value: transfected with GFP


title: TAK_1826-S_cerevisiae_HydEn-seq_rnh201_RNaseHII


title: 4c


title: TAK_1818-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_NT


title: TAK_1822-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_NT


title: TAK_1817-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_NT


title: TAK_1815-S_cerevisiae_HydEn-seq_pol1-Y869A_rnh201_NT


title: TAK_1816-S_cerevisiae_HydEn-seq_pol1-Y869A_rnh201_NT


title: 2b

value: electroporation only (vectorless)


title: 2a


title: TAK_1810-S_cerevisiae_HydEn-seq_rnh201_NT


title: TAK_1811-S_cerevisiae_HydEn-seq_rnh201_NT


title: 14wks_Eed_WT_2

value: pancreatic islets

value: WT


title: 14wks_Eed_WT_1


title: 14wks_Eed_WT_3


title: TAK_1374-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_RNaseHII


title: 14wks_Eed_KO_1

value: Eed -/-


title: 14wks_Eed_KO_2


title: 14wks_Eed_KO_3


title: TAK_1372-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_RNaseHII

value: pol3-L612G rnh201delta


title: AD_B_Ch2: (FAD-BIX2 ChIP)

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 124 Sherman Hall

department: Physiology and Biophysics

institute: University at Buffalo

description: processed data file: FAD_BIX_vs_FAD_peak_compare_table.tsv

data_processing:
The Illumina Hiseq 2500 was used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Frist at all, we use FastQC performs basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below: (1) Remove low-quality reads: The reads that mean quality value less than 20 were removed; (2) Remove the reads that contain more than 15 percent N bases; (3) Remove adapters. Remove the reads that alignment with the adapter sequence; (4) Drop reads blow the 18 bases long after trimming; (5) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last,we use FastQC performs basic statistics on the quality of the clean reads.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Genome_build: mm9
Supplementary_files_format_and_content: Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Tab-delimited text files include values of distribute of chromosome, peak width, fold enrichment, significant level and peak summit number per peak for each Sample …

source_name: BIX01294-treated FAD mice

extract_protocol:
PFC slices were punched from two wild-type mice, two FAD mice and two BIX01294-treated FAD mice, and cross-linked with 1% formaldehyde for 12 min at room temperature. Glycine was used to quench the cross-link. After washing, the tissues were homogenized and sonicated to get sheared chromatin.
The library preparations were sequenced on an Illumina Hiseq platform and 50 bp single-end reads or 150 bp paired-end reads were generated.

value: prefrontal cortex

tag: age

value: 5-6 months old


title: TAK_1370-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_RNaseHII

value: pol2-M644G rnh201delta

value: RNaseHII


title: TAK_1371-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_RNaseHII


title: 14wks_Eed_KO_4


title: 2c


title: AD_B_In2: (FAD-BIX2 input)


title: TAK_1367-S_cerevisiae_HydEn-seq_pol1-Y869A_rnh201_RNaseHII


title: AD_Ch_2: (FAD2 ChIP)

description: processed data file: FAD_vs_WT_peak_compare_table.tsv

source_name: FAD mice


title: TAK_1356-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_NT


title: AD_B_Ch1: (FAD-BIX1 ChIP)


title: TAK_1363-S_cerevisiae_HydEn-seq_rnh201_RNaseHII


title: TAK_1358-S_cerevisiae_HydEn-seq_pol3-L612G_rnh201_NT


title: AD_In_2: (FAD2 input)


title: AD_In_1: (FAD1 input)


title: AD_Ch_1: (FAD1 ChIP)


title: TAK_1354-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_NT


title: CYP Light 3

city: Wien

first: Zsuzsanna

last: Mérai

address: 1030 Wien Dr. Bohr-Gasse 3.

country: Austria

institute: Gregor Mendel Institute

data_processing:
Basecalling was done by using RTA software version 1.18.54.0
Files were generated by bcl2fastq tool version 2.17.1 and bam files were generated by fastq2bam tool version 0.7.
The sequence libraries were processed using Trimmomatic with options “ILLUMINACLIP:adaptors:2:20:8, SLIDINGWINDOW:4:15, TRAILING:15, HEADCROP:12, MINLENGTH:20”
Chloroplast, mitochondrial and ribosomal RNA (rRNA) sequences were filtered out to reduce the complexity of the dataset prior to mapping the reads to the genome by using Bowtie 2 version 2.2.3 with options “-D 20, -R 3, -N 1, -L 20, -i S,1,0.50, --end-to-end” and mapping the reads against the chloroplast (GenBank: AP000423.1), mitochondria (GenBank: Y08501.2) and rRNA (GenBank: X52320.1) sequences of A. thaliana.
Trimmed and filtered reads were mapped against the Aethionema arabicum genome version 2.5, using Bowtie2 with the same options as when filtering, and uniquely mapped reads were kept.
Mapped reads per feature were counted using HTSeq-count version 0.6.1 with the options “–s no –t gene –m union”.
Genome_build: id 33968 v2.5    https://genomevolution.org/coge/
Supplementary_files_format_and_content: xls matrix table file includes Aethionema gene model IDs, gene length, TAIR10IDs, TAIR10 description, Raw Counts and RPKM values for each sample.

organism: Aethionema arabicum

source_name: imbibed seed

extract_protocol:
Intact, non-germinating seeds were collected into liquid nitrogen. RNA was extracted as described at Chang et. al. 1993 (http://dx.doi.org/10.1007/BF02670468) followed by additional purification using columns (QIAGEN RNeasy Kit, Cat. No. 74104).
Libraries were constructed from 600 ng RNA using Lexogen SENSE mRNA seq library Prep Kit (Cat. No. 009) including  Poly(A) RNA Selection Kit (Cat. No. 039).

tag: accession

value: Cyprus

value: seed

value: 23 hours kept under 100µmol m-2s-1 white light


title: TAK_1351-S_cerevisiae_HydEn-seq_pol1-Y869A_rnh201_NT

value: pol1-Y869A rnh201delta


title: TAK_1353-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_NT


title: TAK_1355-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_NT


title: CYP Light 2


title: WT_In_2: (WT2 input)

source_name: wild-type mice


title: TAK_1347-S_cerevisiae_HydEn-seq_rnh201_NT


title: WT_Ch_1: (WT1 ChIP)


title: TAK_1346-S_cerevisiae_HydEn-seq_rnh201_NT


title: CYP Dark 3

value: 23 hours kept in darkness


title: WT_In_1: (WT1 input)


title: TAK_1369-S_cerevisiae_HydEn-seq_pol2-M644G_rnh201_RNaseHII


title: CYP Dark 2


title: CYP Dark 1


title: TUR Light 3

value: Turkish ES1020


title: AD_B_In1: (FAD-BIX1 input)


title: TUR Light 2


title: TAK_1362-S_cerevisiae_HydEn-seq_rnh201_RNaseHII


title: TUR Light 1


title: TUR Dark 3


title: TUR Dark 1


title: WT_Ch_2: (WT2 ChIP)


title: TUR Dark 2


title: CYP Light 1


title: TAK_2034-S_pombe_HydEn-seq_rnh201_RNaseHII

organism: Schizosaccharomyces pombe


title: TAK_2033-S_pombe_HydEn-seq_cdc6-L591G_rnh201_RNaseHII

value: cdc6-L591G rnh201delta


title: C. crescentus spdR(D64E) replicate 2

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
FastQ files from Illumina HiSeq were processed using CLC genomics workbench (Qiagen), RNA-seq data analysis pipeline. Reads were mapped to the Caulobacter crescentus NA1000 genome (accession CP001340)
Genome_build: GenBank accession CP001340

organism: Caulobacter vibrioides

source_name: whole bacterial cells

growth_protocol: Strains grown on PYE agar plates were inoculated into 5 ml of M2X medium in 3 biological replicates for each strain, and grown overnight on a rolling incubator at 30°C. Cultures were diluted to OD660nm of 0.008 into 8 ml of fresh M2X and grown in the same manner until they reached OD660nm of 0.30 – 0.35. At this point, 6 ml of each biological replicate were collected by centrifugation at 15,000 × g for 1.5 min.

extract_protocol:
This cell pellet was resuspended in 1 ml of TRIzol and stored at -80˚ C.  The sample was then heated for 10 min at 65°C and 200 µl of chloroform was added, mixed and incubated at room temperature for 5 min. Samples were centrifuged at 15,000 × g for 15 min at 4°C. The clear aqueous phase was transferred to a new tube and 0.7 volume of cold 100% isopropanol was added. Samples were then saved at -80°C overnight. The overnight precipitation was centrifuged at 15,000 × for 30 min at 4°C and the resulting nucleic acid pellet was washed twice with cold 70% ethanol. The pellet was centrifuged again at 15,000 × for 30 min at 4°C, ethanol was removed and the pellet was allowed to dry.  The nucleic acid pellet was resuspended with nuclease-free water. The samples were treated with with Turbo DNase (Invitrogen) and clean-up was performed with RNeasy Mini Kit (Qiagen).
TruSeq stranded total RNA kit was used to prepare RNA-seq library, per manufacturer (Illumina) protocol

treatment_protocol: Strains were not treated; we were assessing transcript levels across the three genetic backgrounds

tag: genotype/variation

value: spdR phosphomimic strain (SpdR(D64E))


title: C. crescentus spdR(D64E) replicate 1


title: C. crescentus spdR(D64E) replicate 3


title: C. crescentus ΔspdR replicate 3

value: spdR response regulator deletion strain (delta-spdR)


title: TAK_2032-S_pombe_HydEn-seq_cdc6-L591G_rnh201_RNaseHII


title: Cuticle Control2

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

country: China

institute: Weifang University

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC，including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database，Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Supplementary_files_format_and_content: tab-delimited text files includeTPM values for each Sample

organism: Antheraea pernyi

source_name: cuticle

extract_protocol:
Cuticles were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Approximately 10 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cuticle


title: Cuticle Control3


title: Cuticle ApNPV3


title: Cuticle ApNPV1


title: Cuticle ApNPV2


title: Infected 10

city: Copenhagen

first: Huria

last: Marnis

address: Stigbøjlen 7

department: Veterinary and Animals science

country: Denmark

institute: Copenhagen university

data_processing:
Illumina Casava software used for basecalling: SCS2.7/RTA1.7
Reads were aligned to the Baltic cod reference genome (genome https://figshare.com/articles/Transcript_and_genome_assemblies_of_Atlantic_cod/3408247) using TopHat (version 2.0.5)
The resulting files were filtered using SAMtools (version 0.1.18) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9)
To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scalling factor, we employed library size estimates determined using the R/Bioconductor (release 2.11) package DESeq85. Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Correction for false positives is included in the statistical analysis of gene expression through DESeq.
Genome_build: gadMor2_annotation_complete.gff.gz
Supplementary_files_format_and_content: FG1818_All_mapped_reads_2.xlsx; Scores represent counts

organism: Gadus morhua

source_name: Liver

extract_protocol:
Liver samples placed in 1.5 mL tubes containing Lysis Solution and 2-mercaptoethanol were homogenized by TissueLyser II (Qiagen, USA). Total RNA was extracted using RTN350 (Sigma-Aldrich), according to the manufacturer’s instruction and subsequently, DNase treated with DNase I (Thermo Scientific, USA)
Quality and integrity of the total RNA were checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent, Amstelveen, Netherlands). Illumina RNAseq libraries were prepared from 500 ng total RNA using the Illumina TruSeqTM Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions (Illumina Inc. San Diego, CA, USA).

tag: infection

value: Contracaecum osculatum


title: TAK_2031-S_pombe_HydEn-seq_cdc20-M630F_rnh201_RNaseHII

value: cdc20-M630F rnh201delta


title: TAK_2013-S_pombe_HydEn-seq_rnh201_NT

value: NT (non-treatment control)


title: C. crescentus ΔspdR replicate 1


title: TAK_2012-S_pombe_HydEn-seq_cdc6-L591G_rnh201_NT


title: Infected 9


title: Infected 8


title: Wild type C. crescentus replicate 2

value: wild type CB15


title: Wild type C. crescentus replicate 3


title: Infected 7


title: Cuticle Control1


title: TAK_2011-S_pombe_HydEn-seq_cdc6-L591G_rnh201_NT


title: Infected 6


title: TAK_2010-S_pombe_HydEn-seq_cdc20-M630F_rnh201_NT


title: TAK_1968-S_pombe_HydEn-seq_cdc6-L591G_rnh201_NT


title: TAK_1967-S_pombe_HydEn-seq_cdc6-L591G_rnh201_NT


title: C. crescentus ΔspdR replicate 2


title: Infected 5


title: Infected 3


title: Infected 4


title: Infected 2


title: TAK_1966-S_pombe_HydEn-seq_cdc20-M630F_rnh201_NT


title: TAK_1961-S_pombe_HydEn-seq_cdc6-L591G_rnh201_NT


title: Control 10

value: control


title: Control 9


title: Infected 1


title: TAK_1960-S_pombe_HydEn-seq_cdc6-L591G_rnh201_NT


title: 40%C_2h rep3

city: Wuhan

first: Juanping

last: Wang

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to THN1 whole genome using bowtie v2.3.4.3
mRNA abundance was estimated by the number of uniquely mapped reads per kilobase per million reads (RPKM) method
Genome_build: Novosphingobium sp. THN1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Novosphingobium sp. THN1

source_name: cells

growth_protocol: Cells were grown in R2A medium and 40%C R2A medium

extract_protocol:
RNA was extracted from filters using an E.Z.N.A. Bacterial RNA kit (Omega) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCLR was then spiked into the culture at a final concentration of 1.5 mg/ L. The three main carbon ingredients of R2A medium were reduced to 40% as carbon reduction treatment.

value: 2h after MCLR treatment under 40%C R2A medium


title: Control 7


title: 40%C_2h rep2


title: Control 8


title: 40%C_2h rep1


title: TAK_1959-S_pombe_HydEn-seq_cdc20-M630F_rnh201_NT


title: Control 5


title: TAK_1950-S_pombe_HydEn-seq_rnh201_RNaseHII

value: RNaseHII


title: Wild type C. crescentus replicate 1


title: Control 6


title: TAK_1953-S_pombe_HydEn-seq_cdc6-L591G_rnh201_RNaseHII


title: Control 4


title: 100%C_2h rep3

value: 2h after MCLR treatment under 100%C R2A medium


title: MBE02 rep 2

city: Bhavnagar

first: Sandeep

last: Sharma

state: Gujarat

address: Waghawadi Road

department: Department of Biotechnology & Phycology

country: India

institute: CSIR-CSMCRI

data_processing:
Clean reads were obtained by eliminating the adapter sequences, ambiguous reads (reads with unknown nucleotides “N” larger than 5%), and low-quality sequences (reads with more than 10% quality threshold (QV) < 20 phred score) than 10% quality threshold (QV) < 20 phred score) were eliminated
To generate peanut reference transcriptome sequence, reads were aligned to the genome of peanut progenitors, A. duranensis (A genome) and A. ipaensis (B genome) (Bertioli et al, Nature Genetics 48, 438-446, 2016) , using Tophat  and, aligned sequences were assembled with trinity using genome guided strategy as described by Clevenger et al, Fontiers in Plant Science 7, 1446 (2016); Peng, Z et al Sci. Rep. 7, 40066 (2017)
Differential expression analysis was performed between control and MBE02-treated  samples by employing a negative binomial distribution model in DESeq package
Supplementary_files_format_and_content: Counts and differential expression

organism: Arachis hypogaea

source_name: Peanut, MBE02-treated

growth_protocol: Peanut seeds were germinated and grown in half MS medium for 12 days before treating with the rhizobatceria treatment

extract_protocol:
Total RNA was extratced with Plant RNAeasy mini kit with DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 12 days of growth, peanuts were treated with MBE02 rhizobacteria (1x10e6 cells/ml) and roots were collected after one week

value: rhizobacteria MBE02

value: Roots


title: TAK_1964-S_pombe_HydEn-seq_rnh201_NT


title: TAK_1947-S_pombe_HydEn-seq_cdc6-L591G_rnh201_RNaseHII


title: 100%C_2h rep1


title: TAK_1946-S_pombe_HydEn-seq_cdc6-L591G_rnh201_RNaseHII


title: MBE02 rep1


title: Control 3


title: Control 2


title: 100%C_0h rep3

value: 0h after MCLR treatment under 100%C R2A medium


title: TAK_1954-S_pombe_HydEn-seq_cdc6-L591G_rnh201_RNaseHII


title: Control rep2

source_name: Peanut, untreated


title: TAK_1957-S_pombe_HydEn-seq_rnh201_NT


title: Control rep1


title: Control 1


title: 100%C_0h rep2


title: TAK_1945-S_pombe_HydEn-seq_cdc20-M630F_rnh201_RNaseHII


title: TAK_1943-S_pombe_HydEn-seq_rnh201_RNaseHII


title: TAK_1952-S_pombe_HydEn-seq_cdc20-M630F_rnh201_RNaseHII


title: 100%C_2h rep2


title: 100%C_0h rep1


title: pBKSM

status: Public on Jan 29 2019

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

data_processing:
Paired-end sequencing reads were mapped to mm10 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: induced neural stem cell

growth_protocol: Mouse embryonic fibroblasts(MEFs) were derived from genetically modifed mouse embryos at embryonic day 13.5 after carefully removing the head and all the internal organs including the spinal cord. Control neural stem cell(cNSCs) were extracted from cerebral cortex of embryo at embryonic day 13.5. induced iNSCs were generated by using polycistronic vector or monocistronic vector. MEFs were infected with lentivirus or retrovirus and induced with neural stem cell medium.

extract_protocol:
RNA-Seq experiments with pooled RNA samples extracted from 2-3 biological replicates
Libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6-Pou5f1 x 129X1/SvJ

value: Embryonic fibroblast


title: pOKSM


title: cNSCs

source_name: neural stem cell

value: OG2/ROSA26 heterozygous female mice

value: Brain


title: MEFs

source_name: Mouse fibroblasts


title: mcBKSM_clone_3


title: DTA_iNSCs

value: Unknown

value: Oct4-CreER x Rosa26-loxSTOPlox-DTA mouse


title: Healthy Control 6

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were trimmed with trimmomatic to remove adapters and aligned to hg19 genome with Hisat2 aligner in transcriptome mode.
PCR duplicates were removoved with Picard tools Mark Duplicates
Read count on genes was performed with htseq-count
The counts were used for differential expression analysis using DeSeq2 R package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes DESEQ2 normalized values for each Sample. Only expressed genes with normalized count > 1 in atleast 4 samples were retained for further differential expression analaysis

source_name: Skin

extract_protocol:
Total RNA was isolated from each tissue sample using the RNeasy Plus Universal kit (Qiagen, Valencia, USA) as per the manufacturer’s protocol and instructions
Stranded whole transcriptome sequencing using the Sureselect Stranded RNAseq kit from Agilent and Ribozero Gold kit from Illumina

value: Skin

tag: disease

value: Healthy Control


title: Healthy Control 2


title: Case 6

value: frontal fibrosing alopecia


title: Healthy Control 3


title: Healthy Control 1


title: Case 4


title: Healthy Control 5


title: Case 7


title: Healthy Control 7


title: Case 3


title: Healthy Control 4


title: Case 5


title: Case 2


title: Case 1


title: LDN SH rep 2

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

description:
Index sequence: TAGCTT
Lane: 2
processed data files:
LDN-readCounts.txt
LDN-FPKMs.txt

data_processing:
Sequence reads were aligned to the mm10 mouse reference genome sequence using tophat version 2.0.12 running Bowtie2-2.2.3.
Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to tophat during the alignment step
The aligned reads were sorted using samtools-0.1.19, then read counts per gene were obtained from mapped reads using HTSeq-0.6.0
EdgeR version 3.8.6 (using limma-3.22.7) in R-3.1.1 was used to identify differentially expressed genes.
Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file of sequencing read counts per gene
Supplementary_files_format_and_content: tab-delimited txt file represents the normalized expression data as FPKM, produced by EdgeR

source_name: DRG

extract_protocol:
For whole DRG, RNA was extracted using RNeasy kit (Qiagen), according to manufacturer’s guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 7.5 was used for library preparation. For Large diameter DRG neurons, laser capture microdissection was performed to select for neurons with diameter of at least 30 microns. RNA was extracted using Arcturus PicoPure RNA isolation kit (Life Technologies), following manufacturers protocol. RNA concentrations and quality were measured using Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor between 6 and 7 were used for library preparation.
For whole DRG, libraries were generated using the TruSeq mRNA Sample Preparation Kit  (Illumina, San Diego CA) at Ospedale San Raffaele according to the Sample Preparation Guide protocol. Ligation and library integrity was verified using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent). Sample libraries ligated with unique adapter sequences were multiplexed and were sequenced using Illumina HiSeq 2500 100-cycle, pair end sequencing.  For laser captured DRGs, libraries were prepared using the RiboZero ScriptSeq V2 kit working from the low input protocol using 100 ng of RNA per sample.  Libraries were sequenced using Illumina HiSeq 2500 generating 125 bp, paired end reads

treatment_protocol: Mice (5-8 weeks old)  were housed for 10 days in EE vs SH.

value: Large Diameter Neurons from DRG

value: 5-8 weeks old

tag: environment

value: Standard Housing (SH)


title: LDN EE rep 3

description:
Index sequence: ACTTGA
Lane: 3
processed data files:
LDN-readCounts.txt
LDN-FPKMs.txt

value: Environmental Enrichment (EE)


title: LDN SH rep 3

description:
Index sequence: GGCTAC
Lane: 3
processed data files:
LDN-readCounts.txt
LDN-FPKMs.txt


title: LDN EE rep 2

description:
Index sequence: CAGATC
Lane: 3
processed data files:
LDN-readCounts.txt
LDN-FPKMs.txt


title: LDN EE rep 1

description:
Index sequence: TTAGGC
Lane: 1
processed data files:
LDN-readCounts.txt
LDN-FPKMs.txt


title: EE rep3

description:
Index sequence: ACTGAT
Lane: 6
processed data files:
WholeDRG-readCounts.txt
WholeDRG-FPKMs.txt

value: whole DRG


title: LDN SH rep 1

description:
Index sequence: GATCAG
Lane: 3
processed data files:
LDN-readCounts.txt
LDN-FPKMs.txt


title: EE rep2

description:
Index sequence: GTGGCC
Lane: 5
processed data files:
WholeDRG-readCounts.txt
WholeDRG-FPKMs.txt


title: SH rep3

description:
Index sequence: CGTACG
Lane: 6
processed data files:
WholeDRG-readCounts.txt
WholeDRG-FPKMs.txt


title: mcBKSM_clone_1


title: SH rep1

description:
Index sequence: ATCACG
Lane: 4
processed data files:
WholeDRG-readCounts.txt
WholeDRG-FPKMs.txt


title: EE rep1

description:
Index sequence: ACTTGA
Lane: 4
processed data files:
WholeDRG-readCounts.txt
WholeDRG-FPKMs.txt


title: DKO_Treg_1

city: New York

first: Stefan

last: Feske

address: 550 First Avenue

institute: New York University School of Medicine

data_processing:
Base calling and demultiplexing were performed using the Illumina bcl2fastq software v1.8.4
Sequenced reads were mapped to the mm10 reference genome using STAR/2.7
Feature counts 1.22.2 was used to generate the matrix of read counts for annotated genomic features
The DESeq2 package (Bioconductor v3.3.0) in the R statistical programming environment was utilized to calculate differential gene statistical comparisons
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing normalized matrix of read counts which includes values for all features and all samples

source_name: DKO Treg unstim

growth_protocol: FACS-sorted cells, some CD4+CD25hi Treg cells; unstimulated and stimulated for 16 h in vitro with 1 ug/ml plate bound anti-CD3/CD28 in fully complemented RPMI

extract_protocol:
RNA was extracted using the Quiagen MicroRNAeasy kit with Dnase I digestion
Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101) was used with 100ng of input RNA for the construction of sequencing libraries

treatment_protocol: unstimulated or 16 h in vitro stimulation with 1 ug/ml plate bound anti-CD3/CD28

tag: cells

value: Foxp3+CD25+ Treg cells

value: Stim1 fl/f Stim2 fl/fll Foxp3-YFPcre


title: WT_Treg_3

source_name: WT Treg unstim

value: WT


title: DKO_Treg_16h-2

source_name: DKO Treg 16h anti-CD3/CD28


title: DKO_Treg_2


title: WT_Treg_16h-2

source_name: WT Treg 16h anti-CD3/CD28


title: DKO_Treg_16h-1


title: WT_Treg_16h-1


title: CNs 6h rep2

first: Soojin

last: Shim

address: Kwan-ak ro

institute: Seoul National University

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat.
Gene expression level was measured with Cufflinks v2.1.1 using the gene annotation database of the species. To improve the accuracy of the measurement, multi-read-correction and frag-bias-correct options were applied. All other options were set to default values.
Differential expression analysis was performed by Cuffdiff. To enhance the analysis accuracy, multi-read-correction and frag-bias-correct options were applied. All other options were set to default values. DEGs were identified based on the qvalue threshold less than 0.05 for correcting errors caused by multiple-testing.
Genome_build: ENSEMBL ver.77 (GRCm38 / mm10)
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: NALT_CNs 6h

extract_protocol:
NALT was removed and RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/C

value: post natal week 6

value: CNs 6h

value: Nasal-associated lymphoid tissue (NALT)


title: CNs 12h rep2

source_name: NALT_CNs 12h

value: CNs 12h


title: TF 6h rep1

source_name: NALT_TF 6h

value: TF 6h


title: CNs 6h rep1


title: PBS 6h rep2

source_name: NALT_PBS 6h

value: PBS 6h


title: TF 6h rep2


title: PBS 12h rep1

source_name: NALT_PBS 12h

value: PBS 12h


title: MDH 6h rep2

source_name: NALT_MDH 6h

value: MDH 6h


title: MDH 12h rep2

source_name: NALT_MDH 12h

value: MDH 12h


title: MDH 1h rep2

source_name: NALT_MDH 1h

value: MDH 1h


title: WT_Treg_4


title: MDH 12h rep1


title: TF 12h rep2

source_name: NALT_TF 12h

value: TF 12h


title: MDH 1h rep1


title: CNs 12h rep1


title: PBS 6h rep1


title: PBS 12h rep2


title: TF 12h rep1


title: MDH 6h rep1


title: TF 1h rep2

source_name: NALT_TF 1h

value: TF 1h


title: SH rep2

description:
Index sequence: TAGCTT
Lane: 5
processed data files:
WholeDRG-readCounts.txt
WholeDRG-FPKMs.txt

value: whole DRG

value: 5-8 weeks old

value: Standard Housing (SH)


title: TF 1h rep1


title: CNs 1h rep2

source_name: NALT_CNs 1h

value: CNs 1h


title: PBS 1h rep2

source_name: NALT_PBS 1h

value: BALB/C

value: PBS 1h


title: PBS 1h rep1

value: post natal week 6


title: SUM159 WT

city: Ann Arbor

first: Yu-Chih

last: Chen

state: MI

address: 1301 Beal Ave.

institute: University of Michigan

data_processing:
Bowtie and Tophat read aligner
Cufflink
Cuffdiff
Genome_build: hg19 genome
Supplementary_files_format_and_content: Cuffdiff output to compare the gene expression between wild-type and PAI1 altered SUM159 cells

source_name: Breast cancer cell line

growth_protocol: SUM159 cells were cultured in F-12 media supplemented with 10% fetal bovine serum, 1% Pen/Strep, 1% Glutamine, 5 μg/mL hydrocortisone, and 1 μg/mL insulin.

extract_protocol:
Total RNA was extracted using the RNeasy kit from QIAGEN following the manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We cloned human full-length PAI1 fused to NanoBiT (Promega) with a Tev-cleavable linker into the pLVX-Puro vector (ClonTech) (PAI1) and verified products by sequencing. We produced recombinant lentiviral vectors and transduced target cells. We subsequently transduced cells with the PAI1 viral vector and used puromycin selection for cells stably expressing PAI1. We confirmed expression of PAI1 in these cells through qRT-PCR and luminescence of NanoBiT.

tag: cell line

value: SUM159 breast cancer cell line

value: WT


title: Wandering_larvae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep2

city: Cardiff

first: Kevin

middle: van der

last: Graaf

address: Museum Avenue

department: Cardiff School of Biosciences

institute: Cardiff University

data_processing:
Data analysis was done via the webbrowser GenePattern. Reads were mapped to the reference genome Dm3 (UCSC) with Bowtie 1.1.1. The tuxedo suite v2.0.2 was used to process the mapped reads through Cufflinks, Cuffmerge and Cuffdiff. The data from Cuffdiff was imported to excel and contained the significant changes in transcript expression, splicing, and promoter use. All programs used their default settings in GenePattern for analysis.
The gene expression was calculated in FPKM values during Cuffdiff analysis.
Genome_build: Dm3 (UCSC)
Supplementary_files_format_and_content: Excel files

organism: Drosophila melanogaster

source_name: Whole larvae

growth_protocol: Larvae were maintained in standard food vials containing cornmeal, yeast, dextrose and plant agar. Proprionic acid and Nipagen (10% p-hydroxy benzoic acid methyl ester) were added as anti-microbial and anti-fungal, respectively.

extract_protocol:
RNA was extracted with Trizol reagent. ScriptSeq RNA-Seq Library preparation Kit (Illumina) was used with 0.5ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. All samples were 100bp paired-end sequenced on an Illumina HiSeq 2500 using standard mode.

treatment_protocol: Larvae were put in vial that contained 0.05% bromophenol blue added to the food. Wandering larvae were 3rd instar larvae with blue guts, stationary larvae were stationary and had either clear guts or light blue-ish guts and white prepupae were in the first hour of the pupa phase with a white pupal case.

value: Whole larvae

value: yw

value: Wandering larvae


title: White_Prepupae-w1118_Rep2

value: White prepupae


title: Stationary_larvae-w1118_Rep1

value: Stationary larvae


title: White_Prepupae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep3


title: Wandering_larvae-w1118_Rep2


title: White_Prepupae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep1


title: Stationary_larvae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep3


title: White_Prepupae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep2


title: Wandering_larvae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep1


title: Nxt1 DG05102/Nxt1 Z2-0488_rep3

description:
gene_exp_diff.xls
gene_intron_list.xlsx

data_processing:
Reads were mapped to reference genome r6.13 (FlyBase) with BDGP6.87 as GTF file using TopHat v2.1.1 with Bowtie v1.1.1. The mapped reads were then processed with the tuxedo suite v2.2.1 through Cufflinks, Cuffmerge, CuffQuant and Cuffdiff. The output of Cuffdiff was imported to excel for further analysis. All programs used their default setting for analysis.
Genome_build: r6.13 (FlyBase)
Supplementary_files_format_and_content: Excel files

source_name: Larval carcass

extract_protocol:
3rd instar stationary larvae were dissected in a magnetic chamber and all internal tissues were removed. The larval carcasses were put in PBS and flash frozen in liquid nitrogen. RNA was extracted with Trizol reagent. TruSeq Stranded mRNA Library Prep (Illumina) was used with 0.5ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Larvae were put in vial that contained 0.05% bromophenol blue added to the food. Stationary larvae were typically stationary and had white or light blue-ish guts.

value: Larval carcass

value: 3rd instar stationary larvae


title: Nxt1 DG05102/Nxt1 Z2-0488_rep2

description:
gene_exp_diff.xls
gene_intron_list.xlsx


title: White_Prepupae-w1118_Rep1


title: Wandering_larvae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep3


title: Stationary_larvae-w1118_Rep2


title: Stationary_larvae-w1118_Rep3


title: Wandering_larvae-w1118_Rep1


title: Wandering_larvae-w1118_Rep3


title: w1118_rep2

description:
gene_exp_diff.xls
gene_intron_list.xlsx


title: w1118_rep3

description:
gene_exp_diff.xls
gene_intron_list.xlsx


title: CNs 1h rep1

value: Nasal-associated lymphoid tissue (NALT)


title: Chicken Replicate 3

city: New Haven

first: Viktor

last: Feketa

state: CT

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University

description: Chicken

data_processing:
Primary analysis performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.36 (Bolger et al., 2014) with default parameters
Filtered high-quality reads from all samples were aligned to both duck and chicken reference genomes using STAR aligner v2.5.4b with default parameters (Dobin et al., 2013).
Aligned reads were counted by featureCounts program within the Subread package v1.6.2 with default parameters (Liao et al., 2014).
Raw read counts were processed and converted to “reads per kilobase gene length per million mapped reads” (RPKM) values by EdgeR v3.22.3 (Robinson et al., 2010).
To compare gene expression estimates between samples from different species, gene lists and corresponding RPKM values from duck and chicken gene annotations were merged based on the common gene symbol.
Supplementary_files_format_and_content: Raw read counts were processed and converted to “reads per kilobase gene length per million mapped reads” (RPKM) values by EdgeR v3.22.3. RPKM values from 3 biological replicates within each species were averaged and reported in the final data table. To compare gene expression estimates between samples from different species, gene lists and corresponding RPKM values from duck and chicken gene annotations were merged based on the common gene symbol. To maximize the number of matching gene symbols between annotations from different species, gene symbols from the NCBI annotation were converted to consensus gene symbols using the following gene ID conversion databases: DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/home.jsp), Ensembl databases of gene orthologs (www.ensembl.org), and the NCBI gene symbol synonyms database (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz). In case of gene orthologs with a common gene symbol between duck and chicken annotations, final count data for samples from all duck species comes from reads aligned to the duck genome, while count data for samples from chicken comes from reads aligned to the chicken genome. In case of genes without a matching gene ortholog in the other annotation (i.e. for duck genes without an ortholog in chicken, and vice versa), final count data for all samples comes from reads aligned to the corresponding genome only (i.e. only to duck genome in case of duck genes). The final data table (in .xlsx format) contains averaged RPKM values for each sample for each gene in the merged gene annotation as described above. Description of final data table columns: GeneSymbol_Consensus: a common gene symbol after merging duck and chicken annotations; GeneSymbol_Duck: original gene symbol from the annotation (.gff file) for duck genes; NCBI_Gene_ID_Duck: corresponding Gene ID from NCBI Gene Database; GeneSymbol_Chick: original gene symbol from the annotation for chicken genes; NCBI_Gene_ID_Chick: corresponding Gene ID from NCBI Gene Database; SourceGenome: source of data values for a particluar gene as described in the merging strategy (i.e. from reads aligned to the Duck or Chicken genome, or both, depending on whether the common gene symbol was present in the annotations). S1-S7_rpkms (Species): average RPKM values over 3 replicate samples for the given species.

organism: Gallus gallus

source_name: Trigeminal Ganglion

growth_protocol: Eggs of bird species were incubated at 37°C and 55%-75% humidity. Embryos were extracted for dissection when they had broken through the inner shell membrane (24-48 hrs before hatching)

extract_protocol:
Trigeminal ganglia were dissected from embryos, flash-frozen and stored at -80°C until RNA isolation. Total RNA was isolated from the stored trigeminal ganglia using the TRIzol reagent (ThermoFisher, Waltham, MA) according to manufacturer’s instructions. RNA quality and integrity was confirmed by running on Agilent Bioanalyzer, with RINs in the range of 7.7-8.6.
mRNA was purified from ~500 ng total RNA with oligo-dT beads. Strand-specific sequencing libraries were prepared using the KAPA mRNA Hyper Prep kit (Roche Sequencing, Pleasanton, CA).

value: Embryonic Day 19-21


title: SUM159 PAI1

value: PAI1 transfected


title: Stationary_larvae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep2


title: White_Prepupae-w1118_Rep3


title: w1118_rep1

description:
gene_exp_diff.xls
gene_intron_list.xlsx


title: Stationary_larvae-Nxt1 DG05102 / Nxt1 Z2-0488_Rep1


title: Nxt1 DG05102/Nxt1 Z2-0488_rep1

description:
gene_exp_diff.xls
gene_intron_list.xlsx


title: SWAN-71 HGF 24 h

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

address: Aruna Asaf Ali Marg

institute: NAtional Institute of Immunology

data_processing:
CLC Genomics Workbench 6.5.1. software used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to Human mature miRNA (miRBase release 21) accounting for a maximum of two gaps or mismatches in each sequence.
Unpaired group comparisons, based on Transcript Per Million (TPM), were chosen as expression values for comparison.
Kal’s Z test statistical analyses, based on p value < 0.05, fold change ± 1.5 and read count > 10 were used to filter the differentially expressed miRNA.
Genome_build: Human mature miRNA (miRBase release 21)
Supplementary_files_format_and_content: tab-delimited text files which include read count, normalized count and p-value for each Sample.

source_name: SWAN-71 cells

growth_protocol: SWAN-71 cells were grown in DMEM  supplemented with 10 % FBS.

extract_protocol:
total RNA was isolated using standard Trizol reagent. TruSeq Small RNA sample prep kit was used with 1µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation protocol

treatment_protocol: SWAN-71 cells were starved for 4h in  DMEM  plain medium and treated with 50 ng/ml HGF for 24 h. Control SWAN-71 cells were kept in  DMEM  plain medium for 24 h.

value: SWAN-71 cell line (telomerase immortalized first-trimester trophoblast cells)

value: trophoblast

value: HGF 24 h


title: SWAN-71 untreated2

value: untreated


title: SWAN-71 IFN-gamma 24 h

treatment_protocol: SWAN-71 cells were starved for 4h in  DMEM  plain medium and treated with 10 ng/ml IFN-gamma for 24 h. Control SWAN-71 cells were kept in  DMEM  plain medium for 24 h.

value: IFN-gamma 24 h


title: HTR-8/SVneo untreated RNA

data_processing:
CLC Genomics Workbench 6.5.1. software used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to Human Genome GRCH37.p.13 accounting for a maximum of two gaps or mismatches in each sequence.
Unpaired group comparisons, based on Reads per Kilobase per Million (RPKM), were chosen as expression values for comparison.
Kal’s Z test statistical analyses, based on p value < 0.05, fold change ± 1.5 and read count > 10 were used to filter the differentially expressed mRNA.
Genome_build: Human Genome GRCH37.p.13
Supplementary_files_format_and_content: tab-delimited text files which include read count, normalized count and p-value for each Sample.

source_name: HTR-8/SVneo cells

growth_protocol: HTR-8/SVneo cells were grown in 1:1 DMEM + HAM's supplemented with 10 % FBS.

extract_protocol:
total RNA was isolated using standard Trizol reagent. TruSeq RNA Library Prep Kit v2 was used with 1µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq  RNA Sample Preparation protocol

treatment_protocol: HTR-8/SVneo cells were starved for 4h in 1:1 DMEM + HAM's F12 plain medium and treated with 10 ng/ml IFN-gamma for 24 h. Control HTR-8/SVneo cells were kept in 1:1 DMEM + HAM's F12 plain medium for 24 h.

value: HTR-8/SVneo trophoblast cell line (SV40 T antigen immortalized)


title: SWAN-71 untreated


title: HTR-8/SVneo untreated

treatment_protocol: HTR-8/SVneo cells were starved for 4h in 1:1 DMEM + HAM's F12 plain medium and treated with 50 ng/ml HGF for 24 h. Control HTR-8/SVneo cells were kept in 1:1 DMEM + HAM's F12 plain medium for 24 h.


title: SWAN71 EGF 24 h

source_name: SWAN71 cells

treatment_protocol: SWAN-71 cells were starved for 4h in  DMEM  plain medium and treated with 10 ng/ml EGF for 24 h. Control SWAN-71 cells were kept in  DMEM  plain medium for 24 h.

value: SWAN71 cell line (telomerase immortalized first-trimester trophoblast cells)

value: EGF 24 h


title: SWAN71 untreated


title: HTR-8/SVneo HGF 24 h


title: Input_ChIPseq_1

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drive, CCSR 2145c

institute: Stanford University

data_processing:
bowtie used for alignment.
peaks called using MACS
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: TetO-TFAP2C hESC differentiation at Day7 with Dox

growth_protocol: In vitro differentiation of TetO-TFAP2C H9 hESCs: To study the function of TFAP2C in surface ectoderm differentiation, TetO-TFAP2C H9 hESCs were induced with 2 mg/ml Doxycycline(Dox) in E6 medium without RA/BMP4 for 7 days. The resulting cells were imaged and collected for subsequent analysis.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared following the NEBNext protocol (NEBNext ChIP-Seq Library Prep kit Cat #E6240S/L)

value: early epidemal differentiated human emryonic stem cell (hESC)

tag: treatment and stage

value: early differentiaiton with Dox for 7 days

tag: chip antibody


title: 13_TFAP2C_ChIPseq

value: TFAP2C; Santa Cruz Cat #sc-8977X


title: Chicken Replicate 2

description: Chicken


title: 14_TFAP2C_ChIPseq


title: Input_ChIPseq_2


title: 10_H3K9m3_ChIPseq

value: H3K9m3; Abcam Cat #ab8898


title: 7_H3K4m1_ChIPseq

value: H3K4m1; Abcam Cat #ab8895


title: HTR-8/SVneo IFN-gamma 24 h

tag: tissue


title: 5_H3K4m3_ChIPseq

tag: cell type

value: H3K4m3; Active Motif Cat #39159


title: 8_H3K4m1_ChIPseq

tag: genotype


title: Chicken Replicate 1

description: Chicken


title: 3_H3K27m3_ChIPseq

value: H3K27m3; Active Motif Cat #39155


title: 1_H3K27ac_ChIPseq

value: H3K27ac; Active Motif Cat #39133


title: HTR-8/SVneo untreated2


title: 9_H3K9m3_ChIPseq


title: HTR-8/SVneo IFN-gamma 24 h RNA


title: 6_H3K4m3_ChIPseq


title: 2_H3K27ac_ChIPseq


title: seCLIP WT Ago2 IP

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

data_processing:
Library strategy: seCLIP
seCLIP libraries were analyzed by Illumina HiSeq 2000.
Identification of seCLIP clusters enriched against size-matched input (SMinput) were performed as previously described (Van Nostrand, E. L. et al., Nature methods 13, 508-514, (2016)). First, obtained sequences were processed for adaptor removal, and reads mapping to the repetitive elements were removed. Remaining reads were aligned to the mm9 reference genome assembly using STAR (v2.5.1b), and seCLIP clusters for IP samples were identified using CLIPper peak calling algorithm (https://github.com/yeolab/eclip) with the following parameters: --bonferrroni --superlocal --threshold binomial (Lovci, M. T. et al. Nat Struct Mol Biol 20, 1434-1442 (2013)). Finally, peak normalization vs SMinput was performed, and enriched seCLIP clusters were extracted.
Genome_build: mm9
Supplementary_files_format_and_content: Summary txt file includes the information of enriched seCLIP clusters above SM_input, including chromosome, start, end, log10(p-value seCLIP vs SMInput), log2(fold-enrichment in seCLIP vs SMInput), and strand.

source_name: primary chondrocytes

growth_protocol: Mouse primary rib chondrocytes were isolated from the frontal part of the lib cage of 7 day-old mice and cultured in standard culture conditions.

extract_protocol:
Mouse primary rib chondrocytes were UV-crosslinked and harvested.
seCLIP were performed in mouse wild-type and mutant primary chondrocytes using Ago2 and Ybx1 antibodies, as previously described (Van Nostrand, E. L. et al., Nature methods 13, 508-514, (2016)., Van Nostrand, E. L. et al. Methods Mol Biol 1648, 177-200, (2017).). Anti-Ago2 antibody (2D4), and anti-Ybx1 antibody (D2A11, #9744S) were from Wako and Cell Signaling Technology, respectively.

value: chondrocytes

tag: genotype and drug

value: miR-140 WT


title: seCLIP WT Ybx1 IP


title: Pekin duck Replicate 3

description: Pekin duck

organism: Anas platyrhynchos

value: Embryonic Day 25-26


title: seCLIP GG Ago2 IP

value: miR-140 G/G


title: seCLIP GG Ybx1 IP


title: Pekin duck Replicate 1

description: Pekin duck


title: Pekin duck Replicate 2

description: Pekin duck


title: Control3

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC，including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database，Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Supplementary_files_format_and_content: tab-delimited text files includeTPM values for each Sample

source_name: Hemolymph

extract_protocol:
Hemolymph were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Approximately 10 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hemolymph

value: control


title: Control1


title: ApNPV1

value: ApNPV


title: ApNPV2


title: Ruddy duck Replicate 3

description: Ruddy duck

organism: Oxyura jamaicensis

value: Embryonic Day 30-31


title: Control2


title: Ruddy duck Replicate 1

description: Ruddy duck


title: Ruddy duck Replicate 2

description: Ruddy duck


title: Wood duck Replicate 3

description: Wood duck

organism: Aix sponsa

value: Embryonic Day 28-31


title: Wood duck Replicate 2

description: Wood duck


title: Harlequin duck Replicate 3

description: Harlequin duck

organism: Histrionicus histrionicus

value: Embryonic Day 28-29


title: Q_M

organism: Quercus mongolica

source_name: Leaf

extract_protocol:
The  leaves of Q. mongolica were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Approximately 10 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf


title: Lesser Scaup Replicate 3

description: Lesser Scaup

organism: Aythya affinis


title: Harlequin duck Replicate 1

description: Harlequin duck


title: Lesser Scaup Replicate 1

description: Lesser Scaup


title: Lesser Scaup Replicate 2

description: Lesser Scaup


title: Harlequin duck Replicate 2

description: Harlequin duck


title: Q_L

organism: Quercus wutaishanica

extract_protocol:
The  leaves of Q. liaotungensis were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Approximately 10 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Black duck Replicate 3

description: Black duck

organism: Anas rubripes

value: Embryonic Day 21-22


title: PF_D3

city: Shenyang

first: Li

last: Xue

address: Dongling Road No. 120

institute: Shenyang Agricultural University

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

organism: Fragaria x ananassa

source_name: Pink-flowered strawberry

extract_protocol:
RTotal RNA was extracted using a modified CTAB method, and treated with RNase-free DNase I (Takara, Dalian, China) to remove genomic DNA contamination. The total RNA quantity and purity were detected by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. The mRNA-seq sample preparation kit (Illumina, San Diego, USA) was used with 10 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: petal


title: Black duck Replicate 2

description: Black duck


title: ApNPV3


title: Black duck Replicate 1

description: Black duck


title: PF_D2


title: WT + apicidin rep3

city: Aurora

first: Alexander

last: Horswill

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Paired-end reads mapped using SeqMan NGen version 14 (DNAStar).
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using ArrayStar version 14 (DNAStar).
Genome_build: CP000255.1
Supplementary_files_format_and_content: csv files containing total raw counts for each replicate and average RPKM values for each condition

organism: Staphylococcus aureus subsp. aureus USA300

source_name: WT + apicidin rep3

growth_protocol: S. aureus cultures were grown in a 48-well plate to an OD600 of 4 in tryptic soy broth supplemented with 1% DMSO (vehicle control) or 100 μM apicidin.

extract_protocol:
1 h lysis step with lysostaphin followed by RNA purification using Qiagen RNeasy Mini Kit.
rRNA depleted using Ribo-Zero rRNA Removal kit for Gram positive bacteria (Illumina) and libraries prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: 2 min treatment with RNAprotect (Qiagen).

tag: strain

value: wildtype

tag: treatment

value: apicidin


title: WT + apicidin rep1

source_name: WT + apicidin rep1


title: wild type, with 3-OH-C10-HSL, replicate 2

city: Seattle

first: Mitchell

middle: William

last: Pesesky

state: WA

address: 616 NE Northlake Place

institute: University of Washington

data_processing:
Alignment was performed using BWA version 0.7.12-r1044 using the BWA-MEM algorithm and default parameters.
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a.
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.6.1p1 in the ‘intersection-nonempty’ mode.
Differential abundance analysis was performed with DESeq2 1.2.10 using R 3.3.0.
Genome_build: CP033381
Supplementary_files_format_and_content: *.dat files are two columns: locus tag and read count. At the bottom of the file, a few summary read alignment statistics are given.

organism: Methylomonas sp. LW13

source_name: exponential phase culture

growth_protocol: Methylomonas sp. strain LW13 was cultured in an atmosphere of 25% methane in air. For routine culturing plates were incubated at room temperature in sealed jars (Oxoid Limited), while liquid cultures were grown at 18ºC in 250-ml glass serum bottles (Kimble Chase) or 18- by 150-mm tubes (Bellco Glass) sealed with rubber stoppers and aluminum seals (Wheaton) shaken at 200 rpm. Cultures were grown in nitrate mineral salts (NMS) medium (38) containing 0.2 g/L MgSO4·7H2O, 0.2 g/L CaCl2·6H2O, 1 g/L KNO3, and 30 µM LaCl as well as 1X trace elements. 500X trace elements contains 1.0 g/L Na2-EDTA, 2.0 g/L FeSO4·7H2O, 0.8 g/L ZnSO4·7H2O, 0.03 g/L MnCl2·4H2O, 0.03 g/L H3BO3, 0.2 g/L CoCl2·6H2O, 0.6 g/L CuCl2·2H2O, 0.02 g/L NiCl2·6H2O, and 0.05 g/L Na2MoO·2H2O. A final concentration of 5.8 mM phosphate buffer, pH 6.8 was added immediately before use.

extract_protocol:
Cell pellets were lysed by bead beating with 0.1-mm zirconia-silica beads (Biospec Products) in 1 mL TRIzol (Thermo Fisher Scientific). The lysate was then separated according to the TRIzol instructions, and subsequently 1.5 volumes of 100% ethanol was added to the aqueous phase of the extract which was then used as the input for an RNeasy RNA isolation kit (Qiagen). The resulting elution was then digested using Ambion DNase I (Thermo Fisher Scientific) for 30 minutes at 37ºC before being re-purified via RNeasy RNA isolation kit with the addition of an on-column DNase (Qiagen) digestion step for 15 minutes at room temperature. The resulting purified RNA was checked for DNA contamination by PCR using the universal 16S primers 27F and 1492R.
cDNA library preparation and RNA sequencing were performed by GENEWIZ using Illumina HiSeq 2x150 (pair ended) reads.

treatment_protocol: Growing cultures of Methylomonas sp. strain LW13 were subdiluted to OD600nm 0.01 and added to bottles containing dried 3-OH-C10-HSL (or solvent control) resulting in a final concentration of 2 µM signal. RNA was extracted during log phase (OD600nm 0.4-0.6). Briefly, cultures were chilled on ice and then centrifuged at 5000 rpm for 15 minutes at 4ºC. Pellets were subsequently flash frozen in liquid nitrogen and stored at -80ºC until further processing.

value: wild type

value: with 3-OH-C10-HSL


title: PF_Z3


title: wild type, with 3-OH-C10-HSL, replicate 1


title: Δagr + DMSO rep3

source_name: Δagr + DMSO rep3

value: delta agr::tet

value: DMSO


title: Wood duck Replicate 1

description: Wood duck


title: wild type, no 3-OH-C10-HSL, replicate 1

value: no 3-OH-C10-HSL


title: Δagr + DMSO rep2

source_name: Δagr + DMSO rep2


title: WT + apicidin rep2

source_name: WT + apicidin rep2


title: wild type, no 3-OH-C10-HSL, replicate 2


title: Δagr + DMSO rep1

source_name: Δagr + DMSO rep1


title: mmsR-, with 3-OH-C10-HSL, replicate 2

value: mmsR-


title: PF_L3


title: mmsR-, with 3-OH-C10-HSL, replicate 1


title: PF_L2


title: mmsR-, no 3-OH-C10-HSL, replicate 2


title: WT + DMSO rep3

description:
LAC_vs_agr.csv
DMSO_vs_apicidin.csv

source_name: WT + DMSO rep3


title: WT + DMSO rep2

description:
LAC_vs_agr.csv
DMSO_vs_apicidin.csv

source_name: WT + DMSO rep2


title: mmsR-, no 3-OH-C10-HSL, replicate 1


title: PF_L1


title: PF_D1


title: WT + DMSO rep1

description:
LAC_vs_agr.csv
DMSO_vs_apicidin.csv

source_name: WT + DMSO rep1


title: NxC_SC1: nrpd1 x Col LCM Seed Coat Replicate 1

status: Public on Jan 28 2019

city: Austin

first: Z Jeffrey

middle: Jeffrey

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Collected via laser microdissection

data_processing:
Reads clipped to remove 3' Illumina TRUseq small RNA adapter. Reads under 15nt in length discarded
Bowtie 1.0 was ued to map reads against A. thaliana  TAIR10 ribosomal RNA sequences, allowing for no mismatches. Only non-mapping reads  24nt in length were retained
Reads mapped to the TAIR10 genome allowing for no mismatches. Genome was divided into 100bp bins, and scored to determine the number of mapped reads in each bin, with reads mapping to multiple genome positions  weighted based on the number of mapping positions.
Scaling factors for each sample were applied based on miRNA mapping distribution.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph

organism: Arabidopsis thaliana

source_name: Laser microdissected seed coat from seeds resulting from a cross between nrpd1 and Col-0

growth_protocol: All plants were grown under an illumination cycle of 16-h day and 8-h night at 22oC (day) and 20oC (night).

extract_protocol:
total RNA collected from LCM collection tubes using RNAqueous-Micro Kit
TruSeq Small RNA

treatment_protocol: Flowers in the floral stage 12C were manually emasculated and pollinated at 48 hours after emasculation.

value: Seed coat

tag: Stage

value: 6 Days After Pollination

tag: cross

value: nrpd1 x Col-0


title: NxC_ES4: nrpd1 x Col LCM Endsoperm Replicate 4

description: Collected via laser microdissection

source_name: Laser microdissected endosperm from seeds resulting from a cross between nrpd1 and Col-0

value: Endosperm


title: NxC_SC4: nrpd1 x Col LCM Seed Coat Replicate 4

description: Collected via laser microdissection


title: PF_Z2


title: NxC_ES1: nrpd1 x Col LCM Endsoperm Replicate 1

description: Collected via laser microdissection


title: CxN_ES4: Col x nrpd1 LCM Endsoperm Replicate 4

description: Collected via laser microdissection

source_name: Laser microdissected endosperm from seeds resulting from a cross between Col-0 and nrpd1

value: Col-0 x nrpd1


title: C9-TTR-SIG

status: Public on Jan 23 2019

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

data_processing:
Quality filtering was performed using cutadapt v. 1.7.1.
Reads were mapped against the human reference genome using the STAR aligner v.2.5.2a.
Read counts per gene were obtained using RSEM program v.1.2.31 and the Ensembl gtf annotation file.
Following analyses were performed using R. Differential expression analysis was performed with the limma v.3.34.5 and edger v.3.20.6 packages.
Genome_build: Ensembl gtf annotation file (release GRCh38.10)
Supplementary_files_format_and_content: *.genes.results: Tab-delimited text files include TPM and FPKM values for each Sample.

organism: Homo sapiens

source_name: Colon biopsies

extract_protocol:
Tissue RNA was isolated by RNeasy Kit (Qiagen, Spain) according to the manufacturer's instructions. RNA were quantified by NanoDrop spectrophotometer (NanoDrop Technologies, USA). The purity and integrity of the total RNA were assessed via 2100 Bioanalyzer (Agilent, Germany). All RNA samples analyzed had a RNA Integrity Number ≥ 7.
Barcoded RNA sequencing libraries were prepared from 100 ng total RNA using Illumina’s TruSeq stranded mRNA kit according to the manufacturer’s instructions.
Libraries were subjected to paired-end sequencing (101 bp) on a HiSeq-4000 platform (Illumina, San Diego, CA).

value: Healthy non-IBD

value: Colon biopsy

tag: week of hsct treatment

value: C

tag: hsct responder

tag: sescd global

tag: cdai

tag: Sex

value: female

tag: individual id


title: CxN_SC4: Col x nrpd1 LCM Seed Coat Replicate 4

description: Collected via laser microdissection

source_name: Laser microdissected seed coat from seeds resulting from a cross between Col-0 and nrpd1


title: PF_Z1

value: petal


title: C8-TTR-SIG

tag: disease


title: C6-TTR-SIG

value: male


title: CxN_SC1: Col x nrpd1 LCM Seed Coat Replicate 1

description: Collected via laser microdissection


title: C7-TTR-SIG


title: C7-TTR-CA


title: C9-TTR-CA


title: C6-TTR-CA


title: C5-TTR-CA


title: C4-TTR-SIG


title: C3-TTR-CA


title: C3-TTR-SIG


title: C4-TTR-CA


title: C20-TTR-SIG


title: C20-TTR-CA


title: C19-TTR-SIG


title: C19-TTR-CA


title: C18-TTR-SIG


title: C18-TTR-CA


title: C16-TTR-CA


title: C16-TTR-SIG


title: C17-TTR-SIG


title: C17-TTR-CA


title: C15-TTR-SIG


title: C11-TTR-SIG


title: C12-TTR-SIG


title: C15-TTR-CA


title: C14-TTR-SIG


title: C12-TTR-CA


title: CxN_ES1: Col x nrpd1 LCM Endsoperm Replicate 1

description: Collected via laser microdissection


title: C13-TTR-SIG


title: C14-TTR-CA


title: C1-TTR-CA


title: C10-TTR-CA


title: C10-TTR-SIG


title: C1-TTR-SIG


title: C11-TTR-CA


title: 36-T52-TTR-CII

description: Individual 33 and individual 36 refer to the same patient (but during a different phase of the treatment).

value: Crohn's disease (CD)

value: YES


title: 35-T52-TTR-CIA

description: Individual 29 and individual 35 refer to the same patient (but during a different phase of the treatment).

value: NO


title: 36-T26-TTR-CI


title: 35-T26-TTR-CIA


title: 29-S0-TTR-CIA


title: 23-T52-TTR-CII

description: Individual 15 and individual 23 refer to the same patient (but during a different phase of the treatment).


title: 23-T99-TTR-CIA


title: 23-T26-TTR-CII


title: 15-T52-TTR-CII


title: Input_MagoKD_Ser2P

status: Public on Jan 22 2019

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description:
Mago_Input
MNase-Seq and ChIP-Seq experiments share input samples
Input DNA sequencing Mago knockdown (Mago_Ab5095_1, Mago_Ab5095_2, Mago_Mnase_3 input control)
cell culture

data_processing:
The data was sequenced on a HiSeq2500 in a high output run with a readlength of  58 bp PE (TruSeq SBS Kit v3) .   Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Libraries were demultiplexed using 6 bp front tags. After sorting the tags were trimmed + the added T were trimmed (7 bp in total)
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalized bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol.  Custom adaptors with front tag were used in the protocol.

treatment_protocol: 1. S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.  2. MNase: S2R+ cells were fixed with 1% formaldehyde for 10 min at room temperature. Cells were harvested and 20 million nuclei were spun at 3,500 g at 4°C for 10 min. Nuclear Pellet was resuspended in 300 μl of MNase digestion buffer (0.5 mM spermidine, 0.075% NP40, 50 mM NaCl, 10mM Tris-HCl, pH 7.5, 5mM MgCl2, 1mM CaCl2, 1mM β‐mercaptoethanol and complete protease inhibitors). Reaction was spun at 3,200g, 4°C for 10 min and resuspended in 50 μl of MNase digestion buffer and digested with 30U of MNase at 37°C for 10 min at 300 rpm in mixing block. The MNase digestion reaction was quenched with EDTA at 10 mM final concentration. After 10 min on ice, the neclei were washed once with 1 ml of RIPA buffer (140 mM NaCl and complete protease inhibitors). Pellet was resuspended in 300 μl of RIPA buffer (140mM) and sonicated (3 cycles,medium intensity, 30 s on/off intervals) and centrifuged at 18,000g, 4°C for 10 min

value: none (Input DNA Mago Knockdown)

tag: cell line

value: S2R+ Cells

value: Embryonic


title: Input_controlKD_Ser2P

description:
WT_Input
MNase-Seq and ChIP-Seq experiments share input samples
Input DNA sequencing control knockdown (WT_mnase_3, WT_Ab5095_1, WT_Ab5095_2 input control)
cell culture

tag: chip antibody

value: none (Input DNA Ctrl Knockdown)


title: Control KD_Ser2P_Rep2

description:
WT_Ab5095_2
ChIP Seq of Ser2P Pol II in Ctrl Knockdown condition, Rep2
Cell Culture

value: anti Ser2P (Abcam, catalog# Ab5095, lot# GR154006)


title: Control KD_Ser2P_Rep1

description:
WT_Ab5095_1
ChIP Seq of Ser2P Pol II in Ctrl Knockdown condition, Rep1
Cell Culture


title: MagoKD_Ser2P_Rep2

description:
Mago_Ab5095_2
ChIP Seq of Ser2P Pol II in Mago Knockdown condition, Rep2
Cell Culture


title: 33-T52-TTR-CIA

tag: tissue


title: C8-TTR-CA


title: 233360

status: Public on Jan 18 2019

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Data quality was assessed using FastQC v.0.11.2
Trimmed reads were screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.3.7
RSeQC package v.2.6.1 was used to assess read distribution, positional read duplication and confirm strandedness of alignments
Raw trimmed reads were aligned to the reference genome hg19 using Tophat v.2.0.13
Tophat alignments were processed to extract raw read counts for genes using htseq-count v.0.5.4p2
Raw gene counts were loaded and sample-normalized using DESeq v.1.18.0
Differential analysis was performed also in edgeR v3.8.6
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq_count.txt
Supplementary_files_format_and_content: edgeR_merged_wRPKM_tn20150828_GLMM_20170614dm.txt: Differential expression results.

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using QIAGEN QIAsymphony DNA Midi kit.
RNA libraries were prepared using Illumina TruSeq RNA Sample prep kit V2

tag: task force

tag: harvesting time

value: VAL - ALL PHASES

tag: cohort

tag: post deployment time

tag: aggregatebatch

tag: phase

value: I

tag: ptsd diagnosis

tag: date processed

tag: gender

value: Male

tag: age group


title: 227283

value: VAL - June 2012 Samples


title: 212869

value: PET- June 2011 Samples

value: II


title: 233343


title: 233354


title: 219107

value: March, 2012

value: PET - March 2012 Samples

value: III


title: MagoKD_Ser2P_Rep1

description:
Mago_Ab5095_1
ChIP Seq of Ser2P Pol II in Mago Knockdown condition, Rep1
Cell Culture

tag: cell type


title: 233760


title: 226140


title: 219098


title: 233353


title: 233560


title: 212644


title: 233351


title: 233569

value: Female


title: 233570


title: 212656


title: 227286


title: 219104


title: 233568


title: 233759


title: 226146


title: 212713


title: 219101


title: 225655


title: 233355


title: 233340


title: 227280


title: 233358


title: 233348


title: 4_H3K27m3_ChIPseq

source_name: TetO-TFAP2C hESC differentiation at Day7 with Dox

value: early epidemal differentiated human emryonic stem cell (hESC)

tag: genotype

tag: treatment and stage

value: early differentiaiton with Dox for 7 days

value: H3K27m3; Active Motif Cat #39155


title: 212864


title: 233567


title: 233352


title: 233341


title: 233344


title: 225654


title: 212652


title: 233336


title: 226147


title: 219086


title: 227285


title: 233339


title: 225653


title: 233571


title: 212874


title: 233546


title: 227287


title: SNIP3

type: genomic

city: Beijing

first: Zheng

last: Yang

address: No.1 Dongjiaominxiang

institute: Beijing Tongren Hospital

description: sinonasal inverted papilloma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450K BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio V2011.1 Methylation Module 1.9.0

label: Cy5 and Cy3

source_name: Sinonasal

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: condition

value: SNIP


title: 227284


title: 233558


title: 226142


title: 225647


title: 227281


title: 227282


title: 227278


title: 233342


title: 212648


title: SCC arising in SNIP1

description: quamous cell carcinomas arising in SNIP

value: SCC arising in SNIP


title: SNIP1

description: sinonasal inverted papilloma


title: 233338


title: SCC arising in SNIP5

description: quamous cell carcinomas arising in SNIP


title: SCC arising in SNIP2

description: quamous cell carcinomas arising in SNIP


title: 219112


title: 233359


title: SNIP2

description: sinonasal inverted papilloma


title: 212640


title: SCC arising in SNIP4

description: quamous cell carcinomas arising in SNIP


title: 233349


title: 219092


title: 226143


title: 219095


title: SNIP6

description: sinonasal inverted papilloma


title: 212860


title: SNIP4

description: sinonasal inverted papilloma


title: SCC arising in SNIP3

description: quamous cell carcinomas arising in SNIP


title: 233356


title: 233350


title: 227279


title: SNIP5

description: sinonasal inverted papilloma


title: 212702


title: 233761


title: 219080


title: 233758


title: 233555


title: 219089


title: 233561


title: 212706


title: 212698


title: 233564


title: 219083


title: 227277


title: 226141


title: 226144


title: 233345


title: 20_Stat3C_IL23

status: Public on Jan 17 2019

data_processing:
Alignment to reference genome utiizing TopHat 2.1.1
Gene counting utilizing htseq 0.11.1
Count normalizing utilizing DESeq2/1.22.2
Genome_build: mm10
Supplementary_files_format_and_content: csv

organism: Mus musculus

source_name: in vitro differentiated pathogenic Th17 cells

growth_protocol: naïve CD4 T cells were stimulated with plate bound anti-CD3 and anti-CD28 in the presence of IL-6, IL-1b and IL-23 for 2 days

extract_protocol:
RNA was extracted using the Quiagen MicroRNAeasy kit with Dnase I digestion
Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101) was used with 100ng of input RNA for the construction of sequencing libraries

tag: strain

value: pathogenic Th17 cells

value: Stat3CSTOPfl/fl CD4-Cre


title: 24_S1S3_IL23

value: Stim1fl/fl Stat3CSTOPfl/fl CD4-Cre


title: 23_S1S3_IL23


title: 21_Stat3C_IL23


title: 22_S1S3_IL23


title: 19_Stat3C_IL23


title: FOXP1 ChIPseq in human tonsilar Germinal Center CD77+ B cells

status: Public on Jan 16 2019

first: Ashley

middle: Stephen

last: Doane

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg38, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg38 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg38 build
Supplementary_files_format_and_content: bigwig, bigbed, narrowPeak, and bed formats

source_name: Germinal Center CD77+ B cells

growth_protocol: cultured cells, IMDM+10%FBS

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with H3K27ac antibody (abcam 4729) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.
Libraries were prepared using the Illumina Truseq ChIPseq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

value: Primary tonsilar B cells

tag: chip antibody

value: FOXP1 (ab4729, Rabbit, 2 ug)


title: input DNA for FOXP1 ChIPseq in human tonsilar Naïve IgD+ B cells

source_name: Naïve IgD+ B cells

tag: tissue


title: 233540

tag: task force

value: VAL - ALL PHASES

value: Male


title: input DNA for FOXP1 ChIPseq in human tonsilar Germinal Center CD77+ B cells


title: PRO-Seq of 96 h infected flavopiridol-treated HFF (Towne)

city: Iowa City

first: David

middle: H

last: Price

state: Iowa

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.4.4
Alignment of trimmed reads to hg38 using bowtie 1.2 (retain unmapped reads; Towne samples: --trim5 4 and --trim3 4)
Alignment of unmapped reads to Genbank FJ616285.1 using bowtie 1.2
Towne samples: filter duplicate mapped reads with dedup (https://github.com/P-TEFb/dedup)
Generate bedgraphs using bedtools genomecov 2.26
Convert bedgraphs to bigwigs using kentUtils
Upload hg38-mapped tracks to UCSC genome browser
Upload HCMV-mapped tracks to a custom track hub (https://github.com/P-TEFb/trackHub_HCMV)
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, PRO-Cap pileups, or PRO-Cap 5' read positions
Supplementary_files_format_and_content: bigbed files were generated from bed files using kentUtils bedToBigBed program

molecule: nuclear RNA

source_name: human foreskin fibroblast

growth_protocol: HFF were kept at 100% confluence at least one week before infection.

extract_protocol:
All PRO-Seq and PRO-Cap protocols are detailed in the manuscript. Nuclei were rapidly isolated as described in Nilson, et al. 2017 (10.1093/nar/gkx724).
Please consult the manuscript, Nilson, et al. 2017 (10.1093/nar/gkx724), and Mahat, et al. 2016 (10.1038/nprot.2016.086).

treatment_protocol: Infection details are in the manuscript. As indicated, 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest.

tag: hcmv strain

value: Towne varS

tag: infection duration

tag: method

value: PRO-Seq


title: PRO-Seq of 96 h infected DMSO-treated HFF (Towne)


title: PRO-Seq of 4 h infected flavopiridol-treated HFF (TB40/E)

data_processing:
Adapter trimming using trim_galore 0.4.4
Alignment of trimmed reads to hg38 using bowtie 1.2 (retain unmapped reads)
Alignment of unmapped reads to Genbank FJ616285.1 using bowtie 1.2
Generate bedgraphs using bedtools genomecov 2.26
Convert bedgraphs to bigwigs using kentUtils
Upload hg38-mapped tracks to UCSC genome browser
Upload HCMV-mapped tracks to a custom track hub (https://github.com/P-TEFb/trackHub_HCMV)
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, PRO-Cap pileups, or PRO-Cap 5' read positions
Supplementary_files_format_and_content: bigbed files were generated from bed files using kentUtils bedToBigBed program

value: 4 h


title: PRO-Seq of uninfected DMSO-treated HFF (TB40/E)

value: uninfected


title: PRO-Seq of 4 h infected DMSO-treated HFF (TB40/E)


title: PRO-Cap of uninfected flavopiridol-treated HFF (Towne)

value: PRO-Cap


title: PRO-Seq of uninfected flavopiridol-treated HFF (Towne)


title: PRO-Cap of uninfected DMSO-treated HFF (Towne)


title: PRO-Cap of 96 h infected flavopiridol-treated HFF (Towne)


title: 233357

tag: harvesting time

tag: cohort

tag: post deployment time

tag: aggregatebatch

value: I