title: spp1 knockout galactose 60 mins

value: BY4741 RPB3-3xFLAG spp1{delta}

value: RPB3-3xFLAG-HisMX6, spp1::KanMX6


title: Liver_Male_Age_83

status: Public on Jul 04 2019

type: RNA

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

country: USA

institute: US-EPA

description: Gene expression data

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven

scan_protocol: Arrays were scanned on an Affymetrix GeneChip® scanner.

data_processing: Microarray data analysis was performed using Rosetta Resolver®

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Affymetrix recommended protocol using Affymetrix Human Genome U133 Plus 2.0 GeneChips®

extract_protocol: Total RNA was isolated from human livers according to the TriReagent procedure

treatment_protocol: Human livers, male and female, approximately 21-45 years old and 69+ years old, were obtained frozen from CellzDirect (Durham, NC).

tag: gender

value: Male

tag: age

value: old


title: Testis, 3/6328   cre+   lox/lox

type: SRA

city: Turku

first: Emmi

last: Rotgers

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA12

library_source: transcriptomic

data_processing:
The 44 libraries were pooled into a single pool
The samples were sequenced in a single run with Illumina MiSeq instrument using v2 sequencing chemistry.
Single-read sequencing with 1 x 50 bp read length was used, followed by 6 bp + 8 bp dual index run.
Technical quality of the MiSeq run was good and the cluster amount was as expected. Greater than 90% of all bases above Q30 was requested.
The results were submitted to the Illumina BaseSpace data-management and analysis interphase.
The TruSeq Targeted RNA sequencing application v1.0 was used to analyze differential expression of the transcripts in the experimental groups. Briefly, the depth of sequencing between samples was estimated and the expression level for each replicate were normalized based on the total number of aligned reads. The normalized transcript abundance was modeled by a negative binomial distribution model and this model was used to derive a p-value for the differential expression of each transcript. Finally, the application corrected for multiple hypothesis testing by adjusting the p-value for false discovery rate (FDR) by using the Benjamini-Hochberg method.
Genome_build: Hprt, Rpl19 and Ppia were used as reference genes for normalization during the analysis.
Supplementary_files_format_and_content: The TruSeq Targeted RNA sequencing application v1.0 was used to analyze differential expression of the transcripts in the experimental groups.

organism: Mus musculus

source_name: testis

extract_protocol:
Testes were removed, flash frozen on dry ice and total RNA was isolated from P10 (control only) and adult mouse testis (n=4-5/group) using the RNeasy Mini kit (cat. # 74104, Qiagen). Subsequently, the obtained total RNA was treated with RNase-free DNase (cat. # 79254, Qiagen) and purified using the RNeasy MinElute Clean-up kit (cat. # 74204, Qiagen). RNA quality and concentration were determined using Nanodrop.
The library preparation and sequencing were performed at the FFGC (Finnish Functional Genomics Centre, Turku, Finland). Prior to the library preparation the quality of the total RNA samples was ensured using Agilent Bioanalyzer 2100 and Advanced Analytical Fragment Analyzer. Total RNA samples were pure, intact and all samples had similar quality. Bioanalyzer RIN values were > 9.0. Fifty ng of RNA was taken for the library preparation. Library preparation was done according to Illumina TruSeq® Targeted RNA Expression Guide (part # 15034665).

tag: strain

tag: genotype

tag: tissue

value: testis


title: H3K36me3 20mins after rapamycin Input

city: Oxford

first: Jane

last: Mellor

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Reads were aligned to the S cerevisiae genome (build sacCer3) using bowtie2 with standard parameters. Prior to this, reads were first aligned to S. Pombe 2007 build (ASM294v2) to determine normalisation factors, and these aligned reads removed from subsequent analysis.
File type conversion from .sam to .bam, filtering of low quality reads, sorting, and other formattting were performed with Samtools. Genome wide coverage files were generatived with bedtools.
Data-sets were normalised according to total S pombe read counts, and read counts determined at individual S cerevisiae genes using codes written in MATLAB.
Genome_build: sacCer3
Supplementary_files_format_and_content: Excel file contains spike-in normalised H3K4me3 and H3K36me3 levels at 5,222 S cerevisiare genes in a window between the TSS and a point 300bp downstream, approximately corresponding to positions of +1 and +2 nucleosomes.

molecule: genomic DNA

organism: Saccharomyces cerevisiae BY4741

source_name: Log-phase budding yeast

growth_protocol: Cells were grown in 25 mL YPD (1% yeast extract (Difco), 1% bactopeptone, 2% glucose) overnight. This was used to inoculate 1 L of YPD in a 2 L flask to give a starting OD600 of 0.2. 2 L of cells were grown (30°C, 170 rpm) to OD600 of 0.65 (mid-log) .

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 10 uL of anti-H3K4me3 (Millipore, 05-745R) or anti-H3K36me3 (abcam, ab9050) were used for precipitation
500 ng of RNA was used for library preparation with the Lexogen 3’ end RNA-seq library prep kit.

treatment_protocol: Before DNA purification, 25 % S. pombe cells were added (vol. at OD 0.6) as a spike-in control. . Rapamycin was added to a final concentration of 1 ug/mL and samples for RNA-seq were taken at indicated timepoints.

value: BY4741 Anchor-Away

value: MATa; his3D1; leu2D0; ura3D0; tor1D1; fpr1D; RPL13-2xFKBP12-NATMX6.

value: Log-phase budding yeast


title: hNCCs-DMSO-rep3

city: Stanford

first: Margot

middle: Elizabeth

last: Bowen

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Reads were aligned to the genome using HISAT2 version 2.0.4
The number of reads mapping to each gene in the Ensembl database was counted using HTSeq-count version 0.6.1
Differential gene expression analysis was performed using DESeq2 version 1.14.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Bowen_hNCCs_hSMCs_counts.txt: file containing the number of reads in each library that mapped to each gene in the Ensembl database
Supplementary_files_format_and_content: Bowen_Deseq2_NCCNutlin_NCCDMSO.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing Nutlin3a-treated hNCCs (n=3) to DMSO-treated hNCCs (n=3)
Supplementary_files_format_and_content: Bowen_Deseq2_SMCNutlin_SMCDMSO.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing Nutlin3a-treated hSMCs (n=3) to DMSO-treated hSMCs (n=3)
Supplementary_files_format_and_content: Bowen_Deseq2_SMC_NCC.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing DMSO-treated hSMCs (n=3) to DMSO-treated hNCCs (n=3)

molecule: polyA RNA

source_name: neural crest cells, generated from H9 human embryonic stem cells

growth_protocol: H9 human embryonic stem cell colonies were detached using collagenase (2mg/ml, diluted in KnockOut DMEM) and clusters of 100-200 cells were plated in cranial neural crest cell (CNCC) differentiation medium (1:1 Neurobasal medium and D-MEM F-12 medium [Invitrogen]) supplemented with 0.5x B-27 supplement with Vitamin A (50x stock, Gemini Bio-Products), 0.5x N-2 supplement (100x stock, Gemini Bio-Products), 0.5x Glutamax-I supplement (100x stock, ThermoFisher), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich) and 5 μg/ml bovine insulin (Sigma-Aldrich)) to form neuroepithelial spheres. After seven days of differentiation, neuroepithelial spheres attached to the dish and migratory CNCCs began to form at the periphery of the spheres. After a further 3-4 days of differentiation, cells were passaged using Accutase onto fibronectin-coated plates in CNCC early maintenance media (1:1 Neurobasal medium and D-MEM F-12 medium (Invitrogen) supplemented with 0.5x B-27 supplement with Vitamin A (50x stock, Gemini Bio-Products ##400-160), 0.5x N-2 supplement (100x stock, Gemini Bio-Products #400-163), 0.5x Glutamax-I supplement (100x stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich) and 1 mg/ml bovine serum albumin (serum replacement grade, Gemini Bio-Products #700-104P)). After 1-2 passages, CNCCs were transitioned into long term maintenance media (CNCC early maintenance media supplemented with 3µM ChIRON 99021 (Selleck, CHIR-99021) and 50pg/ml BMP2 (Peprotech)). After 4 passages, CNCCs were either maintained in long term maintenance media for an additional 2 days, or were differentiated towards the smooth muscle cell lineage for 2 days in DMEM (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Omega).

extract_protocol:
RNA was extracted using Trizol
RNA-seq libraries were prepared for Illumina sequencing by Novogene Corporation

treatment_protocol: Cells were treated with 10 µM Nutlin-3a (Millipore Sigma) or 0.001% DMSO (vehicle control) and harvested after 8 hours for RNA-seq

tag: treatment

value: DMSO


title: Liver_Male_Age_73

description: Gene expression data

growth_protocol: Human livers, male and female, approximately 21-45 years old and 69+ years old


title: Liver_Male_Age_76

description: Gene expression data


title: H3K36me3 20mins after rapamycin IP


title: Testis, 1/6386  cre+   lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA10


title: H3K36me3 0mins after rapamycin Input


title: Testis, 10/6264  cre+  lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA11


title: hNCCs-Nutlin3a-rep2


title: hSMCs-Nutlin3a-rep2

source_name: early-stage smooth muscle cells, generated from H9 human embryonic stem cells


title: Testis, 4/6336  cre+    lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA09


title: H3K36me3 0mins after rapamycin IP


title: hSMCs-DMSO-rep2


title: Testis, 3/6156 cre+  lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA08


title: Liver_Male_Age_70

description: Gene expression data


title: hSMCs-Nutlin3a-rep1


title: hNCCs-DMSO-rep2


title: Liver_Male_Age_61

description: Gene expression data


title: spp1 knockout 2nd repeat 120 minutes after rapamycin

data_processing:
Reads were aligned to the S cerevisiae genome (build sacCer3) using bowtie2 with standard parameters. Prior to this, reads were first aligned to S. Pombe 2007 build (ASM294v2) to determine normalisation factors, and these aligned reads removed from subsequent analysis.
File type conversion from .sam to .bam, filtering of low quality reads, sorting, and other formattting were performed with Samtools. Genome wide coverage files were generatived with bedtools.
Data-sets were normalised according to total S pombe read counts, and read counts determined at individual S cerevisiae genes using codes written in MATLAB.
Genome_build: sacCer3
Supplementary_files_format_and_content: Excel file contains RNA transcript levels at 5,222 S cerevisiare genes in a window between the Poly(A) site  and a point 300bp upstream.

extract_protocol:
Pelleted cells were resuspended in TES (10 mM Tris pH 7.5, 10 mM EDTA pH 8, 0.5 % SDS). RNA was then extracted with phenol:chloroform followed by ethanol precipitation.
500 ng of RNA was used for library preparation with the Lexogen 3’ end RNA-seq library prep kit.

treatment_protocol: Before RNA purification, 25 % S. pombe cells were added (vol. at OD 0.6) as a spike-in control. . Rapamycin was added to a final concentration of 1 ug/mL and samples for RNA-seq were taken at indicated timepoints.

value: MATa; his3D1; leu2D0; ura3D0; tor1D1; fpr1D; RPL13-2xFKBP12-NATMX6; spp1D::KanMX6.


title: spp1 knockout 1st repeat 120 minutes after rapamycin


title: Testis, 13/6092 cre+  lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA07


title: Liver_Female_Age_24

description: Gene expression data

value: Female

value: young


title: hNCCs-Nutlin3a-rep1


title: Testis, b. 24.8. 5.

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA05

value: WT


title: Liver_Female_Age_33

description: Gene expression data


title: spp1 knockout 2nd repeat 90 minutes after rapamycin


title: Liver_Male_Age_69

description: Gene expression data


title: Liver_Female_Age_37

description: Gene expression data


title: Testis, b. 8.9. 3.

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA04


title: hNCCs-DMSO-rep1


title: spp1 knockout 1st repeat 60 minutes after rapamycin


title: hSMCs-DMSO-rep1


title: Liver_Female_Age_34

description: Gene expression data


title: Testis, b. 6.10. 2

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA03


title: spp1 knockout 2nd repeat 60 minutes after rapamycin


title: spp1 knockout 2nd repeat 40 minutes after rapamycin


title: Testis, b. 6.10 3.

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA02


title: Testis, 3/6087 cre+  lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA06


title: Testis, b.24.8 6.

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA01


title: spp1 knockout 1st repeat 90 minutes after rapamycin


title: Liver_Female_Age_72

description: Gene expression data


title: AIV-infected LMH sample 1 at 12 hpi

city: Guangzhou

first: Min

last: Feng

address: wushan road

country: China

institute: South China Agricultural University

data_processing:
Sequenced reads were filtered by fastp (v0.18.0) with parameters -q 20 -u 50 -n 15 -l 50.
Mapped to GCF_000002315.5 by HISAT2 (v2.1.0) after removal of gallus rRNA sequences
Reconstructed transcripts by Stringtie, and calculated FPKM(Fragments Per Kilobase of transcript per Million mapped reads)
Genome_build: GCF_000002315.5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Gallus gallus

source_name: AIV-infected LMH at 12 hpi

growth_protocol: DF1 and LMH cells were respectively grown in Dulbecco’s modified Eagle’s medium (DMEM) or DMEM Nutrient Mixture F-12(DMEM/F-12) (Gibco) supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) at 37°C and 5% CO2.

extract_protocol:
Total RNA were respectively extracted from DF1 or LMH cells infected with HN strain at 6 h. p. i and 12 h. p. i using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. For every time point, each sample was collected in duplication. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
Illumina HiSeq 4000 (generating 150 bp paired-end reads)

treatment_protocol: H9N2 AIV infection experiments were performed on the monolayers of DF1 or LMH cells in 6-well plates. 1×106 cells per well were infected with H9N2 subtype HN strain at 0.1 MOI. The medium for cultivation of H9N2 virus contained 0.25 μg / mL TPCK-trypsin. Culture supernatants were collected at 6, and 12 hours post infection (h. p. i), respectively. After centrifugation at 2000 rpm for 10 min to remove cellular debris, samples were further analyzed for the virus titer determined by a hemagglutination (HA) assay.

tag: cell line

value: LMH

tag: infection

value: H9N2 subtype HN strain

tag: time point

value: 12 hpi


title: AIV-infected LMH sample 2 at 6 hpi

source_name: AIV-infected LMH at 6 hpi

value: 6 hpi


title: Liver_Female_Age_84

description: Gene expression data


title: Liver_Female_Age_36

description: Gene expression data


title: Liver_Female_Age_86

description: Gene expression data


title: AIV-infected LMH sample 1 at 6 hpi


title: Liver_Female_Age_71

description: Gene expression data


title: spp1 knockout 2nd repeat 20 minutes after rapamycin

value: BY4741 RPB3-3xFLAG spp1{delta}


title: spp1 knockout 1st repeat 20 minutes after rapamycin


title: Normal LMH sample 2

source_name: Normal LMH

value: none (control)


title: FUL TFUL2-rep1

city: Haifa

first: Eliezer

last: Lifschitz

address: Technion City

department: Faculty of Biology

country: Israel

institute: Technion

data_processing:
Library quality control was conducted using FASTQC, version 0.11.5
Sequences were trimmed by quality using trim galore
Sequences were aligned  using Tophat2, version 2.1.0 (uses Bowtie2 version 2.2.6).
Raw gene expression levels were counted by HTseq-count, version 0.6.1
Genome_build: ITAG version 2.5 genome (ftp://ftp.sgn.cornell.edu/genomes/Solanum_lycopersicum/annotation/ITAG2.5_release),
Supplementary_files_format_and_content: counts

organism: Solanum lycopersicum

source_name: stem

extract_protocol:
Five, seemingly homogeneous plants were selected from a larger population to represent the natural variation among greenhouse tomato plants. Independent stem samples consisted of 5 mid-segments of internodes harvested in duplicates 2 h after dawn. Total RNA was extracted using the RNeasy Mini Kit (Qiagen), and treated with DNase I using the RNase-Free DNase set (Qiagen)
RNA samples were processed for sequencing, quality control, and differential expression analysis at the Technion Genome Center. Libraries of single 50 bp reads were prepared using the Ilumina TruSeq RNA library preparation kit v2. The barcoded libraries were sequenced on Ilumina Hiseq 2500, six samples per lane (~30,000,000 reads). If an experiment included more than 6 samples, each sample was divided equally, in all the lanes.

tag: experiment

value: FUL

tag: genotype/variation


title: Normal LMH sample 1


title: spp1 knockout 1st repeat 40 minutes after rapamycin


title: spp1 knockout 2nd repeat 0 minutes after rapamycin


title: AIV-infected DF1 sample 2 at 12 hpi

source_name: AIV-infected DF1 at 12 hpi


title: FUL SFT-rep2


title: FUL SFT-rep1


title: spp1 knockout 1st repeat 0 minutes after rapamycin


title: FUL TFUL2-rep2


title: FUL WT-rep2


title: wild-type 2nd repeat 120 minutes after rapamycin


title: FUL WT-rep1


title: Cre Eed rep3

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v02.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the formula = 10^6*C / (NL/10^3).
Genome_build: mm8

source_name: calvaria

growth_protocol: Bone chips were incubated in Collagenase II overnight, after which the collagenase was spun out and replaced with alpha-MEM until cells reached 80% confluency.

extract_protocol:
Cell media replaced with Trizol reagent to extract total RNA. Agilent RNA 6000 Nano Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: Control cells were incubated with Adenovirus-YFP for three days; treated cells were incubated with Adenovirus-Cre.

value: bone

value: post natal day 10

value: Eedfl/fl


title: Cre Eed rep2

source_name: Calvaria


title: AIV-infected DF1 sample 2 at 6 hpi

source_name: AIV-infected DF1 at 6 hpi


title: wild-type 1st repeat 120 minutes after rapamycin

value: BY4741 Anchor-Away

value: MATa; his3D1; leu2D0; ura3D0; tor1D1; fpr1D; RPL13-2xFKBP12-NATMX6.


title: AIV-infected DF1 sample 1 at 12 hpi


title: HUVEC from batch 1 overexpressing P2Y2

city: Vienna

first: Wolfgang

last: Holnthoner

address: Donaueschingenstrasse 13

department: Ludwig Boltzmann Institute for Experimental and Clinical Traumatology

country: Austria

institute: Austrian Cluster for Tissue Regeneration

description: Gene array data from HUVEC that were retrovirally infected with cDNA for P2Y2-YFP

hyb_protocol: Purified and fragmented cRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 arrays following the manufacturer’s recommendations.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: CEL files were summarized in the Affymetrix Console Software (version 1.4.1.46) using the Robust Multi-array Average (RMA) normalization algorithm (3’ Expression Arrays: RMA, log2).

source_name: HUVEC passage 6 overexpressing P2Y2-YFP, batch 1

label_protocol: Biotinylated cRNA were prepared using the GeneChip HT 3' IVT Express Kit from 2µg total RNA.

growth_protocol: Cells wer routinely cultured in EGM-2 (Lonza)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were retrovirally infected with different plasmids as indicated, expanded and grown to confluency before RNA isolation

tag: cell type

value: HUVEC

value: overexpressing purinergic receptor P2Y2


title: Ginkgo GinFT-rep2

value: Ginkgo


title: HUVEC from batch 1 overexpressing YFP

description: Gene array data from HUVEC that were retrovirally infected with cDNA for YFP

source_name: HUVEC passage 6 overexpressing YFP, batch 1

value: control


title: HUVEC from batch 2 overexpressing P2Y2

source_name: HUVEC passage 6 overexpressing P2Y2-YFP, batch 2


title: wild-type 2nd repeat 90 minutes after rapamycin

value: Log-phase budding yeast


title: Cre Eed rep1


title: AIV-infected DF1 sample 1 at 6 hpi


title: Ginkgo GinFT-rep1


title: Normal DF1 sample 2

source_name: Normal DF1


title: Heat Shock noFT_noHS-rep2

value: Heat Shock

value: Untreated sft


title: DCMA3

city: Calgary

first: Steven

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw FASTQ files were generated using Illumina NextSeq Control software (version 2.02). For RNA-Seq analysis, initial sequencing quality was inspected using FASTQC. Next,transcript counts were estimated using kallisto with human reference transcriptome built from refseq database using linux command ;wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.*.rna.fna.gz;
Quantification of raw transcript counts for each dataset by using following command:    kallisto --single -l 180 -s 20 ; pachterlab.github.io/kallisto/
Expression testing:  Differential gene expression from the kallisto counts data was performed using the Bioconductor package DESeq2. Read counts for control and patient fibroblasts were compared to determine the log2-fold change in abundance for each transcript. Raw p-values were adjusted for multiple comparisons with the Benjamini-Hochberg method
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: DCMA_dermal fibroblasts

extract_protocol:
Total RNA was extracted from DCMA fibroblasts (n=4) and control fibroblasts (n=4) using the RNA extraction Mini kit (Invitrogen) according to the manufacturer’s protocol. RNA purity was assessed and quantified using Nanodrop and a Qubit 2.0 fluorometer (ThermoFisher Scientific). The sequencing library was prepared using 2 μg of RNA and the TruSeq Stranded mRNA library preparation kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: pediatric patient with dilated cardiomyopathy with ataxia syndrome (DCMA)

value: dermal fibroblasts

tag: passages


title: Testis, 30/7007 cre+   E2F3 wt/wt Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA29

source_name: testis

value: mix:B6, C57BL/6, FVB

value: SCRbKO

value: testis


title: YFP Eed rep2

value: bone


title: AIV-infected LMH sample 2 at 12 hpi

value: LMH

value: H9N2 subtype HN strain

value: 12 hpi


title: YFP Eed rep3

value: post natal day 10

value: Eedfl/fl


title: wild-type 2nd repeat 60 minutes after rapamycin

source_name: Log-phase budding yeast

value: BY4741 Anchor-Away

value: MATa; his3D1; leu2D0; ura3D0; tor1D1; fpr1D; RPL13-2xFKBP12-NATMX6.


title: Normal DF1 sample 1

value: none (control)


title: Heat Shock noFT_noHS-rep1


title: wild-type 1st repeat 60 minutes after rapamycin

value: Log-phase budding yeast


title: YFP Eed rep1


title: HUVEC from batch 2 overexpressing YFP

source_name: HUVEC passage 6 overexpressing YFP, batch 2

value: HUVEC

value: control


title: H47_GO

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4)
Reads were mapped to the reference genome (Oar_v3.1) using the software package Tophat2 (version: 2.1.1).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.2.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.2.1) was used for merging together each of the assemblies with the reference sheep annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Sheep genome assembly: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Ovis aries

source_name: Testicle

extract_protocol:
RNA extraction was performed using Trizol® reagent, and quality of the obtained RNA was determined using a nanodrop spectrophotometer (OD260/OD280) to determine purity, as well as an agarose gel electrophoresis to observe potential RNA degradation and contamination. The RNA integrity was assessed using an Agilent Bioanalyzer, with RNA integrity number (RIN) values between 8 and 10.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with Illumina’s HiSeq 3000.

value: Testicle

value: 60 days

tag: breed

value: Santa Ines

value: Maternal Gossypol-rich (Cottonseed) Diet


title: Heat Shock noFT_Hsrep-2

value: Heat Shock

value: Treated sft


title: wild-type 2nd repeat 40 minutes after rapamycin


title: H44_CT

value: Maternal Control Diet


title: Cre rep2

data_processing:
BGISEQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v02.2.5 with parameters -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: Excel, gene expression

growth_protocol: Calvarial bone chips were sterilically isolated, incubated in DMEM containing 10% fetal bovine serum, antibiotics, and 0.02% collagenase II overnight.  Collagenase was then removed, and culture medium was replaced with alpha-MEM containing 10% fetal bovine serum and antibiotics .  Cells were then split, and grown until cells reached 80% confluency.  Then cells were infected with adenovirus expressing Cre or YFP.  Adenovirus concentration was empirically dtermied to achieve >80% infection efficincy.  RNA was extracted 3 days after the viral infection.

extract_protocol:
Trizol reagent to extract total RNA followed by Zymo spin column purification.
mRNA was enriched by polyA selection.  Agilent RNA 6000 Nano Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 protocols (perfomed by BGI)  Single-end 30 million reads.

treatment_protocol: Cells were cultured for three days after a singe dose of adenovirus treatment.  Amounts of adenovirus was empirically determined to achieve >80% infection efficiency.

value: bone


title: Heat Shock noFT_HS-rep1


title: wild-type 1st repeat 40 minutes after rapamycin


title: H41_GO


title: Cre rep1


title: Heat Shock FT_noHS-rep2

value: Untreated sft pHS:FT


title: wild-type 2nd repeat 20 minutes after rapamycin


title: wild-type 1st repeat 20 minutes after rapamycin


title: YFP rep1

value: post natal day 10


title: wild-type 2nd repeat 0 minutes after rapamycin


title: Heat Shock FT_HS-rep2

value: Treated sft pHS:FT


title: H35_GO


title: wild-type 1st repeat 0 minutes after rapamycin

value: BY4741 Anchor-Away


title: Temporal lobe cortex, HI hMeDIP 3

city: Shanghai

first: Yunpeng

last: Zhang

address: Longhang Road 1508 Jinshan distinct

department: jinshan hospital

institute: Fudan university

data_processing:
Library strategy: hMeDIP-Seq
FASTQ sequence files obtained were aligned to the reference genome of rats in UCSC databank (RGSC6.0/rn6) using Bowtie
Only unique non-duplicate reads were used for peak calling and annotation by HOMER (hypergeometric optimization of motif enrichment) software
DhMRs between control and HI rats were determined by comparing 5hmC peak levels by Model-based Analysis of ChIP-Seq (MACS) software
Genome_build: rn6
Supplementary_files_format_and_content: .bw

organism: Rattus norvegicus

source_name: temporal lobe cortex

extract_protocol:
Brains were removed,and genomic DNA was isolated from the temporal cortex and immunoprecipitated by using an anti-5hmC antibody (Active Motif, United States, Cat. No. 39769).
Genomic DNA was sonicated and sequenced using the Illumina Hiseq2000 and Nextseq system (Illumina, United States) in accordance with the manufacturer’s instructions.

tag: disease state

value: hypoxic-ischemic neonatal model of cerebral palsy

value: SD

value: temporal lobe cortex

value: postnatal day 31

tag: antibody

value: anti-5hmC antibody (Active Motif, Cat. No. 39769)


title: H37_CT

value: Testicle


title: H32_CT

value: 60 days


title: Graft wt//SFT-rep2

value: Graft


title: Temporal lobe cortex, HI hMeDIP 2


title: Heat Shock FT_HS-rep1


title: spp1 H3K4me3

data_processing:
Reads were aligned to the S cerevisiae genome (build sacCer3) using bowtie2 with standard parameters. Prior to this, reads were first aligned to S. Pombe 2007 build (ASM294v2) to determine normalisation factors, and these aligned reads removed from subsequent analysis.
File type conversion from .sam to .bam, filtering of low quality reads, sorting, and other formattting were performed with Samtools. Genome wide coverage files were generatived with bedtools.
Data-sets were normalised according to total S pombe read counts, and read counts determined at individual S cerevisiae genes using codes written in MATLAB.
Genome_build: sacCer3
Supplementary_files_format_and_content: Excel file contains spike-in normalised H3K4me3 levels at 5,222 S cerevisiare genes at region 300bp downstream of TSS, approximately corresponding to positions of +1 and +2 nucleosomes.

growth_protocol: Yeast grown to OD 0.6 in YPD (10 g/l Difco yeast extract, 10 g/l Bacto peptone, 10 g/l glucose)

extract_protocol:
Lysates were clarified from MNase-treated nuclei and histone-DNA complexes were isolated with antibody. 25% (vol. at OD 0.6) S.pombe cells were added as a spike-in control. 10 uL of anti-H3K4me3 (Millipore, 05-745R) were used for precipitation
Libraries were prepared using the NEBNext Ultra II DNA Library Kit (NEB) and sequenced on an Illumina Nextseq 500 platform

value: Log-phase budding yeast


title: Temporal lobe cortex, HI hMeDIP 1


title: Graft sp//SFT-rep2


title: spp1 knockout


title: YFP rep2


title: H29_CT

value: Santa Ines


title: Temporal lobe cortex, Control hMeDIP 3

value: control


title: wild-type H3K4me3

value: MATa; his3{delta}1; leu2{delta}0; ura3{delta}0


title: Temporal lobe cortex, Control hMeDIP 2


title: H31_CT

value: Maternal Control Diet


title: Heat Shock FT_noHS-rep1

value: Heat Shock

value: Untreated sft pHS:FT


title: H25_GO

value: Maternal Gossypol-rich (Cottonseed) Diet


title: H39_CT


title: Graft sft//wt-rep2

value: sft//sft


title: wild-type input


title: H22_CT


title: Graft sft//SFT-rep2


title: Temporal lobe cortex, Control hMeDIP 1


title: 5-HT and fluoxetine treated 3

city: Los Angeles

first: Thomas

middle: C

last: Fung

address: 610 Charles E Young Dr. East

institute: University of California, Los Angeles

description: 5ht flx 3

data_processing:
Read alignment, transcript quantification and differential gene expression were performed with Rockhopper software
Genome_build: Turicibacter sanguinis PC909 genome (GCF_000178255.1)
Supplementary_files_format_and_content: "Turicibacter RNAseq transcript list" is an Excel file listing all mapped transcripts with gene descriptions, transcript abundance and statistics for differential expression between groups

organism: Turicibacter sanguinis

source_name: bacteria

growth_protocol: Turicibacter sanguinis MOL361 was grown in Schaedler broth for approximately 16 hours at 37C under anaerobic conditions

extract_protocol:
Cells was were washed with PBS, lysed in TE containing triton and lysozyme, and total RNA was extracted with the RNAeasy Mini Kit with double DNAse digestion
rRNA was removed using the RiboZero Gram Positive Bacteria Kit (Illumina) and library preparation was performed using the TruSeq Stranded RNA kit (Illumina)

treatment_protocol: Bacterial cultures were treated with vehicle, 5-HT (200 uM), fluoxetine (200 uM) or 5-HT plus fluoxetine for 4 hours at 37C under anaerobic conditions

value: 5-HT and fluoxetine treated


title: H20_CT


title: neonatal_rat_cardiomyocyte_yap siRNA_3

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Primary sequencing data was conducted with a BGISEQ-500 50SE at 20M reads per sample.
Raw reads are subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which are aligned to the reference sequences.
"Dirty" raw reads are reads which contain the sequence of adaptor, high content of unknown bases and low quality reads, and are removed before analysis.
Bowtie2 was used to map clean reads to reference gene, and HISAT used to reference genome.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM)  method is used to calculated expression level.
Genome_build: rn6
Supplementary_files_format_and_content: Excel files containing FPKM values for expression levels.

source_name: neonatal rat, cardiomyocyte, yap siRNA, replicate 3

growth_protocol: Cardiomyocytes were incubated in DMEM supplemented with 15% FBS and penicillin-streptomycin.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific) phenol cholorform extraction.
RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low-input poly-A BGISEQ-500RSRNASeq(Transcriptome) protocol.

treatment_protocol: After 16 hours, the cells were transfected using mission siRNA transfection reagent (Sigma) with two different siRNAs each at a concentration of 25 nM designed against the target gene of interest. Forty-eight hours post transfection cells were collected in Trizol for RNA extraction.

value: Sprague Dawley

value: cardiomyocyte

tag: sirna treatment

value: yap siRNA


title: neonatal_rat_cardiomyocyte_yap siRNA_2

source_name: neonatal rat, cardiomyocyte, yap siRNA, replicate 2


title: 5-HT and fluoxetine treated 2

description: 5ht flx 2


title: 5-HT and fluoxetine treated 1

description: 5ht flx 1


title: neonatal_rat_cardiomyocyte_yap siRNA_1

source_name: neonatal rat, cardiomyocyte, yap siRNA, replicate 1


title: Graft sp//SFT-rep1

source_name: stem


title: H10_GO

tag: age


title: Graft wt//SFT-rep1


title: Graft wt//wt-rep2

value: WT//WT


title: H48_GO

value: Testicle


title: Graft sft//wt-rep1


title: H12_GO

value: 60 days


title: Graft sft//SFT-rep1

value: Graft


title: neonatal_rat_cardiomyocyte_negative control_2

source_name: neonatal rat, cardiomyocyte, negative siRNA, replicate 2

tag: strain

value: negative siRNA


title: neonatal_rat_cardiomyocyte_negative control_3

source_name: neonatal rat, cardiomyocyte, negative siRNA, replicate 3


title: fluoxetine treated 2

description: flx 2

value: fluoxetine treated


title: Graft wt//wt-rep1


title: wild-type 1st repeat 90 minutes after rapamycin

value: BY4741 Anchor-Away

tag: genotype

value: MATa; his3D1; leu2D0; ura3D0; tor1D1; fpr1D; RPL13-2xFKBP12-NATMX6.

value: Log-phase budding yeast


title: H08_GO

tag: tissue

value: Santa Ines


title: neonatal_rat_cardiomyocyte_negative control_1

source_name: neonatal rat, cardiomyocyte, negative siRNA, replicate 1


title: H06_CT

tag: treatment

value: Maternal Control Diet


title: H01_GO

value: Maternal Gossypol-rich (Cottonseed) Diet


title: SFT Over Expression sft-rep2

value: SFT Over Expression

value: SFT


title: neonatal_rat_cardiomyocyte_llgl1.2_3

source_name: neonatal rat, cardiomyocyte, llgl1 and llgl2 siRNA, replicate 3

value: Sprague Dawley

value: llgl1 and llgl2 siRNA


title: 5-HT treated 3

description: 5ht 3

value: 5-HT treated


title: fluoxetine treated 1

description: flx 1


title: SFT Over Expression WT-rep2

value: WT


title: neonatal_rat_cardiomyocyte_llgl1.2_2

source_name: neonatal rat, cardiomyocyte, llgl1 and llgl2 siRNA, replicate 2

value: cardiomyocyte


title: 5-HT treated 2

description: 5ht 2


title: 2LP

city: Southport

first: Greg

last: Tram

state: Queensland

address: Parklands Drive

department: Institute for Glycomics

country: Australia

institute: Griffith University

description: C. jejuni_processed_data_files.xls

data_processing:
Raw reads were trimmed of Illumina TruSeq sequencing adapters, filtered for an average Phred Q score minimum of >30 and minimum read length of 32nt after trimming. Reads were further processed by trimming 3’ ends of bases with <30 Q scores.
Processed output files were aligned to the C. jejuni NCTC 11168 genome using Bowtie2 (v2.2.5).
Output .sam files were converted to .bam format using Samtools (v0.1.19), and name-sorted prior to input into HTSeq (v0.6.1). HTSeq counting was performed in union mode.
Differential gene expression analysis was performed using edgeR and R package.
Genome_build: GCA_000009085.1
Supplementary_files_format_and_content: The .xls file contains raw counts from HTSeq showing the abundance of each genomic feature across the samples.

organism: Campylobacter jejuni

source_name: Planktonic cell extract

growth_protocol: Planktonic cultures (LP) of C. jejuni strains were grown from an overnight plate culture, which was used to inoculate 250 mL of heart infusion broth. These cultures were incubated under microaerobic conditions at 42°C and 120 x rpm for 12 hrs. Biofilm samples (BF) were grown from overnight culture of C. jejuni which was diluted to an OD600 of 0.75 in mueller hinton broth. 10 mL of the cell suspension was then inoculated into glass petri dishes and incubated aerobically at 42°C for 48 hours. Samples were then harvested in 4 M guanidine thiocyanate in a 1% sodium lauryl sarcosine solution.

extract_protocol:
Samples were carefully laid over a 3.5 mL cushion of 5.7 M cesium chloride in 0.1 M EDTA in an OptiSeal polypropylene centrifuge tube with the remaining volume of the tube being filled with RNAse water. Samples were centrifuged at 27,000 x rpm for 16 hrs at 4°C in an Optima L-100 XP ultracentrifuge using a SW32Ti rotor. Following centrifugation, the upper phase was removed and the tubes were cut before being allowed to completely drain. The RNA pellet was washed in 100 µL 70% ethanol before being resuspended in 120 µL tris EDTA (TE) / sodium dodecyl sulfate (SDS) with 80 µL of TE being used to dissolve remaining RNA. 650 µL of chilled ethanol was added to resuspended samples in addition to 10 µL sodium acetate to precipitate RNA. Samples were centrifuged at 14,000 x rpm in a Microfuge 22R centrifuge for 15 mins at 4°C. The supernatant was removed and a further 650 µL of 75% ethanol was used to wash the pellet. Samples were centrifuged for a further 5 mins at 14,000 x rpm and the supernatant removed. Pellets were allowed to air dry before resuspension in RNase free water. Quality and concentration of RNA was assessed using a Nanodrop 2000.
RNA library construction was carried out using strand- specific Illumina TruSeq technology and DNA library construction was carried out using Illumina Nextera XT technology.

tag: state

value: Planktonic


title: neonatal_rat_cardiomyocyte_llgl1.2_1

source_name: neonatal rat, cardiomyocyte, llgl1 and llgl2 siRNA, replicate 1


title: fluoxetine treated 3

description: flx 3


title: SFT Over Expression sft-rep1


title: SFT Over Expression pTFT-rep2

value: pSFT-SFT


title: 5-HT treated 1

description: 5ht 1


title: 3BF

description: C. jejuni_processed_data_files.xls

source_name: Biofilm extract

value: Biofilm


title: 1LP

description: C. jejuni_processed_data_files.xls


title: 6 hpo embryos

city: Wuhan

first: Wei

last: Peng

address: Shizishan Street No. 1, Hongshan District, Wuhan,Hubei  430070, P.R. China

institute: Huazhong Agricultural University

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identied as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 20.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi).
The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12) (2) number of base pairs in the stem region of the predicted hairpin (>=16) (3) cutoff of free energy (kCal/mol <=15) (4) length of hairpin (up and down stems + terminal loop >=50) (5) length of hairpin loop (<=200). (6) number of nucleotides in one bulge in mature region (<=4) (7) number of biased errors in one bulge in mature region(<=2) (8) number of biased bulges in mature region (<=2) (9) number of errors in mature region (<=4) (10) number of base pairs in the mature region of the predicted hairpin (>=12) (11) percent of mature in stem (>=80).
Genome_build: ASM78921v1

organism: Bactrocera dorsalis

source_name: 6 post-oviposition (hpo) embryos

extract_protocol:
5, 6 and 7 post-oviposition (hpo) embryos were collected and immediately stored in RNAlater® Solution (Ambion). Total RNAs were extracted using Trizol reagent (Invitrogen, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with total RNA for the construction of sequencing libraries.
Small RNA libraries were generated from the three samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

value: embryos

value: 6 post-oviposition (hpo)


title: control 3

description: ctl 3

value: control


title: 7 hpo embryos

source_name: 7 post-oviposition (hpo) embryos

value: 7 post-oviposition (hpo)


title: 1BF

description: C. jejuni_processed_data_files.xls


title: control 2

description: ctl 2


title: control 1

description: ctl 1


title: SFT Over Expression WT-rep1


title: Human_kidney_MazF

status: Public on Jul 03 2019

first: Zhang

state: Guangdong

address: Xingangxi Roda 135#

institute: Sun Yat-sen University

data_processing:
Library strategy: Aim-seq
The raw reads were filtered adaptors by cutadapt with at least 15 bp remaining length of paired-end reads. The clean reads were mapped to the reference genome (hg19) using Hisat2.
Reads with ACA/TGT motif internal or at the end were used to identify transcriptome-wide candidate m6A sites.
The RNAfold program of ViennaRNA package was used to predict intramolecular secondary structure of each read which supported the candidate sites, and sites with the high pairing probability were discarded.
The FTO demethylation treatment was negative control. Only the sites with at least 10% methylation ratio decrease in FTO treatment were retained as m6A sites.
Genome_build: hg19,mm10,rn6
Supplementary_files_format_and_content: text format with the information of chromosome number, site loction, strand, #reads with internal ACA in MazF, #reads sum in MazF,#reads with internal ACA in FTO, #reads sum in FTO, in one or more replicates

source_name: Human kidney tissue

growth_protocol: Human HEK293T cell line was cultured with DMEM (Corning) supplemented with 10% (v/v) FBS (Gibco) at 37℃ in the presence of 5% CO2, and tested to be negative for mycoplasma contamination.

extract_protocol:
Total RNA from HEK293T cells was extracted using Trizol reagent (Thermo Fisher Scientific) and the mRNA was purified using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, Cat. No. 61006). The mRNA of human tissues (brain, liver and kidney), mouse tissues (brain, liver, heart, testis and kidney) and rat tissues (brain, liver and kidney) were purchased from Takara Bio.
mRNA samples were heated to denature and digested into fragments by MazF (Takara) at 37℃ for 30 min. The fragmented mRNA was purified and end-repaired using T4 polynucleotide kinase at 37℃ for 30 min. The sample was purified for small RNA library construction.
Parallel samples demethylated by FTO in advance were as the negative controls. The FTO treatment was in 20 ul of reaction mixture containing 100-200 ng mRNA, 2.5 ug FTO demethylase, 283 μM of (NH4)2Fe(SO4)2·6H2O, 300 μM of α-KG, 2 mM of L-ascorbic acid, 20 U RNase inhibitor and 50 mM of Tris·HCl buffer (pH 7.5). After incubating at room temperature for 3h, the reaction was stopped by adding 40 mM EDTA.
Small RNA library construction protocol

value: kidney

value: MazF


title: 2BF

description: C. jejuni_processed_data_files.xls


title: Human_kidney_FTO

value: FTO-MazF


title: Human_liver_FTO

source_name: Human liver tissue

value: liver


title: Human_brain_FTO

source_name: Human brain tissue

value: brain


title: HEK293_MazF_rep3

source_name: human HEK293 cell line

tag: cell line


title: HEK293_FTO_rep2


title: HEK293_FTO_rep3


title: HEK293_MazF_rep2


title: HEK293_FTO_rep1


title: HEK293_MazF_rep1


title: 3LP

description: C. jejuni_processed_data_files.xls


title: SFT Over Expression pTFT-rep1

value: SFT Over Expression


title: 5 hpo embryos

source_name: 5 post-oviposition (hpo) embryos

value: 5 post-oviposition (hpo)


title: RT0240

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

data_processing:
Discarded reads that do not span entire sgID-BC region
Read pairs with mismatches were discarded.
Reads with barcodes containing indels were excluded.
Read pileups were generated.
For any given pileup, smaller pileups within a distance of two bases were excluded.
Estimates of cancer cell number were determined by multiplying counts for each pileup by the cancer cell number comprised within the spike-in controls and dividing by the average number of reads for the three spike-in controls.
Genome_build: Custom Lentiviral Amplicon
Supplementary_files_format_and_content: Estimated tumor sizes.

source_name: Tumor-Bearing Lung

growth_protocol: Lung tumors were allowed to develop over the course of four months.

extract_protocol: The harvesting of genomic DNA and preparation of tumor barcode sequencing libraries were performed as described in Rogers et al. 2013 Nature Methods

value: mixed BL6/129


title: RT0252


title: RT0092


title: RT0095


title: RT0088


title: RT0253


title: RT0081


title: RT0098


title: RT0238


title: CM0904


title: Human_liver_MazF


title: CM0896


title: HC0328


title: CM0871


title: RT0254


title: Human_brain_MazF


title: HC0222


title: HC0277


title: HC0211


title: HC0318


title: HC0258


title: Liver_Female_Age_80

address: 109 TW Alexander Dr.

description: Gene expression data

data_processing: Microarray data analysis was performed using Rosetta Resolver®

extract_protocol: Total RNA was isolated from human livers according to the TriReagent procedure

tag: gender

value: Female

value: old


title: WT Tim3-_Day8_rep5

city: Freising

first: Dietmar

last: Zehn

address: Weihenstephaner Berg 3

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

description:
sample name in processed data file:
L10-D8-Tox-WT5-Tim3n_S10

data_processing:
Sequencing quality was assessed with fastqc
Filtering was performed by trimmomatic v0.36
Mapping was performed by STAR v2.5.3a with genome Mus_musculus.GRCm38
Counting by htseq v0.9.1 with annotation Mus_musculus.GRCm38.91
multiqc v1.2 was applied for supervising results from STAR and fastqc
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include raw readcount values for each Sample

source_name: WT Tim3-_Day8

extract_protocol:
RNA was extracted using the Agencourt RNAdvance Cell v2 kit (A47942, Beckman Coulter). RNA integrity number (RIN) and yield were assessed using RNA 6000 Pico Kit (5067-1513, Agilent).
cDNA synthesis and PCR amplification using 1 ng of total RNA from each sample was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634891, Takara/Clontech). After cDNA synthesis, each sample was subjected to 12 cycles of PCR amplification. The generated amplicons were assessed and their concentration was determined with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). 150 pg of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). After PCR amplification of the fragmented libraries, the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 µl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010, Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems).

value: WT

tag: cell population

tag: collection day

value: T-cells


title: WT Tim3-_Day8_rep4

description:
sample name in processed data file:
L8-D8-Tox-WT4-Tim3n_S8

tag: cell type


title: WT Tim3-_Day8_rep3

description:
sample name in processed data file:
L6-D8-Tox-WT3-Tim3n_S6


title: CM0893

first: Christopher


title: WT Tim3-_Day8_rep2

description:
sample name in processed data file:
L4-D8-Tox-WT2-Tim3n_S4


title: CM0873


title: ToxKO_Tim3- Day8_rep4

description:
sample name in processed data file:
L18-D8-Tox-KO4-Tim3n_S3

source_name: ToxKO_Tim3- Day8

value: ToxKO


title: WT Tim3-_Day8_rep1

description:
sample name in processed data file:
L2-D8-Tox-WT1-Tim3n_S2


title: WT Tim3+_Day8_rep1

description:
sample name in processed data file:
L1-D8-Tox-WT1-Tim3p_S1

source_name: WT Tim3+_Day8


title: ToxKO_Tim3+ Day8_rep4

description:
sample name in processed data file:
L17-D8-Tox-KO4-Tim3p_S2

source_name: ToxKO_Tim3+ Day8


title: ToxKO_Tim3+ Day8_rep5

description:
sample name in processed data file:
L19-D8-Tox-KO5-Tim3p_S4


title: WT Tim3+_Day8_rep3

description:
sample name in processed data file:
L5-D8-Tox-WT3-Tim3p_S5


title: ToxKO_Tim3+ Day8_rep1

description:
sample name in processed data file:
L11-D8-Tox-KO1-Tim3p_S11


title: ToxKO_Tim3- Day8_rep2

description:
sample name in processed data file:
L14-D8-Tox-KO2-Tim3n_S14


title: ToxKO_Tim3- Day8_rep5

description:
sample name in processed data file:
L20-D8-Tox-KO5-Tim3n_S5


title: WT Tim3+_Day8_rep5

description:
sample name in processed data file:
L9-D8-Tox-WT5-Tim3p_S9


title: HC0332


title: ToxKO_Tim3- Day8_rep3

description:
sample name in processed data file:
L16-D8-Tox-KO3-Tim3n_S1


title: WT_Day20_rep5

description:
sample name in processed data file:
L25-D20-Tox-WT5_S10

tag: developmental stage


title: HC0214


title: WT Tim3+_Day8_rep2

description:
sample name in processed data file:
L3-D8-Tox-WT2-Tim3p_S3


title: ToxKO_Tim3+ Day8_rep3

description:
sample name in processed data file:
L15-D8-Tox-KO3-Tim3p_S15


title: WT_Day20_rep2

description:
sample name in processed data file:
L22-D20-Tox-WT2_S7


title: WT_Day20_rep1

description:
sample name in processed data file:
L21-D20-Tox-WT1_S6


title: WT_Day20_rep3

description:
sample name in processed data file:
L23-D20-Tox-WT3_S8


title: ToxKO_Day20_rep5

description:
sample name in processed data file:
L30-D20-Tox-KO5_S15


title: ToxKO_Day20_rep4

description:
sample name in processed data file:
L29-D20-Tox-KO4_S14


title: WT Tim3+_Day8_rep4

description:
sample name in processed data file:
L7-D8-Tox-WT4-Tim3p_S7


title: ToxKO_Day20_rep2

description:
sample name in processed data file:
L27-D20-Tox-KO2_S12


title: ToxKO_Tim3- Day8_rep1

description:
sample name in processed data file:
L12-D8-Tox-KO1-Tim3n_S12


title: ToxKO_Day20_rep3

description:
sample name in processed data file:
L28-D20-Tox-KO3_S13


title: ToxKO_Tim3+ Day8_rep2

description:
sample name in processed data file:
L13-D8-Tox-KO2-Tim3p_S13


title: ToxKO_Day20_rep1

description:
sample name in processed data file:
L26-D20-Tox-KO1_S11


title: WT_Day8_rep2

description:
name in processed data file:
L23-Seq29-FA-12-WT-I

data_processing:
Sequencing quality was assessed with fastqc
Filtering was performed by trimmomatic v0.36
Mapping was performed by STAR v2.5.3a with genome Mus_musculus.GRCm38
Counting by htseq v0.9.1 with annotation Mus_musculus.GRCm38.91
multiqc v1.2 was applied for supervising results from STAR and fastqc
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include raw and normalized readcount values for each Sample


title: WT_Day8_rep5

description:
name in processed data file:
L29-Seq29-FA-15-WT-I


title: WT_Day8_rep4

description:
name in processed data file:
L27-Seq29-FA-14-WT-I


title: ToxKO_Day8_rep5

description:
name in processed data file:
L30-Seq29-FA-15-KO-I

value: Tox KO


title: WT_Day8_rep1

description:
name in processed data file:
L21-Seq29-FA-11-WT-I


title: ToxKO_Day8_rep4

description:
name in processed data file:
L28-Seq29-FA-14-KO-I


title: LKS-WT-Replicate1

first: David

middle: T

last: Scadden

state: MA

address: 185 cambridge street

department: CRM

institute: MGH

description: Gene expression data in LLP cells

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, genecount values are provided.

source_name: Mouse bone marrow HSPC

growth_protocol: Cells were freshly isolated and sorted from mouse bone marrow for total RNA extraction

extract_protocol:
For RNA-seq, total RNAs were extracted using RNeasy micro kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.

value: LKS cells

value: Mouse bone marrow HSPC


title: LKS-KO

description: Gene expression data in LLP cells


title: LKS-WT-Replicate2

description: Gene expression data in LLP cells


title: WT_Day20_rep4

description:
sample name in processed data file:
L24-D20-Tox-WT4_S9


title: ToxKO_Day8_rep2

description:
name in processed data file:
L24-Seq29-FA-12-KO-I


title: NS_ATAC_GMT_w6_rep3

city: San Francisco

first: Nicole

last: Stone

address: 1650 Owens St.

institute: Gladstone Institutes - UCSF

description:
accessible genomic DNA
This data was originally generated for comparison of the original reprogramming protocol (Ieda et al. 2010) vs an updated protocol using Tgfβ and Wnt inhibitors to improve reprogramming efficiency (Mohamed et al. 2017). However, this comparison was abandoned for the final manuscript, and some samples were thus excluded from further analysis.

data_processing:
Reads were aligned to the mm9 genomic assembly using bowtie2 with options: -X 600 --no-mixed --no-discordant.
Duplicate reads were removed using Picard MarkDuplicates (http://broadinstitute.github.io/picard).
Peaks were called using macs2 callpeak with options: -p 0.1 --nomodel --shift 100 --extsize 200 -B --SPMR --call-summits.
Peaks identified in at least two of three replicates were considered concordant. Next, regions for further analysis were determined by first estimating counts in each of the replicate samples for each of the time-points across a merged set of 307,204 concordant peaks, then normalizing the counts for differences in sequencing depths and estimating the association with time using the likelihood ratio tests based on negative binomial generalized log-linear model in bioconductor package edgeR.
Clustering was performed on the 10,000 regions with most significant association from the 100,691 regions passing an FDR threshold of 0.05 using the bioconductor package HOPACH and visualized using pheatmap in R (Laan, van der Laan, and Pollard 2003).
Genome_build: mm9
Supplementary_files_format_and_content: normalized counts per peak matrix in csv format

source_name: neonatal mouse heart

extract_protocol:
We prepared iCM, single-factor, and fibroblast samples for ATAC-seq as previously described (Buenrostro et al. 2013). Aliquots of 10,000–50,000 cells were spun down (310 RCF for 3 minutes) and washed with 200 μL of chilled PBS. Samples were lysed with 200 μL of chilled lysis buffer (20 mM Tris-HCl (pH 8.0), 85 mM KCl, 0.5% NP-40) and spun down at 500 RCF for 5 minutes. Nuclear pellets were transposed with 25 μL of Tagment DNA Buffer, 2.5 μL of Tagment DNA Enzyme (Nextera Sample prep Kit from Illumina, cat #FC-121-1030), and 22.5 μL of nuclease-free H2O. The samples were incubated at 37°C for 30 minutes and stored at −20°C. Transposed samples were purified using the QIAGEN MinElute Reaction Cleanup Kit (cat #28204).
Libraries were amplified using 25 μL of NEBNext High Fidelity 2x PCR Master Mix, 1.25 μM Nextera custom primer, 1.25 μM Nextera custom primers with unique barcodes, and nuclease-free H2O. We amplified samples using the following PCR conditions: 72°C for 5 minutes; 98°C for 30 seconds; and cycled at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Half of each sample was amplified for 12 cycles, MinElute purified and assessed by bioanalyzer for library quality. Samples concentration was quantified by Qbit before pooling. Samples were sequenced at 100PE on the Illumina HiSeq 2500 at either the Harvard FAS core or the UCSF CAT core.

treatment_protocol: Direct cardiac reprogramming was performed on neonatal mouse cardiac fibroblasts as previously described (Ieda et al. 2010; Qian et al. 2013). Briefly, tissue explants from αMHC-GFP+ neonatal mouse hearts are cultured for ~10 days, allowing expansion of fibroblast population. Thy1+/αMHC-GFP- cells, largely fibroblasts, are isolated by fluorescence-activated cell sorting (FACS), infected with freshly prepared Gata4, Mef2c, and Tbx5 (GMT) retroviruses, and cultured with or without Tgfβ and Wnt inhibitors (sb431542 and xav939, respectively; Mohamed et al. 2017) prior to FACS harvest of αMHC-GFP+ or dsRed+ cells at time points following reprogramming initiation. We completed three biological replicates per condition.

value: alpha-MHC-GFP

tag: exogenous retroviral expression

value: Gata4, Mef2c, Tbx5

tag: chemical treatment

tag: reprogramming time point

value: day 42

value: alpha-MHC-GFP+ sorted induced cardiomyocytes


title: NS_ATAC_GMT_w6_rep1


title: NS_ATAC_GMT_w4_rep3

value: day 28


title: NS_ATAC_GMT_w4_rep2


title: NS_ATAC_GMT_w2_rep3

value: day 14


title: NS_ATAC_GMT_w2_rep1


title: NS_ATAC_GMT_w2_rep2


title: NS_ATAC_GMT_w1_rep3

value: day 7


title: WT_Day8_rep3

description:
name in processed data file:
L25-Seq29-FA-13-WT-I


title: NS_ATAC_GMT_w1_rep1


title: NS_ATAC_GMT_w1_rep2


title: NS_ATAC_Fibroblastwchem_rep3

value: dsRed

value: day 2

value: dsRed+ sorted fibroblasts (control infection)


title: NS_ATAC_Fibroblastwchem_rep1


title: NS_ATAC_Fibroblastwchem_rep2


title: ToxKO_Day8_rep1

description:
name in processed data file:
L22-Seq29-FA-11-KO-I


title: NS_ATAC_GMT_w6_rep2


title: NS_ATAC_CM_rep3

value: alpha-MHC-GFP+ neonatal cardiac myocytes collected from p0 pups. Hearts were minced and digested with collagenase to singularize cells prior to FACS.


title: NS_ATAC_CM_rep1


title: ToxKO_Day8_rep3

description:
name in processed data file:
L26-Seq29-FA-13-KO-I


title: NS_ATAC_GMTwchem_w3_rep3

description:
accessible genomic DNA
Bulk_Atac_Count_Data.csv

value: day 21


title: NS_ATAC_GMTwchem_w3_rep1


title: NS_ATAC_CM_rep2


title: NS_ATAC_GMTwchem_w3_rep2


title: NS_ATAC_GMTwchem_w2_rep2


title: NS_ATAC_GMTwchem_w2_rep1


title: NS_ATAC_GMT_w4_rep1


title: NS_ATAC_GMTwchem_w1_rep3


title: NS_ATAC_GMTwchem_w1_rep2


title: NS_ATAC_GMTwchem_w2_rep3


title: NS_ATAC_GMTwchem_w1_rep1


title: NS_ATAC_GMTwchem_d3_rep3

value: day 3


title: NS_ATAC_GMTwchem_d3_rep2


title: NS_ATAC_GMTwchem_d3_rep1


title: NS_ATAC_GMTwchem_d2_rep3


title: NS_ATAC_Fibroblast_rep3


title: NS_ATAC_GMTwchem_d2_rep2


title: NS_ATAC_GMTwchem_d2_rep1


title: NS_ATAC_Fibroblast_rep2


title: NS_ATAC_Fibroblast_rep1


title: NS_RNA_GMTwchem_w2_rep3

description:
Table.BulkRNA.csv
GMTc_Wk2.id_a_S08.Mar16

data_processing:
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf (http://code.google.com/p/ea-utils). Sequence quality control was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Alignment of the provided samples to the mm9 reference genome was performed using Bowtie 2.2.4 (Langmead and Salzberg 2012).
Reads were assigned to genes using "featureCounts"(Langmead and Salzberg 2012; Liao, Smyth, and Shi 2014), part of the Subread suite (http://subread.sourceforge.net/), and gene-level counts were arrived at using Ensembl gene annotation, in GTF format.
We calculated differential expression p-values using edgeR, an R package available through Bioconductor (Robinson, McCarthy, and Smyth 2010). We first filtered out genes where there were not at least two samples with at least 5 (raw) reads. Once these genes are removed, we recalculate the counts per million for each gene (CPM) and filter out any genes with a CPM above 20,000. After excluding these genes, we re-normalize remaining genes using calcNormFactors (TMM) ("weighted trimmed mean of M-values") in edgeR (Robinson, McCarthy, and Smyth 2010; Robinson and Oshlack 2010). Calculation of p-values is performed in edgeR for the differential expression between samples. Finally we use the built-in R function "p.adjust" to calculate the FDR (false discovery rate) for each p-value, using the Benjamini-Hochberg method (Benjamini and Hochberg 1995).
We used GO-Elite to generate biological ontology terms (Zambon et al. 2012).
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression matrix in csv format containing raw counts, normalized counts, and differential expression output from EdgeR

extract_protocol:
Total RNA was isolated using the miRNeasy Micro Kit (Qiagen).
Bulk RNA-seq libraries were prepared with the Ovation RNA-seq System v2 kit (NuGEN). RNA-seq libraries were assessed by Bioanalyzer and quantified by qPCR (KAPA). Libraries were pooled and sequenced at 100PE on the Illumina HiSeq 2500 at the Harvard FAS core.

value: neonatal mouse heart


title: NS_RNA_GMTwchem_w3_rep3

description:
Table.BulkRNA.csv
GMTc_Wk3.id_b_S10.Mar16


title: NS_RNA_GMTwchem_w3_rep1

description:
Table.BulkRNA.csv
GMTc_Wk3.id_126.Jan16


title: NS_RNA_GMTwchem_w3_rep2

description:
Table.BulkRNA.csv
GMTc_Wk3.id_a_S09.Mar16


title: NS_RNA_GMTwchem_w2_rep2

description:
Table.BulkRNA.csv
GMTc_Wk2.id_116.Jan16


title: NS_RNA_GMTwchem_w1_rep2

description:
Table.BulkRNA.csv
GMTc_Wk1.id_101.Jan16


title: NS_RNA_GMTwchem_w1_rep3

description:
Table.BulkRNA.csv
GMTc_Wk1.id_114.Jan16


title: NS_RNA_GMTwchem_w2_rep1

description:
Table.BulkRNA.csv
GMTc_Wk2.id_109.Jan16


title: NS_RNA_GMTwchem_d3_rep2

description:
Table.BulkRNA.csv
GMTc_Wk0d3.id_107.Jan16


title: NS_RNA_GMTwchem_d2_rep3

description:
Table.BulkRNA.csv
GMTc_Wk0d2.id_b_S07.Mar16


title: NS_RNA_GMTwchem_w1_rep1

description:
Table.BulkRNA.csv
GMTc_Wk1.id_096.Jan16


title: NS_RNA_GMTwchem_d2_rep2

description:
Table.BulkRNA.csv
GMTc_Wk0d2.id_a_S06.Mar16


title: NS_RNA_GMTwchem_d1_rep3

description:
Table.BulkRNA.csv
GMTc_Wk0d1.id_b_S05.Mar16

value: day 1


title: NS_RNA_GMTwchem_d2_rep1

description:
Table.BulkRNA.csv
GMTc_Wk0d2.id_102.Jan16


title: NS_RNA_GMTwchem_d3_rep1

description:
Table.BulkRNA.csv
GMTc_Wk0d3.id_098.Jan16


title: NS_RNA_GMTwchem_d3_rep3

description:
Table.BulkRNA.csv
GMTc_Wk0d3.id_121.Jan16


title: NS_RNA_GMTwchem_d1_rep1

description:
Table.BulkRNA.csv
GMTc_Wk0d1.id_111.Jan16


title: NS_RNA_GMT_w6_rep3

description:
Table.BulkRNA.csv
GMT__Wk6.id_59.Nov15


title: NS_RNA_GMT_w6_rep2

description:
Table.BulkRNA.csv
GMT__Wk6.id_58.Nov15


title: NS_RNA_GMT_w6_rep1

description:
Table.BulkRNA.csv
GMT__Wk6.id_55_60.Nov15


title: NS_RNA_GMTwchem_d1_rep2

description:
Table.BulkRNA.csv
GMTc_Wk0d1.id_a_S04.Mar16


title: NS_RNA_GMT_w4_rep2

description:
Table.BulkRNA.csv
GMT__Wk4.id_67.Nov15


title: NS_RNA_GMT_w2_rep3

description:
Table.BulkRNA.csv
GMT__Wk2.id_11.Jun14


title: NS_RNA_GMT_w1_rep3

description:
Table.BulkRNA.csv
GMT__Wk1.id_22.Sep14


title: NS_RNA_GMT_w4_rep3

description:
Table.BulkRNA.csv
GMT__Wk4.id_68.Nov15


title: NS_RNA_GMT_w4_rep1

description:
Table.BulkRNA.csv
GMT__Wk4.id_54.Nov15


title: NS_RNA_GMT_w2_rep1

description:
Table.BulkRNA.csv
GMT__Wk2.id_01_02_10_16.Sep14


title: NS_RNA_GMT_w1_rep2

description:
Table.BulkRNA.csv
GMT__Wk1.id_18_20_24_33.Jan15


title: Rat_1

city: Provo

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description: Counts of reads in each gene

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the HG38 or RN6 transcriptome using STAR
Genome_build: HG38 or RN6
Supplementary_files_format_and_content: Count files were generated using HTSeq-count.

source_name: Primary Schwann Cells

extract_protocol:
Qiagen RNEasy
Epicentre RiboZero

treatment_protocol: Cells were taken upon passage 2

value: Primary Schwann Cells

tag: passage

value: Passage 2


title: Rat_2

description: Counts of reads in each gene


title: Rat_3

description: Counts of reads in each gene


title: NS_RNA_Fibroblastwchem_rep3

description:
Table.BulkRNA.csv
GMTc_Wk0d2_dsRed.id_c_S03.Mar16

value: alpha-MHC-GFP


title: NS_RNA_GMT_w1_rep1

description:
Table.BulkRNA.csv
GMT__Wk1.id_084.Jan16

value: Gata4, Mef2c, Tbx5


title: NS_RNA_Fibroblastwchem_rep2

description:
Table.BulkRNA.csv
GMTc_Wk0d2_dsRed.id_b_S02.Mar16


title: day_plus1_5p

description:
Single cell transcriptomes from cardiac reprogramming
plus1_5p_paper.csv.gz
gem.group = - # at end of cell barcode in processed data file

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (2.0.1) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v2.2.
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene-cell barcode expression matrix in csv format

growth_protocol: Timed matings were set up between mice heterozygous for the Hand2 null allele. Morning of plug detection was considered E0.5 and embryos were harvested at embryonic day (E)7.75, E8.25 or E9.25

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell V(D)J Kit (PN-1000006) and the Chromium i7 Multiplex Kit (PN-120262).

value: plus 1

tag: gem.group in supplementary file 1


title: day_plus14_pos

description:
Single cell transcriptomes from cardiac reprogramming
m1_1_2_3_7_14P_paper.csv.gz
gem.group = - # at end of cell barcode in processed data file

value: plus 14


title: day_plus7

value: plus 7


title: NS_RNA_Fibroblastwchem_rep1

description:
Table.BulkRNA.csv
GMTc_Wk0d2_dsRed.id_a_S01.Mar16


title: day_plus3

value: plus 3


title: NS_RNA_Fibroblast_rep1

description:
Table.BulkRNA.csv
dsRed.id_035.Jan15

value: day 7


title: NS_RNA_Fibroblast_rep2

description:
Table.BulkRNA.csv
dsRed.id_09.Jun14

value: dsRed


title: day_plus2

value: plus 2


title: NS_RNA_Fibroblast_rep3

description:
Table.BulkRNA.csv
dsRed.id_13.Sep14

value: dsRed+ sorted fibroblasts (control infection)


title: NS_RNA_GMT_w2_rep2

description:
Table.BulkRNA.csv
GMT__Wk2.id_05_08_12.Jun14

value: day 14

value: alpha-MHC-GFP+ sorted induced cardiomyocytes


title: NS_RNA_neoCM_rep3

description:
Table.BulkRNA.csv
neonatCM.id_03_bc16.Jun15

value: alpha-MHC-GFP+ neonatal cardiac myocytes collected from p0 pups. Hearts were minced and digested with collagenase to singularize cells prior to FACS.


title: NS_RNA_neoCM_rep2

description:
Table.BulkRNA.csv
neonatCM.id_02_bc15.Jun15

value: neonatal mouse heart


title: ToxKO P14 T-cells_Day 13

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by bwa
nucleosome free reads were extracted and nucleosome free peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: nucleosome free peaks in bed format

extract_protocol:
Cells were washed and lysed to generate a crude nuclei preparation
Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters.  DNA fragments were PCR amplified and subsequently purified using Qiagen MinElute PCR Purification Kit (Qiagen, Maryland, USA). Final library quality and quantity was analyzed and measured by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit3.0 Fluorometer (Life Technologies, Carlsbad, CA), respectively.

value: P14 T-cells

value: ToxKO

tag: infection

value: LCMV Armstrong, LCMV-c13 and LCMV mixed c13 infection

tag: time

value: day 13


title: WT P14 T-cells_Day 13

tag: genotype

value: WT


title: WT P14 T-cells_Day 8

value: LCMV-c13 infection

value: day 8


title: day_plus1

tag: strain

value: alpha-MHC-GFP

value: Gata4, Mef2c, Tbx5

value: plus 1


title: NS_RNA_neoCM_rep1

description:
Table.BulkRNA.csv
neonatCM.id_01_bc14.Jun15

tag: tissue


title: miCLIP_MEF_1

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: miCLIP

data_processing:
Library strategy: miCLIP
For miCLIP,  adapters and low-quality based were trimmed using flexbar v2.5: flexbar -n 20 -as AGATCGGAAGAGCGGTTCAG -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -p Read2.fastq
Reads were then demultiplexed using pyBarcodeFilter.py and de-deduplicted using pyFastqDuplicateRemover.py from the pyCRAC software suite, and processed for the CTK iCLIP/miCLIP protocol. Second mate reads were reverse complimented and concatenated a with the first read file and aligned to GRCh38 (or mm10 for MEFs) using bwa v0.7.17: bwa aln -t 4 -n 0.06 -q 20 GRCh38.fasta ConcatendatedReads.fasta > AlignedReads.sai
Aligned reads were then processed as in miCLIP using C to T transitions to identify m6A sites. PCIF1 KO was used as a negative control for WT to determine regions in the genome which are dependent on PCIF1 and are thus m6Am. Ad hoc analyses were performed on the command line making extensive use of bedtools and deeptools.
Ribo-seq was trimmed and demultiplexed as with miCLIP. These reads and those for SLAM-seq were aligned first to the ribosomal DNA, and those that unmapped were mapped to the transcriptome using STAR aligner.
miCLIP Barcodes: WT: NNNCAAT; KO1: NNNGGTT; KO2: NNNTTGT; MEF1: NNNGGCG; MEF2: NNNCCGG
Genome_build: hg38/mm10
Supplementary_files_format_and_content: Processed data are in bed files: m6A.DRACH.FDR01.bed files contain called m6A sites with FDR<0.1; strict_putatitive_m6Am.bed contains the PCIF1-dependent bins; m6Am_locations.binsFINAL.bed contains the coordinates for the m6Am nucleotide in each region

source_name: MEF

extract_protocol:
Total RNA was harvested using Trizol, and polyA mRNA was enriched using 2 rounds of Dynabead oligoDT selection.
Libraries were constructed using either NEBNext Ultra II Directional RNA library prep kit (inputs/SLAM-seq), or using the miCLIP cloning protocol (miCLIP/Ribo-seq)

value: MEF

tag: antibody


title: miCLIP_MEF_2

description: miCLIP

tag: cell line


title: NS_SF.ATAC_T_rep2

description:
accessible genomic DNA
SF.ChIP.ATAC_featureCounts.txt

data_processing:
Reads were aligned to the mm9 genomic assembly using bowtie2 with options: -X 600 --no-mixed --no-discordant.
Duplicate reads were removed using Picard MarkDuplicates (http://broadinstitute.github.io/picard).
For each of the replicate samples, reads were assigned to regions of interest using featureCounts.
Counts were normalized for differences in sequencing depths for each replicate.
Genome_build: mm9
Supplementary_files_format_and_content: Text file containing normalized counts per region matrix

extract_protocol:
We prepared samples for ATAC-seq as previously described (Buenrostro et al. 2013). Aliquots of 50,000 cells were spun down (310 RCF for 3 minutes) and washed with 200 μL of chilled PBS. Samples were lysed with 200 μL of chilled lysis buffer (20 mM Tris-HCl (pH 8.0), 85 mM KCl, 0.5% NP-40) and spun down at 500 RCF for 5 minutes. Nuclear pellets were transposed with 25 μL of Tagment DNA Buffer, 2.5 μL of Tagment DNA Enzyme (Nextera Sample prep Kit from Illumina, cat #FC-121-1030), and 22.5 μL of nuclease-free H2O. The samples were incubated at 37°C for 30 minutes and stored at −20°C. Transposed samples were purified using the QIAGEN MinElute Reaction Cleanup Kit (cat #28204).
Libraries were amplified using 25 μL of NEBNext High Fidelity 2x PCR Master Mix, 1.25 μM Nextera custom primer, 1.25 μM Nextera custom primers with unique barcodes, and nuclease-free H2O. We amplified samples using the following PCR conditions: 72°C for 5 minutes; 98°C for 30 seconds; and cycled at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Half of each sample was amplified for 12 cycles, MinElute purified and assessed by bioanalyzer for library quality. Samples concentration was quantified by Qbit before pooling. Samples were sequenced at 100PE on the Illumina HiSeq 4000 at the UCSF CAT core.

treatment_protocol: Exogenous overexpression of reprogramming factors using retrovirus was performed as previously described (Ieda et al. 2010; Qian et al. 2013), on immortalized neonatal cardiac fibroblasts expressing large T antigen. Cells were infected with freshly prepared Gata4, Mef2c, and/or Tbx5 (GMT) retroviruses, and cultured with Tgfβ and Wnt inhibitors (sb431542 and xav939, respectively; Mohamed et al. 2017) prior to transposition of unsorted cell populations at day 2. We completed three biological replicates per condition.

value: neonatal cardiac fibroblast cell line expressing large T antigen

value: day 2


title: NS_SF.ATAC_T_rep1


title: day_minus1

value: minus 1


title: NS_SF.ATAC_MT_rep1

value: Mef2c, Tbx5


title: NS_SF.ATAC_M_rep1


title: NS_SF.ATAC_GT_rep3

value: Gata4, Tbx5


title: NS_SF.ATAC_M_rep2


title: NS_SF.ATAC_T_rep3


title: NS_SF.ATAC_GT_rep2


title: ToxKO P14 T-cells_Day 8


title: NS_SF.ATAC_GT_rep1


title: NS_SF.ATAC_GMT_rep3


title: NS_SF.ATAC_GMT_rep2


title: D28_Acute_rep3

description: Gene expression profile

hyb_protocol: Agilent mouse GE v2 Microarrays (4x44K) was used in combination with a one-color based hybridization protocol and was performed as described in the manufacturer’s instructions.

scan_protocol: Signals on the microarrays were detected using the Agilent DNA Microarray Scanner (Scan Control A.8.4.1 Software, Agilent Technologies)

data_processing:
Data were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1-107_Sep09 and Grid: 028005_D_F_20130207
GeneSpring GX12 (for Supp. Fig 1A) and GeneSpring GX13.0 (for Supp. Fig 1B)  (Agilent Technologies) was used to normalize and analyze the raw data as well for quality control.

label_protocol: performed by the company

extract_protocol: RNA extraction was performed by the company which also did the gene array. T cell lysates were provided frozen. Final disruption and homogenization of the cell lysates was achieved by using QIAshredder columns (Qiagen) after addition of RLT-buffer containing  Beta-mercaptoethanol. Total RNA was then isolated using the RNeasy Mini Kit (Qiagen) following manufacturer's instructions. The principle of this kit is a silica membrane-based purification of total RNA. Final volume of the eluate was 40  ul. An aliquot of the total RNA samples was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (peqlab). The 2100 Bioanalyzer (Agilent Technologies) allows for analysis of total RNA samples by capillary electrophoresis. The RNA is separated according to fragment size, and results are returned as electropherograms and virtual gel images.  An index for RNA quality, the so-called RIN (RNA integrity number), is derived from the electrophoretic profile. The RIN scale ranges from 1 to 10. A RIN of 10 denotes an excellent RNA quality, while a RIN value of 1 indicates massive degradation. For RIN calculation, the algorithm does not rely on the 28S/18S-rRNA ratio alone, but takes into account the entire electrophoretic profile (e.g. the fraction of short degraded RNA species).  All samples were analyzed using RNA 6000 Pico LabChip Kits (Agilent Technologies).

value: T-cells


title: NS_SF.ATAC_MT_rep2


title: D28_Chronic_rep4

description: Gene expression profile


title: Chronic_rep3

description: Gene expression proflie

source_name: Chronic


title: D28_Acute_rep2

description: Gene expression profile


title: D28_Acute_rep4

description: Gene expression profile


title: D28_Chronic_rep5

description: Gene expression profile


title: Acute_rep3

description: Gene expression proflie

source_name: Acute


title: D28_Chronic_rep3

description: Gene expression profile


title: D28_Acute_rep1

description: Gene expression profile


title: S6Tm  rep3

city: Rochester

first: Yasuhiro

last: Ikeda

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: RNA seq S6Tm vs S6Ct down TOP30.xlsx / RNA seq S6Tm vs S6Ct up TOP30 .xlsx / RNA seq S6Tm vs S5Tm up top 30.xlsx / RNA seq S6Tmvs S5Tm down top 30.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: beta cells

growth_protocol: The basic differentiation strategy without viral vector transduction was a modified version of the previously published protocols.

extract_protocol:
A total 200 ng RNA from differentiated iPSCs at indicated time points was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiating iPSC were transduced with PDX1 at S1, NGN3 at S4, and MAFA at S6.

value: iPSCs-derived beta cells

tag: treatment

value: PNM


title: S6Tm  rep2


title: S6Tm  rep1


title: S6Ct rep3

value: control


title: NS_SF.ATAC_G_rep2


title: D28_Chronic_rep1

description: Gene expression profile


title: NS_SF.ATAC_GM_rep2

value: Gata4, Mef2c


title: Chronic_rep4

description: Gene expression proflie


title: NS_SF.ATAC_GM_rep1


title: NS_SF.ATAC_GM_rep3


title: D28_Chronic_rep2

description: Gene expression profile


title: Acute_rep4

description: Gene expression proflie


title: NS_SF.ATAC_GMT_rep1


title: NS_SF.ATAC_M_rep3


title: S6Ct rep2


title: S6Ct rep1


title: Acute_rep2

description: Gene expression proflie


title: Chronic_rep1

description: Gene expression proflie


title: S5Tm  rep3

description: RNA seq S5Tm vs S5Ct DOWN TOP30 .xlsx  / RNA seq S5Tm vs S5Ct up TOP30 .xlsx / RNA seq S6Tm vs S5Tm up top 30.xlsx / RNA seq S6Tmvs S5Tm down top 30.xlsx


title: Chronic_rep2

description: Gene expression proflie


title: NS_SF.ATAC_Fibroblastwchem_rep3

description:
accessible genomic DNA
This data was originally generated for comparison of the original reprogramming protocol (Ieda et al. 2010) vs an updated protocol using Tgfβ and Wnt inhibitors to improve reprogramming efficiency (Mohamed et al. 2017). However, this comparison was abandoned for the final manuscript, and some samples were thus excluded from further analysis.

value: Fibroblast negative control

value: dsRed


title: NS_SF.ATAC_G_rep3


title: NS_SF.ATAC_Fibroblastwchem_rep2


title: NS_SF.ATAC_G_rep1


title: S5Tm  rep2


title: Acute_rep1

description: Gene expression proflie


title: NS_SF.ATAC_Fibroblast_rep3


title: S5Tm rep1


title: S5Ct  rep2


title: S5Ct rep3


title: S5Ct rep1


title: Human_3

description: Counts of reads in each gene

value: Primary Schwann Cells

value: Passage 2


title: Human_2

description: Counts of reads in each gene


title: NS_SF.ATAC_Fibroblastwchem_rep1

value: alpha-MHC-GFP


title: subcutaneous adipose_4

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Paired-end reads were aligned to hg19 and mm9 genomes using Tophat2 (v2.2.0.12) with default parameters. Gene expression analysis was performed using Cufflinks2 (v2.2.1).
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: bed file with chromosomal coordinates and count (5th column) of back-spliced junctions for circRNAs.

source_name: Tissue

extract_protocol:
Ribosome-depleted RNA from 3 biological replicates of human visceral (omental) and subcutaneous adipose, as well as mouse epididymal and inguinal adipose, was extracted using Trizol (Life Technologies) and purified using RNeasy kit (Qiagen).
Replicates from the same tissue type were pooled into one sample for library preparation (4 samples in total), processed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on the Illumina HiSeq2000 platform.

value: subcutaneous adipose


title: TEST_3

city: Urumqi

first: yan

last: pu

state: State...

address: Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, P.R. China

institute: Institute of Cancer Research

data_processing:
The original image data file obtained from high-flux sequencing(such as illuminahiseqtm2500/miseq)is converted into sequencing sequences by base-based identification analysis. We call it Rawdata or rawreads. The results are stored in fastq file format, which includes sequence information of sequencing sequences and corresponding sequencing quality information.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed. The statistical enrichment of differential expression genes in KEGG pathway was implemented by the clusterProfiler R package.
Genome_build: hg38
Supplementary_files_format_and_content: File includes readcounts and fpkms for each Sample

source_name: renal cell carcinoma  cells

growth_protocol: The 786-O and ACHN cell lines were used in this study. The two cell lines were grown in 1640 medium (HyClone, Los Angeles, CA, USA) supplemented with 10% fetal bovine serum (Gibco, CarIsbad, CA, USA).

extract_protocol:
The RNA-Seq experiments were performed by Novogene (Beijing, China). Briefly, a total amount of 3 µg RNA per sample was isolated using TRIzol reagent (Invitrogen) and used as input material for the RNA sample preparations.
Double-stranded complementary DNAs are synthesized using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. The cDNAs are then fragmented by nebulization and the standard Illumina protocol is followed thereafter, to create the mRNA-seq library.
After the sample was tested, the library was constructed by small rna sample pre kit, and the special structure of 3 'and 5' ends of small rna (5 'end had complete phosphate group and 3' terminal hydroxyl group) was used. Total rna was used as the starting sample, small rna ends were directly added to both ends of small rna, and then cdna. was synthesized by reverse transcription. Then the target dna fragment was isolated by pcr amplification and page gel electrophoresis, and the cdna library was recovered by gel cutting.
After the library was constructed, the library was first quantitated using qubit2.0, the library was diluted to 1 ng/ ul, then the insert size of the library was detected using the agilent 2100, and the insert size met the expected value, and the effective concentration of the library was accurately quantified using the q-pcr method (library effective concentration> 2 nm) to ensure the quality of the library.
After the library was qualified, the different libraries were sequenced according to the effective concentration and the amount of the target lower machine data volume after the histo/ misq sequencing.

treatment_protocol: pLenti-EF1a-EGFP-F2A-Puro-CMV NOAT113026, NF-κB over- expression vector and their respective NC (negative control) vectors were purchased from Obio (Obio, Shanghai, China), and stable transfection was operated according to the vector’s instructions. The multiplicity of infection (MOI) values were as follows: 786-O MOI=10 and ACHN MOI=20. The overexpression efficiency was measured by q-PCR.

tag: cell lines

value: 786-O and ACHN cell lines

value: renal cell carcinoma  cells

value: NOAT113026 overexpression


title: Human_1

description: Counts of reads in each gene


title: NC_3


title: NC_1


title: subcutaneous adipose_3


title: TEST_1


title: subcutaneous adipose_2


title: TEST_2


title: visceral adipose_4

value: visceral adipose


title: NC_2


title: visceral adipose_2


title: subcutaneous adipose_1


title: 293T_TotRNA_TM_rep2

city: La Jolla

middle: Farid

last: Martinez

address: 10010 N Torrey Pines Rf

department: Peptide Biology Laboratories

institute: Salk Institute for Biological Studies

description: processed data file: All_cell_lines_novel_coding_smORFs.txt

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2).
For Ribo-Seq short fragment RNA samples, reads were first trimmed of 3' adaptor sequence (AGATCGGAAGAGCACACGTCT) using fastx_clipper version 0.0.13 with the parameters: fastx_clipper -Q33 -l 20 -n. Trimmed reads were then aligned to a contaminant database of rRNA and tRNA sequences using Star version 2.5.2b with the parameters: --outSAMstrandField intronMotif --outReadsUnmapped Fastx --genomeDir /genomes/hg19cont.star --runThreadN 16. Unaligned reads were then aligned to hg19 with refGene annotations using the parameters: --outFilterMismatchNmax 2 --outFilterMultimapNmax 4 --chimScoreSeparation 10 --chimScoreMin 20 --chimSegmentMin 15 --outSAMattributes All --outSAMstrandField intronMotif. Secondary alignments were filtered out with samtools version 1.3 using the parameters: view -b -F 0X100. RibORF was used to score translation of smORFs. smORFs with RibORF scores of 0.7 and greater were considered translated. Any smORFs found to overlap with UCSC annotated CDS regions using bedtools version 2.25 or had BLASTP scores of 40 or greater against the Human RefSeq database were filtered out.
For RNA-Seq, reads were aligned to the hg19 using the STAR version 2.5.1b using the parameters: --outFilterIntronMotifs RemoveNoncanonical. Cufflinks was used for de novo transcriptome assembly of RNA-Seq data using parameters --multi-read-correct --frag-bias-correct and --library-type fr-firststrand options. Other parameters were set to default values. The resulting transcriptome was then 3-frame translated into ORFs using custom software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: All_cell_lines_novel_coding_smORFs.txt: Tab-delimited text file containing the coordinates for all identified novel protein-coding smORFs, including microprotein sequence, exons, start site type, number of exons, cell lines detected in, samples detected in, average RPKM for each cell line, and PhyloCSF score for each exon.
Supplementary_files_format_and_content: Transcripts assembled by Cufflinks for HeLa-S3 and K562 in gtf format.

source_name: HEK293T (Human Embryonic Kidney)

growth_protocol: All cell lines were maintained at 37ºC with 5% CO2. HEK293T and HeLa-S3 cells were grown in DMEM supplemented with 10% FBS. K562 cells were grown in RPMI 1640 supplemented with 10% FBS.

extract_protocol:
For accompanying short fragment total RNA-Seq experiments, 50 µL of cell lysate from cells prepped for Ribo-Seq was removed and RNA was extracted by acid phenol:chloroform extract followed by isopropanol precipitation. Total RNA was then heat fragmented at 95ºC for 25 min prior to library construction.
Ribo-Seq and short fragment RNA-Seq libraries were prepared utilizing the Illumina TruSeq Ribo Profile kit according to the manufacturer's instructions.

treatment_protocol: For ER stress experiments, cells were treated with either 0.1% DMSO, 5µg/mL tunicamycin (TM), or 1µM thapsigargin (TG) for 4 h at 37ºC.

value: Human Embryonic Kidney

value: Tunicamycin


title: HeLa-S3_TotalRNA

description: processed data file: HeLa-S3_Cufflinks_transcript_assembly.gtf

source_name: HeLa-S3 (Human Cervix Adenocarcinoma)

extract_protocol:
For paired-end sequencing, total RNA for RNA-Seq was prepared using the Qiagen RNeasy kit with gDNA elimination columns according to the manufacturer's instructions.
RNA-Seq libraries were prepared utilizing both the Illumina TruSeq Stranded mRNA kit and the Illumina TruSeq Stranded Total RNA kit according to manufacturer instructions.

value: Human Cervix Adenocarcinoma


title: 293T_TotRNA_TG_rep1

value: Thapsigargin


title: visceral adipose_3


title: NS_SF.ATAC_Fibroblast_rep1

value: neonatal cardiac fibroblast cell line expressing large T antigen

value: day 2


title: NS_SF.ATAC_Fibroblast_rep2


title: 293T_TotRNA_TG_rep2


title: visceral adipose_1