title: tissue- crohn's disease- 10.7 year old female

first: Jocelyn

last: Silvester

address: 300 Longwood Avenue

institute: Boston Children's Hospital

value: Female

tag: disease type

value: Crohn's Disease

value: colon biopsy


title: MTAC-P-1

status: Public on Oct 29 2019

type: RNA

city: Shanghai

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

country: China

institute: Chinese Academy of Sciences

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

molecule: total RNA

organism: Homo sapiens

source_name: human lung cancer cell line

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US),

growth_protocol: Cells were cultured in DMEM medium with 10%FBS and passaged every other day.

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

tag: tissue

value: lung

tag: cell line

value: resistant cell line established by mild-TKI treatment


title: tissue- control- 14.5 year old female

city: Boston

middle: Anne

state: Massachusetts

department: Gastroenterology

country: USA

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip Human Gene 1.0 ST array at 45°C for 16–20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
The Affymetrix Power Tools software package was used to generate probe set (transcript cluster) level measurements using the analysis workflow specification   “-a rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish” to the apt-probeset-summarize program, corresponding to RMA background correction of the perfect match probes, followed by quantile normalization and median polish summarization. This procedure, and each subsequent step in the analysis, was carried out independently for the colon and blood samples (i.e., all colon samples were processed as a single batch, and all blood samples were processed as a single batch).  The Affymetrix Power Tools software package was used to generate probe set (transcript cluster) level measurements using the analysis workflow specification   “-a rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish” to the apt-probeset-summarize program, corresponding to RMA background correction of the perfect match probes, followed by quantile normalization and median polish summarization. This procedure, and each subsequent step in the analysis, was carried out independently for the colon and blood samples (i.e., all colon samples were processed as a single batch, and all blood samples were processed as a single batch).
HuGene-1_0-st-v1.r3.pgf

label: biotin

source_name: colon

label_protocol: Biotin-labeled target for microarray experiment was prepared using 100 nanograms of total RNA, and cDNA was synthesized using the GeneChip Whole Transcript (WT) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix, Santa Clara, CA)

growth_protocol: not applicable

extract_protocol: Paxgene Blood RNA system (PreAnalytiX, Hombrechtikon, Switzerland) was used in conjunction with RNeasy mini kits (Qiagen, Valencia, CA) according to manufacturer instructions

treatment_protocol: not applicable

tag: gender

tag: age

value: Control


title: Rev1-dde: IP

type: genomic

city: Madrid

first: Rodrigo

last: Bermejo

address: Calle Ramiro de Maeztu 9

department: Center for Biological Research (CIB-CSIC)

country: Spain

institute: Spanish National Research Council (CSIC)

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP fraction of Rev1-myc ubp10D ubp12D elg1D 80Sc18.16 HU

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol

growth_protocol: Cells were grown in YPD

extract_protocol: Extracton was performed as described in Bermejo et al., 2011.

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml), S synchronization release from factor block in 200 mM HU, G2 synchronization released from alpha factor block in nocodazole 15 μg/ml, S 16C synchronization release from factor block at 16C

tag: strain

tag: phase

value: S-phase

tag: treatment

value: HU


title: Smore Seq Ribo depletion Replicate 2

type: SRA

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

library_source: transcriptomic

data_processing:
Basecalls performed using BCL2Fastq.
Sequencing reads were aligned to the SacCer3 genome assembly using BWA 0.6.2 or 0.7.7
Data were filtered using the following specifications…
For wig files, reads were converted to signal using bedtools genomecov.
Count files were produced using featurecount.
Genome_build: sacCer3

source_name: cells grown in liquid YPD media to an OD600 of .8

growth_protocol: Cells were grown overnight in liquid YPD media to an OD600 of .8.

extract_protocol:
MNase-ChIP-seq and ChIP-seq ibraries were prepared according to the NEBNext ChIP-seq library-prep kit instructions for Illumina sequencing (Catalog# E6240L).
Smore seq libraries were contructed using the protocol call described in Park 2014 "Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements" and the NEBNext Multiplex Small RNA library prep kit for Illumina sequencing (Catalog# E7300L).

treatment_protocol: Cultures used for MNase-ChIP-seq and ChIP-seq were fixed by treating with 1% formaldehyde for 30 minutes.

tag: genotype/variation

value: Wildtype

value: Ribo depletion


title: blood- control- 8.6 year old male

source_name: blood

value: Male

value: peripheral whole blood


title: Rev1-dd: SUP

source_name: SUP of Rev1-myc ubp10D ubp12D 71Sc72.13 HU


title: Smore Seq Ribo depletion Replicate 1


title: Rev1-dd: IP

source_name: IP fraction of Rev1-myc ubp10D ubp12D 71Sc72.13 HU


title: C57BL CornOil rep1

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing:
Raw array data (CEL files) were loaded into the R statistical environment using the oligo package (v3.6) of the BioConductor library. Gene and ProbeSet annotation was performed using moex10sttranscriptcluster.db (v3.6) and moex10stprobeset.db (v3.6) packages. Data were normalized using the RMA algorithm. Data were assessed for distributional homogeneity; no obvious outliers were detected. Only ProbeSets with annotation core databases were used for the analysis. Differential abundance analysis was performed using the limma package (v3.2) for R. Linear modeling was performed to contrast each TCDD dose to control. Standard errors of coefficients were adjusted using an empirical Bayes model. Model-based t-tests were applied to test for significance, followed by false discovery rate adjustment for multiple testing. To detect alternative splicing events, an entropy base measure for splicing prediction was performed using the ARH package.
RMA-normalized signal intensities. Probeset_ID = Affymetrix probeset id; Transcript_ID = Affymetrix transcript id; Exon_info = Affymetrix exon cluster id (as provided by the moex10sttranscriptcluster.db package)

organism: Mus musculus

source_name: liver, male C57BL/6, corn oil treated

growth_protocol: Animals were housed singly in Makrolon cages with pelleted Altromin 1314 feed and tap water available ab libitum. The housing environment was maintained at 21°C with 50 ± 10% relative humidity and artificial illumination on a 12/12 hour light/dark cycle.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated by oral gavage with a single bolus of either one dosage of TCDD (5 or 500 μg/kg) dissolved in corn oil vehicle or corn oil alone (10mL/kg).

tag: genotype

value: WT

tag: Sex

value: Liver

value: 12-15 weeks

value: Corn Oil vehicle

tag: exposure time

value: 19 hours


title: del-Htz1 Ino80-Myc-Tag Input

library_source: genomic

value: del-Htz1 Ino80-Myc-Tag

tag: chip antibody


title: C57BL TCDD 5 μg/kg rep2

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

source_name: liver, male C57BL/6, TCDD treated, 5 μg/kg

value: 5 μg/kg TCDD


title: Rev1: SUP

source_name: SUP of Rev1-myc wt 62Sc29.09 HU


title: blood-ulcerative colitis- 13.2 year old male

value: UC - L colitis


title: del-Htz1 Ino80-Myc-Tag ChIP


title: C57BL TCDD 5 μg/kg rep3

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: Ubp10 elg1D: SUP

source_name: SUP of Ubp12-myc wt 77Sc40.15 HU


title: Wildtype Ino80-Myc-Tag Input

value: Wildtype Ino80-Myc-Tag


title: blood-ulcerative colitis- 14.9 year old male

value: UC - pancolitis


title: Ddc2: SUP

source_name: SUP of Ddc2-myc wt HU


title: Ubp10 elg1D: IP

source_name: IP fraction of Ubp12-myc wt 77Sc40.15 HU


title: Wildtype Ino80-Myc-Tag ChIP


title: blood-ulcerative colitis- 11.6 year old male


title: tissue- crohn's disease- 9.5 year old male

value: Crohn's Disease

value: colon biopsy


title: del-Htz1 Swr1-Myc-Tag Input

value: del-Htz1 Swr1-Myc-Tag


title: blood-ulcerative colitis- 15.2 year old male


title: blood-ulcerative colitis- 16.9 year old male


title: C57BL TCDD 5 μg/kg rep1


title: del-Htz1 Swr1-Myc-Tag ChIP


title: Ubp10: SUP

source_name: SUP of Ubp10-myc wt 59Sc57.09 HU

value: S-phase

value: HU


title: blood-crohn's disease- 14.6 year old female

value: Female


title: Wildtype Swr1-Myc-Tag Input

value: Wildtype Swr1-Myc-Tag


title: Ubp10: IP

source_name: IP fraction of Ubp10-myc wt 59Sc57.09 HU


title: Ubp12: IP

source_name: IP fraction of Ubp12-myc wt 71Sc01.12 HU


title: C57BL TCDD 500 μg/kg rep1

source_name: liver, male C57BL/6, TCDD treated, 500 μg/kg

value: WT

value: Male

value: 500 μg/kg TCDD


title: Htz1-Tap-Tag MNase Input Replicate 2

description: nucleosomal DNA

data_processing:
Library strategy: MNase-ChIP-seq
Basecalls performed using BCL2Fastq.
Sequencing reads were aligned to the SacCer3 genome assembly using BWA 0.6.2 or 0.7.7
Data were filtered using the following specifications…
For wig files, reads were converted to signal using bedtools genomecov.
Count files were produced using featurecount.
Genome_build: sacCer3


title: Wildtype Swr1-Myc-Tag ChIP


title: Ubp12: SUP

source_name: SUP of Ubp12-myc wt 71Sc01.12 HU


title: C57BL CornOil rep5

value: Liver

value: 12-15 weeks

value: Corn Oil vehicle


title: C57BL TCDD 500 μg/kg rep2

value: 19 hours


title: C57BL TCDD 500 μg/kg rep3


title: Htz1-Tap-Tag MNase ChIP Replicate 2

description: nucleosomal DNA


title: S17: Bronchial lymph node

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

data_processing:
Adapter trimmed sequence reads were received in FASTQ format and assessed for quality using FastQC (version 0.11.7) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned to the bovine genome UMD3.1 using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.5.2b) (Dobin et al., 2013).
Read counts were generated by converting aligned reads into counts per gene using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.5.2b) (Dobin et al., 2013).
Genome_build: UMD3.1
Supplementary_files_format_and_content: Microsoft excel comma separated values file containing raw counts of sequencing reads for the features of interest

organism: Bos taurus

source_name: Bronchial lymph node

extract_protocol:
Bronchial lymph nodes were removed, flash frozen on dry ice, and RNA was harvested using the Qiagen RNeasy Plus Universal Mini Kit (Qiagen LTD, Manchester, UK). Extracted RNA was shipped frozen at -80oC on dry ice to the University of Missouri’s DNA Core Facility for RNA-Seq library preparation (Illumina TruSeq stranded mRNA Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bronchial lymph node

value: BRSV challenged

tag: house

value: C

tag: breed

value: Holstein-Friesian


title: blood-crohn's disease- 12.3 year old female

value: Crohn's Disease

value: peripheral whole blood


title: S18: Bronchial lymph node


title: blood-ulcerative colitis- 16.2 year old male

value: UC - pancolitis


title: S16: Bronchial lymph node


title: S15: Bronchial lymph node


title: Rev1: IP

source_name: IP fraction of Rev1-myc wt 62Sc29.09 HU

value: S-phase

value: HU


title: S13: Bronchial lymph node


title: S14: Bronchial lymph node


title: blood-crohn's disease- 15.9 year old male


title: lecrk-VI.2-2/Psm-3, biological rep3

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Gene expression data

hyb_protocol: Following fragmentation, 11 ug of biotin-labeled aRNAs were hybridized with rotation at 45°C for 16 hr to the Affymetrix GeneChip Arabidopsis Genome ATH1 Array.  The arrays were washed and stained with the reagents supplied in GeneChip® Hybridization Wash and Stain kit (Affymetrix) on an Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using a GeneChip® 7G Scanner (Affymetrix).

data_processing: The data were normalized using RMA normalization approach with Affy R package.

organism: Arabidopsis thaliana

source_name: lecrk-VI.2-2, Psm, 48 hr, replicate 3

label_protocol: All microarray sample preparation used the GeneChip® 3’ IVT Plus Express kit (Affymetrix, Santa Clara, CA), and reactions were done following the manufacturer’s protocols.  Briefly, cDNA was synthesized from 500 ng of total RNA and template for in vitro transcription (IVT) during which a biotin-modified nucleotide was incorporated. The biotin-labeled aRNA was then purified and fragmented.

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Sunshine MVP, Sun Gro Horticulture, Agawam, MA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol: About 100 mg leaf tissues were ground into a fine powder in liquid nitrogen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS).  After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol.  After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol.  The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min.  After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.

treatment_protocol: Psm bacteria were resuspended in 10 mM MgCl2 (OD600 = 0.002). Three lower leaves on each Arabidopsis plant were infiltrated with the bacterial suspension or 10 mM MgCl2 using a 1-mL needleless syringe. Two days later, two systemic leaves were collected for RNA extraction.

value: systemic tissues

tag: ecotype


title: S11: Bronchial lymph node

value: B


title: blood-crohn's disease- 12.9 year old male

source_name: blood

value: Male


title: lecrk-VI.2-2/Psm-2, biological rep2

description: Gene expression data

source_name: lecrk-VI.2-2, Psm, 48 hr, replicate 2


title: S12: Bronchial lymph node


title: blood-crohn's disease- 9.5 year old male


title: blood-crohn's disease- 17.1 year old female

value: Female


title: blood-crohn's disease- 8.2 year old female


title: blood-ulcerative colitis- 11.3 year old female


title: blood- control- 13.4 year old male

value: Control


title: lecrk-VI.2-2/Psm-1, biological rep1

description: Gene expression data

source_name: lecrk-VI.2-2, Psm, 48 hr, replicate 1


title: S10: Bronchial lymph node


title: lecrk-VI.2-2/MgCl2-2, biological rep2

description: Gene expression data

source_name: lecrk-VI.2-2, MgCl2, 48 hr, replicate 2


title: blood-crohn's disease- 14.7 year old male


title: tissue- ulcerative colitis- 12.8 year old female

source_name: colon

value: colon biopsy


title: lecrk-VI.2-2/MgCl2-1, biological rep1

description: Gene expression data

source_name: lecrk-VI.2-2, MgCl2, 48 hr, replicate 1


title: blood-crohn's disease- 12.8 year old female


title: blood-crohn's disease- 16.3 year old male


title: bak1-5/Psm-1, biological rep1

description: Gene expression data

source_name: bak1-5, Psm, 48 hr, replicate 1


title: bak1-5/Psm-2, biological rep2

description: Gene expression data

source_name: bak1-5, Psm, 48 hr, replicate 2


title: S9: Bronchial lymph node


title: lecrk-VI.2-2/MgCl2-3, biological rep3

description: Gene expression data

source_name: lecrk-VI.2-2, MgCl2, 48 hr, replicate 3


title: blood-crohn's disease- 16 year old male


title: blood-crohn's disease- 14.2 year old female


title: S8: Bronchial lymph node


title: S7: Bronchial lymph node


title: S6: Bronchial lymph node

value: control

value: A


title: S5: Bronchial lymph node

value: Bronchial lymph node


title: bak1-5/MgCl2-3, biological rep3

description: Gene expression data

source_name: bak1-5, MgCl2, 48 hr, replicate 3


title: S3: Bronchial lymph node


title: S4: Bronchial lymph node


title: S2: Bronchial lymph node


title: bak1-5/MgCl2-2, biological rep2

description: Gene expression data

source_name: bak1-5, MgCl2, 48 hr, replicate 2


title: blood-crohn's disease- 10.4 year old male


title: Col-0/Psm-3, biological rep3

description: Gene expression data

source_name: Col-0, Psm, 48 hr, replicate 3

value: wildtype


title: blood- IBD- 14 year old male

value: IBDU


title: bak1-5/MgCl2-1, biological rep1

description: Gene expression data

source_name: bak1-5, MgCl2, 48 hr, replicate 1


title: blood-ulcerative colitis- 17 year old male


title: blood-crohn's disease-11.3 year old male


title: S1: Bronchial lymph node

value: Holstein-Friesian


title: bak1-5/Psm-3, biological rep3

description: Gene expression data

source_name: bak1-5, Psm, 48 hr, replicate 3


title: X453_NC

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

description: X453_NC FPKM

data_processing:
BGI500 own software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters v1.5.2, then mapped to Gallus_gallus-5.0 genome using bowtie2 v2. 2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
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: GCF_000001405.25_GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Human breast cancer cell lines MDA-MB-453 was obtained from the Chinese Academy of Sciences Cell Bank and Cellbio (China) and cultured and stored according to their instructions.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: Human breast cancer cell lines MDA-MB-453 was seeded in 6-well dishes the night before to give 60-70% confluence for plasmid and 40-50% for miRNA or siRNA transfection. Cells were transfected using Lipofectamine 2000 (invitrogen), according to the manufacturer’s instructions in the following day. At 48 h post-transfection, cells were harvested for qRT-PCR analysis.


title: X453_NC_r1

description: X453_NC_r1 FPKM


title: Col-0/Psm-1, biological rep1

description: Gene expression data

source_name: Col-0, Psm, 48 hr, replicate 1


title: Col-0/Psm-2, biological rep2

description: Gene expression data

source_name: Col-0, Psm, 48 hr, replicate 2


title: blood- control- 13.2 year old female


title: blood- control- 15.5 year old male

value: Control (E.coli) --> CD


title: blood-ulcerative colitis- 8.3 year old female

value: UC - L colitis

value: peripheral whole blood


title: blood-crohn's disease- 16.4 year old female2

value: Crohn's Disease


title: blood-ulcerative colitis- 14.4 year old male


title: Col-0/MgCl2-2, biological rep2

description: Gene expression data

source_name: Col-0, MgCl2, 48 hr, replicate 2


title: CHR11-FLAG-1

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.2.6 with parameters -k 1 -N 1 -p 20 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f  BAM -p 1e-3 -g 1.2e8  --bdg --nolambda --nomodel
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

source_name: Arabidopsis seedlings

growth_protocol: seeds were grown on MS plates with a 16 h light/8 h dark photoperiod at 22ºC for 12 days and harvested for the next-step experiment

extract_protocol:
12-day-old seedling were collected. Nucleosome were extracted and sonicated. Protein-DNA complexes were extracted using antibody. DNA fragments were extracted for library construction.
libraries were prepared for ChIP-seq

tag: seedling

value: Arabidopsis seedlings

value: CHR11-Flag + wild type

tag: antibody

value: FLAG


title: CHR11-FLAG-2


title: blood- control- 10.1 year old male

source_name: blood

value: Male

tag: disease type

tag: tissue


title: blood-crohn's disease- 8.4 year old male

tag: gender


title: X453_NC_r2

description: X453_NC_r2 FPKM

tag: cell line


title: Col-0/MgCl2-1, biological rep1

description: Gene expression data

source_name: Col-0, MgCl2, 48 hr, replicate 1

value: systemic tissues


title: PIE1-FLAG-2

value: PIE1-Flag + wild type


title: Col-0/MgCl2-3, biological rep3

description: Gene expression data

source_name: Col-0, MgCl2, 48 hr, replicate 3


title: X453_2_r2

description: X453_2_r2 FPKM

source_name: MDA-MB-453_Linc00673 knockdown

value: Linc00673 knockdown


title: X453_2_r1

description: X453_2_r1 FPKM


title: PIE1-FLAG-1


title: X453_2

description: X453_2 FPKM


title: blood- IBD- 14.2 year old male

tag: age

value: IBD w/ oral


title: X453_1_r2

description: X453_1_r2 FPKM


title: X453_1_r1

description: X453_1_r1 FPKM


title: pie1-H3


title: X453_1

description: X453_1 FPKM


title: mbd9-H3


title: WT-H3

value: wild type


title: blood- control- 13.2 year old male

value: Control


title: chr1117-H2AZ-2


title: blood-crohn's disease- 17 year old male


title: WT-FLAG-2


title: blood-ulcerative colitis- 12.7 year old female

value: Female

value: UC - pancolitis


title: pie1-H2AZ-1


title: WT-FLAG-1


title: pie1-H2AZ-2


title: mbd9-H2AZ-2


title: blood- control- 8.5 year old male


title: blood- control- 18.3 year old female


title: blood-ulcerative colitis- 16.1 year old female


title: blood- control- 15.3 year old male

value: Control--> CD


title: Patient 61, glomerulus

data_processing: Raw array data (CEL files) were loaded into the R statistical environment (v3.3.1) using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. An updated Probe to Entrez Gene ID map, hta20hsentrezgcdf (v20.0.0), was used for annotation.

source_name: Patient 61, glomerular tissue

extract_protocol: Total RNA was isolated from micro-dissected glomerular and tubulointerstitial comparments by silica gel columns and diluted in 30 μL RNase-free water.

tag: subject id

value: Patient 61

tag: class

tag: subclass

value: glomerular tissue


title: Patient 40, glomerulus

source_name: Patient 40, glomerular tissue

value: Patient 40


title: mbd9-H2AZ-1

tag: genotype


title: chr1117-H2AZ-1


title: Patient 40, tubulointerstitium

source_name: Patient 40, tubulointersticial tissue

value: tubulointersticial tissue


title: blood-ulcerative colitis- 8.6 year old female

value: peripheral whole blood


title: WT-H2AZ

value: Arabidopsis seedlings


title: blood- control- 11.5 year old female


title: hta911-2

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 TAIR10 whole genome using HISAT-2.1.0 with default parameters
High-throughput sequencing reads were normalized by edgeR TMM algorithm
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each Sample
Supplementary_files_format_and_content: logFC

extract_protocol:
12-day-old seedling were collected for RNA extraction. Total RNA was extracted by Trizol and precipitated by isopropanol
libraries were prepared for mRNA-seq

tag: seedlings

tag: genetype


title: blood-crohn's disease- 14.6 year old male

value: Crohn's Disease


title: Patient 59, glomerulus

source_name: Patient 59, glomerular tissue

value: Patient 59


title: Patient 21, tubulointerstitium

source_name: Patient 21, tubulointersticial tissue

value: Patient 21


title: Patient 61, tubulointerstitium

source_name: Patient 61, tubulointersticial tissue


title: blood-crohn's disease- 18.7 year old male

value: Male


title: hta911-1


title: chr1117-2


title: blood-crohn's disease- 13.6 yr old male


title: blood- control- 10.9 year old male


title: Patient 54, glomerulus

source_name: Patient 54, glomerular tissue

value: Patient 54


title: Patient 53, glomerulus

source_name: Patient 53, glomerular tissue

value: Patient 53


title: blood-ulcerative colitis- 16.3 year old male


title: Patient 58, glomerulus

source_name: Patient 58, glomerular tissue

value: Patient 58


title: pie1-2


title: chr1117-1


title: Patient 55, glomerulus

source_name: Patient 55, glomerular tissue

value: Patient 55


title: mbd9-2


title: pie1-1


title: blood- control- 16.9 year old female

value: Female

value: Control


title: mbd9-1


title: WT-2

value: wild type


title: blood-crohn's disease- 9.2 year old male


title: blood- control- 18.5 year old female


title: Patient 44, glomerulus

source_name: Patient 44, glomerular tissue

value: Patient 44


title: Patient 45, glomerulus

source_name: Patient 45, glomerular tissue

value: Patient 45

value: glomerular tissue


title: E70

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

institute: Public Health Agency of Canada

data_processing:
CutAdapt was used to remove the adapter sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC), removing any reads that did not contain the adapter
Trimmomatic was used to for sliding window trimming of low qaulity base-calls, and to remove reads with average quality < 20 and length < 18
Bowtie 2 was used to align reads to the Univec contaminant reference file, unaliged reads were kept for the next step
Bowtie 2 was used to align reads to the rRNA reference file, unaligned reads were kept for the next step
Bowtie 2 was used to align reads to the GRCh38 reference genome using "very-sensitive-end-to-end" settings
FeatureCounts was used to map the aligned reads to known miRNAs using the miRBase human miRNA  reference annotation using the following settings: GFF feature type = "miRNA"; GFF gene = "Name"; Strand specificity = "Stranded forward";
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files with raw read counts for each miRNA detected from miRBase v22 human annotation

organism: Cervus canadensis

source_name: Serum

extract_protocol:
Norgen plasma/serum RNA purification mini kit
TruSeq small RNA library preparation kit

tag: method for prion disease status

value: CWD (+) by IHC on brain obex tissue

tag: cwd status

value: Pos

tag: scrapie status


title: E69


title: Patient 52, glomerulus

source_name: Patient 52, glomerular tissue

value: Patient 52


title: Patient 43, glomerulus

source_name: Patient 43, glomerular tissue

value: Patient 43


title: blood- control- 14.5 year old female

source_name: blood

value: Control - infect

value: peripheral whole blood


title: blood- control- 16.4 year old female


title: Patient 49, glomerulus

source_name: Patient 49, glomerular tissue

value: Patient 49


title: E68


title: Patient 47, glomerulus

source_name: Patient 47, glomerular tissue

value: Patient 47


title: WT-1

source_name: Arabidopsis seedlings

value: Arabidopsis seedlings


title: blood-crohn's disease- 12.8 year old male

value: Male

value: Crohn's Disease


title: Patient 42, glomerulus

source_name: Patient 42, glomerular tissue

value: Patient 42


title: blood-crohn's disease- 16.4 year old female

value: Female


title: blood- control- 8.3 year old male

value: Control


title: blood-crohn's disease- 17.1 year old male


title: blood- control- 11.2 year old female

value: Control - celiac


title: Patient 35, glomerulus

source_name: Patient 35, glomerular tissue

value: Patient 35


title: blood- control- 8.2 year old male


title: blood- control- 14.7 year old female


title: blood-crohn's disease- 8.6 year old male


title: Patient 39, glomerulus

source_name: Patient 39, glomerular tissue

value: Patient 39

value: glomerular tissue


title: Patient 30, glomerulus

source_name: Patient 30, glomerular tissue

value: Patient 30


title: Patient 37, glomerulus

source_name: Patient 37, glomerular tissue

value: Patient 37


title: blood-ulcerative colitis- 14.8 year old male

value: UC - pancolitis


title: E66

value: CWD (+) by IHC on brain obex tissue

value: Pos


title: Patient 41, glomerulus

source_name: Patient 41, glomerular tissue

value: Patient 41


title: E65


title: E67


title: E64


title: E62


title: E63


title: blood- control- 11.1 year old male

value: peripheral whole blood


title: Patient 27, glomerulus

source_name: Patient 27, glomerular tissue

value: Patient 27


title: blood- control- 14.2 year old male

value: Male


title: Patient 26, glomerulus

source_name: Patient 26, glomerular tissue

value: Patient 26


title: blood- control- 15.1 year old male


title: blood- control- 16.7 year old female


title: Patient 23, glomerulus

source_name: Patient 23, glomerular tissue

value: Patient 23


title: blood- control- 15.5 year old female

value: Female


title: E60


title: E58


title: Patient 28, glomerulus

source_name: Patient 28, glomerular tissue

value: Patient 28


title: Patient 29, glomerulus

source_name: Patient 29, glomerular tissue

value: Patient 29


title: Patient 20, glomerulus

source_name: Patient 20, glomerular tissue

value: Patient 20


title: blood- control- 11.4 year old male

value: Control


title: Patient 22, glomerulus

source_name: Patient 22, glomerular tissue

value: Patient 22

value: glomerular tissue


title: E56

source_name: Serum


title: E61


title: blood-crohn's disease- 8.3 year old female

source_name: blood

value: Crohn's Disease


title: E57


title: blood-ulcerative colitis- 15.8 year old male

value: UC - proctitis


title: E55

value: CWD (+) by IHC on brain obex tissue


title: E59

value: Pos


title: Patient 19, glomerulus

source_name: Patient 19, glomerular tissue

value: Patient 19


title: blood-crohn's disease- 15.8 year old male

value: peripheral whole blood


title: E54


title: blood- control- 16.1 year old female


title: E53


title: Patient 16, glomerulus

source_name: Patient 16, glomerular tissue

value: Patient 16


title: Patient 15, glomerulus

source_name: Patient 15, glomerular tissue

value: Patient 15


title: blood-crohn's disease- 13.8 year old male

value: Male


title: Patient 17, glomerulus

source_name: Patient 17, glomerular tissue

value: Patient 17


title: Patient 18, glomerulus

source_name: Patient 18, glomerular tissue

value: Patient 18


title: E52

value: CWD (-) by IHC on brain obex tissue

value: Neg


title: E51


title: E50


title: Patient 14, glomerulus

source_name: Patient 14, glomerular tissue

value: Patient 14


title: E49


title: blood- control- 16.2 year old female2

value: Female

value: Control


title: E48


title: Patient 13, glomerulus

source_name: Patient 13, glomerular tissue

value: Patient 13

value: glomerular tissue


title: blood-crohn's disease- 11.1 year old male

value: Crohn's Disease


title: Patient 12, glomerulus

source_name: Patient 12, glomerular tissue

value: Patient 12


title: blood-crohn's disease- 14.4 year old male


title: Patient 5, glomerulus

source_name: Patient 5, glomerular tissue

value: Patient 5


title: blood- control- 16.2 year old female


title: blood- control- 13.4 year old female


title: Patient 10, glomerulus

source_name: Patient 10, glomerular tissue

value: Patient 10


title: Patient 11, glomerulus

source_name: Patient 11, glomerular tissue

value: Patient 11


title: blood-ulcerative colitis- 17.3 year old female

value: UC - pancolitis

value: peripheral whole blood


title: E47


title: blood-crohn's disease- 13.6 year old male

value: Male


title: Patient 4, glomerulus

source_name: Patient 4, glomerular tissue

value: Patient 4


title: blood- control- 15.2 year old female

value: Control - infect


title: E45

value: CWD (-) by IHC on brain obex tissue


title: E44

value: Neg


title: blood- control- 16.9 year old male


title: E43


title: E42


title: E41


title: E46


title: E40


title: Patient 3, glomerulus

source_name: Patient 3, glomerular tissue

value: Patient 3


title: E39


title: E38


title: Patient 60, tubulointerstitium

source_name: Patient 60, tubulointersticial tissue

value: Patient 60

value: tubulointersticial tissue


title: blood- control- 17.9 year old male

value: Control


title: blood-crohn's disease- 10.9 year old female

value: Female


title: blood-crohn's disease- 15.9 year old female

value: Crohn's Disease


title: Patient 1, glomerulus

source_name: Patient 1, glomerular tissue

value: Patient 1

value: glomerular tissue


title: blood- control- 18.6 year old female


title: E37

source_name: Serum


title: Patient 2, glomerulus

source_name: Patient 2, glomerular tissue

value: Patient 2


title: blood- control - 17.5 year old male

source_name: blood


title: Patient 58, tubulointerstitium

source_name: Patient 58, tubulointersticial tissue

value: Patient 58


title: Patient 59, tubulointerstitium

source_name: Patient 59, tubulointersticial tissue

value: Patient 59


title: Patient 56, tubulointerstitium

source_name: Patient 56, tubulointersticial tissue

value: Patient 56


title: blood-crohn's disease- 11.5 year old female

value: peripheral whole blood


title: blood-crohn's disease- 13.1 year old male

value: Male


title: E36


title: blood- control - 10.5 year old female


title: Patient 53, tubulointerstitium

source_name: Patient 53, tubulointersticial tissue

value: Patient 53


title: Patient 52, tubulointerstitium

source_name: Patient 52, tubulointersticial tissue

value: Patient 52


title: E35

value: CWD (-) by IHC on brain obex tissue

value: Neg


title: Patient 57, tubulointerstitium

source_name: Patient 57, tubulointersticial tissue

value: Patient 57


title: blood- control - 16.2 year old male


title: Patient 51, tubulointerstitium

source_name: Patient 51, tubulointersticial tissue

value: Patient 51

value: tubulointersticial tissue


title: blood-crohn's disease- 11.8 year old female

value: Female


title: E34

value: CWD (+) by IHC on brain obex tissue

value: Pos


title: blood- control - 9.4 year old female

value: Control - infect


title: C57BL TCDD 500 μg/kg rep2

data_processing: Each genotype was pre-processed separately. Raw array data (CEL files) were loaded into the R statistical environment (v3.4.3) using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm (each genotype processed separately). Two samples (one DBA and one rWT) were identified as an outlier; this was removed and remaining samples re-processed. Updated Probe to Entrez Gene ID maps, mogene11stmmentrezgcdf (v22.0.0) and mogene20stmmentrezgcdf (v22.0.0), were used for annotation. Genotypes were then combined and batch correction performed using ComBat (R package sva v3.24.4).

source_name: liver, male C57BL/6, TCDD treated, 500 μg/kg

tag: strain

value: WT

tag: Sex

value: Liver

value: 12-15 weeks

tag: agent

value: TCDD

tag: dose

value: 500 μg/kg

tag: time (exposure)

value: 19 hours


title: Patient 49, tubulointerstitium

source_name: Patient 49, tubulointersticial tissue

value: Patient 49

tag: tissue


title: E33


title: C57BL TCDD 500 μg/kg rep3

value: Male


title: blood-ulcerative colitis - 12.8 year old female

tag: gender

tag: disease type

value: UC - pancolitis

value: peripheral whole blood


title: Patient 54, tubulointerstitium

source_name: Patient 54, tubulointersticial tissue

tag: subject id

value: Patient 54


title: C57BL TCDD 500 μg/kg rep4

tag: age


title: E32


title: E31


title: C57BL TCDD 500 μg/kg rep1


title: E30


title: C57BL TCDD 5 μg/kg rep3

source_name: liver, male C57BL/6, TCDD treated, 5 μg/kg

value: 5 μg/kg


title: Patient 47, tubulointerstitium

source_name: Patient 47, tubulointersticial tissue

value: Patient 47

tag: class

tag: subclass

value: tubulointersticial tissue


title: C57BL TCDD 5 μg/kg rep4

tag: genotype


title: C57BL TCDD 5 μg/kg rep2


title: Patient 46, tubulointerstitium

source_name: Patient 46, tubulointersticial tissue

value: Patient 46


title: E29

value: CWD (+) by IHC on brain obex tissue

value: Pos


title: blood-crohn's disease - 10.7 year old female

value: Female

value: Crohn's Disease


title: blood-crohn's disease - 10.5 year old male


title: Patient 39, tubulointerstitium

source_name: Patient 39, tubulointersticial tissue

value: Patient 39


title: Patient 37, tubulointerstitium

source_name: Patient 37, tubulointersticial tissue

value: Patient 37


title: Patient 42, tubulointerstitium

source_name: Patient 42, tubulointersticial tissue

value: Patient 42


title: blood- control- 18.1 year old female

source_name: blood

value: Control


title: C57BL TCDD 5 μg/kg rep1

value: WT

value: Liver

value: 12-15 weeks

value: TCDD

value: 19 hours


title: E28

source_name: Serum


title: E27


title: 2xSCS70-2

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Data were analyzed by the MAP-RSeq pipeline developed by the Mayo Clinic Bioinformatics Core (Kalari et al., BMC Bioinformatics 2014;15:224)
RSeQC software was used for estimating the distance between paired end reads, evaluating the sequencing depth for alternate splicing analysis, determining the rate of duplicate reads, evaluating coverage of reads across genes, and more
Paired-end reads were aligned by TopHat 2.0.6 against the mm10 genome build using the bowtie1 aligner option
Gene counts were generated using HTseq software and gene annotation files are obtained from Illumina
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene counts with corresponding RPKM values

source_name: Cells derived from H-2Kb-tsA58 gastric tunica muscularis

growth_protocol: Cell line was cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) at 39.5°C and without interferon-gamma

extract_protocol:
Qiagen miRNeasy
Illumina TruSeq mRNA Sample Preparation Kit v2

tag: cel line

value: Interstitial cells of Cajal (ICC) projenitor cell line

tag: cell type


title: LNA29 treatment RNA-seq Rep #3

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-9

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9, rn6, and hg19 for mouse, rat, and monkey small RNA-seq, mm10 and rn6 for mouse and rat RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

source_name: liver

extract_protocol:
RNA extraction protocol not provided.
Libraries were prepared according to the Illumina TruSeq polyA+ Sample Prep Kit protocol

value: liver


title: 2xSCS2F10-2

source_name: Cells derived from C57BL/6J gastric tunica muscularis

growth_protocol: Cell line was cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) plus 5% cell-free chick embryo extract (CEE; Accurate Chemical) at 37°C


title: E26

tag: method for prion disease status

tag: cwd status


title: blood-crohn's disease - 9.5 year old male

value: Male

value: peripheral whole blood


title: LNA29 treatment RNA-seq Rep #2

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-8

tag: strain


title: blood- control-14.5 year-female


title: C57BL CornOil rep4

source_name: liver, male C57BL/6, corn oil treated

tag: Sex

value: corn oil vehicle

value: control


title: C57BL CornOil rep3

tag: agent


title: C57BL CornOil rep2

tag: dose


title: Patient 31, tubulointerstitium

source_name: Patient 31, tubulointersticial tissue

value: Patient 31

value: tubulointersticial tissue


title: Patient 28, tubulointerstitium

source_name: Patient 28, tubulointersticial tissue

value: Patient 28


title: C57BL CornOil rep1

tag: time (exposure)


title: Patient 34, tubulointerstitium

source_name: Patient 34, tubulointersticial tissue

value: Patient 34

tag: tissue


title: LNA29 treatment RNA-seq Rep #1

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-7


title: E24

value: CWD (+) by IHC on brain obex tissue

value: Pos

tag: scrapie status


title: LNA29 control RNA-seq Rep #6

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-6


title: E25


title: iPSC myotube-SDDF-ATACseq-Exp3

city: Minneapolis

first: Alessandro

last: Magli

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
ATAC-seq analysis. Reads were aligned to the human genome (hg38) using Bowtie2 with the following parameters: -q -I 38 -X 2000 --local --dovetail --no-mixed --no-discordant. Aligned reads were filtered for PCR duplicates using Samtools and then processes with MACS 2.1 with the following parameters: --nomodel --nolambda --keep-dup all --call-summits -q 0.05 -B. Bigwig files for visualization on IGV were generated by converting the bedgraph files obtained from MACS2 using the Kent tool bedGraphToBigWig. To identify peaks unique to DMSO and SDDF-treated cells, we used the BEDTools package: summits from DMSO- or SDDF-treated cells were extended 50bp in both directions and then compared pairwise with BEDTools intersect (Rep1_vs_Rep2, Rep1_vs_Rep3, Rep2_vs_Rep3). Common peaks from the 3 comparisons (DMSO or SDDF) were then combined in a unique list and filtered using BEDTools merge. DMSO and SDDF peaks were then compared using BEDTools intersect using the -v function and a minimum overlap of 60% (-f 0.6 -F 0.6). Analysis of differential accessibility was performed by generating a list of peaks representative of all samples using the peak summits identified by MACS2. Each summit was extended 50bp in both directions and the resulting lists of peaks were combined, sorted and merged to obtain a dataset of unique and non-overlapping loci. This list was then used to extrapolate the sequencing depth coverage from each sample bedgraph file. Coverage files were then analyzed using DEseq2  to identify loci with differential chromatin accessibility.
RNA-seq analysis: 75bp FastQ paired-end reads (n=20.9 Million per sample) were trimmed using Trimmomatic (v 0.33). Quality control on raw sequence data was performed with FastQC. Reads were mapped to the human genome (hg38) reference using Hisat2 (v2.1.0). Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLC genomics work bench (Qiagen) using raw read counts. We filtered the generated list based on a minimum 2X Absolute Fold Change and FDR corrected p < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq: processed files contain the list of peak summits identified by MACS2 in each replicate
Supplementary_files_format_and_content: RNA-seq: processed files contain tab-delimited expression values following analysis using EdgeR

source_name: iPSC myotube-SDDF

growth_protocol: Human iPSC were differentiated into myogenic progenitors using conditional expression of PAX7. Myogenic progenitors were induced to terminally differentiate in a serum free low nutrient medium supplemented with vehicle (DMSO) or small molecules (SDDF)

extract_protocol:
Total RNA was extracted in TRIzol reagent and column purified with DNAse treatment using the Purelink RNA mini kit as per manufacturer's instructions
RNA-seq: Dual-indexed libraries were generated using the TruSeq stranded mRNA library kit
ATAC-seq: 50,000cells from 2-day DMSO- and SDDF-treated cultures were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes, after which transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10µl Elution Buffer. Final libraries were generated by primer extension of the transposed DNA followed by PCR amplification using Illumina-compatible adapter-barcodes.

treatment_protocol: Myotubes were generated upon a 5-day treatment with vehicle (DMSO) or small molecules (SDDF)

value: Human iPSC derived myotubes

tag: treatment

value: S/Da/De/F (SDDF)

tag: time

value: 2-day treatment


title: iPSC myotube-SDDF-ATACseq-Exp2


title: Patient 27, tubulointerstitium

source_name: Patient 27, tubulointersticial tissue

tag: subject id

value: Patient 27


title: iPSC myotube-SDDF-ATACseq-Exp1


title: E22


title: LNA29 control RNA-seq Rep #4

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-4


title: LNA29 control RNA-seq Rep #5

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-5


title: Patient 29, tubulointerstitium

source_name: Patient 29, tubulointersticial tissue

value: Patient 29

tag: class


title: iPSC myotube-DMSO-ATACseq-Exp3

source_name: iPSC myotube-DMSO

value: DMSO


title: E23


title: Patient 26, tubulointerstitium

source_name: Patient 26, tubulointersticial tissue

value: Patient 26

tag: subclass


title: E21


title: iPSC myotube-DMSO-ATACseq-Exp2


title: Patient 25, tubulointerstitium

source_name: Patient 25, tubulointersticial tissue

value: Patient 25


title: Patient 24, tubulointerstitium

source_name: Patient 24, tubulointersticial tissue

value: Patient 24


title: LNA29 control RNA-seq Rep #3

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-3

value: liver


title: Patient 23, tubulointerstitium

source_name: Patient 23, tubulointersticial tissue

value: Patient 23


title: E20


title: LNA29 control RNA-seq Rep #2

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-2


title: E19


title: E18


title: LNA29 control RNA-seq Rep #1

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-1


title: iPSC myotube-DMSO-ATACseq-Exp1


title: LNA29 treatment RNA-seq Rep #5

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-11


title: LNA29 treatment RNA-seq Rep #4

description:
RNA
LNA-29 treatment of mice
lna29_normalizedCounts.csv
Sample name:
LNA29-10


title: E17

value: CWD (-) by IHC on brain obex tissue

value: Neg


title: E16


title: Patient 19, tubulointerstitium

source_name: Patient 19, tubulointersticial tissue

value: Patient 19

value: tubulointersticial tissue


title: si-YTHDF3-2_input

city: Guangzhou

first: Wen

last: Ni

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

description:
Protocol: MeRIP-seq
si6292_input

data_processing:
The total cell RNA is fragmented into ~100-nt-long oligonucleotides using fragmentation buffer (part # CS220011) under elevated temperature.
The Magna ChIP Protein A/G Magnetic Beads were subjected to incubate for 30 minutes at room temperature with m6A-specific antibody (Part # MABE1006) in IP buffer.
Then eluted RNA and analyzed MeRIPed RNA by deep sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files includeFPKM values for each Sample …

source_name: Colorectal cancer cell

growth_protocol: The base medium for this cell line is ATCC formulated McCoy's 5a Medium Modified. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

extract_protocol:
siRNA method according to the manufacturer's instructions of jetPRIME Kit (Polyplus, Strasbourg, France).
Total RNA was extracted using Trizol reagent (Takara, Dalian, China). Agilent 2100 Bioanalyzer (Agilent, CA, USA) and NanoDrop 2000 (Thermo Fisher, MA, USA) was used to analyze the total RNA quality and quantity.
The total cell RNA is fragmented into ~100-nt-long oligonucleotides using fragmentation buffer (part # CS220011) under elevated temperature. Then validation of post-fragmentation size distribution by Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Kit. The Magna ChIP Protein A/G Magnetic Beads were subjected to incubate for 30 minutes at room temperature with m6A-specific antibody (Part # MABE1006) in IP buffer. The mixture was then incubated with MeRIP reaction mixture for 2 hours at 4°C. Then eluted RNA and analyzed MeRIPed RNA by deep sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

tag: cell line

value: Colorectal cancer cell

value: colon

tag: genotype/variation

tag: rip antibody


title: Patient 18, tubulointerstitium

source_name: Patient 18, tubulointersticial tissue

value: Patient 18


title: E15

source_name: Serum

tag: method for prion disease status


title: Patient 20, tubulointerstitium

source_name: Patient 20, tubulointersticial tissue

value: Patient 20


title: si-YTHDF3-2_IP

description:
Protocol: MeRIP-seq
si6292_IP

tag: cell type

value: m6A-specific antibody (Part # MABE1006)


title: iPSC myotube-DMSO-RNAseq-Exp4

value: Human iPSC derived myotubes

value: 5-day treatment


title: iPSC myotube-DMSO-RNAseq-Exp2

value: DMSO


title: iPSC myotube-DMSO-RNAseq-Exp1


title: si-YTHDF3-1_IP

description:
Protocol: MeRIP-seq
si6291_IP


title: E14

tag: cwd status


title: Patient 17, tubulointerstitium

source_name: Patient 17, tubulointersticial tissue

value: Patient 17


title: E12


title: E13


title: H12

organism: Mesocricetus auratus

value: collected 90 dpi following treatment with 263K scrapie brain homogenate

value: Pos


title: si-YTHDF3-1_input

description:
Protocol: MeRIP-seq
si6291_input


title: H11


title: E11


title: Patient 16, tubulointerstitium

source_name: Patient 16, tubulointersticial tissue

value: Patient 16


title: Patient 22, tubulointerstitium

source_name: Patient 22, tubulointersticial tissue

value: Patient 22


title: NC-2_IP

description:
Protocol: MeRIP-seq
nc2_IP

value: si-control transcript


title: NC-2_input

description:
Protocol: MeRIP-seq
nc2_input


title: H10


title: E10

value: CWD (-) by IHC on brain obex tissue

value: Neg


title: H9


title: H8


title: E9


title: NC-1_input

description:
Protocol: MeRIP-seq
nc1_input


title: NC-1_IP

description:
Protocol: MeRIP-seq
nc1_IP


title: Patient 14, tubulointerstitium

source_name: Patient 14, tubulointersticial tissue

value: Patient 14

value: tubulointersticial tissue


title: H7


title: E7


title: Patient 15, tubulointerstitium

source_name: Patient 15, tubulointersticial tissue

value: Patient 15


title: H6

value: collected 90 dpi following treatment with non-infectious brain homogenate


title: Patient 12, tubulointerstitium

source_name: Patient 12, tubulointersticial tissue

value: Patient 12


title: Patient 13, tubulointerstitium

source_name: Patient 13, tubulointersticial tissue

value: Patient 13


title: E6


title: Patient 11, tubulointerstitium

source_name: Patient 11, tubulointersticial tissue

value: Patient 11


title: Patient 9, tubulointerstitium

source_name: Patient 9, tubulointersticial tissue

value: Patient 9


title: E5


title: Patient 10, tubulointerstitium

source_name: Patient 10, tubulointersticial tissue

value: Patient 10


title: Patient 7, tubulointerstitium

source_name: Patient 7, tubulointersticial tissue

value: Patient 7


title: H4


title: E4


title: E8


title: H3


title: H2


title: E3


title: E2


title: E1


title: H5


title: H1


title: FEC on CIM NPK, biological rep4

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

description: Gene expression data from FEC on CIM NPK

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Manihot esculenta

source_name: FEC on CIM NPK

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

growth_protocol: Friable embryogenic callus (FEC) was inducded as follows; Somatic Embryo (SE) was induced from axillary buds in nodal stem of in vitro plantlets during 2 months old as 3-4 weeks interval. To produce the axillary bud, all leaves of in vitro plant (length 20-30 mm) were removed and 20-30 mm of single-nodal-stems were prepared. The induced SEs on CIM were transferred to Driver and Kuniyuki Walnut media (DKW) including 2 µM of CuSO4 and 12 mg/L of picloram, and incubated for 2 weeks at 28◦C in the dark.SE was transferred to nitrogen, phosphate and potassium limited MS media with 2 µM of CuSO4 and 12 mg/L of picloram (CIM-NPK) and FEC was induced from SE on CIM-NPK media.

extract_protocol: Total RNA from FEC was purified according to manual protocol using RNeasy Plant Mini kit protocol (QIAGEN) followed by Plant RNA reagent protocol (Invitrogen). The total RNA quality was evaluated by electrophoresis with the bioanalyzer system (Agilent, USA). The total RNA was stored at -80ºC until further use.

treatment_protocol: Induced FECs were cultivated on CIM–NPK media and FEC cultivated on CIM media for 1 month. We collected the cultivated FECs.

value: friable embryogenic callus (FECs)


title: DMSO-control biological replicate #2

status: Public on Oct 28 2019

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Read quality control diagnostic analyses using FastQC version 0.11.8.
Reads were trimmed using Trimmomatic version 0.32.
Trimmed reads were truncated to 30bp using fastx_trimmer from the FASTX Toolkit version 0.0.13.
Truncated reads were mapped to the zebrafish GRCz10 assembly using bowtie version 1.0.0 (parameters: --chunkmds 520 -y -v 2 --best --strata -m 3 -k 1 -S -p 8).
Read alignments to the mitochondrial genome were filtered out from SAM files and SAM files converted to BAM files using samtools version 0.1.18.
Nuclease accessible peaks were called using the callpeak function in MACS2 (version 2.1.1.20160309; using parameters -f BAM -g 146444456 -nomodel -nolabbda -keep-dup all -call-summits -q 0.001 -B) and Ensembl (version 85) annotation.
Differential binding events were called using the bdgdiff function in MACS2 (parameters used were -C {8,5}).
Motifs within peaks were predicted and annotated using HOMER (version 4.8).
Genome_build: Zv10
Supplementary_files_format_and_content: BED files of ATAC peaks for each sample

organism: Danio rerio

source_name: blood

growth_protocol: Adult AB zebrafish were housed and maintained in tanks at 28oC and exposed to a 14:10 hour light:dark cycle.

extract_protocol:
Transposed DNA was purfied using the QIAGEN MinElute PCR Purification Kit.
ATAC-Seq library protocol as described by Buenrostro J et al., Curr Protoc Mol Bio. 2015; 109: 21.29.1-9.

treatment_protocol: DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development, and then fish were maintained to adulthood under normal conditions.

value: blood

tag: age

value: 11 months


title: DMSO-control biological replicate #3

value: 10 months


title: Patient 6, tubulointerstitium

source_name: Patient 6, tubulointersticial tissue

value: Patient 6


title: cortisol-treated biological replicate #3


title: cortisol-treated biological replicate #2


title: DMSO-control biological replicate #1

value: 12 months


title: cortisol-treated biological replicate #1


title: Patient 2, tubulointerstitium

source_name: Patient 2, tubulointersticial tissue

value: Patient 2


title: Patient 1, tubulointerstitium

source_name: Patient 1, tubulointerstitial tissue

value: Patient 1

value: tubulointerstitial tissue


title: FEC on CIM NPK, biological rep3


title: Patient 5, tubulointerstitium

source_name: Patient 5, tubulointersticial tissue

value: Patient 5

value: tubulointersticial tissue


title: Patient 4, tubulointerstitium

source_name: Patient 4, tubulointersticial tissue

value: Patient 4


title: FEC on CIM, biological rep4

description: Gene expression data from FEC on CIM

source_name: FEC on CIM


title: FEC on CIM, biological rep3

description: Gene expression data from FEC on CIM


title: FEC on CIM NPK, biological rep2


title: FEC on CIM NPK, biological rep1


title: FEC on CIM, biological rep1

description: Gene expression data from FEC on CIM


title: NPCs, CTRL2_CT1.0_D8

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

data_processing:
Basecalls performed using CASAVA version 1.7
Sequences are aligned to transcriptome with Salmon (v0.8.2)
Transcripts Per Million were calculated by Salmon(v0.8.2)by defalut parameters
Genome_build: hg38
Supplementary_files_format_and_content: TPMs

molecule: polyA RNA

source_name: Neural progenitor cells

extract_protocol:
Total RNA was isolated from cells collected at different time points using TRIzol Reagent (Invitrogen). Isolated RNA was enriched by Poly(A) tails and fragmented. Sequencing libraries were prepared according to Illumina manufacturer instruction. Paired-end RNA-seq of 2x100 base pair reads were sequenced on Illumina Hiseq2000 platform or 2x150 base pair reads were sequenced on Hiseq X-ten
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human ES-derived neural progenitor cells

tag: genotype

value: wild type

tag: timepoint


title: NPCs, CTRL2_CT2.0_D8


title: NPCs, CTRL2_CT4.0RA_D8


title: NPCs, CTRL2_CT3.0_D8


title: Patient 3, tubulointerstitium

source_name: Patient 3, tubulointersticial tissue

value: Patient 3


title: NPCs, CTRL2_CT0.4_D8


title: NPCs, CTRL2_IWP2_D8


title: FEC on CIM, biological rep2

description: Gene expression data from FEC on CIM


title: NPCs, CTRL1_CT4.0RA_D8


title: NPCs, CTRL2_CT4.0_D8


title: NPCs, CTRL1_CT4.0_D8


title: NPCs, CTRL1_Untreated_D8


title: NPCs, CTRL1_CT0.4_D8


title: NPCs, CTRL1_CT1.0_D8


title: NPCs, CTRL1_IWP2_D8


title: NPCs, CTRL1_CT3.0_D8


title: NPCs, CTRL1_CT2.0_D8


title: NPCs, CTRL1_CT0.8_D8


title: NPCs, CTRL2_CT4.0RA_D4


title: NPCs, CTRL2_CT3.0_D4


title: NPCs, CTRL2_CT2.0_D4


title: NPCs, CTRL2_CT1.0_D4


title: NPCs, CTRL2_CT0.8_D4


title: NPCs, CTRL2_IWP2_D4


title: NPCs, CTRL2_Untreated_D4


title: NPCs, CTRL2_Untreated_D8


title: NPCs, CTRL1_CT4.0RA_D4


title: NPCs, CTRL1_CT4.0_D4


title: NPCs, CTRL1_CT0.8_D4


title: NPCs, CTRL1_CT1.0_D4


title: NPCs, CTRL1_CT2.0_D4


title: NPCs, CTRL1_Untreated_D4


title: NPCs, CTRL1_IWP2_D4


title: CTRL2_ES

source_name: Human embryonic stem cell

value: human embryonic stem cell


title: CTRL1_ES


title: NPCs, CTRL2_CT4.0_D4


title: WT_b-catenin_Input

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to hg19 genome assembly by bowtie2 (v2.3.2) by default parameters.
Peaks were called using MACS2 (v2.1.0) with setting: fdr-q (0.01).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files were generated by MACS2, the score represents number of bp fall into the single base pair region.

source_name: Neural epithelial cells

extract_protocol:
Neural epithelial cell lysates were clarified from sonicated nuclei and SOX21 complexes or b-catenin-DNA complexes were immunoprecipitated with SOX21 antibody (R&D AF3538) or b-catenin antibody (BD Biosciences, 610154), respectively. Protein A and G Magnetic Dynabeads were used to capture antibody-bound protein-DNA complexes.
The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding “A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq X-ten platforms.

value: Human ES-derived neural epithelial cells

tag: time point

value: Day 5

tag: chip antibody


title: SOX21KO_b-catenin_ChIP

value: b-catenin (BD Biosciences, 610154)


title: WT2-D8

description:
PolyA RNA
processed data file: WT_vs_SOX21-KO.gene_expression.TPM.csv

data_processing:
Basecalls performed using CASAVA version 1.7.
Sequences are aligned to transcriptome with Salmon (v0.8.2).
Transcripts Per Million were calculated by Salmon (v0.8.2) by default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: *.gene_expression.TPM.csv: Comma-separated text files include TPM values for all samples.

extract_protocol:
Total RNA was isolated from cells collected at different time points using TRIzol Reagent (Invitrogen). Isolated RNA was enriched by Poly(A) tails and fragmented.
RNA sequencing libraries were prepared according to Illumina manufacturer instruction. Paired-end RNA-seq of 2x100 base pair reads were sequenced on Illumina Hiseq2000 platform, or 2x150 base pair reads were sequenced on Hiseq X-ten, or 50 base pair reads were sequenced on Illumina MiSeq.

value: Day 8


title: S13-D8


title: S23-D8


title: S23-D4

value: Day 4


title: NPCs, CTRL2_CT0.4_D4


title: SOX21_Input


title: WT2-D4


title: WT1-D4


title: S13-D4


title: WT1-D8


title: NPCs, CTRL1_CT3.0_D4


title: NPCs, CTRL1_CT0.4_D4


title: T1948_S9

city: Zurich

first: Anna

last: Lindholm

address: Winterthurerstrasse 190

department: Department of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

data_processing:
Reads were aligned with STAR STAR-2.5.1b with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the R method Rsubread::featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: text files holding gread counts per gene

extract_protocol:
Ovaries, Testis, Liver: Ambio PureLink RNA Mini Kit with Trizol and a Dnase step; Brain: phenol-chloroform protocol
illumina TruSeq Stranded mRNA Library Kit

tag: sibling

tag: litter

tag: Sex

value: M

tag: tissue

value: Testis


title: T1927_S11


title: T1949_S10

value: wt; +/t


title: T1928_S12


title: WT_b-catenin_ChIP


title: T1961_S12


title: T1916_S15


title: T1960_S11


title: SOX21KO_b-catenin_Input


title: T1915_S14


title: SOX21_ChIP


title: T1901_S10


title: T1903_S11


title: T1894_S9


title: T1892_S8


title: NPCs, CTRL2_CT0.8_D8

tag: treatment


title: O1981_S15

value: F

value: Ovaries


title: O1929_S15


title: O1951_S12


title: O1952_S13


title: O1924_S10


title: O1899_S14


title: O1921_S9


title: O1908_S12


title: O1909_S13


title: O1914_S9


title: O1913_S15


title: O1895_S13


title: L1971_S3

value: Liver


title: L1960_S4


title: L1961_S5


title: L1948_S2


title: L1936_S6


title: L1929_S8


title: L1928_S5


title: L1949_S3


title: L1931_S1


title: L1927_S4


title: O1931_S8


title: O1980_S14


title: L1921_S2


title: L1916_S1


title: L1913_S1


title: L1908_S5


title: L1901_S3


title: L1899_S7


title: L1894_S2


title: L1903_S4


title: 1981_S15

value: Brain


title: L1973_S4


title: L1938_S7


title: 1980_S14


title: L1892_S1


title: L1924_S3


title: 1973_S11


title: 1951_S12


title: 1949_S3


title: 1931_S1


title: 1938_S14


title: 1952_S13


title: 1948_S2


title: 1936_S13


title: L1915_S7


title: L1909_S6


title: L1914_S2


title: L1895_S6


title: LTBItt_5

city: Hannover

first: Leonardo

middle: SILVA

last: de Araujo

address: Feodor-Lynen strasse 7

country: Germany

institute: Twincore

data_processing:
The FASTQ files were preprocessed (FastQC 0.11.2)
adaptors trimmed (Cutadapt 1.7.1)
aligned to the human genome hg38 (STAR 2.4.1d)
counted (featureCounts 1.4.6) on the Oasis 2.0 web platform.
Transcripts with <5 reads in at least one sample were excluded.
Normalized and evaluated for differentially expressed transcripts using DESeq2 (v. 1.16)  on the Oasis 2.0 web platform
Genome_build: Homo sapiens hg38

source_name: LTBItt, blood

extract_protocol:
Whole blood was collected in PAXgene RNA tubes (PreAnalytiX, SWZ) and was stored at -80°C for <2 years before RNA extraction. Total RNA (including small RNA) was isolated using the PAXgene Blood miRNA Kit (PreAnalytiX, SWZ), which is indicated for the isolation and purification of total RNA longer than 18 nucleotides. The manufacturer’s instructions were followed at both stages. Total RNA was quantified with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, EUA) and RNA integrity was assessed via agarose gel electrophoresis.
One microgram RNA was used for cDNA library preparation (TruSeq Small RNA Sample Preparation® Kit, Illumina, San Diego, CA) following the manufacturer’s protocols. RNAseq was performed on an Illumina HiSeq® 2500 Sequencing System (Illumina, San Diego, CA), generating 50 bp single reads and ≈16 million reads passing filter for each sample.

tag: group

value: ttLTBI

value: blood


title: LTBItt_6


title: 1929_S15


title: 1921_S9


title: LTBItt_3


title: LTBItt_2


title: LTBItt_1


title: 1914_S9


title: 1913_S8


title: 1903_S4


title: 1901_S3


title: 1971_S10


title: 1899_S7


title: 1895_S6


title: LTBI_20

source_name: LTBI, blood

value: LTBI


title: LTBI_19


title: LTBI_18


title: CAF2

city: La Jolla

first: Paul

middle: A

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

description: Gene expression of human pancreatic CAFs

hyb_protocol: Standard Affymetrix protocol using HG U133 plus 2.0 array

scan_protocol: Affymetrix GeneAtlas System

data_processing: Data were analyzed in R using the 'affy' package, with data normalized using the MAS 5.0 method

source_name: Human Pancreatic CAFs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

growth_protocol: Human pancreatic CAFs were cultured in DMEM with 30% FBS, 1% Penn-Strep at 5% CO2 at 37C

extract_protocol: RNA was isolated using the Qiagen Rneasy mini kit, with on-column Dnase-1 digestion

value: Pancreatic cancer-associated fibroblasts (CAFs)


title: LTBI_17


title: LTBItt_4


title: 1892_S1


title: LTBI_15


title: 1924_S10


title: LTBI_14


title: 1915_S7


title: LTBI_13


title: LTBI_16


title: LTBI_10


title: LTBI_11


title: 1894_S2


title: LTBI_8


title: LTBI_12


title: LTBI_6


title: LTBI_5


title: LTBI_7


title: LTBI_3


title: LTBI_4


title: LTBI_2


title: Mouse ESC Day 0

city: Boston

first: Daniel

middle: E

last: Wagner

state: MA

address: 200 Longwood Ave, Harvard Medical School, Systems Biology, Warren Alpert 536

department: Systems Biology

institute: Harvard Medical School

description:
LibraryName(s):
DEW209
DEW210

processed data file:
mmESC_X.csv.gz
mmESC_CellData.csv.gz
mmESC_GeneData.csv.gz

data_processing:
inDrops FASTQ files were demultiplexed and processed using a custom python pipeline as previously described (see Zilionis et al., Nature Protocols 2017 and https://github.com/indrops/).
Sequencing reads were first sorted according to sample of origin.  Each library is associated with 4 reads (R1:biological, R2: cell barcode part 1 , R3: library index ,R4: cell barcode part2, UMI)
Each cDNA read was trimmed using Trimomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16).
Cell-specific barcodes for each cDNA read wereÂ then matched against a set of pre-determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded.
cDNAÂ reads were then aligned to a reference transcriptome using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 200 -m 200 -best -strata -a).  Reference transcriptomes were built from mouse GRCm38 (Accession: GCF_000001635.20) or human GRCh37 (Accesion:Â GCF_000001405.13) genome assemblies. Mapped reads were then processed into counts of UMI-filtered transcripts per gene.
UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads.  This determination was made by inspecting a weighted histogram of UMI counts for each cell barcode, and thresholding only the top ~95% of the largest (and often the only) mode of the distribution.
UMI counts matrices originating from the same biological sample were combined into a single table.
Cells were filtered to remove cells that were highly similar to "simulated doublets", i.e. linear combinations of random pairs of observed cells (Wolock et al, BioRxiv 2018).
Genome_build: GRCm38
Genome_build: GRCh37
Supplementary_files_format_and_content:
X.csv: Raw UMI-filtered counts.  Matrix columns are transcripts, rows are single cells.
CellData.csv: Identifiers for single cells corresponding to the rows of X.csv.  Unique cell identifiers are in the following format: LibraryName_CellBarcodePart1_CellBarcodePart2.  Numbers of UMIS and genes detected, clustering assignments, and collection timepoint (if applicable) are included for each cell.
GeneData.csv: Gene names corresponding to the columns of X.csv. "Highly variable gene" flags are included.

source_name: E14 ESC

extract_protocol:
For generating cell suspensions from mouse embryo tailbuds, E9.5 embryos (25-28 somite stage) from CD-1 IGS mice (Charles River) were collected and the posterior part of the embryo, including the last 3 pairs of somites, was carefully dissected from two littermate embryos and subsequently processed as separate samples. Tissues were collected in PBS and dissociated in TrypLE Express for 10 min at 37ºC. Cells were rinsed in PBS/EDTA, transferred to 0.5% BSA in PBS, mechanically separated by trituration and run through a 30 µm cell strainer. Cells were spun down at 200 g for 4 min at 4ºC and resuspended in 100 µl 0.5% BSA in PBS.
For generating cell suspensions from human IPSC differentiated cultures, 3x10^4 MSGN1-Venus cells were seeded on Matrigel-coated 24-well plates 48 hours prior to differentiation. Cells were differentiated as described. All samples (days 1-4 and hiPS control samples) were dissociated, collected and captured on an inDrops setup on the same day, two biological replicates per sample. For dissociation, cells were briefly rinsed in PBS, and incubated in TrypLE Express (Gibco) for 5 min at 37ºC. Dissociated cells were run through a 30 µm cell strainer, spun down at 200g for 4 min at 4ºC and resuspended in 100 µl 0.5% BSA in PBS.
For generating cell suspensions from mouse ESC differentiated cultures, 1x10^4 pMsgn1-Venus cells were seeded on fibronectin-coated 6-well plates and differentiated as described. Samples for days 0 and days 2-5 were dissociated in TryplE Express (Gibco) for 3-10 minutes, washed several times in PBS, passed through a 40 µm cell strainer and resuspended in 0.1% BSA in PBS with Opti-Prep at a final density of 200,000 cells/ml. All samples were dissociated, collected and captured on the same day in biological duplicates.
Single-cell RNA-Seq libraries were prepared using a protocol customized for the inDrops platform (see Zilionis et al., Nature Protocols 2017)
Single-cell RNA-Seq (inDrops V3)

value: mouse embryonic stem cells (ESC)

value: wild type

tag: developmental stage

value: Day 0


title: ExC_11

source_name: ExC, blood

value: ExC


title: ExC_13


title: Mouse ESC Day 4

description:
LibraryName(s):
DEW219
DEW220
DEW227
DEW228

processed data file:
mmESC_X.csv.gz
mmESC_CellData.csv.gz
mmESC_GeneData.csv.gz

tag: genotype/variation


title: Mouse ESC Day 2

description:
LibraryName(s):
DEW213
DEW214

processed data file:
mmESC_X.csv.gz
mmESC_CellData.csv.gz
mmESC_GeneData.csv.gz

value: Day 2


title: ExC_12


title: CAF3


title: ExC_10


title: Mouse ESC Day 5

description:
LibraryName(s):
DEW221
DEW222
DEW230
DEW231

processed data file:
mmESC_X.csv.gz
mmESC_CellData.csv.gz
mmESC_GeneData.csv.gz

value: Day 5


title: ExC_14


title: Mouse ESC Day 3

description:
LibraryName(s):
DEW216
DEW217
DEW224
DEW225

processed data file:
mmESC_X.csv.gz
mmESC_CellData.csv.gz
mmESC_GeneData.csv.gz

value: Day 3


title: LTBI_21


title: ExC_8


title: Mouse E9.5 Posterior

description:
Single-cell RNA-Seq (inDrops)

LibraryName(s):
OP010
OP011

Processed data files:
mmE95_X.csv.gz
mmE95_CellData.csv.gz
mmE95_GeneData.csv.gz

source_name: Mouse Embryo Dissociated Cells

extract_protocol:
For generating cell suspensions from mouse embryo tailbuds, E9.5 embryos (25-28 somite stage) from CD-1 IGS mice (Charles River) were collected and the posterior part of the embryo, including the last 3 pairs of somites, was carefully dissected from two littermate embryos and subsequently processed as separate samples. Tissues were collected in PBS and dissociated in TrypLE Express for 10 min at 37ºC. Cells were rinsed in PBS/EDTA, transferred to 0.5% BSA in PBS, mechanically separated by trituration and run through a 30 µm cell strainer. Cells were spun down at 200 g for 4 min at 4ºC and resuspended in 100 µl 0.5% BSA in PBS.
For generating cell suspensions from human IPSC differentiated cultures, 3x10^4 MSGN1-Venus cells were seeded on Matrigel-coated 24-well plates 48 hours prior to differentiation. Cells were differentiated as described. All samples (days 1-4 and hiPS control samples) were dissociated, collected and captured on an inDrops setup on the same day, two biological replicates per sample. For dissociation, cells were briefly rinsed in PBS, and incubated in TrypLE Express (Gibco) for 5 min at 37ºC. Dissociated cells were run through a 30 µm cell strainer, spun down at 200g for 4 min at 4ºC and resuspended in 100 µl 0.5% BSA in PBS.
For generating cell suspensions from mouse ESC differentiated cultures, 1x10^4 pMsgn1-Venus cells were seeded on fibronectin-coated 6-well plates and differentiated as described. Samples for days 0 and days 2-5 were dissociated in TryplE Express (Gibco) for 3-10 minutes, washed several times in PBS, passed through a 40 µm cell strainer and resuspended in 0.1% BSA in PBS with Opti-Prep at a final density of 200,000 cells/ml. All samples were dissociated, collected and captured on the same day in biological duplicates.
Single-cell RNA-Seq libraries were prepared using a protocol customized for the inDrops platform (see Zilionis et al., Nature Protocols 2017)

tag: strain

value: embryonic cells


title: LTBI_9


title: LTBI_1


title: SRDX9b

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

description: GFP:IDD4:SRDX is driven by the UBIQUITIN10 (AT4G05320) promoter

data_processing:
Sequenced files were trimmed to remove adapter sequences and low quality base pairs using Trimmomatic V0.36
Trimmed sequences were aligned to the TAIR10 genome using TOPHAT V2.1.1
Reads per gene was calculated using SubReads package, and FPKM was calculated using cufflinks package.
Correlation between replicates was checked using multiBamSummary.
Differential expression was calculated using cuffdiff V2.2.1
Genome_build: TAIR10
Supplementary_files_format_and_content: fpkm.xlsx

growth_protocol: 14 day-old seedlings were grown under long-day conditions on sugar-free MS (Murashige and Skoog) plates at 23oC

extract_protocol:
The whole 14 day-old seedlings were used for total RNA extraction.
mRNA library generation followed by paired end sequencing (HiSeq 2500)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

value: 14 day-old seedling


title: ExC_7


title: SRDX9a


title: ExC_9


title: ExC_5


title: ExC_4


title: Wildtype b

value: wildtype


title: ExC_6


title: ExC_3


title: TB_8

source_name: TB, blood

value: TB


title: TB_6


title: TB_7


title: Human IPSC Day 4

description:
Single-cell RNA-Seq (inDrops)

LibraryName(s):
OP008
OP009

Processed data files:
hsIPSC_X.csv.gz
hsIPSC_CellData.csv.gz
hsIPSC_GeneData.csv.gz

source_name: NCRM1 IPSC

tag: cell type

value: iPSC in vitro cultures

value: Day 4


title: Human IPSC Day 1

description:
Single-cell RNA-Seq (inDrops)

LibraryName(s):
OP002
OP003

Processed data files:
hsIPSC_X.csv.gz
hsIPSC_CellData.csv.gz
hsIPSC_GeneData.csv.gz

value: Day 1


title: Human IPSC Day 2

description:
Single-cell RNA-Seq (inDrops)

LibraryName(s):
OP004
OP005

Processed data files:
hsIPSC_X.csv.gz
hsIPSC_CellData.csv.gz
hsIPSC_GeneData.csv.gz


title: SRDX2a


title: SRDX2b


title: TB_5

value: blood


title: 1916_S8

value: M

value: wt; +/t

value: Brain


title: TB_4


title: Patient_23_cancer

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

data_processing:
To control RNA-seq data quality, the RNA-seq reads with Phred base quality ≥ 20 were filtered using Sickle (version 1.33).
The remaining reads were mapped to human reference genome (CRCh37/hg19) using STAR (version 2.5.2b) with parameters "--alignIntronmin 61 --alignIntronMax 265006 --outFilterMultiMapNmax 20 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90".
Read counts were estimated with BAM files using featureCounts (version 1.5.1) with parameters "--minOverlap 60 -s 2 -p -B -C".
Genome_build: hg19
Supplementary_files_format_and_content: Estimated read counts

source_name: ESCC tumor tissue

extract_protocol:
Total RNA was extracted from ESCC tissues using TRIzol reagent (Invitrogen) for construction of RNA-seq libraries.
The sequencing library was prepared from 1 ug of total RNA using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (RS-122-2203).

value: ESCC

value: cancer


title: TB_3


title: Wildtype a


title: Patient_22_cancer


title: ExC_2

value: ExC


title: Human IPSC Day 3

description:
Single-cell RNA-Seq (inDrops)

LibraryName(s):
OP006
OP007

Processed data files:
hsIPSC_X.csv.gz
hsIPSC_CellData.csv.gz
hsIPSC_GeneData.csv.gz

value: wild type


title: Human IPSC Day 0

description:
Single-cell RNA-Seq (inDrops)

LibraryName(s):
OP001

Processed data files:
hsIPSC_X.csv.gz
hsIPSC_CellData.csv.gz
hsIPSC_GeneData.csv.gz

value: Day 0


title: TB_1


title: ExC_1


title: TB_2


title: HUVEC polyA RNA-Seq

city: Baltimore

first: Akhilesh

last: Pandey

state: MARYLAND

address: 733 N Broadway

institute: Johns Hopkins School of Medicine

description: Transcriptome profiling of primay human umbelical vein endothelial cells

data_processing:
CASAVA for base calling
Adaptor trimming and quality trimming using 'Fqtrim v0.9.5'
Alignment using HISAT2 v2.0.1
Assembly and quantification using StringTie v1.3.3, HTSeq 0.6.1p1 and RNA-SeQC v1.1.8
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: GTF
Supplementary_files_format_and_content: HTSeq count

source_name: Human umbelical vein endothelial cells

growth_protocol: Primary human umbilical vein endothelial cells (HUVEC) were obtained from Lonza (Catalog No. CC-2517) and were cultured as per the manufacturer’s specifications. Briefly, ~1.2 million cells were seeded in a 10-cm cell culture dish in endothelial basal medium (EGM BulletKit, Catalog No. CC-3124, Lonza) supplemented with growth factors including BBE (Bovine Brain Extract, w/ heparin), hEGF, hydrocortisone, ascorbic acid, GA-1000 (gentamicin, amphotericin B) and 2% FBS. The cells were grown in 5% CO2 at 37°C for six passages and were harvested at 70-80% confluency for protein and RNA extraction.

extract_protocol:
Total RNA was isolated from HUVEC cells using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. Total RNA isolated was quantified and assessed for quality using Agilent BioAnalyzer.
High quality DNase treated-total RNA from HUVECs was used for library preparation using TruSeq stranded mRNA library preparation kit from Illumina and sequenced on HiSeq2500 according to the manufacturer's guidelines. Briefly, mRNA enrichment from total RNA was carried out by polyA tail capture using oligo-DT beads prior to heat-based fragmentation and elution of mRNA. The eluted fragments were converted to cDNA and their 3' ends were adenylated. Adapters consisting of index sequences were then ligated to the adenylated cDNA, prior to limited cycle PCR amplification of the adapter ligated cDNA fragments. Amplified libraries were size-selected, clustered and sequenced after analyzing the quality of the library using BioAnalyzer. Quality checked library was sequenced using Illumina HiSeq 2500 in the high output mode to obtain 100bp paired-end reads.

value: Endothelial cells

value: Human umbelical vein endothelial cells


title: Patient_23_normal

source_name: ESCC adjacent normal tissue

value: normal


title: Patient_20_cancer


title: Patient_21_normal


title: fit +Fe Root Biological Rep2

city: Hanover

first: Mary Lou

last: Guerinot

state: NH

address: 78 College St

department: Biological Sciences

institute: Dartmouth College

description: Gene expression data from roots

hyb_protocol: Labelled cRNA were hybridized on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array following standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to the standard Affymetrix protocol.

data_processing: Dara were normalized from .cel files using the RMA protocol.

source_name: Arabidopsis root

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol.

growth_protocol: Plants were grown on Gamborg's B5 medium for 14 days and transferred to +Fe or -Fe conditions for 3 days.

extract_protocol: Total RNA was extracted using a Rnease Mini kit (Qiagen) following manufacturer's instruction.

treatment_protocol: Basal medium was prepared with 2 mM Ca(NO3)2, 0.75 mM K2SO4, 0.65 mM MgSO4, 0.1 mM KH2PO4, 10 µM H3BO3, 0.1 µM MnSO4, 0.05 µM CuSO4, 0.05 µM ZnSO4, 0.005 µM (NH3)6Mo7O24, 1 mM MES, 0.7% (w/v) type M agar, and adjusted to pH 6.0. For +Fe conditions, 50 µM Fe(III)-EDTA was added to the agar medium. The iron chelator ferrozine [3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine sulfonate] (HACH Chemical) was added at 300 µM to the agar medium for -Fe conditions.

value: fit

value: +Fe

value: root


title: WT +Fe Root Biological Rep2

description: Gene expression data from roots

value: WT


title: Patient_20_normal


title: fit -Fe Root Biological Rep2

description: Gene expression data from roots

value: -Fe


title: fit +Fe Root Biological Rep1

description: Gene expression data from roots


title: Patient_22_normal


title: Patient_19_cancer


title: WT -Fe Root Biological Rep2

description: Gene expression data from roots


title: WT +Fe Root Biological Rep1

description: Gene expression data from roots


title: LC_rep10

city: Shang hai

first: Yi-yu

last: Lu

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark, Pudong New Area

institute: Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Images were processed using RMA normalization with Nimblegen DEVA software.

source_name: PBMC

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using a “two-step’’ protocol as described previously[33]. The total RNA of leukocytes from the whole blood was extracted using TRIzol® Reagent (Invitrogen, Carlsbad, CA, US) and saved at -80℃. A quality control was carried out with NanoDrop ND-1000.

tag: diagnosis

value: liver cirrhosis

value: PBMC


title: fit -Fe Root Biological Rep1

description: Gene expression data from roots


title: LC_rep9


title: HCC_rep10

value: hepatocellular carcinoma


title: LC_rep8


title: LC_rep7


title: HCC_rep9


title: LC_rep6


title: WT -Fe Root Biological Rep1

description: Gene expression data from roots


title: LC_rep5


title: Patient_21_cancer


title: Patient_19_normal


title: Patient_18_cancer


title: CHB_rep10

value: chronic hepatitis B


title: HCC_rep8


title: HCC_rep7


title: CHB_rep9


title: CHB_rep8


title: CHB_rep7


title: HCC_rep6


title: CHB_rep6


title: Patient_18_normal

value: ESCC


title: Patient_17_normal


title: Patient_16_cancer

value: cancer


title: Patient_17_cancer


title: Patient_15_cancer


title: Patient_15_normal


title: Patient_16_normal


title: Patient_14_cancer


title: Patient_14_normal


title: HCC_rep4


title: LC_rep4


title: CHB_rep5


title: Patient_13_cancer

data_processing:
To control RNA-seq data quality, the RNA-seq reads with Phred base quality ≥ 20 were filtered using Sickle (version 1.33).
The remaining reads were mapped to human reference genome (CRCh37/hg19) using STAR (version 2.5.2b) with parameters "--alignIntronmin 61 --alignIntronMax 265006 --outFilterMultiMapNmax 20 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90".
Read counts were estimated with BAM files using featureCounts (version 1.5.1) with parameters "--minOverlap 60 -s 2 -p -B -C".
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each samples.


title: HBVC_rep1

value: hepatitis B virus carrier


title: HCC_rep5


title: CD36KO-oxLDL_rep3

city: Milwaukee

first: Yiliang

last: Chen

state: WI

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
GSPMC NGS sequencer was used for base-calling
FastQC application provides quality control checks on raw sequence data. Then the software MAPRSeq3 was used to map the reads to reference genome and generate fetured counts
The software MAPRSeq3 also provide normalized values (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include RPKM values for each sample

source_name: macrophage

growth_protocol: All cells were maintained in RPMI1640 plus 10% FBS until treatment

extract_protocol:
Total RNA were isolated using RNeasy Mini Kit (Qiagen) according to the user manual
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 20μg/ml oxLDL for 8h before cell lysis for RNA isolation

value: peritoneal macrophage

value: CD36 KO


title: LC_rep3


title: CHB_rep2


title: HBVC_rep3


title: CHB_rep4


title: HCC_rep3


title: HBVC_rep2


title: HC_rep2

value: healthy control


title: LC_rep2


title: HC_rep1


title: HCC_rep2


title: HC_rep3


title: CHB_rep1


title: LC_rep1


title: CD36KO-control_rep3


title: HCC_rep1


title: Patient_12_normal


title: CD36KO-oxLDL_rep1


title: Patient_11_cancer


title: CD36KO-control_rep2


title: CHB_rep3


title: mrna_37_WT_w/o_CHX_1

city: Bethesda

first: Shardul

last: Kulkarni

state: MD

address: 49 Convent Drive, Rm 2C08

institute: NICHD, NIH

data_processing:
The ribosome profiling and mRNA sequencing data were processed as described in Ingolia, N.T. (2010). Genome-wide translational profiling by ribosome footprinting.  Methods Enzymol. 470, 119–142. Breifly, the sequnce linker and the first nucleotide of each read were removed using fastx_toolkit/0.0.13 (fastx_clipper and fastx_trimmer, respectively). Ribosome RNAs were removed using bowtie/2-2.2.5  alignment agains year ribosome RNA sequences.The non-rRNA reads were mapped to yeast geneome sacCer3 (http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz)using TopHat/2.0.13.
Wiggle files were produced from the alignment files using RiboSeq (https://github.com/ingolia-lab/RiboSeq). each for genes on the Watson or Crick strand. A combined alignment file (Bam file) was generated using two alignment files (one for each of the two biological replicates). The combined files were generated for both RPF samples (ribo-seq) and total RNA samples (mrna) for 20 °C, 30 °C and 37 °C. Wiggle files were generated from this combined alignment file. Files were generated for each gene on the Watson or Crick strand. The tracks were visualized using Integrative Genomics Viewer (IGV 2.4.14). The tracks were normalized according to total number of mapped reads in the combined file by adjusting the scale.

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 37°C,without treatment with cycloheximide before harvesting.

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 500 µg/ml cycloheximide. Total mRNA isolated from whole cell extract using miRNeasy minikt (Qiagen). Total RNA fragmentation, Size selection,  linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223. Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to to remove ribosome contamination after linker ligation step.
RNA-Seq

tag: temperature


title: CD36KO-control_rep1

tag: genotype


title: Patient_11_normal


title: WT-oxLDL_rep2

value: wild type


title: WT-oxLDL_rep3


title: mrna_30_WT_w/o_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 30°C,without treatment with cycloheximide before harvesting.


title: Patient_10_cancer


title: Patient_10_normal

value: normal


title: mrna_20_WT_w/o_CHX_2

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 20°C,without treatment with cycloheximide before harvesting.


title: WT-control_rep2


title: WT-oxLDL_rep1


title: Patient_08_cancer


title: mrna_20_WT_w/o_CHX_1


title: mrna_37_WT_w/o_CHX_2


title: Patient_09_cancer


title: WT-control_rep3


title: WT-control_rep1


title: Patient_09_normal