title: Ani1_D3

description: Cynomolgus macaque

source_name: Whole blood, oral 100PFU, day 3

value: 100 PFU

value: Oral


title: Healthy_NOTNV11LH2E

status: Public on Nov 09 2017

type: SRA

city: Tartu

first: Viktorija

last: Kukushkina

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

library_source: transcriptomic

data_processing:
Data quality was checked with fastQC v.0.11.3 before and after preprocessing step.
Adapter removal and trimming with Trimmomatic tool v. 0.32. Parameters:  PE, -phred33,ILLUMINACLIP:/gpfs/depoofs/a73038/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa:2:30:10:8:'true', LEADING:3, TRAILING:3, HEADCROP:11, SLIDINGWINDOW:4:30, MINLEN:36.
Low quality reads removal was made with fastq_quality_filter from Fastx toolkit v. 0.0.13. Parameters: -Q33, -q 30, -p 50
Good quality reads were mapped using TopHat v. 2.0.11. Parameters: --bowtie1, -p 12, --mate-inner-dist 300, --mate-std-dev 100, --library-type fr-firststrand. Bam files name sorted with picard-tools-1.102 SortSam script. Parameters: SO=queryname.
Raw read counts were counted with HTSeq-count v.0.6.1. Parameters: --format=bam, --stranded=reverse, --type=exon, --idattr=gene_id. Annotation GTF version: Ensembl v.75
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count tab delimited matrix, edgeR CountsPerMillion comma delimited matrix.

molecule: total RNA

organism: Homo sapiens

source_name: Endometrium

extract_protocol:
Tissue samples were extracted with Pipelle® catheters under sterile conditions from 23-36-year-old  healthy and IVF women in with BMI of 19-29 Kg/m2, rinsed with PBS and processed immediately or frozen at -80 °C.
Up to 30 mg of the tissue was homogenized in the presence of QIAzol reagent (Qiagen) and processed using miRNeasy Mini kit (Qiagen), following manufacturer's protocol. miRNA content was decreased using Qiagen's MinElute protocol. Purified RNA quality was assigned with Bioanalyzer (Agilent Technologies).cDNA libraries were generated from ~1 μg of endometrial total RNA using Illumina TruSeq Stranded technology (Illumina), followed by cDNA quality control with Bioanalyzer

tag: gender

value: Female

tag: tissue

value: Endometrium

tag: receptivity time-point

tag: country of origin

value: Estonia

tag: tissue state

value: Healthy

tag: sequencing batch


title: Healthy_NOTNV04LH8E


title: Healthy_NOTNV04LH2E


title: E10_rep2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

description: Otocysts from E10.5 embryos replicate 2

library_source: genomic

data_processing:
Alignment: reads were aligned using mm9 assembly as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bigWig format for visualization of nucleosome free signal (fragment lengh < 130 bp)

molecule: genomic DNA

organism: Mus musculus

source_name: Otocysts from E10.5 embryos

growth_protocol: Wild-type C57BL/6 mice

extract_protocol:
E10.5 mouse otocysts or E14 mouse cochleae were dissected, tissue was digested with Collagenase (C0130, Sigma, 0.3mg/ml) during 45 minutes at 37ºC and cells were suspended and counted in a Neubauer chamber.
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: LY411575 treatment (University of Dundee, UK, 100nM) was performed overnight on E14 mouse cochlea previous to ATAC-Seq procedure in a DMEM media with 1% FBS with L-glutamine and antibiotics

tag: strain

tag: genotype/variation

value: WT

value: otocysts

tag: developmental stage

tag: treatment

value: control


title: Ani1_D6

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

country: USA

institute: Cleveland Clinic Lerner Research Institute

description: Cynomolgus macaque

data_processing:
Base calls generated on a HiSeq 2500 using paired end 2x100bp dual-index format.
Trimmed with FASTX-Toolkit v0.0.14.
Alignment: Tophat v2.1.0 with Bowtie2 v2.2.6.
Count Tables generated with HTSeq v0.5.4.
Genome_build: Macaca_fascicularis_5.0 (GCF_000364345.1)
Supplementary_files_format_and_content: *txt: Tab-delimited text file contains unnormalized count data from HTSeq output.

organism: Macaca fascicularis

source_name: Whole blood, oral 100PFU, day 6

extract_protocol:
Previously flash-frozen whole blood (250ul) treated with 750ul of Trizol.
PureLink RNA Mini Kit.
TruSeq Stranded Total RNA Library Prep Kit (Illumina) on Silicone G3 Liquid Handling Robot (PerkinElmer).

treatment_protocol: Cynomolgus macaques were infected with Ebola variant Makona at three different doses and three different routes of infection.

value: Whole blood

tag: status

value: Infected

tag: virus

value: EBOV Makona

tag: virus dose

tag: infection route

tag: dpi

tag: animal id


title: E14-WT_rep1

description: Otocysts from E14 embryos (WT) replicate 1

source_name: Otocysts from E14 embryos (WT)


title: Healthy_NOTNV12LH2E


title: Ani3_D0

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 10PFU, day 0

value: Control

value: 10 PFU

value: Intramuscular


title: Ani1_D10

description: Cynomolgus macaque

source_name: Whole blood, oral 100PFU, day 10


title: Healthy_NOTNV03LH8E


title: Ani1_D0

description: Cynomolgus macaque

source_name: Whole blood, oral 100PFU, day 0


title: Healthy_NOTNV03LH2E


title: E10_rep1

description: Otocysts from E10.5 embryos replicate 1


title: 20150605.B-Kurtulus_group4

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

description: group 4

data_processing:
Basecalls performed using CASAVA 1.8 and convered into fastq files with bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl canFam3.1 genome assembly using STAR-2.5.1b with following parameters: --outFilterMultimapNmax 50   --outFilterMatchNmin 30   --outFilterMismatchNmax 10   --outFilterMismatchNoverLmax 0.05   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --chimSegmentMin 15   --chimScoreMin 15   --chimScoreSeparation 10   --chimJunctionOverhangMin 15   --sjdbOverhang 150
Counts were generated by Rsubread 1.18.0 with the following parameters: 'Multimapping reads : primary only', 'Multi-overlapping reads : counted', 'Overlapping bases : 10'
Genome_build: CanFam3.1
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

organism: Canis lupus familiaris

source_name: canine corpus luteum

extract_protocol:
Total RNA was extracted using TRIzol® Reagent following the manufacturer's protocol (Invitrogen, Carlsbad, CA, USA). The RNA purity and quantity was measured with a NanoDrop 2000C® spectrophotometer (Thermo Fischer Scientific AG, Reinach, CH). Further purification of RNA was performed by the RNeasy® Mini Kit (Qiagen GmbH, Hilden, DE). RNA integrity was assessed with the Agilent 2200 TapeStation System. The RNA integrity numbers (RIN) ranged from 7.2 to 9.5.
The quality and quantity of isolated RNA was determined with Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of enriched libraries were validated using the Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq PE Cluster Kit v4-cBot-HS or TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc., California, USA) were used for cluster generation using 10 pM of pooled normalized libraries on the cBOT System. Sequencing was performed on the Illumina HiSeq 2500 single end 125 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc.).

tag: condition

value: midgestation

value: corpus luteum


title: SC8

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: iBAT, 6ºC, mouse 3

data_processing:
The fastq files were checked for quality control using FastQC (version 0.10.1).
Tha raw fastq are aligned against the mouse reference genome (Ensembl GRCm38) using the aligner STAR (version 2.4.2a) (Dobin et al., 2013). Gene expression quantification was done with STAR (using the --quantMode GeneCounts option) to generate uniquely mapped read counts at the gene level.
Differential expression analysis was performed with edgeR (version 3.14.0) (Robinson et al., 2010) using the count matrix as input.
Genome_build: mm10
Supplementary_files_format_and_content: BIOIFX-051_rawreadcount.txt - (tab delimited) (raw read counts)

source_name: interscapular brown fat

growth_protocol: Mice were grow from 10 weeks old to 14 weeks old at different ambient temperatures.

extract_protocol:
Tissues were disrupt using Tysseu lyser and Qiazol reagent. Further total RNA isolation was done using the RNeasy Quiagen Kit.  Contaminating DNA was eliminated with DNA-Free kit from Ambion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acclimation to ambient temperatures.

tag: age

value: 14 weeks old

tag: genotype

value: wild type

value: Severe Cold Temperatue, 6ºC

value: interscapular brown fat


title: 20150605.B-Gold_group4

description: group 4

tag: tissue


title: SC6

description: iBAT, 6ºC, mouse 2


title: Healthy_NOTNV02LH2E

tag: gender

value: Female

value: Endometrium

tag: receptivity time-point

tag: country of origin

value: Estonia


title: 20150605.B-Dardanel_group4

description: group 4


title: Healthy_NOTNV11LH8E

tag: tissue state

value: Healthy

tag: sequencing batch


title: 20150605.B-Turgay_group4

description: group 4


title: R8

description: iBAT, 22ºC, mouse 4

tag: strain

value: Room Temperature, 22ºC


title: SC7

description: iBAT, 6ºC, mouse 1

tag: treatment


title: Healthy_NOTNV01LH8E


title: 20150605.B-Nescafe_group4

description: group 2


title: R4

description: iBAT, 22ºC, mouse 3


title: 20150605.B-Zeynep_group2

description: group 2

value: antigestagen


title: Healthy_NOT1213LH2E


title: SC4

description: iBAT, 6ºC, mouse 4


title: 20150605.B-Mara_group3

description: group 3

value: luteal regression


title: R2

description: iBAT, 22ºC, mouse 2


title: Healthy_NOT1210LH2E


title: T8

description: iBAT, 30ºC, mouse 4

value: Thermoneutral, 30ºC


title: 20150605.B-Lissy_group3

description: group 3


title: T5

description: iBAT, 30ºC, mouse 3


title: Healthy_NOTNV02LH8E


title: 20150605.B-Birnur_group2

description: group 2


title: T2

description: iBAT, 30ºC, mouse 2


title: Healthy_NOTNV01LH2E


title: RT_AKT2_KO4

description: iBAT, 22ºC, KO 4

data_processing:
The fastq files were checked for quality control using FastQC (version 0.10.1).
Tha raw fastq are aligned against the mouse reference genome (Ensembl GRCm38) using the aligner STAR (version 2.4.2a) (Dobin et al., 2013). Gene expression quantification was done with  STAR (using the --quantMode GeneCounts option) to generate uniquely mapped read counts at the gene level.
Differential expression analysis was performed with edgeR  (version 3.14.0) (Robinson et al., 2010) using the count matrix as input.
Genome_build: mm10
Supplementary_files_format_and_content: BIOIFX-069_rawreadcount.txt - (tab delited) (raw read counts)

growth_protocol: Mice were grow from 9 weeks old to 13 weeks old at different ambient temperatures.

value: AKT2 KO4

value: 13 weeks old


title: T1

description: iBAT, 30ºC, mouse 1


title: 20150605.B-Citir_group2

description: group 2


title: 20150605.B-Suzan_group2

description: group 2


title: 3hitNSCs_replicate1 (4C-Seq)

city: New York

first: Aram

middle: S

last: Modrek

state: NY

address: 460 E 26th Street

department: Radiation Oncology

institute: New York University School of Medicine

data_processing:
Library strategy: 4C-Seq
4C-Seq data were aligned and processed as described previously using 4C-ker (Raviram et al., 2016). Differential analysis was performed in the near-bait region (2 Mb surrounding the bait) using an adjusted p value of 0.001.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

source_name: hESC derived NSCs

growth_protocol: Human neural stem cells were grown in neural stem cell media: Neural Stem Cell Medium (NSCM) composed of DMEM/F12 (Invitrogen), N2 (Invitrogen), 20 ug/mL Insulin (Invitrogen), 1:1000 B27 (Invitrogen), 1.6 g/L glucose (Fisher) and 20 ng/mL EGF and FGF2 (R&D Systems).

extract_protocol:
4C-seq libraries prepared according to (Rocha et al., 2016)
To generate a 4C library for sequencing, we modified a recent protocol (Rocha et al., 2016) as follows: To capture interactions from the SOX2 promoter, the following primer pairs were used: 5’-TCCACTCTCTTGTTGGGATC-3’, and 5’-CTTCTAGTCGGGACTGTGAG-3’ with DpnII and Csp6I for restriction digests. For the generation of 4C libraries, 10e7 vector NSCs and 3-hit NSCs in duplicates were collected, immediately fixed, and processed accordingly. Illumina adapters were added to the primers before generation of 4C libraries for multiplexed sequencing. 4C libraries were subjected to Agilent Tapestation quality control and quantified with qPCR. Libraries were then sequenced on Illumina HiSeq 2500 sequencers with 50-nucleotide single-end reads.

value: R132H-IDH1 and P53 shRNA and ATRX shRNA

tag: genotype/variation

value: mutant-IDH1 and P53 knockdown and ATRX knockdown


title: controlNSCs_replicate2 (4C-Seq)

value: control


title: controlNSCs_replicate1 (4C-Seq)


title: 20150605.B-Senta_group1

description: group 1

value: luteolysis

value: corpus luteum


title: R1

description: iBAT, 22ºC, mouse 1

value: 14 weeks old

value: wild type


title: Healthy_NOT1213LH8E

value: Female


title: 20150605.B-Seran_group2

description: group 2


title: RT_AKT2_KO3

description: iBAT, 22ºC, KO 3

value: AKT2 KO3

value: interscapular brown fat


title: RT_AKT2_KO2

description: iBAT, 22ºC, KO 2

value: AKT2 KO2


title: Healthy_NOT1210LH8E

value: Endometrium

value: Estonia

value: Healthy


title: 20150605.B-Kimba_group1

description: group 1


title: 2hitNSCs_replicate2 (RNA-Seq)

data_processing:
Sequencing results were analyzed using the Tuxedo suite, as described in (Trapnell et al., 2012)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values, differential expression, cluster assignment

molecule: polyA RNA

extract_protocol:
RNA extracted and purified with the RNeasy Micro Kit (Qiagen) in duplicates
Libraries were generated using TrueSeq mRNA preparation kits (Illumina)

treatment_protocol: All samples were grown and treated the same way.

value: R132H-IDH1 and P53 shRNA

value: mutant IDH1 and p53 knockdown


title: 2hitNSCs_replicate1 (RNA-Seq)


title: 3hitNSCs_replicate1 (RNA-Seq)


title: RT_WT2

description: iBAT, 22ºC, wildtype 2

value: Wild Type2

value: Room Temperature, 22ºC

value: 13 weeks old


title: 3hitNSCs_replicate2 (RNA-Seq)

value: R132H-IDH1 and P53 shRNA and ATRX shRNA

value: mutant-IDH1 and P53 knockdown and ATRX knockdown


title: RT_WT3

description: iBAT, 22ºC, wildtype 3

value: Wild Type3


title: RT_AKT2_KO1

description: iBAT, 22ºC, KO 1

value: AKT2 KO1


title: 1hitNSCs_replicate2 (RNA-Seq)


title: 1hitNSCs_replicate1 (RNA-Seq)


title: RT_WT1

description: iBAT, 22ºC, wildtype 1

value: Wild Type1


title: controlNSCs_replicate2 (RNA-Seq)

value: control


title: controlNSCs_replicate1 (RNA-Seq)


title: TN_AKT2_KO4

description: iBAT, 30ºC, KO 4

value: AKT2 KO4

value: Thermoneutral, 30ºC


title: TN_AKT2_KO3

description: iBAT, 30ºC, KO 3

value: AKT2 KO3

value: interscapular brown fat


title: TN_AKT2_KO2

description: iBAT, 30ºC, KO 2

value: AKT2 KO2


title: TN_AKT2_KO1

description: iBAT, 30ºC, KO 1


title: RT_WT4

description: iBAT, 22ºC, wildtype 4

value: Wild Type4


title: 20150605.B-Amy_group1

description: group 1

value: luteolysis

value: corpus luteum


title: TN_WT3

description: iBAT, 30ºC, wildtype 3


title: late S NOMe-GPS

city: Shanghai

first: Huaibing

last: Luo

address: 130# Dongan Rd

department: Institute of Biomedical Science

country: China

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
Quality control with Trim Galore
Reads alignment to hg19 with Bsseq
GC and CG methylation level calling
Genome_build: hg19
Supplementary_files_format_and_content: GCH.txt files contain the following columns: chr,start,end,strand,sequence,methylation level. WCG.txt files contain the following columns: chr,start,end,strand,sequence,methylation level, C coverage, T coverage.

growth_protocol: HepG2 cells was cultured in recommended condition at 37 ℃ and 5% CO2 , with DMEM high glucose medium containing 10% FBS.Cells were resuspended in PBS and subjected to fluorescence activated cell sorting to collect cells at 4 different phases of the cell cycle according to the DNA content, namely G0/G1, S1, S2 and G2/M, referring to G0/G1 phase, early S phase, late S phase and G2/M phase respectively.

extract_protocol:
genomic DNA was purified with spin column( Qiagen ) according to manufacturer’s instruction.
End repair followed by 3' end configuration, adapter ligation, bisulfite treatment and amplification

treatment_protocol: Nuclei was washed and resuspended in 500 ul ice cold GpC methyltransferase buffer (New England BioLabs), and sonicated to fragments larger than 1kb using biorupter. Sonicated chromatin was then incubated with 20u GpC methyltransferase and 1.5ul SAM (New England BioLabs) at a total volume of 150ul, the reaction was incubated at 37 ℃ for 4 hours, and 0.5 ul SAM was added to each reaction per hour.

tag: cell line

tag: cell cycle stage

value: late S


title: early S NOMe-GPS

value: early S


title: G0/G1 NOMe-GPS


title: TN_WT4

description: iBAT, 30ºC, wildtype 4

value: 13 weeks old


title: G2/M NOMe-GPS


title: CHIP_H3K27me3_morula_Kdm6bMUT_1

city: Boston

first: Lan

last: Jiang

state: Massachusetts

address: 200 Longwood Ave

institute: Boston Children Hospital

data_processing:
Reads of RNA-seq were mapped to the reference genome mm9 with STAR.  Uniquely mapped reads were subsequently quantified with reference annotation (UCSC gene models) using featureCounts from subread-v1.5.1(Liao et al. 2014). After the library size was normalized, the expression level of each gene was resented as normalized FPKM (fragments per kilobase of exon per million mapped fragments). The Pearson correlation coefficient (r) of gene expression level was calculated to indicate the correlation between duplicates.
All ULI-NChIP reads were trimmed for adaptor sequence, low quality and low complexity reads, then were aligned to the mouse reference genome (mm9) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters “ –t –q –N 1 –L 25”. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. Peaks calling are performed using macs2 callpeak with parameters “--broad –broad-cutoff  0.1  --SPMR --nomodel  --extsize 300 -g mm -q 0.05 “.
Genome_build: mm9
Supplementary_files_format_and_content: bed/peak files for CHIP-seq data; tab-delimited text files include FPKM values for each RNA Sample

source_name: early embyro

growth_protocol: All animal studies were performed in accordance with guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. MII-stage oocytes were collected from 8 week-old superovulated B6D2F1/J (BDF1) females by injecting 7.5 I.U. of PMSG (Millipore) and hCG (Millipore). For in vitro fertilization (IVF), MII oocytes were inseminated with activated spermatozoa obtained from the caudal epididymides of adult BDF1 male mice in the HTF medium supplemented with 10 mg/ml bovine serum albumin (BSA; Sigma-Aldrich). Spermatozoa capacitation was attained by 1 h incubation in the HTF medium. Zygotes were transferred into M2 media containing 10 μg/ml cytochalasin B (Sigma-Aldrich) at 10 hpf. Zona pellucidae were cut by a Piezo impact-driven micromanipulator and the pronuclei were isolated from the zygotes. At 12 hpf (PN5-stage), isolated pronuclei were washed with 0.2% BSA/PBS, transferred into Eppendorf LoBind 1.5 ml tubes, and placed on ice until DNase I treatment. For each experiment, 150-200 pronuclei were collected and prepared for liDNase-seq. The parental pronuclei were distinguished by (1) the distance from the second polar body and (2) the size of the pronucleus. Zygotes and preimplantation embryos were cultured in a humidified atmosphere with 5% CO2/95% air at 37.8°C.

extract_protocol:
All animal studies were performed in accordance with guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. MII-stage oocytes were collected from 8 week-old B6D2F1/J (BDF1) females superovulated by injecting 7.5 I.U. of PMSG (Millipore) and hCG (Millipore). For in vitro fertilization (IVF), MII oocytes were inseminated with activated spermatozoa obtained from the caudal epididymis of adult BDF1 or PWK (Jackson Laboratory, 003715) males in HTF medium supplemented with 10 mg/ml bovine serum albumin (BSA; Sigma-Aldrich). Spermatozoa capacitation was attained by 1 h incubation in the HTF medium. Zygotes were transferred to KSOM and cultured in a humidified atmosphere with 5% CO2/95% air at 37.8°C.
RNAseq was performed from whole E3.5 blastocysts (BDF1 X PWK). Each replicate used a pool of 40 embryos. RNA-seq libraries were prepared as previously described (Inoue et al. 2017) with minor modifications. Briefly, reverse transcription and cDNA amplification were performed using whole embryo lysates with SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 634890). cDNAs were then fragmented using Tagmentation with Nextera XT DNA library prep kit (Illumina). The fragmented cDNAs were amplified using Nextera PCR master mix according to the manufacturer’s instruction. Single end 100 bp sequencing was performed on a HiSeq2500 sequencer (Illumina). The ULI-NChIP was performed as described previously (Brind’Amour et al. 2015) with the following several modifications. First, we used Beckman SPRIselect beads (Beckman Coulter), instead of Agencourt Ampure XP beads. Second, the sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufactures' instruction. Third, PCR amplification was performed using Kapa Hifi hotstart readymix (Kapa Biosystems). Lastly, no size selection step was needed. The library was quantified by Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32854) and Agilent high sensitivity assay kit (Agilent Technologies). The libraries were sequenced on a Hiseq2500 with single-end 150 bp reads (Illumina). The H3K27me3 antibody was purchased from Diagenode (C15410069). Before incubation with the antibody, 10% volume of the chromatin lysate was taken for input samples, and the input samples also proceed to the library construction followed by sequencing.

treatment_protocol: MII oocytes were collected from superovulated 8 week-old BDF1 females and inseminated with BDF1 sperm. At 2.5 hpf, fertilized oocytes were transferred into M2 media and mRNA was injected using a Piezo impact-driven micromanipulator (Prime Tech Ltd., Ibaraki, Japan). mRNA injection was completed by 4 hpf. The mRNA concentrations of Kdm6bWT and Kdm6bMUT were 1.8 μg/μl, and those of Kdm4dWT and Kdm4dMUT were 1.5 μg/μl. When preparing Kdm6b-injected PG embryos, MII oocytes were chemically activated by treating with 3 mM SrCl2 in Ca2+-free KSOM containing 5 μg/ml cytochalasin B. At 4 hrs post-activation (hpa), the embryos were washed with KSOM. At 5 hpa, they were injected with mRNA.

tag: cell type

value: Morula embyro

value: Kdm6bMuT injected


title: CHIP_H3K27me3_morula_Kdm6bWT_1

value: Kdm6bWT injected


title: E14.5_WT_rep2

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
mRNA-Seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, aligned to the mouse genome (dm3) using Bowtie/Tophat (v1.3.1) with default parameters.
Uniquely mapped reads were assembled into transcripts guided by reference annotation (FlyBase r5.43) with Cuffdiff (v1.3.0) to calculate gene expression levels which measured as Fragment Per Kilobase per Million mapped fragments (FPKM) and identify differentially expressed genes with FDR < 0.05.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene which FPKM large than 1 at least in one sample.

source_name: Sympathetic ganglion

growth_protocol: Sympathetic ganglion were dissected from E11.5 or E14.5 wild-type and isl1 mutant embryos. To dissect the Sympathetic ganglion of E11.5 embryos，Fluorescence stereoscope was used.

extract_protocol:
RNA was prepared using the RNeasy Micro kit (Qiagen) following the manufacturer’s instructions. The quality of the resulting RNA was verified by the relative intensity of rRNA bands using a Agilent 2100 Bioanalyzer, and RNA was quantified using a Nanodrop ND-1000 spectrophotometer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissue stored in liquid nitrogen. The ganglia for the same genotype from about 10 embryos with the same genotype were pooled at the time of RNA extraction.

value: Wild type

tag: Stage

value: embryonic day 14.5


title: Input_morula_Kdm6bWT_1

value: No injection


title: TN_WT2

description: iBAT, 30ºC, wildtype 2

value: Wild Type2


title: RNA_Blastocyst_Kdm6bWT_rep2

description: Allelic gene expression in Kdm6bWT- and Kdm6bMut-injected hybrid blastocyst embryos.xlsx


title: E14.5_Isl1-MUT_rep2

value: Isl1 mutation


title: Input_morula_Kdm6bMUT_1


title: RNA_Blastocyst_Kdm6bMuT_rep1


title: TN_WT1

description: iBAT, 30ºC, wildtype 1

value: Wild Type1

value: Thermoneutral, 30ºC


title: RNA_Blastocyst_Kdm6bWT_rep1


title: E14.5_WT_rep1


title: E11.5_Isl1-KO_rep2

value: embryonic day 11.5


title: RNA_Blastocyst_Kdm6bMuT_rep2


title: E14.5_Isl1-MUT_rep1


title: E11.5_Isl1-KO_rep1


title: E11.5_WT_rep1


title: ChIP_Islet1

data_processing:
ChIP-seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, then mapped to dm3 whole genome using bowtie v0.12.7 with parameters:–p 8 -t -v 2 -m 1
The uniquely mapped nucleosomal reads were used to identify Islet1 genome wide binding sites through the peak-calling tool macs14
Genome_build: mm9
Supplementary_files_format_and_content: bed file for nucleosome positions includes nucleosome name, location (chromatin, start, end)

source_name: sympathetic neurons

growth_protocol: Sympathetic ganglion were dissected from E12.5 - E14.5 wild-type embryos.The ganglia from about 20 embryos were pooled and digested with trypsin (0.1%) for 10 minutes with periodical pipetting, and clear supernatants were collected in a 15-ml tube. The digestion was   repeated until Sympathetic ganglion tissue was totally digested. The cell suspension was filtered through a 40-um filter unit (Fisher Scientific) . Sympathetic neurons were resuspended in 0.5 ml DMEM medium.

extract_protocol:
100-300bp chromatin fragments were obtained after sonication with indicated condition. Immunoprecipitated DNA-ISL1 complexes were captured by Isl1 antibody (Abcam, USA)-beads complex.Immunoprecipitated DNAs were obtained by extraction with phenol chloroform after incubated on metal bath under the condition of 65 ℃ over night.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Briefly, 50000 cells  were cross-linked with 1% formaldehyde and quenched with 2.5M glycine (Sigma, USA), and then, harvested in a 0.5 mL tube (Eppendorf, Germany). 100-300bp chromatin fragments were obtained after sonication with indicated condition. 5% total chromatin fragments were transferred and setted as Input. Immunoprecipitated DNA-ISLT1 complexes were captured by IsLT1 antibody (Abcom, USA)-beads complex, and then, library was performed on beads.

value: sympathetic neurons

tag: chip antibody

value: rabbit anti-ISL1

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.


title: Ref_8H_a

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3  whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and HISAT software (Kim D, Langmead B and Salzberg SL, Nature Methods, 2015).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium sample

growth_protocol: Strains were grown at 30 °C in Minimal Medium (MM) or Compete Medium (CM) prepared as described previously. Media of auxotrophic strains (N593 ΔkusA, ΔaraR) were supplemented with 1.22 g L-1 uridine. All liquid cultures were incubated in the rotary shaker at 250 rpm. In transfer experiment, freshly harvested spores were pre-grown for 16h in CM with 2% (w/v) D-fructose. The mycelium was then harvested by filtration over sterile cheesecloth, washed with MM and ~2.5 g (wet weight) was transferred to 50 mL MM with 1 % (w/v) sugar beet pectin. After 2 and 8h of incubation, the mycelium was harvested by vacuum filtration, dried between two sheets of paper and frozen in liquid nitrogen. The culture filtrate was harvested, centrifuged and frozen. All samples were stored in -20°C until being processed.

extract_protocol:
RNA was extracted from grinded mycelia using TRIzol® reagent (Invitrogen, Breda, the Netherlands) and purified with NucleoSpin® RNA II Clean-up kit (Macherey-Nagel) with rDNase treatment. The RNA quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: N593 delta-kusA (reference strain)

tag: sampling time

tag: genotype

value: N593 delta-kusA (cspA1, pyrG-, kusA::amdS)


title: Ref_2H_b


title: 3hitNSCs_replicate2 (4C-Seq)

tag: condition

value: R132H-IDH1 and P53 shRNA and ATRX shRNA

value: mutant-IDH1 and P53 knockdown and ATRX knockdown


title: R_8H_b

value: delta-rhaR

value: cspA1, pyrG-, kusA::amdS, delta-rhaR::pyrG


title: Ref_2H_a


title: R_8H_a


title: R_2H_a


title: R_2H_b


title: E11.5_WT_rep2

value: Wild type


title: GR_2H_b

value: delta-gaaRdelta-rhaR

value: cspA1, pyrG-, kusA::amdS, delta-rhaR::pyrG, delta-gaaR::hph


title: GAR_8H_b

value: delta-gaaRdelta-araRdelta-rhaR

value: cspA1, pyrG-, kusA::amdS, delta-rhaR::pyrG, delta-araR::hph, delta-gaaR::phle


title: GR_8H_b


title: GR_8H_a


title: zfp-1-1(RNAi) C

city: Dallas

first: James

last: Collins

state: TX

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern

data_processing:
 bcl2fastq v2.17
Reads were aligned to Schistosoma mansoni genome with STAR
Differential expression analysis was performed with DESeq2
Genome_build: Version 6

organism: Schistosoma mansoni

source_name: Male posterior somatic tissue

growth_protocol: Parasites perfused from mice and cultured in Basch Media 169 at 37C at 5% CO2.

extract_protocol:
Trizol
TruSeq Stranded mRNA Library Preparation

treatment_protocol: Parasites were treated with control or zfp-1-1 dsRNA.  Total RNA was extracted at D17 follwin the first dsRNA treatment.

value: NMRI

value: zfp-1-1 dsRNA


title: GR_2H_a


title: GAR_2H_b


title: GAR_8H_a


title: zfp-1-1(RNAi) B


title: ChIP_Islet1_input

tag: tissue


title: Ref_8H_b


title: zfp-1-1(RNAi) A


title: Control RNAi B

value: control


title: Control RNAi C


title: G_2H_a

value: delta-gaaR

value: cspA1, pyrG-, kusA::amdS, delta-gaaR::pyrG


title: G_2H_b


title: Control RNAi A


title: AR_8H_b

value: delta-araRdelta-rhaR

value: cspA1, pyrG-, kusA::amdS, delta-rhaR::pyrG, delta-araR::hph


title: AR_8H_a


title: ΔraiR3 D. pulchra exposed

city: Sydney

first: Nandan

middle: P

last: Deshpande

state: NSW

address: Kensington Campus

department: School of Biotechnology and Biological Sciences

country: Australia

institute: Systems Biology Initiative

data_processing:
Quality trimming using DynamicTrim.pl and LengthSort.pl scripts from SolexaQA
Read mapping using Bowtie v1.1.2
counting mapped-reads using featureCounts: a ultrafast and accurate read summarization program
Genome_build: Nautella_sp_R11 : GCF_000156255.1_ASM15625v1
Supplementary_files_format_and_content: combined file of raw read counts for all samples

organism: Phaeobacter italicus

source_name: Bacteria cell cultures

growth_protocol: N. italica R11 WT and ΔraiR strains were cultured for 6.5 hours to a late logarithmic phase, washed and re-suspended in Br-ASW to an OD600 = 0.8.

extract_protocol:
Immediately following incubation, N. italica R11 cells were removed and pelleted by centrifugation (1000 x g for 5 minutes) and the total RNA extracted and purified using a TRIzol Plus RNA Purification Kit (Invitrogen, USA)with on column Dnase treatment. The RNA was assessed on a Bioanalyzer (Agilent, USA) to determine the total RNA quality and quantity.
RNA-seq libraries for each sample were constructed using a ScriptSeq v2 RNA-seq Library Preparation Kit (Illumina, USA), which also included a Ribo-Zero ribosomal RNA depletion step. Resulting cDNA was sequenced on the Illumina NextSeq 500 platform using a single read, 75 bp, high-output sequencing kit. Sequencing was performed at the Ramaciotti Centre for Genomics at UNSW.

treatment_protocol: Ten millilitres of each strain was added to a 25 cm2 tissue culture flask with a vented cap (Sarstedt, Germany) containing stressed D. pulchra and incubated at 25°C with 80 rpm shaking for two hours. Each strain was also incubated without D. pulchra under the same conditions, representing the control treatment. The experiment was performed in triplicate for each strain and treatment.

value: RaiR gene disruption mutant

value: exposure to D. pulchra treatment


title: AR_2H_b


title: ΔraiR2 D. pulchra exposed


title: ΔraiR1 D. pulchra exposed


title: WT3  D. pulchra exposed

value: wild type


title: GAR_2H_a


title: WT2  D. pulchra exposed


title: ΔraiR3 Control


title: AG_2H_b

value: delta-araRdelta-gaaR

value: cspA1, pyrG-, kusA::amdS, delta-gaaR::pyrG, delta-araR::hph


title: WT1  D. pulchra exposed


title: ΔraiR1 Control


title: G_8H_b


title: AG_8H_a


title: AG_8H_b


title: AG_2H_a


title: G_8H_a


title: ΔraiR2 Control


title: WT3 Control


title: A_8H_a

value: delta-araR

value: cspA1, pyrG-, kusA::amdS, delta-araR::hph


title: A_2H_b


title: CQ_Na24h

city: Chengdu

first: Qi

last: Wu

address: Shiling town, Longquanyi District,

institute: Chengdu University

data_processing:
The adapter, Ns and low-quality reads were trimmed and filtered by cutadapt.
Transcriptome was assembled with Trinity (version 2.1.1) and annotated with Transdecoder
Longest ORFs were annotated by blastp with Swiss-prot, NR, Pfam and GO database
Sequenced reads were aligned to the transcriptome with Bowtie2 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by RSEM
Supplementary_files_format_and_content: text file contain the read count, FPKM and annotaion of each genes assembled from Trinity of each sample. The FASTA file of assembled transcripts is available on the series record.

organism: Fagopyrum tataricum

growth_protocol: The seeds were sown and grown in small pots (12 centimeters in diameter and 10 centimeters in depth) at the density of 40 seeds for each pot. After germination, the seedlings were cultured in a growth chamber under controlled conditions: 23◦C, 12 hours (h) for dark, and 25◦C, 12 h for light with light intensity at 100 umol.m-2.s-1. The humidity was about 65% with watering supplied every three days.

extract_protocol:
Total RNA were extracted from 2 weeks old seedlings using Qiagen RNeasy plant mini kit.
RNA libraries were prepared for sequencing using standard dUTP strand-specific RNA-seq library  protocols

treatment_protocol: After growth for two weeks, the seedlings were subjected to salinity treatment by supplying with 200mM sodium chloride solution

tag: development stage

value: 2 weeks after germination

value: aerial parts of seedling plants

tag: treatment time


title: CQ_0h


title: WT2 Control


title: A_2H_a


title: WT1 Control


title: AR_2H_a


title: WT4

status: Public on Nov 08 2017

city: Montpellier

first: Julie

last: Perroy

address: 141 rue de la Cardonille

country: France

institute: CNRS

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using bcl2fastq 2.17 (Illumina).
Alignment was performed with TopHat 2.1.1 (with Bowtie 2.2.8) to the mm10 version of the Mus muculus genome. The transcript annotation was retrieved from UCSC on May 23, 2014.
Counting of reads aligned to a gene was performed with HTSeq-count 0.6.1p1.
Genome_build: Mus musculus 10 (mm10)
Supplementary_files_format_and_content: Tab-separated text file. First column is the gene identifier (Gene symbol|Entrez gene ID), the following columns are the raw counts (non-normalized) for each sample.

source_name: Wfs1-CreERT2:RiboTag Hippocampus

extract_protocol:
After Hippocampus dissection, HA-Rpl22 were immunoprecipitated. Total RNA was extracted from ribosome-mRNA complexes using RNeasy Microkit (Qiagen) followed by in-column DNAse treatment to remove genomic DNA contamination. Quality and quantity of RNA samples were both assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). Six biological replicates, each one composed of a pool of 4 to 6 mice, were used for RNAseq analysis.
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.
Stranded RNA-seq

value: CA1 pyramidal cells


title: WT6


title: A_8H_b


title: WT2


title: WT3


title: WT1


title: KO5


title: KO3


title: KO2


title: KO4


title: KO1


title: WT5


title: High-fat diet_mRNA; e_HP_2

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

country: South Korea

institute: Chosun University

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
Mapped to M. musculus whole genome using STAR v2.4.0
Transcripts were assembled and quantitated using Cufflinks v2.1.1
Genome_build: M. musculus Ensembl 72
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "ND","HP", and "HR" sample.

source_name: Mouse Epididymal adipose tissue

growth_protocol: Thirty male C57BL/6J mice (four-week-old, male) were obtained from the Jackson Laboratories (Bar Harbor, ME, USA). All mice were individually housed under a constant temperature (24°C) and 12-h light/dark cycle and, fed a normal chow diet for acclimation for 1 week after arrival.

extract_protocol:
Total RNA was extracted from the adipose tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following  manufacturer's protocols.

treatment_protocol: At 5 weeks of age, they were randomly divided into 3 groups of 10 mice per each group and fed a normal diet (ND), high-fat diet-prone (HP), HFD-resistant (HR) for 12 weeks

tag: age

value: 17 weeks

value: epididymal adipose tissue

tag: Sex

value: male


title: High-fat diet_mRNA; e_HR_1

tag: strain


title: Normal diet_mRNA; L_ND_2

source_name: Mouse liver

value: liver


title: High-fat diet_mRNA; L_HR_3


title: High-fat diet_mRNA; L_HP_1


title: High-fat diet_mRNA; L_HP_3


title: Normal diet_mRNA; L_ND_3


title: High-fat diet_mRNA; L_HR_2


title: High-fat diet_mRNA; L_HR_1


title: Normal diet_mRNA; e_ND_3


title: High-fat diet_mRNA; e_HP_3


title: Normal diet_mRNA; L_ND_1


title: High-fat diet_mRNA; e_HR_2


title: High-fat diet_mRNA; L_HP_2


title: Normal diet_mRNA; e_ND_2


title: Normal diet_mRNA; e_ND_1


title: High-fat diet_mRNA; e_HP_1


title: KO6


title: High-fat diet_mRNA; e_HR_3


title: T2DM_infarct_zone_1

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description: Myocardial infarction was induced by ligating left anterior descending artery (LAD). Total RNA was isolated from remote, Infarct and border zones at day 7 after myocardial infarction. Poly (A)+RNA fraction was subjected to RNA sequencing using Illumina HiSeq.

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: UCSC Bedgraphs are provided

source_name: Type 2 diabetic mouse myocardium including infarcted and border region

extract_protocol:
Hearts were collected at day 7 after LAD ligation and stored in RNA later solution. Total RNA was isolated from remote, border and infarct zones of cardiac tissue using RNeasy Fibrous Tissue Mini Kit (QIAGEN Finland, Helsinki, Finland) according to manufacturer's instructions.
Total RNA was enriched for Poly (A)+ RNA with MicroPoly (A) Purist Kit (Ambion, Austin, TX, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation. Dephosphorylation reactions were mixed with 2 x Novex TBE-Urea sample buffer (Invitrogen), briefly denatured and loaded on a Novex denaturing 15% polyacrylamide TBE-urea gel according to the manufacturer’s instructions. Fragments of 50-300 nucleotides in length were gel purified .  Also the poly (A)+ tailing and cDNA synthesis was performed the next day. However, for reverse transcription oligos with custom barcodes (underlined) were used: 5’phosCA/TG/AC/GTGATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’. After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligos. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of ~150-200 bps were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 8 cycles. The final product was ran on Novex 10%TBE gel, gel purified as above and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA). The library was sequenced for 50 cycles on the Illumina HiSeq 2000 according to the manufacturer’s instructions.

treatment_protocol: Mice under general anesthesia with isoflurane (2%) were subjected to small left thoracotomy. The heart was temporarily exteriorized, and a 6.0 silk suture was placed 2 mm below the origin of the LAD. The heart was replaced immediately into the thoracic cavity, and all thoracic air was evacuated to avoid pneumothorax. Sham operations were performed by passing the suture around the LAD without ligation. Following MI, the animals remained supervised until fully conscious.

value: IGF-II/LDLR-/-ApoB100/100 , with C57BL/6J background

tag: zone of isolation

value: infarcted


title: T2DM_infarct_zone_3


title: T2DM_Remote_zone_3

source_name: Type 2 diabetic mouse myocardium including remote region

value: remote


title: Control_Infarct_zone_1

source_name: Control mouse myocardium including infarcted and border region

value: control


title: T2DM_infarct_zone_2


title: T2DM_Remote_zone_1


title: Control_Infarct_zone_3


title: Control_Infarct_zone_2


title: SUN Rep 3

first: Ravi

last: Iyengar

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Step 1: Initialize directory structure and required datasets and programs, by creating a directory tree, extracting the contents of gzipped files, and adjusting directory variables in data-processing programs.
Step 2: Create a set of index files of the mRNA RefSeq human genome reference library for BWA, by running Build-Genome-Index.BWA.Human.GEO.sh in a command terminal (details in References/Human_RefSeq/refMrna_ERCC_polyAstrip.hg19.fa.README.txt).
Step 3: Align a set of mRNA-sequencing data files to the mRNA RefSeq human genome reference library and count the number of aligned sequences for each reference gene, by running run-alignment-analysis.GEO.sh in a command terminal.
Step 4: Add experiment design information to the gene read counts tables, by running "Rscript Convert-DGE-Samples-Read-Counts.GEO.R" a command terminal.
Genome_build: mRNA RefSeq human genome reference library based on UCSC hg19 reference
Supplementary_files_format_and_content: DGE.CTRL-SOR-SUN.UniqueMap.UMI.tsv: the read counts table of the uniquely aligned sequence fragments tagged with unique molecular identifiers (UMIs) measured by 3'-DGE method
Supplementary_files_format_and_content: DGE.CTRL-SOR-SUN.UniqueMap.NonUMI.tsv: the read counts table of the uniquely aligned sequence fragments without UMI tags measured by 3'-DGE method
Supplementary_files_format_and_content: DGE.CTRL-SOR-SUN.MultiMap.NonUMI.tsv: the read counts table of the non-uniquely aligned sequence fragments without UMI tags measured by 3'-DGE method

source_name: Primary cardiomyocytes

growth_protocol: Cultured under growth conditions with antibiotic free growth media and differentiated for four weeks with antibiotic free differentiation media (see DToxS SOP CE – 1.0: PromoCell Cardiomyocyte Subculture, DToxS SOP CE – 2.0: PromoCell Cardiomyocyte Plating for Drug Test)

extract_protocol:
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Library was constructed using universal adapters, sample barcodes, unique molecular identifiers using a template switching reverse transcriptase (see DToxS SOP A – 6.0: High-throughput mRNA Seq Library Construction for 3' Digital Gene Expression)

treatment_protocol: Fully confluent and differentiated cells were treated with drugs or vehicle (DMSO) for 48 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)

tag: source organ

value: Heart

value: cardiac myocytes

tag: vendor

value: PromoCell

tag: cat #

tag: lot #

tag: treatment time (hrs)

tag: treatment condition

value: Sunitinib

tag: concentration

tag: well

tag: investigative unit

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: SUN Rep 4

tag: cell type


title: SUN Rep 1


title: SUN Rep 2


title: SOR Rep 3

value: Sorafenib

value: 1 uM


title: SOR Rep 2


title: T2DM_Remote_zone_2

tag: strain

tag: condition

tag: zone of isolation


title: CTRL Rep 5

tag: source organ

tag: vendor

tag: cat #

value: Vehicle Control


title: CTRL Rep 4

tag: lot #

tag: treatment time (hrs)

tag: treatment condition


title: CTRL Rep 7

tag: concentration

tag: well

tag: investigative unit


title: Control_Remote_zone_3

source_name: Control mouse myocardium including remote region


title: Control_Remote_zone_2


title: Control_Remote_zone_1


title: CTRL Rep 6

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280


title: CTRL Rep 8

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: CTRL Rep 1

tag: cell type


title: SUN.A.7.14.0.16

data_processing:
Step 1: Initialize directory structure and required datasets and programs, by creating a directory tree, extracting the contents of gzipped files, and adjusting directory variables in data-processing programs.
Step 2: Obtain a copy of UCSC's human genome reference library (version hg19), by following the instructions in References/UCSC/hg19/Sequence/genome.hg19.fa.README.txt.
Step 3: Create a set of index files of the human genome reference library for STAR, by running Programs/Build-Genome-Index.STAR.Human.GEO.sh a command terminal (details in References/UCSC/hg19/STAR_index_2.5.1b/STAR_index_2.5.1b.README.txt).
Step 4: Align a set of mRNA-sequencing data files to the human genome reference library, by running Programs/Align-RNA-Seq-Reads.STAR.Human.GEO.sh in a command terminal.
Step 5: Count the number of aligned sequences for each reference gene, by running Programs/Count-RNA-Seq-Reads.FeatureCounts.GEO.sh twice: one with an input argument of 0 and the other with 1, in a command terminal.
Step 6: Add experiment design information to the gene read counts tables, by running "Rscript Programs/Convert-Conv-Samples-Read-Counts.GEO.R" in a command terminal.
Genome_build: UCSC human genome reference library (version hg19)
Supplementary_files_format_and_content: Conv.CTRL-SOR-SUN.MultiMap.NonUMI.tsv: Read counts table of the non-uniquely aligned sequence fragments measured by conventional method.
Supplementary_files_format_and_content: Conv.CTRL-SOR-SUN.UniqueMap.NonUMI.tsv: Read counts table of the uniquely aligned sequence fragments measured by conventional method.

extract_protocol:
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Library was prepared using 200 ng of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions


title: CTRL Rep 2


title: SOR Rep 1


title: CTRL Rep 3


title: SUN.A.6.9.0.14


title: SUN.A.6.8.0.13


title: SOR.A.8.2.0.12


title: Input_DNA_Replicate1

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

data_processing:
Sequencing reads were processed to remove adapters using Trimmomatic (v0.35) with the settings “ILLUMINACLIP: TruSeq3-SE.fa:2:30:12:1 MAXINFO:50:0.95 LEADING:3 TRAILING:3 MINLEN:50”, and then trimmed from the low quality end to a uniform length of 50bp using fastx_trimmer from the FASTX-Toolkit (v0.0.14).
Reads were aligned to the mouse genome (mm10) using bowtie2 (v2.2.6) with the options “--end-to-end --very-sensitive”.
Regions of Isl1 enrichment in ChIP libraries compared to input chromatin control libraries were determined using the macs2 (version 2.1.0.20150731) callpeak function with the options "--bdg --SPMR --qvalue=0.01".
Genome_build: mm10
Supplementary_files_format_and_content: Bed files of regions with significant Isl1 enrichment were created by extracting the first 6 columns of the narrowPeak files created by macs2.
Supplementary_files_format_and_content: ChIP signal visualized as fold enrichment compared to background were generated from treatment and control bedGraph files using macs2 bdgcmp with the option "--method=FE". BedGraph files were converted to bigWig using BEDtools slopBed command and the bedClip and bedGraphToBigWig from UCSC Kent Utilities as implemented in the bdg2bw script by Tao Liu (https://gist.github.com/taoliu/2469050).

source_name: embryonic genital tubercle

growth_protocol: Normal gestation

extract_protocol:
After cross-linking in 1% formaldehyde in PBS for 20 minutes, tissues were rinsed and treated with trypsin for 5 min. Samples were then homogenized with a Branson 450 Sonifier (at low amplitude for 30 seconds, 100% duty cycle). The homogenates were sheared in a Bioruptor set to high for 15 cycles (30 seconds on, 30 seconds rest) to generate a chromatin size range of 150–400bp. PureProteomeTM Protein G Magnetic Beads (Millipore) were pre-incubated with 5 μg anti-ISL1 rabbit monoclonal antibody (Abcam #EP4182), and the beads were incubated overnight with 500 μg of the sheared E14.5 GT chromatin. After washing, immune complexes were eluted from the beads, and protein-DNA crosslinks were reversed by incubating at 65 °C overnight. After treatment with RNase followed by Proteinase K, samples were purified over MicroChIP DiaPure columns (Diagenode, Inc.).
All ChIP and input chromatin control libraries were produced using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, #E7645S) as directed by the manufacturer. Libraries were sequenced at the Georgia Genomic Facility on an Illumina NextSeq 500 to produce 75bp SE reads.

tag: strain

tag: tissue

value: embryonic genital tubercle

tag: age

tag: genotype

value: wildtype

tag: chip antibody


title: Isl1_ChIP_Replicate1

value: anti-ISL1 rabbit monoclonal (Abcam #EP4182)


title: Isl1_ChIP_Replicate2


title: Input_DNA_Replicate2


title: SOR.A.7.4.0.11

tag: source organ

tag: vendor

tag: cat #

tag: lot #

tag: treatment time (hrs)


title: SOR.A.7.3.0.10

tag: treatment condition

tag: concentration

tag: well

tag: investigative unit

tag: sample id


title: SOR.A.6.5.0.9

tag: rna amount (ng)

tag: nanodrop 260/280

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: SOR Rep 4

tag: cell type


title: SUN.A.7.13.0.15


title: CTRL.A.8.1.0.8


title: CTRL.A.6.3.0.6


title: CTRL.A.7.1.0.7


title: CTRL.A.6.2.0.5


title: tbx5_9pos

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: Ensembl genebuild 75 (Danio rerio assembly Zv9).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

organism: Danio rerio

source_name: Heart

growth_protocol: All experiments were conducted with adult zebrafish between 6 and 9 months of age, raised at a density of 3 fish/l.

extract_protocol:
RNA was extracted using Arcturus Pico Pure (Thermofisher) following manufacturer instructions.
0.6 ng of total RNA was used to generate barcoded RNA-seq libraries using the Ovation Single Cell RNA-Seq System (NuGEN) with two rounds of library amplification.  The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads.  4 biological replicates consisting of 5 pooled hearts were used per sample.

treatment_protocol: GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tg(tbx5:GFP)/(myl7:nucDsRed) double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.

tag: age

value: Adult

tag: tissue

tag: pair


title: CTRL.A.6.1.0.4

tag: source organ

tag: vendor

tag: cat #


title: tbx5_8neg


title: tbx5_8pos


title: CTRL.A.5.1.0.2

tag: lot #

tag: treatment time (hrs)

tag: treatment condition


title: tbx5_10pos


title: tbx5_2neg


title: tbx5_2pos


title: tbx5_10neg


title: CTRL.A.4.1.0.1

tag: concentration

tag: well

tag: investigative unit


title: CTRL.A.5.2.0.3

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280


title: HCT116 CDK8as/as, 3MB, Hypoxia, replicate 1

status: Public on Nov 07 2017

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description:
total RNA from 3MB treated Hypoxic CDK8as/as HCT116 cells
S1778_HCT116cdk8as_hypox3MB

data_processing:
Signal processing, base-calling and removal of barcode and adapter sequences was carried out automatically by the Torrent Suite Software (Life Technologies)
FASTQC v0.11.2 was used to determine sequence quality
fastx-trimmer from the fastx_0.0.13.2 toolkit was used to trim reads to 150bp
fastx-clipper from the fastx_0.0.13.2 toolkit was used to remove reads shorter than 30bp
Alignment to the Human genome (hg19/GRCh37) was carried out using GSNAP (gsnap_2015-06-12) with a mismatch setting of 3%
Reads were then filtered to remove low quality mapped reads (MAPQ < 10) and non-unique reads were removed by SAMtools (0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Raw count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene --mode=intersection-nonempty)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts for each sample
Supplementary_files_format_and_content: Normalized bigwig files using deeptools 2.2.2 (--binSize=1 --minMappingQuality 10 –normalizeUsingRPKM)

growth_protocol: All cell lines were plated 24 hours prior to treatment.

extract_protocol:
RNA was extracted using TRI reagent, according to manufacturer's instructions. Total RNA quality was assessed using Bioanalyzer RNA Pico chips (Agilent). PolyA RNA was purified from 15 g of total RNA using the Dynabeads mRNA Direct micro kit (Life Technologies) according to the manufacturer’s instructions.
Libraries for Ion Torrent sequencing were prepared using the Ion Total RNAseq v2 kit (Life Technologies), according to the manufacturer’s instructions.

treatment_protocol: 24 hours at 1% oxygen

tag: cell line

value: colorectal adenocarcinoma

tag: genotype/variation

tag: treatment

tag: culture condition

value: hypoxia (1% O2 24hrs)


title: HCT116 CDK8as/as, DMSO, Normoxia, replicate 2

description:
total RNA from DMSO treated Normoxic CDK8as/as HCT116 cells
S1757_HCT116cdk8as_normDMSO

tag: cell type

value: DMSO

value: normoxia


title: HCT116 CDK8as/as, DMSO, Hypoxia, replicate 1

description:
total RNA from DMSO treated Hypoxic CDK8as/as HCT116 cells
S1775_HCT116cdk8as_hypoxDMSO


title: HCT116 CDK8as/as, 3MB, Hypoxia, replicate 2

description:
total RNA from 3MB treated Hypoxic CDK8as/as HCT116 cells
S1766_HCT116cdk8as_hypox3MB


title: HCT116 WT, 3MB, Hypoxia, replicate 2

description:
total RNA from 3MB treated Hypoxic wt HCT116 cells
S1765_HCT116wt_hypox3MB

value: WT


title: HCT116 CDK8as/as, DMSO, Normoxia, replicate 1

description:
total RNA from DMSO treated Normoxic CDK8as/as HCT116 cells
S1769_HCT116cdk8as_normDMSO


title: HCT116 CDK8as/as, 3MB, Normoxia, replicate 1

description:
total RNA from 3MB treated Normoxic CDK8as/as HCT116 cells
S1772_HCT116cdk8as_norm3MB


title: HCT116 WT, 3MB, Normoxia, replicate 2

description:
total RNA from 3MB treated Normoxic wt HCT116 cells
S1759_HCT116wt_norm3MB


title: HCT116 CDK8as/as, DMSO, Hypoxia, replicate 2

description:
total RNA from DMSO treated Hypoxic CDK8as/as HCT116 cells
S1763_HCT116cdk8as_hypoxDMSO


title: HCT116 WT, 3MB, Normoxia, replicate 1

description:
total RNA from 3MB treated Normoxic wt HCT116 cells
S1771_HCT116wt_norm3MB


title: HCT116 WT, DMSO, Hypoxia, replicate 2

description:
total RNA from DMSO treated Hypoxic wt HCT116 cells
S1762_HCT116wt_hypoxDMSO


title: HCT116 WT, 3MB, Hypoxia, replicate 1

description:
total RNA from 3MB treated Hypoxic wt HCT116 cells
S1777_HCT116wt_hypox3MB


title: HCT116 WT, DMSO, Hypoxia, replicate 1

description:
total RNA from DMSO treated Hypoxic wt HCT116 cells
S1774_HCT116wt_hypoxDMSO


title: HCT116 WT, DMSO, Normoxia, replicate 2

description:
total RNA from DMSO treated Normoxic wt HCT116 cells
S1756_HCT116wt_normDMSO


title: tbx5_9neg

tag: age

tag: tissue

tag: pair


title: HCT116 WT, DMSO, Normoxia, replicate 1

description:
total RNA from DMSO treated Normoxic wt HCT116 cells
S1768_HCT116wt_normDMSO


title: control IgG Tri-13

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.4.2, trimming for TrueSeq and polyA sequences. Reads were aligned to mouse genome build mm10 using STAR aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID
Supplementary_files_format_and_content: RNAseq_NormExpr_DESeq2

source_name: Lung tumor (CD45neg cells)

growth_protocol: Tumor growth took place during 25 weeks, after which treatment was initiated

extract_protocol:
CD45neg cells of lung tumors were isolated and RNA was harvested using Trizol reagent. TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500ng total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment (anti-Ly6G or control IgG) occured during 2 weeks, 3 injections per week, 10mg/kg i.p.

tag: strain

value: Lung tumor (CD45neg cells)

tag: genotype

value: Kras(LSL-G12D/WT); p53(Flox/Flox)

tag: antibody treatment

value: control IgG

tag: neutrophil infiltration

value: High


title: control IgG Tri-15


title: HCT116 CDK8as/as, 3MB, Normoxia, replicate 2

description:
total RNA from 3MB treated Normoxic CDK8as/as HCT116 cells
S1760_HCT116cdk8as_norm3MB


title: control IgG Tri-9


title: anti-Ly6G Tri-6

value: Low


title: control IgG Tri-14


title: control IgG Tri-10


title: anti-Ly6G Tri-2


title: anti-Ly6G Tri-4


title: anti-Ly6G Tri-5


title: control IgG Tri-8


title: S9_1_stroma_LH2

city: Tartu

first: Viktorija

last: Kukushkina

address: Riia 23b

institute: Estonian Genome Center, University of Tartu

data_processing:
Read starts with 6 bp UMI, 6 bp barcode and 3 bp GGG (outcome of template switching). Following is sequence of transcript
The data QC, preprocessing, mapping, and gene counting, normalizing was made using STRTprep pipeline (Krjutškov K, Katayama S, Saare M, Vera-Rodriguez M, Lubenets D, Samuel K, et al. Single-cell transcriptome analysis of endometrial tissue. Hum Reprod. 2016 Feb 13. [PMID: 26874359])
The pipeline mapping step was made with TopHat2 - -bowtie1.
The pipeline counting step was made with HTSeq-count.
The raw read counts were spike-in normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files:one contain raw gene counts (reads_all.txt.gz), the other one contains spike-in normalized gene counts for each sample (nreads.txt.gz).

source_name: endometrium stroma

extract_protocol:
Endometrial biopsies were collected with endometrial suction Pipelle catheter (Laboratoire CCD, France). Briefly the biopsied tissue samples were dissociated, endometrial stromal cells were stained with fluorocrome-conjugated mouse anti-human CD13 monoclonal antibody (clone TUK1, R-Phycoerythrin, Invitrogen, USA), epithelial cells were stained simultaneously with fluorocrome-conjugated mouse anti-human CD9 monoclonal antibody (clone MEM-61, FITC, Novus Biologicals, USA) and all dead cells were stained with DAPI (Invitrogen, USA).CD9 or CD13 positive and DAPI negative (alive) cells were sorted into a TRIzol Reagent and RNA were extracted immediately after the lysis of cells.
Bulk-RNA full transcriptome analysis of FACS sorted endometrial cells was performed by the RNA-seq method, following the single-cell tagged reverse transcription (STRT) protocol with modifications (Krjutškov et al., 2016). 10 ng of high-quality input of cell-type specific RNA was converted to cDNA and amplified to form an Illumina-compatible library.
STRT (detailed protocol in PubMed ID 26874359), RNA-seq

tag: menstrual cycle phase

value: early secretory

tag: country of origin

value: Spain

tag: library

value: endometrium stroma


title: S6_2_stroma_LH8

value: mid secretory


title: anti-Ly6G Tri-3


title: S9_2_stroma_LH2


title: S33_2_stroma_LH8


title: S4_2_stroma_LH2


title: S24_2_stroma_LH8


title: S22_2_stroma_LH2


title: anti-Ly6G Tri-1


title: S21_2_stroma_LH8


title: S2_1_stroma_LH8


title: S21_1_stroma_LH8


title: S19_1_stroma_LH2


title: S16_2_stroma_LH8


title: S6_1_stroma_LH8


title: S13_2_stroma_LH2


title: S13_1_stroma_LH2


title: S11_2_stroma_LH8


title: S4_1_stroma_LH2


title: S5_1_epithelium_LH8

source_name: endometrium epithelium

value: endometrium epithelium


title: S11_1_stroma_LH8


title: S5_2_epithelium_LH8


title: S7_2_epithelium_LH8


title: S30_1_epithelium_LH2


title: S8_2_epithelium_LH2


title: S30_2_epithelium_LH2


title: S22_1_stroma_LH2


title: S18_2_epithelium_LH2


title: S12_1_epithelium_LH2


title: S17_1_epithelium_LH8


title: S14_2_epithelium_LH8


title: S3_2_epithelium_LH2


title: S20_1_epithelium_LH8


title: S3_1_epithelium_LH2


title: S14_1_epithelium_LH8


title: S23_2_epithelium_LH8


title: S17_2_epithelium_LH8


title: S1_1_epithelium_LH8


title: 4E_1_stroma_LH8

value: Estonia


title: 34E_1_stroma_LH2


title: 38E_2_stroma_LH2


title: 4E_2_stroma_LH8


title: 41E_1_stroma_LH9


title: 36E_2_stroma_LH8


title: S8_1_epithelium_LH2


title: 30E_2_stroma_LH8


title: 2E_2_stroma_LH8


title: 2E_1_stroma_LH8


title: 28E_1_stroma_LH8


title: 28E_2_stroma_LH8


title: 26E_1_stroma_LH2


title: 23E_2_stroma_LH2


title: 22E_1_stroma_LH8


title: 18E_2_stroma_LH2


title: 16E_1_stroma_LH8


title: 20E_1_stroma_LH8


title: S10_2_epithelium_LH8


title: 10E_2_stroma_LH2


title: 8E_2_stroma_LH2


title: 12E_2_stroma_LH2


title: 16E_2_stroma_LH8


title: 12E_1_stroma_LH2


title: 3E_2_epithelium_LH8


title: 7E_2_epithelium_LH2


title: 40E_2_epithelium_LH8


title: 14E_1_stroma_LH2


title: 3E_1_epithelium_LH8


title: 35E_2_epithelium_LH8


title: 29E_1_epithelium_LH8


title: 35E_1_epithelium_LH8


title: 7E_1_epithelium_LH2


title: 31E_1_epithelium_LH2


title: 29E_2_epithelium_LH8


title: 27E_2_epithelium_LH8


title: 27E_1_epithelium_LH8


title: 24E_2_epithelium_LH2


title: 24E_1_epithelium_LH2


title: 1E_1_epithelium_LH8


title: 21E_2_epithelium_LH8


title: 17E_1_epithelium_LH2


title: 17E_2_epithelium_LH2


title: 15E_2_epithelium_LH8


title: 11E_2_epithelium_LH2


title: 9E_2_epithelium_LH2


title: 15E_1_epithelium_LH8


title: mko1_h3k4me3

city: Chapel Hill

first: Karl

middle: B.

last: Shpargel

state: NC

address: 120 Mason Farm Road

institute: University of North Carolina

data_processing:
Trimmed reads from fastq sequence files: trimmomatic SE with options: -threads 1 -phred33 SLIDINGWINDOW:4:15 MINLEN:30 LEADING:3 TRAILING:3
Aligned RNA-seq to get bam-file: tophat2 with options: --library-type fr-firststrand -p 1 --no-novel-juncs -G MM9_UCSC_genes.gtf MM9_UCSC_Bowtie2Index_genome
Aligned ChIP-seq to get sam-file: bowtie2 with options: -x MM9_UCSC_Bowtie2Index_genome
Samtools to convert sam to bam-file: samtools view with options: -S -b -F 4 -q 30
Merged biological replicates of input, wt, and fko bam-files: samtools merge
Created bedgraph from bam-file: bedtools genomecov with options: -split -bg -scale 10000000/total_counts -g MM9_UCSC_ChromInfo.txt
Created bigWig from bedgraph: bedGraphToBigWig
Calculated RNA-seq read counts for each gene: samtools view bam-file put into htseq-count with options: --stranded=reverse -m intersection-nonempty - MM9_UCSC_genes.gtf
Identified broadPeak ChIP-seq enrichment peaks from wt or fko merged bam-files: macs2 callpeak with options (example is wt h3k4me3): -t wtall_k4_merge_aligned_reads_sort.bam -c wt_in2_merge_aligned_reads_sort.bam --broad -g mm --broad-cutoff 0.1
Calculated H3K27me3 ChIP-seq read counts at all broadPeaks: catenated wt and fko peaks, and used bedtools coverage to calculate coverage from individual bam-files
Calculated H3K4me3 ChIP-seq read counts at all broadPeaks: catenated wt and fko peaks, and used bedtools multicov to calculate coverage from individual bam-files
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, TSV htseq-count rna read counts, macs2 broadPeak bed file

source_name: Cranial Neural Crest

growth_protocol: O9-1 basal growth media: DMEM/15% FBS/2 mM L-glutamine/penstrept media was conditioned overnight with primary MEFs, filtered, and supplemented with 0.1 mM minimum essential medium (MEM) non-essential amino acids, 1 mM sodium pyruvate, 55 μM β-mercaptoethanol, 25 ng/mL bFGF, and 1,000 U/mL LIF.

extract_protocol:
For RNA isolation, cranial neural crest were sorted into Trizol LS and processed accordingly. For ChIP, sorted cranial neural crest were pelleted in PBS, frozen cell pellets were thawed, digested with Micrococcal Nuclease, and antibody ChIP isolated histone-DNA complexes. For O9-1 ChIP, cells were fixed with 0.3% Formaldehyde for 30 minutes at 4 degrees, nuclei were isolated by Dounce homogenization, digested with Micrococcal Nuclease, and antibody ChIP isolated histone-DNA complexes.
RNA-seq: KAPA KK8420 Stranded mRNA-seq Kit for mRNA isolation, cDNA production, Illumina TruSeq adapter ligation, and library amplification. For ChIP-seq: KAPA KK8502 Hyper Prep Kit for Illumina TruSeq adapter ligation and library amplification.

treatment_protocol: Cranial neural crest were dissected from Wnt1-Cre, Rosa-Tomato embryos rostral from the maxilla and anterior to the otic vesicle, dissociated in HBSS/0.25% Trypsin/0.7 mg/ml DNase I, resuspended in RPMI/10%FBS/2%BSA/100ng/ml DAPI, and sorted for Tomato fluorescence and DAPI exclusion.

tag: Stage

value: Embryonic day E12.5

value: Wnt1-Cre, Rosa-Tomato flow sorted cranial neural crest

value: Utx fl/y, Wnt1-Cre:mko

tag: Sex

value: male

tag: antibody

tag: antibody vendor/catalog

value: Abcam ab8580


title: o91_utx

source_name: O9-1 Primary Cranial Neural Crest Line

value: Isolated Embryonic day E8.5 line

value: Wnt1-Cre, Rosa-GFP flow sorted cranial neural crest

value: WT Wnt1-Cre:wt

value: UTX

value: Cell Signaling D3Q1I (33510)


title: o91_imput

value: Input, none


title: 11E_1_epithelium_LH2

value: early secretory


title: wt_merged_h3k4me3


title: fko3_h3k4me3

value: Utx fl/fl, Wnt1-Cre:fko

value: female


title: wt1_h3k4me3


title: fko_merged_h3k4me3


title: wt2_h3k4me3


title: wt_input_2


title: input_2_merged

value: wt and fko merged


title: fko_input_2


title: wt3_h3k4me3


title: 19E_2_epithelium_LH8

value: mid secretory

value: endometrium epithelium


title: fko_merged_h3k27me3

value: Embryonic day E12.5

value: Abcam ab6002


title: 19E_1_epithelium_LH8

value: Estonia


title: fko2_h3k27me3

value: Wnt1-Cre, Rosa-Tomato flow sorted cranial neural crest


title: wt3_h3k27me3

value: male


title: wt_merged_h3k27me3


title: wt2_h3k27me3


title: JR1967

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: s-SHIP High 3

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r -10. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 0.  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mammary epithelial cells

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

tag: cell population

value: s-SHIP High


title: fko1_h3k4me3

value: Abcam ab8580


title: input_1_merged


title: fko2_h3k4me3


title: JR1966

description: s-SHIP Low 3

value: s-SHIP Low


title: JR1964

description: s-SHIP High 2


title: wt1_h3k27me3

value: WT Wnt1-Cre:wt


title: fko_input_1


title: wt_input_1


title: mko1_h3k27me3

value: Utx fl/y, Wnt1-Cre:mko


title: fko_merged_rna


title: JR1962

description: s-SHIP Neg 2

value: s-SHIP Neg


title: JR1961

description: s-SHIP High 1


title: mko_merged_rna


title: fko1_rna


title: JR1959

description: s-SHIP Neg 1


title: fko1_h3k27me3


title: JR1960

description: s-SHIP Low 1


title: WRKY75RNAi

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing:
Bowtie for alignment, v2, default parameter
Cufflink for expression profiling, V2.1.0, default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: WRKY75RNAi vs Col down-regulatedgenes.xls
Supplementary_files_format_and_content: WRKY75RNAi vs Col up-regulatedgenes.xls
Supplementary_files_format_and_content: RPKM

organism: Arabidopsis thaliana

source_name: third and fourth leaves

extract_protocol:
RNAeasy Kit
stander Illumina mRNA-seq protocol

tag: ecotype

tag: genotype/variation


title: fko2_rna


title: Arabidopsis Col-0

value: wildtype


title: wt_merged_rna


title: mko1_rna


title: fko3_h3k27me3

value: Utx fl/fl, Wnt1-Cre:fko


title: JR1965

description: s-SHIP Neg 3


title: wt2_rna


title: H3K9me3_IL1RN

city: Salt Lake City

first: Jay

last: Gertz

address: 2000 Circle of Hope Dr.

institute: University of Utah

data_processing:
Sequence reads in fastq format were aligned to hg19 using bowtie with the following parameters: -m 1 -t --best -q -S -l 32 -e 80 -n 2
Sam alignments were converted to sorted bams using samtools
Peaks were called with MACS2 using a p-value cutoff of 1e-10 and the mfold parameter bounded between 15 and 100
During peak calling, read pileups were stored as bedGraphs
Genome_build: Hg19
Supplementary_files_format_and_content: bigWigs contain read pileups generated from MACS2 bedGraphs

source_name: Ishikawa SID4x-dCas9-KRAB

growth_protocol: Cells were maintained in RPMI

extract_protocol:
20 million cells per ChIP were crosslinked in 1% formaldehyde for 10 minutes at room temperature.  Crosslinking was stopped with 125 mM Glycine and nuclei were extracted. Chromatin was sonicated using an Epishear Probe Sonicator (Active Motif) for 3 minutes at 40% power. c-MYC (D3N8F) antibody (Cell Signaling Technology) was used for immunoprecipitation and an input sample for each cell line served as the control.
Libraries were constructed using a standard Illumina library construction protocol.

tag: grna treatment

value: Enhancer-I

tag: drug treatment

tag: growth conditions

value: charcoal-stripped RPMI


title: H3K9me3_EnhI


title: FLAG_EnhI

value: FLAG


title: wt1_rna

tag: tissue


title: LCMV_No Help_004

city: New York

first: Tomasz

last: Ahrends

address: 1230 York Ave

institute: The Rockefellere University

description: processed data file: COMP1_DE_Table.txt

data_processing:
RNA-seq reads were aligned to the GRCm38_77 build of the Mus musculus genome using Tophat (version 2.0.12)
Differential expression analysis was performed using Bioconductor R package edgeR
Genome_build: GRCm38.77
Supplementary_files_format_and_content: Data files include list of differentially expressed genes between 2 groups: COMP1 (LCMV Help vs LCMV No Help), COMP3 (Help vs. No Help), COMP4 (No Help vs. No Help + aCD27) and COMP5 (Help vs. Help + CD70). All files include logFC, logCPM, P-value and FDR value for each gene as determined by edgeR.

source_name: spleen

extract_protocol:
CD8 T cells were FACS-sorted from the spleens of vaccinated mice based on tetramer+ CD8+ phenotype. RNA was isolated using TriZol reagent. Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: CD8 T cells

value: spleen

tag: strain


title: LCMV_No Help_005

description: processed data file: COMP1_DE_Table.txt


title: LCMV_No Help_002

description: processed data file: COMP1_DE_Table.txt


title: JR1963

description: s-SHIP Low 2


title: ER_EnhiE2_rep2

value: ER alpha

value: 10 nM E2

tag: time point


title: ER_IL1E2_rep2

value: Control


title: LCMV_No Help_003

description: processed data file: COMP1_DE_Table.txt


title: ER_IL1E2_rep1


title: mko2_rna

value: Embryonic day E12.5

value: Wnt1-Cre, Rosa-Tomato flow sorted cranial neural crest

tag: genotype

value: male


title: Ishikawa RNA pol II_E2

source_name: Ishikawa endometrial cancer cell line

value: RNA polymerase II


title: LCMV_Help_005

description: processed data file: COMP1_DE_Table.txt


title: ER_EnhiE2_rep1


title: LCMV_Help_003

description: processed data file: COMP1_DE_Table.txt


title: LCMV_Help_004

description: processed data file: COMP1_DE_Table.txt


title: Ishikawa H3K27ac_Strip


title: H3K27ac_IL1RNE2


title: Ishikawa RNA pol II_DMSO

value: DMSO


title: LCMV_Help_002

description: processed data file: COMP1_DE_Table.txt


title: Ishikawa H3K27ac_Regular

value: 1 nM E2

value: regular RPMI (with phenol red)

value: 6 days


title: H3K27ac_EnhiE2


title: H3K27ac_IL1RN


title: LCMV_Help_001

description: processed data file: COMP1_DE_Table.txt


title: P10-2_ATAC-seq

city: Basel

first: Botond

last: Roska

address: Maulbeerstrasse 66

institute: FMI

data_processing:
Preprocessing of reads and analysis was performed using the statistical software R using the QuasR package. Briefly, adaptor sequences (CTGTCTCTTATACACA) were removed from the 5’-ends of both reads using preprocessReads, and truncated reads were further trimmed by one more base to allow for paired-end alignment to a reference mouse genome (GRCm38/mm10) with qAlign, which internally uses bowtie [Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)]. Around 70% of the obtained reads could be mapped.
Peaks were identified on a pool of all samples using macs2 version 2.1.0.20140616 [Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] using parameters --nomodel --shift 0 --gsize 1.87e9 --qvalue 0.10. The number of reads in each sample was then quantified in these peak regions. Mean counts for each time point were determined and log2 transformed (adding 1 count to each value to avoid minus infinity values).
Outliers were removed by removing the ten highest peaks.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text files include RPKM values for each timepoint

source_name: Cone photoreceptor

extract_protocol:
Both retinas from mice age P3, P6, and P9 were used for the ATACseq experiment. For each time point, three mice were used. Only male mice were used to avoid any influence from X-chromosome inactivation. A protocol from Siegert et al. (Nature Neuroscience 2012) was used to dissociate retinal cells. Retinas were dissected in HBSS and incubated in an activated papain solution for 5 min at 37 °C. After removing the papain solution, retinas were washed with HBSS containing 2% FCS and then dissociated in HBSS containing 2% by triturating the tissue with a fire-polished Pasteur pipette. The suspension was filtered before FACS sorting. Single-cell suspensions were obtained after FACS sorting into PBS/10%FCS.
ATACseq was performed according to Buenrostro et al. (Nature Methods, 2013), with minor modifications. Briefly, 50,000 cells were used per transposition reaction. Cells were collected and lysed in cold lysis buffer (10mM Tris-HCl pH 8.0; 10mM NaCl; 3mM MgCl2; 0.5% NP40).  Transposition was done as reported in Buenrostro et al. (Nature Methods, 2013), steps 6 – 12, and PCR amplification was done according to steps 13 – 18. Briefly, during the amplification reaction, PCR primers were used as mentioned in the supplemental material from Buenrostro et al. (Nature Methods, 2013). Amplified libraries were cleaned up using AMPure XP beads in a DNA:beads ratio of 1:1.8. Further size selection of the library prior to sequencing was avoided. The Nextera DNA Library Preparation Kit was used for library preparation. Multiple experiments were sequenced per lane (up to 3 per lane). Libraries were sequenced paired-end 100 bp reads using the Illumina HiSeq 2500.

value: Retina

value: Cone photoreceptor

tag: developmental stage

value: Chrnb4-GFP hetero


title: P10-1_ATAC-seq


title: P10-3_ATAC-seq


title: P6-3_ATAC-seq


title: Control_gRNAs_8hrE2_rep2

data_processing:
Sequence reads in fastq format were aligned to hg19 using HISAT2 (Kim et al., 2015) with the following parameters: --dta -t -p 10 --no-unal --rna-strandness R.
HTseq (Anders et al., 2015) was used to generate normalized counts for RefSeq genes.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files have normalized read counts for RefSeq genes for each Sample

source_name: Control gRNAs, 8hr E2

growth_protocol: Stable lines were grown in estrogen-depleted media for 5-7 days prior to guide RNA transfection.

extract_protocol:
RNA was isolated via direct lysis with Buffer RLT-Plus (Qiagen) with 1% beta-mercaptoethanol (Sigma).
100 ng of each sample was processed using KAPA Stranded mRNA-seq kit (KAPA Biosystems).

treatment_protocol: Cells were treated with E2 at ~72 hours post transfection.

tag: fusion

tag: guide rnas transfected

value: pool of 4 gRNAs targeting IL1RN promoter

tag: treatment

value: estradiol, 8 hr 10 nM E2

value: Ishikawa endometrial cancer


title: Control_gRNAs_noE2_rep2

source_name: Control gRNAs, no E2

value: control


title: EnhancerI_noE2_rep2

source_name: EnhancerI, no E2

value: pool of 42 gRNAs targeting 10 ERBS


title: P6-1_ATAC-seq

tag: Sex


title: P6-2_ATAC-seq


title: P3-2_ATAC-seq


title: Control_gRNAs_noE2_rep1


title: LCMV_No Help_001

description: processed data file: COMP1_DE_Table.txt

value: CD8 T cells

value: spleen


title: EnhancerI_8hrE2_rep2

source_name: EnhancerI, 8hr E2


title: P3-3_ATAC-seq


title: P3-1_ATAC-seq


title: EnhancerI_8hrE2_rep1


title: P12-3_RNA-seq

data_processing:
Base calling and quality scoring is performed using RTA v1.17.21.3. Fastq files generation and demultiplexing was done using bcl2fastq v1.8.4.
Analysis was performed using the statistical software R using the QuasR package
Sequences were mapped to a reference mouse genome (GRCm38/mm10) using splicedAlignment=TRUE, which internally uses SpliceMap counted per gene (using known gene annotation from UCSC) and normalized to the gene length and library size (RPKM = reads per kilobase transcript and million reads in library)
Outliers were excluded from the analysis by removing the highest of the 39 values for each gene. The mean of the technical triplicates was calculated and a threshold was set to remove noise. To find the optimal threshold, different thresholds were applied and a curve was fitted to the resulting data set. The skewness of the curve was used as a measure of normal distribution. The threshold that resulted in the skewness closest to zero was chosen (threshold 1.645 RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text files include RPKM values for each timepoint

extract_protocol:
A protocol from Siegert et al. (Nature Neuroscience 2012) was used to dissociate retinal cells. Retinas were dissected in HBSS and incubated in an activated papain solution for 5 min at 37 °C. After removing the papain solution, retinas were washed with HBSS containing 2% FCS and then dissociated in HBSS containing 2% by triturating the tissue with a fire-polished Pasteur pipette. The suspension was filtered before FACS sorting. Per time point (P0 till P12), we FACS-sorted three retinas, each from a different animal. If 20,000 cells could not be obtained from one retina, retinas of different animals were pooled. Cells where sorted using a BD Influx™ cell sorter (Becton, Dickinson and Company, BD Biosciences, San Jose, CA USA) with the BD FACS™ Sortware sorter software (Version 1.01.654). The sort was performed with a 100 μm nozzle tip, at a sheath pressure of 19.0 psi, and a frequency of 28.90 kHz. The following gates were set: gate 1 was forward scatter FSC-Area against side scatter SSC-Area, gate 2 was FSC-Width against FSC-Height, gate 3 was SSC-Width against SSC-Height, and gate 4 was 530/40 (488 nm) against 710/50 (561 nm). RNA isolation was done using the Pico Pure kit. Total RNA amplification was done using the NuGEn Ovation RNA-Seq System V2 followed by library preparation with the Illumian TruSeq Nano DNA Sample prep protocol. Samples were sequenced in the Hiseq in 50 cycles, producing single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed


title: P12-1_RNA-seq


title: P12-2_RNA-seq


title: P11-3_RNA-seq


title: H3K27ac_Enhi

tag: antibody

value: Enhancer-I

value: charcoal-stripped RPMI


title: P11-2_RNA-seq


title: SAHA Rep1

city: Boston

first: Pin-Ji

last: Lei

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
RNASeq raw data quality control by FastQC
RNASeq raw data clean performed by cutadapt
RNASeq data mapping to hg19 reference genome by tophat2 with at most two mismatch. Cuflinks was used for differential expression gene analysis.Gene ontology analysis was performed using DAVID (http://david.abcc.ncifcrf.gov)
Genome_build: hg19

growth_protocol: U2OS cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% penicillin and streptomycin.

extract_protocol:
10ug total RNA as initiation, and mRNA purification was performed by NEBNext mRNA isolation and fragmentation module.
Rubicon ThruPLEX DNA-seq 48D kit was used for RNASeq ibrary construction. Brifely, about 100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 15 cycles for each library and gel selection was used for library size selection and purification.

treatment_protocol: U2OS cells were treated with 0.5%(V/V) DMSO, 10μM GSK 343 for 24h, 20μM GSK-J4 for 12h, 20μM BRD4770 for 24h, 20μM VPA for 24h, 50μM UNC1215 for 24h, 1mM 2-PCPA for 12h, 5μM Rapamycin for 24h, 1μM SAHA for 24h, 5μM BIX-01294 for 12h.  RNA-Seq was used to analyze transcriptome profilings under different drugs stimulation.

tag: cell line

value: 1μM SAHA for 24


title: UNC1215 Rep1

value: 50μM UNC1215 for 24h


title: P11-1_RNA-seq


title: BRD4770 Rep1

value: 20μM BRD4770 for 24h


title: P10-3_RNA-seq


title: GSK-J4 Rep1

value: 20μM GSK-J4 for 12h


title: BIX-01294 Rep1

value: 5μM BIX-01294 for 12h


title: P10-2_RNA-seq

value: Retina

value: Cone photoreceptor


title: Rapamycin Rep2

value: 5μM Rapamycin for 24h


title: P10-1_RNA-seq

value: Chrnb4-GFP hetero


title: P9-3_RNA-seq


title: Control_gRNAs_8hrE2_rep1

value: pool of 4 gRNAs targeting IL1RN promoter

value: estradiol, 8 hr 10 nM E2

value: Ishikawa endometrial cancer


title: Rapamycin Rep1


title: P9-2_RNA-seq


title: P9-1_RNA-seq


title: P8-3_RNA-seq


title: 2PCPA Rep2

value: 1mM 2-PCPA for 12h


title: 2PCPA Rep1


title: P8-2_RNA-seq


title: VPA Rep1

value: 20μM VPA for 24h


title: DMSO Rep2


title: P8-1_RNA-seq

value: mixed


title: P7-3_RNA-seq


title: P7-2_RNA-seq


title: P7-1_RNA-seq


title: P6-3_RNA-seq


title: 161130-wt-AC403-i16_KOH

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

data_processing:
All reads were trimmed for quality and adaptor sequence with cutadapt 1.2.1 (-m 15 -q 10–match-read-wildcards). Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligonucleotides used in the preparation of these libraries using Bowtie 0.12.8 (DOI: 10.1186/gb-2009-10-3-r25) and the flags -m1 -v2. All pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the sacCer3 S. cerevisiae UCSC reference genome (-m1 -v2 -X10000–best). Single-end alignments were then performed with mate 1 of all unaligned pairs with the flags -m1 -v2.
Genome_build: UCSC (sacCer3)
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: Strains were grown overnight at 30°C with shaking at 180 rpm and used to inoculate larger YPDA cultures at a start OD600 of 0.1. Cultures were grown until OD600 of 0.3 – 0.5 and 15 OD units were spun down, rinsed briefly with water, re-pelleted and stored at -20°C.

extract_protocol:
Genomic DNA was isolated using the MasterPure Yeast DNA Purification Kit (Epicentre) without the optional RNaseA treatment. For strains where large variation in relative ribonucleotide incorporation percentages was observed between the analyzed isolates, the analysis was repeated from cultures where the presence of the correct dNTP pool imbalance was verified  by HPLC analysis as previously described (Jia et al., 2015), and only the pool-verified samples were included in the analysis (rnh201∆; rnr1-Q288A; rnr1-Q288A rnh201∆; rnr1-Y285A; rnr1-Y285A,Q288E and rnr1-Y285A,Q288E rnh201∆). Two or more isolates were analyzed for each strain, except for rnr1-Y285A,Q288E and rnr1-Y285A,Q288E rnh201∆ where two replicates of one isolate were sequenced.
RNA residues in genomic DNA from S. cerevisiae were mapped by HydEn-seq by hydrolyzing 1 µg DNA with 0.3 M KOH for 2 h at 55 °C. To calculate the number of ribonucleotides per mtDNA molecule, we treated 1 µg DNA with 10 U of PmeI and the digests were purified with HighPrep PCR beads (MagBio), before the KCl or KOH treatment. After ethanol precipitation, the DNA fragments were treated for 3 min at 85 °C, phosphorylated with 10 U of 3′-phosphatase-minus T4 polynucleotide kinase (New England BioLabs) for 30 min at 37 °C, heat inactivated for 20 min at 65 °C and purified with HighPrep PCR beads (MagBio). Phosphorylated products were treated for 3 min at 85 °C, ligated to oligo ARC140 overnight at room temperature with 10 U of T4 RNA ligase, 25% PEG 8000 and 1 mM CoCl3(NH3)6, and purified with HighPrep PCR beads (MagBio). Ligated products were treated for 3 min at 85 °C. The ARC76–ARC77 adaptor was annealed to the second strand for 5 min at room temperature. The second strand was synthesized with 4 U of T7 DNA polymerase (New England BioLabs) and purified with HighPrep PCR beads (MagBio). Libraries were purified, quantified with a Qubit fluorometric instrument (ThermoFisher Scientific) and 50-base paired-end sequenced on an Illumina NextSeq500 instrument, to identify the location of the free 5´-ends.

value: WT

tag: digest

value: no


title: P5-3_RNA-seq


title: 161130-wt-AC402-i15_KOH


title: P6-2_RNA-seq


title: P6-1_RNA-seq


title: GSK343 Rep2

value: 10μM GSK 343 for 24h


title: 161130-Y285A-DK8a-i18_KOH


title: 161130-PW18-5f-i14_KOH

source_name: rnh Y285A Q288E

value: rnh Y285A Q288E


title: GSK343 Rep1


title: P5-2_RNA-seq


title: 161130-PW12-3fx-i21_KOH

source_name: rnh

value: rnh


title: 161130-Cut-PW21-8c-i12_KOH

source_name: rnh D57N TRP sml1D crt1D PmeI

value: rnh D57N TRP sml1D crt1D

value: PmeI


title: 161130-JAK17-4i-i13_KOH


title: 161130-PW12-3cx-i20_KOH


title: P5-1_RNA-seq

value: Retina


title: P4-2_RNA-seq

value: Cone photoreceptor


title: EnhancerI_noE2_rep1

value: pool of 42 gRNAs targeting 10 ERBS

value: control


title: DMSO Rep1


title: P4-3_RNA-seq

value: Chrnb4-GFP hetero


title: 161130-Cut-PW21-5b-i11_KOH


title: P4-1_RNA-seq


title: 161130-Cut-PW12-3f-i4_KOH

source_name: rnh PmeI


title: 161130-Y285A-DK8e-i19_KOH


title: P3-2_RNA-seq


title: P3-3_RNA-seq


title: 161130-Cut-PW12-3c-i3_KOH


title: 161130-Cut-PW10-7f1-i9_KOH

source_name: D57N TRP sml1D crt1D PmeI

value: D57N TRP sml1D crt1D


title: 161130-Cut-AC402-2-i2_KOH

source_name: WT PmeI


title: P2-3_RNA-seq


title: P3-1_RNA-seq


title: P1-1_RNA-seq


title: P1-3_RNA-seq


title: P1-2_RNA-seq


title: P2-2_RNA-seq


title: 160912_PW18-5fx1-KOH


title: 160912_PW13-3cx-KOH

source_name: rnh Q288A

value: rnh Q288A


title: 160912_PW13-6dx-KOH


title: P0-3_RNA-seq


title: 161130-Cut-AC402-1-i1_KOH


title: 160912_DK10c-KOH


title: 160912_JAK17-4ix1-KOH


title: 161130-Cut-PW10-7f2-i10_KOH


title: 160912_DK10ex-KOH


title: 160615_ACP18-D57N-KOH-160310

source_name: D57N TRP

value: D57N TRP


title: 160615_ACP20-D57N-Q288E-KOH-160310


title: 160912_AC402-PmeI-500ng-KOH

source_name: WT AC402 PmeI

value: WT AC402


title: P0-1_RNA-seq

value: mixed


title: P0-2_RNA-seq


title: P2-1_RNA-seq


title: 160615_ACP17-D57N-crt-sml1-KOH-160310

source_name: D57N TRP sml1D crt1D


title: 160615_ACP12-Q288E-KOH-160310


title: 160524_PW123h_KOH


title: mouse lung high rep3

city: Princeton

first: Celeste

middle: M

last: Nelson

state: NJ

address: 303 Hoyt Laboratory

department: Chemical & Biological Engineering

institute: Princeton University

description: mouse lung high rep3

data_processing:
1. Basecalls performed by Illumina RTA version 1.18.64.0
2. PhiX removal using alignment with Bowtie version 1.1.1
3. Demulitiplexing performed by Galaxy's Enhanced Barcode Splitter v 1.1
4. Illumina TruSeq Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) trimmed with Cutadapt (Galaxy version 1.6) with default parameters
5. Alignment to mm10 genome using Tophat (Galaxy version 0.9) with the following settings: --library_type (first-strand), --GTF (UCSC mm10 GTF file), --no-novel-juncs
6. Gene counts generated using htseq-count (Galaxy version 0.6.1galaxy1) with default parameters
7. Differential expression analysis performed using DESeq2  (Galaxy Version 2.1.8.3)
* Step 3 produced the raw data files below
* Step 6 produced the raw count files that were fed into the differential expression analysis with DESeq2 (one possible "processed data file")
* Step 7 produced the lists of fold change and p-values (another possible "processed data file")
Genome_build: mm10

source_name: embryonic mouse lung

growth_protocol: (i) embryonic mouse lungs at E12.5 were cultured under low or high pressure for 48 hours prior to RNA extraction or (ii) embryonic mouse lungs were isolated from pregnant mice at E12.5, E13.5 and E14.5 prior to RNA extraction

extract_protocol:
RNA was isolated from a pool of 6 embryonic mouse lungs (cultured under low pressure and E12.5) and pool of 3 embryonic mouse lung (cultured under high pressure, E13.5 and E14.5) using QIAGEN Rneasy fibrous tissue kit.
PrepX RNA-Seq for Illumina Library Kit, from WaferGen

value: wildtype

tag: age

value: isolated at embryonic E12.5, cultured ex vivo for 48 hours


title: mouse lung high rep1

description: mouse lung high rep1


title: mouse lung low rep3

description: mouse lung low rep3


title: mouse lung low rep2

description: mouse lung low rep2


title: 160524_PW123d_KOH

value: no


title: mouse lung high rep2

description: mouse lung high rep2


title: E14.5 mouse lung rep1

description: E14.5 mouse lung rep1

value: embryonic E14.5


title: E14.5 mouse lung rep3

description: E14.5 mouse lung rep3


title: 160204_ARC119-PW215b-KOH

source_name: rnh D57N TRP sml1D crt1D


title: 160204_ARC117-PW203b-KOH

source_name: rnh D57N TRP

value: rnh D57N TRP


title: E14.5 mouse lung rep2

description: E14.5 mouse lung rep2


title: 160204_ARC118-PW204a-KOH


title: mouse lung low rep1

description: mouse lung low rep1


title: 160615_ACP16-D57N-crt-sml1-KOH-160310


title: E13.5 mouse lung rep3

description: E13.5 mouse lung rep3

value: embryonic E13.5


title: E13.5 mouse lung rep1

description: E13.5 mouse lung rep1


title: E13.5 mouse lung rep2

description: E13.5 mouse lung rep2


title: 160204_ARC116-PW194a-KOH

source_name: rnh Q288E

value: rnh Q288E


title: 160204_ARC111-PW172b-KOH

source_name: rnh D57N Q288E

value: rnh D57N Q288E


title: 160204_ARC115-PW193c-KOH


title: 160204_ARC112-PW174b-KOH


title: E12.5 mouse lung rep3

description: E12.5 mouse lung rep3

value: embryonic E12.5


title: 160204_ARC109-PW164b-KOH

source_name: rnh Y285F

value: rnh Y285F


title: 160204_ARC108-PW156h-KOH

source_name: rnh Y285A

value: rnh Y285A


title: 160204_ARC110-PW165h-KOH


title: 160204_ARC107-PW157d-KOH


title: 150313_ACH15-150202_KOH


title: E12.5 mouse lung rep1

description: E12.5 mouse lung rep1


title: 160204_ARC120-PW218c-KOH

value: rnh D57N TRP sml1D crt1D


title: 150313_ACH14-150202_KOH


title: 150313_ACH11-150202_KOH


title: 150313_ACH02-150202_KOH

source_name: WT

value: WT


title: 150313_ACH10-150202_KOH