title: miRNA CR2, replicate 2

city: Orlando

first: Augusto

last: Schneider

state: FL

address: 6900 Lake Nona Blvd

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

data_processing:
IlluminaCasava1.8 software was used for basecalling; all reads use phred33 quality scores.
Sequence reads were processed using sRNAToolBox, available at: http://bioinfo5.ugr.es/srnatoolbox/. Reference: Rueda et al. (2015) - doi: 10.1093/nar/gkv555.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: rhemac8
Supplementary_files_format_and_content: tab-delimited text file include raw count values for each sample in separate columns.

organism: Macaca mulatta

source_name: Plasma

extract_protocol:
Total RNA was extracted from plasma using the miRNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma

tag: age

value: 26.13 years

value: male

tag: diet

value: 30% calorie restriction


title: ATAC_ctrl_D10_B

status: Public on Aug 04 2017

type: SRA

city: Saint Louis

first: Matthew

middle: James

last: McCoy

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

country: USA

institute: Washington University in St. Louis

description: Induced with non-specific miRNA for 10 days.

library_source: genomic

data_processing:
ATAC-seq reads were trimmed for Nextera adapter sequences using TrimGalore.
Trimmed ATAC reads were aligned to the hg19 genome assembly using bowtie2.
Duplicate reads were discarded with Picard and uniquely mapped reads were used.
Peaks in each sample were called using Homer findPeaks. Peaks called from all the samples were combined together.
Raw reads mapped on the combined peaks were counted using HTSeq-count.
Differential peaks were identified using edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: Human adult fibroblasts

growth_protocol: Human 22 yr adult fibroblasts (NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research, GM02171) were maintained in fibroblast media comprised of Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone), 0.01% β- mercaptoethanol (Life Technologies), 1% non-essential amino acids, 1% sodium pyruvate, 1% GlutaMAX, 1% 1M HEPES buffer solution and 1% penicillin/streptomycin solution (all from Invitrogen) and never passaged more than 15 times.

extract_protocol:
DNA fragments were collected by column-based purification after tagmentation.
ATAC-seq was performed as previously described (Buenrostro et al., 2013). Briefly, 50,000 cells were collected for ATAC-seq library preparation at Ctrl day 10, miNs day 10, miNs day 20, shBRG1 Day20 and shEGFP day 20. Transposition reaction was carried out with Nextera Tn5 Transposase for 30 min at 37 °C. Library fragments were amplified for optimal amplification condition. Final libraries were purified using AMPure XP beads (Ampure) and sequenced with 50 bp paired-end reads on Illumina HiSeq 2500 or 75 bp paired-end reads on Illumina NextSeq 500.

treatment_protocol: 1.8x10^6 cells were seeded onto Costar 6 well cell culture vessels (Corning; 300,000 cells/well). The following day, each plate was transduced with 10 ml of unconcentrated lentivirus containing a doxycycline inducible miR-9/9*-124 vector (Victor et al., 2014) or a non-specific microRNA control vector (miR-NS) and polybrene (8 μg/mL ; Sigma-Aldrich). The following day media was changed to fresh fibroblast media (2 mL per well) supplemented with Dox. After 2 days, fresh fibroblast media was changed and supplemented with Dox and antibiotics for respective vectors (see Table 1). Seven days post-transduction, cells were first washed 2x with 3 mL sterile PBS, then 1 ml of 0.25% Trypsin (Gibco) was added to each plate then placed in an incubator. Cells were monitored every 2 minutes, as soon as cells began to detach (no more than 6 minutes), 4 ml of MEF media supplemented with 1 μg/mL Dox was added to each plate. Cells were transferred to Primaria modified 10 cm plates (Corning) and 5 ml fresh fibroblast media supplemented with 1 μg/mL Dox was added to a final volume of 10 ml. The following day media was changed to Neuronal Media (Sciencell) supplemented with Dox, valproic acid (1 mM; EMD Millipore) dibutyryl cAMP (200 μM; Sigma-Aldrich), BDNF, and NT-3 (all 10 ng/ml, Peprotech), Retinoic Acid (1 uM; Sigma-Aldrich), and 4% FBS. Dox was replenished every two days and half the media was changed every 4 days.

tag: cell line

tag: cell type

value: adult fibroblasts

tag: treatment

value: non-specific miRNA

tag: timepoint


title: miRNA CR4, replicate 4

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: 25.22 years

tag: Sex


title: ATAC_ctrl_D10_A


title: ATAC_miNs_D10_A

description: Induced with miR-9/9*-124 for 10 days.


title: miRNA CR5, replicate 5

value: 25.26 years


title: miRNA CR1, replicate 1

value: 25.69 years


title: miRNA CO5, replicate 5

value: 26.31 years

value: Ad libitum diet


title: Sample 27_ZFG-16-08_11

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

description: processed data: DESeq_yellow_uninfected_vs_yellow_infected.xlsx

data_processing:
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (Anders et al., 2015)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; Transcripts; Longest transcript length; Total length; sample x; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Anguilla anguilla

source_name: yellow eel_infected

growth_protocol: European eels were caught by local fishermen and kept in freshwater for a few days.

extract_protocol:
Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2.

treatment_protocol: Prior to dissection, animals were either killed with an overdose of tricaine methanosulfonate or anesthetized with tricaine methanosulfonate and subsequently decerebrated. The swimbladder was dissected, freed from connective tissue to reveal the actual gas gland tissue, immediately shock frozen in liquid nitrogen and stored at -80°C until futher use.

tag: developmental stage

value: yellow eel

tag: infection status

value: infected

value: swimbladder; gas gland tissue


title: melXmel_cyc14C_sl06

city: Stanford

first: Peter

middle: Acuña

last: Combs

state: CA

address: Gilbert Rm 309, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the melanogaster genome with interspecific polymorphisms masked with Ns using STAR v.2.4.2a, with arguments --clip5pNbases 6 --outSAMattributes MD NH
Absolute expression was called using cufflinks v.2.2.1 with arguments --multi-read-correct --frag-bias-correct, and using the --mask-file argument to exclude a set of ribosomal, tRNA, microRNA, and histone features.
Allele-specific expression was called using ASEr commit cfe619c69a (https://github.com/TheFraserLab/ASEr/commit/cfe619c69a31f4600670859a82aae4378381b648)
Genome_build: FlyBase r5.57
Supplementary_files_format_and_content: Tab-delimited text files containing absolute expression (.fpkms) and allele-specific (.ase) expression data for each sample.
ase_summary.tsv (Tab-separated file with complete matrix of allele-specific expression values)
expr_summary.tsv (Tab-separated file with complete matrix of absolute expression values)

organism: Drosophila melanogaster

growth_protocol: 25C incubator. 2 hour lay, age to appropriate stage in incubator.

extract_protocol:
TRIzol Extraction with 1ug of glycogen
SMART-seq2 with minor modifications (see Combs & Eisen, 2015)

treatment_protocol: Methanol fixation of embryos

tag: strain(s)

value: embryonic blastoderm cycle 14C


title: miRNA CO2, replicate 2

value: 25.54 years


title: miRNA CO3, replicate 3

value: 25.36 years


title: Sample 25_ZFG-16-08_09


title: miRNA CO4, replicate 4

value: plasma

value: 25.39 years


title: miRNA CO1, replicate 1

value: 25.44 years

value: male


title: ATAC_miNs_D20_B

description: Induced with miR-9/9*-124 for 20 days.

value: adult fibroblasts


title: Sample 24_ZFG-16-08_08


title: Sample 26_ZFG-16-08_10


title: Sample 21_ZFG-16-08_05

source_name: yellow eel_uninfected

value: uninfected


title: Sample 23_ZFG-16-08_07


title: ATAC_miNs_D20_A

description: Induced with miR-9/9*-124 for 20 days.


title: Sample 22_ZFG-16-08_06


title: simXsim_cyc14C_sl26

organism: Drosophila simulans


title: simXsim_cyc14C_sl25


title: Sample 20_ZFG-16-08_04


title: simXsim_cyc14C_sl27


title: simXsim_cyc14C_sl24


title: Sample 19_ZFG-16-08_03


title: simXsim_cyc14C_sl23


title: Sample 18_ZFG-16-08_02


title: simXsim_cyc14C_sl22


title: Sample 17_IL-14-12_17


title: simXsim_cyc14C_sl21


title: simXsim_cyc14C_sl20


title: Sample 15_IL-14-12_15


title: Sample 14_IL-14-12_14


title: simXsim_cyc14C_sl18


title: simXsim_cyc14C_sl13


title: simXsim_cyc14C_sl16


title: simXsim_cyc14C_sl17


title: simXsim_cyc14C_sl08


title: simXsim_cyc14C_sl10


title: simXsim_cyc14C_sl07


title: simXsim_cyc14C_sl12


title: simXsim_cyc14C_sl11


title: Sample 11_IL-14-12_11

description: processed data: DESeq_silver_uninfected_vs_silver_infected.xlsx

source_name: silver eel_infected

value: silver eel


title: simXsim_cyc14C_sl09


title: Sample 10_IL-14-12_10


title: simXsim_cyc14C_sl05


title: simXsim_cyc14C_sl04


title: Sample 16_IL-14-12_16


title: miRNA CR3, replicate 3

value: 25.00 years

value: 30% calorie restriction


title: simXsim_cyc14C_sl02


title: simXsim_cyc14C_sl01


title: Sample 8_IL-14-12_8


title: simXsim_cyc14C_sl03


title: simXmel_cyc14C_rep2_sl27

organism: Drosophila melanogaster x Drosophila simulans

tag: hybrid

value: (Drosophila simulans F) x (Drosophila melanogaster M) F1 Hybrid


title: simXmel_cyc14C_rep2_sl26


title: simXsim_cyc14C_sl15


title: Sample 13_IL-14-12_13


title: simXmel_cyc14C_rep2_sl25


title: simXsim_cyc14C_sl14


title: simXsim_cyc14C_sl19


title: simXmel_cyc14C_rep2_sl24


title: Sample 5_IL-14-12_5


title: simXmel_cyc14C_rep2_sl23


title: simXmel_cyc14C_rep2_sl21


title: simXmel_cyc14C_rep2_sl22


title: simXmel_cyc14C_rep2_sl20


title: simXsim_cyc14C_sl06


title: Sample 1_IL-14-12_1


title: simXmel_cyc14C_rep2_sl15


title: simXmel_cyc14C_rep2_sl19


title: simXmel_cyc14C_rep2_sl17


title: simXmel_cyc14C_rep2_sl16


title: simXmel_cyc14C_rep2_sl13


title: simXmel_cyc14C_rep2_sl14


title: simXmel_cyc14C_rep2_sl12


title: SG-bam-2

city: Beijing

first: Zhaohui

last: Wang

address: No 1 Westbeichen Road

country: China

institute: Institute of genetics and developmental biology

description: mutant testes containing mainly germ cells arrested at mitosis

data_processing:
Base-calling were performed using RTA and CASAVA.
The quality of sequencing data was estimated using FastQC (v0.11.3). Then adaptors and low quality bases were removed using Trimmomatic (v0.33).
RNA-seq reads were mapped to Drosophila melanogaster genome (dm6) using TopHat (version 2.1.0) (Kim et al., 2013) with parameters only allowing uniquely mapped reads. The mapped reads were assembled using Cufflinks (version 2.2.1) with dm6 annotation as the reference (Trapnell et al., 2013). The assembled transcripts were merged and annotated using Cuffcompare (version 2.2.1) with dm6 annotation as the reference. The expression levels of each gene were then calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using Cuffdiff (version 2.2.1) with default parameters.
Only the extension of 3’UTR but not new isoforms due to alternative splicing was the focus of this study.  To identify 3' UTR extensions, RNA-seq reads that mapped to the downstream of the shortest annotated 3' UTR were collected. The initial 3' UTR extensions were contiguously assembled from the 3' end of the shortest annotated 3' UTR with a 10-nt resolution. The initial extension was able to extend to next 10-nt bin only if the FPKM of the assembled extension (FPKMext) ≥1 and the FPKM of the 10-nt bin (FPKMbin) ≥1.  Next, the assembled transcript extension in one condition was compared to that in the other condition, and only the overhangs were defined as final 3' UTR extensions. The final extensions were kept if their lengths were at least 200 nt and their FPKMs were at least 2-fold greater in one condition than another condition.  P < 0.05 and adjusted P< 0.1 were used as cutoffs to define differentially expressed 3' UTR extensions. The P value and adjusted P value were calculated using DESeq2 (Love et al. 2014).
Genome_build: DM6
Supplementary_files_format_and_content: Excel files

source_name: testis

extract_protocol:
For SG &SC, the cDNA libraries were constructed following SMARTer Ultra Low Input RNA Kit for Sequencing-v3 (Clonetech, 634848) with 12 PCR cycles, and purified using the Agencourt Ampure XP Kit (Beckman Coulter, A63880). For tut,bam or bgcn mutants, total RNAs from tut (tut3), bam (bamBG/bamΔ86) or bgcn (bgcn20093/bgcnQS2) mutant testes were extracted using Trizol (Invitrogen, 15596-026).mRNAs were enriched from total RNAs using Dynabeads mRNA DIRECT Kit (Invitrogen, 61012).
For SG&SC, The full-length cDNA outputs were processed with the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1024). For tut, bam or bgcn mutant, RNA-seq libraries were generated using the mRNA-Seq Sample Preparation kit (Illumina, RS-930-1001) following manufacturer instructions.

tag: Stage

value: mitotic germ cells

tag: genotype

value: bam mutant

value: testis


title: SG-bam-1


title: Sample 7_IL-14-12_7

value: infected

value: swimbladder; gas gland tissue


title: simXmel_cyc14C_rep2_sl09

value: embryonic blastoderm cycle 14C


title: simXmel_cyc14C_rep2_sl08


title: simXmel_cyc14C_rep2_sl07


title: SG-tut-2

value: tut mutant


title: simXmel_cyc14C_rep2_sl06


title: SG-bgcn-1

value: bcgn mutant


title: simXmel_cyc14C_rep2_sl04


title: simXmel_cyc14C_rep2_sl03


title: simXmel_cyc14C_rep2_sl18


title: simXmel_cyc14C_rep2_sl05


title: simXmel_cyc14C_rep2_sl02


title: simXmel_cyc14C_rep2_sl01


title: SG-3

description: laser disssected

value: wild type


title: SG-2

description: laser disssected


title: IL2RGA_rep3_bulkRNA

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

description: source_type: tissue

data_processing:
Demultiplexed reads were aligned using STAR(Dobin et al., 2013) to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCounts(Liao Y, Smyth GK and Shi W 2014).
Genome_build: GRCz10
Supplementary_files_format_and_content: text file with raw counts

molecule: polyA RNA

organism: Danio rerio

source_name: whole kidney marrow

extract_protocol:
Wild-type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2-Mercaptoethanol, followed by RNA isolation using the RNAeasy Mini kit (QIAGEN).
100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike-in.

value: kidney marrow


title: SG-bgcn-2


title: melXsim_cyc14C_rep3_sl27

value: (Drosophila melanogaster F) x (Drosophila simulans M) F1 Hybrid


title: IL2RGA_rep2_bulkRNA

description: source_type: tissue


title: SG-1

description: laser disssected


title: melXsim_cyc14C_rep3_sl26


title: simXmel_cyc14C_rep2_sl10


title: IL2RGA_rep1_bulkRNA

description: source_type: tissue


title: SC-3

description: laser disssected

value: meiotic germ cells


title: melXsim_cyc14C_rep3_sl25


title: melXsim_cyc14C_rep3_sl24


title: SC-1

description: laser disssected


title: melXsim_cyc14C_rep3_sl23


title: SC-2

description: laser disssected


title: SG-tut-1


title: melXsim_cyc14C_rep3_sl21


title: PRKDC.IL2RGA_rep1_bulkRNA

description: source_type: tissue


title: melXsim_cyc14C_rep3_sl22


title: PRKDC_rep3_bulkRNA

description: source_type: tissue

value: PRKDC


title: melXsim_cyc14C_rep3_sl20


title: PRKDC_rep2_bulkRNA

description: source_type: tissue


title: melXsim_cyc14C_rep3_sl19


title: melXsim_cyc14C_rep3_sl18


title: melXsim_cyc14C_rep3_sl17


title: WT_rep2_bulkRNA

description: source_type: tissue

value: wildtype


title: ILB_9583_IonTorrent

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description:
[processed data files:]
IonTorrent.GSNAP.gene_quant.txt
IonTorrent.STAR.gene_quant.txt
IonTorrent.STAR_PLUS_BOWTIE2.gene_quant.txt

data_processing:
We aligned fastq files from both platforms using STAR v2.5.1b, GSNAP release 2015-12-31 (v8), or a combination of STAR and Bowtie2 v2.2.9. For the STAR + Bowtie2 combination, we first aligned reads to the genome using STAR and extracted all unmapped reads from the resulting BAM files. Next, we used Bowtie2 to align all of these unmapped reads to the reference genome. Lastly, we used custom perl scripts to merge the Bowtie2 alignments with the STAR alignment, replacing entries for the unaligned reads with the mapping information from Bowtie2.
To normalize the data within a given platform/aligner combination, we used the Pipeline Of RNA-Seq Transformations (PORT - v0.8.1-beta). Briefly, PORT filters out potential confounding factors like reads mapping to rRNA sequences and mitochondrial DNA. Next, PORT determines the input dataset with the fewest number of gene-mapping reads and re-samples all datasets to have the same number of reads, thus accounting for batch effects and differences in sequencing depth between samples.
In addition to normalization, we also used PORT to quantify the normalized, gene-level read counts for each of our datasets. For quantification, we used the gene models from the Ensembl v67 annotation.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

organism: Mus musculus

source_name: Liver

growth_protocol: Twelve-week old male C57/B6J mice were acquiered from Jackson Labs.

extract_protocol:
Mice were sacrificed and liver samples were dissected and snap-frozen in liquid nitrogen. RNA was extracted from the liver tissue using TRIzol and Qiagen Rneasy Mini Kit, according to manufacturers’ protocols.
Ion Torrent: Total RNA was poly-A selected using Ambion’s (ThermoFisher) Dynabeads mRNA Direct Micro Purification kit. About 100 ng poly-A RNA was used to prepare strand-specific barcoded RNA library with the Ion Total RNA-Seq kit v2.0 following manufacturer’s protocol. The library quality was checked by running on the BioAnalyzer and the concentration was determined from the analysis profile. Ten barcoded libraries were pooled together on an equimolar basis and run using three PIv3 chips on an Ion Torrent Proton using HiQ chemistry.

Illumina: 200 ng total RNA from each liver sample was prepared for Illumina sequencing according to the manufacturer’s protocol using the TruSeq Stranded mRNA Sample Preparation Kit.  Following preparation, library quality was assessed using a Bioanalyzer. Libraries from all samples were pooled together and sequenced using an Illumina HiSeq 2500 (125 bp paired-end reads).

treatment_protocol: Four hours prior to tissue collection, mice were treated with either 20 µg/Kg of IL-1B or saline.

tag: strain

value: 12 weeks

value: Liver

value: male

value: IL-1 Beta


title: melXsim_cyc14C_rep3_sl16


title: PRKDC_rep1_bulkRNA

description: source_type: tissue


title: WT_rep1_bulkRNA

description: source_type: tissue


title: melXsim_cyc14C_rep3_sl15


title: PRKDC.IL2RGA_rep3_bulkRNA

description: source_type: tissue


title: melXsim_cyc14C_rep3_sl13


title: ILB_9579_IonTorrent


title: melXsim_cyc14C_rep3_sl14


title: melXsim_cyc14C_rep3_sl11


title: simXmel_cyc14C_rep2_sl11

value: (Drosophila simulans F) x (Drosophila melanogaster M) F1 Hybrid


title: ILB_9578_IonTorrent


title: ILB_9577_IonTorrent


title: melXsim_cyc14C_rep3_sl10


title: UNT_9580_IonTorrent

value: saline


title: melXsim_cyc14C_rep3_sl09


title: UNT_9576_IonTorrent


title: WT_rep3_bulkRNA

description: source_type: tissue


title: UNT_9575_IonTorrent


title: UNT_9574_IonTorrent


title: melXsim_cyc14C_rep3_sl04


title: melXsim_cyc14C_rep3_sl05


title: ILB_9582_IonTorrent


title: melXsim_cyc14C_rep3_sl02


title: WT treated with AC2P36, pH 5.7 rep 2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplexe and converte reads to FASTQ format
Trimmomatic (v0.30)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie  was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determin counts per gene feature in the M. tuberculosis CDC1551 genome
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the edgeR package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as .csv spreadsheets and represents the average of 2 biological replicates
Supplementary_files_format_and_content: SupplementalTableS1: Normalized counts and differential expression Pyruvate pH 7.0 vs Glycerol pH 7.0 (AC2P36 vs DMSO pH 7.0)
Supplementary_files_format_and_content: SupplementalTableS2: Normalized counts and differential expression Glycerol pH 5.7 vs Glycerol pH 7.0 (AC2P36 vs DMSO pH 5.7)
Supplementary_files_format_and_content: SupplementalTable S3: Normalized counts and differential expression Glycerol pH 5.7 vs Glycerol pH 7.0 (DMSO pH 5.7 vs DMSO pH 7.0)

organism: Mycobacterium tuberculosis CDC1551

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 was grown at 37ºC in T-25 vented, standing tissue culture flasks in 8 mL of buffered 7H9 medium (pH 7.0 or 5.7) lacking catalase to an OD600 of 0.5.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Mtb cultures were subsequently treated with 10 µM AC2P36. For the control, cultures treated with an equal amount of DMSO.  Following a 4 h incubation period, RNA was isolated from the bacterial cultures and used for RNA-seq. For each condition, 2 biological replicates were performed.

tag: chemical treatment

tag: ph


title: WT treated with AC2P36, pH 5.7 rep 1


title: WT treated with AC2P36, pH 7.0 rep 2


title: melXsim_cyc14C_rep3_sl06


title: melXsim_cyc14C_rep3_sl03


title: WT treated with AC2P36, pH 7.0 rep 1


title: melXsim_cyc14C_rep3_sl12


title: WT treated with DMSO, pH 5.7 rep 2

value: DMSO


title: melXsim_cyc14C_rep3_sl01


title: UNT_9584_IonTorrent

tag: age


title: melXsim_cyc14C_rep2_sl26


title: WT treated with DMSO, pH 5.7 rep 1


title: WT treated with DMSO, pH 7.0 rep 2


title: melXsim_cyc14C_rep3_sl08


title: melXsim_cyc14C_rep2_sl24


title: WT treated with DMSO, pH 7.0 rep 1


title: melXsim_cyc14C_rep2_sl25


title: melXsim_cyc14C_rep2_sl23


title: melXsim_cyc14C_rep2_sl22


title: melXsim_cyc14C_rep3_sl07


title: 5_N2K12_EARLY2

city: GA

last: Sonowal

state: Atlanta

address: 144 Whitehead Bldg., 615 Michael St.

department: Pathology & Laboratory Medicine

institute: Emory University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim galore, and masked for low-complexity or low-quality sequence.
The sequence reads that passed quality filters were analyzed using ce6 with STAR aligner with default parameters followed by
gene count estimation by HTSeq-count 0.6.1p2 for transcript abundances.
Differentially-expressed genes were called at a false discovery rate (FDR) of 0.05% using the DESeq2 package in R.
Genome_build: C elegans ucsc ce6
Supplementary_files_format_and_content: text files contain gene count data fr each condition and csv file contains list of differentially expressed with fold change that passed false discovery rate of 0.05

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Worms were grown at 16 degree celsius on stadard NGM plates.

extract_protocol:
Worms were grown in respective conditions since embryo stage. RNA was extracted with Trizol with multiple freeze-thaw cycles and was purified using Rneasy Plus Mini kit (Qiagen) before sending for sequencing.
Atleast two biological replicates for each condition was considered for RNA-Seq with each containing purified RNA from ~150 adults worms
RNA libraries were prepared for sequencing using standard Illumina protocols
cDNA libraries for RNA-Seq

treatment_protocol: Worms were grown on two types of bacterial strain of E. coli, K12 and delta-tnaA strain since the embryo stage.

value: 3 d


title: 6_N2K12_EARLY3


title: 4_N2K12_EARLY1


title: melXsim_cyc14C_rep2_sl21

value: embryonic blastoderm cycle 14C


title: melXsim_cyc14C_rep2_sl20


title: 3_N2tnaA_EARLY3


title: melXsim_cyc14C_rep2_sl19


title: 37_AHRK12_LATE1


title: melXsim_cyc14C_rep2_sl17


title: 2_N2tnaA_EARLY2


title: melXsim_cyc14C_rep2_sl16


title: 39_AHRK12_LATE3


title: melXsim_cyc14C_rep2_sl15


title: melXsim_cyc14C_rep2_sl18


title: 16_N2K12_LATE1


title: melXsim_cyc14C_rep2_sl14


title: 14_N2tnaA_LATE2


title: 15_N2tnaA_LATE3


title: melXsim_cyc14C_rep2_sl12


title: melXsim_cyc14C_rep2_sl11


title: melXsim_cyc14C_rep2_sl13


title: melXsim_cyc14C_rep2_sl09


title: melXsim_cyc14C_rep2_sl10


title: WT3a_M140_1_GMP RRBS-seq

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: biological replicate 1

data_processing:
Fastq files aligned with bsmap 2.74 in RRBS mode using the following parameters: -g 1 -w 5 -D C-CGG -p 8 -R -s 12 -S 42 -u; methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z --ct-snp=no-action
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

source_name: Idh2 mutant GMPs

growth_protocol: Freshly sorted mouse megarkaryocyte erythroid progenitor(MEP,Lin-cKit+, Sca1-, CD34-, Cd16/32-); Granulocyte Macrophage Progenitor(GMP,Lin-cKit+, Sca1-, CD34+, Cd16/32+) from each genotype

extract_protocol:
Extract DNA using Qiagen Allprep Micro kit.
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were treated with sodium bisulfite (Qiagen)

value: Murine bone marrow derived primary GMPs

tag: cell surface marker

value: Mx1-cre-;Dnmt3af/f;Idh2 R140Q


title: PRKDC.IL2RGA_rep2_bulkRNA

description: source_type: tissue


title: WT3a_GFP_2_GMP RRBS-seq

description: biological replicate 2

source_name: WT GMPs


title: WT3a_M140_2_MEP RRBS-seq

description: biological replicate 2

source_name: Idh2 mutant MEPs

value: Murine bone marrow derived primary MEPs


title: WT3a_M140_1_MEP RRBS-seq

description: biological replicate 1


title: melXsim_cyc14C_rep2_sl07


title: WT3a_M140_2_GMP RRBS-seq

description: biological replicate 2


title: melXsim_cyc14C_rep2_sl08


title: WT3a_GFP_2_MEP RRBS-seq

description: biological replicate 2

source_name: WT MEPs


title: melXsim_cyc14C_rep2_sl05


title: 18_N2K12_LATE3


title: WT3a_GFP_1_GMP RRBS-seq

description: biological replicate 1


title: melXsim_cyc14C_rep2_sl03


title: melXsim_cyc14C_rep2_sl06


title: KO3a_M140_3 RRBS-seq

description: biological replicate 3

source_name: Dnmt3a knockout Idh2 mutant HSPCs

value: Murine bone marrow derived maligant HSPCs

value: Mx1-cre+;Dnmt3a-/-;Idh2 R140Q


title: KO3a_M140_2 RRBS-seq

description: biological replicate 2


title: melXsim_cyc14C_rep2_sl02

value: (Drosophila melanogaster F) x (Drosophila simulans M) F1 Hybrid


title: KO3a_GFP_2_MEP RRBS-seq

description: biological replicate 2

source_name: Dnmt3a knockout MEPs


title: KO3a_M140_1 RRBS-seq

description: biological replicate 1


title: simXmel_cyc14C_rep1_sl25


title: melXsim_cyc14C_rep2_sl01


title: KO3a_GFP_2_GMP RRBS-seq

description: biological replicate 2

source_name: Dnmt3a knockout GMPs


title: simXmel_cyc14C_rep1_sl24


title: simXmel_cyc14C_rep1_sl23


title: simXmel_cyc14C_rep1_sl22


title: KO3a_GFP_1_GMP RRBS-seq

description: biological replicate 1


title: WT3a_GFP_1_MEP RRBS-seq

description: biological replicate 1


title: simXmel_cyc14C_rep1_sl19


title: WT3a_GFP_3_GMP RNA-seq

description: biological replicate 3 of MEPs from Dnmt3a WT

data_processing:
Reads were aligned with Tophat 2.0.10 to both refseq transcriptome and mm9 genome using parameters: -p 12 --library-type fr-unstranded --read-realign-edit-dist 0 --min-anchor-length 6 --microexon-search --transcriptome-index=mm9_refseq. The refseq transcriptome gtf file was obtained from the Illumina iGenomes collection as recommended by the software developers
Refseq reference-based transcript assembly and transcript quantification were performed by Cufflinks 2.1.1 using parameters: --max-bundle-frags 500000 -p 16 -u -A 0.16 -b -M -g
Differential expression of Refseq genes was assessed by Cuffdiff 2.1.1 using parameters: -b -M -p 12 --min-reps-for-js-test 2 -u
Genome_build: mm9
Supplementary_files_format_and_content: gene_exp.diff is a tab separated text file of the Cuffdiff output for differential gene expression analysis of the following groups: KO3a_GFP_M, MEPs from Dnmt3a KO genotype primary transplant; KO3a_M140_2nd, MEP-like HSPCs from Dnmt3aKO;Idh2 mutant genotype secondary transplant; WT3a_GFP_M, MEPs from Dnmt3a WT genotype primary transplant;WT3a_M140_M, MEPs from Dnmt3a WT;Idh2 mutant genotype primary transplant. The remaining files are tab separated text files of the Cufflinks output for gene level expression abundance measurements produced by Cufflinks for each sample.

source_name: Bone marrow

growth_protocol: Sca1+ enriched Dnmt3a KO or Dnmt3a WT cells were transduced with retroviruses expressing MSCV-Idh2R140Q-IRES-GFP mutant, MSCV-Idh2-IRES-GFP, or MSCV-IRES-GFP control transgenes and injected into lethally irradiated recipients. Freshly sorted mouse megarkaryocyte erythroid progenitor(MEP,Lin-cKit+, Sca1-, CD34-, Cd16/32-); Granulocyte Macrophage Progenitor(GMP,Lin-cKit+, Sca1-, CD34+, Cd16/32+) from each genotype were collected from a primary or secondary transplant recipient.

extract_protocol:
Extract RNA using Qiagen Allprep Micro kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection


title: WT3a_WTIDH2_1_MEP RNA-seq

description:
biological replicate 1 of MEPs from Dnmt3a WT;Idh2 WT
processed data file: gene_exp.diff


title: WT3a_GFP_2_GMP RNA-seq

description: biological replicate 2 of GMPs from Dnmt3a WT


title: WT3a_GFP_2_MEP RNA-seq

description:
biological replicate 2 of GMPs from Dnmt3a WT
processed data file: gene_exp.diff


title: simXmel_cyc14C_rep1_sl20


title: WT3a_WTIDH2_1_GMP RNA-seq

description: biological replicate 1 of GMPs from Dnmt3a WT;Idh2 WT


title: WT3a_GFP_3_MEP RNA-seq

description:
biological replicate 3 of MEPs from Dnmt3a WT
processed data file: gene_exp.diff


title: simXmel_cyc14C_rep1_sl18


title: WT3a_GFP_1_MEP RNA-seq

description:
biological replicate 1 of MEPs from Dnmt3a WT
processed data file: gene_exp.diff


title: simXmel_cyc14C_rep1_sl15


title: WT3a_GFP_1_GMP RNA-seq

description: biological replicate 1 of GMPs from Dnmt3a WT


title: simXmel_cyc14C_rep1_sl16


title: KO3a_M140_3 RNA-seq

description:
biological replicate 3 of MEP-like HSPCs from Dnmt3a KO;Idh2 mutant
processed data file: gene_exp.diff

value: Murine bone marrow derived maligant MEP-like HSPCs


title: KO3a_M140_2 RNA-seq

description:
biological replicate 2 of MEP-like HSPCs from Dnmt3a KO;Idh2 mutant
processed data file: gene_exp.diff


title: simXmel_cyc14C_rep1_sl13


title: simXmel_cyc14C_rep1_sl12


title: simXmel_cyc14C_rep1_sl11


title: KO3a_GFP_1_MEP RRBS-seq

description: biological replicate 1


title: KO3a_M140_1 RNA-seq

description:
biological replicate 1 of MEP-like HSPCs from Dnmt3a KO;Idh2 mutant
processed data file: gene_exp.diff


title: KO3a_GFP_2_MEP RNA-seq

description:
biological replicate 2 of MEPs from Dnmt3a KO
processed data file: gene_exp.diff


title: KO3a_GFP_2_GMP RNA-seq

description: biological replicate 2 of GMPs from Dnmt3a KO


title: simXmel_cyc14C_rep1_sl10


title: simXmel_cyc14C_rep1_sl09


title: KO3a_GFP_1_MEP RNA-seq

description:
biological replicate 1 of MEPs from Dnmt3a KO
processed data file: gene_exp.diff


title: simXmel_cyc14C_rep1_sl08


title: KO3a_GFP_1_GMP RNA-seq

description: biological replicate 1 of GMPs from Dnmt3a KO


title: simXmel_cyc14C_rep1_sl07


title: WT3a_M140_2_GMP RNA-seq

description: biological replicate 2 of GMPs from Dnmt3a WT;Idh2 mutant


title: WT3a_M140_2_MEP RNA-seq

description:
biological replicate 2 of MEPs from Dnmt3a WT;Idh2 mutant
processed data file: gene_exp.diff


title: WT3a_M140_1_MEP RNA-seq

description:
biological replicate 1 of MEPs from Dnmt3a WT;Idh2 mutant
processed data file: gene_exp.diff


title: simXmel_cyc14C_rep1_sl06


title: simXmel_cyc14C_rep1_sl14


title: WT3a_M140_1_GMP RNA-seq

description: biological replicate 1 of GMPs from Dnmt3a WT;Idh2 mutant


title: simXmel_cyc14C_rep1_sl02


title: simXmel_cyc14C_rep1_sl01


title: simXmel_cyc14C_rep1_sl03


title: melXsim_cyc14C_rep1_sl27


title: melXsim_cyc14C_rep1_sl26


title: melXsim_cyc14C_rep1_sl24


title: melXsim_cyc14C_rep1_sl22


title: melXsim_cyc14C_rep1_sl25


title: melXsim_cyc14C_rep1_sl21


title: melXsim_cyc14C_rep1_sl23


title: melXsim_cyc14C_rep1_sl20


title: melXsim_cyc14C_rep1_sl17


title: melXsim_cyc14C_rep1_sl18


title: melXsim_cyc14C_rep1_sl15


title: melXsim_cyc14C_rep1_sl14


title: melXsim_cyc14C_rep1_sl16


title: simXmel_cyc14C_rep1_sl05


title: melXsim_cyc14C_rep1_sl13


title: simXmel_cyc14C_rep1_sl04


title: melXsim_cyc14C_rep1_sl11


title: melXsim_cyc14C_rep1_sl10


title: melXsim_cyc14C_rep1_sl12


title: melXsim_cyc14C_rep1_sl08


title: melXsim_cyc14C_rep1_sl07


title: melXsim_cyc14C_rep1_sl09


title: melXsim_cyc14C_rep1_sl06


title: melXsim_cyc14C_rep1_sl05


title: melXsim_cyc14C_rep1_sl19


title: melXsim_cyc14C_rep1_sl02


title: Col-0×Ak-1 rep1

status: Public on Aug 03 2017

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

data_processing:
RNA-seq reads of Col-0 were mapped to Arabidopsis TAIR 10 using TopHat software (version 2.0.8b, http://ccb.jhu.edu/software/tophat/index.shtml) with parameters set to a minimum intron length 20, maximum intron length 6000, and a maximum of 2 mismatches. To decrease the mapping bias for Per-1 and Aa-0 RNA-seq reads, we created Per-1 and Aa-0 reference genomes using SNP data from Arabidopsis 1001 genomes website according to method described45. RNA-seq reads of Per-1 and Aa-0 were mapped to Per-1 and Aa-0 reference genomes, respectively. To analyze the RNA-seq data of Col-0×Per-1 and Col-0×Aa-0, we aligned the sequencing reads to both of the Col reference genome and updated Per-1 and Aa-0 reference genome. Only unique mapped reads were extracted for the following analysis. Then, fragments per kilobase of exon model per million mapped fragments (FPKM) for each gene was calculated by Cufflinks (version 2.0.2, http://cole-trapnell-lab.github.io/cufflinks/), which represented the expression level of each gene. Following the previous study46, a threshold of 1 for FPKM was used to identify expressed genes.
differentially expressed genes among two parents and the hybrid were identified using the GLM method in edgeR package (version 3.12.0, http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) with FDR of 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: First leaf

growth_protocol: plants were grown on Murashige and Skoog plates containing 1% sucrose for 14 days

extract_protocol:
RNA was harvested using RNeasy plant mini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit V2 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: Leaf

value: day 14


title: melXsim_cyc14C_rep1_sl01


title: Ak-1 rep1


title: melXsim_cyc14C_rep1_sl04


title: Col-0×Per-1 rep1


title: Col-0×Per-1 rep2


title: Ak-1 rep2


title: Col-0×Ak-1 rep2


title: Col-0×Aa-0 rep2


title: Col-0×Aa-0 rep1


title: simXmel_cyc14C_rep1_sl21


title: Per-1 rep2


title: Aa-0 rep2


title: Per-1 rep1


title: Col-0 rep4


title: Col-0 rep3


title: Aa-0 rep1


title: Col-0 rep1


title: melXsim_cyc14C_rep1_sl03


title: melXsim_cyc14C_rep2_sl04


title: WT Nucleoplasmic Total RNA rep-1 run-2

city: Freiburg

first: Thomas

last: Jenuwein

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Nucleoplasmic Total RNA from mouse embryonic stem cells

data_processing:
bcl2fastq version 2.17.1.14
Tophat2.0.13 with default parameters were used to align to the mouse mm10 genome.
The alignment file was split into uniquely mapping and multi-mapped/unmapped reads, and the unmapped reads were converted into fastq file using samtools-1.3.
The multi-mapped/unmapped reads were the used to determine fractional counts over repetitive elements using RepEnrich and the Repeatmasker mm10 genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 input count matrices were created using RepEnrich

source_name: Embryonic Stem cells

growth_protocol: ES cells were grown on gelatin coated plates with ES medium ( DMEM supplemented with 15% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM and LIF). MEFs were grown in DMEM supplemented with 10% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM. In vitro differentiation to NPCs was carried out as described before (Bibel et al., 2007)

extract_protocol:
Wild-type mouse ES cells from one confluent maxi dish were trypsinized and collected by centrifugation at 1200 rpm for 3 min in 15 ml falcon tubes. The cell pellet was resuspended in PBS and the cell number determined using a CASY-counter. 2x107 cells were resuspended in 200 μl of cold cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 min. The lysate was layered onto 500 μl of cold sucrose buffer (10 mM Tris pH 7.5, 150 mM NaCl, 24% sucrose w/v), and centrifuged in microfuge tubes at 14,000 rpm for 10 min at 4°C. The supernatant recovered after this spin (~700 μl) represents the cytoplasmic fraction. The nuclear pellet was gently resuspended in 200 μl of cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT. An additional 200 μl of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40, 1 mM DTT) was added to the samples, followed by pulsed vortexing and incubation on ice for 1 min. Samples were then centrifuged in microfuge tubes for 2 min at 14,000 rpm at 4°C. The supernatant from this spin represents the soluble nuclear fraction (nucleoplasm), while the remaining insoluble part represents the chromatin pellet.
TrueSeq total RNA
TrueSeq mRNA

value: wild type

value: Embryonic Stem cells

tag: fraction

value: nucleoplasmic

tag: sequencing run


title: WT Nucleoplasmic Total RNA rep-2 run-2


title: WT Chromatin-associated polyA RNA rep-2 run-2

description: Chromatin-associated polyA RNA from mouse embryonic stem cells

value: chromatin-associated


title: WT Nucleoplasmic polyA RNA rep-1 run-2

description: Nucleoplasmic polyA RNA from mouse embryonic stem cells


title: WT Nucleoplasmic polyA RNA rep-3 run-1


title: WT Chromatin-associated Total RNA rep-2 run-2

description: Chromatin-associated Total RNA from mouse embryonic stem cells


title: WT Chromatin-associated Total RNA rep-3 run-2


title: WT Chromatin-associated Total RNA rep-3 run-1


title: WT Nucleoplasmic polyA RNA rep-3 run-2


title: WT Nucleoplasmic polyA RNA rep-1 run-1


title: WT Nucleoplasmic polyA RNA rep-2 run-1


title: WT Chromatin-associated polyA RNA rep-1 run-1


title: WT Chromatin-associated Total RNA rep-1 run-2


title: WT Nucleoplasmic Total RNA rep-3 run-1


title: WT Chromatin-associated polyA RNA rep-1 run-2


title: WT Chromatin-associated Total RNA rep-2 run-1


title: WT Nucleoplasmic Total RNA rep-2 run-1


title: WT Nucleoplasmic Total RNA rep-1 run-1


title: WT Nucleoplasmic polyA RNA rep-2 run-2


title: WT Chromatin-associated polyA RNA rep-3 run-1


title: Col-0 rep2


first: Naresh

middle: Singh

last: Redhu

state: Massachusetts

address: 300 Longwood Ave, Enders 670

department: GI/Nutrition

institute: Boston Children's hospital

description:
LP Macrophages from 12 Week old Il10rb-/- (KO)
12WK2

data_processing:
Trim_galore
TopHat
HtSeq
DeSeq
Genome_build: mm10
Supplementary_files_format_and_content: csv of normalized expression values

source_name: Colonic lamina propria macrophages

growth_protocol: Colonic lamina propria macrophages were isolated ex vivo and FACS sorted directly in lysis buffer for RNA extraction

extract_protocol:
Lamina propria leukocytes were isolated following Shouval et al, Immunity 2014 protocol.
Clontech (TaKaRa) SmartSeq v4 Rubicon

treatment_protocol: All samples untreated (ex vivo direct analysis)

value: 12 week-old

tag: cell type


description:
LP Macrophages from 3 Week old Il10rb-/- (KO)
3WK1

value: 3 week-old


description:
LP Macrophages from 12 Week old Il10rb+/- (het)
12WH2

value: Il10rb+/- (het)


title: WT Nucleoplasmic Total RNA rep-3 run-2


title: WT Chromatin-associated polyA RNA rep-2 run-1


title: WT Chromatin-associated polyA RNA rep-3 run-2


description:
LP Macrophages from 1 Week old Il10rb+/- (het)
1WH1

value: 1 week-old


description:
LP Macrophages from 1 Week old Il10rb-/- (KO)
1WK1


title: Chinese Red Steppes 6

city: Changchun

first: Xibi

last: Fang

address: No. 5333 Xian Road

institute: Jilin University

data_processing:
Read sequences produced by the Illumina pipeline in FastQ format were first pre-processed through in-house perl scripts.
Firstly, as a subset of reads contained all of part of the 3’adapter oligonucleotide sequence, every read was scanned for the adapter sequence, and if detected the read was filtered out.
Secondly, since some reads had N (unknown base) in their sequences, the percentage of Ns in each read was calculated, and if the percentage of Ns was larger than 10% the read was removed.
Thirdly, reads with low quality (PHRED score <= 5, and percentage of the low quality bases >= 50%) were trimmed. At the same time, Q20, Q30 and GC content of the data were calculated.
The remaining reads that passed the filters were called as clean reads and all of the subsequent analyses were based on them.
After filtering the low quality reads, the clean reads data were aligned to the Ensemble bovine reference genome (Bos taurus UMD_3.1.1) and the methylation of mC sites were detected using Bismark (version 0.12.5).
Genome_build: Bos taurus UMD_3.1.1
Supplementary_files_format_and_content: Bismark software (version 0.12.5; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome with the default parameters. The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The results of methylation extractor were transformed into bigWig format for visualization using IGV browser.

organism: Bos taurus

source_name: longissimus muscle

growth_protocol: The cattle in both groups were raised under normal similar conditions on a diet of corn and hay with access to feed and water ad libitum.

extract_protocol:
DNA was extracted from longissimus muscle tissues with the DNA extraction kit (Tiangen, Beijing, China) according to the manufacturer’s protocol and concentration of the genomic DNA was determined with a NanoDrop ND-2000 UV spectrophotometer (Thermo Fisher Scientific Inc., USA).
5.2 mg genomic DNA spiked with 26 ng lambda DNA were fragmented to 200-300bp by sonication with a focused-ultra sonicator (Covaris, Woburn, MA, USA), followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA according to the manufacturer’s protocol. After DNA bisulfite conversion, single-strand DNA fragments were PCR amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2X) (Kapa Biosystems, Wilmington, MA, USA).

tag: breed

value: Chinese Red Steppes cattle

value: adult

value: 28 months

value: muscle tissue


title: Chinese Red Steppes 4

value: Chinese Red Steppes  cattle

tag: tissue


title: Chinese Red Steppes 5


title: wagyu 120719

value: Japanese black (Wagyu) cattle


title: wagyu 120921


title: Wagyu 120616


title: simXmel_cyc14C_rep1_sl17

value: (Drosophila simulans F) x (Drosophila melanogaster M) F1 Hybrid

value: embryonic blastoderm cycle 14C


title: WT rep2

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

description: Sample name: 1wc3wt

data_processing:
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and quality assessed with the FastQC Version 1.0.0 App.
Sequences were trimmed to 125bp by cutting 10bp from the 5'-end and 16bp from the 3'end using the FASTQ Toolkit Version 2.2.0 App.
Trimmed sequences were aligned to mus musculus mm10 genome using the TopHat Alignment Version 1.0.0 App.
Transcripts were assembled and differential expression was determined using the BaseSpace Cufflinks Assembly and DE Version 1.1.0 App selecting mm10 reference genome and "Stranded" polyA enriched sequences.
FPKM tables and CuffDiff results of differential gene expression of were downloaded and significantly expressed genes (FDR<0.05, FPKM>5) with >1.5-fold up/downregulation were used for subsequent analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files contain FPKM values for each sample and summary differential gene expression data.

source_name: Ventricle Tissue

extract_protocol:
Ventricles were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
polyA RNA was enriched and stranded libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA sample preparation kit. 151bp paired-end libraries with SBS chemistry were sequenced on the Illumina HiSeq4000 sequencer.

tag: Sex

value: male

value: heart ventricle

value: post natal day 21

value: WT


title: Cdk8Tg rep1

description: Sample name: 1db3tg

tag: developmental stage


title: WT rep4

description: Sample name: 1wc9wt


title: Cdk8Tg rep4

description: Sample name: 1wc8tg


title: Cdk8Tg rep5

description: Sample name: 1wc10t


title: not4D+Not4RRM Replicate 3

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

description:
Not4 RRM Expresser culture.
Processed data file: read_counts.txt

data_processing:
The sequencing run here had a mean read length of 225 bp.
These were aligned to S. cerevisiae S288C genome coding reference (Saccharomyces cerevisiae strain S288C Reference Genome Sequence in SGD) using RNA-STAR.
Reads were normalized with TPM. Gene expression was analyzed using fold change 1.5, student t test < 0.05 and FDR <0.05.
Genome_build: S. cerevisiae S288C genome R64-2-1 2014_11_18
Supplementary_files_format_and_content: read_counts.txt: Tab-delimited text file containing read counts for each gene across all six samples.

organism: Saccharomyces cerevisiae

source_name: Yeast culture, not4D+Not4RRM

extract_protocol:
Total RNA was extracted from whole cell cultures using the Qiagen RNA isolation kit. Its quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).
1µg of total RNA was enriched for Poly A RNA using the Dynabeads® mRNA DIRECT™ Micro Purification Kit according to manufacturer’s standard protocol. The resulting enriched RNA samples were then used to prepare barcoded libraries for sequencing using the Ion Total RNAseq V2 kit and the Ion Xpress 1-48 Barcode kit. Libraries were amplified 16 cycles and the quality of the libraries was confirmed on an Agilent Bioanalyzer using a DNA High Sensitivity chip. The libraries were pooled based on concentrations from the High Sensitivity chip, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer.

tag: strain/background

tag: expression


title: Cdk8Tg rep3

description: Sample name: 1wc2tg


title: WT rep1

description: Sample name: 1db6wt


title: WT rep5

description: Sample name: 2cb6wt


title: not4D+Not4WT Replicate 3

description:
Not4 WT Expresser culture.
Processed data file: read_counts.txt

source_name: Yeast culture, not4D+Not4WT


title: not4D+Not4RRM Replicate 1


title: SL147674

city: Huntsville

first: Ryne

last: Ramaker

state: AL

address: 601 Genome Way

department: Genetics

institute: University of Alabama at Birmingham

description: RNA-sequencing of fresh frozen liver tissue

data_processing:
Reads trimmed with TrimGalore with default settings
Reads aligned to raw count table with STAR v2.4.2 with ENCODE standard settings
Genome_build: GRCh37_E75
Supplementary_files_format_and_content: Tab-delimeted text file containing raw count levels of each gene

source_name: Child Liver

extract_protocol:
Total RNA was extracted from fresh frozen liver tissue that had been homogenized to a fine powder with the Norgen Total RNA Preparation Kit.  RNA was polyA selected with the Dynabeads mRNA Purification Kit. cDNA was prepared using the ThermoFisher High-Capacity RNA-to-cDNA Kit.  RNA-seq libraries were prepared with the Nextera DNA Library Sample Prep Kit.
PolyA selection, Transposase-mediated construction

tag: tissue type

value: Flash frozen liver tissue


title: SL147673


title: not4D+Not4RRM Replicate 2


description:
LP Macrophages from 3 Week old Il10rb+/- (het)
3WH1


title: WT rep3

description: Sample name: 1wc4wt


title: SL147675


title: not4D+Not4WT Replicate 2


title: SL147678

source_name: Adult Liver


title: SL147676


title: not4D+Not4WT Replicate 1


title: Cdk8Tg rep2

description: Sample name: 1dd4tg


title: int-c.5 (GSHO 2003) 1327Z

city: Cologne

first: Kurt

last: Stueber

address: Carl von Linne-Weg 10

department: Genome Centre

institute: Max Planck Institute for Plant Breeding Research

data_processing:
BWA-MEM was used for alingment of the reads, Salmon was used to extract transcript per million (TPM) values.
Log fold change values comparing mutant versus wildtype at different developmental stages were obtained using Limma-Voom
Genome_build: As reference a combined set public available data of HC and LC predicted coding sequences of barley cv. Morex (The International Barley Genome Sequencing Consortium 2012) was used.
Variant calling was performed with GATK UnifiedGenotyper (Version 3.1-1) on on processed alignment files using a combined set of High Confidence (HC) and Low confidence (LC) predicted coding sequences of barley cv. Morix (TBGC, 2012) as reference.
Supplementary_files_format_and_content: Excel sheet with log fold changes comparing the different states, vcf file with varant information

organism: Hordeum vulgare

source_name: apex tissue

growth_protocol: Plants were grown under long day conditions (16h, 22°C day; 8h, 18°C night)

extract_protocol:
Main shoot apex tissue was isolated at Waddington stage W3.5 and 5.5 and frozen in liquid nitrogen. Tissue was ground, dissolved in 500 mL TRIzol reagent (Invitrogen), incubated for 5 min at room temperature after which, 100 mL of chloroform was added. The sample was homogenized, incubated for 2 min, and centrifuged for 15 min at 4°C  followed by phase separation (keeping the aqueous phase). Next, isopropanol was added and incubated  for 10 min at room temperature and further purified using an RNA easy Micro Kit (Qiagen). Residual DNA was removed using a DNA-free kit (Ambion). The quality of the RNA was tested using a bio analyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Waddington stage 5.5

tag: genetic background

value: IL in cv. Bowman

tag: phenotype


title: int-c.5 (GSHO 2003) 1327Y


title: SL147679


title: Mmu N H3K27me3 replicate 2

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

institute: TUD Dresden University of Technology

description:
Mmu_N_K27_2
processed data file: Mmu_N_K27.bigWig

data_processing:
Reads were mapped using bowtie v1.0.0 (-best -m 1)
Duplicate reads were removed at the library level using picardtools markDuplicates
Peaks were called using Macs2
Read extension to 200bp was done using bedtools slop
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig after normalization using genomeCoverageBed
Supplementary_files_format_and_content: *Peak files: Histone methylation peaks were identified using MACS2 with 'default' parameters for H3K4me3 and the 'broad' peak option for H3K27me3.

source_name: Mmu N H3K27me3

extract_protocol:
ChIP was performed using the LowCell ChIP kit (Diagenode) and DNA was purified using the IPure kit (Diagenode) according to manufacturer’s instructions.
DNA was subjected to NGS library preparation using the MicroPlex Template Preparation Kit from Diagenode.

tag: strain

value: neuron

tag: chip antibody

value: anti-H3K27me3 (Cell Signaling, 9733S, C36B11, Lot 8)


title: Mmu Input replicate 1

description:
Mmu_Input_1
processed data file: Mmu_Input.bigWig

source_name: Mmu Input

value: pooled


title: WT Chromatin-associated Total RNA rep-1 run-1

tag: genotype

value: wild type

value: Embryonic Stem cells

value: chromatin-associated


title: Mmu aRG-N H3K27me3 tech replicate 2

description:
Mmu_aRG-N_K27_2
processed data file: Mmu_aRG-N_K27.bigWig

source_name: Mmu aRG-N H3K27me3 tech

value: neurogenic apical radial glia


title: int-c.5 (GSHO 2003) 1327V

value: Waddington stage 3.5


title: vrs1 (GSHO 1907) 1327AW


title: siFGF13_rep3

city: Rehovot

first: Moshe

last: Oren

address: Herzl Street

department: Department of Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Fastq files for each sample were generated by the usage of Illumina CASAVA-1.8.2 software (basecalling)
Reads were aligned to the Homo sapiens hg19 genome, using Tophat (v2.0.10).
Counting reads on genes annotated in RefSeq hg19, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq (v1.18.0)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: Excel file includes the normalized counts (DESeq Normalization)

source_name: H460_ FGF13 siRNAs

growth_protocol: H460 cells were routinely maintained at 37°C in a 5% CO2 humidified incubator and were grown in DMEM plus 10% heat-inactivated FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from flash-frozen cell pellets with the miRNeasy kit (Qiagen), according to the manufacturer's instructions.
TruSeq RNA sample preparation Kit v2 protocol (Illumina)

treatment_protocol: Control (Non-Targeting siRNA Pool) and FGF13 (SMARTpool) siRNAs were purchased from Dharmacon and transfected at a final concentration of 20 nM. siRNA transfections were performed with Dharmafect 1 reagent (Dharmacon), following the manufacturer's instructions.

tag: cell line

value: Non-small cell lung cancer cell line (NSCLC)

tag: transfected with

value: FGF13 siRNAs


title: siC_rep3

source_name: H460_Control siRNA

value: Control siRNA


title: Mmu aRG-N H3K27me3 tech replicate 1

description:
Mmu_aRG-N_K27_1
processed data file: Mmu_aRG-N_K27.bigWig


title: int-c.5 (GSHO 2003) 1327U


title: Mmu N H3K27me3 replicate 1

description:
Mmu_N_K27_1
processed data file: Mmu_N_K27.bigWig


title: SL147680


title: siC_rep2


title: siFGF13_rep2


title: siFGF13_rep1


title: Mmu bRG H3K27me3 replicate 2

description:
Mmu_bRG_K27_2
processed data file: Mmu_bRG_K27.bigWig

source_name: Mmu bRG H3K27me3

value: basal radial glia


title: vrs1 (GSHO 1907) 1327AX


title: int-c.5 (GSHO 2003) 1327W


title: int-c.5 (GSHO 2003) 1327X


title: Mmu aRG-P H3K27me3 replicate 2

description:
Mmu_aRG-P_K27_2
processed data file: Mmu_aRG-P_K27.bigWig

source_name: Mmu aRG-P H3K27me3

value: proliferative apical radial glia


title: vrs1 (GSHO 1907) 1327AV


title: Mmu Input replicate 2

description:
Mmu_Input_2
processed data file: Mmu_Input.bigWig


title: siC_rep1


title: Mmu aRG-P H3K27me3 replicate 1

description:
Mmu_aRG-P_K27_1
processed data file: Mmu_aRG-P_K27.bigWig


title: SL147677


title: vrs1 (GSHO 1907) 1327AU


title: Mmu NEC H3K27me3 replicate 2

description:
Mmu_NEC_K27_2
processed data file: Mmu_NEC_K27.bigWig

source_name: Mmu NEC H3K27me3

value: neuroepithelial cell


title: vrs1 (GSHO 1907) 1327AT


title: Mmu NEC H3K27me3 replicate 1

description:
Mmu_NEC_K27_1
processed data file: Mmu_NEC_K27.bigWig


title: 647762_HuTSCM

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (trimglore) and mapped to the hg19 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: hg19
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: HuTSCM

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.
Whole genome bisulfite sequencing

tag: individual

value: TSCM subject#2


title: 647761_HuTCM

source_name: HuTCM

value: TCM subject#2


title: Mmu bRG H3K27me3 replicate 1

description:
Mmu_bRG_K27_1
processed data file: Mmu_bRG_K27.bigWig


title: vrs1 (GSHO 1907) 1327AS

value: IL in cv. Bowman


title: Mmu N H3K4me3 replicate 2

description:
Mmu_N_K4_2
processed data file: Mmu_N_K4.bigWig

source_name: Mmu N H3K4me3

value: neuron

value: anti-H3K4me3 (Cell Signaling, 9751S, LC42,D8, Lot 7)


title: vrs4.k (GSHO 1986) 1327AR

value: Waddington stage 5.5


title: vrs4.k (GSHO 1986) 1327AQ


title: vrs4.k (GSHO 1986) 1327AN


title: 647760_HuTEM

source_name: HuTEM

value: TEM subject#2


title: 383227_TCMD204

value: TCM subject#1


title: 383226_TEMD203

value: TEM subject#1


title: Mmu aRG-P H3K4me3 replicate 2

description:
Mmu_aRG-P_K4_2
processed data file: Mmu_aRG-P_K4.bigWig

source_name: Mmu aRG-P H3K4me3


title: Mmu bRG H3K4me3 replicate 2

description:
Mmu_bRG_K4_2
processed data file: Mmu_bRG_K4.bigWig

source_name: Mmu bRG H3K4me3


title: vrs4.k (GSHO 1986) 1327AM


title: Lamin B1 ChIP-Seq following SHM induction replicate 2

city: London

first: Andrejs

last: Braun

state: London

address: Charterhouse Square,

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Raw reads were mapped to the human genome (hg19) using the Bowtie 2 alignment software. PCR duplicates were removed using Picard's MarkDuplicates program
To avoid any normalization bias, each pair of aligned input and ChIP BAM files were further processed to have the same read depth, by using Picard's DownsampleSam program on the larger of the two files.
Lamin B1 enriched regions were defined using the enriched domain detector algorithm  (EDD) as previously described
The aligned peaks were then visualised using the Interactive Genome Browser (IGV)
Genome_build: hg19
Supplementary_files_format_and_content: genome coverage binary tdf files were generated to be viewed using IGVtools

source_name: BL2 cell line

growth_protocol: BL2 cell line maintained in antibiotic-free RPMI 1640 medium with 10% FCS and 2 mM L-glutamine

extract_protocol:
Lysates were clarified from sonicated nuclei and Lamin B1-DNA complexes were isolated with antibody.
Library was prepared using Nextera DNA Library Preparation Kit essentially as described by manufacturer

treatment_protocol: Cells were incubated at 0.4x106 cells/ml in RPMI medium, containing 2.5 µg/ml of biotinylated anti−human IgM (clone UCHB1 Caltag Laboratories, Buckingham, UK), of anti-CD19 (clone RFB9, in-house, Southampton, UK) and anti-CD21 (clone HB135, in-house, Southampton, UK) for 20 min at 4 °C. Cells were washed and then resuspended in RPMI medium containing streptavidin-conjugated magnetic beads (5−7 beads/cell) (Dynabeads M280, Thermo-Fisher, UK) and incubated with agitation at 4 °C for 20 min. Complete RPMI medium containing 2% serum was added to the activated cells, followed by incubation at 37 °C

value: Lamin B1 (Abcam ab1648)

value: Burkitt's lymphoma

tag: immunology

value: CD3 -, CD10 +, CD13 -, CD19 +, CD20 +, CD34 -, CD37 +, CD38 +, cyCD79a +, CD80 +, CD138 -, HLA-DR +, sm/cyIgG -, sm/cyIgM +, sm/cykappa -, sm/cylambda +


title: vrs4.k (GSHO 1986) 1327AP


title: int-a.1 (GSHO 2055) 1327AF


title: 383225_TSD202

value: TSCM subject#1


title: Lamin B1 ChIP-Seq in control cell population replicate 2

tag: cell type


title: 383224_TND201

value: TN subject #1


title: int-a.1 (GSHO 2055) 1327AE


title: Mmu aRG-N H3K4me3 replicate 2

description:
Mmu_aRG-N_K4_2
processed data file: Mmu_aRG-N_K4.bigWig

source_name: Mmu aRG-N H3K4me3

value: neurogenic apical radial glia


title: Mmu aRG-P H3K4me3 replicate 1

description:
Mmu_aRG-P_K4_1
processed data file: Mmu_aRG-P_K4.bigWig

value: proliferative apical radial glia


title: vrs4.k (GSHO 1986) 1327AO

source_name: apex tissue

value: Waddington stage 3.5


title: Mmu NEC H3K4me3 replicate 2

description:
Mmu_NEC_K4_2
processed data file: Mmu_NEC_K4.bigWig

source_name: Mmu NEC H3K4me3

value: neuroepithelial cell


title: Lamin B1 ChIP-Seq following SHM induction replicate 1


title: Mmu aRG-N H3K4me3 replicate 1

description:
Mmu_aRG-N_K4_1
processed data file: Mmu_aRG-N_K4.bigWig


title: Lamin B1 ChIP-Seq in control cell population replicate 1


title: int-a.1 (GSHO 2055) 1327AD


title: Mmu NEC H3K4me3 replicate 1

description:
Mmu_NEC_K4_1
processed data file: Mmu_NEC_K4.bigWig


title: Mmu bRG H3K4me3 replicate 1

description:
Mmu_bRG_K4_1
processed data file: Mmu_bRG_K4.bigWig

value: basal radial glia


title: 647759_HuTN

source_name: HuTN

value: TN subject #2


title: Mmu N H3K4me3 replicate 1

description:
Mmu_N_K4_1
processed data file: Mmu_N_K4.bigWig

value: neuron


title: Mmu NEC replicate 4

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were trimmed with cutadapt (-m 20 -q 25)
Trimmed Reads were mapped using tophat v2.0.11 (-G $gtfFile -g1)
Abundance estimation was performed using cuffdiff (v2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM normalized expressoin score tables as provided by cummerbund::countMatrix

source_name: NEC

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Complete cDNA was synthesized from half of the isolated mRNA with SmartScribe reverse transcriptase (Clontech) using a universally tailed poly-dT primer and template switching oligos. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase (12 cylces). After ultrasonic shearing of the amplified cDNA (Covaris S2), samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs), in brief: fragments were end repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Subsequently, the NGS libraries were finalized by a universally primed PCR amplification (15 cycles). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75-bp single end sequencing on the Illumina HiSeq 2000 platform providing on average 35 Mio reads per sample.

value: neural progenitor cells


title: Mmu NEC replicate 5


title: Mmu NEC replicate 3


title: Bowman 1327H

value: Waddington stage 5.5

value: cv. Bowman

value: Bowman 1327H 1327H


title: int-a.1 (GSHO 2055) 1327AA

value: IL in cv. Bowman


title: Bowman 1327G

value: Bowman 1327G 1327G


title: Mmu NEC replicate 1


title: Mmu NEC replicate 2


title: Bowman 1327E

value: Bowman 1327E 1327E


title: Bowman 1327D

value: Bowman 1327D 1327D


title: Bowman 1327C

value: Bowman 1327C 1327C


title: U87MG-control

city: Seoul

first: Seon Yong

last: Lee

address: 145 Anam-ro, Seungbuk-gu

country: South Korea

institute: Korea University

data_processing:
Data were processed using Complete Genomics RNA-seq program.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: GRCh38.p4
Supplementary_files_format_and_content: Excel spreadsheet format which includes contents; 1) NCBI gene accession ID, 2) Gene length, 3) Means of FPKM values for each experimental sets, 4) Log2 ratio of gene expression, 5) Probability value (PA), 6) Gene symbol, 7) Gene description, 8) KEGG orthology, 9) GO component, 10) GO function, 11) GO process, 12) Blast nr

growth_protocol: U87MG cells were grown in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and gentamicin sulfate (50 μg/ml).

extract_protocol:
Total RNA was isolated from U87MG cells using TRIzol reagent (3 prime) according to the manufacturer's instructions.
Libraries were prepared for RNA-seq by using CG RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) coporation.

value: Glioblastoma cells

tag: cell line source gender

value: male

tag: cell line source age

value: 44 years

tag: cell line source tissue

value: Brain

value: pCDH-CMV-MCS-EF1-Puro (U87MG-control)


title: Bowman 1327A

tag: developmental stage

value: Waddington stage 3.5

value: Bowman 1327A 1327A


title: Bowman 1327B

value: Bowman 1327B 1327B


title: KO_IP2

status: Public on Aug 02 2017

city: Edinburgh

first: Emily

last: Osterweil

address: Hugh Robson building

institute: University of Edinburgh

description:
TRAP IP
Ribosome bound mRNA

data_processing:
Alignment to ensembl V80 with STAR aligner 2.4.0i
read count per gene level with feature count 1.4.6-p2
DEseq2 run with betaprior=FALSE. Littermates were paired for this analysis
Genome_build: mm10
Supplementary_files_format_and_content: read count data used for DESeq2 (WTKOIN and WTKOIP). IP and IN data are in separate files with sample IDs on first column. DESeq2 output from IP comparison and IN comparison (ip.Res and in.Res). All in csv format

source_name: CA1 pyramidal cells

growth_protocol: All experiments are done with p25 -p32 male littermate paired mice.

extract_protocol:
Hippocampus was rapidly removed and homogenised. RNA samples were amplified with RNAseq V2 ovation kit before library construction.
Libraries were constructed using Wafergen’s PrepX Complete ILMN 32i DNA Library Kit (cat number 400076) using the Apollo 324. Ligation of adapters was performed using Illumina Adapters within the Multiplexing Sample Preparation Oliogonucleotide Kit.

tag: tissue/cell type

value: CA1 pyramidal cells

value: Fmr1 KO

tag: gender


title: WT_IP2

description:
TRAP IP
Ribosome bound mRNA

value: WT


title: WT_IP3

description:
TRAP IP
Ribosome bound mRNA


title: KO_IN3

description:
Input
Total RNA

source_name: Hippocampus

value: Hippocampus


title: KO_IP3

description:
TRAP IP
Ribosome bound mRNA


title: KO_IP1

description:
TRAP IP
Ribosome bound mRNA


title: int-a.1 (GSHO 2055) 1327AC

value: IL in cv. Bowman


title: KO_IN1

description:
Input
Total RNA


title: U87MG-CD133

source_name: U87MG_CD133 overexpression

value: pCDH-CMV-CD133-EF1-Puro (U87MG-CD133)


title: WT_IN2

description:
Input
Total RNA


title: WT_IN3

description:
Input
Total RNA


title: WT_IN1

description:
Input
Total RNA


title: WT_IP1

description:
TRAP IP
Ribosome bound mRNA


title: int-a.1 (GSHO 2055) 1327AB


title: Bowman 1327F

value: Waddington stage 5.5

value: cv. Bowman

value: Bowman 1327F 1327F


title: AEG_1CKO_chow_3230 biological rep1

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Gene expression data from hepatocyte-specific AEG-1 knockout mice

data_processing:
At each processing step, sequenced reads were QC'd using FastQC.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic 0.33, and mapped to mm10 whole genome (autosomes and sex chromosomes only) using subread 1.4.6-p4
Read counts were calculated using featureCounts 1.4.6-p4 over Mus_musculus.GRCm38.83 GTF file from ENSEMBL
# Program:featureCounts v1.4.6-p4; Command:"featureCounts" "-t" "exon" "-g" "gene_id" "-a" "/home/sequencing/data/ExtData/UCSC/mm10/Mus_musculus.GRCm38.83_filt.gtf" "-o" "counts.txt" "02_subread-align/AEG_1CKO_HFD_2660.bam" "02_subread-align/AEG_1CKO_HFD_2662.bam" "02_subread-align/AEG_1CKO_HFD_2666.bam" "02_subread-align/AEG_1CKO_chow_3230.bam" "02_subread-align/AEG_1CKO_chow_3231.bam" "02_subread-align/AEG_1CKO_chow_3232.bam" "02_subread-align/WT_HFD_2659.bam" "02_subread-align/WT_HFD_2661.bam" "02_subread-align/WT_HFD_2665.bam" "02_subread-align/WT_chow_2776.bam" "02_subread-align/WT_chow_2777.bam" "02_subread-align/WT_chow_3354.bam"
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Hepatocyte-specific AEG-1 knockout mice

growth_protocol: Livers were harvested from chow-fed 12 wks old AEG-1fl/fl and AEG-1DHEP mice.

extract_protocol:
Trizol extraction of total RNA was performed using QIAGEN columns according to the manufacturer's instruction.
Total RNA, extracted using Qiagen miRNAeasy mini kit (Qiagen, Valencia, CA) from livers of 3 adult mice per group, was employed for RNA sequencing. RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and sequenced on Illumina HiSeq2500 platform per manufacturer's protocol.

treatment_protocol: No treatment.

tag: strain background

tag: genotype/variation

value: Hepatocyte-specific AEG-1 knockout mice

tag: age

value: 12 wks

tag: tissue

value: liver


title: WT_chow_3354 biological rep3

description: Gene expression data from mice control

source_name: control mice

value: control mice


title: WT_chow_2776 biological rep1

description: Gene expression data from mice control


title: AEG_1CKO_chow_3231 biological rep2


title: AEG_1CKO_chow_3232 biological rep3


title: KO_IN2

description:
Input
Total RNA

tag: strain

value: male


title: Sample_0160_serum

city: Kiel

first: Matthias

last: Hübenthal

state: SH

address: Rosalind-Franklin-Str. 9

department: Dermatology, Venereology and Allergy

institute: University Hospital Schleswig-Holstein

data_processing:
Raw sequence reads were trimmed for adapters using cutadapt v1.3. Trimmed reads that were shorter than 17 bp and the low quality reads were discarded.
Pre-processed reads mapped (blastn v2.2.30) to viral genomes (RefSeq), viral precursors (miRBase 21) and human non-miRNA short RNAs (RFam) were removed.
Filtered reads were mapped to known miRNA sequences (miRBase 21) using miraligner with default parameters.
The miRNA-arms (±3 nucleotides from canonical mature sequnce and 1 mismatch allowed) and isomiR counts were generated using isomiRs (v1.5.0) bioconductor package.
Supplementary_files_format_and_content: Compressed miraligner output file *.mirna.gz (tab delimited text file). The content is explained in detail: http://seqcluster.readthedocs.io/mirna_annotation.html#manual-of-miraligner-java

source_name: serum

extract_protocol:
Total RNA including small RNA from MACS/FACS sorted cell types was extracted using the mirVana RNA Isolation Kit (Ambion). For whole blood samples, PAXgene Blood miRNA Kit (Qiagen) was used. For serum samples the Qiagen miRNeasy Serum and Plasma kit was used and exosomes were processed using the Total Exosome Isolation Reagent and the Total Exosome RNA and Protein Isolation Kit (Life Technologies). All isolation protocols were conducted according to the manufacturer's instructions, without modification.
Illumina TruSeq Small RNA sample preparation protocol

tag: sample type

value: serum


title: Sample_0161_serum


title: Sample_0154_serum


title: Sample_0157_exosomes

source_name: exosomes

value: exosomes


title: Sample_0158_exosomes


title: Sample_0159_serum


title: Sample_0153_serum


title: Sample_0151_serum


title: Sample_0152_exosomes


title: Sample_0148_serum


title: Sample_0149_exosomes


title: Sample_0150_serum


title: Sample_0150_exosomes


title: Sample_0149_serum


title: Sample_0151_exosomes


title: Sample_0152_serum


title: Sample_0162_serum


title: WT_chow_2777 biological rep2

description: Gene expression data from mice control


title: Sample_0148_exosomes


title: Sample_0156_exosomes


title: Sample_0147_serum


title: Sample_0147_exosomes


title: Sample_0154_exosomes


title: Sample_0146_exosomes


title: Sample_0145_serum


title: Sample_0153_exosomes


title: Sample_0146_serum


title: Sample_0155_exosomes


title: Sample_0145_exosomes


title: Sample_0144_exosomes


title: Sample_0143_exosomes


title: Sample_0141_exosomes


title: Sample_0144_serum


title: Sample_0140_serum


title: Sample_0143_serum


title: Sample_0141_serum


title: Sample_0142_exosomes


title: Sample_0140_exosomes


title: Sample_0139_serum


title: Sample_0136_exosomes


title: Sample_0139_exosomes


title: Sample_0135_serum


title: Sample_0138_serum


title: Sample_0136_serum


title: Sample_0135_exosomes


title: Sample_0138_exosomes


title: Sample_0134_serum


title: Sample_0137_serum


title: Sample_0137_exosomes


title: Sample_0131_serum


title: Sample_0132_serum


title: Sample_0130_exosomes


title: Sample_0129_serum


title: Sample_0134_exosomes


title: Sample_0133_serum


title: Sample_0132_exosomes


title: Sample_0133_exosomes


title: Sample_0127_exosomes


title: Sample_0131_exosomes


title: Sample_0142_serum


title: Sample_0125_exosomes


title: Sample_0130_serum


title: Sample_0129_exosomes


title: Sample_0122_exosomes


title: Sample_0123_serum


title: Sample_0128_exosomes


title: Sample_0128_serum


title: Sample_0127_serum


title: Sample_0121_exosomes


title: Sample_0115_WB

source_name: whole blood

value: whole blood


title: Sample_0114_WB


title: Sample_0116_WB


title: Sample_0126_serum


title: Sample_0125_serum


title: Sample_0111_WB


title: Sample_0112_WB


title: Sample_0124_exosomes


title: Sample_0124_serum


title: Sample_0107_WB


title: Sample_0106_WB


title: Sample_0123_exosomes


title: Sample_0122_serum


title: Sample_0104_WB


title: Sample_0121_serum


title: Sample_0118_WB


title: Sample_0120_WB


title: Sample_0101_WB


title: Sample_0117_WB


title: Sample_0119_WB


title: Sample_0126_exosomes


title: Sample_0095_WB


title: Sample_0096_WB


title: Sample_0113_WB


title: Sample_0110_WB


title: Sample_0109_WB


title: Sample_0089_WB


title: Sample_0108_WB


title: Sample_0090_WB


title: Sample_0105_WB


title: Sample_0100_WB


title: Sample_0102_WB


title: Sample_0098_WB


title: Sample_0099_WB


title: Sample_0086_WB


title: Sample_0097_WB


title: Sample_0082_WB


title: Sample_0093_WB


title: Sample_0092_WB


title: Sample_0078_WB


title: Sample_0094_WB


title: Sample_0091_WB


title: Sample_0077_WB


title: Sample_0088_WB


title: Sample_0085_WB


title: Sample_0075_WB


title: Sample_0084_WB


title: Sample_0087_WB


title: Sample_0083_WB


title: Sample_0070_WB


title: Sample_0069_WB


title: Sample_0072_WB


title: Sample_0073_WB


title: Sample_0080_WB


title: Sample_0071_WB


title: Sample_0079_WB


title: Sample_0076_WB


title: Sample_0067_WB


title: Sample_0064_WB


title: Sample_0065_WB


title: Sample_0081_WB


title: Sample_0066_WB


title: Sample_0068_WB


title: Sample_0062_WB


title: Sample_0061_WB


title: Sample_0063_WB


title: Sample_0059_WB


title: Sample_0074_WB


title: Sample_0060_WB


title: Sample_0057_WB


title: Sample_0054_WB


title: Sample_0056_WB


title: Sample_0055_WB


title: Sample_0053_WB


title: Sample_0052_WB


title: Sample_0051_WB


title: Sample_0050_WB


title: Sample_0048_WB


title: Sample_0046_WB


title: Sample_0044_WB


title: Sample_0049_WB


title: Sample_0043_CD235a

source_name: CD235a cells

tag: leukocytes

tag: erythrocytes

tag: hematocrit

value: blood cell population CD235a


title: Sample_0103_WB


title: Sample_0058_WB


title: Sample_0043_CD19

source_name: CD19 cells

tag: individual

value: blood cell population CD19


title: Sample_0043_CD15

source_name: CD15 cells

value: blood cell population CD15


title: Sample_0043_CD14

source_name: CD14 cells

value: blood cell population CD14


title: Sample_0042_CD235a


title: Sample_0043_CD8

source_name: CD8 cells

value: blood cell population CD8


title: Sample_0042_CD56

source_name: CD56 cells

value: blood cell population CD56


title: Sample_0042_CD15


title: Sample_0042_CD4

source_name: CD4 cells

value: blood cell population CD4


title: Sample_0042_CD8


title: Sample_0043_CD4


title: Sample_0042_CD14


title: Sample_0041_CD235a

value: female

tag: purity


title: Sample_0041_CD56


title: Sample_0041_CD4


title: Sample_0041_CD15


title: Sample_0042_CD19


title: Sample_0041_CD8


title: Sample_0040_CD235a


title: Sample_0047_WB


title: Sample_0045_WB


title: Sample_0040_CD56


title: Sample_0040_CD15


title: Sample_0040_CD19


title: Sample_0040_CD8


title: Sample_0040_CD14


title: Sample_0043_CD56


title: Sample_0040_CD4


title: Sample_0039_CD235a


title: Sample_0039_CD15


title: Sample_0041_CD19


title: Sample_0038_CD56


title: Sample_0039_CD14


title: Sample_0038_CD19


title: Sample_0039_CD56


title: Sample_0039_CD8


title: Sample_0039_CD4


title: Sample_0038_CD15


title: Sample_0038_CD235a


title: Sample_0037_CD235a


title: Sample_0037_CD56


title: Sample_0038_CD4


title: Sample_0038_CD14


title: Sample_0037_CD19


title: Sample_0038_CD8


title: Sample_0037_CD15


title: Sample_0037_CD14


title: Sample_0041_CD14


title: Sample_0036_CD56


title: Sample_0037_CD4


title: Sample_0036_CD15


title: Sample_0036_CD14


title: Sample_0039_CD19


title: Sample_0036_CD8


title: Sample_0037_CD8


title: Sample_0035_CD235a


title: Sample_0035_CD56


title: Sample_0036_CD4


title: Sample_0035_CD19


title: Sample_0034_CD56


title: Sample_0035_CD4


title: Sample_0034_CD235a


title: Sample_0035_CD14


title: Sample_0034_CD15


title: Sample_0035_CD8


title: Sample_0033_CD19


title: Sample_0033_CD56


title: Sample_0033_CD235a


title: Sample_0034_CD14


title: Sample_0033_CD14


title: Sample_0035_CD15


title: Sample_0036_CD235a


title: Sample_0034_CD8


title: Sample_0033_CD15


title: Sample_0032_CD15


title: Sample_0032_CD56


title: Sample_0032_CD19


title: Sample_0032_CD14


title: Sample_0032_CD8


title: Sample_0034_CD4


title: Sample_0033_CD8


title: Sample_0034_CD19


title: Sample_0032_CD4


title: Sample_0036_CD19


title: Sample_0031_CD15


title: Sample_0031_CD19


title: Sample_0031_CD56


title: Sample_0031_CD8


title: Sample_0031_CD14


title: Sample_0030_CD235a


title: Sample_0030_CD19


title: Sample_0030_CD14


title: Sample_0030_CD4


title: Sample_0029_CD19


title: Sample_0030_CD56


title: Sample_0029_CD15


title: Sample_0029_CD14


title: Sample_0029_CD56


title: Sample_0030_CD15


title: Sample_0029_CD8


title: Sample_0031_CD4


title: Sample_0028_CD235a


title: Sample_0030_CD8


title: Sample_0028_CD8


title: Sample_0028_CD14


title: Sample_0028_CD15


title: Sample_0028_CD4


title: Sample_0027_CD235a


title: Sample_0028_CD56


title: Sample_0027_CD56


title: Sample_0027_CD14


title: Sample_0027_CD15


title: Sample_0027_CD8


title: Sample_0033_CD4


title: Sample_0026_CD235a


title: Sample_0027_CD19


title: Sample_0026_CD56


title: Sample_0029_CD235a


title: Sample_0028_CD19


title: Sample_0025_CD235a


title: Sample_0026_CD4


title: Sample_0026_CD8


title: Sample_0026_CD14


title: Sample_0024_CD235a


title: Sample_0025_CD56


title: Sample_0025_CD15


title: Sample_0025_CD19


title: Sample_0026_CD19


title: Sample_0025_CD8


title: Sample_0024_CD19


title: Sample_0025_CD4


title: Sample_0024_CD15


title: Sample_0024_CD14


title: Sample_0024_CD8


title: Sample_0027_CD4


title: Sample_0024_CD4


title: Sample_0023_CD56


title: Sample_0023_CD235a


title: Sample_0026_CD15


title: Sample_0023_CD19


title: Sample_0023_CD15


title: Sample_0023_CD4


title: Sample_0023_CD8


title: Sample_0023_CD14


title: Sample_0022_CD235a


title: Sample_0022_CD56


title: Sample_0022_CD19


title: Sample_0025_CD14


title: Sample_0022_CD4


title: Sample_0024_CD56


title: Sample_0021_CD235a


title: Sample_0021_CD56


title: Sample_0022_CD15


title: Sample_0022_CD8


title: Sample_0021_CD15


title: Sample_0021_CD19


title: Sample_0021_CD8


title: Sample_0021_CD4


title: Sample_0020_CD56


title: Sample_0020_CD14


title: Sample_0020_CD15


title: Sample_0020_CD8


title: Sample_0019_CD235a


title: Sample_0019_CD15


title: Sample_0019_CD19


title: Sample_0019_CD14


title: Sample_0020_CD19


title: Sample_0018_CD235a


title: Sample_0019_CD56


title: Sample_0019_CD8


title: Sample_0019_CD4


title: Sample_0022_CD14


title: Sample_0018_CD56


title: Sample_0018_CD19


title: Sample_0018_CD15


title: Sample_0021_CD14


title: Sample_0017_CD19


title: Sample_0018_CD14


title: Sample_0017_CD56


title: Sample_0020_CD235a


title: Sample_0017_CD14


title: Sample_0018_CD8


title: Sample_0020_CD4


title: Sample_0017_CD4


title: Sample_0016_CD56


title: Sample_0016_CD15


title: Sample_0016_CD235a


title: Sample_0016_CD14


title: Sample_0016_CD19


title: Sample_0015_CD235a


title: Sample_0015_CD19


title: Sample_0016_CD4


title: Sample_0015_CD56


title: Sample_0015_CD14


title: Sample_0016_CD8


title: Sample_0015_CD8


title: Sample_0017_CD235a


title: Sample_0015_CD15


title: Sample_0018_CD4


title: Sample_0014_CD15


title: Sample_0014_CD235a


title: Sample_0014_CD56


title: Sample_0015_CD4


title: Sample_0017_CD8


title: Sample_0017_CD15


title: Sample_0014_CD19


title: Sample_0013_CD56


title: Sample_0013_CD235a


title: Sample_0014_CD8


title: Sample_0013_CD19


title: Sample_0013_CD15


title: Sample_0013_CD14


title: Sample_0013_CD8


title: Sample_0013_CD4


title: Sample_0014_CD14


title: Sample_0012_CD235a


title: Sample_0012_CD56


title: Sample_0012_CD15


title: Sample_0012_CD19


title: Sample_0012_CD14


title: Sample_0011_CD56


title: Sample_0012_CD4


title: Sample_0011_CD235a


title: Sample_0014_CD4


title: Sample_0011_CD14


title: Sample_0011_CD8


title: Sample_0011_CD19


title: Sample_0011_CD15


title: Sample_0011_CD4


title: Sample_0010_CD235a


title: Sample_0010_CD19


title: Sample_0010_CD56


title: Sample_0010_CD8


title: Sample_0010_CD15


title: Sample_0009_CD14


title: Sample_0009_CD4


title: Sample_0012_CD8


title: Sample_0008_CD235a


title: Sample_0009_CD8


title: Sample_0008_CD19


title: Sample_0007_CD19


title: Sample_0007_CD56


title: Sample_0010_CD14


title: Sample_0010_CD4


title: Sample_0007_CD15


title: Sample_0008_CD8


title: Sample_0007_CD14


title: Sample_0009_CD15


title: Sample_0009_CD235a


title: Sample_0008_CD56


title: Sample_0008_CD14


title: Sample_0009_CD56


title: Sample_0009_CD19


title: Sample_0006_CD56


title: Sample_0008_CD15


title: Sample_0006_CD15


title: Sample_0006_CD14


title: Sample_0006_CD8


title: Sample_0007_CD235a


title: Sample_0006_CD4


title: Sample_0008_CD4


title: Sample_0007_CD4


title: Sample_0005_CD14


title: Sample_0005_CD15


title: Sample_0006_CD19


title: Sample_0007_CD8


title: Sample_0005_CD235a


title: Sample_0006_CD235a


title: Sample_0005_CD56


title: Sample_0004_CD19


title: Sample_0005_CD8


title: Sample_0003_CD56


title: Sample_0004_CD8


title: Sample_0003_CD19


title: Sample_0005_CD4


title: Sample_0004_CD56


title: Sample_0004_CD235a


title: Sample_0003_CD15


title: Sample_0004_CD14


title: Sample_0004_CD4


title: Sample_0002_CD235a


title: Sample_0003_CD4


title: Sample_0003_CD8


title: Sample_0003_CD235a


title: Sample_0003_CD14


title: Sample_0002_CD56


title: Sample_0002_CD15


title: Sample_0005_CD19


title: Sample_0002_CD19


title: Sample_0002_CD14


title: Sample_0002_CD4


title: Sample_0002_CD8


title: Sample_0001_CD56


title: Sample_0001_CD19


title: Sample_0004_CD15


title: Sample_0001_CD8


title: Sample_0001_CD15


title: Sample_0001_CD14


title: Sample_0001_CD4


title: NB1643_Input

city: Philadelphia

first: John

middle: M

last: Maris

state: Pennsylvania

address: 3501 Civic Center Blvd, CTRB

institute: Children's Hospital of Philadelphia

data_processing:
Trim Galore v0.4.1 was used for quality trimming with --fastqc parameter to provide quality control metrics on the trimmed sequences.
Bowtie v1.1.2 was used to align the trimmed reads to the hg19 reference genome using parameters --best --strata -m1 -n2.
Samtools v1.3.1 was used to remove duplicates from the aligned reads usng the rmdup command
MACS2 v2.1.0.20150731 was used to call significant peaks using the callpeak command with parameters -B to save extended fragment pileup at every bp into a bedGraph file format, --call-summits to find subpeak summits in each enriched peak region, -q 0.05 to set FDR cutoff and --SPMR option to get normalized peak value in units of signal per million reads. The two biological replicates of NB-1643 were pooled together.
Bedtools v2.26.0 intersect command was used to filter the called peaks for any artifacts that tend to show high signal such as centromeric, telomeric and satellite repeats using the blacklisted regions defined by UCSC.
Genome_build: hg19
Supplementary_files_format_and_content: The bigWig (.bw) files were generated using UCSC's bedGraphToBigWig utility by converting bedGraph output of MACS2 to bigWig for visualization in IGV; The _peaks.txt files were generated by MACS2 and contain information about each called peak like chromosomal coordinates, pileup, -log10(pvalue), -log10(qvalue); The filtered peak (_peaks.filtered.narrowPeak) files were obtained after filtering out the blacklisted regions and contain the peak locations of signal enrichment together with peak summit, fold-change, pvalue and qvalue.

source_name: NB-1643 neuroblastoma cells

growth_protocol: Cells were grown to 80% confluence on 15cm tissue culture plates in 20ml of medium. NGP and Kelly cells were grown in RPMI with 10% FBS, 1% L-glutamine and 1% Penn/Strep. NB-1643 cells were grown in IMDM with 20% FBS, 1% L-glutamine and 1% Penn/Strep.

extract_protocol:
Cells were lysed in 5 pellet volumes of FA lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 1.0% Triton-X-100, 0.1% SDS, 0.1% Deoxycholate), supplemented with fresh protease inhibitors and DTT. Beads were washed 3x in ChIP Wash Buffer (0.1% SDS,1.0% Tritotn-X-100, 2mM EDTA pH 8.0, 150mM NaCl, 20mM Tris-HCL pH8.0)and once with Final Wash Buffer (0.1% SDS, 1.0% Triton-X-100, 2mM EDTA pH8.0, 500mM NaCl, 20mM Tris-HCL pH 8.0)
NEB Ultra manufacturer's instructions

treatment_protocol: 415ul of 37% formaldehyde (final concentration 0.75%) was added to the medium and rocked for 10 min to fix cells and 1.5ml of 2.5M glycine (finalconcentration 0.18M) was added to quench the formaldehyde and the plate was rocked for an additional 5 min.

tag: chip antibody

tag: cell line

tag: cell type

value: Neuroblastoma

tag: mycn status

value: amplified


title: Kelly_Input

source_name: Kelly neuroblastoma cells

value: Kelly


title: NGP_Input

source_name: NGP neuroblastoma cells

value: NGP


title: Kelly_MYCN_ChIPSeq

value: B8.4b (Santa Cruz, Catalog# sc-53993, Lot# K1315)


title: NB1643_MYCN_ChIPSeq

description:
NB1643-MYCN replicate 1
NB1643-MYCN replicate 2


title: AB1247_L1_S2_R1 IL4-IL10_fatty

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

data_processing:
Illumina RTA v. 2.4.6 software (NextSeq System Suite v2.0) was used for basecalling.
Bcl files output by Illumina NextSeq500 sequencer were converted to fastq format with Bcl2fastq v2.16.
The reads were aligned to the mouse mm10 genome with TopHat2 (v. 2.0.8) set for first strand mRNA and a median fragment size of 280b in Partek Flow (Build 4.0.15.0702).
Aligned reads were mapped to the mouse RefSeq transcriptome (2015-0804) with the Partek Flow (Build 4.0.15.0702) EM algorithm function, then exported as counts per gene.
Read counts per gene were normalized as Reads per Million (aligned) reads by sample (RPM), shifted by +1, converted to log2, and normalized by the upper quantile across samples with JMP/Genomics 7.0 (SAS Institute Inc., Cary N.C.).
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Tab-delimited text file with counts per gene per sample (output of Partek E/M mapping algorithm)
Supplementary_files_format_and_content: Tab-delimited text file with normalized and filtered counts per gene per sample (as described)

source_name: Liver Tissue

growth_protocol: Male mice were obtained from Taconic Farms at 6-8 weeks of age, all genotypes are on a C57Bl6 background.

extract_protocol:
Livers were perfused and approximately 10-20 mg of liver tissue was collected for RNA isolation.  Samples were homogenized in 750 ul of Trizol reagent in a Precellys homogenizer with stainless steel beads. A chloroform extraction was performed and RNA was isolated using MagMAX-96 Total RNA Isolation Kit (Life Technologies) according to manufacturer’s protocol with DNase treatment.
Libraries were prepared with Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Product # RS-122-2101) using nominal input of 3 ug total RNA per sample following the standard protocol document “Illumina TruSeq Stranded mRNA Sample Preparation Guide” (Part # 15031047 Revision E, October 2013).

treatment_protocol: Wild type, IL-4 knockout and IL-10/IL-4 double knockout mice on normal or high fat diet;. mice were fed with either normal chow or 60%kcal from fat diet (Harlan TD.06414) for 15 weeks

tag: background strain

tag: genotype

value: IL-10/4 dKO

value: liver

tag: diet

value: high fat diet


title: AB1245_L1_S4_R1 IL4-IL10_fatty


title: AB1246_L1_S3_R1 IL4-IL10_fatty


title: AB1239_L1_S9_R1 IL4_fatty

value: IL-4 KO


title: AB1236_L1_S11_R1 IL4_fatty


title: AB1244_L1_S5_R1 IL4-IL10_normal

value: normal


title: AB1241_L1_S8_R1 IL4-IL10_normal


title: AB1238_L1_S10_R1 IL4_fatty


title: AB1242_L1_S7_R1 IL4-IL10_normal


title: NGP_MYCN_ChIPSeq


title: AB1229_L1_S18_R1 WT_fatty

value: wild type


title: AB1233_L1_S14_R1 IL4_normal


title: AB1230_L1_S17_R1 WT_fatty


title: AB1234_L1_S13_R1 IL4_normal


title: AB1243_L1_S6_R1 IL4-IL10_normal


title: AB1227_L1_S19_R1 WT_fatty


title: AB1226_L1_S20_R1 WT_normal


title: AB1224_L1_S22_R1 WT_normal


title: ChIP-seq AR R1-D567 non radiated control cells

city: Dallas

first: Ganesh

middle: V

last: Raj

address: 5323 Harry Hines Blvd

department: Department of Urology

institute: UT SOUTHWESTERN MEDICAL CENTER

data_processing:
Basecalling was done using bcl2fastq/2.17
Fastq files were trimmed for quality and adapters using fastq-mcf (ea-utils/1.1.2-806)
Fastq files were mapped to hg19 (UCSC) using bowtie/2.2.3
Reads with mapping quality less than 10 were removed using samtools/1.2-2-gf8a6274
Duplicates were removed using picard-tools/1.127
Normalized bigwig files were made using homer/v4.8.3
Peak calling was done using MACS/2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files contain normalized read coverage
Supplementary_files_format_and_content: narrowPeak files are bed files with peaks in narrowPeak format

growth_protocol: RPMI 1640 medium supplemented with 10% (vol/vol) FBS in a 5% CO2 incubator at 37 °C

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturer's protocol (Diagenode). ChIP DNA was isolated and purified (IPure Kit, Diagenode) from samples.
Next- generation sequencing library preparation using KAPA Hyper Prep kit (KAPA Biosystems) using TruSeq adapters (Integrated DNA Technologies). A quality check of the purified libraries was carried out using the Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were radiated with 10 Gy, and fixed in formaldehyde. They were lysed to carry out ChIPs using RNApolII antibody (Biolegend, 920101) and Androgen Receptor (SCBT, sc-816)

value: Transcription activator-like effector nuclease genetically-engineered cell lines derived from CWR-R1 PCa cells

tag: sample group

value: non-radiated control cells

value: Androgen Receptor (SCBT, sc-816)


title: AB1225_L1_S21_R1 WT_normal


title: AB1248_L1_S1_R1 IL4-IL10_fatty


title: ChIP-seq RNApolII R1-D567 non radiated control cells

value: RNApolII antibody (Biolegend, 920101)


title: Input R1-D567 non radiated control cells


title: Input R1-D567 Radiated cells

value: radiated cells


title: ChIP-seq AR R1-D567 Radiated cells