title: H1_TKO_ESC_R2_DNA_Methylation_HELP_assay

description:
library selection: restriction digest
DNA methylation HELP assay
Processed data file: WT_ESC_vs_H1_TKO_ESC_DNA_methylation_assay_HELP.txt.gz

data_processing:
Library strategy: HELP
Hi-C : Reads from both ends were mapped separately single end with bwa aln with default parameters. Uniquely mapped reads were sorted and paired by read ID using samtools. Mapped pairs were filtered to remove reads coming from the same or neighboring restriction fragments. Filtered pairs were deduplicated to remove PCR duplicates and valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files.
DNase Hypersensitivity : Aligned reads in bam files are those 36bp reads that aligned uniquely (Bowtie) to the reference (NCBI37/mm9) and contain no more than 2 mismatches. DNaseI-sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004).
DNA methylation HELP tagging data was processed with the WASP pipeline (version 3.0.31 (rev. 3822). Reads were aligned with Illumina's CASAVA and ELAND v. 1.7.0 allowing 2 mismatches in the first 32bp and no more than 10 alignments for each read. HELP angles were computed as described in (Suzuki et al. 2010).
RNA-Seq : We aligned 2x100 paired-end reads of 2 replicate WT ESC RNA-seq libraries and 3 replicate H1 TKO ESC RNA-seq libraries to the reference genome (NCBI37/mm9) with TopHat and used Cufflinks and CuffDiff for differential expression analysis of RNA-seq expression for a non-redundant collection of 20876 known RefSeq transcripts. We considered genes with a marginal p-value smaller than 0.05 and an absolute log2 fold-change  bigger than 1 to be differentially expressed.
ChIP-Seq : Reads from all different libraries were aligned to the reference genome (NCBI37/mm9) with bowtie2 with default settings and the --qc-filter switch. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/) and were removed from the data for subsequent analyses. Regions significantly enriched for H3K4me1, H3K4me3, H3K27me3 and H3K9me3 compared to matched input samples were identified using the MACS2 peak caller with default settings. For the H3K9me3 and H3K27me3 histone marks, the parameter - - broad was set. Analysis of differential ChIP enrichment was done using diffReps with parameters -me gt –pval 0.001 --frag 150.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files; ChIP-Seq peaks called by MACS2 are in peaks.bed.gz files; DNaseI-hypersensitive sites called with the HOTSPOT algorithm in mm9.bed.gz files; DNA methylation HELP angles are in HELP.txt.gz file; RNA-Seq FPKM values are in FPKM.txt.gz file.

source_name: H1 TKO embryonic stem cells

extract_protocol: Suzuki et al. 2010 (Genome Biology 2010).

tag: strain/background

value: embryonic stem cell line

tag: genotype/variation

value: H1c, H1d, H1e triple-null


title: LNA-miR27-TGFb

status: Public on Nov 30 2015

type: SRA

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
Paired-end reads were mapped to mm9 assembly with the TopHat program (version 2.0.9.) (Trapnell et al., 2009) using the UCSC mm9 GTF file.
FPKM data was generated with Cufflinks (version 2.1.1.).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: 6samples_TGFb_FKPM.txt': Tab-delimited text file includes FPKMs for each sample.

molecule: total RNA

organism: Mus musculus

source_name: mouse endothelial cells, miR27 inhibitor and TGF-beta

growth_protocol: MS-1 cells were obtained from American Type Culture Collection, and maintained in Minimum Essential Medium-Alpha (MEM-α) medium (Invitrogen) supplemented with 10% fetal calf serum (FCS), 50 units/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
Total RNA were collected, and rRNAs were depleted with Ribo-Zero™ Magnetic Kit (Epicentre).
Total RNAs were subjected to library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and KAPA HiFi DNA polymerase (NIPPON Genetics), and analyzed by Illumina HiSeq 2000.

treatment_protocol: MS-1 cells transfected with miRNA inhibitors were cultured in the absence or presence of 1 ng/ml of TGF-β2 for 72 hours.

tag: cell line

tag: cell type

value: mouse endothelial cells

tag: treatment

value: miR27 inhibitor and TGF-beta


title: LNA-miR31-cont

source_name: mouse endothelial cells, miR31 inhibitor

value: miR31 inhibitor


title: LNA-miR27-cont

source_name: mouse endothelial cells, miR27 inhibitor

value: miR27 inhibitor


title: H1_TKO_ESC_R1_DNA_Methylation_HELP_assay

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

molecule: genomic DNA

growth_protocol:
Wild-type ES cell line was derived from littermate male blastocysts produced from matings of N7 backcrossed C57BL/6 triple heterozygous H1 mutant parents. The transgenic lines are further described in Fan et al. Cell 2005 (PMID 16377562).
WT and H1 TKO ES cells were grown on irradiated mouse embryonic fibroblasts in DMEM (high glucose, Gibco) with 15% FBS, 1x non-essential amino acids (NEAA; Gibco), 1x penicillin–streptomycin (Gibco), 1:1,000 b-mercaptoethanol (Invitrogen), 1x L-glutamine (Gibco) and 1,000 U/ml leukaemia inhibitory factor (LIF; Gibco).


title: LNA-NC-TGFb

source_name: mouse endothelial cells, TGF-beta

value: TGF-beta


title: LNA-miR31-TGFb

source_name: mouse endothelial cells, miR31 inhibitor and TGF-beta

value: miR31 inhibitor and TGF-beta


title: Non-targeting RNAseq Replicate1

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

country: USA

institute: University of North Carolina Chapel Hill

data_processing:
Alignment - tophat -p 8 --library-type fr-firststrand
Quantification - HTSeq- count htseq-count -s reverse -m intersection-strict -i gene_name -
Differential expression analysis - DESeq2 using gencode V16 transcripts ( see differential_expression_test.R in associated code repository)
Genome_build: hg19
Supplementary_files_format_and_content: htseq counts for all genes(rows) x samples (columns)  and depth and length normalized values for each gene (count_data_rpkm.csv)

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human hepatocellular carcinoma cells (HepG2) were grown in DMEM with 10% Fetal Bovine Serum and penicillin and streptomycin

extract_protocol:
RNA was extracted by Trizol purification and cleaned using a Qiagen RNAeasy column using manufacturers instruction
Strand specific libraries were constructed using the dUTP incorporation method

treatment_protocol: Cells were treated with 50nM siRNA for 72 hours using Lipofectamine RNAimax

value: hepatocellular carcinoma

tag: sirna vendor

value: Dharmacon

tag: catolog number


title: WT_ESC_R2_DNA_Methylation_HELP_assay

source_name: WT embryonic stem cells

value: WT


title: 0827.phf5a_kd_861

city: Cleveland

first: Christopher

middle: G.

last: Hubert

state: OH

address: 9500 Euclid Ave.

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic

description: regulated.phf5a_kd_861.down.0827.list.txt, regulated.phf5a_kd_861.up.0827.list.txt

data_processing:
We used previously published annotations of competing 3' and 5' splice sites, mutually exclusive exons, and skipped exons (Wang et al., 2008). For each splicing event, we assigned it to its most likely parent isoform and assessed whether it was likely to induce nonsense-mediated decay (if it introduced an in-frame stop codon at least 50 bp upstream of a splice junction). We furthermore enumerated all constitutive junctions, where a constitutive junction was defined as a splice junction for which neither the 5' nor 3' splice site was annotated as possibly spliced to another 3' or 5' (respectively) splice site in either Ensembl or UCSC.
We mapped the raw FASTQ files using Bowtie version 0.12.8 (Langmead et al., 2009) and TopHat version 1.3.3 (Trapnell et al., 2009).
We mapped to the genome, all splice junctions in the annotations described above, and all possible splice junctions that could result from skipping of exons in our gene annotations. To reduce the false positive rate of mapping, we did not allow novel junction discovery and furthermore required at least 6 bp of overhang on either side of splice sites.
In order to detect changes in all classes of splicing events with equal statistical power, we used only reads crossing the minimal identifying splice junctions for each event and tested for changes in splicing following PHF5A KD using the binomial proportion test, which is appropriate for RNA-seq data, where the number of reads is variable. We described this approach previously (Bradley et al., 2012). To fairly assess retention of constitutive introns, we treated reads crossing the 5' splice site (the 3' end of the upstream exon) with at least 6 bp of overhang in both the exon and intron as identifying reads. We required p-value < 0.01 and a change of at least 10% in isoform ratio.
We sought to obtain the most comprehensive set of splicing events affected by PHF5A. We therefore took the union of the events detected using the approach described above with events identified with a binomial proportion test on the reads assigned to each isoform by MISO version 0.4.4 (Katz et al., 2010), which uses a Bayesian approach to assign non-identifying reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text containing splicing event coordinates, prediction of nonsense-mediated decay, p-value, and gene information

source_name: glioblastoma

growth_protocol: Grown in serum-free media supplemented with N2, B27, EGF, FGF, L-Glutamine, Sodium Pyruvate, on Laminin coated plates. Samples indicated as CB660 are neural stem cells and samples indicated as either G166 or 0827 are glioblastoma.

extract_protocol:
Trizol
We prepared poly (A)-selected single-end RNA-seq libraries using the Illumina TruSeq protocol and sequenced all libraries on the HiSeq 2000 instrument with a read length of 99 bp.

treatment_protocol: shRNA knockdown using pGIPZ lentivirus followed by puromycin selection of positively infected cells. Clone #861 shRNA sequence is ATAATATGAGACTAGTGGG. Clone #402 shRNA sequence is AGTGTTAAACAAGTAAATG.

value: glioblastoma

tag: lentivirus

value: :pGIPZ

tag: shRNA seq

value: ATAATATGAGACTAGTGGG


title: WT_ESC_R1_DNA_Methylation_HELP_assay


title: Arid2 RNAseq Replicate3

value: Life Technologies


title: Arid2 RNAseq Replicate2


title: Arid1b RNAseq Replicate3


title: Arid1b RNAseq Replicate2


title: Arid2 RNAseq Replicate1


title: Arid1a RNAseq Replicate2


title: Arid1a RNAseq Replicate4


title: Arid1b RNAseq Replicate1


title: Arid1a RNAseq Replicate5


title: Input

data_processing:
Align with bowtie2
Filter Duplicates
Merge alignments
Call peaks using macs --broadpeak -q 0.01
Create wig files
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and bigbed

extract_protocol:
Chromatin Immunoprecipitation on 2e7 cells using antibodies noted in Samples section
NEB Next Reagents for Illumina Sequencing

tag: antibody

value: none (input)


title: Arid1a RNAseq Replicate1


title: Snf5 ChIP Replicate 2

value: Bethyl - A301-087A

tag: antibody lot


title: Snf5 ChIP Replicate 1


title: Arid2 RNAseq Replicate5


title: Arid1a ChIP Replicate1

value: Santa Cruz -  sc-32761X


title: Arid1a ChIP Replicate 2


title: LNA-NC-cont

source_name: mouse endothelial cells, control

value: control


title: Arid2 ChIP Replicate 1

value: Bethyl - A302-230A


title: untreated SiHa RNA-seq

first: Jennifer

last: Webster-Cyriaque

state: NC

address: 385 S. Columbia St.

department: Dental Research

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were aligned to the hg19 genome assembly using TopHat version 2.0.9, using the Ensembl gtf, with default parameters.
RPKM was calculated using CuffLinks version 2.1.1, with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values

source_name: untreated SiHa cells

growth_protocol: DMEM supplemented with 5% FBS and 1% penicillin-strepomycin

extract_protocol:
Cells were harvested and RNA was isolated using Trizol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SiHa

value: cervical cancer cell line with integrated HPV16


title: Arid1b ChIP Replicate 2

value: Santa Cruz - sc-32762X


title: Arid1b ChIP Replicate 1


title: S18

city: Stanford

first: Livia

middle: Zarnescu

last: Yanez

state: California

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

data_processing:
Adapter clipping and trimming using fastq_quality_trimmer and fastx_clipper
Align reads to hg18 using STAR aligner
Convert files from sam to bam format and sort reads by name
Output read counts using HTSeq-count
Obtain adjusted expression values using edgeR and ComBat packages in R
Genome_build: hg18
Supplementary_files_format_and_content: Processed files contain read counts for each gene ([sample name]_paired_count.txt). There is also a file adjusted_expression_data.txt which contains all the data values used to generate figures along with adjusted_expression_qvals.txt which contains the q-values for all genes.

source_name: Human zygote (2PN)

extract_protocol:
SMARTer® Ultra™ Low RNA kit (Clontech)
NEBNext® DNA Sample Prep Master Mix Set (New England Biolabs)

treatment_protocol: micropipette aspiration to measure mechanical parameters

tag: tissue type

value: embryo

tag: developmental stage

value: 2PN zygote

tag: predicted viability

value: good


title: S22

value: bad


title: S20


title: S19


title: S21


title: L-11-3284

city: Cincinnati

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: prenatal control diet exposed PND21 mammary glands

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to rn4 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: rn4
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

organism: Rattus norvegicus

source_name: mammary gland_CTL

extract_protocol:
RNAs were extracted using Qiagen Rneasy Lipid kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: mammary gland

tag: age

tag: diet

value: Control (CTL)


title: L-9-3282


title: S16


title: L-10-3283


title: L-14-3289


title: L-7-3280


title: Arid1a RNAseq Replicate3

value: hepatocellular carcinoma

value: Dharmacon


title: L-6-3276

description: prenatal high fat butter exposed PND21 mammary glands

source_name: mammary gland_HFB

value: High fat butter (HFB)


title: S13


title: S12


title: S11


title: L-5-3274


title: Arid2 ChIP Replicate 2


title: L-4-3273


title: S14


title: S9


title: S10


title: S8


title: L-1-3270


title: S17


title: S7


title: L-2-3271


title: S6


title: S3


title: S2


title: L-8-3281


title: S1


title: JSC.6200 Johnson Space Center study

city: College Station

first: Nancy

middle: D.

last: Turner

state: TX

address: 2253 TAMU

department: Nutrition & Food Science

institute: Texas A&M University

description:
Johnson Space Center study
table.from_biom_w_taxonomyJSCSTS

library_source: metagenomic

data_processing:
454 Life Sciences GS Data Analysis Software package using standard parameters
The combined raw sequencing data were de-multiplexed and filtered by QIIME
Data were denoised using Denoiser software
Sequences were grouped into OTUs at a 97% level to approximate species-level phylotypes using Uclust
Supplementary_files_format_and_content: Text file containing taxonomy classification and abundances from biom

organism: rat gut metagenome

source_name: feces

extract_protocol:
Total DNA was isolated from fecal samples using Qiagen's protocol
Initial amplification of the V1-V2 region of the bacterial 16S rDNA was performed on total DNA isolated from fecal samples. Each sample was individually gel purified using the E-Gel Electrophoresis System. To ensure equal representation of each sample in the sequencing run, each barcoded sample was standardized by calculating equimolar amounts prior to pooling. Pooled samples of the 16S rDNA multiplexed amplicons were sequenced on a Roche 454 Genome Sequencer FLX Titanium instrument using the GS FLX Titanium XLR70 sequencing reagents and protocols.

treatment_protocol: Radiation, diet, microgravity

tag: strain

value: Sprague-Dawley

tag: radiation

value: Fractionated low LET gamma (3 Gy)

value: High Fe diet

tag: microgravity

value: Weightbearing


title: JSC.6199 Johnson Space Center study


title: S5


title: JSC.6201 Johnson Space Center study


title: JSC.6202 Johnson Space Center study


title: JSC.6197 Johnson Space Center study


title: JSC.6198 Johnson Space Center study


title: H1_TKO_ESC_H3K27me3_IP_R1

description: Processed data file: H1_TKO_ESC_H3K27me3_peaks.bed.gz

data_processing:
Hi-C : Reads from both ends were mapped separately single end with bwa aln with default parameters. Uniquely mapped reads were sorted and paired by read ID using samtools. Mapped pairs were filtered to remove reads coming from the same or neighboring restriction fragments. Filtered pairs were deduplicated to remove PCR duplicates and valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files.
DNase Hypersensitivity : Aligned reads in bam files are those 36bp reads that aligned uniquely (Bowtie) to the reference (NCBI37/mm9) and contain no more than 2 mismatches. DNaseI-sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004).
DNA methylation HELP tagging data was processed with the WASP pipeline (version 3.0.31 (rev. 3822). Reads were aligned with Illumina's CASAVA and ELAND v. 1.7.0 allowing 2 mismatches in the first 32bp and no more than 10 alignments for each read. HELP angles were computed as described in (Suzuki et al. 2010).
RNA-Seq : We aligned 2x100 paired-end reads of 2 replicate WT ESC RNA-seq libraries and 3 replicate H1 TKO ESC RNA-seq libraries to the reference genome (NCBI37/mm9) with TopHat and used Cufflinks and CuffDiff for differential expression analysis of RNA-seq expression for a non-redundant collection of 20876 known RefSeq transcripts. We considered genes with a marginal p-value smaller than 0.05 and an absolute log2 fold-change  bigger than 1 to be differentially expressed.
ChIP-Seq : Reads from all different libraries were aligned to the reference genome (NCBI37/mm9) with bowtie2 with default settings and the --qc-filter switch. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/) and were removed from the data for subsequent analyses. Regions significantly enriched for H3K4me1, H3K4me3, H3K27me3 and H3K9me3 compared to matched input samples were identified using the MACS2 peak caller with default settings. For the H3K9me3 and H3K27me3 histone marks, the parameter - - broad was set. Analysis of differential ChIP enrichment was done using diffReps with parameters -me gt –pval 0.001 --frag 150.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files; ChIP-Seq peaks called by MACS2 are in peaks.bed.gz files; DNaseI-hypersensitive sites called with the HOTSPOT algorithm in mm9.bed.gz files; DNA methylation HELP angles are in HELP.txt.gz file; RNA-Seq FPKM values are in FPKM.txt.gz file.

source_name: H1 TKO embryonic stem cells, H3K27me3 ChIP

extract_protocol: TruSeq DNA sample preparation kit (Illumina).

tag: strain/background

tag: cell type

value: embryonic stem cell line

tag: genotype/variation

value: H1c, H1d, H1e triple-null

tag: chip antibody

value: H3K27me3 (Abcam ab6002)


title: H1_TKO_ESC_H3K9me3_H3K27me3_input

description:
Processed data file: H1_TKO_ESC_H3K9me3_peaks.bed.gz
Processed data file: H1_TKO_ESC_H3K27me3_peaks.bed.gz

source_name: H1 TKO embryonic stem cells, H3K9me3 H3K27me3 input


title: WT_ESC_H3K9me3_H3K27me3_input

description:
Processed data file: WT_ESC_H3K9me3_peaks.bed.gz
Processed data file: WT_ESC_H3K27me3_peaks.bed.gz

source_name: WT embryonic stem cells, H3K9me3 H3K27me3 input

value: WT


title: JSC.6194 Johnson Space Center study

value: Low Fe diet


title: JSC.6195 Johnson Space Center study


title: H1_TKO_ESC_H3K27me3_IP_R2


title: JSC.6196 Johnson Space Center study


title: WT_ESC_H3K27me3_IP_R2

description: Processed data file: WT_ESC_H3K27me3_peaks.bed.gz

source_name: WT embryonic stem cells, H3K27me3 ChIP


title: L-3-3272


title: WT_ESC_H3K27me3_IP_R1


title: JSC.6192 Johnson Space Center study


title: S4

value: embryo

value: 2PN zygote


title: JSC.6193 Johnson Space Center study


title: H1_TKO_ESC_H3K9me3_IP_R1

description: Processed data file: H1_TKO_ESC_H3K9me3_peaks.bed.gz

source_name: H1 TKO embryonic stem cells, H3K9me3 ChIP

value: H3K9me3 (Abcam ab8898)


title: H1_TKO_ESC_H3K9me3_IP_R2


title: JSC.6191 Johnson Space Center study


title: JSC.6190 Johnson Space Center study


title: WT_ESC_H3K9me3_IP_R2

description: Processed data file: WT_ESC_H3K9me3_peaks.bed.gz

source_name: WT embryonic stem cells, H3K9me3 ChIP


title: JSC.6189 Johnson Space Center study


title: JSC.6188 Johnson Space Center study


title: SHAM.LUN Brookhaven National laboratory study

description:
Brookhaven National laboratory study
SHAM.LUNOTUs

organism: mouse gut metagenome

value: SHAM irradiated

value: Chow

value: 1/6 G partial weight bearing


title: JSC.6187 Johnson Space Center study


title: SHAM.CC Brookhaven National laboratory study

description:
Brookhaven National laboratory study
SHAM.CCOTUs


title: LUN.RE Brookhaven National laboratory study

description:
Brookhaven National laboratory study
LUN.REOTUs

value: High LET silicon radiation (0.05 Gy)


title: CC.RE Brookhaven National laboratory study

description:
Brookhaven National laboratory study
CC.RE OTUs


title: STS135.G40 Space Shuttle 135 study

description:
Space Shuttle 135 study
table.from_biom_w_taxonomyJSCSTS

value: Mixed space radiation

value: AEM


title: S15

value: good


title: STS135.G36 Space Shuttle 135 study


title: JSC.6183 Johnson Space Center study

value: Sprague-Dawley

value: High Fe diet


title: JSC.6184 Johnson Space Center study

value: Weightbearing


title: JSC.6186 Johnson Space Center study


title: JSC.6182 Johnson Space Center study


title: JSC.6185 Johnson Space Center study


title: STS135.G28 Space Shuttle 135 study


title: STS135.G24 Space Shuttle 135 study


title: JSC.6181 Johnson Space Center study


title: JSC.6180 Johnson Space Center study


title: STS135.G32 Space Shuttle 135 study


title: STS135.G20 Space Shuttle 135 study


title: STS135.G16 Space Shuttle 135 study


title: STS135.F66 Space Shuttle 135 study

value: Microgravity


title: STS135.F74 Space Shuttle 135 study


title: JSC.6178 Johnson Space Center study


title: STS135.F60 Space Shuttle 135 study


title: JSC.6175 Johnson Space Center study


title: JSC.6173 Johnson Space Center study


title: STS135.F58 Space Shuttle 135 study


title: JSC.6174 Johnson Space Center study


title: JSC.6171 Johnson Space Center study


title: Sample7_hpSC_DA_Progenitor

status: Public on Nov 29 2015

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Twelve bases were trimmed from the five prime end of each read using FASTX (version 0.0.13)
The adaptors were then trimmed using Trim Galore (version 0.2.2) and then mapped to hg19 reference genome using Tophat (version 2.0.6)
Samtools (version 0.1.17) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes1 and annotated using RefSeq (archive-2012-03-09-03-24-410). Genes that did not have at least one sample with at least five reads were removed from the analysis.
The data was normalized using the R (version 3.0.1) package DESeq (version 1.12.0)
Differential expression analysis and heat maps were done using Qlucore Omics Explorer 2.3
ANOVA of all three cell types and t-test of NSC and DAP were performed (q<0.01)
Functional annotation analysis was done using DAVID
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx including DESeq normalized counts filtered for genes with at least 5 reads in at least one sample

source_name: Dopaminergic Neuron Precursors

extract_protocol:
RNA was isolated from cells (RNeasy Plus Mini kit, Qiagen), quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent).
Approximately 600 ng was used as input for the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol.  Briefly, poly-A containing mRNA molecules are purified using a reagent containing poly-T oligo-attached magnetic beads. After purification, the mRNA is fragmented and first strand cDNA is produced using random primers and reverse transcriptase.  Second strand cDNA synthesis is then prepared using DNA Polymerase I and RNase H.  The cDNA is then ligated to indexed Illumina adapters and enriched with PCR to create the cDNA library.

value: hpSC derived Dopaminergic Neuron Precursors

tag: cell line


title: Sample9_hpSC_DA_Progenitor


title: STS135.F64 Space Shuttle 135 study


title: Sample5_hpSC_NSC

source_name: Neural Stem Cells

value: hpSC derived Neural Stem Cells


title: Sample6_hpSC_NSC


title: Sample3_hpSC_Undiff

source_name: Human Parthenogenic Stem Cells

value: Human Parthenogenic Stem Cells


title: JSC.6179 Johnson Space Center study

value: Low Fe diet


title: JSC.6177 Johnson Space Center study


title: WT_ESC_H3K9me3_IP_R1

value: embryonic stem cell line

value: WT


title: STS135.F52 Space Shuttle 135 study


title: Sample2_hpSC_Undiff


title: non-polyA RNAs from nuclear extract, seedling

status: Public on Nov 28 2015

city: Beijing

first: Yijun

last: Qi

address: #7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences

description: Strand-specific RNA-seq

data_processing:
Illumina Casava1.7 software was used for base-calling.
Adaptor sequences in the sequencing reads were removed using Cutadapt v1.0 with parameters '-O 4 -e 0.13 -m 35'.
Trimmed reads with a length no shorter than 35nt were aligned to Arabidopsis genome using TopHat v1.3.1 with parameters '-g 5 -i 20 -I 50000 -G TAIR10.gtf --solexa1.3-quals --library-type fr-secondstrand'.
For each sample, transcripts were assembled independently using Cufflinks v1.3.0 with parameters '--min-intron-length 20 -I 50000 -g TAIR10.gtf --library-type fr-secondstrand --min-frags-per-transfrag 1 -u'.
All assemblies from each samples as well as TAIR annotation (v10) were merged together by Cuffmerge using default parameters.
Cuffdiff were used to estimate the expression levels of each transcript in all samples.
genome build: TAIR10
processed data files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis ecotype Col-0 was surface steriled and planted on 1/2 MS medium. The culture condition was: 16 hour with light at 23℃, 70% humity, 8 hours without light at 18℃, 70% humity. 2 weeks old seedlings were harvested. The rest were transferred to soil medium for addtional two weeks and the inflorescence was harvested.

extract_protocol: The total RNA was extracted by using TRIzol reagent (Invitrogen, Cat. No. 15596018) with its standard protocol. RNAs were first fragmented by partial alkaline hydrolysis and separated on 12% PAGE gel. RNAs ranging from ~50 to ~75  were ligated to 3’ RNA adaptor and then ligated to 5’ RNA adaptor. The ligation products were then reverse transcribed to first strand cDNA, followed by PCR amplification.

treatment_protocol: no treatment

tag: ecotype

value: seedling

value: 14-day old

tag: molecule

value: non-polyA RNA, rRNA depleted


title: mock RIP-seq, seedling

data_processing:
Library strategy: RIP-Seq
Illumina Casava1.7 software was used for basecalling.
Adaptor sequences in the sequencing reads were removed using Cutadapt v1.0 with parameters '-O 4 -e 0.13 -m 18'.
Trimmed reads with a length no shorter than 18nt were aligned to Arabidopsis genome using TopHat v1.3.1 with parameters '-g 5 -i 20 -I 50000 -G TAIR10.gtf --solexa1.3-quals'.
The number of reads overlapping with long non-coding RNAs were counted using SAMtools v0.1.16.
Raw read numbers were normalized to reads per million sequenced reads(RPM).
genome build: TAIR10
processed data files format and content: tab-delimited text files include RPM values for each Sample.

source_name: mock RIP-seq, seedling

growth_protocol: Arabidopsis ecotype Col-0 and transgenic plant (35S::myc-CLF clf-2) were surface steriled and planted on 1/2 MS medium. The culture condition was: 16 hour with light at 23℃, 70% humity, 8 hours without light at 18℃, 70% humity. 2 weeks old seedlings were harvested.

extract_protocol: The total RNA was extracted by using TRIzol reagent (Invitrogen, Cat. No. 15596018) with its standard protocol. Co-immunoprecipitated RNAs were reversed transcribed to cDNA by first-strand cDNA synthesis kit, and then, the second strand synthesis reaction was performed with Double-strand cDNA synthesis kit. Subsequently, the double strand cDNA were performed with a standard DNA library preparation protocol. RIP-seq: Anti-c-myc, Cat. No. 11 667 203 001, Roche

value: RNA


title: total RNAs from nuclear extract, seedling

description: Strand-specific RNA-seq

value: total RNA, rRNA depleted


title: total RNAs from nuclear extract, inflorescence

description: Strand-specific RNA-seq

value: inflorescence

value: 28-day old


title: JSC.6176 Johnson Space Center study

value: Sprague-Dawley

value: SHAM irradiated


title: polyA+ RNAs from whole cell extract, inflorescence

description: Strand-specific RNA-seq

value: polyA+ RNA


title: STS135.F54 Space Shuttle 135 study

value: Mixed space radiation

value: AEM

value: Microgravity


title: JSC.6172 Johnson Space Center study

value: Weightbearing


title: non-polyA RNAs from cytoplasmic extract, seedling

description: Strand-specific RNA-seq


title: total RNAs from whole cell extract, seedling

description: Strand-specific RNA-seq


title: Sample8_hpSC_DA_Progenitor

value: hpSC derived Dopaminergic Neuron Precursors


title: Sample4_hpSC_NSC

value: hpSC derived Neural Stem Cells


title: non-polyA RNAs from whole cell extract, seedling

description: Strand-specific RNA-seq


title: polyA+ RNAs from whole cell extract, seedling

description: Strand-specific RNA-seq


title: dHNF4 ChIP C

city: Salt Lake City

first: Carl

middle: S

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah, School of Medicine

description: mixed population (males and females)

data_processing:
MACS2 and Useq ScanSeqs (FDR80) were each used identified using USeq FindNeighboringGenes and UCSC dm3 ensGene gene tables
Genome_build: dm3
Supplementary_files_format_and_content: excel spreadsheet of significant dHNF4 enrichment peaks with Nearest Neighbor genes (within 10kb) listed in order of proximity to peak. Genes found to be downregulated in dHNF4 mutants (by RNAseq) are highlighted in tan as high confidence direct targets of dHNF4

organism: Drosophila melanogaster

source_name: mautre adults_whole animal_males + females_dHNF4 ChIP

growth_protocol: Bottles of flies cultures at room temperature on standard cornmeal-based lab media. Mixed population (males and females) of adults ranging from newly eclosed to 2 week old animals were collected for chromatin isolation.

extract_protocol:
Protocol was followed esentially as described previously (Schwartz, B.E., Larochelle, S., Suter, B., and Lis, J.T. 2003 Mol Cell Biol). Briefly, crude nuclei were isolated and sonicated to aquire an average fragment size ~300 bp followed by IP using rat-anti-dHNF4 antibody and protein G dynabeads (Life Technologies)
Libraries were prepared using NEB ChIPseq library prep kit

tag: strain background

value: mature adults

value: whole animal

tag: gender

value: mixed


title: ov-5DPA RNA-seq R11_rep1

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

data_processing:
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: bigWig

organism: Solanum lycopersicum

source_name: ovule of 5DPA fruit

growth_protocol: the tomato plants were grown in greenhouse on soil

extract_protocol:
the fruits of different stages were collected and the ovule and ovary wall were dissected under microscope. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

value: ovule

tag: Stage


title: ov-5DPA RNA-seq R11_rep2


title: ow-5DPA RNA-seq R12_rep2

source_name: ovule wall/pericarp of 5DPA fruit

value: ovary wall/pericarp


title: CLF RIP-seq, seedling

source_name: CLF RIP-seq, seedling

value: seedling

tag: developmental stage

value: 14-day old

value: RNA


title: dHNF4 ChIP B

description: mixed population (males and females)

tag: tissue


title: dHNF4 ChIP D

description: mixed population (males and females)


title: ow-2DPA RNA-seq R08_rep1

source_name: ovule wall/pericarp of 2DPA fruit


title: ov-2DPA RNA-seq R07_rep2

source_name: ovule of 2DPA fruit


title: dHNF4 ChIP A

description: mixed population (males and females)


title: Input D

description: mixed population (males and females)

source_name: mautre adults_whole animal_males + females_input


title: total RNAs from cytoplasmic extract, seedling

description: Strand-specific RNA-seq

value: total RNA, rRNA depleted


title: ov-2DPA RNA-seq R07_rep1


title: ow-0DPAe RNA-seq R06_rep2

source_name: ovary wall/pericarp of 0DPAe (emasculated) fruit

value: 0DPA (emasculated at -2DPA)


title: ow-0DPAe RNA-seq R06_rep1


title: Input C

description: mixed population (males and females)


title: Input B

description: mixed population (males and females)


title: dHNF4 mutant bio replicate 4

data_processing:
Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly.
nohup java -jar -Xmx20G ~/AppsUSeq/OverdispersedRegionScanSeqs -s ODRSS/ -t BamAlignments/HNF4Mut/ -c BamAlignments/Control/ -u dm3EnsGenes.ucsc.gz -o -p -v D_melanogaster_Apr_2006 &> ODRSS/odrss.log.txt &
for x in $(ls *bam); do echo $x; java -jar -Xmx10G ~/AppsUSeq/SamParser -v D_melanogaster_Apr_2006 -f $x -r PD_$x -m 0 -a 120; done
nohup java -jar -Xmx10G ~/AppsUSeq/MultipleReplicaScanSeqs -s MRSS/ -t BamAlignments/HNF4Mut/ -c BamAlignments/Control/ -p 0 -w 200 -f 1 -b &> MRSS/mrss.log.txt &
jj ~/AppsUSeq/EnrichedRegionMaker -f MRSS/binaryWindowData.swi.zip -i 0,1 -s 10,1 -r dm3EnsGenes_Exons.bed.gz -b 1000jj ~/AppsUSeq/EnrichedRegionMaker -f MRSS/binaryWindowData.swi.zip -i 0,1 -s 10,1 -r dm3EnsGenes_Exons.bed.gz -b 1000 -m
Genome_build: dm3
Supplementary_files_format_and_content: Matrix excel file for differential mRNA adundance in treatment (T, aka dHNF4 mutants) versus control (C) samples including gene ID number, gene name, FDR, and log2 values

source_name: dHNF4 mutant_adult males

growth_protocol: Flies were cultured under density-controlled conditions (~60 larvae per vial) raised on 3% sugar diet, then 5 day old adults were transferred to 15% sugar diet for 3 days prior to sample collection.

extract_protocol:
Total RNA was extracted from dHNF4 mutants and genetically-matched control adult males (8 days old) using TriPure isolation reagent (Roche) followed by further purification/cleanup by RNeasy kit (QIAGEN)
RNA from 4 biological replicates (n=40 flies per sample) per genotype was polyA-selected and assembled into barcoded libraries and pooled into a single-flow cell lane for Illumina HighSeq2000 50-cycle single-read sequencing,

value: dHNF4 mutant

tag: strain info.

tag: gender/age

value: adult male

value: whole-animal


title: Input A

description: mixed population (males and females)


title: ow-5DPA RNA-seq R12_rep1


title: dHNF4 mutant bio replicate 3


title: ov-0DPAe RNA-seq R05_rep2

source_name: ovule of 0DPAe (emasculated) fruit


title: ow-1DPA RNA-seq R04_rep2

source_name: ovule wall/pericarp of 1DPA fruit


title: dHNF4 mutant bio replicate 2


title: ow-1DPA RNA-seq R04_rep1


title: ow-2DPA RNA-seq R08_rep2


title: ov-1DPA RNA-seq R03_rep2

source_name: ovule of 1DPA fruit

value: 1DPA (days post anthesis)


title: ov-1DPA RNA-seq R03_rep1


title: Control bio replicate 3

source_name: control_adult males

value: control

value: EP/KG precise excision transheterozygote


title: dHNF4 mutant bio replicate 1


title: Control bio replicate 2


title: Control bio replicate 1


title: PREG7

status: Public on Nov 27 2015

city: Måløv

first: Jeannette

middle: Schlichting

last: Kirkegaard

address: Novo Nordisk park

department: Department of islet and stem cell biology

country: Denmark

institute: Novo Nordisk A/S

description: Pregnant 3

data_processing:
Raw reads received as Fastq files from Beijing Genomics Institute (BGI), China.
FASTX-Toolkit fastq_quality_trimmer with options -t 30 -l 25 used to quality trim 3prime end to Q30
FASTX-Toolkit fastq_quality_filter with options -q 5 -p 100 used to remove reads with Ns
For mapping reads to transcripts, we used Tophat version 2.0.12 with options --segment-mismatches 2 --segment-length 25 --max-multihits 1  --solexa1.3-quals --transcriptome-index=transcriptome_idx --mate-inner-dist 100 --mate-std-dev 50 -G /novo/omdb/genome.indices/Mmusculus/GRCm38r77/feature/Mmusculus_GRCm38r77.gtf /novo/omdb/genome.indices/Mmusculus/GRCm38r77/bowtie_index/Mmusculus_GRCm38r77 /novo/omdb/pds02/PDS1073/data/NGSp_atlas/jobId03/PREG3_1.fq.gz /novo/omdb/pds02/PDS1073/data/NGSp_atlas/jobId03/PREG3_2.fq.gz > /data27/omdb.pds/PDS1073/data/Ensg77_atlas/jobId01/PREG3_tophat.log 2>&1 && ln -s /data27/omdb.pds/PDS1073/data/Ensg77_atlas/jobId01/PREG3/accepted_hits.bam /data27/omdb.pds/PDS1073/data/Ensg77_atlas/jobId01/PREG3.bam
For counts, HTSeq version 0.5.3p3 was used with options  --stranded=no --mode=intersection-nonempty --idattr=gene_id
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel fil: Meanreads for n=3 pregnant and n=3 non-pregnant mice, Fold change, P-value, FDR, Log2 (Pregnant/Nonpregnant), SwissProt accession and length is given.

source_name: Gestational day 14.5

growth_protocol: All mouse experiments were performed in accordance with institutional and national regulations and approved by Danish Animal Experimentation Inspectorate, the Ministry of Justice, Denmark. Animals were kept in a 12 hour light/dark interval at room temperature and were daily subjected to visual health control

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QIAGEN, Chatsworth, CA). RNA with a RIN value above 7 was used for sequencing.
Truseq Transcriptome library

treatment_protocol: Islet were isolated by injection of inject of ice-cold Liberase TL (Roche)/DNase I (BioNordica) solution into the common bile duct. Pancreata were digested and islet were hand-picked.

tag: strain

value: Islets


title: NP8

description: Non Pregnant 2

source_name: Littermates


title: NP12

description: Non Pregnant 3


title: PREG6

description: Pregnant 2


title: Control bio replicate 4

value: EP/KG (p-element precise excisions) transheterozygote


title: PREG3

description: Pregnant 1


title: IPJ2015_003

city: Kyoto

first: Kosuke

last: Kawaguchi

address: 54 Kawaharacho Shogoin Sakyo-ku

institute: Kyoto University

data_processing:
The Ion Proton reads were analyzed using the AmpliSeqRNA analysis plugin, v4.2.1, in the Torrent Suite Software (Life Technologies)
Reads per million reads (RPM):Counts the number of sequences obtained for all cDNA amplicons
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Monocytes

extract_protocol:
RNA was harvested using Trizol reagent.  Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (#A26325) was used with 1 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion torrent protocols

value: Monocytes

tag: disease state

value: healthy

tag: source

value: Peripheral blood mononuclear cells


title: IPJ2015_007


title: TG ASO Rep 2 (8w)

city: Houston

first: Yehezkel

last: Sztainberg

address: 1250 Moursond

institute: Baylor College of Medicine

data_processing:
Illumina HiSeq 2000 software used for basecalling
Raw reads were first groomed by removing adapters from both the 3’- and 5’-ends, then mapped to mm10 using TopHat v2.0.9
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under the exons of the gene (union of all the exons of the gene). This read counts obtained are analogous to the expression level of the gene. Using the obtained read counts, differential gene analyses were carried out using the DESeq package and glm.nb function in the R environment.
Genome_build: mm10
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Hippocampus

growth_protocol: standard animal house conditions

extract_protocol:
Mice were euthanized under anesthesia and the hippocampi were quickly dissected over ice. Total RNA was extracted using miRNeasy minikit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. Isolated RNA was eluted in RNase-free water and submitted to the Genomic and RNA Profiling Core at Baylor College of Medicine. Sample quality checks using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100 were conducted.
A double-stranded DNA library was created using 250 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flow-cell. First, cDNA was created using the fragmented 3’ poly(A) selected portion of total RNA and random primers. During second strand synthesis, dTTP is replaced with dUTP which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3’ end and finally ligating unique adapters to the ends. The ligated products were then amplified using 15 cycles of PCR. The resulting libraries were quantitated using the NanoDrop spectrophotometer and fragment size assessed with the Agilent Bioanalyzer. A qPCR quantitation was performed on the libraries to determine the concentration of adapter ligated fragments using Applied Biosystems ViiA7 Real-Time PCR System and a KAPA Library Quant Kit. Using the concentration from the ViiA7 qPCR machine, 21pM of library was loaded onto a flowcell and amplified by bridge amplification using the Illumina cBot machine. A paired-end 100 cycle run was used to sequence the flow-cell on a HiSeq Sequencing System.

treatment_protocol: 7-8-week old F1 hybrid (FVB/N x 129S6/SvEv) MECP2-TG mice were gradually infused with 500µg MECP2-ASO or control-ASO into the right ventricles of the brains using micro-osmotic pumps designed to deliver the molecule at a constant rate over a four-week period. We performed RNA-seq analysis in the hippocampus at two different time points after the initiation of the treatment: 4 weeks after initiation of treatment, and 8 weeks after initiation of treatment.

value: F1 hybrid FVB/N x 129S6/SvEv

value: Hippocampus

tag: genotype

value: TG ASO

tag: time after treatment initiation

value: 8 weeks


title: IPJ2015_004

source_name: Macrophages

tag: cell type

value: Macrophages


title: NP7

description: Non Pregnant 1


title: TG ASO Rep 3 (8w)


title: ov-0DPAe RNA-seq R05_rep1

value: ovule

value: 0DPA (emasculated at -2DPA)


title: TG ctrl Rep 3 (8w)

value: TG ctrl


title: IPJ2015_008


title: S_6_low RFI pool

city: Armidale

first: WIJDAN

last: AL-HUSSEINI

state: NSW

address: UNE

department: Centre for Genetics Analysis and Applications, School of Environmental and Rural Science

country: Australia

institute: University of New England

description: Total RNA were collected from 13 animals from low RFI line

data_processing:
Raw sequence reads were processed with a Perl script to remove low quality reads, adaptor seq, and to count the reads into read-count files
Sequenced reads were trimmed for adaptor sequence then aligned  to bovine genome B. taurus, UMD v3.0 using Bowtie
Sequencing data analysied and mapped to bovine microRNAs database, miRBase v.19 using miRanalyzer
Supplementary_files_format_and_content: tab-delimited text files

organism: Bos taurus

source_name: liver biopsies_bulls

growth_protocol: Angus bulls resulting from approximately three generations of divergent selection for RFI, which were established in 1993 at the Agricultural Research Centre, Trangie, NSW, Australia.Bulls were born in 2005 and, when approximately one year-of-age, their growth and feed intake were measured. Post-weaning RFI for each animal  was calculated using a linear regression of daily feed intake on mean metabolic mid-test weight and average daily gain

extract_protocol:
Total RNA from liver was isolated using TRI reagent.2 pools of total RNA were constructed from 13 high-RFI animals and 13 low-RFI animals with equal quantities (1 µg of RNA) from each animal.
Libraries of small RNAs were prepared using the “Preparing Samples for Small RNA Sequencing Using the Alternative v1.5 Protocol". The libraries were sequenced on the Illumina Genome Analyzer IIx using Single-Read Cluster Generation Kit v2 (Cat. no. FC-103–2001; Illumina) and 36 Cycle Sequencing Kit v4 (Cat. no. FC-104–4002).

tag: breed

value: Angus cattle

tag: Sex

value: male

tag: residual feed intake (rfi)

value: low

tag: age of animals at biopsy

value: 13 months

value: liver biopsies


title: WT Rep 3 (8w)

value: WT


title: S_7_High RFI pool

description: Total RNA were collected from 13 animals from high RFI line

value: high


title: TG ctrl Rep 1 (8w)


title: TG ctrl Rep 2 (8w)


title: WT Rep 2 (8w)


title: TG ASO Rep 1 (8w)


title: WT Rep 1 (8w)


title: TG ASO Rep 2 (4w)

value: 4 weeks


title: TG ASO Rep 1 (4w)


title: TG ctrl Rep 3 (4w)


title: WT Rep 3 (4w)


title: TG ctrl Rep 1 (4w)


title: WT Rep 1 (4w)


title: F/TG/Cre TMX Rep 3

treatment_protocol: 8- to 9-week-old mice were injected with tamoxifen or vehicle intraperitoneally at a dose of 100 mg/kg, 3 alternative days a week for 4 weeks.

value: F1 hybrid FVB/N x C57Bl/6

value: F/TG/Cre TMX


title: F/TG/Cre veh Rep 2

value: Hippocampus

value: F/TG/Cre veh


title: F/TG/Cre TMX Rep 2


title: F/TG/Cre veh Rep 3


title: F/TG/Cre TMX Rep 1


title: F/TG/Cre veh Rep 1


title: F/TG Rep 3

value: F/TG


title: F/TG Rep 2


title: Flox Rep 1

value: Flox


title: TG ASO Rep 3 (4w)

value: F1 hybrid FVB/N x 129S6/SvEv

value: TG ASO


title: Timecourse 3 no labeling (background)

status: Public on Nov 26 2015

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNATCACGN

data_processing:
Raw fastq files were demultiplexed using pyBarcodeFilter version 2.3.3 from the pyCRAC tool suite (Webb et al Genome Biology 2014; version 1.2.2.3).
Quality trimming and removal of 3' Adapter sequences (5'AGATCGGAAGAGCACACG-3' ) was removed using Flexbar (version 2.4)
Reads were aligned to the Saccharomyces_cerevisiae.R64-1-1.75  reference genome using STAR (version 2.4.2a) at default settings. Read counts (FPKMs) were calculated using pysam
The splicing ratio, i.e., the mRNA proportion is then calculated from the aligned reads either by direct methods or using a probabilistic method (details provided in supplementary data of the manuscript); code for the probabilistic method is available at http://isplice.sourceforge.net.
Genome_build: Saccharomyces_cerevisiae.R64-1-1.75 (ENSEMBL)
Supplementary_files_format_and_content: Processed data files are Excel spreadsheets containing the data used for generating the figures in the manuscript.

organism: Saccharomyces cerevisiae

source_name: Ribosomal RNA depleted total RNA

growth_protocol: Cultures were grown in SD -Ura–Leu to OD600 of 0.8. Cultures remained at 30ºC and were shaken throughout the experiment. Large (600 ml) cultures were used for es4tU-seq experiments.

extract_protocol:
RNA was isolated using a standard hot-phenol extraction. Biotinylation was performed on 2 mg of RNA. The incubation at 65°C was for only 15 minutes to reduce RNA degradation. The RNA was purified using 2ml Zeba columns (Thermo), as per manufacturer's instructions, and ethanol precipitated. Biotinylated RNA was extracted using streptavidin C1 Dynabeads (Life Technologies).  Fifty µl of beads were equilibrated in NaPTMg (i.e. 0.2M NaCl, 0.1M Sodium phosphate pH 6.8, 25mM MgCl2 and 0.4% Tween) then blocked in NaPTMg and 1µg/µl glycogen for 20minutes.  The biotinylated RNA was purified for 30 minutes with the dynabeads at 4°C in NaPTMg.  The beads were washed 3 times in NaPTMg and twice with TEN1000 (i.e. 10mM Tris Cl pH 7.5, 1mM EDTA pH8 and 1M NaCl). All bead block, incubation and wash volumes were 400µl.  The RNA was eluted twice with 50µl of 0.7M beta-mercaptoethanol for 5 minutes at room temperature before being ethanol precipitated with 20µg glycogen -20°C for at least 2hours and re-suspended in 10µl DEPC treated H2O.
RNA-seq libraries were produced essentially as described previously (Hector et al Nucleic Acids Research 2014). Briefly, between 100-250ng of (thiolated) RNA was fragmented in Superscript reverse transcription buffer for five minutes at 95ºC.  Fragmented RNA was subsequently randomly primed as described (Hector et al Nucleic Acids Research 2014). The cDNAs were ligated to 5' adapters (see barcodes below) using CircLigase 2 for six hours at 65ºC according to manufacturer's procedures. Libraries were amplified using PCR primers listed below. The cDNA products were amplified (16-20 cycles) using Pfu Polymerase (Promega) using standard cycling conditions (Tm = 55ºC)

treatment_protocol: Cells were treated with 500 µM 4tU for the appropriate time. Cells were snap frozen in methanol at -70ºC to rapidly halt transcription

tag: assayed molecule

value: rRNA depleted total RNA


title: Flox Rep 2


title: F/TG Rep 1


title: Timecourse 1 no labeling (background)

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNTGACCAN

source_name: Nascent RNA isolated using an ultrashort 4-thio-Uracil

value: thiolated RNA


title: Flox Rep 3


title: WT Dox

city: Dalian

first: Qingkai

last: Yang

state: Liaoning

address: 9 Western Lvshun South Road

department: 9 Western Lvshun South Road

institute: Institute of Cancer Stem Cell, DaLian Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using segemehl v0.1.7 with parameters -F 1
Data were filtered using the following specifications:Only reads uniquely aligned to the mm9 assembly.
Genome_build: mm9
Supplementary_files_format_and_content: txt contains counts of high-quality CG and TG at each sampled CpG in [Sample].
<chrom> is the number of chromosome for mm9
<posi> is the positiation for mm9
<rC_n> is the number of CGs observed in the negative strand DNA
<rC_p> is the number of CGs observed in the positive strand DNA
<rT_n> is the number of TGs observed in the negative strand DNA
<rT_p> is the number of TGs observed in the positive strand DNA
<me> is the methlation leverl of this site(0~1)

source_name: Cultured MEF cells

extract_protocol:
genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions
bisulphite converted DNA was amplified, fragmented and sequenced fellowing standard Illumina protocol

tag: strain background

value: Cultured MEF cells

tag: genotype/variation

value: wild type

tag: treated with

value: Doxorubicin


title: Pml KO

value: Pml knockout

value: none (control)


title: Pml KO Dox


title: TG ctrl Rep 2 (4w)

tag: tissue

value: TG ctrl


title: mTEC_Male_2

city: Montréal

first: Maude

last: Dumont-Lagacé

state: Quebec

address: 2950 chemin de la polytechnique

country: Canada

institute: IRIC - Université de Montréal

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: Medullary thymic epithelial cells

growth_protocol: Primary cells were extracted with enzymatic digestion and cell sorting from 6 month-old C57BL6 mice housed under specific-pathogen-free conditions in sterile ventilated racks. Cx male : mice were castrated at 4 weeks of age (before puberty).

extract_protocol:
Total RNA was isolated using TrizolTM as recommended by the manufacturer (Invitrogen), and then further purified using RNeasy Micro columns (Qiagen).
Transcriptome libraries were made using the TruSeq RNA Sample Prep Kit (v2) (Illumina) following the manufacturer’s protocols.

value: Male

tag: castration status

value: not castrated

value: mTECs


title: mTEC_Cxmale_1

value: male

value: castrated at 4 weeks of age


title: mTEC_Female_3

value: Female


title: mTEC_Male_1


title: mTEC_Male_3


title: WT Rep 2 (4w)

value: Hippocampus

value: WT

value: 4 weeks


title: mTEC_Female_2


title: cTEC_Male_2

source_name: Cortical thymic epithelial cells

value: cTECs


title: cTEC_Cxmale_3


title: cTEC_Cxmale_2


title: cTEC_Male_3


title: cTEC_Male_1


title: cTEC_Cxmale_1


title: mTEC_Cxmale_3


title: LSK DKO BR1 RNA-Seq

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

description: RNA-seq Sample

data_processing:
The reads that passed illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences and spike-in controls.
The reads were then aligned to UCSC mm9 reference genome using TopHat (v1.4.1). Dustscores were calculated with PRINSEQ Lite (v0.20.3) and low-complexity reads (DUST>4) were removed from BAM files
Alignment results were parsed via the SAMtools to generate SAM files. Read counts to each genomic feature were obtained with htseq count program (v0.6.00) using the union option.
Genome_build: mm9
Supplementary_files_format_and_content: Estimated RPKM values (txt)

source_name: Bone marrow

growth_protocol: Mice were housed in a pathogen-free animal facility at the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee

extract_protocol:
Total RNA was extracted from two biological replicates each of WT and Tet2/3 DKO LSK cells using Purelink RNA Micro kit (Invitrogen).
Using 10 ng of total RNA, cDNA was synthesized and amplified using SMARTer® UltraTM Low Input RNA for Illumina® Sequencing-HV (Clontech® Laboratories, Inc.). RNA-Seq libraries were constructed using Nextera® XT DNA Sample Preparation kit (Illumina) and single end sequencing was performed using the Illumina HiSeq 2500 on Rapid Run mode.

treatment_protocol: bone marrow cells were flushed out of femurs and tibiae in Hanks' balanced salt solution (HBSS, Gibco Invitrogen) containing 2% FBS and 10 mM HEPES (Gibco Invitrogen). Prior to sorting of LSK  cells in the bone marrow, we depleted lineage positive cells as follows. Red cell-depleted total bone marrow cells were incubated with Biotin-conjugated Mouse Hematopoietic Lineage Panel (eBioscience) at 4oC for 20 min. After washing with 1X PBS containing 1% FBS, cells were incubated with Dynabeads® Biotin Binder (Life Technologies) at 4oC for 30 min and Lin- cells were purified by magnetic separation, followed by staining with antibodies against c-Kit, Sca-1 and PerCP-Cy5.5 and sorting using FACSAria II.

value: bone marrow LSK

value: Tet2/3 double knock out

value: Hematopietic stem/progenitor cells


title: cTEC_Female_3


title: WT

value: Cultured MEF cells

value: wild type


title: LSK DKO BR2 RNA-Seq

description: RNA-seq Sample


title: WGBS seq DKO LSK BR3

description: bisulfite conversion

data_processing:
Fastq files from sequiencing were mapped against the mm9 genome using BSmap v2.74 and the parameters -v 4 -w 2 -r 0 -q 20 -R -p 12
To remove multiple mappers as well as methylation bias, BSeQC v1.0.3 with default parameters and -l 101_101 (Read length 100)
For each CpG covered by a given sample, the levels of methylation were calculated using methratio.py, script from BSmap tool with the parameters -z -t 0 -x CG -i "correct"
The methratio calling from all samples was merged into one big table (The MasterTable) containig all CpGs covered by at least one read in any of the samples.
Genome_build: mm9
Supplementary_files_format_and_content: Tabular format text, Mastertable, containing all the methylation info for the 6 samples (3 WT & 3 Tet2/3 DKO). The mastertable contains the CpG coverage and the total reads indication methylation in a given CpG for all samples. If a sample does not cover this CpG this is indicated with a NA in the methylation column and with zero coverage

source_name: Tet2/Tet3 DKO LSK cells biological replicate (BR) 3

extract_protocol:
After isolation of the cells, DNA was isolated using the PureLink DNA isolation  kit (Life Technologies), according to the instructions of the manufacturer.
For WGBS library construction, genomic DNA was fragmented using a Covaris sonication system (Covaris S2). DNA libraries were constructed using the Illumina TruSeq Nano DNA sample preparation kit. Adapter ligated libraries were bisulfite-treated using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA). Enrichment PCR was done using TrueSeq primer mix and Pfu TurboCx hotstart DNA polymerase (Stratagene).

value: LSK cells

value: Tet2/3 DKO mice


title: cTEC_Female_1


title: LSK WT BR2 RNA-Seq

description: RNA-seq Sample


title: LSK WT BR1 RNA-Seq

description: RNA-seq Sample


title: WGBS seq DKO LSK BR2

description: bisulfite conversion

source_name: Tet2/Tet3 DKO LSK cells biological replicate (BR) 2


title: WGBS seq WT LSK BR3

description: bisulfite conversion

source_name: wild type LSK cells biological replicate (BR) 3

value: Wild Type


title: WGBS seq DKO LSK BR1

description: bisulfite conversion

source_name: Tet2/Tet3 DKO LSK cells biological replicate (BR) 1


title: WGBS seq WT LSK BR2

description: bisulfite conversion

source_name: wild type LSK cells biological replicate (BR) 2


title: mTEC_Female_1


title: WGBS seq WT LSK BR1

description: bisulfite conversion

source_name: wild type LSK cells biological replicate (BR) 1


title: Fertile bud

city: Wuhan

first: Jingyin

last: Yu

address: No.2, Xudong Second Road, Wuchang District

department: Department of Genomics and Molecular Biology

institute: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Unigenes of Brassica napus in NCBI.
Clean tags mapped to reference sequences from multiple genes were filtered, and the remaining clean tags were designated as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)
Genome_build: UniGene Build #17: http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=3708
Supplementary_files_format_and_content: The files (Fer.fq and Ste.fq) stored information about read sequences and quality.The files (Fer.GeneExpression.txt and Ste.GeneExpression.txt) showed that the number of unambiguous clean tags for each gene was calculated and then normalized to TPM

organism: Brassica napus

source_name: Fertile bud

extract_protocol:
Total RNA from five sterile and fertile individual plants, respectively was extracted using the TRIzol reagent (Invitrogen). After precipitation, RNA was purified with Qiagen’s RNeasy Kit with on-column DNase digestion according to the manufacturer’s instructions. Purified RNA samples were dissolved in diethylpyrocarbonate-treated H2O, and the concentration determined spectroscopycally. The quality of the RNA was assessed on 1.0 % denaturing agarose gel in combination with the Bioanalyzer 2100 (Agilent). For Solexa sequencing, at least 6 μg of total RNA (≥400 ng/μL) was used
For Solexa sequencing, at least 6 μg of total RNA (≥400 ng/μL) was used

tag: developmental stage

value: less than 2 mm in diameter

value: young floral bud

tag: phenotype

value: fertile

tag: genetic background

value: hybrid between novel restorer line NR1 and Nsa CMS line


title: Sterile bud

source_name: Sterile bud

value: sterile


title: DLD1-Cas9

status: Public on Nov 25 2015

city: Toronto

first: Jason

last: Moffat

state: ON

address: 160 College St

department: CCBR

institute: University of Toronto

description: RNAseq of Cas9 knock-in

data_processing:
TopHat v2.0.13
command line:  tophat --transcriptome-index gencode.v19.annotation -T hg19 [fastq file]
Cufflinks v2.0.2
command ine:  cufflinks -G gencode.v19.annotation.gtf accepted_hits.bam
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet of log2(fpkm+0.01) for protein coding genes

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% Penicillin/Streptomycin (Life Technologies). HeLa, DLD1, and hTERT RPE1 cells were maintained in DMEM with high glucose and pyruvate (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% Penicillin/Streptomycin (Life Technologies). The patient-derived GBM514 glioblastoma cell line was kindly provided by Peter Dirks’ laboratory at SickKids, Toronto. GBM cells were cultured as described in Pollard et al. 2009.

extract_protocol:
RNA was extracted from Cas9-expressing cell lines using TriReagent (Sigma) according to manufacturer's instructions
RNA sequencing libraries were prepared with Illumina TruSeq V2 RNA library preparation kit according to manufacturer's directions. Multiplexed libraries (HCT116 only) were sequenced on a single read High Output Illumina NextSeq500 flow cell (version 1 chemistry) with a read length of 61bp.

treatment_protocol: HCT116, HeLa, DLD1, hTERT RPE1 and GBM514 cells were infected with virus carrying the Cas9-2A-Blasticidin expressing cassette and infected cells were selected with blasticidin (5 ug/ml). After 10 days of selection, single cells were sorted onto 96-well plates with a BD FACS Aria IIu cell sorter at low pressure (20 PSI) using a 100 micron nozzle or by manual seeding of a single cell suspension at 0.6 cells/96 well plates. Independent clones were isolated and FLAG-Cas9 expression was determined using Western blot analysis.

value: Cas9 knock-in


title: HCT116-Cas9

description: RNAseq of Cas9 knock-in


title: GBM-Cas9

description: RNAseq of Cas9 knock-in


title: cTEC_Female_2

tag: strain

value: Female


title: Soleus

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

data_processing:
Basecalling with Illumina GAPipeline-1.4.0
Alignment with Tophat v1.0.14
Gene expression profiling with 5'RNA-seq software package
5pr comparisons with 5'RNA-seq software package
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are in bigWig format (.wig.gz). The bigWig format is for display of dense, continuous data that will be displayed in the UCSC Genome Browser as a graph.

source_name: soleus muscle tissue

extract_protocol:
TRIzol-based, following manufacturer's protocol.
RNA-sequencing libraries were constructed with random hexamer priming. To reduce biological variation, RNA was pooled from three biological replicates. Uniform amplification of the cDNA library was achieved with amplification cycles before the reaction reached saturation determined with qPCR. Enhanced sequencing at 5' ends of transcripts to sensitively query chages in start-site usage (intact polyA RNA, no fragmentation of RNA or cDNA, size selection, linear amplification).

value: soleus muscle

value: Black Swiss

value: Male

tag: age

value: 4-6 weeks


title: TA

source_name: tibialis anterior muscle tissue

value: tibialis anterior muscle


title: Ventricle

source_name: left vetricle cardiac muscle

value: left vetricle cardiac muscle


title: Late Immature Neuron D233.1

city: Seattle

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

description: Technical replicate of cell D233

data_processing:
Image analysis and base calling were performed using Illumina real time analysis v1.13.48 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files using CASAVA v1.8.2 software.
Adapters were trimmed with the “trim_galore” utility from the cutadapt package (v1.2.1)
Sequencing libraries were analyzed with TopHat (v2.0.14) and Cufflinks (v.2.2.1) to generate normalized FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include coordinates of gene annotations, abundance measurements in Fpkm for genes and Fpkm values for Olfr genes considered as positive expression.

source_name: Olfactory epithelium

growth_protocol: Single cells were manually isolated from dissociated mouse olfactory epithelium.

extract_protocol: Single cell cDNA libraries were prepared using oligo(dT) primed cDNA synthesis followed by PCR amplification of cDNAs (Malnic et al, 1999, Cell, 96:713.  Libraries were prepared for sequencing using the TruSeq DNA sample prep kit (Illumina)

value: Late Immature Neuron


title: Late Immature Neuron D230.1

description: Technical replicate of cell D230


title: Early Immature Neuron D244.1

description: Technical replicate of cell D244

value: Early Immature Neuron


title: Mature Neuron D251.1

description: Technical replicate of cell D251

value: Mature Neuron


title: Mature Neuron D95


title: Diaphragm

source_name: diaphragm muscle tissue

value: diaphragm muscle


title: Mature Neuron D223


title: Late Immature Neuron D250.1

description: Technical replicate of cell D250


title: Mature Neuron D254


title: Mature Neuron D243.1

description: Technical replicate of cell D243


title: Early Immature Neuron D187.1

description: Technical replicate of cell D187


title: RPE1-Cas9

description: RNAseq of Cas9 knock-in


title: Mature Neuron D81


title: Mature Neuron D265


title: Mature Neuron D240


title: Mature Neuron D245


title: Mature Neuron D232


title: Mature Neuron D253


title: Mature Neuron D260


title: Mature Neuron D55


title: Mature Neuron D97


title: Mature Neuron D255


title: Mature Neuron D274


title: Mature Neuron D29


title: Early Immature Neuron D200.1

description: Technical replicate of cell D200


title: Mature Neuron D259


title: Mature Neuron D261


title: Mature Neuron D262


title: Mature Neuron D342


title: Mature Neuron D251


title: Mature Neuron D316


title: Late Immature Neuron D234


title: Mature Neuron D433


title: Mature Neuron D243


title: Late Immature Neuron D77


title: Mature Neuron D213


title: Late Immature Neuron D412


title: Late Immature Neuron D233


title: Late Immature Neuron D250


title: Late Immature Neuron D432


title: H3K27me3 ChIP-seq, seedling

data_processing:
Illumina Casava1.7 software was used for basecalling.
Adaptor sequences in the sequencing reads were removed using Cutadapt v1.0 with default parameters.
Trimmed reads were aligned to Arabidopsis genome using Bowtie v0.12.7   with parameters '-m 1 -v 3 --best --strata'.
BCP (version 1.1) was used to call peaks for H3K27me3 modification in no control model.
Target genes/lncRNAs were indentified by at least 200bp/100bp overlapped regoin with the peak regions.
genome build: TAIR10
processed data files format and content: wig files include the H3K27me3 signial intensity for each sample

source_name: H3K27me3 ChIP-seq, seedling

extract_protocol: Genomic DNA was purified by using DNeasy Plant Mini Kit (Qiagen,Cat. No. 69104) with its standard protocol. Co-immunoprecipitated DNAs were ligated to adaports and followed by PCR amplification. ChIP-seq:  Anti-trimethyl-Histone H3 (Lys27), Cat. # 07-449, Millipore

tag: ecotype

value: seedling

value: 14-day old

tag: molecule

value: genomic DNA


title: Sample1_hpSC_Undiff

data_processing:
Twelve bases were trimmed from the five prime end of each read using FASTX (version 0.0.13)
The adaptors were then trimmed using Trim Galore (version 0.2.2) and then mapped to hg19 reference genome using Tophat (version 2.0.6)
Samtools (version 0.1.17) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes1 and annotated using RefSeq (archive-2012-03-09-03-24-410). Genes that did not have at least one sample with at least five reads were removed from the analysis.
The data was normalized using the R (version 3.0.1) package DESeq (version 1.12.0)
Differential expression analysis and heat maps were done using Qlucore Omics Explorer 2.3
ANOVA of all three cell types and t-test of NSC and DAP were performed (q<0.01)
Functional annotation analysis was done using DAVID
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx including DESeq normalized counts filtered for genes with at least 5 reads in at least one sample

source_name: Human Parthenogenic Stem Cells

extract_protocol:
RNA was isolated from cells (RNeasy Plus Mini kit, Qiagen), quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent).
Approximately 600 ng was used as input for the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol.  Briefly, poly-A containing mRNA molecules are purified using a reagent containing poly-T oligo-attached magnetic beads. After purification, the mRNA is fragmented and first strand cDNA is produced using random primers and reverse transcriptase.  Second strand cDNA synthesis is then prepared using DNA Polymerase I and RNase H.  The cDNA is then ligated to indexed Illumina adapters and enriched with PCR to create the cDNA library.

tag: cell type

value: Human Parthenogenic Stem Cells

tag: cell line


title: Late Immature Neuron D406


title: Late Immature Neuron D344


title: Late Immature Neuron D230


title: Late Immature Neuron D334


title: Late Immature Neuron D343


title: Early Immature Neuron D202


title: Mature Neuron D329


title: Early Immature Neuron D192


title: Early Immature Neuron D168


title: Early Immature Neuron D378


title: Early Immature Neuron D425


title: Early Immature Neuron D401


title: Early Immature Neuron D317


title: Early Immature Neuron D431


title: Early Immature Neuron D362


title: Early Immature Neuron D336


title: Early Immature Neuron D200


title: Early Immature Neuron D347


title: Early Immature Neuron D434


title: Early Immature Neuron D417


title: Early Immature Neuron D197


title: Late Immature Neuron D199


title: Early Immature Neuron D373


title: Early Immature Neuron D187


title: Early Immature Neuron D318


title: Early Immature Neuron D371


title: Early Immature Neuron D332


title: Late Immature Neuron D205


title: Early Immature Neuron D411


title: Early Immature Neuron D244


title: Precursor D178

value: Precursor


title: Early Immature Neuron D215


title: Early Immature Neuron D394


title: Early Immature Neuron D424


title: Precursor D179


title: Precursor D319


title: Early Immature Neuron D357


title: Precursor D398


title: Precursor D345


title: Precursor D195


title: Progenitor D330

value: Progenitor


title: Progenitor D393


title: Progenitor D169


title: Precursor D374


title: Progenitor D174


title: Precursor D383


title: Progenitor D337


title: Progenitor D170


title: Progenitor D189


title: Progenitor D175


title: Progenitor D184


title: Progenitor D172


title: T440 RNA-seq

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
DNase-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed from further analysis in each library.
We identified Dnase I hypersensitive sites in Enocode data and our small cell number Pico-seq data using MACS.
Genome_build: hg18
Supplementary_files_format_and_content: Bed: plan text file. Each line is one read. The six columns are chrom, start position, end position, length, alignment score and strand.

source_name: formalin-fixed paraffin-embedded tissue

growth_protocol: NIH/3T3 tet-on 3G cells (Clontech cat# 631197) were cultured in DMEM (Invitrogen cat# 10566-016) supplemented with 10% FBS ( Sigma cat# F4135-500ML) and 100U/ml Penicillin-Streptomycin (Invitrogen cat# 15140-122). Mouse ES cells were cultured as described in G. Hu et al. (Cell Stem Cell, 2013).

extract_protocol:
For DNase I digestion, 0.2 to 1 unit of Dnase I was added to the cells and incubated at 37°C for 5 minutes. The reaction was stopped by adding 80 ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EDTA), 1 ul of 20mg/ml Proteinase K and 5 ul of 6ng/ul circular carrier DNA. The mixture was incubated at 55°C for 1 hour and DNA purified by Phenol-chloroform extraction, followed by precipitation with ethanol in the presence of glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.

treatment_protocol: Single cell suspension after trypsinization was used for DAPI staining immediately before sorting by flow cytometry. Single live cells were sorted and deposited directly into each tubes of a PCR strip-tube, which containing 30 ul cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Triton X-100).

tag: patient

value: follicular thyroid carcinoma

value: tumor


title: N440 RNA-seq_rep3

value: normal


title: T440 RNA-seq_rep2


title: N440 RNA-seq


title: N131 Dnase1_rep

description: Dnase-seq

value: papillary thyroid carcinoma


title: T131 Dnase1_rep

description: Dnase-seq


title: N440 RNA-seq_rep4


title: Precursor D242


title: T131 Dnase1

description: Dnase-seq


title: T797 DNase1

description: Dnase-seq


title: N797 DNase1

description: Dnase-seq


title: T957 DNase1

description: Dnase-seq


title: T440  DNase1_rep

description: Dnase-seq


title: N440 DNase1_rep

description: Dnase-seq


title: T440  DNase1

description: Dnase-seq


title: N440 DNase1

description: Dnase-seq


title: Progenitor D203


title: S1 single-end

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: directional single-end RNA-seq

data_processing:
After quality control analysis of raw sequencing datasets, RNA-seq sequences were aligned to the rice genome using TopHat. Then the mapped sequences of each sample were assembled by Cufflinks. Fragments per kilobase of exon per million fragments mapped of assembled transcripts (FPKM) were calculated and normalized using Cuffcompare and Cuffdiff with global normalization parameters.
Genome_build: Oryza sativa L. ssp. Japonica, MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

organism: Oryza sativa Japonica Group

source_name: milk grains

growth_protocol: Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini kit. Total RNA was treated with Turbo DNase I (Life Technologies AM2238) according to product specification. DNase I treated RNA was then applied again to an RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to the manufacturer’s instructions.
Sequencing libraries were prepared using the Illumina Stranded mRNA sample Prep kit, set A (RS-122-2101, Illumina Inc.) according to the manufacturer's instructions.  The quality and size of cDNA libraries for sequencing were checked using the Agilent 2200 TapeStation system (Agilent Inc.). The libraries were sequenced for 100 cycles on HiseqTM 2500 (Illumina Inc.)

value: milk grains


title: L2 single-end

description: directional single-end RNA-seq

source_name: leaves sampled after flowering

value: leaves sampled after flowering


title: R1 single-end

description: directional single-end RNA-seq

source_name: roots sampled before flowering

value: roots sampled before flowering


title: R2 single-end

description: directional single-end RNA-seq

source_name: roots sampled after flowering

value: roots sampled after flowering


title: T440 RNA-seq_rep3


title: S2 single-end

description: directional single-end RNA-seq

source_name: mature seeds

value: mature seeds


title: T440 RNA-seq_rep4


title: L1 single-end

description: directional single-end RNA-seq

source_name: leaves sampled before flowering

value: leaves sampled before flowering


title: N440 RNA-seq_rep2


title: F2 single-end

description: directional single-end RNA-seq

source_name: flowers

value: flowers


title: Early Immature Neuron D331

value: Early Immature Neuron


title: F1 single-end

description: directional single-end RNA-seq

source_name: flower buds

value: flower buds


title: MfaT009

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

institute: Chinese Academic of Science

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.6 mapping to reference genome
count counting
Genome_build: mfa5.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Macaca fascicularis

source_name: brain tissue of aborted newborn MECP2 transgenic monkey

extract_protocol:
Total RNA was extracted from brain tissues of wild-type or MECP2 transgenic monkey by Trizol reagent (Invitrogen) separately.
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

tag: genotype

value: MECP2 transgenic

value: 3 years

value: cortical region


title: directional RNA-seq T35

city: Nijmegen

first: Richard

middle: Csaba

last: Bartfai

address: Geert Groteplein 26-26

department: Department of Molecular Biology

institute: Radboud University

data_processing:
Illumina Casava 1.8.2 software for base calling. We only used the bcl to fast conversion.
The single-end RNA-seq samples were mapped with BWA (Version 0.6.2-r126, default parameters) to either the complete P. falciparum assembly for the genomic tracks or the spliced transcriptome for transcript quantification (PlasmoDB 6.1) and filtered to mapping quality ≥15. Between 13.9 and 24.9 million reads mapped to transcripts.
Paired-end reads were clipped to 72bp (FASTX Toolkit, 0.0.13.2) and mapped with BWA (0.6.2-r126) to the PlasmoDB 6.1 assembly. We decided to trim MNase-seq reads to 72bp, to be able to map sub-nucleosomal fragments shorter than 100bp, but retain decent mappability of the sequence reads. The paired-end mapping was done such that up to 1000 alternative alignment positions were reported for each read (bwa sampe –n 1000). Subsequently, read pairs aligning with mapping quality below 30 or aligning to more than a single position with alignment pair distances below 1 kb were discarded using a custom script.
Genome_build: PlasmoDB 6.1
Supplementary_files_format_and_content: .raw.bedGraphFull: Raw coverage by full length fragments for paired-end or 92 bp reads for single-end.  .scale1.bedGraphFull: Normalized coverage per site (ni) calculated as ni = ri × g/b, where ri is the raw coverage (.raw.bedGraphFull) covering the sites i in the sample, b is the total number of bases in fragments, and g is the genome size. Therefore, a normalized coverage value of 1 represents the coverage expected if fragments are randomly distributed across the genome.  .scaled.*.scale1.bedGraphFull: Normalized RNA-seq coverage as in .scale1.bedGraphFull multiplied by scaling constants representing the estimated total RNA content per cell.  gDNArs*: As a means to control for amplification and sequencing biases we sequenced a sonicated genomic DNA sample, which unavoidably has a different distribution of fragment lengths than MNase-digested and nucleosome-protected DNA. To avoid potential biases associated with such differences in the insert-size distributions (ISD), we transformed the ISD of the gDNA control using a sampling approach. For every MNase-seq sample we created a resampled gDNA control with a matching ISD. To that aim, for every insert-size the number of fragments was calculated based on the target ISD and a desired total number of 150 million fragments. Fragments were then randomly selected from the fragments of that length out of the 274 million gDNA fragments.  Samples T40 & Tall: T40 represents the pooled fragments of samples T40A-4511 and T40B-4513. Tall represents the pooled fragments of T5-4504, T10-4505, T15-4506, T20-4507, T25-4508, T30-4509, T35-4510, and T40.

organism: Plasmodium falciparum

source_name: red blood cell stage, 27-35 hours post invasion

growth_protocol: 3D7 Plasmodium falciparum blood-stage parasites obtained from the Swiss Tropical and Public Health Institute (Basel, Switzerland - a kind gift from Dr. T. Voss) were cultured in standard RPMI medium supplemented with 10% human serum and 0.2% NaHCO3 in 2.5% human O+ red blood cells. 75 cm2 tissue culture flasks were incubated at 37ºC in candle jars under low oxygen conditions. Multiple rounds of panning were performed as described in (Noviyanti et al., 2001) with the following modifications, to obtain a parasite population homogenously expressing a single var gene (var2csa, PF3D7_1200600). In short, CSA coated plates were blocked using 1% casein sodium salt from bovine milk (Sigma C8654-500G) solution and washed three times with RPMI media before parasites were allowed to bind for 30 min at 37 ºC without agitation followed by 5 RPMI washes. Bound parasites were collected in RPMI media supplemented with serum and NaHCO3 and allowed to grow to ~5-10% parasitemia before the next round of panning was performed.  Preferential expression of var2csa and silencing of all other var genes was verified by RT-qPCR prior to synchronization with multiple rounds of sorbitol treatments. After a final Percoll gradient centrifugation human red blood cells were added with a few hours delay as in (Bartfai et al., 2010), to prevent “premature” invasion and therefore ensure better synchronicity of the culture. The blood was pre-filtered twice over sterile PlasmoPure (EuroProxima) filters to remove human white blood cells. T0 was set as the time when the first invasions were observed, resulting in an ~8 hour synchronicity window for >95% of parasites. Cross-linked nuclei (for MNase-Seq) and RNA (for RNA-Seq) were collected every 5 hours. Medium was changed at least every 10 hours, but not within 10 hours from collection. For T25 and T30 collections culture volume was doubled at the T9, for T35 and T40 collections at the T18 media change, respectively. Cultures were divided over separate culture flasks (20ml each), but mixed upon every media change.

extract_protocol:
Cross-linked nuclei and RNA were collected from the pooled culture flasks of the same batch of synchronized parasites to ensure completely matched nucleosome-positioning and transcriptome.    MNase-seq and pellet Control:  Formaldehyde was immediately added to 37 ºC parasite cultures to a 1% final concentration, followed by 15 min incubation at 37 ºC while shaking. Cross-linking reaction was quenched by addition of 0.125M glycine (final concentration) and all subsequent steps were performed at 4 ºC unless noted otherwise. Parasites were isolated from red blood cells by 0.05% saponin lysis, followed by the isolation of parasite nuclei on a 0.25 M sucrose cushion using cell lysis buffer (10 mM Tris pH8, 3 mM MgCl2, 0.2% NP40, Roche Protease Inhibitor Cocktail). Isolated nuclei were divided over multiple aliquots, which were used to determine the optimal digestion time for each time-point. Enzymatic digestion of the chromatin was performed in digestion buffer (50 mM Tris pH7.4, 4 mM MgCl2, 1mM CaCl2, 0.075% NP40, 1mM DTT, Roche Protease Inhibitor Cocktail) with 0.5 U MNase and 100 U Exonuclease III in 150 µl aliquots for 3.5-14 min at a 37 ºC waterbath with regular agitation. Digestion reactions were stopped by addition of 1 reaction volume quenching solution (2% Triton X100, 0.6% SDS, 300 mM NaCl, 6 mM EDTA, Roche Protease Inhibitor Cocktail) and placed at 4 ºC. Nuclei were mildly sonicated for 6x 10 sec (setting low, BioruptorTM Next Gen, Diagenode) to free the cross-linked nucleosomes from the nuclear membranes and the supernatant containing soluble chromatin was collected after centrifugation for 10 min at 9800 x g (this is the X-linked chromatin used for MNase-Seq input and α-H4 ChIP reactions). Nuclear pellets were decrosslinked (see conditions below) to assess whether the material residing with the nuclear membranes is equally distributed over the genome or enriched for certain genomic regions (pellet control). DNA yield from the pellet of each time-point was quantified and DNA size distribution was confirmed to be marginally higher in size-range to MNase digested soluble chromatin. Since for the T15 time-point the highest percentage of chromatin remained with the nuclear membranes, this sample was selected for sequencing as the pellet control. MNase-Seq chromatin and nuclear pellets were decrosslinked overnight at a 45 ºC shaking heatblock in decrosslinking buffer (1% SDS, 0.1 M NaHCO3, 1 M NaCl) after which DNA was isolated via QIAquick column purification (Qiagen). Digestion efficiency was verified on 2% agarose gel. Importantly, to enable, as much as possible, differentiation of technical variation from biological variation between the different samples, a technical replicate was included for the T40 time-point, where two different aliquots from the same nuclear collection were independently digested and processed for MNase-Seq. These technical replicates were called T40A and T40B and for most analysis sequence reads from both samples were combined (T40 sample).  Chromatin Immunoprecipitation:  200ng X-linked T40-stage chromatin (from sample T40A) in ChIP buffer (20 mM Tris pH8, 2 mM EDTA, 1% Triton-X100, 0.15% SDS, 150 mM NaCl, Roche Protease Inhibitor Cocktail) was incubated with 1 µg α-H4 core antibody (Abcam Ab17036, lot GR8733-1) or 1 µg normal rabbit IgG control antibody (Upstate 12-370, lot DAM1421465) O/N while rotating at 4 ºC. 10 µl ProtA Dynabeads (Life Technologies 10008D) and 10 µl ProtG Dynabeads (Life Technologies 10009D) were added to each reaction and allowed to rotate for another 2 hours at 4 ºC, after which ChIPs were washed with 400 µl wash buffer: 1x ChIP wash 1 (20 mM Tris pH8, 2 mM EDTA, 1% Triton-X100, 0.1% SDS, 150 mM NaCl), 2x ChIP wash 2 (20 mM Tris pH8, 2 mM EDTA, 1% Triton-X100, 0.1% SDS, 500 mM NaCl), 2x ChIP wash 3 (10 mM Tris pH8, 1 mM EDTA). Reactions were rotated for 5 min at 4 ºC in between each wash. Immunoprecipitated chromatin was eluted in elution buffer (1% SDS, 0.1M NaHCO3) during 20 min rotation at RT and decrosslinked as described above (“MNase-Seq and pellet control” section). ChIP reaction efficiency with α-H4 core and control antibody was verified by qPCR.    Genomic DNA extraction and fragmentation:  Genomic DNA was extracted from sorbitol synchronized ring stage 3D7 Plasmodium falciparum cultures of the same strain as was used for MNase-Seq. Cultures were PlasmoPure (EuroProxima) filtered before collection. Native nuclei collection, proteinase K treatment and genomic DNA isolation were performed as described in (Bartfai et al., 2010) with the following modifications. An RNaseA incubation step ensured degradation of RNA. gDNA was fragmented using a BioruptorTM Next Gen (Diagenode) to a ~100-400 bp range.    RNA isolation:  Total RNA isolation and oligo-dT-selection to enrich for polyA+ mRNA were performed as described elsewhere (Hoeijmakers et al., 2013a) with addition of an extra in-solution DNase treatment (TURBO DNase, Ambion) to remove contaminating gDNA. Integrity of total RNA was confirmed on 1.5% agarose gel and gDNA contamination was tested by qPCR.
MNase/gDNA Sequencing library preparation:   10 ng of MNase-Seq inputs, gDNA control, T15 pellet control and 5.7 ng of T40 α-H4 ChIP DNA were used to generate sequencing libraries. All samples were first end repaired, a 3’ A-overhang added and NextFlex barcoded adapters (Bio Scientific) were as described in (Hoeijmakers et al., 2011). Adapter ligation was followed by 2 successive Agencourt AMPure XP bead purifications (Beckman Coulter) and library amplification by an in-house Plasmodium-optimized kapa PCR amplication protocol. 2x kapa HiFi HotStart ready-mix (KAPA Biosystems) and NextFlex primers were used for 9 cycles of PCR amplification using the following conditions: 98 ºC for 2 min, (9 cycles of: 98 ºC for 20 sec, 62 ºC for 3 min), 62 ºC for 5 min. Libraries were again Agencourt AMPure XP bead purified before sequencing. Importantly, no size-selection step was applied to the MNase-Seq input and control libraries allowing assessment of the full range of DNA fragments resulting from enzymatic chromatin digestion and in silico size-selection of paired-end sequenced libraries.    cDNA synthesis and preparation of strand-specific RNA-seq libraries:  2 µg of total RNA-equivalent polyA+ mRNA was fragmented by hydrolysis as described in (Hoeijmakers et al., 2013a). cDNA synthesis was modified as follows from (Hoeijmakers et al., 2013a) to allow maintenance of directional information for strand-specific RNA-Seq. During first strand synthesis 0.2 µg Actinomycin D was included in the reaction and a 15 min 70 ºC enzyme deactivation step was included after first strand synthesis followed by QIAquick MinElute purification (Qiagen) of the first strand cDNA. During second strand synthesis dTTP was replaced by dUTPs, resulting in incorporation of U-bases instead of T-bases in the second cDNA strand only. 4 ng double-stranded cDNA was used for sequencing library preparation as described above (“Sequencing library preparation” section) with the following adaptation: after adapter ligation a 15 min incubation at 37 ºC with USER enzyme (New England Biolabs) ensured degradation of the second cDNA strand specifically (by degrading the U-base containing strand) thereby retaining directional information for sequencing. Subsequently, 4 cycles of Plasmodium-optimized kapa pre-PCR (for details see “Sequencing library preparation” section) were performed, followed by size-selection of 200-300bp cDNA fragments and subsequent amplification of another 9 cycles of Plasmodium-optimized kapa PCR resulting in total 13 cycles of PCR amplification.

value: medium schizont

tag: selection


title: MfaT005

value: 1 year


title: N957 DNase1

description: Dnase-seq

value: follicular thyroid carcinoma


title: directional RNA-seq T40

source_name: red blood cell stage, 32-40 hours post invasion

value: late schizont


title: Mfa25

source_name: brain tissue of aborted newborn wild-type monkey

value: wild-type


title: MfaD017

source_name: brain tissue of aborted newborn FMR1 knockout monkey

value: FMR1 knockout


title: directional RNA-seq T25

source_name: red blood cell stage, 17-25 hours post invasion

value: late trophozoite


title: MfaT007


title: directional RNA-seq T20

source_name: red blood cell stage, 12-20 hours post invasion

value: early trophozoite


title: directional RNA-seq T30

source_name: red blood cell stage, 22-30 hours post invasion

value: early schizont


title: MfaD012_3-1


title: directional RNA-seq T15

source_name: red blood cell stage, 7-15 hours post invasion

value: late ring stage


title: MfaD189-4

source_name: brain tissue of aborted newborn MECP2 knockout monkey

value: MECP2 knockout


title: MfaD189-5


title: directional RNA-seq T10

source_name: red blood cell stage, 2-10 hours post invasion

value: medium ring stage


title: directional RNA-seq T5

source_name: red blood cell stage, 40-5 hours post invasion

value: early ring stage


title: MfaD189-3


title: MfaD02-3


title: MfaD02-5


title: MNase-seq Pellet T15


title: MNase-seq αH4 ChIP T40A


title: MNase-seq T40B


title: MfaD02-4


title: MfaD013-3


title: MfaD013-2


title: sonicated gDNA

source_name: red blood cell stage, 0-20 hours post invasion

value: ring stage


title: Mfa009-3


title: MfaD013-1


title: Mfa009-2


title: Mfa009-1


title: MNase-seq T40A


title: MNase-seq T30


title: Mfa198-3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.6 mapping to reference genome
Counts counting
Genome_build: mfa5.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

value: MECP2 transgenic


title: MNase-seq T35


title: MNase-seq T5

source_name: red blood cell stage, 40-5 h post invasion


title: MNase-seq T10


title: MNase-seq T15


title: MNase-seq T20


title: MNase-seq T25


title: Mfa198-2


title: Mfa198-1


title: Infected Low Sensitive 3 hours after infection

city: Moscow

first: Alina

last: Artcibasova

address: Samory Mashela, 1

country: Russia

institute: Federal Research Center of Pediatric Hematology, Oncology and Immunology

data_processing:
FASTQ to FASTA conversion
The adapter sequence (5’-TGGAATTCTCGGGTGCCAAGG-3’) was clipped from the 3’-end of raw reads, and reads shorter than 16nt were discarded.
Remaining sequences were mapped to miRBase human microRNA reference using the short-read aligner Bowtie [19261174], up to two mismatches were allowed. The sequences that failed to map to the genome were mapped against the artificially introduced sequences. The multiplicity count of mapped sequences was normalized to the total number of reads that mapped to the genome.
Aligned reads were attributed to known microRNAs using processing with SAMTools
Prior analysis, quantile normalization was done for microarray gene expression data. AI and WI samples were treated as the "case" samples. Pre-experimental normal samples were used as the controls. The analysis was done separately for HCMV infection high and low sensitive cell cultures. The data were normalised using preprocessCore quantile normalisation in R.
Genome_build: miRBase human microRNAs
Supplementary_files_format_and_content: text file with mapped and normalized data for each sample

source_name: human adult skin fibroblasts (line HAF-1608)

growth_protocol: The cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM, PanEco, Moscow, Russia) supplemented with 10% fetal bovine serum (FBS, PanEco), 2 mM L-glutamine and 50 ug/ml gentamicin at 37°C in 5% CO2. The cells were maintained by regular passages when confluence was reached. To obtain cells in G0 phase of cell cycle the cells of both lines were cultured in DMEM with 0.2% FBS for 48 hours.

extract_protocol:
Short RNA fractions were cloned from total RNA extracts. Non-coding RNAs within a 19–33 nt window were isolated from 12% polyacrylamide gels. 3’- and 5’-linkers were ligated, and products were reverse-transcribed using Superscript III (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols. Following PCR amplification, the libraries were sequenced using the Illumina GAIIx platform in accordance with Illumina protocols (Illumina, USA).

treatment_protocol: Cells HELF- 977 and HAF-1608 synchronized in G0 phase were infected with HCMV at multiplicity of infection of 3 or mock-infected. Viral inoculum was added to the cells and allowed to adsorb for 60 min at 37°C in 5% CO2. Then virus inoculum was removed and replaced with fresh medium.

tag: sensitivity

value: Low

value: adult skin fibroblasts

tag: infection

value: HCMV at multiplicity of infection of 3


title: Norm Low Sensitive


title: Mfa132-3

value: cortical region


title: Infected High Sensitive 3 hours without infection

source_name: human embryonic lung fibroblast (line HELF-977)

value: High

value: embryonic lung fibroblast

value: mock