title: 3T3-L1 WT_d(-2)_rep1

city: Beijing

first: fan

last: yi

address: Xue Yuan Road 38

department: Peking University

institute: State Key Laboratory of Natural and Biomimetic Drugs

description: Gene expression in  3T3-L1 WT cells differentiated on day (-2)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays (G2534A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed  at room temperature with GE Wash Buffer 1 (Agilent) and GE Wash buffer 2 (Agilent) with 37°C GE, then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v11.0.1.1).

source_name: 3T3-L1 wildtype preadipocytes induced with MDI cocktail on day (-2)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed byRNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 3T3-L1 Pre-adipocytes were cultured in DMEM supplemented with 10% newborn calf serum (Gibco), passaged at 70–80% confluence.

extract_protocol: RNA was prepared using TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. RNA clean-up was performed with RNasey Mini Kit(Qiagen p/n 74104). Quantification and quality of RNA was monitored with NanoDrop ND-1000

treatment_protocol: After cells reached confluence (day 0), cells were induced to differentiate by changing the culture medium to DMEM supplemented with MDI (0.5 mM 3-isobutyl-1-methyxanthine (Sigma),1 μM dexamethasone (Sigma) and 167 nM insulin (Sigma)) every two days.

value: 3T3-L1 adipocytes

tag: time point

tag: shRNA

value: wildtype


title: 3T3-L1 WT_d(0)_rep1

status: Public on Dec 15 2018

type: RNA

country: China

description: Gene expression in  3T3-L1 WT cells differentiated on day (0)

molecule: total RNA

organism: Mus musculus

source_name: 3T3-L1 wildtype preadipocytes induced with MDI cocktail on day (0)

tag: cell type

value: day (0)


title: 3T3-L1 WT_d(+2)_rep1

description: Gene expression in  3T3-L1 WT cells differentiated on day (+2)

source_name: 3T3-L1 wildtype preadipocytes induced with MDI cocktail on day (+2)


title: SCN_Cont-Pio_3

type: SRA

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

country: USA

institute: University of North Dakota

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Tuxedo suite of sequence analysis programs. Reads were mapped to the NCBI reference mouse transcriptome (NCBI 37) to identify transcripts.
Mapped reads were processed using the Cufflinks algorithm to calculate fragments per kilobase of exon per million mapped reads (FPKM), as presented in Trapnell et al., Nature Protocol 2012, which accurately reflects the RNA transcript number normalized for RNA length and total number of mapped reads.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: sciatic nerve

extract_protocol:
Tissues [sciatic nerve (SCN), dorsal root ganglia (DRG), kidney glomerui, and kidney cortex] were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) 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: tissue

value: sciatic nerve

tag: agent

value: pioglitazone

tag: diabetes-type

value: db+

tag: strain

value: BKS.Cg-m +/+ Leprdb/J

tag: age

value: 16-week old


title: SCN_dbdb_6

value: dbdb


title: 3T3-L1 WT_d(+4)_rep1

description: Gene expression in  3T3-L1 WT cells differentiated on day (+4)

source_name: 3T3-L1 wildtype preadipocytes induced with MDI cocktail on day (+4)


title: SCN_Cont-Pio_2


title: sh8_d(-2)_rep1

description: Gene expression in  shRNA-8 cells differentiated on day (-2)

source_name: 3T3-L1 preadipocytes stably transfected with slincRAD shRNA-8 induced with MDI cocktail on day (-2)


title: alphaPM_peudoislets_

city: Kyoto

first: Kenichiro

last: Furuyama

state: Kyoto

address: 53 Shogoinkawahara-cho, Sakyo-ku

department: Life Science Frontiers

country: Japan

institute: CiRA, Kyoto University

data_processing:
The Cell Ranger software pipeline (ver.2.1, 10xGenomics) was used to demultiplex cellular barcodes, map reads to the transcriptome using the STAR aligner to produce a sparse cell/gene matrix.
This is a 10xGenomics scRNA-seq data, so our data include the paired-end Read 1 (containing the 16 bp 10x Barcode and 10 bpUMI) and Read 2 (used to sequence the cDNA fragment) and the sample index in the i7 index read.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample

organism: Homo sapiens

source_name: pancreas

extract_protocol:
Single-cell capture and extraction procedures were performed using the Chromium Controller (10xGenomics) and the Single Cell 3? Library Kit v2 (PN-120236, PN-120237, PN-120262) according to manufacture's instructions.
The cDNA libraries were constructed using the Single Cell 3? Library Kit v2 (PN-120236, PN-120237, PN-120262) according to the manufacture's protocol.2

treatment_protocol: Pseudoislets (?GFP, ?PM or BetaGFP) and graft (?PM) were dissociated into single-cells, and single, viable and GFP+ cells were sorted on a Moflo Astrios (Beckman Coulter) system. n an

tag: cell-type

value: alpha-cellsp

tag: protocol

value: 1 week  cultured

tag: transduction

value: PM


title: alphaPM_graftsS

value: grafted


title: sh8_d(0)_rep1

description: Gene expression in  shRNA-8 cells differentiated on day (0)

source_name: 3T3-L1 preadipocytes stably transfected with slincRAD shRNA-8 induced with MDI cocktail on day (+0)


title: sh8_d(+2)_rep1

description: Gene expression in  shRNA-8 cells differentiated on day (+2)

source_name: 3T3-L1 preadipocytes stably transfected with slincRAD shRNA-8 induced with MDI cocktail on day (+2)


title: SCN_Cont-Pio_1


title: BetaGFP_pseudoisletsL

value: Beta-cellsp

value: GFP


title: SCN_Cont_6


title: SCN_Cont_4


title: alphaGFP_pseudoisletsl


title: SCN_Cont_5


title: SCN_Cont_3


title: SCN_Cont_2


title: SSc-ILD_02

city: Chicago

first: Alexander

middle: V

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
BaseCalls: HCS 3.4.0 software.
Fastq files were generated using bcl2fastq software (Illumina) as part of CellRanger V2.0 pipeline (10x Genomics) using mkfastq command.
Fastq files processed using CellRanger V2.0 pipeline (10x Genomics), mapping was done to GRCh38 version of human genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw and filtered matrices in HDF5 format.

source_name: Lung

growth_protocol: not applicable.

extract_protocol:
The lungs were infused with 1 mL dispase (Corning) with DNase I (Sigma). Lungs were incubated at room temperature with gentle agitation for 45 minutes, followed by gentle teasing using forceps into small (1-2 mm) fragments and incubation in digestion buffer for another 15 minutes. Resulting suspension was passed through passed through 70 μm cell strainer (Falcon), washed with DMEM (Corning) supplemented with 5% FBS (Corning), pelleted by centrifugation and erythrocytes were lysed using BD Pharm Lyse (BD Biosciences). Resulting single cell suspension was kept in DMEM/FBS and passed through 40 μm cell strainer (Falcon) two times. Cells were counted using Cellometer K2 (Nexcelom) with nucleic acid binding dyes acridine orange (AO) to calculate total number of nucleated cells and propidium iodide (PI) to count dead cells. All manipulations were performed using wide bore tips (Axygen).
10x Genomics, 3' single-cell RNA-seq, V2 chemistry (Protocol CG00052 Rev B).
single-cell RNA-seq (10x Genomics) sequenced on Illumina HiSeq 4000, 1 librar per lane.

treatment_protocol: not applicable.

tag: disease condition

value: Systemic slcerosis-associated interstitial lung disease


title: Triple stimuli + Rapamycin

city: Otsu

first: Shinji

last: Kume

state: Shiga

address: Seta Tsukinowa-cho

department: Medicine

institute: Shiga University of Medical Science

description:
1% HG Pal R
Triple stimuli + Rapamycin

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mProx24 cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: mProx24 cell were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C and 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Subconfluent cells were incubated at 37°C and 1% O2 with same medium for 12 h, followed by stimulation with 150 μM of palmitate bound to bovine serum albumin (0.15%) for 9 hours. 0.4μg/ml Rapamycin was treated for 12 h before stimulation with palmitate.

value: proximal tubular cell

tag: cell line

value: mProx24 cell


title: SCN_Cont_1


title: Donor_08

value: Donor


title: MGL_165

city: Columbus

first: Kristina

middle: Grace

last: Witcher

state: OH

address: 460 Medical Center Dr

department: Neuroscience

institute: Ohio State University

data_processing:
FASTQ files were aligned to mm10 reference genome using STAR aligner
DESeq2 was used to generate normalized counts
Genome_build: mm10
Supplementary_files_format_and_content: csv of DESeq2 normalized counts

source_name: Sorted microglia

extract_protocol:
Microglia were fluorescence-activated cell sorted (FACS) based on expression of CD11b and CD45 (intermediate) from whole-brain homogenate. Cells were immediately lysed and RNA was extracted using the PicoPure kit per manufacterers recommendations (Arcturus). Coronal brain sections were collected immediately at time of sacrifice and flash frozen in liquid nitrogen. RNA was extracted using Trizol per manufacturers protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq, 25mil 75bp SE reads

treatment_protocol: Mice were either fed vehicle diet (CON) or administered PLX5622 (1200ppm in AIN7A chow) for 3 weeks followed by 3 weeks of wash-out (REPOP)

value: BALB/c

value: 2 months

tag: developmental stage

value: ADULT

tag: treatment

value: REPOP

value: Sorted microglia

tag: known experimental batch

value: THREE


title: MGL_166

value: CON


title: MGL_164

value: 22 months

value: AGED


title: Triple stimuli

description:
1% HG Pal
Triple stimuli


title: High glucose

description:
20% HG PBS
High glucose


title: High FFAs

description:
20% NG Pal
High FFAs


title: MGL_161


title: MGL_160


title: Donor_07


title: Myositis_ILD_01

value: Myositis-associated interstitial lng disease


title: CD31+CD105low

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
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 a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: H1 cell line

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 3 days.

extract_protocol:
H1 drived 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: CD31+CD34+CD105lowHEPs derived from day4 of hematopoietic differentiation


title: MGL_159


title: Hypoxia

description:
1% NG PBS
Hypoxia


title: SSc-ILD_01


title: Control

description:
20% NG PBS
Control


title: MGL_157

value: TWO


title: MGL_158


title: sh8_d(+4)_rep1

description: Gene expression in  shRNA-8 cells differentiated on day (+4)

source_name: 3T3-L1 preadipocytes stably transfected with slincRAD shRNA-8 induced with MDI cocktail on day (+4)

value: 3T3-L1 adipocytes


title: MGL_156


title: WT-2

city: Seoul

first: Bongkun

last: Choi

address: Olympic-ro 43-gil

department: Department of Biomedical Sciences

country: South Korea

institute: Asan Medical Center, University of Ulsan College of Medicine

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label: biotin

source_name: wild type mice

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

extract_protocol: RNA extraction

value: aorta

tag: genotype

value: wild type


title: HP_01

value: Hypersensitivity pneumonitis


title: eNOS-KO-19

source_name: endothelial nitric oxide synthase (eNOS)-deficient mice


title: WT-5


title: eNOS-KO-15

value: endothelial nitric oxide synthase (eNOS)-deficient


title: MGL_163

value: BALB/c


title: MGL_162

value: 2 months


title: Donor_05

value: Donor


title: MGL_154

value: ADULT


title: pAVICs Stage 3+KPT biological replicate 3

city: Milwaukee

first: Punashi

last: Dutta

state: WI

address: 8701 Watertown Plank Road

department: Cardiovascular

institute: Medical College of Wisconsin

description:
Nod_KPT-3
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217559

data_processing:
Amplified cDNA libraries suitable for sequencing were prepared from 500 nanograms (ng) of DNA-free total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.; Part # RS-122-2103).
Sequence alignment was performed using TopHat v2.1.0
Based on the quality results, the reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed
The RPKM values were filtered to retain a list of genes with a minimum of approximately 50 mapped reads in one or more samples.
Genome_build: scr3 reference genome
Supplementary_files_format_and_content: .txt files include rpkm for exons and genes for each sample

organism: Sus scrofa

source_name: porcine aortic valve interstitial cells (pAVICs)

growth_protocol: Cells were grown on glass for 5,8 or 12 days (depending on when the stages were observed) in DMEM media

extract_protocol:
RNA was isolated using the RNAeasy kit from Qiagen
Amplified cDNA libraries suitable for sequencing were prepared from 500 nanograms (ng) of DNA-free total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.; Part # RS-122-2103).

treatment_protocol: Stage3+DMSO and Stage3+KPT samples received DMSO/KPT at Stage 3

value: aortic valve interstitial cells

tag: calcification stages & treatment

value: Stage 3+KPT

tag: calcification stimulus

value: glass


title: MGL_152

value: 22 months

value: REPOP

value: Sorted microglia


title: eNOS-KO-11


title: MGL_153


title: MGL_150

value: CON

value: ONE


title: IPF_04

value: Idiopathic pulmonary fibrosis


title: Donor_04


title: MGL_149


title: WT-3

value: aorta


title: pAVICs Stage 3+KPT biological replicate 2

description:
Nod_KPT-2
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217558

tag: cell type


title: IPF_03


title: Donor_06


title: pAVICs Stage 3+KPT biological replicate 1

description:
Nod_KPT-1
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217557

tag: tissue


title: MGL_155

value: AGED

value: TWO


title: pAVICs Stage 3+DMSO biological replicate 3

description:
Nod_DMSO-3
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217556

value: Stage 3+DMSO


title: Donor_03


title: MGL_147

value: BALB/c


title: MGL_148


title: MGL_146

value: 2 months


title: MGL_144


title: Cryobiopsy


title: MGL_143


title: BRSL_166

source_name: Coronal brain section

value: Coronal brain section

value: THREE


title: MGL_145

value: ADULT


title: pAVICs Stage 3+DMSO biological replicate 1

description:
Nod_DMSO-1
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217554

value: aortic valve interstitial cells


title: pAVICs Stage 3+DMSO biological replicate 2

description:
Nod_DMSO-2
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217555

value: glass


title: MGL_151

value: 22 months


title: Donor_02

value: Donor


title: pAVICs Stage 2 biological replicate 3

description:
Day8-3
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217553

value: Stage 2


title: BRSL_165

value: REPOP


title: BRSL_164


title: pAVICs Stage 2 biological replicate 2

description:
Day8-2
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217552


title: IPF_02


title: BRSL_163

value: CON


title: Donor_01


title: Triple stimuli + Rapamycin

description:
1% HG Pal R
Triple stimuli + Rapamycin

hyb_protocol: Labeled samples were incubated at 55℃ for 20 hours with Hybri Spike In, Blocking Agent and HI-PRM Hybridazation Buffer.

scan_protocol: Images were scaned using Agilent Technologies Microarray Scanner, and quantified using Agilent Feature Extraction 10.7.3.1.

label_protocol: 100 ng of total RNA were dephosphorylated with CIP at 37°C for 30 min, then ligated at 16°C for 2 h in the presence of T4 RNA ligase and 3μL pCp-Cy3.

value: proximal tubular cell

value: mProx24 cell


title: BRSL_161


title: Triple stimuli

description:
1% HG Pal
Triple stimuli


title: pAVICs Stage 1 biological replicate 2

description:
Day5-2
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217549

value: aorta

value: Stage 1


title: RPD3 S418A (19)

city: Cambridge

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

data_processing:
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the yeast reference genome transcripts (downloaded from the SGD database) using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Differential gene expression analysis between each each strain and S288c (WT) was performed using DESeq2 v 3.8
Genome_build: R64-2-1 2014_11_18 (SGD database)
Supplementary_files_format_and_content: Tab-delimited files with the “kallisto_” prefix report the reads counts for each transcript, as well as the TPM values. Tab-delimited files with the “deseq_” prefix report the differential gene expression between each strain and the reference in the same growth condition.

organism: Saccharomyces cerevisiae

source_name: Yeast strain culture

growth_protocol: Samples were grown in synthetic defined media until an O.D. concentration of 0.4

extract_protocol:
Total RNA was harvested at O.D. 0.4
Total RNA was extracted using the MasterPure Yeast RNA purification Kit (Biozym, Epicentre)
The samples were quality tested on the Fragment analyzer (AATi/Agilent) using the Standard sensitivity RNA kit (AATi/Agilent), 600 ng of total RNA was used for library preparation. The libraries were prepared using the Truseq Stranded mRNA kit (Illumina) using a Beckman Fxp liquid handler system.

treatment_protocol: Half of the samples were exposed for 4 hours to caffeine with 20mM concentration

value: RPD3 S418A

tag: growth condition

value: Synthetic defined media


title: RPD3 S418A (11)


title: pAVICs Stage 1 biological replicate 3

description:
Day5-3
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217550


title: High FFAs

description:
20% NG Pal
High FFAs


title: BRSL_160

value: BALB/c

value: AGED


title: RPD3 KO (20)

value: RPD3 KO


title: BRSL_159

value: Coronal brain section

value: THREE


title: BRSL_158

value: 2 months

value: ADULT

value: TWO


title: Hypoxia

description:
1% NG PBS
Hypoxia


title: Control

description:
20% NG PBS
Control


title: High glucose

description:
20% HG PBS
High glucose


title: BRSL_157


title: IPF_01

value: Idiopathic pulmonary fibrosis


title: BRSL_156

value: 22 months

value: REPOP


title: pAVICs Stage 2 biological replicate 1

description:
Day8-1
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217551

value: aortic valve interstitial cells

value: Stage 2

value: glass


title: BRSL_155

value: CON


title: BRSL_154


title: RPD3 KO (4)


title: BRSL_162


title: SWI3 S237A (10)

value: SWI3 S237A


title: SWI3 S237A (2)

value: Synthetic defined media


title: C_S3

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

department: Plant Science

institute: South Dakota State University

description: Control whole shoot tissue

data_processing:
FASTQ files were explored using FASTX toolkit and cleaned using Prinseq
The cleaning procedure included, trimming low quality reads from both ends until a bp of Phred quality score >= 20 and filtering out reads having below 20 nt.
Bowtie2 V2.1.0 was used to build the index of reference genome, the 12x sequence of V. vinifera PN40024.
TopHat V2.0.8 was used to map each of the cleaned samples to the bowtie build index and Cufflinks V2.2.2 was used to quantify transcript abundance in terms of RPKM.
Differential gene expression, in WD relative to C treatments, was tested by the Cuffdiff program within Cufflinks using its default parameters. V. vinifera V1 gene annotation was used.
Genome_build: 12x V. vinifera PN40024 (http://genomes.cribi.unipd.it/DATA/)
Supplementary_files_format_and_content: text files containing count, RPKM, or cuffdiff output (as indicated in the file name) with the identifiers at:
http://plants.ensembl.org/Vitis_vinifera/Info/Index
http://www.plantgdb.org/VvGDB/

organism: Vitis riparia

growth_protocol: Spur-pruned, V. riparia Michx. vines were removed from cold storage, root pruned, repotted in 15 L pots, and grown under a long photoperiod (15 h) with 25/20°C ± 3°C day/night temperatures and 600 to 1400 μmol m-2 sec-1 photosynthetic photon flux in a climate-controlled, un-shaded glass greenhouse (En Tech Control Systems Inc., Montrose, MN) in Brookings, SD, USA (44.3°N).

extract_protocol:
Total RNA was extracted from 100 mg of each replicate (n=3) frozen pulverized shoot tips as described by Mathiason K. et al. (2009). Total RNA was extracted from root tips (5 cm) of each replicate (n=3) using the Qiagen Rneasy Midi RNA isolation kit (Qiagen, 75144) according to manufacturer protocol.
Total RNA samples were sent to Cornell University Life Sciences Core Laboratories and single-end sequences were generated using an Illumina HiSeq 2000.

treatment_protocol: Three shoots were allowed to develop on each grapevine; after 30 days growth, when the grapevine shoots had reached 12-15 nodes, 36 grapevines were randomized into two groups:  water deficit (WD) and well-watered control (C).  Five days after randomization, differential water treatments began in replicates (3 vines/ replicate) of each treatment:  WD received no water and C received 2 L of tap water each day.  Root and shoot samples from the 14 d C and WD treatments were used for transcriptomic analysis, as this time point showed distinct physiological differences between treatments.

tag: water condition

value: Control

value: Shoot


title: BRSL_153

tag: strain

value: BALB/c


title: S288c (17)

value: wild type


title: pAVICs Stage 1 biological replicate 1

description:
Day5-1
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217548

value: aorta

value: Stage 1


title: BRSL_152

tag: age

value: AGED

value: Coronal brain section


title: C_S1

description: Control whole shoot tissue


title: BRSL_151

value: TWO


title: S288c (9)


title: RPD3 S418A (3)

value: RPD3 S418A


title: S288c (1)


title: RPD3 KO (12)

value: RPD3 KO


title: BRSL_150

value: 2 months

value: ADULT

value: ONE


title: BRSL_149

value: REPOP


title: WD_S3

description: Water deficit whole shoot tissue

source_name: Water Deficit_Shoot

value: Water Deficit


title: WD_S1

description: Water deficit whole shoot tissue


title: WD_S2

description: Water deficit whole shoot tissue


title: BRSL_148

value: 22 months


title: mir-83 day 12_replicate 1_RNASeq

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description:
miR-83 D12_rep1
Mir-83d12_HVLMNCCXX_L4_1

data_processing:
reads were mapped to the C. elegans genome(ce11) by Bowtie2
edgeR was used to calculate the differential genes
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

organism: Caenorhabditis elegans

source_name: mir-83 day 12

growth_protocol: Worms were cultured on FuDR-containing NGM plates at 20 ℃ until adult day 4 and day 12.

extract_protocol:
Total RNA was extracted using the Trizol method.
Libraries were prepared and sequenced according to Illumina's instructions.

treatment_protocol: Worms were washed with three changes of M9 buffer to remove excess OP50 bacteria.

tag: genotype/variation

value: mir-83 mutant

value: adult day 12

value: whole worms


title: mir-83 day 12_replicate 2_RNASeq

description:
miR-83 D12_rep2
mir83D12_1


title: mir-83 day 4_replicate 2_RNASeq

description:
miR-83 D4_rep2
mir83D4_1

source_name: mir-83 day 4

value: adult day 4


title: C_R3

description: Control whole root tissue

value: Control

value: Root


title: SWI3 S237A (18)

value: SWI3 S237A

value: Synthetic defined media


title: BRSL_147

value: BALB/c

value: AGED

value: CON

value: Coronal brain section


title: C_R2

description: Control whole root tissue


title: BRSL_146

value: 2 months

value: ADULT


title: N2 day 12_replicate 2_RNASeq

description:
N2D12_rep2
N2D12_1

source_name: N2 day 12

value: wild type


title: C_R1

description: Control whole root tissue


title: BRSL_145

value: REPOP

value: ONE


title: N2 day 12_replicate 1_RNASeq

description:
N2D12_rep1
N2d12_HVLMNCCXX_L4_1


title: C_S2

description: Control whole shoot tissue

value: Shoot


title: N2 day 4_replicate 2_RNASeq

description:
N2D4_rep2
N2D4_1

source_name: N2 day 4


title: WD_R1

description: Water deficit whole root tissue

source_name: Water Deficit_Root

value: Water Deficit


title: BRSL_143

value: 22 months


title: N2 day 4_replicate 1_RNASeq

description:
N2D4_rep1
N2-Day4_HNG7CCCXX_L4_1

value: adult day 4

value: whole worms


title: mir-83 day 4_replicate 1_RNASeq

description:
miR-83 D4_rep1
miR-83-Day4_HNG7CCCXX_L4_1

value: mir-83 mutant


title: BRSL_144


title: WD_R2

description: Water deficit whole root tissue

value: Root


title: WD_R3

description: Water deficit whole root tissue


title: Ileum-WT_PCN-Rep5

status: Public on Dec 14 2018

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

country: France

institute: INRAe

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 19 out of 23 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 39860 spots out of 62976 were selected.  The mean signal of the 11 first samples and 12 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 37161 rows each corresponding to a unique ProbeName (provided as data Matrix).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: At sacrifice, the liver, the three parts of the small intestine (duodenum, jejunum, ileum), and the colon were removed and snap-frozen in liquid nitrogen and stored at -80°C until used for RNA extraction. Total RNA was extracted with TRIzol reagent (Invitrogen).

treatment_protocol: Twelve six-week old wild-type (WT) C57BL/6J male mice were purchased from Charles River and 12 Pxr-/- animals (backcrossed on the C57Bl/6J background) are bred for 10y in our animal facility. Mice were acclimatized for two weeks, then randomly allocated to the different experimental groups: wild-type control (WT CONT, n=6), wild-type PCN-treated (WT PCN, n=6), Pxr-/- control (Pxr-/- CONT, n=6), Pxr-/- PCN-treated (Pxr-/- PCN, n=6). PCN-treated mice received a daily intraperitoneal injection of PCN (100 mg/kg) in corn oil for 4 days while control mice received corn oil only. Mice were killed at ZT6, 6 hours after the last PCN injection, in the fed state.

tag: strain background

value: WT

tag: Sex

value: male

value: PCN

value: Ileum

tag: washbatch


title: Ileum-PXRKO_PCN-Rep1

value: PXRKO


title: Ileum-PXRKO_Ctl-Rep3

value: Ctl


title: Ileum-PXRKO_PCN-Rep2


title: Ileum-PXRKO_PCN-Rep3


title: Ileum-WT_Ctl-Rep3


title: Ileum-WT_Ctl-Rep5


title: Ileum-PXRKO_Ctl-Rep2


title: Ileum-WT_Ctl-Rep2


title: Ileum-PXRKO_Ctl-Rep5


title: Ileum-WT_PCN-Rep4


title: Ileum-WT_PCN-Rep2


title: Liver-WT_Ctl-Rep6

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 19 out of 23 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 35218 spots out of 62976 were selected.  The mean signal of the 12 first samples and 11 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the qsmooth method using the qsmooth function from the qsmooth R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32574 rows each corresponding to a unique ProbeName (provided as data Matrix).

value: Liver


title: Ileum-PXRKO_Ctl-Rep1


title: Ileum-WT_PCN-Rep1


title: Ileum-WT_Ctl-Rep4


title: Ileum-WT_Ctl-Rep1


title: Ileum-WT_Ctl-Rep6


title: Liver-PXRKO_Ctl-Rep3


title: Ileum-PXRKO_Ctl-Rep4


title: Liver-PXRKO_PCN-Rep6


title: Ileum-PXRKO_PCN-Rep4


title: Ileum-WT_PCN-Rep3


title: Liver-WT_Ctl-Rep4


title: Liver-WT_PCN-Rep2


title: Ileum-PXRKO_Ctl-Rep6


title: Liver-PXRKO_Ctl-Rep6


title: Ileum-PXRKO_PCN-Rep5


title: Ileum-PXRKO_PCN-Rep6


title: siSRRM1 [r12798]

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

data_processing:
all samples are analyzed by QC
all samples are analyzed by Ericscript
Raw reads were filtered using NGSQC toolkit to retain high quality reads. Gene fusion candidates were predicted using EricScript software with default parameters. Fusions were further filtered based on EricScore (>=0.6) to retain fusions with high confidence of prediction followed by filtering out M/M fusions which are likely to be artifacts (see reference PMC4824105). Output file from EricScript software (MyEric.results.filtered.tsv) were processed using in-house perl scripts.
EricScript produces 3 files in its main output folder. These files are “MyEric.results.filtered.tsv”, “MyEric.results.total.tsv” and “MyEric.Summary.RData”. EricScript produces MyEric.results.total.tsv file and uses its own filtering to select fusions from this file and saves in the MyEric.results.filtered.tsv file. The file MyEric.Summary.Rdata is a temporary file during running the software.
Genome_build: hg38
Supplementary_files_format_and_content: EricScript produces 3 files in its main output folder. These files are “MyEric.results.filtered.tsv”, “MyEric.results.total.tsv” and “MyEric.Summary.RData”. EricScript produces MyEric.results.total.tsv file and uses its own filtering to select fusions from this file and saves in the MyEric.results.filtered.tsv file. The file MyEric.Summary.Rdata is a temporary file during running the software.

source_name: 293T cells with cis-SAGe reporter

growth_protocol: The 293T cells are maintained in DMEM high glucose medium with 10% FBS, 1% Pen/Strep at 37 degree incubator with 5% CO2.

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Knocking down using siRNAs

tag: sirna


title: siSF3B1 [r12797]


title: siN-T [r12796]

value: siN-T


title: Liver-WT_PCN-Rep3


title: Liver-WT_Ctl-Rep2


title: siN-T [S11441]

data_processing:
all samples are analyzed by QC
all samples are analyzed by Ericscript
Raw reads were filtered using NGSQC toolkit to retain high quality reads. Gene fusion candidates were predicted using EricScript software with default parameters. Fusions were further filtered based on EricScore (>=0.6) to retain fusions with high confidence of prediction followed by filtering out M/M fusions which are likely to be artifacts (see reference PMC4824105). Output file from EricScript software (MyEric.results.filtered.tsv) were processed using in-house perl scripts.
EricScript produces 3 files in its main output folder. These files are “MyEric.results.filtered.tsv”, “MyEric.results.total.tsv” and “MyEric.Summary.RData”. EricScript produces MyEric.results.total.tsv file and uses its own filtering to select fusions from this file and saves in the MyEric.results.filtered.tsv file. The file MyEric.Summary.Rdata is a temporary file during running the software.
genome build: hg38
processed data files format and content: EricScript produces 3 files in its main output folder. These files are “MyEric.results.filtered.tsv”, “MyEric.results.total.tsv” and “MyEric.Summary.RData”. EricScript produces MyEric.results.total.tsv file and uses its own filtering to select fusions from this file and saves in the MyEric.results.filtered.tsv file. The file MyEric.Summary.Rdata is a temporary file during running the software.


title: siSRRM1 [S11449]


title: Liver-PXRKO_PCN-Rep3


title: siSF3B1 [S11448]


title: Liver-PXRKO_Ctl-Rep4


title: Liver-PXRKO_Ctl-Rep1


title: Liver-WT_PCN-Rep1


title: Liver-WT_Ctl-Rep5


title: Liver-WT_Ctl-Rep3


title: Liver-PXRKO_PCN-Rep5


title: Liver-PXRKO_Ctl-Rep2


title: Liver-WT_PCN-Rep4


title: Liver-PXRKO_PCN-Rep4


title: Liver-WT_Ctl-Rep1


title: Liver-WT_PCN-Rep5


title: Liver-PXRKO_Ctl-Rep5


title: Liver-PXRKO_PCN-Rep2


title: Liver-PXRKO_PCN-Rep1


title: Patient 2957, Wk4 treatment, technical replicate 2

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

description: Gene expression data from Liver from 53 year old White Male, at Wk4 treatment

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 2.0 ST arrays, incubated at 45°C for 18 hours rotating at 60 rpm in a GeneChip Hybridization oven (Affymetrix Inc, CA).

scan_protocol: Hybridized arrays were washed and stained with GeneChip HWS kit (Affymetrix Inc, CA) using Affymetrix 450 Fluidic Stations.

data_processing: Raw files from Affymetrix Human Gene 2.0 array were preprocessed using RMA in R (Bioconductor oligo package, v.1.34.2).Technical replicates were averaged for each sample and averages were used for further analysis by linear mixed models using the Bioconductor limma package.

label_protocol: Ten nanograms of total RNA from each sample was used for cDNA library preparation using Ovation Pico WTA system V2 kit (NuGEN Technologies Inc, CA).  For each array, 4 ug of cDNA was fragmented and biotin labeled using Encore Biotin module (NUGEN Technologies Inc, CA) and then added with hybridization control reagents (20x Eukaryotic controls and Control Oligo B2, Affymetrix Inc. CA).

extract_protocol: Total RNA extraction from liver tissue was performed on paired liver biopsies using RNeasy kit (Qiagen). The quality of isolated total RNA was assessed using bioanalyzer, (Agilent Technologies, CA) and RIN (RNA Integrity Number); values were generally above 8.0 for most of the samples.

treatment_protocol: Core liver biopsies were immediately placed in RNA later and stored at -80C until handling.

tag: patient id

tag: technical replicate

value: liver

tag: gender

value: Male

tag: race

value: White

tag: disease state

value: HCV genotype 1b-infected patient


title: Patient 2957, Base treatment, technical replicate 1

description: Gene expression data from Liver from 53 year old White Male, at Base treatment

tag: treatment

value: Base


title: Patient 2783, Wk2 treatment, technical replicate 2

description: Gene expression data from Liver from 70 year old African American Female, at Wk2 treatment

value: Female

value: African American


title: Patient 2783, Base treatment, technical replicate 2

description: Gene expression data from Liver from 70 year old African American Female, at Base treatment


title: Patient 2783, Wk2 treatment, technical replicate 1

source_name: Liver from 70 year old African American Female, at Wk2 treatment


title: Patient 2957, Base treatment, technical replicate 2

source_name: Liver from 53 year old White Male, at Base treatment


title: Patient 2168, Wk2 treatment, technical replicate 2

description: Gene expression data from Liver from 68 year old Asian Female, at Wk2 treatment

value: Asian


title: Patient 2783, Base treatment, technical replicate 1

source_name: Liver from 70 year old African American Female, at Base treatment


title: Patient 1505, Wk4 treatment, technical replicate 2

description: Gene expression data from Liver from 69 year old African American Male, at Wk4 treatment


title: Patient 1154, Wk4 treatment, technical replicate 2

description: Gene expression data from Liver from 63 year old White Female, at Wk4 treatment


title: Patient 1230, Base treatment, technical replicate 1

description: Gene expression data from Liver from 61 year old White Male, at Base treatment


title: Patient 1230, Base treatment, technical replicate 2

source_name: Liver from 61 year old White Male, at Base treatment


title: Patient 1230, Wk4 treatment, technical replicate 1

description: Gene expression data from Liver from 61 year old White Male, at Wk4 treatment


title: Patient 1154, Base treatment, technical replicate 2

description: Gene expression data from Liver from 63 year old White Female, at Base treatment


title: Patient 1505, Wk4 treatment, technical replicate 1

source_name: Liver from 69 year old African American Male, at Wk4 treatment


title: Patient 1059, Wk2 treatment, technical replicate 2

description: Gene expression data from Liver from 62 year old White Male, at Wk2 treatment


title: Patient 975, Base treatment, technical replicate 2

description: Gene expression data from Liver from 75 year old African American Female, at Base treatment


title: Patient 1230, Wk4 treatment, technical replicate 2

source_name: Liver from 61 year old White Male, at Wk4 treatment


title: Patient 1154, Wk4 treatment, technical replicate 1

source_name: Liver from 63 year old White Female, at Wk4 treatment


title: Patient 2168, Base treatment, technical replicate 1

description: Gene expression data from Liver from 68 year old Asian Female, at Base treatment


title: Patient 1154, Base treatment, technical replicate 1

source_name: Liver from 63 year old White Female, at Base treatment


title: Patient 2168, Wk2 treatment, technical replicate 1

source_name: Liver from 68 year old Asian Female, at Wk2 treatment


title: Patient 1505, Base treatment, technical replicate 2

description: Gene expression data from Liver from 69 year old African American Male, at Base treatment


title: Patient 1059, Wk2 treatment, technical replicate 1

source_name: Liver from 62 year old White Male, at Wk2 treatment


title: Patient 1059, Base treatment, technical replicate 2

description: Gene expression data from Liver from 62 year old White Male, at Base treatment


title: Patient 1505, Base treatment, technical replicate 1

source_name: Liver from 69 year old African American Male, at Base treatment


title: Patient 1059, Base treatment, technical replicate 1

source_name: Liver from 62 year old White Male, at Base treatment


title: Patient 975, Wk2 treatment, technical replicate 2

description: Gene expression data from Liver from 75 year old African American Female, at Wk2 treatment


title: Patient 814, Wk2 treatment, technical replicate 1

description: Gene expression data from Liver from 53 year old White Female, at Wk2 treatment


title: Patient 975, Wk2 treatment, technical replicate 1

source_name: Liver from 75 year old African American Female, at Wk2 treatment


title: Patient 814, Wk2 treatment, technical replicate 2

source_name: Liver from 53 year old White Female, at Wk2 treatment


title: Patient 2957, Wk4 treatment, technical replicate 1

description: Gene expression data from Liver from 53 year old White Male, at Wk4 treatment


title: Patient 975, Base treatment, technical replicate 1

source_name: Liver from 75 year old African American Female, at Base treatment


title: fragileX_sample_103108GP

city: Los Angeles

first: Grace

last: Xiao

state: CA

address: 610 Charles E. Young Drive S

department: UCLA Department of Integrative Biology and Physiology

institute: UCLA

description:
polyA-selected
fragileX definition: sample derived from patient diagnosed with Fragile X Syndrome

data_processing:
Map fastq reads with HISAT2 hisat2 -q --phred64 -x grch37_tran/genome_tran  --no-unal --reorder --no-mixed
Extract uniquely mapped reads from SAM files
Remap unmapped reads with hyperediting pipeline. In brief, convert all adenosines to guanosines and align to modified hg19 genome where adenosines are also substituted by guanosines.
Obtain uniquely mapped reads pairs from hyperediting pipeline and combine with uniquely mapped reads from first round of read mapping
Identify RNA-DNA differences between mapped reads and hg19 reference genome.
Apply log-likelihood test to determine whether RDD is likely resulted from sequencing error (Bahn et. al. PMID: 21960545)
Apply posterior filters to remove RDD sites that are likely caused by technical artifats (Bahn et. al. PMID: 21960545 and Lee et. al. PMID: 23598527)
Retain only highly prevalent editing sites. In particular, filter for editing sites where both pooled fragile X and pooled controls have at least 10 reads each and where pooled fragile X or pooled controls have editing ratio at least 0.1
Also quantify gene expression as RPKM values over the exon union of ENSEMBL transcripts in hg19.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression (RPKM)

source_name: human frontal cortex

growth_protocol: Tissues

extract_protocol:
Total RNA was extracted using TRIzol from frozen tissues
RNA-Seq libraries were prepared using NEBNext Poly (A) mRNA magnetic isolation module (NEB, E7490) followed by NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB, E7760S) according to manufacturer’s instruction.

value: Brain


title: Patient 513, Base treatment, technical replicate 2

description: Gene expression data from Liver from 41 year old Asian Male, at Base treatment


title: Patient 513, Wk4 treatment, technical replicate 2

description: Gene expression data from Liver from 41 year old Asian Male, at Wk4 treatment


title: Patient 814, Base treatment, technical replicate 2

description: Gene expression data from Liver from 53 year old White Female, at Base treatment


title: Patient 110, Base treatment, technical replicate 2

description: Gene expression data from Liver from 65 year old African American Female, at Base treatment


title: control_sample_103710XX

description:
polyA-selected
control definition: sample derived from control individual


title: control_sample_UCD1407


title: siLOL-1

city: Shanghai

first: Wei

last: Sun

address: Dongan Road 270

department: Department of Musculoskeletal Surgery

institute: Fudan University Shanghai Cancer Center

data_processing:
HiSeq 2000 (Illumina, San Diego, CA) was used for basecalling.
Sequencing reads from the RNA-seq data were aligned using the spliced read aligner HISAT2
Genome_build: The Ensembl human genome assembly (Genome Reference Consortium GRCh38) was supplied as the reference genome.

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were cultured in RPMI-1640.

extract_protocol:
Total RNA were extracted using Trizol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocol

treatment_protocol: NC andLOL siRNA transfected MCF-7 cells were cultured in conditioned medium for 2 days

tag: cell line

tag: transfection

value: siLOL


title: RNA-seq siSCR Rep2

city: Urbana

first: Miroslav

last: Hejna

state: Illinois

address: 1110 West Green Street

department: Department of Physics

institute: University of Illinois

data_processing:
Alignment to genome (hg19) using Bowtie2
Deduplication of aligned reads
Peak calling using Macs2 (narrow peak option for MITF, broad peak option for H3K4me3)
Cuffdiff used for RNA-seq differential expression
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak and broadPeak files of ChIP-seq peaks, CuffDiff differential expression output

source_name: Melanocyte

growth_protocol: Primary human melanocytes were cultured in TIVA medium (Ham’s F-10 (Corning), 7.5% fetal bovine serum (Atlanta Biologicals), 50 ng/ml 12-O-tetradecanoylphorbol-13-acetate, 0.1 mM 3-isobutyl-1-methylxanthine, 1 mM sodium orthovanadate, 1 mM N6,2′-O-Dibutyryladenosine 3′,5′-cyclic monophosphate sodium salt (Sigma-Aldrich)).

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary human melanocytes were transfected with control siRNA pool (siGENOME Non-Targeting siRNA #2 (Dharmacon)) or siRNA pool against MITF (siGENOME MITF siRNA (Dharmacon)) using lipidoid and incubated 72 hours.

value: siSCR


title: siNC

value: siNC


title: fragileX_sample_JS03

tag: tissue


title: Input Melanocyte siSCR

library_source: genomic

molecule: genomic DNA

extract_protocol:
Lysates were prepared from sonicated cells and histone-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from ChIP DNA using the NEBNext ChIP-seq library prep reagent set for Illumina (New England Biolabs) as per manufacturer’s protocol with the following modifications: DNA purification with Qiaquick PCR purification or Minelute PCR purification kits, 2% agarose gel DNA size selection, custom indexed adapters, and 18 cycles of PCR amplification. The libraries were sequenced on an Illumina HiSeq 2000 (single-end, 75 bp).


title: Input Melanocyte siMITF

value: siMITF


title: C1-1772117-118_H12

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis. We rejected cells that had less than 2000 mRNA molecules,  more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a   separate cluster with no specific gene expression (putative damaged or dead cells).  Genes  that were   dete  cted at less than  4 molecules in the whole datasets were eliminated.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

molecule: polyA RNA

source_name: LT-NES SAI2 cell

growth_protocol: Cells were grown in maintanence medium based on DMEM F12 Glutamax Medium (GIBCO, LifeTechnologies) supplemented  with N2 (1:100, GIBCO, LifeTechnologies), B27 (1:1000, GIBCO, LifeTechnologies), and a  combination of growth factors hEGF (10 ng/ml, R&D) and FGF2 (10 ng/ml, R&D).

extract_protocol:
Cells were trypsinized with TrypLE Select and cell resuspensions were kept in maintenance medium with albumin from bovine serum until loading on the Fluidigm chip.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3’ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.

tag: cell type

value: long-term self-renewing neuroepithelial-like stem cells


title: C1-1772117-118_H10


title: ChIP-seq H3K4me3 Melanocyte siSCR

tag: antibody


title: Patient 814, Base treatment, technical replicate 1

source_name: Liver from 53 year old White Female, at Base treatment

tag: age


title: Patient 110, Wk4 treatment, technical replicate 2

description: Gene expression data from Liver from 65 year old African American Female, at Wk4 treatment


title: C1-1772117-118_H07


title: ChIP-seq H3K4me3 Melanocyte siMITF


title: Patient 513, Base treatment, technical replicate 1

source_name: Liver from 41 year old Asian Male, at Base treatment


title: Patient 110, Base treatment, technical replicate 1

source_name: Liver from 65 year old African American Female, at Base treatment


title: C1-1772117-118_H06


title: Patient 110, Wk4 treatment, technical replicate 1

source_name: Liver from 65 year old African American Female, at Wk4 treatment


title: Patient 513, Wk4 treatment, technical replicate 1

source_name: Liver from 41 year old Asian Male, at Wk4 treatment


title: RNA-seq siSCR Rep1


title: RNA-seq siMITF Rep2


title: RNA-seq siMITF Rep1


title: C1-1772117-118_G11


title: C1-1772117-118_G12


title: C1-1772117-118_H11


title: C1-1772117-118_G08


title: C1-1772117-118_G09


title: C1-1772117-118_G10


title: C1-1772117-118_H08


title: C1-1772117-118_H04


title: C1-1772117-118_H03


title: C1-1772117-118_H05


title: C1-1772117-118_G05


title: C1-1772117-118_G03


title: C1-1772117-118_G02


title: C1-1772117-118_G04


title: C1-1772117-118_G06


title: C1-1772117-118_H09


title: C1-1772117-118_F07


title: C1-1772117-118_F10


title: C1-1772117-118_F09


title: C1-1772117-118_F06


title: C1-1772117-118_G01


title: C1-1772117-118_F04


title: C1-1772117-118_F05


title: C1-1772117-118_F02


title: C1-1772117-118_F11


title: C1-1772117-118_E12


title: C1-1772117-118_E10


title: C1-1772117-118_E06


title: C1-1772117-118_E08


title: C1-1772117-118_E09


title: C1-1772117-118_E05


title: C1-1772117-118_E07


title: C1-1772117-118_E03


title: C1-1772117-118_E04


title: C1-1772117-118_F12


title: C1-1772117-118_D12


title: C1-1772117-118_E02


title: C1-1772117-118_D10


title: C1-1772117-118_E01


title: C1-1772117-118_D11


title: C1-1772117-118_D09


title: C1-1772117-118_D07


title: C1-1772117-118_D06


title: C1-1772117-118_D02


title: C1-1772117-118_D05


title: C1-1772117-118_D03


title: C1-1772117-118_D01


title: C1-1772117-118_D04


title: C1-1772117-118_C12


title: C1-1772117-118_C10


title: C1-1772117-118_C11


title: C1-1772117-118_C05


title: C1-1772117-118_C08


title: C1-1772117-118_C06


title: C1-1772117-118_C07


title: C1-1772117-118_C03


title: C1-1772117-118_C04


title: C1-1772117-118_C02


title: C1-1772117-118_B10


title: C1-1772117-118_C01


title: C1-1772117-118_A10


title: C1-1772117-118_A07


title: C1-1772117-118_A12


title: Patient 2168, Base treatment, technical replicate 2

source_name: Liver from 68 year old Asian Female, at Base treatment


title: C1-1772117-118_B11


title: C1-1772117-118_B01


title: C1-1772117-118_B09


title: C1-1772117-118_A09


title: C1-1772117-118_B03


title: C1-1772117-118_B07


title: C1-1772117-118_D08


title: C1-1772117-118_B06


title: C1-1772117-118_B04


title: C1-1772117-118_B05


title: C1-1772117-118_B08


title: C1-1772117-118_B02


title: C1-1772117-118_A08


title: C1-1772117-118_A11


title: C1-1772117-117_H05


title: C1-1772117-118_A01


title: C1-1772117-118_A02


title: C1-1772117-118_A03


title: C1-1772117-117_H11


title: C1-1772117-117_H10


title: C1-1772117-117_H07


title: C1-1772117-117_H06


title: C1-1772117-117_H02


title: C1-1772117-117_F03


title: C1-1772117-117_F08


title: C1-1772117-117_E12


title: C1-1772117-117_G05


title: C1-1772117-117_F01


title: C1-1772117-117_F02


title: C1-1772117-117_F05


title: C1-1772117-117_F09


title: C1-1772117-117_G06


title: C1-1772117-117_E09


title: C1-1772117-117_G03


title: C1-1772117-117_E11


title: C1-1772117-117_E05


title: siLOL-2


title: C1-1772117-117_E02


title: C1-1772117-117_G09


title: C1-1772117-117_E07


title: C1-1772117-117_E04


title: C1-1772117-117_G12


title: C1-1772117-117_D09


title: C1-1772117-117_E08


title: C1-1772117-117_G02


title: C1-1772117-117_D12


title: C1-1772117-117_D06


title: C1-1772117-117_D04


title: C1-1772117-117_D03


title: C1-1772117-117_D02


title: C1-1772117-117_C11


title: C1-1772117-117_C08


title: C1-1772117-117_C06


title: C1-1772117-117_C10


title: C1-1772117-117_C05


title: C1-1772117-117_G11


title: C1-1772117-117_C07


title: C1-1772117-117_C02


title: C1-1772117-117_C01


title: C1-1772117-117_C04


title: C1-1772117-117_D11


title: C1-1772117-117_B12


title: C1-1772117-117_B08


title: C1-1772117-117_B04


title: C1-1772117-117_B09


title: C1-1772117-117_B01


title: C1-1772117-117_B10


title: C1-1772117-117_A12


title: C1-1772117-117_D05


title: C1-1772117-117_B05


title: C1-1772117-117_A11


title: C1-1772117-117_A08


title: C1-1772117-117_A03


title: C1-1772117-117_A02


title: C1-1772117-116_H11


title: C1-1772117-117_A07


title: C1-1772117-116_H08


title: C1-1772117-116_H07


title: C1-1772117-116_H06


title: C1-1772117-116_H05


title: C1-1772117-116_H01


title: C1-1772117-116_H03


title: C1-1772117-116_G12


title: C1-1772117-116_G11


title: C1-1772117-116_G10


title: C1-1772117-116_G06


title: C1-1772117-116_G04


title: C1-1772117-116_G03


title: C1-1772117-116_G05


title: C1-1772117-116_F12


title: C1-1772117-116_F11


title: C1-1772117-116_F07


title: C1-1772117-116_F08


title: C1-1772117-116_F09


title: C1-1772117-116_F06


title: C1-1772117-116_F05


title: C1-1772117-116_F02


title: C1-1772117-116_E11


title: C1-1772117-116_E10


title: C1-1772117-116_E09


title: C1-1772117-116_E07


title: C1-1772117-116_H04


title: C1-1772117-116_E06


title: C1-1772117-116_G09


title: C1-1772117-116_E04


title: C1-1772117-116_E02


title: C1-1772117-116_D10


title: C1-1772117-116_D09


title: C1-1772117-116_E03


title: C1-1772117-116_D12


title: C1-1772117-116_G02


title: C1-1772117-116_D08


title: C1-1772117-116_D04


title: C1-1772117-116_D03


title: C1-1772117-116_F03


title: C1-1772117-116_F10


title: C1-1772117-116_D01


title: C1-1772117-116_C07


title: C1-1772117-116_E12


title: C1-1772117-116_C06


title: C1-1772117-116_C12


title: C1-1772117-116_C04


title: C1-1772117-116_D05


title: C1-1772117-116_D06


title: C1-1772117-116_E05


title: C1-1772117-116_B12


title: C1-1772117-116_C01


title: C1-1772117-116_C03


title: C1-1772117-116_C09


title: C1-1772117-116_B11


title: C1-1772117-116_B09


title: C1-1772117-116_B08


title: C1-1772117-116_B10


title: C1-1772117-116_B05


title: C1-1772117-116_A12


title: C1-1772117-116_B01


title: C1-1772117-116_B03


title: C1-1772117-116_C11


title: C1-1772117-116_A11


title: C1-1772117-116_A06


title: C1-1772117-116_A07


title: C1-1772117-116_A09


title: C1-1772117-116_D02


title: C1-1772117-116_A04


title: C1-1772117-116_A01


title: C1-1772117-116_A03


title: C1-1772117-115_H12


title: C1-1772117-115_H08


title: C1-1772117-115_H09


title: C1-1772117-115_H07


title: C1-1772117-115_H06


title: C1-1772117-115_H10


title: C1-1772117-115_H02


title: C1-1772117-115_H01


title: C1-1772117-115_H03


title: C1-1772117-116_B07


title: C1-1772117-116_B06


title: C1-1772117-115_H04


title: C1-1772117-115_G12


title: C1-1772117-115_G11


title: C1-1772117-116_A08


title: C1-1772117-115_G05


title: C1-1772117-115_G02


title: C1-1772117-115_G06


title: C1-1772117-115_G04


title: C1-1772117-115_G03


title: C1-1772117-115_F12


title: C1-1772117-115_F11


title: C1-1772117-115_H11


title: C1-1772117-115_F08


title: C1-1772117-115_F10


title: C1-1772117-115_F09


title: C1-1772117-115_F06


title: C1-1772117-115_F01


title: C1-1772117-115_F03


title: C1-1772117-115_F05


title: C1-1772117-115_F04


title: C1-1772117-115_E09


title: C1-1772117-115_F02


title: C1-1772117-115_E06


title: C1-1772117-115_G10


title: C1-1772117-115_E07


title: C1-1772117-115_E03


title: C1-1772117-115_D11


title: C1-1772117-115_E04


title: C1-1772117-115_D09


title: C1-1772117-115_G09


title: C1-1772117-115_D07


title: C1-1772117-115_D06


title: C1-1772117-115_D05


title: C1-1772117-115_D02


title: C1-1772117-115_D04


title: C1-1772117-115_C12


title: C1-1772117-115_C09


title: C1-1772117-115_C10


title: C1-1772117-115_E11


title: C1-1772117-115_C05


title: C1-1772117-115_C03


title: C1-1772117-115_C04


title: C1-1772117-115_D12


title: C1-1772117-115_E05


title: C1-1772117-115_C07


title: C1-1772117-115_C11


title: C1-1772117-115_B12


title: C1-1772117-115_C02


title: NC14

city: Pasadena

first: Angelike

last: Stathopoulos

address: 1200 E. California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

description:
YW_nc14_neg.bw
YW_nc14_pos.bw
nc14_genes.fpkm_tracking.gz

data_processing:
(NC13) Libraries 17660 and 18078 were concatenated to produce ~150M raw reads
(NC14) Library 17661
Raw reads were aligned to dm3 and Flybase 20060401 annotation using Tophat 2.0.13 using the parameters –bowtie1 -p20 –library-type fr-unstranded Bowtie1 refers to Bowtie 1.1.1
Aligned reads were quantified with Cufflinks 2.2.1 using the Flybase 20060401 annotation with the default parameters
FPKMs were filtered using custom Python software as per the protocol described in the manuscript
Genome browser tracks were created using bedtools and the UCSC genome browser tools
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files, positive and negative signal. Cufflinks FPKM tables.

organism: Drosophila melanogaster

source_name: Whole embryo extract

extract_protocol:
Individual embryos were staged and flash frozen in Trizol reagent. RNA was extracted and pooled from 50 embryos for each sample.
Libraries were constructed according to the protocol developed in (Lianoglou et. al., GenesDev, 2013) and Illumina protocols.

tag: developmental stage

value: embryo

tag: nuclear cycle


title: C1-1772117-115_B11


title: C1-1772117-115_B09


title: C1-1772117-115_C01


title: C1-1772117-115_B08


title: C1-1772117-115_B06


title: C1-1772117-115_B07


title: C1-1772117-115_B05


title: Blnc1 adipose specific Tg biological rep3

city: Ann Arbor

first: xuyun

last: zhao

state: Michigan

address: 210 washtenaw ave

institute: Life Sciences Institute

description: Gene expression data from Tg mice biological rep3

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse ST 2.1, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.1.1. RMA was used to fit log2 transformed expression values.

source_name: Blnc1 adipose specific Tg, eWAT

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

extract_protocol: mouse eWAT was extracted, immediately frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.

treatment_protocol: WT and Tg mice was fed on HFD diet (D12492, Research Diets) for 21 weeks

tag: strain

value: 8 months

value: male

value: eWAT

tag: genotype

value: Tg

value: HFD


title: Blnc1 adipose specific Tg biological rep2

description: Gene expression data from Tg mice biological rep2


title: Wild type biological rep3

description: Gene expression data from wild type mice biological rep3

source_name: Wild type, eWAT

value: WT


title: rad30-F35A(1-622) rnh201 rad1 rev3 rep3

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

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

source_name: culture

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

value: whole yeast culture

tag: genotype/variation


title: rad30-F35A(1-622) rnh201 rad1 rev3 rep2


title: Wild type biological rep1

description: Gene expression data from wild type mice biological rep1


title: Wild type biological rep2

description: Gene expression data from wild type mice biological rep2


title: Blnc1 adipose specific Tg biological rep1

description: Gene expression data from Tg mice biological rep1


title: rad30-F35A rnh201-P45D-Y219A rad1 rev3 rep3

value: rad30-F35A rnh201-P45D-Y219A rad1 rev3


title: C1-1772117-115_C08


title: C1-1772117-115_B03


title: C1-1772117-115_A12


title: NC13 (Library 18078)

description:
YW_nc13_neg.bw
YW_nc13_pos.bw
nc13_genes.fpkm_tracking.gz


title: rad30-F35A(1-622) rnh201 rad1 rev3 rep1


title: pol1-L868M rnh201 rad1 rev3 rep3

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

extract_protocol:
Genomic DNA was isolated using the MasterPure Yeast DNA Purification Kit (Epicentre) without the optional RNaseA treatment. For strains where large variation in relative ribonucleotide incorporation percentages was observed between the analyzed isolates, the analysis was repeated from cultures where the presence of the correct dNTP pool imbalance was verified  by HPLC analysis as previously described (Jia et al., 2015), and only the pool-verified samples were included in the analysis (rnh201∆; rnr1-Q288A; rnr1-Q288A rnh201∆; rnr1-Y285A; rnr1-Y285A,Q288E and rnr1-Y285A,Q288E rnh201∆). Two or more isolates were analyzed for each strain, except for rnr1-Y285A,Q288E and rnr1-Y285A,Q288E rnh201∆ where two replicates of one isolate were sequenced.
RNA residues in genomic DNA from S. cerevisiae were mapped by HydEn-seq by hydrolyzing 1 µg DNA with 0.3 M KOH for 2 h at 55 °C. After ethanol precipitation, the DNA fragments were treated for 3 min at 85 °C, phosphorylated with 10 U of 3′-phosphatase-minus T4 polynucleotide kinase (New England BioLabs) for 30 min at 37 °C, heat inactivated for 20 min at 65 °C and purified with HighPrep PCR beads (MagBio). Phosphorylated products were treated for 3 min at 85 °C, ligated to oligo ARC140 overnight at room temperature with 10 U of T4 RNA ligase, 25% PEG 8000 and 1 mM CoCl3(NH3)6, and purified with HighPrep PCR beads (MagBio). Ligated products were treated for 3 min at 85 °C. The ARC76–ARC77 adaptor was annealed to the second strand for 5 min at room temperature. The second strand was synthesized with 4 U of T7 DNA polymerase (New England BioLabs) and purified with HighPrep PCR beads (MagBio). Libraries were purified, quantified with a Qubit fluorometric instrument (ThermoFisher Scientific) and 50-base paired-end sequenced on an Illumina NextSeq 500 instrument, to identify the location of the free 5´-ends.

value: pol1-L868M rnh201 rad1 rev3


title: C1-1772117-115_A09


title: C1-1772117-115_A07


title: rad30-F35A rnh201-P45D-Y219A rad1 rev3 rep2


title: C1-1772117-115_A11


title: C1-1772117-115_A08


title: rad30-F35A rnh201-P45D-Y219A rad1 rev3 rep1


title: pol3-L612M rnh201 rad1 rev3 rep3

value: pol3-L612M rnh201 rad1 rev3


title: rnh201 rad1 rev3 L03 rep2

value: rnh201 rad1 rev3 L03


title: NC13 (Library 17660)


title: C1-1772117-115_A06


title: pol2-M644L rnh201 rad1 rev3 rep3

value: pol2-M644L rnh201 rad1 rev3


title: pol2-M644G rnh201 rad1 rev3 rep2

value: pol2-M644G rnh201 rad1 rev3


title: C1-1772117-115_B02


title: C1-1772117-115_A05


title: rnh201 rad1 rev3 W303 rep3

value: rnh201 rad1 rev3 W303


title: rad30F35A rnh201 rad1 rev3 rep3

value: rad30F35A rnh201 rad1 rev3


title: pol3-L612G rnh201 rad1 rev3 rep2

value: pol3-L612G rnh201 rad1 rev3


title: pol1-Y869A rnh201 rad1 rev3 rep2

value: pol1-Y869A rnh201 rad1 rev3


title: pol2-M644L rnh201 rad1 rev3 rep2


title: pol3-L612M rnh201 rad1 rev3 rep2


title: KO WNV 24h rep 2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.0)
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome (mm10) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed. After counst were generated we normalized with voom from the limma package in R.

source_name: Bone marrow dendritic cells

growth_protocol: BMDCs were cultured in complete RPMI supplemented with recombinant mouse IL-4 (40ng/ml, Invivogen) and GM-CSF (40ng/ml, Invivogen) for 7-9 days, changing media on day 3. Cells were kept at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN) with on-column DNase treatment.
KAPA stranded RNA-seq kit with Ribo Erase
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: BMDCs were resuspended in serum-free RPMI with 2.5 MOI of WNV for 1.5 hours with gentle rocking.

tag: time

value: WNV infection

tag: replicate


title: KO WNV 24h rep 3


title: KO WNV 24h rep 1


title: pol2-M644G rnh201 rad1 rev3 rep3


title: KO WNV 12h rep 3


title: rnh201 rad1 rev3 L03 rep3


title: pol1-Y869A rnh201 rad1 rev3 rep1


title: KO WNV 12h rep 2


title: KO WNV 6h rep 3


title: KO WNV 6h rep 2


title: pol1-L868M rnh201 rad1 rev3 rep1


title: rnh201 rad1 rev3 W303 rep2


title: pol3-L612G rnh201 rad1 rev3 rep1


title: pol3-L612M rnh201 rad1 rev3 rep1


title: KO WNV 12h rep 1


title: KO mock 24h rep 2

value: Mock


title: rad30F35A rnh201 rad1 rev3 rep2


title: pol1-Y869A rnh201 rad1 rev3 rep3


title: KO mock 12h rep 3


title: pol2-M644L rnh201 rad1 rev3 rep1


title: KO mock 24h rep 1


title: rnh201 rad1 rev3 L03 rep1


title: KO mock 24h rep 3


title: KO mock 12h rep 1


title: KO mock 12h rep 2


title: pol1-L868M rnh201 rad1 rev3 rep2


title: pol2-M644G rnh201 rad1 rev3 rep1


title: KO mock 6h rep 3


title: rad30F35A rnh201 rad1 rev3 rep1


title: rnh201 rad1 rev3 W303 rep1


title: pol3-L612G rnh201 rad1 rev3 rep3


title: KO WNV 6h rep 1


title: KO mock 6h rep 2


title: Resistant GSC11

city: Houston

first: Dimpy

last: Koul

state: TX

address: 6767 Bertner Ave

institute: MD Anderson Cancer Center

data_processing:
We ran PRADA pipeline.
PRADA aligned RNA-seq reads to a composite reference database composed of whole genome and transcriptome sequences.
PRADA recalibrates BAM and mark duplicates using GATK and picard tools.
PRADA uses RNA-seQC to generate RPKM values
HTseq was used to generate RNA seq counts
Genome_build: hg19 (Ensemble 64)
Supplementary_files_format_and_content: *rpkm.gct files were generated using PRADA. *counts.txt were generated using HTseq using the BAM output from PRADA

source_name: Glioblastoma

growth_protocol: The GSCs were cultured as GBM neurospheres in DMEM/F12 medium containing B27 supplement (Invitrogen, Grand Island, NY), basic fibroblast growth factor, and epidermal growth factor (20 ng/ml each).

extract_protocol:
Total RNA was extracted from control and resistant cells using an RNeasy Mini Kit (Qiagen, Hilden, Germany).  A minimum quantity of 1 g of total RNA was used for RNA Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Half million GSCs were implanted intracranially into each 4-week-old male nude mouse using a guide-screw system. Animals were treated with 40 mg/kg BKM-120 once a day (5 days per week) by oral gavage.Tumor growth was monitored by MRI weekly.The occurence of adaptive reistance was indicated by rapid re-growth of the tumor. Tumor cells were isolated from the corresponding xenograft tumors and established as neurosphere population in vitro.

value: Brain

value: patient-derived glioma sphere-forming cell

value: Glioblastoma

tag: phenotype

value: resistant


title: KO mock 6h rep 1


title: WT WNV 24h rep 3

value: WT


title: Parental GSC711

value: parental


title: Resistant GSC711


title: WT WNV 24h rep 2


title: Parental GSC11


title: WT WNV 12h rep 3


title: WT WNV 24h rep 1


title: WT WNV 12h rep 1


title: WT WNV 6h rep 3


title: WT WNV 6h rep 1


title: HTBE_H3N2_12h_H3K27ac_2

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Adapter sequences were trimmed with fastp 0.12.5
Reads were mapped to the human hg38 genome with Bowtie 2.3.4
Genomic coverage was calculated using deepTools 3.0.1, with binSize=1 and extendReads=150
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files normalized by BPM

growth_protocol: HTBE cells (Lonza) were maintained in PneumaCult-Ex Medium (Stemcell Technologies) according to the manufacturer’s recommendations.

extract_protocol:
Previously described protocols (see PMID: 17512414 and PMID: 17406303) with minor modifications were used: (i) Sonication: A refrigerated Bioruptor (Diagenode) was used . Sonication conditions were optimized to generate DNA fragments of approximately 200-500 bp. (ii) Antibodies (Ab) were coupled with Invitrogen Dynabeads anti-mouse M-280 #112-02, or Dynabeads anti-rabbit M-280 #112-04 for 6hours. Ab-beads and chromatin were then immunoprecipitated overnight. (iii) After the wash steps, reverse crosslinking was carried out at 65°C for 2 hours in a thermomixer programmed for mixing at 700 rpm 2 min on/ min off. ChIP DNA was then isolated, after RNase digestion and proteinase K digestion, using QIAGEN MinElute kit (28004).
For library preparation, 30 ul of ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies, cat# ER0720), and purified end-repaired DNA using the QIAGEN PCR purification kit (28104). DNA END Repair was done using Klenow Fragment (NEB M0212L), and purified DNA was collected with QIAGEN MinElute kit. Ligation of Illlumina/Solexa adapters (#FC-102-1003) to DNA fragments overnight was achieved using T4 DNA ligase (NEB M0202L). Adaptor-ligated DNA fragments were purified with the QIAGEN MinElute kit. 18 cycles of PCR was performed with the Illumina/Solexa primers 1.0 and 2.0, and an aliquot of material was used to check the fragment size on agarose gel. The remaining DNA was column purified and bio-analyzed before sequencing.

treatment_protocol: 24 hours before infection, HTBE cells (Lonza, Donor 4F1289J) were plated at a density of 2 x 10^6 cells in a 10 cm dish. For infection, growth medium was replaced with virus diluted to the appropriate concentration in Pneumacult-Ex complete medium at a total volume of 2 mL. Dishes were incubated in a cell culture incubator with gentle rocking every 15 minutes. After 60 minutes, the inoculum was removed and cells were washed twice washed gently with 5 mL Pneumacult-Ex. 10 mL of Pneumacult-Ex was added and cells were incubated for the specified length of time.

value: Human tracheobronchial epithelial (HTBE) cells

tag: infected with

value: H3N2 influenza virus

tag: time point

value: 12h post-infection

tag: chip antibody

tag: biological replicate


title: HTBE_H3N2_18h_Input_1

value: 18h post-infection

value: none (input)


title: HTBE_H3N2_mock_H3K27ac_1

value: uninfected (mock control)


title: HTBE_H3N2_18h_H3K27ac_2


title: HTBE_H3N2_12h_Input_1


title: WT WNV 6h rep 2

tag: treatment


title: HTBE_H3N2_mock_H3K27ac_2


title: WT mock 24h rep 3


title: HTBE_H3N2_mock_Input_1


title: HTBE_H3N2_18h_H3K27ac_1


title: HTBE_H3N2_12h_H3K27ac_1


title: WT mock 24h rep 1


title: WT mock 12h rep 3


title: WT mock 12h rep 2


title: HTBE_H3N2_06h_H3K27ac_1

value: 06h post-infection


title: HTBE_H3N2_06h_Input_1


title: HTBE_H3N2_06h_H3K27ac_2


title: HTBE_H3N2_03h_Input_1

value: 03h post-infection


title: WT mock 24h rep 2


title: WT mock 12h rep 1


title: WT mock 6h rep 3


title: HTBE_H3N2_03h_H3K27ac_2


title: WT WNV 12h rep 2


title: HTBE_H1N1_mock_Input_1

value: H1N1 influenza virus


title: HTBE_H3N2_03h_H3K27ac_1


title: WT mock 6h rep 1


title: HTBE_H1N1_mock_H3K27ac_2


title: WT mock 6h rep 2


title: HTBE_H1N1_mock_H3K27ac_1


title: Animal-6 85% O2 Exposed

city: Birmingham

first: Manimaran

last: Ramani

state: Alabama

address: 1700, 6TH Ave South

department: Pediatrics

institute: University of Alabama at Birmingham

data_processing:
The Quality of raw data is accessed using tool FASTQC(1.
STAR (version 2.5.3a was used to align the raw RNA-Seq fastq reads to the mouse reference genome from Gencode (Release M13.
The transcripts aligning to the gene features were counted using program HTSeq.
The HTseq output for all replicates were imported into DeSeq2 for detecting differentially expressed genes.
Functional and pathways analysis (statistical overrepresentation test of pathways and GO terms were performed using web tool PANTHER for gene expressed up and down sepearetely.
Additional functional analysis was performed using Ingenuity pathway analysis (IPA.
Genome_build: Gencode (Release M13
Supplementary_files_format_and_content: normalized count are matrix table in tab-delimited text files; differential expression test is standard deseq2 output which includes P-value, fold change and multiple testing correction (fdr

source_name: Hippocamppus

extract_protocol:
Immediately after harvesting, left hippocampal tissue was flash frozen in an Eppendorf tube with steel beads. Tissue was then homogenized using Qiagen tissue lyser  and RLT+BME buffer solution and RNA was isolated using Qiagen RNeasy mini RNA isolation kit
Targeted mRNA-sequencing was performed on the Illumina NextSeq500 as described by the manufacturer

treatment_protocol: Newborn Pups along with their Dams were exposed to 85% oxygen from P2-14 in a normobaric hyperoxia chamber.

value: 85% O2 Exposed

tag: tissue

value: Hippocamppus

tag: postnatal age


title: Animal-5 85% O2 Exposed


title: Animal-2 Room air Exposed

value: Room air exposed


title: HTBE_H1N1_24h_H3K27ac_2

tag: cell type

value: 24h post-infection


title: Animal-1 Room Air Exposed


title: HTBE_H1N1_24h_H3K27ac_1


title: HTBE_H1N1_24h_Input_1


title: Animal-3 Room air Exposed


title: Animal-4 85% O2 Exposed


title: HTBE_H1N1_18h_Input_1


title: HTBE_H1N1_18h_H3K27ac_2


title: HTBE_H1N1_18h_H3K27ac_1


title: HTBE_H1N1_12h_H3K27ac_1


title: HTBE_H1N1_12h_Input_1


title: HTBE_H1N1_06h_Input_1


title: Wt1 overexpression line2 rep 3

city: LA JOLLA

first: Kristin

last: Baldwin

address: 10550 N. Torrey Pines

department: DNC

institute: TSRI

description: Sample 30

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

source_name: iPS cells

growth_protocol: iPSC and ESC were grown in knock-out DMEM supllemented with 15% KSR and LIF

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPS cells

tag: protocol

value: iPSC generated by Wt1 over expression plus Klf4, Oct4, cMyc


title: Mouse embryonic fibroblasts rep1

description: Sample 31

source_name: fibroblasts

tag: age

value: Embryonic day 13.5

value: fibroblasts


title: Wt1 overexpression line2 rep 1

description: Sample 28


title: HTBE_H1N1_12h_H3K27ac_2

value: Human tracheobronchial epithelial (HTBE) cells


title: Wt1 overexpression line1 rep 3

description: Sample 27


title: Mouse embryonic fibroblasts rep2

description: Sample 32


title: HTBE_H1N1_06h_H3K27ac_2


title: HTBE_H1N1_06h_H3K27ac_1


title: Wt1 overexpression line2 rep 2

description: Sample 29


title: Wt1 overexpression line1 rep 1

description: Sample 25


title: Basp1 Kd line2 rep 1

description: Sample 22

value: iPSC generated by Basp1 shRNA plus Klf4, Oct4, cMyc


title: Basp1 Kd line2 rep 2

description: Sample 23


title: OctAb2 rep1

description: Sample 16

value: iPSC generated by antibody plus Klf4, Sox2 cMyc


title: OctAb1 rep3

description: Sample 15


title: OctAb1 rep1

description: Sample 13


title: OctAb2 rep3

description: Sample 18


title: OctAb2 rep2

description: Sample 17


title: Basp1 Kd line1 rep 3

description: Sample 21


title: OctAb1 rep2

description: Sample 14


title: SoxAB1 rep2

description: Sample 11

value: iPSC generated by antibody plus Klf4, Oct4, cMyc


title: SoxAB1 rep3

description: Sample 12


title: SoxAb2 rep1

description: Sample 7


title: SoxAb2 rep3

description: Sample 9


title: SoxAB1 rep1

description: Sample 10


title: Wt1 overexpression line1 rep 2

description: Sample 26


title: Basp1 Kd line2 rep 3

description: Sample 24


title: MCNT rep1

description: Sample 4

source_name: Embryonic stem cell line

tag: cell line

value: Embryonic stem cell line

value: Generated by nuclear transfer


title: Sample 4b-TBX4

city: Beirut

first: Athar

last: Khalil

address: Bliss

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

data_processing:
Illumina RTA v1.18 software used for basecalling.
The bcl binary is converted into Fastq using Illumina package bcl2fastq (v1.8.4)
Alignement to the human reference genome was done using STAR v2.3.0, mapped reads were quantified using feature counts v1.5.4 using default settings.
Genes with raw counts above 5 in more than half of the samples (n=18) were kept, and differential expression analysis was performed using DESeq2.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: tab-delimited text files include RNAseq count values for all samples

source_name: Lung Cancer

growth_protocol: DMEM low Glucose + 10% FBS

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung Adenocarcinoma

tag: passage


title: Sample 5b-TBX5


title: Sample 4c-TBX5


title: Sample 5a-TBX5


title: Sample 3b-TBX3


title: Sample 5c-TBX5


title: Sample 3c-TBX3


title: MCNT rep3

description: Sample 6


title: Sample 3a-TBX3


title: Basp1 Kd line1 rep 2

description: Sample 20


title: Sample 2c-TBX2


title: Basp1 Kd line1 rep 1

description: Sample 19


title: SoxAb2 rep2

description: Sample 8


title: Sample 4a-TBX4


title: Sample 2b-TBX2


title: IMZ21 rep1

description: Sample 1

value: generated by Klf4, Sox2, Oct4, cMyc


title: IMZ21 rep2

description: Sample 2


title: IMZ21 rep3

description: Sample 3


title: Sample 1c-EV


title: Mouse57.12 [miRNA-Seq]

city: Bar Harbor

first: Catherine

last: Kaczorowski

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
KD
Mouse57.12

data_processing:
Raw fastq files (R1 only) were subjected to QC using fastqc (v0.11.3), following which adapter sequences were trimmed using cutadapt (v1.14)
Trimmed reads were then alingned to the Mouse miRNA-precursor miRBase reference (miRBase release 21) using bowtie (v1.0.0)
Following alignment, counts were extracted using featureCounts function from the subread (v1.5.2)  package
Genome_build: mm10
Supplementary_files_format_and_content: miRNA_counts.csv - expected read counts for each miRNA sample
Supplementary_files_format_and_content: miRNAcounts_normalized_rlog.csv - normalized and log transformed count data exported from DESeq2

source_name: Hippocampus

growth_protocol: Male mice (3-5mo) received an injection of either AAV9-shRNA-Hp1bp3 or AAV9-scrmb-shRNA. A minimum of six weeks later, mice were sacrificied and brains harvested for electrophysiology and/or molecular characterization.

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy Mini kit.
miRNA libraries were made with the Illumina TruSeq Small RNA Library Prep Kit

treatment_protocol: The hippocampus was freshly dissected from brain tissue and immediately snap-frozen in liquid nitrogen. Samples were kept at -80C until further use.

tag: strain


title: Sample 1b-EV


title: Sample 1a-EV


title: Mouse56.11 [miRNA-Seq]

description:
CTRL
Mouse56.11

value: AAV-scrmb-shRNA


title: Mouse53.09 [miRNA-Seq]

description:
CTRL
Mouse53.09


title: Mouse55.10 [miRNA-Seq]

description:
CTRL
Mouse55.10


title: Sample 0c-Ctl


title: Mouse49.08 [miRNA-Seq]

description:
KD
Mouse49.08


title: Mouse41.07 [miRNA-Seq]

description:
KD
Mouse41.07


title: Mouse40.06 [miRNA-Seq]

description:
CTRL
Mouse40.06


title: RH4_si-Circ#1

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SI_A_RH4

data_processing:
Illumina Casava1.8 software used for basecalling.
Adapter sequences and poor quality ends were removed using the Trimmomatic software; reads with length < 20 nt after trimming were filtered out.
Reads were mapped to human GRCh38 genome and Ensembl 90 transcriptome using STAR software. Htseq-count software was used to count reads mapping to Ensembl 90 human genes; the overlap resolution mode was set to intersection-strict.
Differential gene expression was performed using edgeR R package after filtering out genes with a CPM (Count Per Million) value less than 1 in at least two samples; TMM normalization was applied independently for myoblast and rhabdomyosarcoma samples. RPKM values were calculated using the edgeR rpkm function.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. Genes are specified using their Ensembl Gene ID.

source_name: RH4 cell line from Alveolar Rhabdomyosarcoma tumor

growth_protocol: Human primary myoblasts and Rhabdomyosarcoma cell lines were maintained in growth conditions

extract_protocol:
Total RNA was extracted with Qiazol reagent (Qiagen) and Direct-zol RNA Miniprep kit (Zymo Research), according to the manufacturer’s protocol. Then RNA was treated with DNase I (New England Biolabs) to remove genomic DNA, according to the manufacturer's instructions.
Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero treatment

treatment_protocol: Cells were transfected with si-SCR or si-Circ 48 hours before being harvested for RNA extraction. 3 pmol siRNA (Dharmacon) and 0,15 μl Dharmafect transfection reagent 1 (Dharmacon) in 150 μl DMEM (Sigma-Aldrich) were added to each 100 μl of culture medium in the plate. Medium was replaced 24h after the transfection.

value: RH4 tumor cell line

value: si-Circ


title: Sample 0b-Ctl


title: Mouse38.05 [miRNA-Seq]

description:
KD
Mouse38.05


title: Sample 0a-Ctl


title: RH4_si-Circ#2

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SI_B_RH4


title: Mouse36.04 [miRNA-Seq]

description:
CTRL
Mouse36.04


title: Mouse35.03 [miRNA-Seq]

description:
KD
Mouse35.03


title: Sample 2a-TBX2


title: Mouse32.02 [miRNA-Seq]

description:
KD
Mouse32.02


title: RD_si-Circ#2

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SI_B_RD

source_name: RD cell line from Embryonal Rhabdomyosarcoma tumor

value: RD tumor cell line


title: RH4_si-SCR#1

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SCR_A_RH4

value: si-SCR


title: RD_si-Circ#1

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SI_A_RD


title: RD_si-SCR#2

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SCR_B_RD


title: RD_si-SCR#1

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SCR_A_RD


title: Mouse55.10 [RNA-Seq]

description: CTRL

data_processing:
Raw fastq files (R1 an R2) were subjected to filtering and triming of poor quality reads and bases using a custom python script
We used rsem (v1.2.12) for alignment and expression estimation of trimmed reads were using Bowtie2 (v2.2.0). Depending of the sample's  strain background, we used either the  C57BL/6J (GRCm38.74) or DBA/2J (build-mm10) genomes, as deemed appropriate.
Genome_build: C57BL/6J (GRCm38.74) or DBA/2J (build-mm10) genomes
Supplementary_files_format_and_content: normalized counts_mrna.csv, normalized counts from DESeq2
Supplementary_files_format_and_content: genes_expected_counts_merge.csv, expected read counts (not normalized, used as DESeq2 input)

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy Mini kit.
Libraries were made with the KAPA Biosystems mRNA Hyper Prep Kit.


title: Myoblasts_si-Circ#1

description:
Processed data file: myoblast_rpkm.tsv
processed data file column header: SI_A

source_name: Primary myoblasts from skeletal muscle

value: wild-type primary myoblast cells


title: Myoblasts_si-SCR#2

description:
Processed data file: myoblast_rpkm.tsv
processed data file column header: SCR_B


title: Myoblasts_si-SCR#1

description:
Processed data file: myoblast_rpkm.tsv
processed data file column header: SCR_A


title: Mouse41.07 [RNA-Seq]

description: KD


title: RH4_si-SCR#2

description:
Processed data file: rhabdomyosarcoma_rpkm.tsv
processed data file column header: SCR_B_RH4