title: M2TG_T-G-_replicate_2

city: Cambridge

first: Rudolf

last: Jaenisch

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Base call using illumina HiSeq 2500 pipeline
Raw fastq files are aligned to a consensus genome using STAR (v.2.5.3.a). The reference transcriptome includes the miR290-295 pri-miRNA or Sox2 and the RGMs on pseudo-chromosomes.
SNPsplit (v0.3.2) splits the reads into four files based on single nucleotide variations (SNV). The reads were either allele specific (for CAST or S129), unassigned (if there are no SNVs present) or conflicting (if the SNVs in the read are from both alleles).
The split read files were quantified using RSEM (v1.2.31) separately for each sample.
Raw counts were then normalized to library using DESeq2 (v1.18.1) for each split.
To obtain sample-level quantifications raw counts were summed over the splits before normalization. Differential expression analysis (DEA) was performed using DESeq2 (v1.18.1) at the level of samples. Samples were corrected for genetic clone and batch effect. All P-values were controlled for false discovery rate (Benjamin-Hochberg procedure).
Genome_build: mm10

source_name: embryonic stem cells

extract_protocol:
0.5 million pre-plated sorted mouse ESCs were sorted and total mRNA was extracted using Direct-zol RNA Miniprep (Zymo Research, Cat#R2050)
Stranded mRNA libraries were prepared using KAPA HyperPrep (SOX2-SE-TG) and TrueSeq Stranded PolyA prep (MIR290-SE-TG) according to manufacturer's protocols

treatment_protocol: LIF/Serum culture on MEF feeders with passaging every 2-3 days. Cells were FACS sorted based on tdTomato and eGFP signals. Cells were pre-plated on gelatin coated plates for 30min-1hr to eliminate MEFs and sorted based on fluorescent signals. 2 independently targeted clones, each clone has 2 independent sortings

value: mouse ES cells

value: CAST/129 F1


title: 024-5921853085_R06C01

status: Public on Jun 15 2019

type: genomic

city: Wenzhou

first: Xiangnan

last: Chen

address: west load of college 268

country: China

institute: Wenzhou Medical University

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
024-5921853085_R06C01_Grn.idat
024-5921853085_R06C01_Red.idat

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).
Genomic gains and losses of 100 kb in length that affected a minimum of 50 and 25 markers, respectively, were initially considered to determine the relevance of duplications and deletions. Breakpoint positions of each CNV were converted to Genome Reference Consortium Human Build 37 patch release 13 (GRCh37.p13).

label: A-DNP, C-Bio

molecule: genomic DNA

organism: Homo sapiens

source_name: patient with intellectual disability phenotype

label_protocol: 250 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was isolated from whole blood with EDTA by using the QIAamp DNA Mini kit (QIAGEN, Germany), following the manufacturer’s instructions. Purified DNA was eluted with 50–200 μL of DNA elution buffer. Sample concentration and purity were detected using the NanoDrop 2000 UV-Vis spectrophotometer (Thermo Scientific, USA).

treatment_protocol: Individuals were considered for inclusion in the study if they met the following criteria: (1) Intelligence Quotient (IQ) < 70 as measured by the China–Wechsler Intelligence Scale for Children; (2) demonstrated neural developmental defects resulting in mental retardation, motor retardation, language delay, epilepsy, etc.; (3) not pregnant (4)no known nongenetic cause of ID, such as perinatal infection, ischemia, hypoxia, etc.; (5) no family history of ID; (6) no obvious genetic metabolic disease; and (7) availability of biological parents to participate in the study. In total, 64 patients with ID (38 males, 26 females; age range: 3–29 years) were enrolled after screening using the aforementioned criteria.

tag: diagnosis

value: intellectual disability

tag: gender

value: female

tag: tissue

value: Peripheral Blood


title: 027-8667011137_R04C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
027-8667011137_R04C01_Grn.idat
027-8667011137_R04C01_Red.idat


title: M2TG_T-G-_replicate_3

type: SRA

state: MA

department: Biology

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: cell type

tag: strain


title: 013-7612835093_R05C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
013-7612835093_R05C01_Grn.idat
013-7612835093_R05C01_Red.idat

value: male


title: 005-6922997087_R02C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
005-6922997087_R02C02_Grn.idat
005-6922997087_R02C02_Red.idat


title: 020-8447245040_R02C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
020-8447245040_R02C01_Grn.idat
020-8447245040_R02C01_Red.idat


title: M2TG_T-G-_replicate_4


title: M2TG_T+G-_replicate_4


title: 056-3999238220_R05C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
056-3999238220_R05C02_Grn.idat
056-3999238220_R05C02_Red.idat


title: 018-8667011137_R05C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
018-8667011137_R05C01_Grn.idat
018-8667011137_R05C01_Red.idat


title: 030-8685016029_R03C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
030-8685016029_R03C02_Grn.idat
030-8685016029_R03C02_Red.idat


title: 016-6066001037_R01C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
016-6066001037_R01C02_Grn.idat
016-6066001037_R01C02_Red.idat


title: 003-5921853148_R06C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
003-5921853148_R06C02_Grn.idat
003-5921853148_R06C02_Red.idat


title: 007-7757444113_R05C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
007-7757444113_R05C02_Grn.idat
007-7757444113_R05C02_Red.idat


title: 019-6923009018_R03C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
019-6923009018_R03C02_Grn.idat
019-6923009018_R03C02_Red.idat


title: M2TG_T-G+_replicate_3


title: M2TG_T-G-_replicate_1


title: 037-9282242053_R05C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
037-9282242053_R05C02_Grn.idat
037-9282242053_R05C02_Red.idat


title: 047-9878596042_R04C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
047-9878596042_R04C02_Grn.idat
047-9878596042_R04C02_Red.idat


title: M2TG_T+G-_replicate_1


title: 006-8667011140_R01C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
006-8667011140_R01C02_Grn.idat
006-8667011140_R01C02_Red.idat


title: 052-9983866099_R03C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
052-9983866099_R03C02_Grn.idat
052-9983866099_R03C02_Red.idat


title: 033-8685016030_R01C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
033-8685016030_R01C01_Grn.idat
033-8685016030_R01C01_Red.idat


title: M2TG_T+G+_replicate_2


title: RNA-seq_human primary fetal astrocytes batch 2_rep1

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

data_processing:
All reads were quality trimmed using TrimGalore 0.4.5 prior to further processing. For libraries having undergone paired-end sequencing, only the first read was used.
Reads were mapped using STAR and GENCODE V19 transcripts were quantified with RSEM using the standard ENCODE parameters.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files including gene expression estimates from RSEM and signal tracks in bigwig format

molecule: total RNA

growth_protocol: Human primary fetal astrocytes were cultured according to the ScienCell protocol (catalog #1801).

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN #74104) according to its protocol.
The TruSeq Stranded mRNA protocol from Illumina was followed for library construction (catalog #RS-122-2101).

value: human primary fetal astrocytes batch 2


title: M2TG_T-G+_replicate_2


title: S2TG_T-G-_replicate_3


title: M2TG_T+G+_replicate_1


title: M2TG_T+G+_replicate_4


title: RNA-seq_human primary fetal astrocytes batch 2_rep2


title: 021-8667011138_R06C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
021-8667011138_R06C01_Grn.idat
021-8667011138_R06C01_Red.idat


title: S2TG_T-G-_replicate_2


title: 014-5921853148_R03C02

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
014-5921853148_R03C02_Grn.idat
014-5921853148_R03C02_Red.idat


title: RNA-seq_iPSC-induced lower motor neurons_rep1

value: iPSC-induced lower motor neurons


title: M2TG_T+G-_replicate_2


title: RNA-seq_iPSC-induced lower motor neurons_rep2


title: S2TG_T-G+_replicate_4


title: M2TG_T+G-_replicate_3


title: RNA-seq_iPSC-derived hippocampal DG-like neurons_rep2


title: S2TG_T-G+_replicate_3


title: M2TG_T-G+_replicate_1


title: S2TG_T-G-_replicate_1


title: RNA-seq_iPSC-derived hippocampal DG-like neurons_rep1


title: ATAC-seq_human primary fetal astrocytes batch 2_rep2

description:
MS130_YSMS11
processed data file:
astrocyte.atac.seq.narrowPeak
astrocyte.atac-seq.bigwig

library_source: genomic

data_processing:
All reads were trimmed to 50 bp prior to processing. For libraries having undergone paired-end sequencing, only the first read was used.
All libaries were processed using the ENCODE ATAC-seq pipeline (December 2017).
Optimal IDR and optimal overlap peaks called by MACS2 were used.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks called using MACS2 and signal tracks in bigwig format

extract_protocol:
Cells were harvested, snap frozen in dry ice, and stored at -80C. Cells were washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with Ampure XP beads.


title: ATAC-seq_human primary fetal astrocytes batch 2_rep1

description:
MS129_YSMS11
processed data file:
astrocyte.atac.seq.narrowPeak
astrocyte.atac-seq.bigwig


title: S2TG_T-G+_replicate_1


title: S2TG_T+G-_replicate_4


title: S2TG_T+G-_replicate_3


title: ATAC-seq_iPSC-derived hippocampal DG-like neurons_rep1

description:
MS144_YSMS17
processed data file:
hippocampal.atac.seq.narrowPeak
hippocampal.atac-seq.bigwig


title: RNA-seq_human primary fetal astrocytes_rep2

source_name: human primary fetal astrocytes

value: human primary fetal astrocytes


title: S2TG_T+G-_replicate_2


title: S2TG_T-G-_replicate_4


title: M2TG_T-G+_replicate_4


title: RNA-seq_human primary fetal astrocytes_rep1


title: RNA-seq_iPSC-induced excitatory neurons_rep2

source_name: iPSC-induced excitatory neurons

value: iPSC-induced excitatory neurons


title: RNA-seq_iPSC-induced excitatory neurons_rep1


title: PCHiC_human primary fetal astrocytes_rep2

description:
JC006
wtc_PASS_hg19.phased.vcf.gz
astrocyte_all.ibed
library strategy: In situ Hi-C followed by promoter capture Hi-C

data_processing:
All reads were quality trimmed using fastp.
Reads were mapped, filtered, and deduplicated using HiCUP 0.7.1 running bowtie2 and retaining ditags with lengths between 100 and 1200 bp.
Paired-end BAM files from HiCUP were converted to CHiCAGO input format and interactions were called using CHiCAGO with minNPerBaits=250 and a score cutoff of 5.
Genome_build: hg19
Supplementary_files_format_and_content: CHiCAGO input files for each biological replicate, CHiCAGO interaction data in IBED format, and WashU interaction files

extract_protocol:
Cells were harvested, fixed in 1% formaldehyde, snap frozen in dry ice, then stored at -80C. Nuclei extraction was performed prior to further processing.
In situ Hi-C was performed using the standard protocol, then 500 ng of the resulting libraries were used to prepare pcHi-C using a custom biotinylated RNA probe set.
In situ Hi-C followed by pcHi-C


title: PCHiC_human primary fetal astrocytes_rep1

description:
JC005
wtc_PASS_hg19.phased.vcf.gz
astrocyte_all.ibed
library strategy: In situ Hi-C followed by promoter capture Hi-C


title: S2TG_T+G+_replicate_4


title: S2TG_T+G+_replicate_2


title: S2TG_T+G+_replicate_1


title: S2TG_T-G+_replicate_2


title: S2TG_T+G+_replicate_3


title: PCHiC_iPSC-induced excitatory neurons_rep3

description:
MS003
wtc_PASS_hg19.phased.vcf.gz
cortical_all.ibed
library strategy: In situ Hi-C followed by promoter capture Hi-C


title: miR290-SE Nanog+RGM+

description: Bisulfite PCR amplicons of the miR290 SE DMR

data_processing:
The resulting 40 bp single-end reads from Illumina had good quality by checking with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Reads were mapped to hg19 using TopHat v2.1.1 with options as “solexa1.3-quals” mode and “no-novel-juncs”. The gene model for TopHat was created by merging knownGene in gtf format with kgXref table, downloaded from the UCSC table browser. The read counts were obtained using the featureCounts function from Subread package with strandness option as –s 2.  Reads were normalized with DESeq2.  The biological replicates in the neuron samples, processed at different time periods, have batch effect as suggested by principle component analysis. Consequently, Combat was used for reducing this batch effect.
Bisulfite-Seq reads were aligned to bisulfite-converted PCR amplicon templates prepared by Bismark v0.21.0, using non-directional directional method provided by Bismark
Methylation information at each CpG position were extracted using Bismark Methylation Extractor
Positional methylation information (average methylation level) was filtered for sufficient converage >1000
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including each CpG position (1st column) average methylation (2nd column)

extract_protocol:
For miR290 SE Nanog+RGM+ DKO and miR290-SE Nanog+RGM+, cells were preplated and sorted based on Nanog-eGFP and RGM-tdTomato signals. For miR290 SE untargeted, cells were preplated.
PCR amplicons were sonicated using Covarius into 150-200bp range. NEBNext® Ultra™ DNA Library Prep Kit for Illumina and NEBNext® Multiplex Oligos for Illumina® were used to construct libraries according to manufacturer’s protocol. Single barcoded library was prepared from sonicated bisulfite PCR amplicon fragments of the miR290 SE wildtype-allele using NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB #E7370S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, NEB #E7335S).

treatment_protocol: LIF/Serum culture on MEF feeders with passaging every 2-3 days. Cells were FACS sorted based on tdTomato and eGFP signals. Cells were pre-plated on gelatin coated plates for 30min-1hr to eliminate MEFs and sorted based on fluorescent signals

tag: genetic background


title: PCHiC_iPSC-induced excitatory neurons_rep2

description:
MS002
wtc_PASS_hg19.phased.vcf.gz
cortical_all.ibed
library strategy: In situ Hi-C followed by promoter capture Hi-C


title: 002-5921853148_R03C01

description:
Infinium HumanCytoSNP-12 v2.1 BeadChips
002-5921853148_R03C01_Grn.idat
002-5921853148_R03C01_Red.idat


title: miR290 SE untargeted

growth_protocol: LIF/Serum culture on MEF feeders with passaging every 2-3 days. Cells were FACS sorted based on tdTomato and eGFP signals


title: PCHiC_iPSC-induced excitatory neurons_rep1

description:
MS001
wtc_PASS_hg19.phased.vcf.gz
cortical_all.ibed
library strategy: In situ Hi-C followed by promoter capture Hi-C


title: S2TG_T+G-_replicate_1


title: ATAC-seq_human primary fetal astrocytes_rep2

description:
MS049
processed data file:
astrocyte.atac.seq.narrowPeak
astrocyte.atac-seq.bigwig


title: miR290 SE Nanog+RGM+ DKO


title: ATAC-seq_human primary fetal astrocytes_rep1

description:
MS048
processed data file:
astrocyte.atac.seq.narrowPeak
astrocyte.atac-seq.bigwig


title: MIR290-SE-TG T-G- input

data_processing:
Base call using illumina HiSeq 2500 pipeline
The resulting 40 bp single-end reads from Illumina had good quality by checking with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Reads were mapped to hg19 using TopHat v2.1.1 with options as “solexa1.3-quals” mode and “no-novel-juncs”. The gene model for TopHat was created by merging knownGene in gtf format with kgXref table, downloaded from the UCSC table browser. The read counts were obtained using the featureCounts function from Subread package with strandness option as –s 2.  Reads were normalized with DESeq2.  The biological replicates in the neuron samples, processed at different time periods, have batch effect as suggested by principle component analysis. Consequently, Combat was used for reducing this batch effect.
Raw reads were aligned to the reference genome mm10 using BWA using default parameters.
Peak calling was done using MACS2.
Peak intensities at SE, promoter and in-between regions are quantified and compared using bamCompare – deepTools 3.0.2 with FPKM from 10bp genomic bins of each sample. SNPs specific to 129 or CAST genomes at SE and promoters were counted from mapped raw reads and SNPs covered by more than 3 reads are accepted for quantification.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files from MACS2 peak-called bedgraph files and generated by bedGraphToBigWig

extract_protocol:
2 million pre-plated sorted mouse ESCs were fixed in 1% formaldehyde for 10min at RT then quenched with 2.5M glycine. ChIP was performed as described in Lesch et al 2013.
Swift ChIP DNA kit, according to manufacture's protocol

tag: chip antibody


title: MIR290-SE-TG T-G+ input


title: ATAC-seq_iPSC-induced excitatory neurons_rep2

description:
LM093
processed data file:
cortical.atac.seq.narrowPeak
cortical.atac-seq.bigwig


title: ATAC-seq_iPSC-induced excitatory neurons_rep1

description:
LM092
processed data file:
cortical.atac.seq.narrowPeak
cortical.atac-seq.bigwig


title: MIR290-SE-TG T+G- input


title: MIR290-SE-TG T+G+ input


title: MIR290-SE-TG T-G+ ChIP


title: Mutant RAF1 S257L/+ PD98059 rep3

city: New York

first: Fabrice

last: Jaffre

state: New York

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medicine

data_processing:
Raw sequencing data from the Ion S5 was analyzed using the Ion Torrent Suite software v5.6 to generate normalized count files for each condition. Files were loaded into RStudio and count tables generated to measure differential gene expression between different conditions (e.g. RAF1 mutant vs isogenic control, ERK5 or MEK1/2 inhibitors vs vehicle) using the DESeq2 package2. Estimations of dispersion were plotted from the count data using the plotDispEsts function. Data were regularized log transformed and a sample matrix was visualized to compare different replicates and conditions. Principal components analysis (PCA) was performed using the prcomp function to separate out different conditions. Assuming a negative binomial distribution of the count data, the DESeq function was used to estimate the fold change of differentially expressed genes between different conditions, and p values were adjusted using the Benjamini Hochberg method.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files representing differential gene expression between different conditions (e.g. RAF1 mutant vs isogenic control, ERK5 or MEK1/2 inhibitors vs vehicle) generating using the DESeq2 package

source_name: iPSC-derived cardiomyocytes

growth_protocol: iPSC-derived cardiomyocytes were differentiated using small molecules that modulate the Wnt-beta catenin pathway. At day 15 of differentiation, the cardiomyocytes were purified for 4 days with DL-Lactate supplementation. At Day 21, cardiomyocytes were replated on 0.1% gelatin coated plates and cultured in RPMI+10% FBS.  At day 24, Total RNA was extracted

extract_protocol:
Total RNA was prepared using the mirVana PARIS purification Kit (ThermoFisher, #AM1556) following the manufacturer’s recommendations. RNA integrity (RIN) was determined using ScreenTape R6K kit on the TapeStation2200 (Agilent Technologies) and only samples with RIN >7 were further used for RNA-sequencing
Isolated total RNA was diluted to 0.95 ng/µl and 10.5 µL was loaded in each reverse transcription reaction with the SuperScript VILO cDNA Synthesis Kit (ThermoFisher, #11754050). Reverse transcription was completed in a thermocycler with the following temperature settings: 42ºC for 30 minutes, 85ºC for 5 minutes and 10ºC on hold. After reverse transcription, libraries were prepared using the Ion Chef (ThermoFisher, #4484177) and the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (ThermoFisher, #A31446). The AmpliSeq Gene Expression Panel includes one primer pair for every gene in the transcriptome, allowing for amplification of a single amplicon for each gene to be sequenced. At the completion of library preparation, libraries from 8 samples were pooled together, templated, and loaded on the Ion 540 Chip (ThermoFisher, #A27765) using the Ion Chef and the Ion 540 Kit Chef (ThermoFisher, #A27759). After templated samples were loaded onto the 540 Chips, each Chip was inserted into the Ion Torrent S5 sequencer (ThermoFisher, #A27212) and 500 flows were applied for each sequencing run. The second Chip was stored at 4ºC during the first sequencing run and removed to room temperature for 30 minutes prior to running the second Chip

treatment_protocol: At Day 22, mutant RAF1 cardiomyocytes were treated with 25 µM BIX02189 or 25 µM PD98059 for 48 hours before total RNA extraction

value: iPSC-derived cardiomyocytes

tag: age

value: Day 24


title: Mutant RAF1 S257L/+ PD98059 rep2


title: Mutant RAF1 S257L/+ PD98059 rep1


title: Mutant RAF1 S257L/+ BIX01289 rep3


title: SOX2-SE-TG T-G- input


title: MIR290-SE-TG T+G- ChIP


title: MIR290-SE-TG T+G+ ChIP


title: SOX2-SE-TG T+G- input


title: Mutant RAF1 S257L/+ rep3


title: Mutant RAF1 S257L/+ BIX01289 rep1


title: SOX2-SE-TG T+G+ input


title: Mutant RAF1 S257L/+ rep2


title: Mutant RAF1 S257L/+ rep1


title: Tomato_PSTVd-M (PARE)

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

department: Biochemistry

country: Canada

institute: Université de Sherbrooke

description:
RNA isolated from PSTVd-M used for PARE analysis
Lycopersicum esculentum
RNA-seq 5’ RACE

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
Sequence containing the 5' adapter sequences (GTCCGAC) were filtered
The filtered sequences were searched against the tomato genome  (taxid:4081) by BLAST in order to detect 5' end of the cleaved site.
Genome_build: tomato  (taxid:4081)
Supplementary_files_format_and_content: Excel file containing the 5' RACE sequences of chloride channel protein CLC-b-like mRNA and the 40S ribosomal protein S3a-like.

organism: Solanum lycopersicum

source_name: leaf tissue

growth_protocol: Plants were grown in a growth chamber at a temperature of 25ºC with 16 h of light and 8 h of darkness.

extract_protocol:
Total RNA from the leaf samples was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA), with modifications. Briefly, 100 mg of leaf sample was ground with 800 µl of Lysis/Binding buffer. Then, 80 µl of miRNA homogenate was added and the resulting solution was mixed by vortexing.  RNA was separated by acid phenol-chloroform extraction followed by DNase RQ1 (Promega, MA) treatment. RNA integrity was examined in a 2100 Bioanalyzer (Agilent Technologies, California, USA).
Total RNA obtained from 21-days post inoculation (dpi) plants were subjected for mRNA purification using GenElute mRNA Mini Prep kit according to the manufacturers instructions (Sigma-Aldrich). An RNA adapter-containing MmeI restriction endonuclease site, 5’-PARE RNA adapter, was ligated to the 5’ uncapped ends of the purified mRNA by incubating at 37ºC for 1 h in the presence of T4 RNA ligase I (New England Biolabs, Inc, MA, USA). The unligated adaptor was removed with GenElute mRNA Mini Prep kit. Obtained RNA products were subjected to cDNA synthesise using Target RT-primer followed by 7 cycles of PCR amplification using 5’-cDNA PCR primer and 3’-cDNA PCR primer. The amplicons were subjected to MmeI restriction endonuclease digestion for 1 h according to the manufacturers instructions (New England Biolabs Inc, MA, USA). The products of were separated on 5% polyacrylamide gel and then the nucleic acid band of approximately 70-bp was eluted using elution buffer (10 mM magnesium acetate tetrahydrate, 0.5 M ammonium acetate, 1 mM EDTA [pH 8.0], 0.1% [w/v] SDS). The eluted products were subjected to 15 cycles of PCR amplification using Illumina universal primer along with Indexed TruSeq 3’ index primers.

treatment_protocol: Tomato plants were inoculated with the 1 µg of the dimeric PSTVd-M transcripts.

tag: cultivar

value: Rutgers

tag: infection

value: PSTVd-M infected

value: leaf


title: SOX2-SE-TG T-G- ChIP


title: Isogenic corrected rep3


title: SOX2-SE-TG T-G+ ChIP


title: SOX2-SE-TG T+G- ChIP


title: Isogenic corrected rep1


title: SOX2-SE-TG T+G+ ChIP


title: MIR290-SE-TG T-G- ChIP


title: Isogenic corrected rep2


title: Mutant RAF1 S257L/+ BIX01289 rep2


title: SOX2-SE-TG T-G+ input


title: Kidney-Norm-118

type: RNA

city: Birmingham

first: Michael

middle: Edward

last: Seifert

state: AL

address: 1600 7th Ave S Lowder 516

institute: UAB School of Medicine

data_processing: Raw gene expression data were background subtracted and normalized to the geometric mean of the expression of 12 housekeeping genes in each sample. Genes with expression counts < 20 were excluded from final analysis.

source_name: Kidney Allograft

label_protocol: Please see manufacturer's protocol for the Nanostring nCounter Vantage RNA WNT Pathways Panel (LBL-10251-03)

extract_protocol: Total RNA was extracted from FFPE sections using Qiagen DNA/RNA FFPE kit

value: kidney

value: No major transplant abnormalities


title: Kidney-TG-227

value: TG


title: Kidney-Norm-228


title: Kidney-TG-178


title: Kidney-Norm-173


title: RNASeq CXCR5+Tim-3- Rep2

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: CXCR5+Tim-3- Rep2

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 0.12.9 and Tophat 2.1.1
Aligned reads are converted to bam format using samtools. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data.
Genome_build: mm10

source_name: splenocytes

growth_protocol: Six- to eight-week-old female C57BL/6J and CD45.1 congenic mice were purchased from the Jackson Laboratory. Chronically LCMV infected mice were generated as follows; Mice were depleted of CD4+ T cells by injecting 300-500 μg of GK1.5 antibody intraperitoneally (i.p.) 2 days prior to infection and again on the day of infection, followed by infecting mice with 2 x 106 pfu of LCMV clone 13 intravenously via tail vein.

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymo Research), with oncolumnDNase digestion. RNA-seq libraries were prepared using 150 ng of total RNA and KAPAStranded mRNA-seq Kit (Kapa Biosystems). Each library was indexed using barcoded primers(BIOO Scientific, Austin, TX) and was amplified for 10 cycles. Then, 200- to 350-bp fragmentsof barcoded PCR products were separated by 2% E-Gels (Thermo Fisher Scientific) and purifiedby Gel DNA Purification Kit (Zymo Research).
PCR products were barcoded (indexed) and sequenced on HiSeq2500 platform.

treatment_protocol: PD-1+CXCR5-Tim-3+CD8+ and PD-1+CXCR5+Tim-3-CD8+ cells (> 3x10e5 cells each) were sorted from pooled splenocytes of chronically LCMV infected mice (> day 40 p.i., n=14-15)

tag: agent

value: chronically LCMV infected

tag: antibody

value: CD8+ T-cell

value: Six- to eight-week-old

tag: Sex


title: RNASeq CXCR5-Tim-3+ Rep2

description: CXCR5-Tim-3+ Rep2

value: female


title: RNASeq CXCR5+Tim-3- Rep3

description: CXCR5+Tim-3- Rep3


title: RNASeq CXCR5+Tim-3- Rep1

description: CXCR5+Tim-3- Rep1


title: RNASeq CXCR5-Tim-3+ Rep3

description: CXCR5-Tim-3+ Rep3


title: RNASeq CXCR5-Tim-3+ Rep1

description: CXCR5-Tim-3+ Rep1


title: Kidney-Norm-121


title: Kidney-Norm-167-2


title: Kidney-ABMR-166-2

value: ABMR


title: Kidney-ABMR-221


title: Kidney-ABMR-222


title: Kidney-Norm-216


title: M2TG_T+G+_replicate_3

value: mouse ES cells

value: CAST/129 F1


title: Kidney-ABMR-217


title: Kidney-Norm-220


title: Kidney-ABMR-215


title: Kidney-ABMR-226


title: Kidney-ABMR-214


title: Kidney-Norm-213


title: Kidney-Norm-210


title: Kidney-Norm-2027


title: Kidney-Norm-212


title: Kidney-TG-203


title: Kidney-Norm-205


title: Kidney-Norm-207


title: Kidney-Norm-208


title: Kidney-Norm-206


title: Kidney-ABMR-202


title: Kidney-Norm-201


title: Kidney-TG-199


title: Kidney-TG-196


title: Kidney-ABMR-197


title: Kidney-Norm-198


title: Kidney-Norm-191


title: Kidney-ABMR-187


title: Kidney-Norm-188


title: Kidney-Norm-189


title: Kidney-Norm-190


title: Kidney-TG-186


title: Kidney-ABMR-180


title: Kidney-ABMR-209


title: Kidney-Norm-183


title: Kidney-TG-179


title: Kidney-Norm-181


title: Kidney-Norm-175


title: Kidney-Norm-170


title: Kidney-Norm-193


title: Kidney-TG-169


title: Kidney-TG-195


title: Kidney-ABMR-185


title: Kidney-Norm-162


title: Kidney-Norm-167


title: Kidney-Norm-168


title: Kidney-TG-159


title: Kidney-ABMR-165


title: Kidney-Norm-163


title: Kidney-TG-158


title: Kidney-ABMR-166


title: Kidney-Norm-160


title: Kidney-ABMR-153


title: Kidney-Norm-139


title: Kidney-TG-156


title: Kidney-TG-152


title: Kidney-Norm-150


title: Kidney-TG-147


title: Kidney-ABMR-155


title: Kidney-Norm-146


title: 920N

city: Guangzhou

first: Dong-liang

address: No.651 Dong Feng East Road

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The samples were used to synthesize double-stranded cDNA, and the cDNA was then labeled and hybridized to the LncRNA Expression Microarray (Arraystar 8x60Kv3.0, Rockville, USA) according to the manufacturer's protocol.

scan_protocol: After hybridization, the arrays were washed, the slides were scanned with an Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing:
Raw data were extracted as pair files using the Agilent Feature Extraction. The random variance model was used to identify the differentially expressed genes.
The paired t-test was used to calculate the P-value. The threshold set for up- and down-regulated genes was a fold change >=4.0 and a P-value <= 0.05, respectively.

source_name: normal colon tissue

label_protocol: The samples were labeled with Cy3.

extract_protocol: Total RNA was extracted from tissues using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

value: normal colon


title: 951N


title: Kidney-TG-138


title: 1049N


title: 946N


title: 1051N


title: 939N


title: 1054N


title: 1043N


title: Kidney-TG-143


title: 933N


title: 1057N


title: 930N


title: Kidney-TG-137


title: Kidney-Norm-136


title: Kidney-TG-135


title: CB HSC, UM171, 6 days, CD90+, biological 1

city: Lund

first: Agatheeswaran

last: Subramaniam

state: Skane Lan

address: BMC A12, 221 84 Lund, Sweden

country: Sweden

institute: Lund universirty

description: Gene expression data

hyb_protocol: 5,5 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Human Gene 2.0 arrays for 16 h at 45° C and 60 rpm in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.3.3 software.

data_processing: Data normalized with Affymetrix GeneChip Expression Console v1.4 Software

label: Biotin

label_protocol: 20 µg of cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated at a fixed ratio relative to dTTP. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin.

growth_protocol: Cells were cultured in SFEM medium supplemted with human SCF, TPO and Flt3L at 37 C.

extract_protocol: RNA was extracted with  Qiagen RNeasy Micro kit (#74126).

treatment_protocol: Compounds stocks were prepared in DMSO and added to the culture media.

value: Cord Blood

value: Hematopoietic Stem Cell (HSC)

tag: treatment


title: 1019N


title: Kidney-TG-134


title: B16_d8_CD45+_Nrp1_Rep1

city: Pittsburgh

first: Chang

middle: of

last: Liu

state: PENNSYLVANIA

address: 200 Lothrop Street, W1028-22A, Biomedical Science Tower

department: Immunology

institute: University of Pittsburgh

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: data was RMA summarized, QC checked by PCA , and batch corrected in Partek Genomics Suite 6.6

source_name: intratumoral CD45+ cells from d6 B16 tumors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 1 ug of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: Tumor infiltrating CD45+ cells were sorted by fluorecence activated cell sorting and directly subjected to cell lysis for RNA extraction.

extract_protocol: Qiagen RNeasy Micro kit was used to extract RNA according to the manufacturer's protocol

treatment_protocol: No in vitro culture or treatment.

value: intratumoral CD45+ cells

tag: tumor model

tag: genotype


title: CB HSC, DMSO 6 days, CD90+, biological 2

description: Gene expression data

value: DMSO


title: 1014N


title: B16_d8_CD45+_FYC_Rep2


title: CB HSC, UM171, 6 days, CD90+, biological 2

description: Gene expression data


title: CB HSC, UM171, 6 days, CD90+, biological 3

description: Gene expression data


title: 1033N


title: B16_d8_CD45+_FYC_Rep1


title: B16_d8_CD45+_Nrp1_Rep2


title: CB HSC, DMSO 6 days, CD90+, biological 3

description: Gene expression data


title: sirD rep3

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

country: Japan

institute: Kagoshima University

data_processing:
Quality check by fastqc
The sequences were mapped to Aspergillus kawachii IFO 4308 genomes using BWA software
CTSS (CAGE detected transcriptional start site) was counted by BEDTools
CAGE-tag 5' coordinates were input for RECLU clustering
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Aspergillus luchuensis

source_name: whole cell

extract_protocol:
Rice koji was frozen by liquid nitrogen and RNA was extracted by RNAiso Plus (Takara Bio). The RNA was purified by SV total RNA isolation system (Promega).
Library for was perfrmed accoding to a previous paper (Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., Hayashizaki, Y., Carninci, P.: CAGE: cap analysis of gene expression, Nat. Methods, 3, 211–222. 2006).

value: sirD


title: B16_d12_CD45+_Nrp1_Rep2

source_name: intratumoral CD45+ cells from d12 B16 tumors


title: sirD rep2


title: 1009N


title: Kidney-Norm-133


title: Kidney-Norm-132


title: sirD rep1


title: B16_d12_CD45+_Nrp1_Rep1


title: CB HSC, DMSO 6 days, CD90+, biological 1

description: Gene expression data


title: Ctrl rep3


title: CB HSC, 2-PCPA, 6 days, EPCR-, biological 2

description: Gene expression data


title: Kidney-ABMR-131


title: Kidney-TG-130


title: B16_d12_CD45+_FYC_Rep2


title: Ctrl rep2


title: B16_d12_CD45+_FYC_Rep1


title: Ctrl rep1


title: CB HSC, 2-PCPA, 6 days, EPCR+, biological 2

description: Gene expression data


title: CB HSC, 2-PCPA, 6 days, EPCR-, biological 1

description: Gene expression data


title: Kidney-Norm-129


title: Kidney-ABMR-126


title: Kidney-ABMR-128


title: pcHi-C_human primary fetal astrocytes batch 2_rep1

description:
MS127
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz

value: human primary fetal astrocytes batch 2


title: pcHi-C_human primary fetal astrocytes batch 2_rep2

description:
MS128
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz


title: MC38_d18_CD45+_FYC_Rep2

source_name: intratumoral CD45+ cells from d18 MC38 tumors


title: MC38_d18_CD45+_FYC_Rep1


title: Kidney-Norm-119

value: kidney


title: Kidney-ABMR-125


title: pcHi-C_iPSC-induced lower motor neurons_rep2

description:
MS140
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz

source_name: pcHi-C_iPSC-induced lower motor neurons

value: iPSC-induced lower motor neurons


title: CB HSC, 2-PCPA, 6 days, EPCR+, biological 1

description: Gene expression data


title: MC38_d18_CD45+_Nrp1_Rep1


title: Kidney-ABMR-117


title: CB HSC, 2-PCPA, 24hrs, Biological 2

description: Gene expression data

source_name: CB HSC, 2-PCPA, 24hrs, Biological 2


title: CB HSC, 2-PCPA, 24hrs, Biological 1

description: Gene expression data

source_name: CB HSC, 2-PCPA, 24hrs, Biological 1


title: MC38_d18_CD45+_Nrp1_Rep2


title: pcHi-C_iPSC-induced lower motor neurons_rep1

description:
MS136
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz


title: CB HSC, DMSO, 24hrs, Biological 3

description: Gene expression data

source_name: CB HSC, DMSO, 24hrs, Biological 3


title: Kidney-Norm-116

value: No major transplant abnormalities


title: MC38_d6_CD45+_FYC_Rep2

source_name: intratumoral CD45+ cells from d6 MC38 tumors


title: CB HSC, DMSO, 24hrs, Biological 2

description: Gene expression data

source_name: CB HSC, DMSO, 24hrs, Biological 2


title: CB HSC, 2-PCPA, 24hrs, Biological 3

description: Gene expression data

source_name: CB HSC, 2-PCPA, 24hrs, Biological 3


title: MC38_d6_CD45+_Nrp1_Rep2


title: SM2676: D39_CEP_RR07_B

city: Odense

first: Mikkel

middle: Girke

last: Jørgensen

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Sourthern Denmark

data_processing:
Reads mapped using Bowtie2 (Langmead and Salzberg, 2012)
Converted to BAM files and sorted via Samtools (Li et al, 2009)
Loaded into SeqMonk  No removal of duplicate reads  Treated as RNA-Seq data  Min mapping quality 20  Primary alignments only
All datasets quantificated via RNA-Seq quantification pipeline in seqmonk  Feature: Gene  Raw counts used
Feature report for all datasets via seqmonk  Annotated to Gene  with exactly overlapping probes   No merging of isoforms  Included all features
Differential Expression calcualted in R via EdgeR  Raw reads for all features in datasets used.  Variation for each gene in dataset replicates calculated and used to it a negative binomial generalized log-linear model to the read counts for each gene.   Genewise statistical test and, calculated fold change
Genome_build: GCA_000014375.1
Supplementary_files_format_and_content: Tab-deliminated file includes, fold-changes, FDR and raw read counts

organism: Streptococcus pneumoniae D39

source_name: D39 overexpressing the response regulator of Two-Component System 7 (SPD_0158)

growth_protocol: Grown in C+Y to OD600 = 0.5

extract_protocol:
Total RNA was extracted with an hot phenol-chloroform protocol, pelleted in ethanol and resuspended in H2O.
Ribosomal RNA was removed with the Ribo-Zero rRNA Removal Kit for Gram-Positive Bacteria (Illumina) according to manufacturers guidelines. Subsequent library preparation was performed using the NEBNext RNA library prep kit for Illumina. Library quality was assessed using the Fragment Analyzer followed by library qPCR quantification (Kapa library quantification kit).

tag: serotype

tag: genotype/variation


title: CB HSC, DMSO, 24hrs, Biological 1

description: Gene expression data

source_name: CB HSC, DMSO, 24hrs, Biological 1


title: Kidney-Norm-194

tag: diagnosis


title: pcHi-C_iPSC-derived hippocampal DG-like neurons_rep2

description:
MS142
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz


title: pcHi-C_iPSC-derived hippocampal DG-like neurons_rep1

description:
MS137
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz


title: Kidney-TG-171

tag: tissue

value: TG


title: SM2675: D39_B

source_name: D39 wildtype

value: wildtype


title: MC38_d6_CD45+_FYC_Rep1

tag: cell type


title: Kidney-Norm-164

source_name: Kidney Allograft


title: SM2672: D39_A

tag: strain


title: Kidney-Norm-154


title: SM2673: D39_CEP_RR07_A

value: overexpressing the response regulator of Two-Component System 7 (SPD_0158)


title: ATAC-seq_iPSC-induced lower motor neurons_rep2

description:
MS138_YSMS16
processed data file:
motor.atac.seq.narrowPeak
motor.atac-seq.bigwig


title: MC38_d12_CD45+_Nrp1_Rep2

source_name: intratumoral CD45+ cells from d12 MC38 tumors


title: MC38_d6_CD45+_Nrp1_Rep1


title: MC38_d12_CD45+_Nrp1_Rep3


title: Kidney-Norm-151


title: ATAC-seq_iPSC-induced lower motor neurons_rep1

description:
MS135_YSMS16
processed data file:
motor.atac.seq.narrowPeak
motor.atac-seq.bigwig


title: ONT_K562_2

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2218 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California: Irvine

data_processing:
Fast5 basecalled with Albacore
Mapping was done using Minimap2 settings for direct-RNA seq
TranscriptClean was used for error correction using the default settings. The splice junction file was obtained using GENCODE v29 using one of the accesory scripts
TALON was used for annotation and quantification. The database was initialized with GENCODE v29
Genome_build: hg38
Supplementary_files_format_and_content: TSV table format;transcript counts

source_name: Lymphoblastoid cell line

growth_protocol: ENCODE protocols cell line specific

extract_protocol:
QIAGEN RNAeasy
Total RNA

value: Lymphoblastoid cell line

tag: cell line


title: ONT_K562_1


title: ATAC-seq_iPSC-derived hippocampal DG-like neurons_rep2

description:
MS145_YSMS21
processed data file:
hippocampal.atac.seq.narrowPeak
hippocampal.atac-seq.bigwig


title: ONT_HepG2_3

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: ONT_HepG2_2


title: Kidney-Norm-148


title: Kidney-ABMR-144

value: ABMR


title: ONT_HepG2_1


title: ONT_GM12878_3


title: MC38_d12_CD45+_FYC_Rep3


title: Kidney-TG-141


title: MC38_d12_CD45+_Nrp1_Rep1


title: ONT_GM12878_2


title: MC38_d12_CD45+_FYC_Rep1


title: MC38_d12_CD45+_FYC_Rep2


title: Kidney-TG-149


title: B16_d18_CD45+_FYC_Rep3

source_name: intratumoral CD45+ cells from d18 B16 tumors


title: B16_d18_CD45+_Nrp1_Rep2


title: B16_d18_CD45+_Nrp1_Rep3


title: ONT_GM12878_1


title: IP_S83A_4

status: Public on Jun 14 2019

first: Rui

last: Sun

state: PA

address: 5117 Centre Avenue, UPMC Hillman Cancer Center Research Pavilion 1.8

department: Department of Microbiology and Molecular Genetics

data_processing:
Reads were trimmed and filtered to remove adaptor sequences with Trim Galore and Cutadapt programs. trim_galore -q 28 --nextera --length 50 --paired; cutadapt -u 20 --length 30
Trimmed sequences were aligned to human genome (hg19) with CLC genomics workbench (QIAGEN)
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...

source_name: 4E-BP1 S83A HeLa cells

growth_protocol: HeLa cells were maintained in DMEM (Corning Cellgro) supplemented with 10% FBS.

extract_protocol:
eIF4G RIP were performed by using RIP-Assay Kit (MBL, RN1001). Collected cell pellets were lysed in 800 μL kit-provided lysis buffer supplemented with protease inhibitors (Roche), RiboLock RNase Inhibitor (Thermo Fisher) and dithiothreitol (DTT) on ice for 10 min. Lysed samples were centrifuged at 12,000 × g for 5 min at 4 °C to collect the supernatant (cell lysate). 80 μL supernatant was set aside as input and the remaining supernatant was divided into two groups. Lysates were incubated with 30 μL protein A/G sepharose beads (Santa Cruz) and 5 μL kit-provided rabbit IgG or eIF4G antibody (MBL, RN002P) overnight at 4 °C. Beads were collected, washed three times with kit-provided wash buffer supplemented with DTT. The immunoprecipitated and input RNA was extracted using Trizol (ThermoFisher).
Double-strand cDNA libraries were prepared with SMART-seq Ultra Low Input Kit (Takara Clontech). Double-strand cDNA libraries were fragmented and indexed using Nextera XT DNA Library Preparation Kit (Illumina). Quality of extracted RNA, double-strand cDNA libraries and Nextera XT DNA Libraries were determined on Bioanalyzer2100 (Agilent).

treatment_protocol: HeLa cells were arrested at G2/M boundary with RO3306, released and synchronized for mitotic entry. Mitotic cells were collected by shake-off, while attached cells were allowed to progress into post-mitosis. Harvested cell pellets were then subjected to RNA-seq and eIF4G RIP-seq. A similar analysis was performed on mitosis-enriched 4E-BP1WT and 4E-BP1S83A cells.


title: IP_WT_4

source_name: 4E-BP1 WT-HeLa cells


title: Kidney-TG-145


title: Kidney-ABMR-122


title: Kidney-Norm-123


title: IP_WT_3


title: Input_WT_4

value: Input


title: IP_S83A_3


title: B16_d18_CD45+_FYC_Rep2


title: Input_S83A_4


title: Input_S83A_3


title: Input_S83A_2


title: IP_PM_PP242

source_name: HeLa cells


title: B16_d18_CD45+_FYC_Rep1


title: B16_d18_CD45+_Nrp1_Rep1


title: Input_PM_PP242


title: Kidney-ABMR-140


title: IP_PM_CtrL


title: IP_M_CtrL


title: IP_M_PP242


title: Input_M_CtrL


title: Input_WT_2


title: IP_S83A_2


title: Input_WT_3


title: OGD, miR-29 virus, replicate 3

first: Mariko

last: Kobayashi

state: NY

address: 1230 York Avenue

department: Molecular Neuro-Oncology

institute: Rockefeller University

description:
ogd-miR29, replicate 3
OM3

data_processing:
Sequencing reads were aligned using the STAR aligner (v2.5.0a) to the mm10 genome (Dobin et al., 2013).
Reads were quantified using  featureCounts v1.4.3-p1  (Liao et al., 2014).
Difference analysis of gene expression changes was carried out in R (www.r-project.org; [Ihaka and Gentleman, 1996]) using Bioconductor (Gentleman et al., 2004) and the package edgeR (Robinson and Oshlack, 2010) applying generalized linear model methods to account for biological variation across replicates (McCarthy et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: matrix of counts (.txt) for all expressed genes, filtered for lowly expressed genes.  Input for difference analysis using EdgeR
Supplementary_files_format_and_content: EdgeR output files (.txt) for pair-wise analysis of OGD-empty vs. sham-empty, and OGD-miR29 vs. OGD-empty

source_name: cortical cultures, OGD

growth_protocol: Neurobasal media supplemented with 1x B27, 5mM Hepes, ph7.2, 5mM GlutaMax, and maintained at 37°C, 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent, precipitated with ethanol, DNase-treated, phenol-chloroform extracted, precipitated once more with ethanol and yields determined by absorption spectroscopy using a NanoDrop (NanoDrop Products).
Purified RNA wre depleted of rRNA using Ribo-Zero protocol (Illumina), RNA-seq libraries were generated following Illumina TruSeq protocol.

treatment_protocol: sham (normoxia) or OGD

value: cortex

tag: biological replicate

value: replicate 3

tag: ogd duration

tag: recovery duration

tag: lenti-virus, moi

value: miR-29c; MOI = 2

tag: library type

value: RNAseq


title: sham, miR-29 virus, replicate 3

description:
sham-miR29, replicate 3
SM3

source_name: cortical cultures, no OGD

tag: age


title: OGD, empty virus, replicate 3

description:
ogd-empty, replicate 3
OE3

value: Empty; MOI = 2


title: sham, empty virus, replicate 3

description:
sham-empty, replicate 3
SE3


title: OGD, miR-29 virus, replicate 2

description:
ogd-miR29, replicate 2
OM2

value: replicate 2


title: sham, miR-29 virus, replicate 2

description:
sham-miR29, replicate 2
SM2


title: sham, empty virus, replicate 2

description:
sham-empty, replicate 2
SE2


title: IP_WT_2


title: OGD, empty virus, replicate 1

description:
ogd-empty, replicate 1
OE1

value: replicate 1


title: sham, empty virus, replicate 1

description:
sham-empty, replicate 1
SE1


title: sham, miR-29 virus, replicate 1

description:
sham-miR29, replicate 1
SM1


title: MCAO ipsilateral RPF, replicate 5

description:
3hr stroke-ipsi, replicate 5
I5

data_processing:
Clipped adapter sequence (TGGAATTCTCGGGTGCCAAGGAACTCC) from demultiplexed reads,  aligned to mouse reference genome using Bowtie2, allowing a maximum of 2 mismatches and applying iterative 3'trimming and retaining only single-hit reads.
Counts of all genes associated with ribosome protected fragments, difference analysis of gene expression changes was carried out in R (www.r-project.org; [Ihaka and Gentleman, 1996]) using Bioconductor (Gentleman et al., 2004) and the package edgeR (Robinson and Oshlack, 2010) applying generalized linear model methods to account for biological variation across replicates (McCarthy et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: matrix of counts for all genes associated with ribosome protected fragments, filtered for low counts, for each replicate of all conditions, sham(S), contralateral(C), ipsilateral(I). Input for difference analysis using EdgeR

source_name: anesthesized and MCAO surgery performed

growth_protocol: standard animal husbandry and breeding of wildtype C57BL6

extract_protocol:
Ribosomal protected fragments isolated from purified monosomes were extracted, gel purified (Urea-PAGE) and selected for 30-50nt size fragments.
RPF libraries were generated following Illumina TruSeq small RNA protocol, PCR amplified 140-160bp fragments (15-35bp inserts + adaptors) isolated and purified for 69bp single-end sequencing on MiSeq (Illumina).

treatment_protocol: Sham or MCAO surgery, cortical tissue dissected

value: cortex - contralateral hemisphere

value: 7-8 weeks

value: replicate 5

tag: reperfusion time point

value: small RNAseq


title: MCAO ipsilateral RPF, replicate 4

description:
3hr stroke-ipsi, replicate 4
I4

value: replicate 4


title: pcHi-C_iPSC-induced lower motor neurons_rep3

description:
MS141
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz

source_name: pcHi-C_iPSC-induced lower motor neurons

value: iPSC-induced lower motor neurons


title: Input_M_PP242

tag: treatment


title: MCAO ipsilateral RPF, replicate 2

description:
3hr stroke-ipsi, replicate 2
I2


title: Input_PM_CtrL


title: MCAO contralateral RPF, replicate 6

description:
3hr stroke-contra, replicate 6
C6

value: replicate 6


title: OGD, miR-29 virus, replicate 1

description:
ogd-miR29, replicate 1
OM1


title: MCAO contralateral RPF, replicate 4

description:
3hr stroke-contra replicate 4
C4


title: MCAO contralateral RPF, replicate 1

description:
3hr stroke-contra, replicate 1
C1


title: sham RPF, replicate 2

description:
sham, replicate 2
S2

source_name: anesthesized and sham surgery performed


title: sham RPF, replicate 1

description:
sham, replicate 1
S1


title: OGD, empty virus, replicate 2

description:
ogd-empty, replicate 2
OE2


title: MCAO contralateral RPF, replicate 5

description:
3hr stroke-contra, replicate 5
C5


title: 24hr MCAO ipsilateral miRNAseq, replicate 3

description:
24hr stroke-ipsi, replicate 3
I3_24hr

data_processing:
Clipped adapter sequence (TGGAATTCTCGGGTGCCAAGGAACTCC) from demultiplexed reads,  aligned to mature mouse miRNA database using novoalign (Novocraft Technologies) applying iterative 3'trimming and retaining only single-hit reads.
Counts of all mature mouse miRNAs generated, difference analysis of gene expression changes was carried out in R (www.r-project.org; [Ihaka and Gentleman, 1996]) using Bioconductor (Gentleman et al., 2004) and the package edgeR (Robinson and Oshlack, 2010) applying generalized linear model methods to account for biological variation across replicates (McCarthy et al., 2012)
Genome_build: mature mouse miRNAs (miRBase)
Supplementary_files_format_and_content: matrix of counts for all mature mouse miRNAs, for each replicate of all conditions, sham(S), contralateral(C), ipsilateral(I), and time points (3-24hr).  Input for difference analysis using EdgeR

extract_protocol:
Total RNA was extracted using Trizol reagent, precipitated with ethanol, DNase-treated, phenol-chloroform extracted, precipitated once more with ethanol and yields determined by absorption spectroscopy using a NanoDrop (NanoDrop Products).
miRNAseq libraries were generated following Illumina TruSeq small RNA protocol, PCR amplified 140-160bp fragments (15-35bp inserts + adaptors) isolated and purified for 69bp single-end sequencing on MiSeq (Illumina).

value: cortex - ipsilateral hemisphere


title: 24hr MCAO ipsilateral miRNAseq, replicate 1

description:
24hr stroke-ipsi, replicate 1
I1_24hr


title: sham RPF, replicate 5

description:
sham, replicate 5
S5


title: 24hr MCAO ipsilateral miRNAseq, replicate 2

description:
24hr stroke-ipsi, replicate 2
I2_24hr


title: 12hr MCAO ipsilateral miRNAseq, replicate 3

description:
12hr stroke-ipsi, replicate 3
I3_12hr


title: 12hr MCAO ipsilateral miRNAseq, replicate 1

description:
12hr stroke-ipsi, replicate 1
I1_12hr


title: 12hr MCAO ipsilateral miRNAseq, replicate 2

description:
12hr stroke-ipsi, replicate 2
I2_12hr


title: MCAO ipsilateral RPF, replicate 6

description:
3hr stroke-ipsi, replicate 6
I6


title: 6hr MCAO ipsilateral miRNAseq, replicate 2

description:
6hr stroke-ipsi, replicate 2
I2_6hr


title: 3hr MCAO ipsilateral miRNAseq, replicate 3

description:
3hr stroke-ipsi, replicate 3
I3_3hr


title: 3hr MCAO ipsilateral miRNAseq, replicate 2

description:
3hr stroke-ipsi, replicate 2
I2_3hr


title: 6hr MCAO ipsilateral miRNAseq, replicate 1

description:
6hr stroke-ipsi, replicate 1
I1_6hr


title: 24hr MCAO contralateral miRNAseq, replicate 3

description:
24hr stroke-contra, replicate 3
C3_24hr


title: 3hr MCAO ipsilateral miRNAseq, replicate 1

description:
3hr stroke-ipsi, replicate 1
I1_3hr


title: 24hr MCAO contralateral miRNAseq, replicate 2

description:
24hr stroke-contra, replicate 2
C2_24hr


title: 24hr MCAO contralateral miRNAseq, replicate 1

description:
24hr stroke-contra, replicate 1
C1_24hr


title: 12hr MCAO contralateral miRNAseq, replicate 3

description:
12hr stroke-contra, replicate 3
C3_12hr


title: 12hr MCAO contralateral miRNAseq, replicate 2

description:
12hr stroke-contra, replicate 2
C2_12hr


title: 6hr MCAO contralateral miRNAseq, replicate 3

description:
6hr stroke-contra, replicate 3
C3_6hr


title: 12hr MCAO contralateral miRNAseq, replicate 1

description:
12hr stroke-contra, replicate 1
C1_12hr


title: 6hr MCAO contralateral miRNAseq, replicate 1

description:
6hr stroke-contra, replicate 1
C1_6hr


title: 3hr MCAO contralateral miRNAseq, replicate 2

description:
3hr stroke-contra replicate 2
C2_3hr


title: 3hr MCAO contralateral miRNAseq, replicate 1

description:
3hr stroke-contra, replicate 1
C1_3hr


title: sham miRNAseq, replicate 1

description:
sham, replicate 1
S1


title: sham miRNAseq, replicate 2

description:
sham, replicate 2
S2


title: 3hr MCAO contralateral miRNAseq, replicate 3

description:
3hr stroke-contra, replicate 3
C3_3hr


title: sham miRNAseq, replicate 3

description:
sham, replicate 3
S3


title: 6hr MCAO ipsilateral miRNAseq, replicate 3

description:
6hr stroke-ipsi, replicate 3
I3_6hr


title: 6hr MCAO contralateral miRNAseq, replicate 2

description:
6hr stroke-contra, replicate 2
C2_6hr


title: WT2

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm10 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: B220+ splenocytes

extract_protocol:
Cells were stored in Trizol and RNA extracted using the Zymogenetics directZol miniprep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B220+ cells were isolated from spleens of 4-5 week old mice of each genotype.

value: B220+ splenocytes

value: Max WT

value: 4-5 weeks


title: WT1


title: EWT3

value: EuMyc Max WT


title: EWT2


title: KO2

value: Max KO


title: EWT1


title: WT3


title: EKO2

value: EuMyc Max KO


title: EKO3


title: EKO1


title: IL6_repl1

city: Seoul

first: Saseong

last: Lee

address: Banp-daero

department: Rheumatology

country: South Korea

institute: The catholic university of korea

description: Gene expression data from mouse splenic CD4+ T cells stimulated with IL6+ConCM in the presence of anti-CD3/CD28 antibodies.

hyb_protocol: The labeled DNA target was hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST array (Affymetrix).

scan_protocol: The hybridized chip was scanned on a GCS3000 scanner (Affymetrix).

data_processing: The data were analyzed with transcriptome analysis console (TAC) software using Affymetrix default analysis settings and normalized with quantile normalization method. To define differentially expressed genes (DEGs), the integrated statistical testing method was used. Briefly, for each gene, two independent tests including two-tailed T-test and log2 median ratio test were performed using the empirical distributions that were obtained by randomly permutating the samples 1000 times. Then the two sets of P values from individual tests were combined to compute the overall P values using the Stouffer’s method. The DEGs were selected when a gene displayed an overall P < 0.05 and when the absolute log2-fold changes were larger than the cutoff. The cutoff value was determined as 1.31, which is larger than the mean absolute values of the 5 and 95 percentiles of the empirical null distribution.

label: biotin

label_protocol: The sense cDNA was then fragmented and biotin-labeled using GeneChip Whole Transcript PLUS reagent kit (Affymetrix).

growth_protocol: Splenic cells were isolated from mice immediately after euthanasia.Then, CD4+ T cells were isolated using magnetic beads. Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from two replicate samples using RNeasy® Mini kit (Qiagen).

treatment_protocol: The cells were treated with PlGFCM, ConCM or IL6(20ng/ml)+ConCM in the presence of anti-CD3/CD28 antibody (1μg/ml) stimulation for 12 hours.

value: Mouse splenic CD4+ T cells

value: IL6+ConCM, anti-CD3/CD28 antibodies


title: IL6_repl2

source_name: CD4+ T cells stimulated with IL6+ConCM in the presence of anti-CD3/CD28 antibodies


title: PlGF_sup_repl2

description: Gene expression data from mouse splenic CD4+ T cells stimulated with PlGFCM in the presence of anti-CD3/CD28 antibodies.

value: PlGFCM, anti-CD3/CD28 antibodies


title: Con_sup_repl2

description: Gene expression data from mouse splenic CD4+ T cells stimulated with ConCM in the presence of anti-CD3/CD28 antibodies.

value: ConCM, anti-CD3/CD28 antibodies


title: Con_sup_repl1

source_name: CD4+ T cells stimulated with ConCM in the presence of anti-CD3/CD28 antibodies


title: PlGF_sup_repl1

source_name: CD4+ T cells stimulated with PlGFCM in the presence of anti-CD3/CD28 antibodies


title: E13.5_wildtype_biorep3

city: Aurora

first: Victor

middle: A

last: Ruthig

state: CO

department: Pediatrics, Section of Developmental Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina Hi-seq 2500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Alignment to mm9 using Bowtie 2 (version 2.2.4) with default settings
Assembly with Cufflinks pipeline (version 2.2.0) (Top-Hat, Cufflinks, Cuffmerge) with default settings
Gene levels quantified using Cuffquant (version 2.2.0)
Differential expression analysis using Cuffdiff (version 2.2.0)
mm9
Output of tab-delimited text files with RPKM and differential expression values for each Sample

source_name: Male Germ Cells

extract_protocol:
testes were collected from genotyped fetuses at E12.5, E13.5 and E14.5, testes were disassociated, male germ cells were purified using FACS for GFP, total RNA was extracted using Qiagen RNeasy Micro Kit (Qiagen #74004)
RNA libraries were prepared for sequencing according to the Smart-seq2 protocol (Picelli et al., 2014) using the Nextera XT DNA Sample Prep Kit (illumina #15032352)

tag: rip antibody

tag: background

tag: allele


title: E14.5_wildtype_biorep4


title: E14.5_mutant_biorep1


title: E14.5_wildtype_biorep3


title: E14.5_mutant_biorep4


title: E14.5_wildtype_biorep2


title: E13.5_wildtype_biorep4


title: E14.5_wildtype_biorep1


title: E14.5_mutant_biorep3


title: E14.5_mutant_biorep2


title: KO3

tag: genotype


title: KO1


title: E13.5_wildtype_biorep2


title: ATAC-seq_iPSC-induced lower motor neurons_rep3

description:
MS139_YSMS16
processed data file:
motor.atac.seq.narrowPeak
motor.atac-seq.bigwig

data_processing:
All reads were trimmed to 50 bp prior to processing. For libraries having undergone paired-end sequencing, only the first read was used.
All libaries were processed using the ENCODE ATAC-seq pipeline (December 2017).
Optimal IDR and optimal overlap peaks called by MACS2 were used.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks called using MACS2 and signal tracks in bigwig format

extract_protocol:
Cells were harvested, snap frozen in dry ice, and stored at -80C. Cells were washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with Ampure XP beads.


title: E13.5_wildtype_biorep1


title: E13.5_mutant_biorep3


title: E13.5_mutant_biorep2


title: E12.5_wildtype_biorep3


title: E12.5_wildtype_biorep4


title: E13.5_mutant_biorep1


title: E12.5_wildtype_biorep2


title: E12.5_mutant_biorep4


title: E12.5_wildtype_biorep1


title: E12.5_mutant_biorep3


title: E12.5_mutant_biorep1


title: E12.5_mutant_biorep2


title: E13.5_mutant_biorep4


title: MNase-seq_EED-GOF_week0_rep2

first: Yumei

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

description: cTNT-EED by AAV9 transduction

data_processing:
MNase-seq reads were filtered by cutadapt (v1.10) with parameters -O 10 -u 1 -U 1.
The reads were aligned to mm10 mouse genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 20 were kept.
Nucleosome occupancy was called using merged BAM files by DANPOS2 (v2.2.2) with parameters -jd 147 --extend 74 -m 1 -c 10000000.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using DANPOS2; scores represented nucleosome occupancy.

source_name: heart

growth_protocol: Mice were kept in the animal house.

extract_protocol:
DNA was extracted with pheno-chloroform. Then DNA fragments with size around 150bp were extracted from gel.
E7370 kit was used for library construction. And Illumina Truseq indexes were used to index samples. The cycle number of the amplification was 4 or 5.

treatment_protocol: Tissue sample was fixed with formaldehyde and then lysed. The lysates were digested by MNase at 37℃. EDTA and SDS were used to stop the digestion. And the digested materials were reverse crosslinked and treated with proteinase K.

value: isolated ventricular cardiomyocytes

tag: developmental stage

value: Adult

value: EED overexpression


title: MNase-seq_EED-GOF_week0_rep3

description: cTNT-EED by AAV9 transduction


title: LR6a

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

description: Sample 34

data_processing:
Bam files generated using TopHat alignment software using Illumina's Basespace
Samples were filtered with normalized read counts across all samples >1
A value of '1' was added to each of the genes across all samples.  This provides a value to genes which show no read counts and allows for appropriate calculations of fold change.  Low abundance transripts are moe influenced by highly expressed transcripts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The processed data file was processed using Tibco Spotfire with OmicsOffice.  This sofware utilizes Cufflinks to generate raw read counts.  Read counts were normalized using DESeq2 through R software.

source_name: LGP2ko RIG-I 6hr 1

extract_protocol:
Total RNA was prepared using the QIAGEN RNeasy Plus Mini Kit
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 2500 in 100-base single-read reactions.

treatment_protocol: WT and Dhx58-/- DCs were CD11c+-purified using EasySep Mouse CD11c Positive Selection Kit II (Stemcell) per the manufacturer’s protocol, and transfected with 20ng PAMP RNA, or left untreated. Cells were plated in biological triplicates for each condition/time point. PAMP RNA-treated cells and time-matched mock-treated cells were collected at 1, 3, and 6h post-agonist transfection in Buffer RLT (QIAGEN).

value: GM-CSF-cultured BM-DCs


title: LM6c

description: Sample 33

source_name: LGP2ko Mock 6hr 3


title: WTR6b

description: Sample 29

source_name: WT RIG-I 6hr 2


title: LM6b

description: Sample 32

source_name: LGP2ko Mock 6hr 2


title: LR6b

description: Sample 35

source_name: LGP2ko RIG-I 6hr 2


title: WTM6a

description: Sample 25

source_name: WT Mock 6hr 1


title: WTM6b

description: Sample 26

source_name: WT Mock 6hr 2


title: WTR6a

description: Sample 28

source_name: WT RIG-I 6hr 1


title: LM6a

description: Sample 31

source_name: LGP2ko Mock 6hr 1


title: WTR6c

description: Sample 30

source_name: WT RIG-I 6hr 3


title: MNase-seq_Control_week0_rep3

description: cTNT-Luciferase by AAV9 transduction

value: WT


title: MNase-seq_EED-GOF_week0_rep1

description: cTNT-EED by AAV9 transduction


title: LR6c

description: Sample 36

source_name: LGP2ko RIG-I 6hr 3


title: MNase-seq_Control_week0_rep2

description: cTNT-Luciferase by AAV9 transduction


title: H2BGFP_input_week2_EED-GOF

data_processing:
The sequencing adaptors were filtered and reads with low quality (average quality <20 or fraction of bases with quality less than 20  >0.5 or fraction of N bases >0.1) were filtered.
High-quality reads were aligned to mm10 mouse genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 20 were kept.
Reads were further analyzed by DANPOS2 (v2.2.2) with parameters -c 10000000 --extend 74
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for H2BGFP ChIP-seq were generated using DANPOS2. Scores represented nucleosome occupancy measured by ChIP signals subtract input.

growth_protocol: Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory animal care. The Dox was mixed with water and was fed to the mice according to experimental requirement.

extract_protocol:
The cardiomyocytes were isolated from the adult mice heart according to previous protocol, and the cardiomyocytes were fixed and then lysed. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP library preparation Kit (NEBE7370). Briefly, DNA was end-repaired. The blunt, phosphorylated ends were treated with TA ligase Master mix and NEBNext Adaptor for Illumina. After adaptor ligation, DNA was PCR amplified with Illumina primers for 15 cycles. The DNA library was purified and the size of DNA fragments was selected by AMPure XP beads. The libraries were then sent to be sequenced.

value: isolated adult ventricular cardiomyocytes

value: adult

tag: chip antibody


title: LM3c

description: Sample 21

source_name: LGP2ko Mock 3hr 3

tag: cell type


title: LR3a

description: Sample 22

source_name: LGP2ko RIG-I 3hr 1

tag: strain


title: LR3b

description: Sample 23

source_name: LGP2ko RIG-I 3hr 2


title: LM3b

description: Sample 20

source_name: LGP2ko Mock 3hr 2


title: WTM6c

description: Sample 27

source_name: WT Mock 6hr 3


title: H2BGFP_input_week0_EED-GOF

source_name: heart


title: LM3a

description: Sample 19

source_name: LGP2ko Mock 3hr 1


title: H2BGFP_input_week2_Control


title: H2BGFP_input_week0_Control


title: WTR3c

description: Sample 18

source_name: WT RIG-I 3hr 3


title: LR3c

description: Sample 24

source_name: LGP2ko RIG-I 3hr 3


title: WTR3b

description: Sample 17

source_name: WT RIG-I 3hr 2


title: WTM3c

description: Sample 15

source_name: WT Mock 3hr 3


title: H2BGFP_week2_EED-GOF_rep2

description: input sample: H2BGFP_input_week2_EED-GOF


title: LR1b

description: Sample 11

source_name: LGP2ko RIG-I 1hr 2


title: LR1a

description: Sample 10

source_name: LGP2ko RIG-I 1hr 1


title: WTM3a

description: Sample 13

source_name: WT Mock 3hr 1


title: MNase-seq_Control_week0_rep1

description: cTNT-Luciferase by AAV9 transduction


title: WTR3a

description: Sample 16

source_name: WT RIG-I 3hr 1


title: LR1c

description: Sample 12

source_name: LGP2ko RIG-I 1hr 3


title: H2BGFP_week0_EED-GOF_rep3

description: input sample: H2BGFP_input_week0_EED-GOF


title: H2BGFP_week2_Control_rep2

description: input sample: H2BGFP_input_week2_Control


title: H2BGFP_week2_Control_rep1


title: H2BGFP_week0_Control_rep2

description: input sample: H2BGFP_input_week0_Control


title: H2BGFP_week0_EED-GOF_rep2


title: H2BGFP_week0_Control_rep1


title: LM1b

description: Sample 8

source_name: LGP2ko Mock 1hr 2


title: MNase-seq_siRNA-Brg1_week0_rep1

description: siRNA-Brg1 by AAV9 transduction

value: BRG1 knockdown


title: WTM3b

description: Sample 14

source_name: WT Mock 3hr 2


title: MNase-seq_siRNA-Brg1_week0_rep2

description: siRNA-Brg1 by AAV9 transduction


title: H2BGFP_week0_Control_rep3


title: WTR1c

description: Sample 6

source_name: WT RIG-I 1hr 3


title: LM1a

description: Sample 7

source_name: LGP2ko Mock 1hr 1


title: MNase-seq_scramble_week0_rep2

description: scramble by AAV9 transduction


title: MNase-seq_scramble_week0_rep1

description: scramble by AAV9 transduction


title: H2BGFP_week2_EED-GOF_rep1


title: H2BGFP_week0_EED-GOF_rep1


title: WTR1a

description: Sample 4

source_name: WT RIG-I 1hr 1


title: WTM1c

description: Sample 3

source_name: WT Mock 1hr 3


title: H2BGFP_input_week3_siRNA-Brg1

description: input DNA

source_name: heart

value: BRG1 knowdown

value: No

tag: input sample


title: WTR1b

description: Sample 5

source_name: WT RIG-I 1hr 2


title: H2BGFP_input_week0_scramble

description: input DNA


title: WTM1b

description: Sample 2

source_name: WT Mock 1hr 2


title: LM1c

description: Sample 9

source_name: LGP2ko Mock 1hr 3


title: H2BGFP_input_week0_siRNA-Brg1

description: input DNA


title: WTM1a

description: Sample 1

source_name: WT Mock 1hr 1


title: RIP_RNA_biorep2

data_processing:
Processing of data was performed as described in Nicholson et al. 2017
After removal of adapter and UMI sequences, reads were mapped to hg19 using TopHat2 (Version ##).
Binding sites were identified using the binning and normalization procedure of Nicholson et al. 2017
IPs were compared to input samples to identify sites enriched in DND1 IPs.
Reads with a low pass filter of >3 reads and >1.5 fold enrichment over input were considered DND1 binding sites.
hg19
Output of tab-delimited text files with total number of sites values for each target

growth_protocol: DO-RIP-seq was performed as described in (Nicholson et al., 2017). Briefly, 5 - 15 cm2 plates of HEK293 cells were grown to 80-90% confluency

extract_protocol:
RNA from IPs was radiolabeled and run on a 10% TBE-Urea gel. RNA fragments from ~25-75 nucleotides were excised and extracted from the gel.
cDNA libraries were prepared using the NEBNext Multiplexing Small RNA Library Prep Set for Illumina with 14-17 rounds of amplification, following the manufacturer’s protocol with the exception that the 5’ RNA adapter was replaced with a custom 5’ adapter compatible with UMI (Unique Molecular Identifier) tagging (Kivioja et al., 2011)
Libraries were sequenced using Illumina HiSeq 2500.

treatment_protocol: cells were transfected with ~35 µg/plate FLAG-DND1 or untagged DND1 (as a negative control), grown for 24hrs, then harvested in PLB (polysome lysis buffer)

value: human embryonic kidney cell derived

value: anti-FLAG


title: H2BGFP_week3_siRNA-Brg1_rep1


title: RIP_RNA_biorep1


title: H2BGFP_week3_siRNA-Brg1_rep2


title: H2BGFP_week3_scramble_rep2


title: input_RNA_biorep2


title: H2BGFP_input_week3_scramble

description: input DNA


title: H2BGFP_week3_scramble_rep1


title: input_RNA_biorep1


title: H2BGFP_week0_scramble_rep1


title: H2BGFP_week0_scramble_rep2


title: LC509_tumor_totalRNA

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

data_processing:
The 3' adaptors (CTGTAGGCACCATCAAT) were trimmed using cutadapt software. Low-quality reads with Phred quality scores lower than 20 (50% of bases) were removed using fastq quality filter.
The reads originated from rRNAs were identified and discarded by aligning the reads to human rRNA sequences (5S, 5.8S, 18S, and 28S ) using Bowtie (version 1.1.2) with no mismatch allowed.
The remaining reads were then mapped to the human genome and spliced transcripts using STAR with following parameters:--outFilterType BySJout --outFilterMismatchNmax 2 --outSAMtype BAM --quantMode TranscriptomeSAM --outFilterMultimapNmax 1 --outFilterMatchNmin 16
Genome_build: custom transcriptome reference fasta file 'GRCh38.transcripts.fa'
Supplementary_files_format_and_content: counts

extract_protocol:
Tumors and adjacent normal tissues from HCC patients were flash-frozen and stored in liquid nitrogen. Prior to the experiments, the tissue samples were crushed into powder in an automatic cryogenic grinder (HORIBA, Freezer/Mill 6770) filled with liquid nitrogen. About 50 mg of each of the powdered samples was lysed in 400 ul of lysis buffer containing 20 mM Tris-HCl (PH 7.4) (Invitrogen, AM9850G), 150mM NaCl (Invitrogen, AM9760G), 5mM MgCl2 (Invitrogen, AM9530G), 1% Triton X-100 (Sigma Aldrich, T8787), 0.1% NP40 (Amresco, E109), 1 mM DTT (Sigma Aldrich, 43816), 25 U/ml DNase I (Invitrogen, AM2239) and 0.1 mg/ml cycloheximide (Inalco, 1758-9310). The mixture was clarified for 10 minutes at 20,000 g at 4°C. 200ul of the clarified lysate was used for purification of the RPF, which will be profiled by ribosome profiling, and 100ul of the lysate was for the total RNA sequencing in parallel.
For RPF, 90 Units of RNase I (Life Technologies, AM2294) for each A260 of the lysate was added to 200 ul of the supernatant and incubated at room temperature for 45 min with gentle mixing. Nuclease digestion was stopped with 15 ul of SUPERase InTM RNase Inhibitor (Life Technologies, AM2696) and chilled on ice. Ribosome-RNA complexes were purified by Sephacryl S400 spin column chromatography (GE Healthcare, 27514001). The ribosome-protected RNA was extracted with Trizol (Invitrogen, 15596018), following the manufacturer’s protocol. Then the ribosomal RNA was depleted using the RiboZero kit (Illumina; MRZH11124), following the manufacturer’s protocol, omitting the 50°C incubation step. Next, the samples were resolved in a 15% Urea gel by electrophoresis, and the fragment at 25-35 nucleotides was excised from the gel. The RNA fragments were then eluted at least 2h in 400ul Nuclease-Free Water, 40 ul of 5 M Ammonium Acetate (Invitrogen, AM9070G) and 2 ul of 10% SDS (Invitrogen, AM9823), followed by Isopropanol (Sigma Aldrich, I9030) precipitation.
Total RNA from the tissue samples was isolated from 100 ul of the clarified tissue lysate with Trizol (Invitrogen, 15596018), and the ribosomal RNA was then depleted using the RiboZero kit (Illumina; MRZH11124). Next, the rRNA-depleted total RNA was fragmented with PNK buffer (NEB, M0201L) at 95˚C for 20min.
Both RPF and fragmented total RNA were cloned and amplified for next-generation sequencing with a tagging-based workflow. In brief, the RNA fragments were end repaired with T4 PNK (NEB, M0201L) and ligated with 3’ adaptor, followed by cDNA synthesis, cDNA gel purification, circularization and PCR amplification20. The sequencing libraries were assessed with a BioAnalyzer and quantified using KAPA SYBR FAST Universal qPCR Kit (Kapa Biosystems, KK4601) prior to and after pooling for sequencing. Library insert sizes were typically about 30bp. The pooled libraries were sequenced on the Illumina HiSeq 2500 platform with a single-end sequencing strategy for 50 cycles.

tag: subject status

value: HCC patient

tag: subject id

tag: tissue type

value: liver tumor

tag: molecule subtype

value: rRNA-depleted, fragmented total RNA


title: LC509_normal_totalRNA

value: adjacent normal liver tissue


title: 24hr MCAO ipsilateral RNAseq, replicate 3

description:
24hr stroke-ipsi, replicate 3
I3_24hr

data_processing:
Sequencing reads were aligned using the STAR aligner (v2.5.0a) to the mm10 genome (Dobin et al., 2013).
Reads were quantified using  featureCounts v1.4.3-p1  (Liao et al., 2014).
Difference analysis of gene expression changes was carried out in R (www.r-project.org; [Ihaka and Gentleman, 1996]) using Bioconductor (Gentleman et al., 2004) and the package edgeR (Robinson and Oshlack, 2010) applying generalized linear model methods to account for biological variation across replicates (McCarthy et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: matrix of counts for all expressed genes, for each replicate of all conditions, sham(S), contralateral(C), ipsilateral(I), and time points (3-24hr). Input for difference analysis using EdgeR

source_name: anesthesized and MCAO surgery performed

growth_protocol: Standard animal husbandry and breeding of wildtype C57BL6

tag: tissue

value: cortex - ipsilateral hemisphere

value: 7-8 weeks

tag: biological replicate

value: replicate 3

tag: library name


title: LC509_tumor_RPF

data_processing:
library strategy: ribo-seq
The 3' adaptors (CTGTAGGCACCATCAAT) were trimmed using cutadapt software. Low-quality reads with Phred quality scores lower than 20 (50% of bases) were removed using fastq quality filter.
The reads originated from rRNAs were identified and discarded by aligning the reads to human rRNA sequences (5S, 5.8S, 18S, and 28S ) using Bowtie (version 1.1.2) with no mismatch allowed.
The remaining reads were then mapped to the human genome and spliced transcripts using STAR with following parameters:--outFilterType BySJout --outFilterMismatchNmax 2 --outSAMtype BAM --quantMode TranscriptomeSAM --outFilterMultimapNmax 1 --outFilterMatchNmin 16
Genome_build: custom transcriptome reference fasta file 'GRCh38.transcripts.fa'
Supplementary_files_format_and_content: counts

value: ribosome-protected mRNA fragment (RPF)


title: H2BGFP_week0_siRNA-Brg1


title: 24hr MCAO ipsilateral RNAseq, replicate 1

description:
24hr stroke-ipsi, replicate 1
I1_24hr

tag: age

value: replicate 1

tag: reperfusion time point


title: LC508_tumor_totalRNA


title: LC508_tumor_RPF


title: LC509_normal_RPF


title: 12hr MCAO ipsilateral RNAseq, replicate 2

description:
12hr stroke-ipsi, replicate 2
I2_12hr

value: replicate 2


title: LC508_normal_totalRNA


title: 12hr MCAO ipsilateral RNAseq, replicate 3

description:
12hr stroke-ipsi, replicate 3
I3_12hr


title: LC508_normal_RPF


title: LC507_tumor_RPF


title: 6hr MCAO ipsilateral RNAseq, replicate 3

description:
6hr stroke-ipsi, replicate 3
I3_6hr


title: LC507_tumor_totalRNA


title: LC507_normal_totalRNA


title: 6hr MCAO ipsilateral RNAseq, replicate 2

description:
6hr stroke-ipsi, replicate 2
I2_6hr


title: 6hr MCAO ipsilateral RNAseq, replicate 1

description:
6hr stroke-ipsi, replicate 1
I1_6hr


title: LC507_normal_RPF


title: 12hr MCAO ipsilateral RNAseq, replicate 1

description:
12hr stroke-ipsi, replicate 1
I1_12hr


title: 3hr MCAO ipsilateral RNAseq, replicate 2

description:
3hr stroke-ipsi, replicate 2
I2_3hr


title: LC506_tumor_RPF


title: 3hr MCAO ipsilateral RNAseq, replicate 1

description:
3hr stroke-ipsi, replicate 1
I1_3hr


title: 24hr MCAO contralateral RNAseq, replicate 3

description:
24hr stroke-contra, replicate 3
C3_24hr

value: cortex - contralateral hemisphere


title: 24hr MCAO contralateral RNAseq, replicate 1

description:
24hr stroke-contra, replicate 1
C1_24hr


title: LC505_tumor_totalRNA


title: 24hr MCAO ipsilateral RNAseq, replicate 2

description:
24hr stroke-ipsi, replicate 2
I2_24hr


title: LC506_normal_RPF


title: 24hr MCAO contralateral RNAseq, replicate 2

description:
24hr stroke-contra, replicate 2
C2_24hr


title: LC505_tumor_RPF


title: 12hr MCAO contralateral RNAseq, replicate 3

description:
12hr stroke-contra, replicate 3
C3_12hr


title: LC505_normal_totalRNA


title: LC502_tumor_RPF


title: 12hr MCAO contralateral RNAseq, replicate 2

description:
12hr stroke-contra, replicate 2
C2_12hr


title: 12hr MCAO contralateral RNAseq, replicate 1

description:
12hr stroke-contra, replicate 1
C1_12hr


title: LC502_tumor_totalRNA


title: LC505_normal_RPF


title: 3hr MCAO ipsilateral RNAseq, replicate 3

description:
3hr stroke-ipsi, replicate 3
I3_3hr


title: 6hr MCAO contralateral RNAseq, replicate 3

description:
6hr stroke-contra, replicate 3
C3_6hr


title: 6hr MCAO contralateral RNAseq, replicate 1

description:
6hr stroke-contra, replicate 1
C1_6hr


title: 6hr MCAO contralateral RNAseq, replicate 2

description:
6hr stroke-contra, replicate 2
C2_6hr


title: LC502_normal_totalRNA


title: LC506_tumor_totalRNA


title: LC501_tumor_totalRNA


title: LC502_normal_RPF


title: 3hr MCAO contralateral RNAseq, replicate 1

description:
3hr stroke-contra, replicate 1
C1_3hr


title: LC501_normal_RPF


title: LC501_normal_totalRNA


title: LC501_tumor_RPF


title: 3hr MCAO contralateral RNAseq, replicate 3

description:
3hr stroke-contra, replicate 3
C3_3hr


title: sham RNAseq, replicate 3

description:
sham, replicate 3
S3

source_name: anesthesized and sham surgery performed

value: cortex


title: LC506_normal_totalRNA


title: LC034_tumor_totalRNA


title: LC034_normal_totalRNA


title: 3hr MCAO contralateral RNAseq, replicate 2

description:
3hr stroke-contra replicate 2
C2_3hr


title: MCAO ipsilateral cortex AGO CLIP, replicate 5

data_processing:
All fastq processing done using fastqx_toolkit-0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/).  Sequencing reads were filtered for quality reads (min:0-6:20,mean:7-50:20), collapsed exact sequences, trimmed 5' degenerate linker, demultiplexed and trimmed 4nt barcode sequence, and clipped 3' adapter sequence (GTGTCAGTCACTTCCAGCGG).
Processed fastq files were aligned to mouse reference genome or miRBase mature mouse miRNA database using novoalign (Novocraft Technologies) applying iterative 3'trimming and retaining only single-hit reads.
Peak calling strategy using CLIP Toolkit command tag2peak.pl was used, applying FDR cut-off of <0.01 over background.  Genomic coordinates for each peak were constructed with standard width of 80nt (+/- 40nt from peak midpoint).  Peaks were assessed for biological complexity and selected for BC3, or represented by at least 3 biological replicates for one of 3 conditions (sham, MCAO-contralateral, or MCAO-ipsilateral).
Genome_build: mm10
Supplementary_files_format_and_content: CLIP tag counts of all BC3 AGO mRNA peaks (mm10 genomic coordinates) for each replicate of all conditions, sham(S), contralateral(C), ipsilateral(I)
Supplementary_files_format_and_content: CLIP tag counts of mature mouse miRNAs for each replicate of all conditions, sham(S), contralateral(C), ipsilateral(I)

extract_protocol:
Argonaute IP, alkaline phosphatase treatment, polynucleotide kinase (PNK) radiolabeling, addition of pre-adenylated 3’ linker, SDS-PAGE, and nitrocellulose transfer and extraction performed.   AGO:RNA complexes excised out of nitrocellulose membrane, followed by proteinase K digestion of AGO protein.
AGO-CLIP footprints were cloned using the Br-dU incorporation and bead-capture strategy.  Barcoded reverse transcription (RT) primers, allowing multiplexing of 3 samples per Hiseq (Illumina) run,50 base pair single-end reads.

treatment_protocol: Sham or MCAO surgery, cortical tissue dissected, homogenized and UV-crosslinked.

tag: ago

value: rna complex:Pooled high and low molecular weight AGO:RNA complexes ~110-150kDa

value: replicate 5


title: sham RNAseq, replicate 2

description:
sham, replicate 2
S2


title: LC034_normal_RPF


title: MCAO ipsilateral cortex AGO CLIP, replicate 4

value: replicate 4


title: sham RNAseq, replicate 1

description:
sham, replicate 1
S1


title: LC033_normal_totalRNA


title: LC033_tumor_RPF


title: MCAO ipsilateral cortex AGO CLIP, replicate 1


title: MCAO ipsilateral cortex AGO CLIP, replicate 2


title: LC001_tumor_totalRNA


title: MCAO contralateral cortex AGO CLIP, replicate 5


title: LC001_tumor_RPF


title: LC033_normal_RPF


title: MCAO contralateral cortex AGO CLIP, replicate 4


title: MCAO contralateral cortex AGO CLIP, replicate 2


title: LC001_normal_totalRNA


title: sham cortex AGO CLIP, replicate 5


title: MCAO contralateral cortex AGO CLIP, replicate 1


title: sham cortex AGO CLIP, replicate 3


title: LC001_normal_RPF


title: LC034_tumor_RPF


title: sham cortex AGO CLIP, replicate 2


title: SSRP1dsRNA_b_RNAseq_Rep2

city: KANSAS CITY

first: Joan

middle: W

last: Conaway

state: Missouri

institute: Stowers Institute for Medical Research

description: poly-A Stranded RNA-Seq

data_processing:
Reads demultiplexed and evaluated for quality
Alignment of reads with STAR (version 2.6.1) to combined genome of hg38 and dm6 with parameter `--quantMode GeneCounts`.
Raw gene counts were imported into edgeR for DGE analysis. The RUVg function in the RUVSeq method was applied to normalize to spike-in (hg38) (Risso, D., Ngai, J., Speed, T.P., and Dudoit, S. (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotech 32, 896-902, https://www.nature.com/articles/nbt.2931; Risso, D. RUVSeq: Remove unwanted variation from RNA-Seq data. https://www.bioconductor.org/packages/RUVSeq)
Table exported from edgeR containing gene values for fold-change, FDR, and FPKM.
Genome_build: dm6 (primary), hg38 (spike-in)
Supplementary_files_format_and_content: Raw gene counts output by STAR and final output table from edgeR

organism: Drosophila melanogaster

source_name: SSRP1 dsRNA b

growth_protocol: Drosophila S2 cells were cultured in Schneider’s media (GIBCO #21720) supplemented with 10% heat-inactivated fetal bovine serum (PAA #A15-701) at 25°C

extract_protocol:
At the end of the 4-day knockdown, Drosophila S2 cells were harvested. Human HEK293T cells were added to the harvested S2 cells (0.8x10e6 human cells / 15x10e6 S2 cells) as spike-in control.  Each Pool of S2 and HEK293T cells was washed twice using 1 X PBS. Total RNA was extracted using the QIAGEN RNeasy mini kit. Libraries were prepared using the Illumina TruSeq Standard mRNA LT sample prep kit and sequenced on the Illumina HiSeq 2500 platform.
RNA-seq libraries were generated from 1ug of high quality total RNA, as assessed using the Bioanalyzer (Agilent). Libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA LT Sample Prep Kit – set A (Illumina, Cat. No. RS-122-2101) kit. The resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50 bp single reads on the Illumina HiSeq 2500 instrument.

treatment_protocol: Drosophila S2 Cells were treated with SSRP1 dsRNA and Spt16 dsRNA to knockdown SSRP1 and Spt16 respectively. S2 cells were treated with eGFP dsRNA as a non-targeting control. Spt16dsRNA_a and Spt16dsRNA_b are two ~400 bp dsRNAs that target non-overlapping regions of the Spt16 mRNA, and SSRP1dsRNA_a and SSRP1dsRNA_b are two ~400 bp dsRNAs that target non-overlapping regions of the SSRP1 mRNA.  Rep1 and Rep2 are biological replicates (independent cultures, independent treatments, independent RNA extractions and libraries).

tag: cell line

tag: knockdown

tag: spike-in cells

value: Human HEK293T cells


title: sham cortex AGO CLIP, replicate 1


title: LC033_tumor_totalRNA


title: SSRP1dsRNA_b_RNAseq_Rep1

description: poly-A Stranded RNA-Seq


title: MNase-seq_Het_rep2

data_processing:
MNase-seq reads were filtered by cutadapt (v1.10) with parameters -O 10 -u 1 -U 1.
The reads were aligned to mm10 mouse genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 20 were kept.
Nucleosome occupancy was called by DANPOS2 (v2.2.2) with parameters -jd 147 --extend 74 -m 1 -c 10000000.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using DANPOS2; scores represented nucleosome occupancy.

value: heart

value: isolated adult ventricular cardiomyocytes

tag: developmental stage

value: adult

tag: genotype

value: WT


title: SSRP1dsRNA_a_RNAseq_Rep2

description: poly-A Stranded RNA-Seq

source_name: SSRP1 dsRNA a


title: Spt16dsRNA_b_RNAseq_Rep2

description: poly-A Stranded RNA-Seq

source_name: Spt16 dsRNA b


title: MNase-seq_Het_rep1

tag: strain

tag: cell type


title: MNase-seq_CKO_rep2

value: cardiac conditional EED knockout


title: SSRP1dsRNA_a_RNAseq_Rep1

description: poly-A Stranded RNA-Seq


title: Spt16dsRNA_b_RNAseq_Rep1

description: poly-A Stranded RNA-Seq


title: MCAO ipsilateral cortex AGO CLIP, replicate 3

value: cortex - ipsilateral hemisphere


title: Spt16dsRNA_a_RNAseq_Rep2

description: poly-A Stranded RNA-Seq

source_name: Spt16 dsRNA a


title: MNase-seq_CKO_rep1


title: Hand2asD/D_rep6 8-wk

first: Xue

last: Han

address: Zhongguancun North Street

department: School of Medicine

data_processing:
Basecalls performed using CASAVA
All RNA-Seq data were mapped to the mouse reference genome (mm9) using TopHat (version 2.0.11). For samples E11.5 hearts and E16.5 ventricles of Hand2asF, reads were assigned to their transcribed strand (Tophat parameter “--library-type=fr-firststrand”).
FPKM was calculated by Cufflink version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for control (heterozygous or wildtype) and homozygous Hand2as KO mice heart tissues

source_name: 8-wk cardiomyocytes

growth_protocol: All animal experiments were conducted in accordance of institutional guidelines for animal welfare and approved by the Institutional Animal Care and Use Committee (IACUC) at Tsinghua University.

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: 8 weeks


title: Hand2asD/D_rep4 8-wk


title: Hand2asD/D_rep5 8-wk


title: Spt16dsRNA_a_RNAseq_Rep1

description: poly-A Stranded RNA-Seq


title: eGFPdsRNA_RNAseq_Rep1

description: poly-A Stranded RNA-Seq

source_name: eGFP (non-targeting control)

value: eGFP (non-targeting control)


title: Hand2asD/D_rep3 8-wk


title: Hand2asD/D_rep2 8-wk


title: Hand2asD/D_rep1 8-wk