title: LOF P53 mouse 3

city: Aurora

first: Enrique

last: Torchia

state: CO

department: Dermatology

institute: University of Denver

data_processing:
Alignment using Tophat 2 (2.1.0)
filter duplicates
Quantify to annotation model (Partek E/M)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts value for each Sample …

source_name: skin

extract_protocol: TruSEQ Stranded mRNA Sample Prep (Illumina) was used with 500 ng of total RNA.  Barcoded samples were pooled and run across 3 lanes of 50bp reads sequencing on the HiSEQ 2500 machine (Illumina). Reads quality was checked using FastQC software.

value: Mix C57BL/6 and 129

tag: tissue

value: skin

tag: age

value: 8-10 weeks


title: LOF P53 mouse 4

status: Public on Oct 30 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype


title: GOF P53 mouse 5


title: GOF P53 mouse 4


title: LOF P53 mouse 5


title: LOF P53 mouse 2


title: LNCaP MKC8866-2

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

description: Sample_14-LN86-2.Aligned.sortedByCoord.out.bam

data_processing:
Sequenced reads were mapped to human reference genome (hg38) using STAR (2.5.2a) with default parameters.
Aligned reads were summarized into gene counts using the featureCounts (v1.5.0) command of the Subread package with default parameters in conjunction with the human gencode annotation file (hg38 release 85).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file containing raw read counts for all samples

organism: Homo sapiens

growth_protocol: LNCaP cells were cultured in regular growth medium (RPMI1640 + 10% FCS + 1%P/S + 1% Glutamine)

extract_protocol:
RNA was harvested using Trizol reagent.
The TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol.

treatment_protocol: For samples 1-8, cells were transfected with either Allstar control siRNA or XBP1-specific siRNA. After two days, the cells were treated with 30 nM thapsigargin for 3 hours. For samples 9-16, LNCaP cells were treated with either DMSO or 10 μM MKC8866 for 24 h before 3h induction with 30 nM thapsigargin.

tag: cell line

value: LNCaP

tag: cell type

value: Human prostate cancer cells

tag: passage

tag: treated with

value: 10 μM MKC8866 for 24hrs


title: GOF P53 mouse 3


title: Aur-AepiDel;GOF P53 mouse 2


title: Aur-AepiDel;GOF P53 mouse 4


title: Aur-AepiDel;GOF P53 mouse 3


title: Aur-AepiDel;LOF P53 mouse 4


title: Aur-AepiDel;GOF P53 mouse 1


title: Aur-AepiDel;LOF P53 mouse 5


title: Aur-AepiDel;LOF P53 mouse 3


title: Aur-AepiDel;LOF P53 mouse 2


title: GOF P53 mouse 1


title: plko_EV2

city: TianJin

first: Hua

middle: Jin

last: Liu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use HISAT2  to map clean reads to genome reference and transcript references.
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by STRINGTIE.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD34+ derived erythroid cells

growth_protocol: CD34+ cells cultured in IMDM medium supplemented with 20% BIT(StemCell Technologies-#9500),5ng/ml IL-3 (sigma, I1646), 100 ng/ml  SCF (Prospec, #CYT-255),10^-6 M Hydrocortisone (sigma, H2270) and 3 U/ml human EPO(ProTech,100-64) for 8 days.

extract_protocol:
CD34+ drived erythroid cells  cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary erythroid cells

tag: cell treatment

value: Empty vector lentivirus-infected primary erythroid cells

value: control

tag: time

value: culture day 8


title: plko_EV1


title: ShPTB1_2

value: shPTBP1 lentivirus-infected primary erythroid cells

value: PTBP1 knockdown


title: LNCaP siCtrl-3

description: Sample_3-LNC-3.Aligned.sortedByCoord.out.bam

tag: transfected with

value: Allstar control siRNA


title: GOF P53 mouse 2


title: U22

tag: treatment

value: shUCA1 lentivirus-infected primary erythroid cells

value: UCA1 knockdown


title: U21


title: P1


title: P2


title: MM6_APRIL1

city: Lund

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

country: Sweden

institute: Lund University

data_processing:
Bcl2FastQ software was used for basecalling.
Sequenced reads were mapped to the hg19 referece genome using Tophat 2.0.13 with parameters -p 2 --keep-fasta-order --no-coverage-search
BAM files were imported to the Qlucore Omics Explorer 3.0 software and normalized using the TMM (Trimmed Mean of M-values) method. Features with less than 10 reads in at least 5 samples were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file of TMM values, fold change and p-values of t-test between control and treated cells for every gene. A rank was created for each gene based on the log10 of the p-value and the direction of the fold change.

source_name: MonoMac 6 cell line

growth_protocol: The MonoMac 6 cells were cultured in RPMI with 10% fetal bovine serum and 1% penicilin/streptomycin.

extract_protocol:
RNA was extracted using the QIAshredder and RNeasy Microkit (QIAgen, Hilden, Germany).
Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The treated group was cultured in the presence of 100 ng/mL of human APRIL (Peprotech) in serum-free RPMI for 24 hours.

value: Blood cell line

value: MonoMac 6

value: Acute monocytic leukemia derived cell line


title: MM6_Ctrl3


title: MM6_APRIL3


title: MM6_APRIL2


title: MM6_APRIL4


title: MM6_Ctrl4


title: MM6_Ctrl1


title: Aur-AepiDel;LOF P53 mouse 1

value: Mix C57BL/6 and 129

value: skin


title: LOF P53 mouse 1

value: 8-10 weeks


title: ShPTB1_1


title: Sample_10-12-10W-2

city: Bethesda

first: Richard

middle: L

last: Proia

state: MD

address: 9000 Rockville Pk Bldg10-9D08

department: NIDDK

institute: NIH

description: Each sample is a pooled of 4-6 individual organoids.

data_processing:
Reads were mapped to the human hg19 reference genome using the ELAND aligner (Illumina).
Bam files were analyzed using Genomatix Software Suite to determine RPKM values (included in the txt files uploaded us processed files). RPKM values were used as gene expression values for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: txt files: Bam files were analyzed using Genomatix Software Suite to determine RPKM values which are included in the txt files uploaded us processed files.

source_name: HEX-corrected cerebral organoids

growth_protocol: Cerebral organoids were generated by aggregation of iPS cells and grown in suspension with constant agitation in growing medium described in Lancaster and Knoblich, 2014, Nat Protoc 9:2329-40.

extract_protocol:
Organoids were harvested at 8 and 10 weeks, pooled and RNA was purified using the Rneasy Mini kit (Qiagen).
Libraries were generated with the TruSeq Stranded mRNA Library Prep Kit (Illumina) starting with 1 ug RNA per pooled sample.

tag: type of ips cells

value: HEX-corrected iPS cells

value: Cerebral organoids generated using iPS cells

tag: time in culture

value: 10 weeks


title: Sample_GSL-10W-1

source_name: Sandhoff cerebral organoids

value: Sandhoff patient iPS cells


title: Sample_10-12-10W-4


title: Sample_GSL-10W-2


title: Sample_10-12-8W-5

value: 8 weeks


title: Sample_GSL-10W-3


title: Sample_10-12-10W-3


title: Sample_10-12-8W-1


title: Sample_GSL-8W-4


title: Sample_10-12-8W-2


title: Sample_GSL-8W-5


title: Sample_GSL-8W-3


title: Sample_10-12-8W-4


title: Sample_GSL-8W-2


title: MM6_Ctrl2


title: LL5

first: Jun

last: Yin

state: Maryland (MD)

address: 35 Convent Drive, Room 1B-1006

department: NINDS

institute: National Institutes of Health

data_processing:
8 bp of 5' end reads were trimmed due to library prepation protocol, while 3' end reads keep the same.
Reads were mapped by Tophat.
Reads uniquely aligned to gene exon region were counted by HTSeq.
Statistical analysis of differential gene expression was carried out using the DESeq2 package in R environment
DEXSeq package were used to count reads mapped to each exon
Genome_build: FLYBASE: dmel_6.05

organism: Drosophila melanogaster

source_name: larval ventral lateral neuron (LNv)

growth_protocol: Drosophila  larvae cultured under LD (12hr light : 12hr dark) and LL (24hr light) conditions for 5 days.

extract_protocol:
FASC sorted LNv neruons were used for total RNA extractions with PicoPure RNA extraction kit.
RNA libraries were prepared using Ovation Single Cell RNA-Seq System (Nugen, 0342HV-32).

value: larval ventral lateral neuron (LNv)

value: LL condition (24hr light)

value: Pdf-Gal4>UAS-CD8::GFP (X chromosome)


title: BE(2)_mock

city: Wuhan

first: Liduan

last: Zheng

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Pathology

institute: Union Hospital, Tongji Medical College

description: Gene expression after stable transfection of empty vector

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: BE(2)-C stably transfected with empty vector

growth_protocol: Human neuroblastoma cell line BE(2)-C was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The FOXD3-AS1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.

value: neuroblastoma

tag: passages

tag: genotype/variation

value: empty vector


title: LL4


title: Sample_GSL-10W-4


title: Sample_10-12-10W-1


title: LL3


title: LL1


title: LL2


title: LD3

value: LD condition (12hr light :12hr dark)


title: 5Y_pancEts-1

first: Qiangsong

last: Tong

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of pancEts-1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: SH-SY5Y stably transfected with pancEts-1

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

treatment_protocol: The pancEts-1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.


title: LD2


title: 5Y_mock

source_name: SH-SY5Y stably transfected with empty vector


title: Patient Healthy Skeletal Tissue, Demethylase Untreated

status: Public on Oct 29 2018

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
Human Healthy Tissue, Untreated
Isolated tRNA
PatientCounts.xlsx

data_processing:
Raw reads were processed using Trimmomatic v 0.32n and custom Python scripts to fully remove traces of adapter.
Processed reads were aligned in Bowtie 1.0 according to the parameters of -t -v 3 -m 10 --best --strata -p 12
Fragments shorter than 15 base pairs during alignment were removed during subsequent analysis.
Further processing using custom C and Python scripts were used to map reads onto tRNA isodecoders.
Lastly, poly-A tail analysis was done by taking isolating reads with poly-A tails greater than 10 nt and aligning them onto reference genomes with polyA appended.
Genome_build: hg19
Supplementary_files_format_and_content: Individual alignment files mapping tRNA to isodecoder with read counts, as well as an aggregate spreadsheet containing map information and tRNA charging ratios
[MERRF_Patient_NoTreatment.map.txt] mapping data
[MERRF_Patient_Treatment.map.txt] mapping data
[WT_Patient_NoTreatment.map.txt] mapping data
[WT_Patient_Treatment.map.txt] mapping data
[PatientCounts.xlsx] Count Data for Patient Sequencing Data
[MyoblastCounts.xlsx] Count Data for Myoblast Sequencing Data

source_name: Patient Skeletal Muscle

growth_protocol: The human control skeletal muscle biopsy was obtained after informed consent, according to Helsinki Declaration, accepted by the Ethical Review Board of Helsinki University Hospital (nr 43/13/03/04/2008). The MERRF skeletal muscle biopsy was obtained after informed consent from a subject with progressive muscle weakness. The skeletal muscle biopsy showed accumulation of COX negative and ragged-red muscle fibers and a high level of heteroplasmy for the mutation m. 8344A>G in tRNALys

extract_protocol:
Total RNA was isolated with Trizol according to the manufacturer’s instructions. Muscle samples were homogenized with a Precellys 24 ( Bertin Technologies). For next generation sequencing all samples were reprecipitated with 0.1 vol 3M Sodium acetate. 3 vol ice cold 100% Ethanol.
Total RNA was isolated by using mirVana miRNA Isolation Kit (Life Technologies). Purified total RNA was deacylated by incubating in 0.1 M tris-HCl, pH 9 at 37°C for 45 min. When necessary, total tRNA was subsequently isolated using a denaturing 10% polyacrylamide gel followed by passive gel elution and ethanol precipitation.
Homemade protocol based on Illumina protocols. Deacylated RNAs with or without the demethylation were first treated with T4 Polynucleotide Kinase (Epicentre) at 37C° for 30 min to further warrant a free 3' hydroxyl group for template switching. Template-switching reactions were performed as described7. Briefly, we used an initial template-primer substrate consisting of a 41-nt RNA oligonucleotide (5’-AGA UCG GAA GAG CAC ACG UCU AGU UCU ACA GUC CGA CGA UC/3SpC3/-3’) that contains Illumina Read1 and Read2 primer-binding sites and a 3’ blocking group (three carbon spacer; IDT) annealed to a complementary 32P-labeled DNA primer with a single-nucleotide 3’ overhang, T, which facilitates the template switch to full-length tRNA that mostly contain a 3’ CCA end. For g2RT template-switching reactions, average 100 ng of demethylated tRNAs or 1 μg of demethylated total RNA were mixed with the initial template-primer substrate (100 nM) and g2RT (1 μM of TeI4cΔEn or 500 nM of GsI-IIC RT) in reaction medium containing 450 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.5, and DTT (1 mM for TeI4cΔEn or 5 mM for GsI-IIC RT). For template-switching with TeI4cΔEn RT, the reactions were pre-incubated at room temperature for 30 min, initiated by adding 25 mM dNTPs to a final concentration of 1 mM and incubating at 60°C for 30 min. For template-switching with GsI-IIC RT, the pre-incubation step is not required. The reactions were terminated by adding 5 M NaOH to a final concentration of 0.25 M, incubating at 95°C for 3 min, and neutralizing with 5M HCl. The cDNAs resulting from template switching were analyzed in a denaturing 6% polyacrylamide gel, electroeluted using a D-tube Dialyzer Maxi with MWCO of 6-8 kDa (EMD Millipore), and ethanol precipitated with 0.3 M sodium acetate in the presence of 25 µg of linear acrylamide (Life Technologies). The purified cDNAs were then circularized with CircLigase II (Epicentre) using manufacture’s protocol with extended incubation time of 5 hours at 60°C, phenol-CIA extracted, ethanol precipitated and amplified with Phusion-HF (Thermo Scientific) using Illumina multiplex (5’- AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GAC GAT C -3’) and barcode (5’- CAA GCA GAA GAC GGC ATA CGA GAT BARCODE GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T -3’) primers for 12 cycles of 98°C for 5 sec, 60°C for 10 sec and 72°C for 10 sec. The PCR products were sequenced on Illumina HiSeq 1000 system.

treatment_protocol: Homoplasmic human myoblasts for wild type or the m.8344 A>G tRNALys mutation were derived from satellite cells from a skeletal muscle biopsy (Boulet et al., 1992) and immortalized with E6/E7 (Lochmüller et al., 1999). Cells were cultured at 37°C and 5% CO2 Cell Applications Inc. Skeletal Muscle Cell Growth Medium (#151-500) supplemented with 50 μg/ml uridine. Retrovirus was generated by transient transfection of retroviral plasmids into the Phoenix amphotropic packaging line (Richter et al., 2015). Cells were used directly following selection with blasticidin.

value: Skeletal Muscle

value: no AlkB-derived enzyme mixture

tag: disease

value: WT

tag: molecule subtype

value: tRNA


title: LD1

tag: tissue

tag: age


title: FLAG_HLF_KSL_HSC

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Reads aligned to mm10 using Bowtie2.
bedGraphs created using bedtools.
bigWigs created using UCSC utilities.
Peaks called using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig: density profile of mapped reads
bed: peaks

molecule: genomic DNA

source_name: Lin-Sca-1+c-Kit+ (LSK) - hematopoietic stem/progenitor cells

growth_protocol: 80,000 WT Lin-Sca-1+c-Kit+ cells were infected on retronectin coated plates (Takara) with either a pMX-GFP control or a pMX-3xFLAG-Hlf/Hlf-IRES-GFP virus and maintained for 5 days in basal OP9 medium supplemented with 50 ng/ml SCF, 10 ng/ml IL-7, 10 ng/ml Flt3L and 5 ng/ml IL-3 (Peprotech).

extract_protocol:
Lysates were clarified from sonicated nuclei following crosslinking with 1% formaldehyde, and histone-DNA complexes were isolated with antibody. For detailed protocol see Wilson et al., Cell Stem Cell. 2010 Oct 8;7(4):532-44, modified in that the sonication was 4 cycles (30 secs on, 30 secs off).
According to Illumina TruSeq DNA Sample Prep Kit

value: LSK

tag: chip antibody

value: α-FLAG (Sigma, catalog# F3165, lot# 114K6081)

tag: genotype

value: FLAG-HLF


title: Patient Healthy Skeletal Tissue, Demethylase Treated

description:
Human Healthy Tissue, Treated
Isolated tRNA
PatientCounts.xlsx

value: AlkB-derived enzyme mixture


title: GFPctrl_KSL_HSC

tag: cell type

value: GFP-ctrl


title: Patient MERRF Skeletal Tissue, Demethylase Treated

description:
Human MERRF Tissue, Treated
Isolated tRNA
PatientCounts.xlsx

value: MERRF


title: Immortalized Cell Line, WT, Demethylase Treated, Technical Replicate 3

description:
Myoblast_WT_Treated_Rep3
TP9, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx

source_name: E6/E7 immortalized cell lines

tag: cell line

value: E6/E7 immortalized cell lines


title: Patient MERRF Skeletal Tissue, Demethylase Untreated

description:
Human MERRF Tissue, Untreated
Isolated tRNA
PatientCounts.xlsx


title: BE(2)_FOXD3_AS1

description: Gene expression after stable transfection of FOXD3-AS1

source_name: BE(2)-C stably transfected with FOXD3-AS1

value: FOXD3-AS1 overexpression


title: Immortalized Cell Line, WT, Demethylase Treated, Technical Replicate 1

description:
Myoblast_WT_Treated_Rep1
TP7, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, WT, Demethylase Untreated, Technical Replicate 2

description:
Myoblast_WT_Untreated_Rep2
TP2, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, WT, Demethylase Treated, Technical Replicate 2

description:
Myoblast_WT_Treated_Rep2
TP8, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, WT, Demethylase Untreated, Technical Replicate 1

description:
Myoblast_WT_Untreated_Rep1
TP1, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, MERRF, Demethylase Untreated, Technical Replicate 3

description:
Myoblast_MERRF_Untreated_Rep3
TP6, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, MERRF, Demethylase Untreated, Technical Replicate 2

description:
Myoblast_MERRF_Untreated_Rep2
TP5, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: LD5

value: larval ventral lateral neuron (LNv)


title: LD4

value: Pdf-Gal4>UAS-CD8::GFP (X chromosome)


title: Immortalized Cell Line, MERRF, Demethylase Treated, Technical Replicate 3

description:
Myoblast_MERRF_Treated_Rep3
TP12, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, MERRF, Demethylase Treated, Technical Replicate 2

description:
Myoblast_MERRF_Treated_Rep2
TP11, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, MERRF, Demethylase Untreated, Technical Replicate 1

description:
Myoblast_MERRF_Untreated_Rep1
TP4, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, WT, Demethylase Untreated, Technical Replicate 3

description:
Myoblast_WT_Untreated_Rep3
TP3, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Immortalized Cell Line, MERRF, Demethylase Treated, Technical Replicate 1

description:
Myoblast_MERRF_Treated_Rep1
TP10, Isolated tRNA from aforementioned sample
MyoblastCounts.xlsx


title: Single-cell 37

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

data_processing:
Bowtie(v 0.12.9) was used to align raw reads  to mm9 transcriptome based on sequence of RefSeq transcripts.
Transcript level reads counts were estimated by eXpress (v 1.5.1)
Expression level of each transcript was eormalizedstnimated by calcNormFactors() function in edgeR.
The count per million (CPM) value was used to further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

source_name: Krt19+ cell and its progeny from Krt19CreERT/Rosa26CAG-EGFP adult mouse liver

extract_protocol:
GFP+ cells in adult mouse liver were FACS sorted. Individual cell was picked into single-cell lysis buffer which contained reverse transcriptase.
RNA libraries were prepared for sequencing using single cell protocols

value: Liver


title: Single-cell 34


title: Single-cell 38


title: Single-cell 33


title: Single-cell 31


title: Single-cell 39


title: Single-cell 36


title: Single-cell 28


title: Single-cell 32


title: Single-cell 30


title: Single-cell 29


title: Single-cell 35


title: Single-cell 25


title: Single-cell 27


title: Single-cell 24


title: Single-cell 23


title: Single-cell 20


title: Single-cell 18


title: Single-cell 19


title: Single-cell 21


title: Single-cell 17


title: Single-cell 16


title: Single-cell 15


title: Single-cell 14


title: Single-cell 13


title: Single-cell 12


title: Single-cell 11


title: Single-cell 10


title: Single-cell 8


title: Single-cell 26


title: Single-cell 4


title: TumorMDSC1

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

data_processing:
Illumina built-in 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
Fragment 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: tab-delimited text files include FPKM values for each Sample ...

source_name: Splenic CD11b+Gr1+ MDSC cells 1 from tumor-bearing mice

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: spleen

value: CD11b+Gr1+ MDSC

tag: pathological/physiological status

value: tumor-bearing mice


title: Single-cell 3


title: Single-cell 6


title: Single-cell 22


title: Single-cell 2


title: TumorMDSC3

source_name: Splenic CD11b+Gr1+ MDSC cells 3 from tumor-bearing mice


title: Single-cell 9


title: NeoNeg1

source_name: Splenic CD45-Ter119+CD71+ cells 1 from neo-natal mice

value: CD45-Ter119+CD71+ cells

value: neonatal mice


title: NeoNeg2

source_name: Splenic CD45-Ter119+CD71+ cells 2 from neo-natal mice


title: NeoPos3

source_name: Splenic CD45+Ter119+CD71+ cells 3 from neo-natal mice

value: CD45+Ter119+CD71+ cells


title: Single-cell 1


title: Single-cell 5


title: TumorMDSC2

source_name: Splenic CD11b+Gr1+ MDSC cells 2 from tumor-bearing mice


title: AnemiaNeg3

source_name: Splenic CD45-Ter119+CD71+ cells 3 from anemia mice

value: anemia mice


title: AnemiaNeg1

source_name: Splenic CD45-Ter119+CD71+ cells 1 from anemia mice


title: AnemiaNeg2

source_name: Splenic CD45-Ter119+CD71+ cells 2 from anemia mice


title: AnemiaPos3

source_name: Splenic CD45+Ter119+CD71+ cells 3 from anemia mice


title: AnemiaPos2

source_name: Splenic CD45+Ter119+CD71+ cells 2 from anemia mice


title: TumorNeg3

source_name: Splenic CD45-Ter119+CD71+ cells 3 from tumor-bearing mice


title: TumorNeg2

source_name: Splenic CD45-Ter119+CD71+ cells 2 from tumor-bearing mice


title: TumorNeg1

source_name: Splenic CD45-Ter119+CD71+ cells 1 from tumor-bearing mice


title: TumorPos3

source_name: Splenic CD45+Ter119+CD71+ cells 3 from tumor-bearing mice


title: Single-cell 7


title: NeoNeg3

source_name: Splenic CD45-Ter119+CD71+ cells 3 from neo-natal mice


title: NeoPos2

source_name: Splenic CD45+Ter119+CD71+ cells 2 from neo-natal mice


title: TumorPos2

source_name: Splenic CD45+Ter119+CD71+ cells 2 from tumor-bearing mice


title: NeoPos1

source_name: Splenic CD45+Ter119+CD71+ cells 1 from neo-natal mice


title: WT1135

status: Public on Oct 27 2018

city: West Lafayette

first: Rosemary

middle: Elizabeth

last: Morman

state: IN

address: 1203 West State Street Rm 181

department: Biology

institute: Purdue University

data_processing:
One replicate for the knockout treatment (KO1163), failed during sequencing and therefore not used for analysis
Reads were filtered using the FASTX toolkit (v 0.0.13) to remove bases with a Phred score below 30 and then aligned with Tophat (v 2.0.6) to the mouse genome
Read counts for each gene were generated using HTSeq (v 0.5.3p7)
Differential expression was determined using edgeR (v 3.03) with a false discovery rate of < 0.05 and a fold-change cut-off of 2
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: edgeR output

source_name: wild type_splenic B cells

growth_protocol: Splenic B cells were activated in culture with 20ug/mL LPS and 20ng/mL IL-4 for 6hrs

extract_protocol:
RNA was extracted with a Total RNA kit from Omega
Paired-end libraries were constructed for each sample and sequenced on an Illumina HiSeq System to a depth of >30 million reads per sample.

tag: strain background

value: wild type

value: B cells


title: TumorPos1

source_name: Splenic CD45+Ter119+CD71+ cells 1 from tumor-bearing mice


title: KO1138

source_name: Batf KO _splenic B cells

value: Batf KO


title: AnemiaPos1

source_name: Splenic CD45+Ter119+CD71+ cells 1 from anemia mice


title: RNAseq_NS-DADm2

first: Ying-Wooi

last: Wan

state: TX

address: One Baylor Plaza

data_processing:
Sequenced reads were mapped to UCSC mm10 whole genome using TopHat2 v2.0.9
Expression level, the raw counts, for each gene was estimated using htseq-count function of HTSeq program on mapped reads.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-deliminted raw counts for each gene, obtained from HTSeq; individual file for eah sample.

source_name: hypothalamus

extract_protocol:
Total RNA was extracted using Trizol and RNAeasy mini kit (Qiagen)
Standard illumina protocols

value: NS-DADm

value: 3-4 month


title: RNAseq_WT1

value: WT


title: RNAseq_WT2


title: RNAseq_NS-DADm3


title: RNAseq_NS-DADm1


title: WT1142


title: WT1165


title: KO1141


title: HDAC3 ChIPseq_IP

description: Chip-IP

data_processing:
ChIP-seq reads from both the runs were pooled
Pooled ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.1.0 with default settings
Sam files were converted and coordinate sorted using samtools version 0.1.19-96b5f2294a
Bigwig files were generated from bam files using deeptools version 2.2.4
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigwig files genarated using deeptools


title: HDAC3 ChIPseq_Input

description: Chip-Input


title: Panc-1 Tet-MIST1 Dox 4

city: Frederick

first: Brad

middle: LaMar

last: Jakubison

address: 1050 Boyles St., Building 539, Room 106

department: Mouse Cancer Genetics

institute: National Cancer Institute

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MPosd4

data_processing:
Standard RTA2 software on the Illumina Hiseq 4000 was used for base calling.
Sequenced reads were trimmed to remove the adapter sequences aligned with matching read and mapped to human genome 19 (hg19) using Tophat.  HTSeq software was used to call genes following sequence alignement.
Differentially expressed genes were identified using DESeq in edgeR bioconductor using the BH statistical test with a significance value cut-off of 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for each cell line includes statisticas, Counts per Million and raw counts

molecule: polyA RNA

source_name: Pancreatic Cancer Cell Line- Panc-1

growth_protocol: Panc-1 Cells were grown using standard procedures.  Cells were grown in high glucose DMEM with 10% Tetracycline-depleted FBS and 1 % penicillin.streptomyocin.

extract_protocol:
8.0 x 10^5 cells were harvested in Qiazol®.  Lysates were run through Qiashredder® columns and mRNA was isolated using the Qiagen miRNeasy extraction kit.
Libraries were construcuted using standard Illumina procedures.

value: Pancreatic Cancer Cell

tag: passage number

value: 1 μg/ml Doxycycline


title: Panc-1 Tet-MIST1 Dox 2

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MPosd2

tag: treatment


title: Panc-1 Tet-MIST1 Dox 1

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MPosd1


title: Panc-1 Tet-MIST1 Dox 3

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MPosd3


title: Panc-1 Tet-MIST1 Control 1

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MNegd1


title: Panc-1 Tet-MIST1 Control 2

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MNegd2


title: Panc-1 Tet-PTF1a Dox 4

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: 4


title: Panc-1 Tet-PTF1a Dox 3

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: 3


title: RNAseq_WT3


title: WT1170


title: Panc-1 Tet-PTF1a Dox 2

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: 2


title: Panc-1 Tet-PTF1a Dox 1

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: 1


title: KO1139


title: Panc-1 Tet-PTF1a Control 4

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: -4


title: Panc-1 Tet-PTF1a Control 3

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: -3


title: Panc-1 Tet-PTF1a Control 2

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: -2


title: TDN

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

description: Small RNA sequencing

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to look for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively. To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: laryngeal squamous carcinoma cells

growth_protocol: TU-177 cells were cultured in MEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted by using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells positive or negative for CD44 and CD133 surface markers were isolated from cultured TU-177 cells by MACS by using CD44 MicroBeads or CD133-PE antibody (Miltenyi Biotec, Gladbach, Germany) according to the manufacturer’s instructions

value: Laryngeal squamous carcinoma cell line TU-177-derived CD133-CD44- cells

tag: cell surface antigen

value: CD133- and CD44-

tag: isolation method

value: Magnetic activated cell sorting


title: Panc-1 Tetone Control 3

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PNegd3


title: Panc-1 Tetone Dox 1

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PPosd1


title: Panc-1 Tet-PTF1a Control 1

description:
processed data file:
PTF1a RNASEQ.txt
Sample name: -1


title: Panc-1 Tetone Control 2

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PNegd2


title: Panc-1 Tet-MIST1 Control 4

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MNegd4


title: Panc-1 Tetone Dox 3

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PPosd3


title: TPT

description: Small RNA sequencing

value: Laryngeal squamous carcinoma cell line TU-177

value: unsorted TU-177 cells


title: Panc-1 Tetone Dox 4

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PPosd4


title: Panc-1 Tet-MIST1 Control 3

description:
processed data file:
MIST1 RNASEQ.txt
Sample name: MNegd3


title: Panc-1 Tetone Dox 2

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PPosd2


title: TDP

description: Small RNA sequencing

value: Laryngeal squamous carcinoma cell line TU-177-derived CD133+CD44+ cancer stem cells

value: CD133+ and CD44+


title: Panc-1 Tetone Control 1

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PNegd1


title: TDP

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
Transcripts predicted with coding potential by either/all of the four tools (CNCI, CPC, Pfam-sca, phyloCSF) were filtered out, and those without coding potential were our candidate set of lncRNAs.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM/TPM values for each Sample

extract_protocol:
Total RNA was extracted by using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: TDN


title: TPT


title: DAC2_HH1_25uM_4day_2

status: Public on Oct 26 2018

city: Philadelphia

first: Hanghang

state: PA

address: 3307 N. Broad Street Pharmacy Allied Health Building, Room 339

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in fastq files to hg19 and generating BAM files
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Samples were performed in two batches. To get rid of batch effects, samples were normalized using RUVr method from the RUVseq package (only for the YB5_HH1_10uM_summary.xlsx file, the other file was not normalized because all samples were performed in one batch).
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. Two files are provided. For the first file (YB5_HH1_10uM_summary.txt),  the first 42 columns are the RPKMs of the individual samples. The following columns are the fold change and FDR of the triplicates of each condition compared against the triplicates of control samples.  For the second file (YB5_HH1_25uM_summary.txt),  the first 9 columns are the RPKMs of the individual samples. The following columns are the fold change and FDR of the triplicates of each condition compared against the triplicates of control samples.

source_name: YB5 colon cancer cell line

growth_protocol: YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were treated daily with 100nM decitabine (5-aza-CdR) for 48h, then with or without either 10uM or 25uM HH1 for an additional four days (one-dose and let the drug in the media for two days. Drug-free media were changed on day three before performing RNA-seq on day four). For dnCDK9 overexpression, viral dnCDK9 was transduced and RNA-seq was performed 72hr after transduction.

value: colon cancer cell line

tag: disease state

value: Dukes' type C, grade IV, colorectal adenocarcinoma

tag: gender

value: female


title: DAC2_HH1_25uM_4day_3


title: DAC2_HH1_25uM_4day_1


title: HH1_25uM_4day_3


title: HH1_25uM_4day_2


title: sihnRNPK RKO cells

city: shanghai

first: Lina

address: Yueyang Road 320

department: Institute for Nutritional Sciences

institute: SIBS，Chinese Academy of sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The stat of mapped reads was list in siNC.gene.MapReadsStat.xls and sihnRNPK.gene.MapReadsStat.xls
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: RKO cells two days after tranfection

extract_protocol:
RKO cells two days after tranfected with siRNA were collected , and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: colorectal cancer (CRC)

value: RKO

value: hnRNPK-/-


title: siNC RKO cells

value: control


title: DAC2_HH1_10uM_4day_2


title: DAC2_HH1_10uM_4day_3


title: HH1_25uM_4day_1


title: Panc-1 Tetone Control 4

description:
processed data file:
Tetone RNASEQ.txt
Sample name: PNegd4


title: DAC2_DMSO_4day_3


title: DAC2_HH1_10uM_4day_1


title: DAC2_DMSO_4day_2


title: DAC2_DMSO_4day_1


title: HH1_10uM_4day_2


title: HH1_10uM_4day_3


title: DMSO_4day_2


title: tet_off_72hr_3

value: tet_off_72hr viral transduction using a TET-off dnCDK9 construct


title: tet_on_72hr_3

value: tet_on_72hr (viral transduction using a TET-off dnCDK9 construct)


title: tet_off_72hr_1


title: tet_on_72hr_1


title: tet_on_72hr_2


title: HH1_10uM_24hr_3


title: HH1_10uM_24hr_2


title: DMSO_24hr_3


title: DMSO_24hr_2


title: DMSO_24hr_1


title: HH1_10uM_4day_1


title: HH1_10uM_8hr_2


title: HH1_10uM_8hr_3


title: DMSO_4day_1


title: DMSO_8hr_1


title: HH1_10uM_4hr_3


title: HH1_10uM_8hr_1


title: DMSO_8hr_3


title: DMSO_8hr_2


title: HH1_10uM_4hr_1


title: DMSO_4hr_3


title: HH1_10uM_4hr_2


title: DMSO_4hr_2


title: HH1_10uM_2hr_3


title: HH1_10uM_2hr_2


title: HH1_10uM_2hr_1


title: DMSO_2hr_2


title: DMSO_2hr_3


title: DMSO_2hr_1


title: 246 V336Y

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using CASAVA 1.8 and convered into fastq files with bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl GRCm38, GRCh37 genome assembly using STAR_2.4.2a with following parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated by countOverlaps from GenomicRanges_1.20.5 with minoverlap 10
Genome_build: GRCm38, GRCh37
Supplementary_files_format_and_content: count file was generated by "countOverlaps" from GenomicRanges package. The numbers are raw counts.

source_name: cell culture

growth_protocol: HEK293 cells stably transfected with MRPS5 wild-type or MRPS5 V336Y mutant expressing constructs were cultured in Dulbecco's MEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA from cell culture samples was isolated using RNeasy Mini Kit (Qiagen). Total RNA from muscle samples was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MRPS5 V336Y


title: 236 WT

value: MRPS5 WT


title: 233 WT


title: 245 V336Y


title: 237 WT


title: 238 WT


title: 235 WT


title: 249 V336Y


title: 260 WT


title: day0_rep1

city: Worcester

first: Guangping

last: Gao

state: Massachusetts

address: Albert Sherman Center (AS6-2011)

department: Gene Therapy Center

institute: University of Massachusetts, Medial School

description: untreated

data_processing:
Primary bioinformatics pipelines were performed by ContigExpress, LLC (New York, NY)
Paired-end reads were mapped to the mouse mm10 referece genome using tophat, version 2.1.0, and bowtie2 version 2.2.6
Transcript assemblies were performed by Cufflinks (v2.2.1) and merged with Cuffmerge using refseq gene annotations and the mm10 reference genome
Cuffdiff was performed to identify differentially expressed genes and transcripts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited fpkm normalized abundances for gene transcripts

source_name: cornea

extract_protocol:
Whole mouse corneas representing three treatment groups: non-treated (day 0), post-operative (day 5), and regression post-operative (day 15) were sent on dry ice to Otogenetics (Atlanta, GA).  RNA was extracted with standard procedures by Otogenetics.
Total RNA was subjected to polyA cDNA synthesis, and libraries were prepared for sequencing using standard Illumina protocols

value: cornea

value: 6-8 week old


title: day15_rep1

description: 15 days post-treatment


title: day5_rep2

description: 5 days post-treatment


title: day0_rep2

description: untreated


title: day15_rep2

description: 15 days post-treatment


title: day5_rep1

description: 5 days post-treatment


title: 22RV1-Input-1

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description:
input DNA
22RV1-IP-OC2-1.vs.Input_peaks.narrowPeak

data_processing:
Reads were aligned to hg19 with bwa 0.7.13-r1126
Data was filtered with Picard to mark duplicates and filter to q20
permissive peak calls were generated with macs2 2.1.1 and the arguments -p 1e-3 --to-large
the final peak set was generated with IDR 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files containing permissive peaks of individual replicates + idr peak set

source_name: 22Rv1 - prostate carcinoma

growth_protocol: 22Rv1 were grown in RPMI-1640 media (Gibco) supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Concentrated DNA ChIP or Input DNA was ligated to specific annealed linkers followed by direct sequencing using the Illumina HiSeq3000, system at the UCLA Clinical Microarray Core.
ChIP-Seq libraries were prepared with the ChIP-IT High Sensitivity kit from Active Motif. Briefly, 80% confluent 22Rv1 were cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to 100-500 bp in a Bioruptor UCD-200 (Diagenode) and incubated overnight with 4μg of antibody (anti-OC2 HPA057058). After RNase A and Proteinase K treatment, ChIP DNA was purified with the column system provided with the kit.


title: DMSO_4hr_1


title: 22RV1-Input-2

description:
input DNA
22RV1-IP-OC2-2.vs.Input_peaks.narrowPeak


title: 22RV1-OC2-2

description:
Chromatin IP against ONECUT2
22RV1-IP-OC2-2.vs.Input_peaks.narrowPeak

value: Anti-ONECUT2 antibody produced in rabbit (Sigma-Aldrich, catalog#)


title: 22RV1-OC2-1

description:
Chromatin IP against ONECUT2
22RV1-IP-OC2-1.vs.Input_peaks.narrowPeak


title: RNaseH1 KOH

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

data_processing:
Library strategy: HydEn-seq
Reads were trimmed for quality and adapter sequence with cutadapt (-m 15 –q 10match-reas-wildcards). Pairs with one or both reads shorter than 15 nts were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligos used in the preparation of these libraries with bowtie sing bowtie 0.12.8 (-m1 -v2), and all pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the hg38 H. sapiens reference mitochondrial genome where the mitochondrial genome was cleaved at position 4,000 and OriH region was religated (-m1 -v2 -X10000 --best). Single-end alignments were then performed using mate 1 of all unaligned pairs (-m1 -v2). The count of 5´ ends of all unique paired-end and single-end alignments were determined and these counts were converted to bedGraph format for visualization.
Genome_build: Human NCBI genome build GRCh38
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

source_name: Patient-derived fibroblast cells

growth_protocol: Patient and control fibroblast cells were grown in DMEM GlutaMAX medium, supplemented with 10 % FBS, PEST and 10 μg/ml uridine in 5 % humidified atmosphere at 37 °C.

extract_protocol:
Approximately 5 × 106 cells were collected and lysed for 30 min at 42 °C in lysis buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 10 % SDS). An equal volume of phenol-chloroform was added, samples were mixed and centrifuged (15,000 g for 5 min, 4 °C). The aqueous phase was saved and 100 mM NaCl and one volume isopropanol were added. After precipitation at -20 °C for one hour, the samples were centrifuged (15,000 g, 20 min, 4 °C) and the pellets were washed with 70 % EtOH. The DNA was resuspended in 100 μl TE buffer. DNA concentrations were measured using the Qubit fluorometric instrument (ThermoFisher Scientific).
Free 5´-ends in mtDNA of fibroblast and patient-derived fibroblast cells were mapped by 5´-End-seq by treating 1 µg DNA with 0.3 M KCl for 2 h at 55 °C. RNA residues in mtDNA of fibroblast and patient-derived fibroblast cells were mapped by HydEn-seq by hydrolyzing 1 µg DNA with 0.3 M KOH for 2 h at 55 °C. After ethanol precipitation, the DNA fragments were treated for 3 min at 85 °C, phosphorylated with 10 U of 3′-phosphatase-minus T4 polynucleotide kinase (New England BioLabs) for 30 min at 37 °C, heat inactivated for 20 min at 65 °C and purified with HighPrep PCR beads (MagBio). Phosphorylated products were treated for 3 min at 85 °C, ligated to oligo ARC140 overnight at room temperature with 10 U of T4 RNA ligase, 25% PEG 8000 and 1 mM CoCl3(NH3)6, and purified with HighPrep PCR beads (MagBio). Ligated products were treated for 3 min at 85 °C. The ARC76–ARC77 adaptor was annealed to the second strand for 5 min at room temperature. The second strand was synthesized with 4 U of T7 DNA polymerase (New England BioLabs) and purified with HighPrep PCR beads (MagBio). Libraries were purified, quantified with a Qubit fluorometric instrument (ThermoFisher Scientific) and 75-base paired-end sequenced on an Illumina NextSeq500 instrument, to identify the location of the free 5´-ends.

tag: genotype/variation


title: RNaseH1 KCl


title: C3 M rep4

status: Public on Oct 25 2018

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Raw sequenced reads were filtered to retain only read pairs with average base quality score of at least 20 for each read.
3’ Illumina universal adapter sequences were removed from each mate using Cutadapt v1.9.1 (parameters: -a AGATCGGAAGAG -O 3). Read pairs less than 30nt were excluded.
Reads were mapped against mm9 reference genome with STAR v2.5.1b (parameters: --runMode alignReads --outSAMtype BAM Unsorted SortedByCoordinate --outMultimapperOrder Random  --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8).
Reads were summarized based on the RefSeq annotations (February 8, 2016) using the featureCounts read quantification program of the Subread v1.5.0-p1 package with default parameters except “-s2 -p” such that reads were counted at the meta-feature level, and multimapping or multi-overlapping reads were not counted.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of raw counts per gene for each sample (n = 20); format = txt.
Supplementary_files_format_and_content: Matrix of transcripts per million (TPM) per gene for each sample (n = 20); format = txt.

source_name: liver

growth_protocol: Female and male C57BL/6N and C3H/HeN mice were obtained from Taconic Farms, Inc. Animals were housed in an AALAC accredited facility at Alion Science and Technology (Durham, NC). All procedures were in compliance with the Animal Welfare Act Regulations, 9 CFR 1-4 with handling and treatment according to the Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Total RNA was extracted from fresh liver tissues, with 5 biological replicates per group. The left lateral liver lobe was rapidly removed and homogenized in Trizol (Thermo Fisher Scientific), and phase separation was performed according to the manufacturer’s instructions. The aqueous phase was then purified using Acid Phenol:Chloroform (Ambion). Following, equal volume of 50% ethanol was added to the aqueous layer and then purified using the RNeasy Mini Kit (Qiagen) with RNase-Free DNase treatment (Qiagen).
Indexed paired end libraries were constructed for each total RNA sample using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina), according to the manufacturer’s instructions. Libraries were randomly distributed to three pools, and each pool was sequenced using the Illumina HiSeq 2500 Sequencing System, run as indexed 125 base paired end reads, at the NIH Intramural Sequencing Center.

value: C3H/HeN (C3)

tag: Sex

value: male

tag: tissue

value: liver

tag: pool


title: C3 M rep5

tag: age


title: Fibroblast KOH

source_name: Fibroblast cells

value: wildtype


title: DMSO_4day_3

tag: cell type

value: colon cancer cell line

value: Dukes' type C, grade IV, colorectal adenocarcinoma


title: C3 M rep1


title: C3 M rep3


title: C3 F rep5

value: female


title: C3 F rep1


title: C3 F rep4


title: C3 F rep3


title: B6 M rep5


title: C3 F rep2


title: B6 M rep4


title: B6 M rep2


title: B6 M rep1


title: B6 F rep5


title: Day 14, replicate 4

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

description:
High fat diet 14 days
fat_D14_28

data_processing:
Basecalls were generated using CASAVA
Resulting reads (2 x 100 bp) were aligned to the mouse genome (Ensembl release 80) using STAR
Uniquely mapped reads were counted against gene annotations from Gencode (version M6) using featureCounts.
Gene expression levels were normalized using TMM and differential expression was assessed using linear modelling and the limma package (R version 3.0).
Genome_build: Ensembl release 80
Supplementary_files_format_and_content: raw counts

source_name: Day 14

extract_protocol:
RNA was isolated from epididymal fat tissue using RNeasy® Mini Kit (Qiagen) according to the manufacturer’s recommendations
Samples were prepared for RNA-seq using Illumina’s TruSeq RNA Sample Preparation Kit

tag: diet

value: High fat diet

tag: time

value: 14 days

value: Adipose tissue


title: B6 F rep4

tag: strain


title: B6 F rep2


title: B6 F rep3


title: B6 M rep3


title: Fibroblast KCl


title: Day 14, replicate 2

description:
High fat diet 14 days
fat_D14_18


title: Day 14, replicate 1

description:
High fat diet 14 days
fat_D14_14


title: Day 14, replicate 3

description:
High fat diet 14 days
fat_D14_22


title: Day 6, replicate 3

description:
High fat diet 6 days
fat_D6_24

source_name: Day 6

value: 6 days


title: Day 6, replicate 4

description:
High fat diet 6 days
fat_D6_29


title: Day 6, replicate 2

description:
High fat diet 6 days
fat_D6_19


title: C3 M rep2


title: Day 6, replicate 1

description:
High fat diet 6 days
fat_D6_15


title: Day 4, replicate 4

description:
High fat diet 4 days
fat_D4_26

source_name: Day 4

value: 4 days


title: B6 F rep1


title: Day 4, replicate 2

description:
High fat diet 4 days
fat_D4_17


title: Day 2, replicate 3

description:
High fat diet 2 days
fat_D2_25

source_name: Day 2

value: 2 days


title: Day 2, replicate 1

description:
High fat diet 2 days
fat_D2_16


title: Day 4, replicate 1

description:
High fat diet 4 days
fat_D4_12


title: Day 4, replicate 3

description:
High fat diet 4 days
fat_D4_21


title: Day 0, replicate 2

description:
Normal chow control
fat_D0_13

source_name: Day 0

value: Normal chow

value: control


title: Day 2, replicate 4

description:
High fat diet 2 days
fat_D2_30


title: Day 2, replicate 2

description:
High fat diet 2 days
fat_D2_20


title: Day 0, replicate 1

description:
Normal chow control
fat_D0_11


title: Day 0, replicate 3

description:
Normal chow control
fat_D0_23


title: WT1-IP

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: No. 6, Tongwei Road, Xuanwu District

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

data_processing:
Library strategy: m6A-seq
Basecalls performed using CASAVA version 1.8.2
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat2.0.13 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 –r 70 --library-type fr-unstranded
peaks were called using MACS version 1.4.2 with the following setting: Pvalue cutoff:0.01
Genome_build: mm10
Supplementary_files_format_and_content: txt file. Peaks

source_name: WT-IP

growth_protocol: mice were maintained under a 12 hr light/12 hr dark (LD) cycle and fed ad libitum with normal rodent chow

extract_protocol:
Total RNA was extracted using TRIzol reagent followed by purification using PolyATtract® mRNA Isolation.Immunoprecipitated RNA fragments and comparable amounts of input were subjected to first-strand cDNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post natal day 21

tag: genotype

value: wild type

tag: ip antibody

value: anti-m6A (Synaptic systems, catalog#:202003, RRID:AB_2279214)


title: WT2-IP


title: WT2-Input

source_name: WT-Input

value: input


title: WT3-Input

value: liver


title: WT3-IP


title: KO3-Input

source_name: KO-Input


title: KO3-IP

source_name: KO-IP


title: KO2-IP


title: KO1-Input


title: KO1-IP


title: KO2-Input


title: KO2

first: Fangzhen

last: Xia

address: South Chongqing Road，NO.280

institute: Shanghai  Jiao  Tong  University  School  of  Medicine

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trinned for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse reference genome (GRCm38, Ensembl build) using Tophat version 2.0.12, yielding an average mapping rate of 90.3 ± 2.3%.
Gene expression levels, which represented as fragments per kilo-base per million mapped reads (FPKM), were obtained for 27180 genes/transcripts annotated using Ensemble release 67.
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with fpkm values.

source_name: bone marrow

extract_protocol:
LSCs of AML murine model were sortted by FACS, and RNA was harvested using Trizol reagent.  library construction following standard TruSeq RNA sample preparation v2 protocol (Illumina).
Library construction following standard TruSeq RNA sample preparation v2 protocol (Illumina). The sequencing libraries were sequenced using the Illumina HiSeq2500 platform.

value: bone marrow

value: LSC

tag: cell markers


title: WT2

value: wildtype


title: WT1


title: WT1-Input


title: KNV rep2

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
The paired-end reads were aligned to the transcript sequences with Bowtie using the following parameters: -v2 -a -m10 -best -strata.
We counted the number of reads mapped to each transcript and divided it by the length of the transcript and the total number of aligned reads to calculate the normalized gene expression value (reads per kilobase per million mapped reads, RPKM). We considered the number of alignment of the read with N hits on the transcripts as 1/N
Genome_build: IWGSC, v2.2
Supplementary_files_format_and_content: tab-delimited text files include read counts for each transcript

organism: Triticum aestivum

source_name: SPIKE TISSUE

growth_protocol: wheat are grown in growth room at 25C under Longday condition (16 h light/8 h dark)

extract_protocol:
Total RNA was isolated using the RNeasy plant mini kit (Qiagen) and treated with DNaseI (Roche) to eliminate contaminating DNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: glume primordium differentiation stage


title: KNVI rep2

value: floret differentiation stage


title: KNIV rep2

value: double ridge stage


title: KNV rep1


title: KNIII rep2

value: single ridge stage


title: KNIV rep1


title: CS Tat (BL43 C-Tat)

city: Bengaluru

first: Ranga

last: Udaykumar

state: Karnataka

address: Jakkur post

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were quality checked for adaptor sequences, then mapped to hg38 whole genome using tophat2 v2.0.13 with default parameters
The aligned reads were subjected to cufflinks assembly of transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Jurkat T-cell line

growth_protocol: The Tet-On stably transduced Jurkat cells were maintained in RPMI1640 supplemneted with 10% Tet-system approved FBS (Clontech Cat#631101 ).

extract_protocol:
The total RNA (free from genomic DNA) was extracted using the RNAqueous-4PCR kit (Life Technologies Cat#AM1914).
RNA libraries were prepared for sequencing using the standard Illumina protocols

treatment_protocol: The Tat expression was induced in the Tet-On stable cells using an optimized dose of Doxycycline (Sigma Cat# D9891) at 800 ng/ml for samples 3 and 4 and 100 ng/ml for samples 1, 2 and 6

value: Stably tranduced Jurkat T-cell line

tag: expression

value: Tetracycline inducible Tat expression

tag: type of tat protein

value: BL43 subtype-C Tat with the signature amino acid residue Serine at position 31


title: CC Tat (BL43 C-Tat)

value: BL43 subtype-C Tat isogenic variant with the residue Cysteine at position 31


title: Empty cntrl (Dox)

value: No Tat expression

value: No Tat Control


title: Empty cntrl (No Dox)


title: SAR-C Tat

value: Consensus subtype-C Tat with signature amino acid residues


title: KNII rep1

value: elongation stage


title: KNII rep2


title: KNI rep1

value: vegetative stage


title: LYEC1

city: Harbin

first: Hui

last: Yuan

state: Heilongjiang

address: XiangFang

institute: Northeast Agricultural University

data_processing:
Clean reads were obtained with in-house Perl scripts, by removing those reads that contained an adapter or poly N sequence and the low-quality reads from the raw reads.
The chicken reference genome and gene annotation files were downloaded from the chicken genome website
The number of reads mapped to each gene was counted with HTSeq v0.6.1, and the gene expression levels were calculated with the FPKM method.
Cufflinks v2.1.1 Reference Annotation Based Transcript (RABT) was used to assemble and identify both the known and novel transcripts from the TopHat results
The differential expression of genes in the black and light-yellow eyelids (three biological replicates per group) was analyzed with DESeq R package (1.18.0).
A GO enrichment analysis of the DEGs was performed with the GOseq R package. GO terms with corrected P value < 0.05 were deemed significantly enriched. The KOBAS software was used to test the statistical enrichment of DEGs in the KEGG pathways.
Genome_build: Galga4 Ensembl release 85
Supplementary_files_format_and_content: FPKMs

organism: Gallus gallus

source_name: LYEC, eyelid

growth_protocol: According to the inclusion criteria, three black-eyelid chickens (BEC1, BEC2, and BEC3) and three light-yellow-eyelid chickens LYEC1, LYEC2, and LYEC3) were chosen randomly and slaughtered 30 weeks after hatching.

extract_protocol:
Total RNAs were isolated from the eyelid tissues of the six chickens with TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacture’s protocol.
The extracted RNA (3 μg per sample) was used to construct a transcriptome library with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Beverly, MA, USA), according to the manufacturer’s protocol. Different index codes were added to each sample library. The libraries were constructed in a series of steps, including cDNA synthesis, blunt ending, addition of adaptors, selection of cDNA fragments, PCR, and purification of the PCR products.

value: Lindian chicken

value: eyelid

tag: tissue color

value: light-yellow


title: LYEC3


title: BEC2

source_name: BEC, eyelid

value: black


title: KO1

value: bone marrow

value: LSC


title: BEC1


title: KNVI rep1

value: floret differentiation stage


title: BEC3


title: LYEC2


title: 243 V336Y

source_name: cell culture

value: MRPS5 V336Y

tag: cell line


title: SAR-B Tat

value: Stably tranduced Jurkat T-cell line

value: Consensus subtype-B Tat with signature amino acid residues


title: wit3

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
kallisto version 0.43.0 was first used to build an index file for the Drosophila reference transcriptome BDGP6 as downloaded from the Ensembl web site (www.ensembl.org, release 86). The sequence reads for each sample were then quantified with the quant function of kallisto.
In-house Perl scripts were used to sum the read counts at the transcript level for each gene and to create a matrix comprising the read counts for all the genes for all the samples.
Differential expression analysis was then performed on the data from that matrix using the R package DESeq2.
Each sample was assessed with the quality control software RNA-SeQC (DeLuca et al., 2012) and the PtR script from the trinity suite (Grabherr et al., 2011). Such quality control showed no outliers, and all the samples were therefore kept for differential expression analyses.
Genome_build: BDGP6
Supplementary_files_format_and_content: *txt: Tab-separated text files with FlyBase gene ids and counts from kallisto.

source_name: ventral nerve cord

growth_protocol: Control and wit L1 larvae grown on grapejuice plates were picked and transferred into vials containing regular agar corn fly food (80 larvae/vial) until dissection, at 25C.

extract_protocol:
The brains from third instar wandering larvae were extracted in ice cold Dulbecco's buffered saline solution (Sigma) and brain lobes were removed. Twenty five ventral nerve cords for each biological replicate were transferred into RNAlaterTM reagent (Qiagen) and stored at 4C. Total RNA was extracted using RNAzol RT(Sigma) following manufacturer protocol.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the TruSeq stranded mRNA library kit (Illumina) on the Illumina Neoprep automated nanofluidic library prep instrument. Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads.

tag: strain/background

tag: genotype/variation

value: ventral nerve cord

value: wandering third instar larval stage

value: female


title: SlincR Morphant TCDD_biorep_3

city: Corvallis

first: Gloria

middle: R

last: Garcia

state: OR

institute: Oregon State University

description: Supplemental File 4.xlxs

data_processing:
HiSeq 3000 system used for base calling
Reads were initially evaluated by FastQC version-0.11.32 to detect major sequencing problems and quality control trimmed with Skewer version-0.1.1273 to remove ends of reads with low mean Phred quality score (options: --mode pe --end-quality 30 --mean-quality 25 --format auto --threads 9)
Trimmed reads were aligned with TopHat version-2.1.1 using the following options optimized for trimmed, paired-end data: --library-type fr-secondstrand --no-discordant --no-mixed --mate-inner-dist 20 --mate-std-dev 180 --min-anchor-length 5 --min-intron-length 10 --max-intron-length 400000 --num-threads 9. Samtools version-1.46 was used to assess the percent of paired aligned reads and to sort aligned reads (BAM) by name using the “flagstat’ and “sort –n -@9” commands, respectively.
Gene counts were estimated using the htseq-count function from HTSeq version-0.6.0 (options: --format=bam --order=name --stranded=yes --type=exon --idattr=gene_id --mode=intersection-nonempty) on the GRCz10 Ensembl (release 89) GTF annotation
The Bioconductor package, edgeR version-3.18.1, was used to normalize counts and identify differentially expressed genes. Briefly, genes were filtered to exclude those with low counts across libraries, only keeping genes expressed in a minimum of four samples with average counts per million reads per sample above 0.62, which corresponds to a minimum read count of 10-20. Differential expression of control versus TCDD exposed control or slincR morphants was determined in edgeR using the quantile-adjusted conditional maximum likelihood (qCML) method to calculate dispersions. The ‘robust=TRUE’ option was used to protect the empirical Bayes estimates against the possibility of outlier genes with wide ranging individual P-values were adjusted for a 5% false discovery rate using the Benjamini-Hochberg method.
To understand the functional consequences of TCDD exposure and slincR knockdown, we performed biological process network enrichment analysis and GO term enrichment on the significant gene list using Metacore GeneGo software. Only enriched biological process networks and GO terms with a FDR-correct p-value ≤ 0.05 were considered significant.
Genome_build: Zv10_89
Supplementary_files_format_and_content: xlxs files with tabs for significant genes, enriched netwrok processes, and GO terms
Supplementary_files_format_and_content: gene counts data: _GEO_Combined_HTSeq-count_table.tab

organism: Danio rerio

source_name: whole 48 hpf embryo

extract_protocol:
Total RNA was extracted from 48 hpf whole embryos using RNAzol (Molecular Research Center, Inc; Cincinnati, OH) and a bullet blender with 0.5 mM zirconium oxide beads (Next Advance, Averill Park, New York) as recommended by the manufacturer. The RNA was purified using the Direct-zol MiniPrep kit (Zymo Research; Irvine, CA) and included an in-column DNase 1 digestion.  RNA quality and quantity was assessed using a SynergyMix microplate reader with the Gen5 Take3 module. RNA integrity was confirmed (RIN score > 8) with an Agilent Bioanalyzer 2100.
Total RNA samples were sent to Oregon State University Center for Genome Research and Biocomputing Core facilities for library preparation and sequencing. mRNA was poly-A selected, and libraries were prepared with the PrepXTM mRNA and Illumina* sequencing workflow (Wafergen Biosystems, Fremont, CA). Paired-end sequencing (150 bp) was conducted with an Illumina HiSeq 3000 sequencer.

treatment_protocol: Shield-stage (~6 hpf) embryos were exposed to 1 ng/mL TCDD (311 nM, 95.3% purity; SUPELCO Solutions Within; Bellfonte, PA) or vehicle (0.1% DMSO) with gentle rocking for 1 hour in 20 mL glass vials (10 embryos/mL). Vials were also gently inverted every 15 minutes to ensure proper mixing. Embryos were rinsed 3 times with fish water and then raised in 100-mm petri dishes.

value: Tropical 5D line

tag: tissue

value: whole 48 hpf embryo

value: SlincR Morphant

tag: agent

value: 1 ng/mL TCDD


title: KNI rep2

city: Shanghai

value: vegetative stage


title: KNIII rep1

value: single ridge stage


title: SlincR Morphant TCDD_biorep_4

description: Supplemental File 4.xlxs


title: wit2

tag: Sex


title: SlincR Morphant TCDD_biorep_1

description: Supplemental File 4.xlxs


title: SlincR Morphant TCDD_biorep_2

description: Supplemental File 4.xlxs


title: SlincR Morphant DMSO_biorep_3

description: Supplemental File 4.xlxs

value: 0.1percent DMSO


title: C4


title: wit1


title: C2


title: SlincR Morphant DMSO_biorep_4

description: Supplemental File 4.xlxs


title: SlincR Morphant DMSO_biorep_1

description: Supplemental File 4.xlxs


title: C1


title: Control Morphant TCDD_biorep_4

description: Supplemental File 3.xlxs

value: Control Morphant


title: Control Morphant TCDD_biorep_3

description: Supplemental File 3.xlxs


title: wit4


title: Control Morphant TCDD_biorep_1

description: Supplemental File 3.xlxs


title: Control Morphant TCDD_biorep_2

description: Supplemental File 3.xlxs


title: HH1_10uM_24hr_1

last: Zhang

source_name: YB5 colon cancer cell line

tag: treatment

tag: cell type

value: colon cancer cell line

tag: disease state

value: Dukes' type C, grade IV, colorectal adenocarcinoma

tag: gender


title: IMA.sample_10758.69_female

status: Public on Oct 24 2018

city: New York

first: Jason

middle: C

last: Kovacic

state: NY

address: 1 Gustave L. Levy Place, Box: 1030

institute: Icahn School of Medicine at Mount Sinai

description: CAD for CABG

data_processing:
Sequencing reads were aligned to the human reference genome with the STAR aligner using default parameters.
GENCODE v.24 annotations were downloaded and exons were merged on a per gene basis. Reads were counted on merged exons using the HTSeq-count program.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file with read counts for all samples

source_name: Internal thoracic artery

extract_protocol:
Total RNA was isolated from freshly sorted live DAPI-CD90+ aorta or ITA cells using an RNeasy Micro Kit (Qiagen). All samples had a 260/280 ratio greater than 1.8.
Amplified cDNA was prepared from total RNA using the Ovation RNA-Seq System V2 Kit (NuGEN, San Carlos, CA) according to manufacturer’s instructions.

value: CD90+ sort

value: Internal thoracic artery

tag: age

tag: coronary artery disease status

value: case


title: Control Morphant DMSO_biorep_3

description: Supplemental File 3.xlxs

tag: strain


title: Control Morphant DMSO_biorep_2

description: Supplemental File 3.xlxs


title: Control Morphant DMSO_biorep_4

description: Supplemental File 3.xlxs


title: Control Morphant DMSO_biorep_1

description: Supplemental File 3.xlxs


title: IMA.sample_10691.59_female

description: CAD for CABG


title: C3

tag: developmental stage


title: SlincR Morphant DMSO_biorep_2

description: Supplemental File 4.xlxs


title: healthy_aorta.sample_11723.27_male

description: No PMH

source_name: Aorta

value: Aorta

value: male

value: control


title: diseased_aorta.sample_10519.56_male

description: +CAD


title: diseased_aorta.sample_10560.82_female

description: +CAD

value: female


title: healthy_aorta.sample_11732.41_female

description: PMH of HTN and smoking


title: IMA.sample_10158.52_female

description: CAD for CABG


title: IMA.sample_10374.65_female

description: CAD for CABG


title: IMA.sample_10509.55_male

description: CAD for CABG


title: diseased_aorta.sample_10053.72_male

description: +CAD


title: healthy_aorta.sample_10363.25_male

description: PMH polysubstance abuse and smoking


title: healthy_aorta.sample_9982.37_male

description: No PMH


title: tet_off_72hr_2

value: tet_off_72hr viral transduction using a TET-off dnCDK9 construct


title: IMA.sample_10531.47_female

description: CAD for CABG


title: RNA-seq_D7_shUbc9_rep2

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
For RNA-seq paired-end reads were mapped applying the 2-pass mapping mode of STAR v2.5.0a; best unique matches of concordant pairs were kept.
Mapped pairs were deduplicated with the Picar toolkit v1.94 and reads summarized over annotations with the featureCounts function of the Rsubread R package v1.26.0.
genome build: mm9
Supplementary_files_format_and_content: tdf files were generated with igvtools v2.3.25. ChIP-seq, ATAC-seq and RNA-seq libraries were merged by pooling the biological replicates. Prior to pooling, quality assurance clustering and principal component analysis were performed to identify and discard outlying replicates. The read coverage of the merged libraries was calculated over non-overlapping windows of 50 bp genome wide and library size normalization was applied to allow comparisons of the read coverage between samples: quantile normalization for the ChIP-seq and ATAC-seq datasets and DESeq2 size normalization for the RNA-seq datasets.
Supplementary_files_format_and_content: bed files with selected peaks were generated by MACS2 and then filtered according to the IDR protocol; tab delimited format: chromosome start end MACS_peak_ID -log10(p-value)*10 . foldChange -log10(p-value) -log10(q-value) relativeSummitPosition
Supplementary_files_format_and_content: RNA-seq_MEF-D4-D7-iPS-ES_shCtr-shUbc9_counts.txt: File with summarized counts (not normalized) for all the RNA-seq samples

source_name: mouse embryonic fibroblast cells E13.5

extract_protocol:
For RNA-Seq: trizol extraction and clean-up using RNeasy kit (QIAGEN). Experiments were done in triplicates.
Libraries prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (# RS-122-2301, Illumina) following manufacturer's protocol. Surplus primers were removed using AMPure XP beads (Agencourt Biosciences Corporation).

value: MEF expressing OKSM for 7 days

tag: passages

tag: genotype


title: RNA-seq_D7_shUbc9_rep3


title: RNA-seq_iPS_shUbc9_rep3

value: iPS derived from MEF


title: RNA-seq_ES_siUbc9_rep3

source_name: mouse embryonic stem cells

value: ES


title: RNA-seq_D4_shUbc9_rep3

value: MEF expressing OKSM for 4 days


title: RNA-seq_D4_shUbc9_rep1


title: RNA-seq_D4_shUbc9_rep2


title: RNA-seq_iPS_shUbc9_rep2


title: RNA-seq_ES_siUbc9_rep1


title: diseased_aorta.sample_10468.81_female

description: +CAD


title: RNA-seq_iPS_shUbc9_rep1


title: RNA-seq_MEF_shUbc9_rep3

value: MEF


title: RNA-seq_ES_siUbc9_rep2


title: RNA-seq_D7_shUbc9_rep1


title: diseased_aorta.sample_10015.71_male

description: +CAD


title: healthy_aorta.sample_10799.44_male

description: No PMH


title: RNA-seq_MEF_shUbc9_rep1


title: RNA-seq_ES_siCtrl_rep3

value: siCtrl


title: RNA-seq_ES_siCtrl_rep1


title: RNA-seq_iPS_shCtrl_rep3

value: shCtrl


title: RNA-seq_ES_siCtrl_rep2


title: RNA-seq_D7_shCtrl_rep1


title: RNA-seq_D7_shCtrl_rep2


title: RNA-seq_D7_shCtrl_rep3


title: RNA-seq_iPS_shCtrl_rep1


title: RNA-seq_MEF_shCtrl_rep3


title: RNA-seq_MEF_shCtrl_rep2


title: RNA-seq_MEF_shCtrl_rep1


title: ATAC-seq_D4_shUbc9_rep3

data_processing:
For ATAC-seq paired-end reads were mapped using the end-to-end mode and the very-sensitive parametrization of bowtie2; concordant pairs were kept (including dovetail) with a maximum fragment size of 2 Kbp.
Mapped pairs were deduplicated with the Picar toolkit v1.94 and retained pairs were then classified according to their correspondent fragment; we restricted the analysis to fragment sizes sufficiently sampled in the ATAC-seq library by selecting read pairs coming from fragments between 50 bp and 2 Kbp.
genome build: mm9
Supplementary_files_format_and_content: tdf files were generated with igvtools v2.3.25. ChIP-seq, ATAC-seq and RNA-seq libraries were merged by pooling the biological replicates. Prior to pooling, quality assurance clustering and principal component analysis were performed to identify and discard outlying replicates. The read coverage of the merged libraries was calculated over non-overlapping windows of 50 bp genome wide and library size normalization was applied to allow comparisons of the read coverage between samples: quantile normalization for the ChIP-seq and ATAC-seq datasets and DESeq2 size normalization for the RNA-seq datasets.
Supplementary_files_format_and_content: bed files with selected peaks were generated by MACS2 and then filtered according to the IDR protocol; tab delimited format: chromosome start end MACS_peak_ID -log10(p-value)*10 . foldChange -log10(p-value) -log10(q-value) relativeSummitPosition
Supplementary_files_format_and_content: RNA-seq_MEF-D4-D7-iPS-ES_shCtr-shUbc9_counts.txt: File with summarized counts (not normalized) for all the RNA-seq samples

extract_protocol:
For ATAC-seq:  according to Buenrostro et al., Nature Methods, 2013. 30min treatment with Tn5 nuclease on isolated nuclei. Experiments were done in triplicates.
Elute transposed DNA was PCR-amplified using barcode primers and purified using PCR Cleanup kit (QIAGEN)


title: ATAC-seq_D4_shUbc9_rep1


title: ChIP-seq_Sox2_D4_shUbc9_rep1

data_processing:
For ChIP-seq single-end reads were mapped to the Mus musculus mm9 reference genome using bowtie1; unique matches with no more than 2 mismatches in the best alignment stratum were kept.
Following the ENCODE guidelines, mapped reads were deduplicated with the Picar toolkit v1.94, blacklisted regions removed with bedtools v2.19.1 and the degree of IP fragment clustering determined with phantompeakqualtools v2.0. Peak calling was performed with MACS2  with default parameters for regular peak calling and using the INPUT library for the estimation of the significance of peak enrichment. Consistency of peak calling among biological replicates and the final set of peaks per condition were determined using the Irreproducible Discovery Rate (IDR) approach.
genome build: mm9
Supplementary_files_format_and_content: tdf files were generated with igvtools v2.3.25. ChIP-seq, ATAC-seq and RNA-seq libraries were merged by pooling the biological replicates. Prior to pooling, quality assurance clustering and principal component analysis were performed to identify and discard outlying replicates. The read coverage of the merged libraries was calculated over non-overlapping windows of 50 bp genome wide and library size normalization was applied to allow comparisons of the read coverage between samples: quantile normalization for the ChIP-seq and ATAC-seq datasets and DESeq2 size normalization for the RNA-seq datasets.
Supplementary_files_format_and_content: bed files with selected peaks were generated by MACS2 and then filtered according to the IDR protocol; tab delimited format: chromosome start end MACS_peak_ID -log10(p-value)*10 . foldChange -log10(p-value) -log10(q-value) relativeSummitPosition
Supplementary_files_format_and_content: RNA-seq_MEF-D4-D7-iPS-ES_shCtr-shUbc9_counts.txt: File with summarized counts (not normalized) for all the RNA-seq samples

extract_protocol:
For ChIP-Seq: 10min formaldehyde fixation followed by sonication (histone marks) or Mnase digestion (transcription factors). Immunoprecipitation was performed using ChIP-IT kit (#53040, Active Motif) following manufacturer's protocol. Experiments were done in duplicates.
Libraries prepared using Microplex library Preparation kit v2 (C05010014, Diagenode) following manufacturer's protocol (V2 02.15). Libraries were size-selected (200-400bp) and clenaed-up using Agencourt AMPure XP beads (#A63881, Beckman).

tag: chip antibody

value: Sox2 (Millipore, AB5603)


title: RNA-seq_D4_shCtrl_rep3


title: ChIP-seq_Oct4_D4_shUbc9_rep2

value: Oct3/4 (Santa Cruz, sc8628)


title: ChIP-seq_INPUT-MNase_D4_shCtrl_rep2


title: ChIP-seq_Oct4_D4_shUbc9_rep1


title: ATAC-seq_D4_shCtrl_rep2


title: ChIP-seq_Klf4_D4_shUbc9_rep2

value: Klf4 (Santa Cruz, sc20691)


title: ChIP-seq_INPUT-MNase_D4_shUbc9_rep2


title: ChIP-seq_INPUT-MNase_D4_shUbc9_rep1


title: ATAC-seq_D4_shUbc9_rep2


title: RNA-seq_D4_shCtrl_rep2


title: ChIP-seq_Sox2_D4_shUbc9_rep2


title: ATAC-seq_D4_shCtrl_rep1


title: ChIP-seq_Klf4_D4_shUbc9_rep1


title: ChIP-seq_Oct4_D4_shCtrl_rep1


title: ChIP-seq_Oct4_D4_shCtrl_rep2


title: ChIP-seq_Klf4_D4_shCtrl_rep1


title: ChIP-seq_INPUT_D4_shUbc9_rep2


title: ChIP-seq_INPUT-MNase_D4_shCtrl_rep1


title: RNA-seq_D4_shCtrl_rep1


title: ChIP-seq_Klf4_D4_shCtrl_rep2


title: ATAC-seq_D4_shCtrl_rep3


title: ChIP-seq_H3K9me3_D4_shUbc9_rep2

value: H3K9me3 (Abcam, ab8898)


title: ChIP-seq_INPUT_D4_shUbc9_rep1


title: ChIP-seq_H3K27me3_D4_shUbc9_rep2

value: H3K27me3 (Millipore, 07-449)


title: ChIP-seq_H3K4me1_D4_shUbc9_rep1

value: H3K4me1 (Abcam, ab8895)


title: ChIP-seq_Sox2_D4_shCtrl_rep1


title: ChIP-seq_H3K27me3_D4_shUbc9_rep1


title: ChIP-seq_H3K27ac_D4_shUbc9_rep1

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq_Sox2_D4_shCtrl_rep2


title: ChIP-seq_H3K27ac_D4_shUbc9_rep2


title: ChIP-seq_H3K27me3_D4_shCtrl_rep2


title: ChIP-seq_H3K27me3_D4_shCtrl_rep1


title: ChIP-seq_H3K4me3_D4_shUbc9_rep1

value: H3K4me3 (Millipore, 17-614)


title: ChIP-seq_H3K9me3_D4_shUbc9_rep1


title: ChIP-seq_H3K27ac_D4_shCtrl_rep1


title: ChIP-seq_INPUT_D4_shCtrl_rep1


title: ChIP-seq_H3K4me1_D4_shCtrl_rep1


title: ChIP-seq_H3K4me1_D4_shCtrl_rep2


title: ChIP-seq_H3K4me3_D4_shUbc9_rep2


title: ChIP-seq_H3K9me3_D4_shCtrl_rep1


title: ChIP-seq_H3K4me1_D4_shUbc9_rep2


title: ChIP-seq_H3K27ac_D4_shCtrl_rep2


title: ChIP-seq_SUMO-2_ES_rep2

value: SUMO-2 (gift from Dr. M. Dasso)

value: wild type


title: ChIP-seq_INPUT_ES_rep2


title: ChIP-seq_H3K4me3_D4_shCtrl_rep1


title: ChIP-seq_SUMO-1_ES_rep2

value: SUMO-1 (Abcam, ab32058)


title: ChIP-seq_SUMO-2_ES_rep1


title: ChIP-seq_SUMO-1_ES_rep1


title: ChIP-seq_H3K9me3_ES_rep2


title: ChIP-seq_INPUT_D4_shCtrl_rep2


title: ChIP-seq_H3K27me3_ES_rep1


title: ChIP-seq_H3K27ac_ES_rep2


title: ChIP-seq_H3K4me3_D4_shCtrl_rep2


title: ChIP-seq_H3K9me3_ES_rep1


title: ChIP-seq_H3K27me3_ES_rep2


title: ChIP-seq_H3K27ac_ES_rep1


title: ChIP-seq_H3K4me1_ES_rep2


title: ChIP-seq_INPUT_MEF_rep2


title: ChIP-seq_SUMO-2_MEF_rep2


title: ChIP-seq_H3K4me1_ES_rep1


title: ChIP-seq_H3K4me3_ES_rep2


title: ChIP-seq_H3K4me3_ES_rep1


title: ChIP-seq_SUMO-1_MEF_rep2


title: ChIP-seq_SUMO-2_MEF_rep1


title: ChIP-seq_SUMO-1_MEF_rep1


title: ChIP-seq_H3K27me3_MEF_rep2


title: ChIP-seq_H3K9me3_MEF_rep1


title: ChIP-seq_H3K27me3_MEF_rep1


title: ChIP-seq_H3K27ac_MEF_rep1


title: ChIP-seq_H3K4me1_MEF_rep2


title: ChIP-seq_H3K4me1_MEF_rep1


title: ChIP-seq_H3K4me3_MEF_rep2


title: ChIP-seq_H3K4me3_MEF_rep1


title: Sample_4340

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
We concatenated reads files into a single .fastq file for each sample.
We checked the quality of the raw reads data for each sample using FastQC (version 0.10.0) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.). We trimmed low quality bases from individual reads using CutAdapt.
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads to the reference mRNA + lncRNA transcriptome (UCSC mm10) using TopHat (version 2.0.9) and Bowtie (version 2.1.0.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis, using UCSC mm10.fa as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Genome_build: mm10
Supplementary_files_format_and_content: Text file of raw mapped read counts

source_name: WT Mouse #1

growth_protocol: Mice were grown on standard chow to 14wks of age.

extract_protocol:
Total RNA was extracted using Trizol extraction (Ambion) according to the manufacturer's instructions. Then, isolated RNAs were reverse transcribed using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) according to the manufacturers recommendations.
cDNA was prepared for sequencing using the TruSeq mRNA-Seq sample prep kit according to manufacturers recommended protocols and sequenced on an Illumina 2000 platform.

treatment_protocol: Mice were sacrificed and the LA/BC muscle was harvested and flash frozen in LN2.

value: levator ani/bulbocavernosus (LA/BC) muscle

value: WT


title: Sample_4342

source_name: WT Mouse #3


title: Sample_4343

source_name: 113Q Mouse #1


title: Sample_4344

source_name: 113Q Mouse #2


title: ChIP-seq_INPUT_MEF_rep1


title: C3B6F1_F_3

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw data was filtered to retain only read pairs with average base quality score of at least 20 for each read.
Reads were mapped against mm9 reference genome with Bismark v0.7.8 (parameters: -X 10000 --non_bs_mm -n 2 -l 50 -e 70 --chunkmbs 1024), using Bowtie v0.12.8 as the underlying alignment tool.
All mapped hits from the same library were combined then deduplicated with the Bismark deduplication script (deduplicate_bismark_alignment_output.pl; from Bismark v0.7.8).
Mapped reads were separated by source strand (plus or minus).
Redudant mapped bases from ovlerapping mapped reads in a read pair were trimmed to avoid bias in quantification of methylation status.  The first 4 and last 1 base from each mate2 read were also clipped due to observed positional methylation bias.
Alignments for multiple libraries from a given animal were combined with MergeSamFiles.jar from the Picard suite (v1.110).
Genomic cytosines were considered validated if at least 75% of mapped bases at the N, N+1, and N+2 positions from both the C67BL/6N and C3H/HeN mice were consistent with the expected reference (mm9) context.  Each genomic cytosine was then categorized by context (CpG, CHG, CHH) and status (validated or unvalidated).  Further analysis was limited to only validated CpG sites.
Percent methylation at each validated CpG sites was calculated as methylated cytosine bases / total cytosine bases, summed over both genomic strands.
Inheritance of methylation status was assessed based on read pairs overlapping both a CpG of interest and a SNV that distinguishes between the local C67BL/6N and C3H/HeN genomes; approximately 2.8M such SNVs were catalogued.
Genome_build: mm9
Supplementary_files_format_and_content: Percent methylation at each validated CpG; format = bigWig.
Supplementary_files_format_and_content: Total methylated and unmethylated cytosine counts per validated CpG (summed over both genomic strands) per animal; format = tab-delimited text.
Supplementary_files_format_and_content: Genomic coordinate and alleles of SNVs in the local C67BL/6N and C3H/HeN genomes; format = tab-delimited text.

source_name: liver

growth_protocol: Animals were maintained in climate controlled rooms (18-26C; 35-65% humidity) on a 12:12hr light:dark cycle in polycarbonate cages with irradiated, heat treated hardwood bedding (Teklad, Indianapolis, IN).  Cotton fiber nestlets (Ancare Corp., Bellmore, NY) were supplied to mice for environmental enrichment.  NIH 31 (Harlan Teklad, Indianapolis, IN) was provided ad libitum.  Reverse osmosis treated water from sterilized bottles with stainless steel sipper tubes was provided ad libitum to all animals and changed weekly.

extract_protocol:
Frozen liver tissues were quickly pulverized with BioPulverizer (Bio Spec Products Inc.) on dry ice. DNA was extracted with Allprep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer's protocol. DNA was further purified by phenol-chloroform extraction followed by ethanol precipitation.
DNA (1 µg) was spiked with 1ng unmethylated lambda DNA (Promega), fragmented using a Covaris E210 (intensity 5, duty cycle 10%, cycles per burst 200; average size  300 bp), end-repaired, A-tailed, and adapter-ligated using Truseq DNA sample prep kit (Illumina) according to the manufacturer's protocol. Adapter-ligated DNA was size selected on a Pippin Prep (Sage Science; 1.5% agarose cassette; targeted DNA size 430bp +/- 120bp). After cleaning up DNA with AMPure XP beads, bisulfite conversion was performed using EpiTect Bisulfite kit (Qiagen) with the following thermal cycles, 95°C 5 minutes, 60°C 25 minutes, 95°C 5 minutes, 60°C 85 minutes, 95°C 5 minutes, 60°C 175 minutes, 95°C 5 minutes, 60°C 180 minutes. After cleaning up DNA with AMPure XP beads DNA was eluted in 17.5 ul.  Two 4 ul aliquots of bisulfite converted DNA were amplified with PfuTurbo Cx Hotstart DNA Polymerase with following thermal cycles, 95°C 5 minutes, 98°C 30 seconds, 12 cycles of (98°C 10 seconds, 65°C 30 seconds, 72°C 30 seconds), 72°C 5 minutes. The two amplification reactions were pooled, cleaned with AMpure XP beads, and stored at -20°C until use.

value: offspring of C3H/HeN dam and C57BL/6N sire

value: female

tag: replicate animal


title: Sample_4345

source_name: 113Q Mouse #3


title: Sample_4341

source_name: WT Mouse #2


title: C3B6F1_F_2


title: ChIP-seq_H3K9me3_MEF_rep2

value: MEF


title: C3B6F1_F_1


title: C3B6F1_M_3

value: male


title: C3B6F1_M_2


title: B6C3F1_F_1

value: offspring of C57BL/6N dam and C3H/HeN sire


title: B6C3F1_F_3


title: B6C3F1_F_2


title: B6C3F1_M_2


title: B6C3F1_M_1


title: B6C3F1_M_3


title: ChIP-seq_H3K27ac_MEF_rep2


title: C3_F_3


title: C3_F_2


title: C3_F_1


title: C3_M_2


title: C3_M_1


title: C3_M_3


title: C3B6F1_M_1