title: DGM-11269_M6_lg (BMP4 study)

value: COPD smoker

value: large airway epithelial cells


title: DGM-11163_M3_lg (BMP4 study)

status: Public on May 28 2020

type: SRA

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include UniqueID with gene ID and location, GeneID, and the FPKM values for all samples

molecule: total RNA

organism: Homo sapiens

source_name: large airway epithelium cells

growth_protocol: Pure populations of nonsmoker, smoker and COPD smoker large airway samples and nonsmoker, smoker and COPD smoker derived large airway basal cells (BC) were obtained and characterized using detailed protocols as previously described (PMID:1572528). Primary BC were maintained in Bronchial Epithelial Growth Media (BEGM, Lonza, Walkersville, MD) and passaged by seeding at a cell density of 3000 cells/cm2 in BEGM with fresh media changed every 2 days (PMID:24298994). RNA sequencing of primary (Passage 0) BC was performed on cells once they had reached 70-80% confluence as well as large airway samples.

extract_protocol:
Total RNA from nonsmoker, smoker and COPD smoker epithelium and harvested basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500. HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

tag: smoking status

tag: cell type

tag: time of serial bronchoscopy (month)


title: GM89G_CTRL

type: RNA

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

hyb_protocol: For transcriptional profiling using the Affymetrix GeneChip Human Transcriptome 2.0 Arrays, 1 ng of total RNA was processed using the WT Pico Kit. Fragmentation, hybridization, and scanning were all performed according to Affymetrix manufacturer’s instructions.

scan_protocol: According to Affymetrix manufacturer’s instructions

data_processing: libaffy-2.1.5/bin/iron --norm-quantile --median-polish using GPL17586 annotation HTA-2_0.na36.hg19

label: biotin

source_name: Tracheal aspirate cells

growth_protocol: Tracheal aspirate cells were collected from intubated preterm infants as detailed below. After instillation of 0.5 ml of normal saline into the endotracheal tube, a suction catheter was introduced into the endotracheal tube and tracheal secretions were aspirated into a sterile mucus trap. The suction catheter was subsequently rinsed with an additional 1.5 ml of sterile saline to clear any remaining aspirate from the catheter into the mucus trap. Cells were collected by centrifugation and resuspended in DMEM with 10% fetal bovine serum, penicillin, and streptomycin. Equal aliquots of resuspended cells were divided between two separate tissue culture treated plates and incubated at 37 ˚C in a humidified environment of 95% air and 5% CO2 to allow macrophage attachment. After 30 min, nonadherent cells were removed by gentle washing and fresh cell culture media was applied.

treatment_protocol: Lipopolysaccharide from E. coli (strain 055:B5, gel purified, Sigma-Aldrich L2637; 250 ng/ml) was added to one of the plates and both were incubated for 4 h at 37 ˚C.

tag: title

tag: nicu

value: UCSD

tag: collection place

value: GM

tag: treatment

value: CTRL

tag: bpd

value: Yes

tag: severity

value: Severe

tag: gender

value: Female

tag: delivery type

value: Cesarean


title: MV-4-11 24hr 100nM INCB059872 B

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

data_processing:
Read alignment performed with TopHat
Differential gene expression determined by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: plain text documents containing averaged RPKM values and calculated differential expression between treatment samples and corresponding control samples

molecule: polyA RNA

extract_protocol:
RNA was harvested using TRIzol reagent.
Libraries were prepared from polyA-enriched RNA by standard Illumina protocols.

tag: cell line

value: acute myeloid leukemia (AML) cell line

value: 100nM INCB059872 for 24hrs


title: DGM-11077_M0_lg (BMP4 study)


title: MV-4-11 3hr 100nM INCB059872 A

value: 100nM INCB059872 for 3hrs


title: GM89H_LPS

label_protocol: According to Affymetrix manufacturer’s instructions

value: LPS


title: GM32H_LPS

extract_protocol: According to Affymetrix manufacturer’s instructions

value: Male


title: MV-4-11 control B

source_name: MV-4-11 control

value: none (control)


title: DGM-10800_M0_lg (BMP4 study)


title: Participant3 AMJaTP2

city: Belgrade

first: Aleksandra

last: Stankovic

address: Mike Petrovica Alasa 12

department: Department of Health and Environment

country: Serbia

institute: VINCA Institute of Nuclear Sciences, University of Belgrade

hyb_protocol: Illumina® Direct Hybridization Assay protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and normalised using quantile normalisation with GenomeStudio software 2011.1 (Illumina)

label_protocol: TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre)

extract_protocol: Lymphocyte Separation Medium (GE Healthcare) protocol for isolation of the PBMC from whole blood samples, followed by TRI Reagent® Solution (Ambion) protocol for extraction of the total RNA from PBMC

tag: subject id

tag: age (years)

value: male

tag: polyphenol dose

value: Aronia melanocarpa juice (AMJ)

tag: intervention point

value: After treatment period 2 (aTP2)


title: MV-4-11 control A


title: GM84A_LPS


title: GMR09A_CTRL

value: RADY

value: GMR

value: Mild

value: Vaginal


title: Participant19 AMJbTP2

value: Before treatment period 2 (bTP2)


title: DGM-10549_M6_lg (BMP4 study)

value: COPD smoker

value: large airway epithelial cells


title: PTBP1-SIM-2

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

data_processing:
RNA-Seq data from eCLIP IP and input samples was analyzed using the ENCODE eCLIP-seq Processing Pipeline (Van Nostrand et al., 2018).
 Raw fastq files were trimmed with Cutadapt as described (Martin, 2011), followed by removal of sequences derived from repetitive elements with STAR aligner, using human RepBase sequences (Bao et al., 2015; Dobin et al., 2013).
Remaining reads were mapped to the hg19 human genome release with STAR aligner.
PTBP1 eCLIP peaks were called with Clipper software and normalized vs the size-matched input control as described (Van Nostrand et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: BAM files of eCLIP peaks called by Clipper

source_name: HEK-293 Flp-In TREx cells

growth_protocol: Flp-In T-REx-293 cells (ThermoFisher Scientific) were maintained at 37°C in ambient oxygen and 5% CO2 in DMEM (Gibco #11965‐092) supplemented with 10% fetal bovine serum (Gibco) and a 1% penicillin, streptomycin, and L‐glutamine mixture (Gibco).

extract_protocol:
Samples were prepared according to the eCLIP protocol (Van Nostrand et al. 2016 Nat Methods.) For each sample, 2x10^7 cells were UV crosslinked at 400mJ/cm2 constant energy. Cells were lysed on ice for 15 min in 1 mL lysis buffer containing 50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, Halt protease inhibitor cocktail (ThermoFisher Scientific). Cells were passed through 27-gauge needles several times before sonication (Biorupter, Diagenode) for 3 min at low setting with 30 second on/30 second off duty cycle at 4°C.
eCLIP and size-matched input libraries were constructed according to the eCLIP protocol (Van Nostrand et al. 2016 Nat Methods.)

treatment_protocol: Polyclonal cells were treated with doxycyline hyclate (1 μg/mL final concentration, ThermoFisher Scientific) for 48-72 hours for induction of transgene expression.

tag: strain

value: FLAG-PTBP1 stably integrated in FRT site


title: DGM-10406_M0_lg (BMP4 study)

tag: smoking status


title: GMR02A_LPS

value: Yes

value: Severe

value: Cesarean


title: GMR10C_LPS

value: LPS

value: Female


title: PTBP1-SIM-1


title: PTBP1-eCLIP-2


title: DGM-10262_M3_lg (BMP4 study)

tag: cell type


title: PTBP1-eCLIP-1


title: Participant4 PLBbTP1

value: placebo beverage (PLB)

value: Before treatment period 1 (bTP1)


title: Participant3 AMJbTP2

value: male

value: Aronia melanocarpa juice (AMJ)


title: DGM-01753_M3_lg (BMP4 study)

tag: time of serial bronchoscopy (month)


title: GM42C_LPS

tag: title

value: UCSD

value: GM

value: Male


title: GMR09C_CTRL

tag: nicu

value: RADY

value: GMR

value: CTRL

value: Mild

value: Vaginal


title: DGM-12446_LA-BC (BMP4 study)

source_name: large airway basal cells

value: COPD smoker

value: basal cells cultured from airway epithelial cells


title: UPF1_isoform_2_RIP-Seq_3

data_processing:
Reads were trimmed using Cutadapt with the following parameters: --match-read-wildcards --times 2 -e 0 -O 5 -q 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG   -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG  -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Trimmed reads were quantified using Kallisto software with parameters --bias -b 1000 -t 16 --single --rf-stranded -l 200 -s 20 and differential expression analysis was performed with Sleuth software.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file contains TPM values for each replicate, average TPM values for each condition, log2 fold-change values for RNA abundance in Input samples, average and individual RIP-Seq efficiency calculations (IP/Input TPM), and statistical parameters from Sleuth analysis of Input RNA-Seq samples.

source_name: HEK-293 Trex_UPF1_isoform_2_RIP-seq

growth_protocol: HEK-293TO cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Mini RNA isolation kit
One μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: HEK-293TO cells were treated with 200 ng/mL doxycycline hyclate to induce transgene expression.

value: HEK-293 Trex cells

tag: genotype/variation

value: Expressing CLIP-UPF1_isoform_2

tag: molecule subtype

value: Affinity-purified RNA


title: GM30D_CTRL

tag: collection place

tag: treatment

tag: bpd

value: Yes

value: Cesarean


title: Participant2 AMJaTP2

tag: gender

value: female

value: After treatment period 2 (aTP2)


title: DGM-11463_M0_LA-BC (BMP4 study)


title: Participant6 AMJaTP2

value: male

value: Aronia melanocarpa juice (AMJ)


title: UPF1_isoform_2_RIP-Seq_2

tag: cell line


title: GM32W_CTRL

value: UCSD

value: GM

tag: severity

value: Severe

value: Male

tag: delivery type


title: Participant14 AMJaTP2

tag: subject id

tag: age (years)

tag: polyphenol dose


title: Participant1 AMJaTP2

tag: intervention point


title: V_TMD10-6M

city: Yokohama

first: Hideko

last: Sone

address: 601 Matanocho Totsuka

country: Japan

institute: Yokohama University of Pharmacy

description: Gene expression after 72hr in 1000nM Thalidomide-exporsed human cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent  028004 SurePrint G3 Human GE 8x60K Microarray Microarrays (G4851B) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Sphere, 72hr, 1000nM Thalidomide, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNA Purification kit (RNaeasy micro, Quiagen Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: embryonic stem-derived neuronalprogenitor cells


title: UPF1_isoform_2_RIP-Seq_1


title: Participant10 AMJaTP2


title: Control Day 25 Rep6

first: Koray Dogan

last: Kaya

address: 6 CENTER DR

department: NEI

institute: NIH

data_processing:
Raw reads passing chastity filter were trimmed for Illumina adapters with Trimmomatic (v0.36) (Bolger et al., 2014).
Trimmed reads were quantified at the transcript level using kallisto (v0.45.0). Then they were summarized to gene level using R package tximport (v1.8) using the option “countFromAbundance=lengthScaledTPM”.
The tximport summarized gene level count values were normalized with TMM and converted to count per million (CPM) using edgeR (v3.20.9)
Differential expression analysis was performed using limma (v3.34.9).
Genome_build: GRCh38.p7 ENSEMBL v82
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...
Supplementary_files_format_and_content: controlde.xlsx: xlsx file containing full de table of time-wise comparison of control samples
Supplementary_files_format_and_content: patientde.xlsx: xlsx file containing full de table of time-wise comparison of patient samples
Supplementary_files_format_and_content: clusterde.xlsx: xlsx file containing cluster membership of de genes with largest FC comparison
Supplementary_files_format_and_content: SummarizedGeneLevelCounts.txt: tab-delimited text file including Gene Level Counts Summarized by txtimport
Supplementary_files_format_and_content: NormalizedCpms.txt: tab-delimited text file including CPM values

source_name: Retinal Organoid differentiated from iPCS

extract_protocol:
Trizol
Illumina Stranded mRNA-Seq

tag: individual

tag: d.e. group name

tag: time point

value: Day 25


title: M17_CTRL

tag: title

tag: nicu

value: CTRL

value: Female


title: DGM-11270_M0_LA-BC (BMP4 study)

tag: smoking status

value: COPD smoker

value: basal cells cultured from airway epithelial cells

tag: time of serial bronchoscopy (month)


title: V_Cont DMSO

description: Gene expression after 72hr in 0.01% DMSO-exporsed human cells

source_name: Sphere, 72hr, 0.01% DMSO, replicate 1


title: UPF1_isoform_1_RIP-Seq_3

source_name: HEK-293 Trex_UPF1_isoform_1_RIP-seq

value: HEK-293 Trex cells

tag: genotype/variation

value: Expressing CLIP-UPF1_isoform_1

tag: molecule subtype

value: Affinity-purified RNA


title: DGM-11261_M6_LA-BC (BMP4 study)


title: GMR08B_LPS

value: RADY

tag: collection place

value: GMR

tag: treatment

value: LPS

tag: bpd

value: Yes

tag: gender

value: Cesarean


title: GMR02G_LPS

tag: severity

tag: delivery type


title: M17_LPS

value: UCSD


title: DGM-11001_M6_LA-BC (BMP4 study)


title: UPF1_isoform_1_RIP-Seq_1

tag: cell line


title: GM70F_LPS

value: GM

value: Moderate


title: DGM-11007_M6_LA-BC (BMP4 study)

tag: cell type


title: DGM-10984_M6_LA-BC (BMP4 study)


title: N_BED-8M

description: Gene expression after 72hr in 10 nM 4OH-BDE47-exporsed human cells

source_name: Sphere, 72hr, 10 nM BDE47, replicate 1

value: embryonic stem-derived neuronalprogenitor cells

value: male


title: GFP_Total_3

source_name: HEK-293 Trex_GFP_total

value: Expressing GFP


title: UPF1_isoform_1_RIP-Seq_2


title: GFP_Total_2


title: DGM-10794_M3_LA-BC (BMP4 study)


title: GM83C_CTRL

value: CTRL

value: Severe

value: Male

value: Vaginal


title: WTA replicate 3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data were aligned and summarized using bowtie version 1.0.1 (Langmead et al., 2009), RSEM version 1.2.15 (Li and Dewey, 2011), samtools/0.1.19 (Li et al., 2009)
Genome_build: ce10 with 2016 UCSC known genes annotation
Supplementary_files_format_and_content: text file of count data
Supplementary_files_format_and_content: text file of log 2 FPKM data that includes an offset of 1 prior to log transformation

organism: Caenorhabditis elegans

source_name: N2 Adult C. elegans

growth_protocol: Strains were maintained at 20°C on Nematode Growth Medium plates containing 3 g/L NaCl, 2.5 g/L peptone and 17 g/L agar supplemented with 1 mM CaCl2, 1 mM MgSO4, 1 mM KPO4 and 5 mg/L cholesterol with E. coli OP50 as a source of food (Brenner, 1974). hira-1(-) indicates hira-1(gk835598).

extract_protocol:
RNA was isolated from N2 and hira-1(gk835598) using the Tissue Ruptor (Qiagen) and TRIzol Reagent (Invitrogen) followed by isopropanol precipitation. Then RNA was further purified using RNeasy Mini Kit (Qiagen).
mRNA was purified by polyA-tail enrichment, fragmented, and reverse transcribed into cDNA (Illumina TruSeq). cDNA samples were then end-repaired, adaptor-ligated using the SPRI-works Fragment Library System I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq sequencer.

tag: genotype

tag: Stage

value: Adult


title: HIL4 replicate 3

source_name: MT23643 L4 C. elegans


title: GFP_Total_1

value: HEK-293 Trex cells


title: HIA replicate 3

source_name: MT23643 Adult C. elegans


title: N_OH-PCB187-8M

description: Gene expression after 72hr in 10 nM OH-PCB187-exporsed human cells

source_name: Sphere, 72hr, 10 nM OH-PCB187, replicate 1


title: N_TMD10-6M


title: UPF1_isoform_2_Total_3

source_name: HEK-293 Trex_UPF1_isoform_2_total

value: Expressing CLIP-UPF1_isoform_2


title: DGM-10406_M12_LA-BC (BMP4 study)

value: COPD smoker

value: basal cells cultured from airway epithelial cells


title: N_BPA10-7M

description: Gene expression after 72hr in 100nM BisphenolA-exporsed human cells

source_name: Sphere, 72hr, 100nM BisphenolA, replicate 1


title: WTL4 replicate 3

source_name: N2 L4 C. elegans


title: N_Sumi Cont DMSO


title: DGM-10262_M6_LA-BC (BMP4 study)


title: DGM-02164_M3_LA-BC (BMP4 study)


title: urt1-1 xrn4-3 replicate2

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

data_processing:
The base calls were acquired from HiSeq 2500 after processing by Illumina RTA 1.18.61.0 and CASAVA pipeline v.1.8.2.
Sequencing quality was assessed with a PhiX reference spiked in the flow-cell that gave an average sequencing error rate of 0.16 % with 92 % of the reference nucleotides having a Q-score >=30 (Phred calculation).
‘TGGAATTCTCGGGTGCCAAG’ sequence corresponding to the 20 nt sequence of the 5' end of the 3’ adapter was searched and removed using in-house Fasteris pipeline.
Trimmed reads of 14 nt to 30nt in length were selected to be mapped to TAIR10 genome using bowtie (v1.0.0) (Langmead et al., 2009, https://doi.org/10.1186/gb-2009-10-3-r25) by permitting up to 1 mismatch. (http://www.arabidopsis.org).
Reads that could map to more than 50 loci were discarded and only the best alignment(s) of each small RNA sequence was kept.
BEDTools suite (v2.17.0, Quinlan and Hall, 2010, https://doi.org/10.1093/bioinformatics/btq033) was then used to annotate and count reads that map to mRNAs using intersectBed and multiBamCov tools, respectively, with default settings. mRNAs were annotated based on TAIR10 annotation (http://www.arabidopsis.org).
Normalized number of reads (Counts per Million) were calculated using the edgeR package (3.26.5).
Genome_build: TAIR10
Supplementary_files_format_and_content: One processed data file is given. It includes the processed data for the two biological replicate of each genotype.
Supplementary_files_format_and_content: Each line corresponds to one mRNA loci and indicates the gene AGI (AGI), the chromosome number (Chr), the gene start coordinate (Start), the gene end coordinate (End), the DNA stand (Strand) and the raw count and CPM for each genotype.
Supplementary_files_format_and_content: Only loci detected with at least 1 read per million for at least 2 samples are shown.

organism: Arabidopsis thaliana

source_name: 24 day-old plantlets

growth_protocol: The plant material corresponds to Arabidopsis plantlets grown for 24 days in vitro on Murashige & Skoog media with 0.8 % agar and 12 hr light (22 °C)/12 hr darkness cycles (18 °C).

extract_protocol:
Total RNA was extracted from seedlings with TRI Reagent® (Molecular Research Center) according to manufacturer’s instructions
Libraries were generated from 3 µg of DNase treated-RNA using the Illumina TruSeq® Small RNA protocol after size selection of 18-30 nt RNA fragments on a denaturing polyacrylamide gel.

value: urt1-1 xrn4-3

tag: biological replicate

value: replicate 2

tag: reference sequence


title: N_Nunc Cont DMSO


title: UPF1_isoform_2_Total_1


title: DGM-00061_M28_LA-BC (BMP4 study)


title: xrn4-3 replicate2


title: GM89G_LPS

source_name: Tracheal aspirate cells

tag: title

tag: nicu

value: UCSD

value: LPS

value: Yes

value: Female

value: Cesarean


title: UPF1_isoform_2_Total_2


title: HIA replicate 2


title: GM83A_LPS

value: GM


title: urt1-1 replicate2


title: DGM-12088_LA-BC (BMP4 study)

source_name: large airway basal cells

tag: smoking status

value: smoker


title: HIA replicate 1


title: UPF1_isoform_1_Total_3

source_name: HEK-293 Trex_UPF1_isoform_1_total

tag: genotype/variation

value: Expressing CLIP-UPF1_isoform_1


title: WTA replicate 2


title: DGM-12005_LA-BC (BMP4 study)


title: UPF1_isoform_1_Total_2


title: DGM-11529_LA-BC (BMP4 study)


title: HIL4 replicate 1


title: HIL4 replicate 2

source_name: MT23643L4 C. elegans


title: WTA replicate 1


title: urt1-1 xrn4-3 replicate1

value: replicate 1


title: DGM-11280_LA-BC (BMP4 study)


title: xrn4-3 replicate1


title: WTL4 replicate 2


title: UPF1_isoform_1_Total_1


title: HIL1 replicate 3

source_name: MT23643L1 C. elegans


title: DGM-10201_M12_LA-BC (BMP4 study)

tag: time of serial bronchoscopy (month)


title: WTL4 replicate 1


title: HIL1 replicate 2

source_name: MT23643 L1 C. elegans


title: DGM-12163_LA-BC (BMP4 study)


title: HSFB (Patient 3) with stretch and TA

city: Xi’an

first: Huayu

last: Zhu

state: Shaanxi

address: Changle Xilu 15

department: Department of Burns and Cutaneous Surgery, Xijing Hospital

country: China

institute: Fourth Military Medical University

description: HSFB (Patient 3) with stretch and TA

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

source_name: HSFB (Patient 3)

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cultured hypertrophic scars fibroblasts (from hypertrophic scar patients) were pelleted and grown in DMEM supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Hypertrophic scars fibroblasts treated with glucocorticoid were seeded in the chambers and subjected to mechanical stretch. Paired HSFBs in the control groups were treated with solvent and subjected to mechanical stretch.

tag: tissue

value: Hypertrophic scar


title: HSFB (Patient 1) with stretch and TA

description: HSFB (Patient 1) with stretch and TA

source_name: HSFB (Patient 1)


title: HIL1 replicate 1


title: HSFB (Patient 2) with stretch and TA

description: HSFB (Patient 2) with stretch and TA

source_name: HSFB (Patient 2)


title: HSFB (Patient 3) with stretch

description: HSFB (Patient 3) with stretch


title: DGM-12748_LA-BC (BMP4 study)

value: nonsmoker


title: urt1-1 replicate1


title: HSFB (Patient 1) with stretch

description: HSFB (Patient 1) with stretch


title: DGM-11156_LA-BC (BMP4 study)


title: Participant10 dAMJbTP3

tag: subject id

tag: age (years)

value: male

tag: polyphenol dose

value: Aronia melanocarpa juice-based beverage (dAMJ)

tag: intervention point

value: Before treatment period 3 (bTP3)


title: WTL1 replicate 2

source_name: N2 L1 C. elegans


title: DGM-02019_LA-BC (BMP4 study)

value: basal cells cultured from airway epithelial cells


title: DGM-10698_M12_LA-BC (BMP4 study)


title: WT replicate2

value: WT


title: DGM-12535_LA-BC (BMP4 study)


title: Fam122a KO repli2

city: Shanghai

first: Manhua

last: Liu

state: China

address: 280, Chong-Qing South Road

department: Pathophysiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina bcl2fastq software used for basecalling.
The raw reads were aligned to the mouse reference genome (GRCm38.p5) using RNA STAR (Version 2.7.1a) and counted using HISAT2 (Version 2.1.0).
Differential expression analysis was performed on the count data using DEGSeq (Version 1.38.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

source_name: LT-HSCs

extract_protocol:
RNA was isolated from FACS-sorted LT-HSCs mixed from 3 animals. The total RNA was extracted by Trizol precipitation method (molecular research center, USA), and two biological replicates were performed. RNA quantification and quality were determined using Agilent RNA 6000 Pico Kit.
Libraries were prepared with TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing using standard Illumina procedures.

tag: strain

tag: age

value: 8-12 weeks

value: LT-HSC

tag: hsc markers

value: LSK CD34- FLk2-

tag: genetype/variation

value: Fam122a KO


title: WTL1 replicate 3

tag: genotype

tag: Stage


title: WT replicate1

tag: biological replicate

tag: reference sequence


title: DGM-12489_LA-BC (BMP4 study)

tag: cell type


title: WT repli2


title: WT repli1


title: P1_CGP_rep3_RNA

city: Los Angeles

first: Neil

last: Segil

state: CA

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

data_processing:
Sequenced reads were mapped to Gencode Mm10v11 genome using STAR (v2.5.4b).
Transcript quantification was performed with RSEM.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.isoforms.results.tsv: Tab-delimited text files of transcript quantification were generated with RSEM.

source_name: Brain

growth_protocol: Brain was dissected from P1 mice and enzymatically dissociated with 0.25% trypsin. Cells were pelleted and resuspended in DMEM/F12 and then FACS purified to collect the Atoh1-GFP positive cells.

extract_protocol:
Cells were FACS purified and collected in RNA lysis buffer. Total RNA was extracted with Quick-RNA Microprep kit (Zymo Research).
Libraries were prepared using QIAseq FX Single Cell RNA Library Kit (Qiagen).

tag: developmental stage

value: post natal day 1

value: Brain


title: DGM-12251_LA-BC (BMP4 study)

tag: smoking status


title: DGM-12334_LA-BC (BMP4 study)


title: P1_CGP_rep2_RNA


title: PeOP30

city: Beijing

first: Zhaobin

last: Zhang

address: Yiheyuan Road 5#

institute: Peking Univ

data_processing:
Illumina Casava1.7 software used for basecalling.
The paired-end reads were quality filtered and trimmed using CLC genomics workbench 12.
Read alignment and gene qulification was perfomed using the  CLC genomics workbench 12 against GRCm38.p6.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for every samples

source_name: uteri

extract_protocol:
The uteri were isolated and frozen in liquid nitrogen,and total RNA was extracted  using TRIzol reagent.Illumina TruSeq RNA Sample Prep Kit (NEB.Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PhOP and PeOP were dissolved in peanut oil (vehicle) to prepare dosages of 3, 30, and 300 mg /kg bw /d, respectively. Mice treated with peanut oil only were used as the peanut oil vehicle control, while those treated with 0.4 mg /kg bw /d E2 were used as the positive control. The mice were treated for three days by oral gavage from PND 21.

value: uterus

value: post natal day 24

tag: agent

value: PeOP (30 mg/kg bw/d)


title: DGM-12203_LA-BC (BMP4 study)


title: PeOP3

tag: tissue

value: PeOP (3 mg/kg bw/d)


title: P1_CGP_rep1_RNA


title: 223 2018: RIP2 KO3 Input

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: RIP2 KO3 Input

data_processing:
Raw FastQ files were aligned against the mm10 rRNA genome using Bowtie1 0.12.9 with 2 mismatches in order to identify rRNA contaminated reads and remove them from the analysis.
Subsequent non-rRNA reads were aligned against the mm10 genome using Bowtie2 2.2.2, allowing for 1 mismatch and reporting best alignment site per read.
Duplicated reads (potential PCR over-amplification artifacts) were identified and removed with sambamba v.0.5.1 using default options.
Per sample counts were obtained with the countOverlaps function from the IRanges package.
DESeq2 was used to identify RBP sites with sample counts at 3'UTR level (using longest 3'UTR per gene), using Bowtie2 aligned reads after removing rRNA contamination,   filtering duplicated reads and removing multihit alignments with MAPQ=0. 3'UTRs were selected as Enriched/Depleted based on a |FC| of 1.5 and a BH adjusted pvalue of 0.10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files mm10 genomic information, and per sample longest 3'UTR raw counts using the countOverlaps function from the IRanges package for reads with MAPQ>0, as well DESeq2 log2 normalized counts and differential expression results for candidate RNA Binding Proteins (WT/KO IP/Input DESeq2 interaction analysis).

source_name: Murine mammary epithelial cells

growth_protocol: Freshly isolated cells were used.

extract_protocol:
Mammary glands were incubated with collagenase/hyaluronidase solution (STEMCELL Technologies), then red blood cells were lysed and cells were further dissociated with trypsin (Sigma), Dispase II (Sigma) and DNAse I (Sigma). Then, epithelial enriched fraction was obtained by EasySep (STEMCELL Technologies).
Poly A purification ( New England Biolabs, catalog # E7490) was only performance on Input samples in only one step of purification. Library generation was done with the kit NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, catalog # E7770), following manufacturer´s instructions and 10-13 cycles of amplification.

treatment_protocol: No specific treatment was used.

value: Murine mammary epithelial cells

tag: rip antibody


title: DGM-12044_LA-BC (BMP4 study)

value: nonsmoker


title: HSFB (Patient 2) with stretch

description: HSFB (Patient 2) with stretch

value: Hypertrophic scar


title: DGM-12027_LA-BC (BMP4 study)


title: PhOP30

value: PhOP (30 mg/kg bw/d)


title: WTL1 replicate 1


title: PhOP3

value: PhOP (3 mg/kg bw/d)


title: 312 2018: RIP3 WT4 IP

description: RIP3 WT4 IP


title: DGM-12023_LA-BC (BMP4 study)

value: basal cells cultured from airway epithelial cells


title: DGM-11963_LA-BC (BMP4 study)


title: DGM-11956_LA-BC (BMP4 study)


title: 313 2018: RIP3 KO4 IP

description: RIP3 KO4 IP


title: 311 2018: RIP3 KO4 Input

description: RIP3 KO4 Input


title: DGM-11213_LA-BC (BMP4 study)


title: ctrl

value: Control


title: D14_iHC_rep3_RNA

source_name: Fibroblast

growth_protocol: MEFs were infected with retroviral overexpression constructs for Six1, Atoh1, Pou4f3 and Gfi1. The cells were reprogrammed for 14 days and then FACS purified to collect the Atoh1-GFP positive cells.

value: embryonic day 14

value: Fibroblast


title: 225 2018: RIP2 KO3 IP

description: RIP2 KO3 IP


title: E2

value: E2 (0.4 mg kg/bw/d)


title: DGM-10500_M12_LA-BC (BMP4 study)

tag: time of serial bronchoscopy (month)


title: 310 2018: RIP3 WT4 Input

description: RIP3 WT4 Input


title: D14_iHC_rep2_RNA


title: 224 2018: RIP2 WT3 IP

description: RIP2 WT3 IP


title: 222 2018: RIP2 WT3 Input

description: RIP2 WT3 Input


title: DGM-10123_LA-BC (BMP4 study)


title: Mut-3

city: Chicago

first: Alexander

last: Guzzetta

state: IL

institute: University of Chicago

data_processing:
50bp reads from Illimuna HiSeq2500 were first evaluated for quality using fastqc. All samples passed initial quality control.
.fastq files were aligned to the mm9 Mus musculus genome using TopHat2 (v2.0.14) running default parameters
Features were assigned to aligned reads in .bam files using feturecounts from the R subread package ( v1.4.6; standard parameters with the following additions: allowMultiOverlap=T, countMultiMappingReads=T)
Raw gene counts were processed by EdgeR using standard parameters. Data were analyzed comparing mutant and to wild type samples. Because the study design was balanced and samples were litter-matched, no additional variables were considered.
Genome_build: mm9
Supplementary_files_format_and_content: .text file containing raw featurecount output

source_name: Mesp1Cre-sorted E7.5 mesoderm from Mesp1-Cre/+;R26-Gli3R-IRES-Venus/+ embryos

extract_protocol:
Embryos used for bulk transcriptome profiling were harvested at E7.5 in 1x ice cold PBS, pooled with their littermates, dissociated with TrypLE (Fisher) reagent for 5 minutes at 37C while shaking at 1,400 rpm in a Fisher Thermomixer, followed by inactivation by addition of 10% FBS in 1x PBS. Cells were spun down at 800 x g for 5 minutes, re-suspended in 10% FBS with a Near-IR dead dye (Life Technologies) and strained through a 40µm mesh prior to FACS. 1000 litter-matched control or mutant cells were directly sorted into lysis buffer for cDNA synthesis and subsequent RNA-seq library preparation.
SMARTer Ultra Low RNA Kit for Illumina sequencing (Clontech) for cDNA generation followed by Nextera XT DNA Library Preparation Kit (Illumina) for library generation.

tag: litter


title: D14_MEF_rep3_RNA

growth_protocol: MEFs were infected with a retroviral overexpression constructs for dsRed. The cells were cultured for 14 days to mimic the iHC culturing protocol and then FACS purified to collect the dsRed positive cells.


title: Wt-3

source_name: Mesp1Cre-sorted E7.5 mesoderm from Mesp1-Cre/+;R26-tdTomato/+ embryos


title: DGM-01624_LA-BC (BMP4 study)


title: Stat5_Adipoq_basal_4

city: Vienna

first: Tobias

last: Suske

state: Vienna

address: Veterinärplatz 1

department: Functional Cancer Genomics

country: Austria

institute: University of Veterinary Medicine

description: STAT5 in thermogenic_fat

data_processing:
Alignments to genome version GRCm38_mm10 and the corresponding Ensgene annotation were accomplished with STAR (STAR_2.5.0b) using default parameters
Expression level estimation was performed with featureCounts (version 1.5.0-p1) with the ‘-t exon’ option .
Differential expression analysis was performed with DESeq2 (1.16.1)
Genes with low expression were filtered out if the size factor normalized row sum was ≤45.
The functions ‘DESeq()’ and ‘results()’ were then applied with default parameters.
Genome_build: GRCm38_mm10
Supplementary_files_format_and_content: 1. mapped bam files sampled from BAT. 5 control and 5 Stat5Adipoq samples  2. Count tables; *.gene_id files consisting of two columns: ncbi_id and counts.  3. DeSeq2 results() full tableDifferential expression analysis table with ncbi_id, gene_symbol, entrez_id.  4. Subsets of the results table using a p value cutoff of 0.05: Up-, Down-, and differentially expressed genes.  5. excel file containing three sheets of the full GO analyses results using either up-, down- or all differentially expressed genes with a P value cutoff < 0.05, respectively.

source_name: Brown Adipose Tissue

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen, Venlo, Netherlands).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

tag: genotype/variation


title: Mut-2


title: DGM-01578_LA-BC (BMP4 study)

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include UniqueID with gene ID and location, GeneID, and the FPKM values for all samples

source_name: large airway basal cells

extract_protocol:
Total RNA from nonsmoker, smoker and COPD smoker epithelium and harvested basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500. HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.


title: Stat5_Adipoq_basal_5

description: STAT5 in thermogenic_fat

tag: strain


title: Stat5_Adipoq_basal_3

description: STAT5 in thermogenic_fat


title: D14_MEF_rep1_RNA


title: D14_MEF_rep2_RNA


title: Wt-2


title: Mut-1


title: DGM-11852_lg (BMP4 study)

source_name: large airway epithelium cells

value: large airway epithelial cells


title: DGM-10447_M0_LA-BC (BMP4 study)


title: DGM-11374_lg (BMP4 study)


title: Stat5_Adipoq_basal_1

description: STAT5 in thermogenic_fat


title: D14_iHC_rep1_RNA


title: Wt-1


title: DGM-10565_M6_lg (BMP4 study)


title: control_basal_5

description: STAT5 in thermogenic_fat

value: wild type


title: DGM-02007_LA-BC (BMP4 study)


title: DGM-10503_M6_lg (BMP4 study)


title: Tumor 7

city: South San Francisco

first: Steffen

last: Durinck

address: 1 DNA Way

institute: Genentech

description:
bulk_RNAseq_tumor_cells.xls
SAM24313957

data_processing:
Illumina Casava 1.8
Sequencing reads were filtered to have at least an average base quality of 23 and were then aligned to GRCm38  using GSNAP
Expression counts per gene were obtained by counting the number of reads aligned uniquely to each gene locus as defined by NCBI and Ensembl gene annotations and RefSeq mRNA sequences
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with gene expression counts

source_name: Homozygous knockout GCGR: tumor

growth_protocol: Animals were maintained in a pathogen-free animal facility under 12hr light/12hr dark cycle with access to a standard rodent chow and water ad libitum

extract_protocol:
FACS sorted alpha cells or dissected tumor tissues were individually processed to generate RNA samples
RNeasy Kit (Qiagen, Hilden, Germany)
TruSeq RNA Sample Preparation kit (Illumina)
N=3 GCGR heterozygous control; N=5 GCGR homozygous knockout; N=7 GCGR homozygous knockout tumors; N=8 non-tumor controls

treatment_protocol: Mice received tamoxifen at 200mg/kg i.p. for 5 days and islets were isolated and dispersed 14-21 days later.

value: Homozygous knockout GCGR

value: tumor

tag: treatment

tag: replicate


title: control_basal_4

description: STAT5 in thermogenic_fat


title: Met-1 TripZ-200c Plus Dox 3

city: Aurora

first: Michelle

middle: M

last: Williams

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Reads generated were mapped to the house mouse genome (GRCM38.p6 FVB_NJ_v1) by gSNAP (CITE2).
Expression (FPKM) derived by Cufflinks (CITE2).
Genome_build: GRCM38.p6 FVB_NJ_v1
Supplementary_files_format_and_content: Differential expression analyzed with ANOVA in R.

source_name: Mouse mammary carcinoma cell line

growth_protocol: Cells grown in attached culture conditions in DMEM + 10% FBS + 1% pen/strep

extract_protocol:
mRNA was extracted using TRIzol and was Bioanalyzed prior to sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in RPMI + 10% FBS + 1% pen/strep ± 1ug/mL doxycycline, 48 hours.

value: 1ug/mL doxycycline

tag: time point

value: 48 hours

value: FVB/nJ


title: Met-1 TripZ-200c Plus Dox 1


title: Tumor 6

description:
bulk_RNAseq_tumor_cells.xls
SAM24313956

tag: genotype


title: Met-1 TripZ-200c Minus Dox 3

value: Vehicle


title: control_basal_3

description: STAT5 in thermogenic_fat


title: Met-1 TripZ-200c Minus Dox 2


title: DGM-10500_M0_lg (BMP4 study)

city: New York

first: Yael

last: Strulovici-Barel

institute: Weill Cornell Medical College

value: nonsmoker


title: Stat5_Adipoq_basal_2

description: STAT5 in thermogenic_fat


title: control_basal_2

description: STAT5 in thermogenic_fat


title: DGM-10284_M6_lg (BMP4 study)


title: Tumor 5

description:
bulk_RNAseq_tumor_cells.xls
SAM24313955


title: Met-1 TripZ-200c Plus Dox 2


title: Met-1 TripZ-200c Minus Dox 1


title: Tumor 4

description:
bulk_RNAseq_tumor_cells.xls
SAM24313954


title: IR_KO2

first: Hao

last: Wang

address: 180 Fenglin Road

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were mapped to the mouse genome mm9 using STAR
The raw read counts were measured with RefSeq genes using Homer and the differential gene expression analysis was carried out using edgeR
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw counts and normalized RPKM values for every gene and every sample.

source_name: Kidney

extract_protocol:
Kidney tissues were collected from mice and quickily fozen in liquid nitrogen. The total RNA of kidney tissues was prepared using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: renal IR injury


title: DGM-10194_M3_lg (BMP4 study)


title: Tumor 3

description:
bulk_RNAseq_tumor_cells.xls
SAM24313953


title: URT1D491/3A replicate 5 Dataset#2

data_processing:
After initial data processing by the MiSeq Control Software v 2.5. (Illumina), base calls were retrieved and further analysed by a suite of home made python scripts (v2.7) using biopython (v1.63) and regex (v2.4) libraries
Data processing pipeline was adapted from (Sikorska et al., 2017). Reads with low quality bases (=<Q10) within the 15 –base random sequence of the read 2 or within the 30 bases downstream the delimiter sequence, were filtered out
Sequences with identical nucleotides in 15 –base random sequence were deduplicated.
Next, 20 nucleotides sequences corresponding to nucleotides of the transcript  were searched into reads 1 to identify the corresponding target mRNAs. One mismatch was tolerated. Matched reads 1 and their corresponding reads 2 were extracted and annotated.
Reads 2 that contain the delimiter sequence were selected and subsequently trimmed from their random and delimiter sequences.
Then, the analysis was divided into two steps.
The aim of the first step was to identify the position of mRNA 3’ extremities and to detect untemplated nucleotides. To do this, the 30 nucleotide sequences downstream of the read 2 delimiter sequence were mapped to the corresponding reference sequence, which goes from the first nucleotide of the transcript that maps the forward PCR2 primer to the end of the mRNA. Up to four mismatches were tolerated, with the exception of the first five nucleotides downstream of the mapping site that had to perfectly map. To map the 3’ end position of reads 2 with untemplated tails, the sequences of the unmatched reads 2 were successively trimmed from their 3’ end, with a one nucleotide trimming step, until they could be mapped to the reference sequence or until a maximum of 30 nucleotide has been removed. For each successfully mapped read 2, untemplated nucleotides at the 3’ end were extracted
The aim of the second step was to analyze long mRNA poly(A) tail. Sequencing of long homopolymeric stretches causes a rapid decrease of sequencing quality, making it impossible to exactly map the 3’ end of mRNA with long poly(A). We thus looked for long T stretches of at least 10 Ts in the read 2 that failed to map the reference sequence. Poly(A) tails were searched with the constraint that it must begin in the first 30 cycles, which means that the maximal length of the added 3’ end modification is limited to 29 nucleotides.
Finally, results from step 1 and 2 were compiled and 3’ extensions were analyzed.
Supplementary_files_format_and_content: One processed data file is given for each of the tree datasets generated in individual Miseq runs. It includes the processed data for each construction and biological replicate. Each line corresponds to one individual reads.
Supplementary_files_format_and_content: For each read, we indicate the read ID (read.ID), the gene AGI (Gene), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), A + non-A tail sequence (extension), A + non-A tail size (extension.size), tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), the biological replicate (rep) and the construction (construction).

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: Nicotiana benthamiana infiltrated leaves of plants grown during 4 weeks on soil with 16 hr light (22 °C) /8 hr (18 °C) darkness cycles.

extract_protocol:
Total RNA was extracted from flowers with TRI Reagent® (Molecular Research Center) according to manufacturer’s instructions
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

treatment_protocol: Different URT1 constructions  were co-inflitrated with a GFP reporter mRNA and P19 (silencing inhibitor) in leaves.

tag: construction

tag: biological replicate

value: replicate 5

tag: dataset


title: IR_KO3


title: DGM-10123_M0_lg (BMP4 study)

tag: cell type


title: Tumor 2

description:
bulk_RNAseq_tumor_cells.xls
SAM24313952


title: control_basal_1

description: STAT5 in thermogenic_fat


title: Tumor 1

description:
bulk_RNAseq_tumor_cells.xls
SAM24313950


title: IR_KO1


title: DGM-01620_lg (BMP4 study)

tag: smoking status


title: m1m2URT1D491/3A replicate 1 Dataset#3

value: replicate 1

tag: reference sequence

value: GFP


title: URT1 replicate 5 Dataset#2


title: Control tissue 8

description:
bulk_RNAseq_tumor_cells.xls
SAM24313948

source_name: Homozygous knockout GCGR: non-tumor pancreatic tissue

value: pancreatic tissue


title: m2URT1D491/3A replicate 1 Dataset#3


title: Control tissue 7

description:
bulk_RNAseq_tumor_cells.xls
SAM24313947


title: ctrl replicate 5 Dataset#2

value: ctrl


title: Elav-GAL4_RT_rep3

city: State College

first: Santhosh

last: Girirajan

state: PA

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Trimmomatic (Bolger et al., 2014) v.0.36 was first used to trim reads as necessary, based on FastQC (bioinformatics.babraham.ac.uk/projects/fastqc) output.
TopHat2 v.2.1.0 (Kim et al., 2013) was used to align the raw sequencing data to the reference fly genome and transcriptome.
HTSeq-Count v.0.6.1 (Anders et al., 2015) was used to calculate raw read counts for each gene.
Genome_build: Dmel 6.08
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts for all transcripts.

organism: Drosophila melanogaster

source_name: Drosophila whole head

growth_protocol: Flies were reared on conventional cornmeal-sucrose-dextrose-yeast medium, at 25°C for Cen, CG14182  and UQCR-C2  knockdwn flies and control, and at room temperature for Sin knockdown flies and control.

extract_protocol:
F1 female progeny were collected in groups of 35-40, quickly frozen in liquid nitrogen, and stored at −80°C. For RNA extraction, heads were separated from the bodies by repetitive cycles of freezing in liquid nitrogen and vortexing. Total RNA was isolated using TRIZOL (Invitrogen, Carlsbad, CA, USA).
We prepared cDNA libraries using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).

tag: tissue

value: whole head

tag: tissue-specific knockdown

value: neuronal

tag: fly gene

value: Control

tag: human homolog

tag: vdrc stock no.

tag: Sex

value: female


title: IR_WT2

tag: strain

value: WT

tag: treatment


title: m1URT1D491/3A replicate 1 Dataset#3


title: Elav-GAL4_RT_rep1


title: Control tissue 5

description:
bulk_RNAseq_tumor_cells.xls
SAM24313943

value: Homozygous knockout GCGR

tag: replicate


title: URT1D491/3A replicate 1 Dataset#3


title: Control tissue 6

description:
bulk_RNAseq_tumor_cells.xls
SAM24313944

tag: genotype


title: KO3

tag: age

value: Healthy control


title: KO1


title: IR_WT1


title: Elav-GAL4_25C_Dicer2_rep2


title: Elav-GAL4_25C_Dicer2_rep3


title: Control tissue 3

description:
bulk_RNAseq_tumor_cells.xls
SAM24313941


title: Control tissue 4

description:
bulk_RNAseq_tumor_cells.xls
SAM24313942


title: ctrl replicate 1 Dataset#3

tag: construction


title: IR_WT3


title: Elav-GAL4_25C_Dicer2_rep1


title: DGM-01774_090416_lg (BMP4 study)

address: 1300 York Avenue

value: large airway epithelial cells


title: URT1 replicate 1 Dataset#3

tag: biological replicate


title: Elav-GAL4_RT_rep2


title: m1m2URT1D491/3A replicate 3 Dataset#3

value: replicate 3

tag: dataset


title: UQCR-C2_rep2


title: Control tissue 2

description:
bulk_RNAseq_tumor_cells.xls
SAM24313940

tag: cell type


title: WT2


title: Control tissue 1

description:
bulk_RNAseq_tumor_cells.xls
SAM24313939


title: UQCR-C2_rep1


title: Alpha cell knockout sorted 4

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653328

source_name: Homozygous knockout GCGR: pancreatic islet

value: alpha cell

value: tamoxifen


title: Sin_rep3

value: Sin


title: Alpha cell knockout sorted 3

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653327


title: URT1D491/3A replicate 3 Dataset#1


title: m2URT1D491/3A replicate 3 Dataset#3


title: KO2


title: Sin_rep2


title: ctrl replicate 4 Dataset#2

value: replicate 4


title: Alpha cell heterozygous sorted 3

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653324

source_name: Heterozygous GCGR: pancreatic islet

value: Heterozygous GCGR


title: CG14182_rep3

value: MOSMO


title: URT1D491/3A replicate 4 Dataset#2


title: Sin_rep1


title: UQCR-C2_rep3


title: m1URT1D491/3A replicate 3 Dataset#3

value: GFP


title: URT1 replicate 3 Dataset#1


title: WT3


title: WT1


title: Alpha cell knockout sorted 5

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653329


title: Alpha cell heterozygous sorted 2

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653323


title: CG14182_rep2


title: URT1 replicate 4 Dataset#2


title: CG14182_rep1


title: URT1D491/3A replicate 3 Dataset#3


title: Cen_rep3

value: Cen


title: Mouse_6 tumor_2

library_source: genomic

data_processing:
Library strategy: DNA-seq
Sequencing reads were mapped using BWA
Local realignment, duplicate marking, and raw variant calling were performed according to GATK best practices
Somatic variant calling on tumor and its matched normal BAM file was performed using Strelka
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with mutations

molecule: genomic DNA

source_name: Pancreatic tumor

extract_protocol:
Agilent SureSelect Human All Exome kit (50 Mb).
N=6 control samples, N=11 tumor samples

value: Pancreatic tumor

tag: mouse number


title: URT1 replicate 3 Dataset#3

tag: reference sequence


title: Cen_rep2

tag: tissue

value: whole head

value: neuronal


title: Mouse_6 tumor_1


title: Alpha cell knockout sorted 1

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653325


title: ctrl replicate 3 Dataset#3

value: ctrl


title: Mouse_5 tumor


title: Alpha cell knockout sorted 2

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653326


title: Tumor Sample 2

data_processing:
Illumina Casava 1.8
Illumina bcl2fastq 2.17
Reads were demultiplexed based on perfect matches to expected barcodes
Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) only considering uniquely mapped reads
Per-gene transcript counts were determined based on the number of unique UMIs for mapped reads overlapping exons in sense orientation, allowing for one mismatch when collapsing UMI sequences
Barcodes were filtered by requiring a minimum number of detected transcripts, where a sample-specific cutoff was set to 0.1 times the total transcript count for cells at rank 30 (the 99th percentile for 3,000 cells)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene x barcode matrix with UMI counts

source_name: Tumor

extract_protocol:
Dissociated islet and tumor cells were individually processed to generate single cell RNA samples
Chromium Single Cell 3’ Library and Gel Bead Kit V2 (10X Genomics)
N=5 single cell libraries

value: tumor

value: GCGR homozygous knockout


title: Cen_rep1

tag: tissue-specific knockdown

value: female


title: m2URT1D491/3A replicate 2 Dataset#3

value: replicate 2


title: Mouse_6 control

source_name: Pancreatic tissue control

value: Pancreatic tissue control


title: m1m2URT1D491/3A replicate 2 Dataset#3


title: Tumor Sample 3


title: ctrl replicate 3 Dataset#1

value: replicate 3


title: URT1D491/3A replicate 2 Dataset#1


title: Alpha cell heterozygous sorted 1

description:
bulk_RNAseq_Alpha_cells.xls
SAM19653322

value: alpha cell

value: tamoxifen


title: Mouse_3 tumor_3


title: Homozygous GCGR Knockout Islets

source_name: Pancreatic islet

value: islet cell


title: Mouse_5 control


title: Mouse_3 control


title: Tumor Sample 1


title: Mouse_3 tumor_2


title: Heterozygous Islets

value: GCGR heterozygous


title: Mouse_3 tumor_1


title: URT1 replicate 2 Dataset#1


title: m1URT1D491/3A replicate 2 Dataset#3


title: ctrl replicate 2 Dataset#1


title: URT1D491/3A replicate 2 Dataset#3


title: Mouse_4 tumor


title: Mouse_4 control


title: Mouse_2 tumor_2


title: ctrl replicate 2 Dataset#3


title: URT1 replicate 2 Dataset#3


title: URT1D491/3A replicate 1 Dataset#1

value: replicate 1


title: Mouse_2 tumor_1


title: CAD I304N Neurite B

first: Matthew

last: Taliaferro

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

data_processing:
Adapters were trimmed from the 3' end of reads using cutadapt
Transcript abundances were calculated using salmon or kallisto against the mm10 or hg38 genomes
Gene abundances were calculated from transcript abundances using tximport
Reads were mapped to mouse genome (mm10 or hg38) using STAR
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: transcript abundances in txt format

source_name: CAD cell line

extract_protocol:
RNA extraction was performed with Qiagen or Zymo Microprep Kits
Illumina TruSeq

value: CAD cell line

tag: cell compartment

value: neurite


title: URT1 replicate 1 Dataset#1


title: Mouse_2 control


title: CAD I304N Neurite A


title: Mouse_1 tumor_2

value: Pancreatic tumor


title: CAD I304N Neurite C


title: ctrl replicate 1 Dataset#1


title: URT1D491/3A replicate 6 Dataset#2

value: replicate 6


title: CAD I304N Soma C

value: soma


title: CAD I304N Soma B


title: CAD I304N Soma A


title: Mouse_1 tumor_1


title: ctrl replicate 6 Dataset#2

value: ctrl


title: Mouse_1 control tissue


title: single cells_INCB059872 6d B

city: Nashville

first: Scott

last: Hiebert

address: 2220 Pierce Ave.

institute: Vanderbilt University

data_processing:
Samples were demultiplexed and single-cell gene expression matrices were generated using Cell Ranger software.
Seurat R package was used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: "filtered_feature_bc_matrix" folder contents from Cell Ranger output (Genes.tsv, Barcodes.tsv, Matrix.mtx)

source_name: lineage-negative bone marrow

extract_protocol:
Bone marrow was harvested from femurs and tibias and stained with BD Pharmingen Biotin Mouse Lineage Panel and streptavidin-PacBlue. Zombie-NIR Fixable Viability Dye was added to each sample at 1:1000 dilution before sorting alive lineage-negative population (PacBlue-/NIR-). Sorted cells were submitted for single-cell RNA-seq using 10X Genomics Chromium Controller.
Barcoded cDNA libraries were prepared according to instructions from 10X Genomics.

treatment_protocol: Mice were treated daily with 10 mg/kg INCB059872 via oral gavage.

value: lineage-negative bone marrow

tag: time (days)


title: single cells_INCB059872 6d A


title: single cells_INCB059872 6d C


title: single cells_INCB059872 4d C


title: URT1 replicate 6 Dataset#2


title: single cells_INCB059872 4d A


title: Fam122a KO repli1

source_name: LT-HSCs

value: 8-12 weeks

value: LT-HSC

tag: hsc markers

value: LSK CD34- FLk2-

tag: genetype/variation

value: Fam122a KO


title: single cells_Control C

tag: strain


title: 14_412_WT-High

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

description: WT sorted EGFP(High) intestinal stem cell population.

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the Fluidic Station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing:
The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.
RMA normalization is performed using R with Version 21 of EntrezGene CDF brainarray.

source_name: WT-High

label_protocol: 1 ng of total RNA is reverse transcribed following the Ovation Pico System V2 (Tecan). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Tecan).

extract_protocol: Cells were sorted directly into lysis buffer and RNA was extracted using the RNeasy Micro Kit (Qiagen).

treatment_protocol: Mice treated with tamoxifen for five consecutive days and sacrificed 1 month after treatment. Intestinal tissue was incubated in 15 mM EDTA in PBS for 25 minutes on ice then vigorously vortexed to release crypts. Crypts were dissociated by incubation in dispase buffer containing 0.3 U/ml dispase (Corning), 0.8 U/ml DNase (Ambion), 10 µM Y-27632 (Enzo) at 37°C for 30 min. Intestinal stem cells and their direct transit amplifying progenitors from individual mice were enriched by sorting CD24(low)/EGFP(High) or CD24(low)/EGFP(Low) populations, respectively.

tag: genotype/variation

value: WT

value: CD24(low)/EGFP(High) intestinal stem cell population


title: single cells_Control B


title: 11_386_Atg7KO-High

description: Atg7KO sorted EGFP(High) intestinal stem cell population.


title: WT rep3

data_processing:
Library strategy: TAIL-seq
The base calling-based pipeline was adapted from Zuber et al. 2016 (doi: 10.1016/j.celrep.2016.02.060) .
The base calls were retrieved after initial data processing by the MiSeq Control Software v 2.6 and the sequences having completely identical nucleotides in the 1st to 15th cycle in read 2 (degenerate bases in 3’ adapter) were deduplicated.
In order to identify transcripts, read 1 sequences were mapped onto the Arabidopsis thaliana reference genome (TAIR 10) using Hisat2 (v2.1.0) (Kim et al. 2015, https://doi.org/10.1038/nmeth.3317).
The resulting alignment was annotated using the intersectBed tool from the BEDTools suite (v2.17.5) (Quinlan and Hall, 2010, https://doi.org/10.1093/bioinformatics/btq033) and the Arabidopsis annotation file TAIR10_GFF3_genes.gff (http://www.arabidopsis.org).
Reads 1 that map onto cytosolic mRNAs and their corresponding reads 2 were extracted and used for further analyses.
Reads 2 that contain the delimiter sequence were selected and subsequently trimmed from their random and delimiter sequences.
A homemade python script was then used to extract poly(A) tails (>5 nt) and their potential 3’ end modification from the remaining read 2. Poly(A) were detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3’ end modification of poly(A) tails was limited to the last 29 nucleotides of insert.
Detected poly(A) and 3’ extensions were finally analyzed for their size and composition using a homemade script based on Python 2.7.
Genome_build: TAIR10
Supplementary_files_format_and_content: One processed data file is given. It includes the processed data for the three biological replicate.
Supplementary_files_format_and_content: For each read, we indicate read ID (read.ID), gene AGI (AGI), TruSeq index (index), biological replicate (rep), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size),  tail sequence (extension), tail size (extension.size), and a tag (classification) indicating the category of the tail.

source_name: flowers

growth_protocol: Arabidopsis plantlets of Col-0 accession were grown on soil with 16 hr light (21 °C) /8h (18 °C) darkness cycles

extract_protocol:
Total RNA was extracted from flowers with TRI Reagent® (Molecular Research Center) according to manufacturer’s instructions
TAILseq libraries according to Chang et al., 2014 (https://doi.org/10.1016/j.molcel.2014.02.007) and Zuber et al., 2016  (doi: 10.1016/j.celrep.2016.02.060) with some modifications of the protocol, see related publication.

value: WT (Col-0)

value: replicate 3


title: WT rep1


title: 13_411_WT-High


title: 09_356_Atg7KO-High


title: 10_348_Atg7KO-High


title: H. pylori infected cells replicate 2

city: Kuala Lumpur

first: Won

middle: Fen

last: Wong

address: Lembah Pantai

department: Department of Medical Microbiology,  Faculty of Medicine

country: Malaysia

institute: University of Malaya

description: RAW264.7 cells infected with Helicobacter pylori at MOI10 for 24 hours

hyb_protocol: cRNA (600 ng) was hybridized onto 8-array slide at10 rpm for 17 h at 65 °C.

scan_protocol: The slide was  scanned on Agilent High Resolution Microarray Scanner (C-model)

data_processing: Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V107.1.1).

source_name: RAW264.7 cells

label_protocol: Total RNA (100 ng) was primed with an oligo-dT containing the recognition site for RNA polymerase. RNA was labelled using Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) to produce cyanine 3-CTP labeled cRNA.

growth_protocol: RAW264.7 cells were purchased from America Type Culture Control (ATCC TIB-71). RAW264.7 cells were cultured in Dulbecco’s Modified Essential Medium supplemented with 10% heat inactivated fetal bovine serum and incubated at 37o C, 5% CO2

extract_protocol: RNA was isolated from cells using TRIzol reagent.

treatment_protocol: ne day prior to inoculation, cells were seeded in a T25 flask at 5 × 105 cells/ml. Cells were then infected with H. pylori SS1 at MOIs of 10 for 24 h.

tag: cell line

value: RAW264.7 (ATCC TIB71)

tag: treatment

value: H. pylori SS1 (MOI10, 24 hours)


title: 12_388_WT-High


title: Effector_Th17_CD30low

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

institute: Chiba University

description: Splenic CD44low CD62Llow CD4+ cells were stimulated under Th17 culture conditions (10 ng/ml IL-6, and 10 ng/ml IL-1β, 10 ng/ml IL-23, 10 µg/ml anti-IL-4 Ab, and 10 µg/ml anti-IFN-γ Ab) for 6 days in vitro. CD30low and CD30high population were sorted by cell sorter.

hyb_protocol: cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using Affymetrix GeneChip Command Console Software (AGCC) and Console Software (Expression Console).

source_name: Six-day cultured Th17 cells generated from primary splenic naive CD4_T cells

label_protocol: Total RNA was labeled using the GeneChip 3' IVT Express Kit.

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

treatment_protocol: Cells were harvested and RNA was immediately isolated.

tag: sorted cells

value: CD44low CD62Llow CD4+


title: H. pylori infected cells replicate 1


title: WT rep2

first: Dominique

last: Gagliardi

institute: CNRS

tag: genotype

value: replicate 2


title: Control uninfected cells replicated 1

description: RAW264.7 cells

value: Uninfected


title: Effector_Th1_CD30high

description: Splenic CD44low CD62Lhi CD4+ were stimulated under Th1 culture conditions (30 U/ml IL-2 culture sup, 100 U/ml IL-12, and 1 µg/ml anti-IL-4 Ab) for 6 days in vitro. CD30low and CD30high population were sorted by cell sorter.

source_name: Six-day cultured Th1 cells generated from primary splenic naive CD4_T cells

value: CD44low CD62Lhi CD4+


title: single cells_INCB059872 4d B


title: Control uninfected cells replicate 2

description: RAW264.7 cells


title: Effector_Th17_CD30high

description: Splenic CD44low CD62Lhi CD4+ cells were stimulated under Th17 culture conditions (10 ng/ml IL-6, and 10 ng/ml IL-1β, 10 ng/ml IL-23, 10 µg/ml anti-IL-4 Ab, and 10 µg/ml anti-IFN-γ Ab) for 6 days in vitro. CD30low and CD30high population were sorted by cell sorter.


title: Effector_Th1_CD30low

description: Splenic CD44low CD62Llow CD4+ were stimulated under Th1 culture conditions (30 U/ml IL-2 culture sup, 100 U/ml IL-12, and 1 µg/ml anti-IL-4 Ab) for 6 days in vitro. CD30low and CD30high population were sorted by cell sorter.


title: 08_411_WT-Low

description: WT sorted EGFP(Low) transit amplifying population.

source_name: WT-Low

value: CD24(low)/EGFP(Low) transit amplifying population


title: 07_409_WT-Low


title: urt1-1 replicate 2 Dataset#2

data_processing:
After initial data processing by the MiSeq Control Software v 2.5. (Illumina), base calls were retrieved and further analysed by a suite of home made python scripts (v2.7) using biopython (v1.63) and regex (v2.4) libraries
Data processing pipeline was adapted from (Sikorska et al., 2017). Reads with low quality bases (=<Q10) within the 15 –base random sequence of the read 2 or within the 30 bases downstream the delimiter sequence, were filtered out
Sequences with identical nucleotides in 15 –base random sequence were deduplicated.
Next, 20 nucleotides sequences corresponding to nucleotides of the transcript  were searched into reads 1 to identify the corresponding target mRNAs. One mismatch was tolerated. Matched reads 1 and their corresponding reads 2 were extracted and annotated.
Reads 2 that contain the delimiter sequence were selected and subsequently trimmed from their random and delimiter sequences.
Then, the analysis was divided into two steps.
The aim of the first step was to identify the position of mRNA 3’ extremities and to detect untemplated nucleotides. To do this, the 30 nucleotide sequences downstream of the read 2 delimiter sequence were mapped to the corresponding reference sequence, which goes from the first nucleotide of the transcript that maps the forward PCR2 primer to the end of the mRNA. Up to four mismatches were tolerated, with the exception of the first five nucleotides downstream of the mapping site that had to perfectly map. To map the 3’ end position of reads 2 with untemplated tails, the sequences of the unmatched reads 2 were successively trimmed from their 3’ end, with a one nucleotide trimming step, until they could be mapped to the reference sequence or until a maximum of 30 nucleotide has been removed. For each successfully mapped read 2, untemplated nucleotides at the 3’ end were extracted
The aim of the second step was to analyze long mRNA poly(A) tail. Sequencing of long homopolymeric stretches causes a rapid decrease of sequencing quality, making it impossible to exactly map the 3’ end of mRNA with long poly(A). We thus looked for long T stretches of at least 10 Ts in the read 2 that failed to map the reference sequence. Poly(A) tails were searched with the constraint that it must begin in the first 30 cycles, which means that the maximal length of the added 3’ end modification is limited to 29 nucleotides.
Finally, results from step 1 and 2 were compiled and  3’ extensions were analyzed.
Genome_build: TAIR10
Supplementary_files_format_and_content: One processed data file is given. It includes the processed data of the 22 Arabidopsis mRNAs for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary_files_format_and_content: For each read, we indicate read ID (read.ID), gene AGI (Gene), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), biological replicate (rep) and genotype (genotype, WT or urt1).

tag: biological replicate


title: 6d INCB059872 B

data_processing:
Trimmomatic-0.32: trim low-quality sequences
Bowtie2: read alignment to mm10
samtools: filter out low quality alignments
Differential gene expression determined by Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: plain text documents containing averaged RPKM values and calculated differential expression between treatment and control

source_name: megakaryocyte progenitor cells

extract_protocol:
Lin- CD41+ CD200r3- murine bone marrow cells were flow-sorted directly into Buffer RLT from Qiagen RNeasy Mini Kit, and RNA was isolated according to manufacturer’s protocol.
Libraries were prepared using Nugen Ovation RNA-Seq System V2 kit.

value: Lin- CD41+ CD200r3- bone marrow


title: 6d INCB059872 A


title: single cells_Control A

value: lineage-negative bone marrow


title: WT replicate 2 Dataset#2

tag: dataset


title: 06_407_WT-Low

tag: cell type


title: 05_341_WT-Low


title: 4d INCB059872 A


title: 4d INCB059872 B


title: urt1-1 replicate 2 Dataset#5


title: urt1-1 replicate 2 Dataset#4


title: control B


title: control A


title: urt1-1 replicate 1 Dataset#4

value: replicate 1


title: 231 Talazoparib replicate 4

city: Baltimore

first: Michael

middle: Jonathan

last: Topper

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

description: DESeq2 Normalized Counts Tal and Mock

data_processing:
fastq files were trimmed using Trimmomatic using SLIDINGWINDOW operation
Trimmed fastq files were aligned to Hg38 using RNA STAR
BAM files from RNA STAR were used as input for featureCounts v1.6.3
featureCount count files were used to generate normalized abundance measurements and were derived using DESeq2 R version 3.4.1 (2017-06-30) -- "Single Candle", DESeq2 version 1.18.1
Genome_build: hg38
Supplementary_files_format_and_content: Matrix tables with normalized gene counts for every gene mock and treated contained in each table.

source_name: MDA-MB-231 cells treated with 10nM Talazoparib for 10 days

growth_protocol: Cell lines were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 10 days  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated from cell pellets using Takara NucleoSpin RNA extraction kit. RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.
RNA-seq libraries were prepared using  SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian without significant modification of standard protocol
Total Transcriptome RNA-seq, ribosomal RNA depletion

treatment_protocol: Cell lines detailed above were treated with the agents indicated above for a period of 10 days

tag: source

value: in-vitro cultured cell lines

tag: Sex

value: Female


title: 231 Mock replicate 2

description: Contained in all processed data files

source_name: MDA-MB-231 cells treated with vehicle


title: 231 Combo replicate 3

description: DESeq2 Normalized Counts Combo and Mock

source_name: MDA-MB-231 cells treated with 500nM Azacitidine and 10nM Talazoparib for 10 days


title: WT replicate 2 Dataset#5

city: Strasbourg

address: 12, rue du General Zimmer

tag: reference sequence


title: A-myb-KO-PS-H3K27Ac-2

city: Cincinnati

first: Akihiko

last: Sakashita

state: Ohio

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Basecalls performed using bcl2fastq version 2.20.0
RNA-seq and ChIP-seq reads were aligned to the mm10 genome using Hisat2 version 2.1.0. and bowtie2 version 2.3.3.1.
For RNA-seq analysis, To quantify uniquely aligned reads on respective annotated transcript loci (NCBI RefSeq transcripts), the htseq-count function with  –s reverse option, part of the HTSeq package
For ChIP-seq analysis, Pearson correlation coefficient (R) in 1 kb bins between biological replicates were calculated with SeqMonk. Peak calling for ATAC- and ChIP-seq data were performed by MACS version 1.4.2 with default arguments; a cut-off P value of 10-25 was used.  Relative ChIP-seq enrichments in respective peak regions were calculated by dividing input controls.
Genome_build: mm10
Supplementary_files_format_and_content: bam files were generated from each alignment step

source_name: mouse pachytene spermatocytes

growth_protocol: For RNA-seq analysis, ES cells were cultured in ESC media (15% FBS, 25 mM HEPES, 1× GlutaMAX, 1× MEM non-essential amino acids, 1× Penicillin/Streptomycin and 0.055 mM β-Mercaptoethanol in DMEM High Glucose (4.5g/l)) with 2i (PD0325901, 1 µM; LC Laboratories and CHIR99021, 3µM, LC Laboratories) and LIF (1300 U/ml, in-house) on cell culture plates coated with 0.2% gelatin, under feeder-free condition. For native ChIP-seq analysis in pachytene spermatocytes, from WT and A-myb mutant testes, we prepared testicular cell suspension from 1 male mouse at ages of 8-12 weeks, and isolated pachytene spermatocytes according to small-scale STA-PUT method described in our previous report (Adam SR, PLoS Genet, 2018).

extract_protocol:
For RNA-seq analysis, total RNA from ES cells on each well of 24 well plate was extracted using an RNeasy Plus Mini Kit (QIAGEN), with gnomic DNA elimination. For ChIP-seq analysis, to extract chromatin, isolated pachytene spermatocytes were suspended in 20 µl of Nuclei EZ Lysis Buffer (SIGMA), and extensively digested chromatin with 2 IU/µl Micrococcal Nuclease (MNase, NEB) at 37℃ for 5 min.
RNA-seq library preparation was carried out using TruSeq Stranded mRNA Library Prep kit (Illumina) following manufacturer’s instructions. ChIP-seq library preparation was carried out by NEBNext Ultra II DNA Library Prep Kit (NEB) following manufacturer’s instructions.

treatment_protocol: In ES cell culture, doxycycline (1 µg/ml) and A-MYB expression were induced at day1 and day2

tag: no. of passages and ages of weeks

value: 8-12 weeks

tag: background strain

tag: chip antibody


title: 04_386_Atg7KO-Low

description: Atg7KO sorted EGFP(Low) transit amplifying population.


title: 03_387_Atg7KO-Low


title: NU1_RST010.3_01

city: Montreal

first: Rene

last: St-Arnaud

state: Quebec

address: 1003 Decarie Blvd

department: Human Genetics

country: Canada

institute: McGill University

description: fraction: whole cell

hyb_protocol: Samples were hybridized to GeneChip system mouse MoGene-2.0 gene ST arrays according to Affymetrix specifications.

scan_protocol: Not provided

data_processing: CEL files containing probe intensity data were analyzed using FlexArray software (version 1.6.2).

label_protocol: Samples were prepared according to Affymetrix specifications.

growth_protocol: The calvaria-derived pre-osteoblast cell line MC3T3-E1 (ATCC CRL-2593) were grown in alpha minimum essential media supplemented with 10% fetal bovine serum (FBS) and a cocktail of 100 U/ml penicillin and 100 µg/ml streptomycin in a humidified 5% CO2 incubator at 37°C.

extract_protocol: Total RNA was isolated from MC3T3-E1 cells differentiated in osteogenic medium for 14 days in the presence of NU7441 (1 μM) or DMSO. Total RNA was purified with RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s guidelines.

treatment_protocol: Cells were plated in complete αMEM medium (Gibco) and grown until confluency. To induce differentiation, the culture medium was freshly supplemented with 50µg/ml ascorbic acid (Sigma-Aldrich) and 10 mM β-glycerophosphate (Sigma-Aldrich). NU7441 (1 µM) or vehicle (DMSO) (Sigma-Aldrich) were added to the media. Cells were harvested for total RNA extraction at day 14.

value: MC3T3-E1 (ATCC CRL-2593)


title: WT replicate 2 Dataset#4

value: WT


title: 02_353_Atg7KO-Low


title: Ctrl3_RST009.3_01

description: fraction: whole cell

value: DMSO


title: Ctrl1_RST007.3_01

description: fraction: whole cell


title: NU2_RST011.3_01

description: fraction: whole cell


title: NU3_RST012.3_01

description: fraction: whole cell


title: Ctrl2_RST008.3_01

description: fraction: whole cell


title: urt1-1 replicate 1 Dataset#2


title: urt1-1 replicate 1 Dataset#5


title: 01_356_Atg7KO-Low


title: WT-PS-H3K27Ac-1


title: WT-PS-H3K27Ac-2


title: 231 Talazoparib replicate 3

description: DESeq2 Normalized Counts Tal and Mock


title: 231 Azacitidine replicate 4

description: DESeq2 Normalized Counts Aza and Mock

source_name: MDA-MB-231 cells treated with 500nM Azacitidine for 10 days


title: WT replicate 1 Dataset#5


title: A-myb-KO-PS-input-2


title: 231 Mock replicate 4

description: Contained in all processed data files


title: WT replicate 1 Dataset#4


title: 231 Azacitidine replicate 3

description: DESeq2 Normalized Counts Aza and Mock


title: 231 Combo replicate 2

description: DESeq2 Normalized Counts Combo and Mock


title: urt1-1 replicate 2 Dataset#1


title: WT replicate 2 Dataset#1


title: WT-PS-input-2


title: WT-PS-input-1


title: 231 Talazoparib replicate 2

description: DESeq2 Normalized Counts Tal and Mock


title: urt1-1 replicate 1 Dataset#1


title: P8AM7 OB

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent Technologies). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven and then washed at room temperature.

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies)

data_processing: Raw data were extracted using Agilent Feature Extraction Software (Agilent Technologies, v11.0.1.1). Background correction, averaging the expression values of duplicated probes and between-sample normalization of raw data were performed using limma35 and R 3.2.1（https://cran.r-project.org/）. Normalization was performed using quantile method.  All expression values for the probes was log2 transformed and normalized between groups using quantile method.

source_name: Aged damaged olfactory bulb in control group

label_protocol: RNA labeling and hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kits (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: RNA was prepared using TRIzol Reagent (Life Technologies) and RNeasy Mini Kits (QIAGEN) following the manufacturer's recommendations. RNA purity and integrity were confirmed based on its OD 260/280 ratio before analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies). Each total RNA sample pooled from 5 biological replicates (two experimental replicate).

treatment_protocol: Septal nasal mucosa were collected from young-adult or aged mice immediately after euthanization, and then snap-freezed with liquid nitrogen.

tag: tissue

value: olfactory bulb

tag: age

value: 16 months

value: methimazole


title: P8A OB

source_name: Aged oldactory bulb in control group

tag: strain

value: control


title: P8AMT7 OB

source_name: Aged damaged olfactory bulb in smoking group

value: cigarette smoke solution and methimazole


title: P8AM14 OB


title: P8AMT14 OB


title: 231 Mock replicate 3

description: Contained in all processed data files


title: A-myb-KO-PS-H3K27Ac-1


title: P9CMT14 OB

source_name: Young damaged olfactory bulb in smoking group

value: 8 weeks


title: P9CMT7 OB


title: WT replicate 1 Dataset#1


title: 231 Azacitidine replicate 2

description: DESeq2 Normalized Counts Aza and Mock


title: A-myb-KO-PS-input-1


title: 231 Talazoparib replicate 1

description: DESeq2 Normalized Counts Tal and Mock


title: P9CM14 OB

source_name: Young damaged olfactory bulb in control group


title: WT replicate 2 Dataset#3

value: replicate 2


title: P9CM7 OB


title: Day3_Dox-plus-1A-MYB-plus-1

source_name: mouse J1 embryonic stem cells

tag: agent

value: Dox+,A-MYB


title: 231 Mock replicate 1

description: Contained in all processed data files


title: Day3_Dox-plus-1A-MYB-plus-2


title: Day3_Dox-minus-1A-MYB-plus-1

value: Dox-, A-MYB


title: urt1-1 replicate 1 Dataset#3

source_name: flowers


title: urt1-1 replicate 2 Dataset#3


title: 231 Combo replicate 1

description: DESeq2 Normalized Counts Combo and Mock


title: P9AMT14

source_name: Aged damaged nasal mucosa in smoking group

value: olfactory epithelium


title: Day3_Dox-plus-2

value: Dox+


title: 231 Azacitidine replicate 1

description: DESeq2 Normalized Counts Aza and Mock

value: in-vitro cultured cell lines


title: Day3_Dox-plus-1


title: P8C OB

source_name: Young olfactory bulb in control group


title: P9AMT7


title: WT replicate 1 Dataset#3

value: replicate 1


title: WT replicate 1 Dataset#2


title: P9AM7

source_name: Aged nasal mucosa in control group


title: INCB059872+AZA B

data_processing:
Samples were demultiplexed and single-cell gene expression matrices were generated using Cell Ranger software.
Seurat R package was used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: "filtered_feature_bc_matrix" folder contents from Cell Ranger output (Features.tsv, Barcodes.tsv, Matrix.mtx)

source_name: bone marrow

growth_protocol: Cells were thawed and cultured in IMDM media containing 10% FBS, 2 mM L-glutamine, 10 ng/mL IL-3, 10 ng/mL Flt3, 10 ng/mL SCF, 10 ng/mL TPO, 5 ng/mL IL-6, 10 μM 2-mercaptoethanol, and 4 μg/mL LDL.

extract_protocol:
Apoptotic cells were removed from the samples using Miltenyi Annexin V Microbead Kit with MACS LS columns. Cells were submitted for single-cell RNA-seq using 10X Genomics Chromium Controller.
Barcoded cDNA libraries were prepared according to instructions from 10X Genomics.

treatment_protocol: Cells were treated for 48 hours with DMSO, 100 nM INCB059872, 500 nM azacitidine, or 100 nM INCB059872 + 500 nM azacitidine.

tag: diagnosis

value: treatment-related acute myeloid leukemia (t-AML) with TP53 mutation and complex genetics

value: bone marrow


title: Day3_Dox-minus-1

value: Dox-


title: p38_KO+flu_rep3

city: Haifa

first: Amir

last: Sapir

state: Israel

address: Abba Khoushy Ave 199

country: Israel

institute: University of Haifa

data_processing:
The libraries were loaded on one lane of an Illumina HiSeq 2500 instrument and were ran by 50 bp single read using V4 reagents at the Technion Genome Center, TechnionIsrael Institute of Technology
Reads were trimmed, collapsed, and then aligned to the WS220 gene transcripts of C. elegans (Worm Base) using Bowtie {Langmead, 2010 #1474}, allowing multiple alignments to include multiple transcripts due to alternative splicing. Of the reads in all samples, 94–95% were mapped to the C. elegans transcriptome.
The DESeq2 package {Love, 2014 #1475} in R was used to identify differentially expressed genes upon the treatment of statins for each strain. PCA analysis revealed a batch effect of biological replica number two, and this batch effect was included in the DESeq2 analysis. The DESeq2 package includes automatic strict filtering of low normalized gene counts to increase power and to ensure reliable results.
Genome_build: WS220
Supplementary_files_format_and_content: DESeq2 analysis output

source_name: C. elegans whole body

growth_protocol: Synchronized wild-type or dlk-1-mutant worms at the L1 stage (approximately 200 worms/plate, four plates per condition) were spotted onto 60 mm NGM plates seeded with 350 ml of OP-50. At the L4 stage (approximately 48 hours later), the worms were washed from the plates with S. basal medium, cleaned from the OP-50 bacteria by washing the worms with S. basal medium three times for five minutes each.

extract_protocol:
Total RNA was extracted using the Direct Zol RNA mini perp kit (Zymo R2070) and was treated with DNase, according to the manufacturer's instructions. The concentration of the mRNA was quantified by both Nanodrop and Qubit (Thermo Fisher Scientific), and RNA was used for library construction and the RNA sequencing procedure.
RNA libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina), according to the manufacturer’s protocol. The libraries were loaded on one lane of an Illumina HiSeq 2500 instrument and were ran by 50 bp single read using V4 reagents at the Technion Genome Center, Technion¬Israel Institute of Technology.

treatment_protocol: Worms were dropped on 55 mm NGM plates that were seeded a day before with 350 ml of OP-50 with or without fluvastatin. After nine hours, the worms were collected and washed with an S. basal medium three times and with RNase-free water two more times.

tag: treatment

value: +flu

tag: whole body

value: whole body


title: p38_KO+flu_rep2

tag: genotype


title: Day3_Dox-minus-1A-MYB-plus-2


title: p38_KO+flu_rep1


title: CAD WT GFP rescue Neurite C

source_name: CAD cell line

tag: cell compartment

value: neurite

value: WT, GFP rescue


title: P9AM14

source_name: Aged damaged nasal mucosa in control group

value: 16 months

value: methimazole


title: CAD WT GFP rescue Neurite B


title: p38_KO-flu_rep3

value: -flu


title: AZA B

value: AZA


title: P8A_2

value: control


title: P9CMT7

source_name: Young damaged nasal mucosa in smoking group

value: 8 weeks

value: cigarette smoke solution and methimazole


title: P9CMT14

value: olfactory epithelium


title: AZA A


title: P9CM14

source_name: Young damaged nasal mucosa in control group


title: p38_KO-flu_rep2


title: CAD WT GFP rescue Soma C

value: soma


title: INCB059872+AZA A


title: CAD WT GFP rescue Neurite A


title: CAD WT GFP rescue Soma B


title: WT+flu_rep3

value: wild-type


title: INCB059872 B

value: treatment-related acute myeloid leukemia (t-AML) with TP53 mutation and complex genetics


title: P9CM7


title: DMSO B

value: DMSO

value: bone marrow


title: P8AT28

source_name: Aged nasal mucosa in smoking group

value: cigarette smoke solution


title: WT+flu_rep2

value: +flu

value: whole body


title: WT+flu_rep1


title: P8C_2

source_name: Young nasal mucosa in control group


title: Day3_Dox-minus-2

value: Dox-


title: CAD WT GFP rescue Soma A

value: WT, GFP rescue


title: CAD FMR1KO Fmr1 rescue Neurite C

value: neurite

value: FMR1 KO, Fmr1 rescue


title: p38_KO-flu_rep1

value: -flu


title: WT-flu_rep3


title: P8AT42

value: 16 months


title: CAD FMR1KO Fmr1 rescue Neurite A


title: P8AT14


title: 24hr INCB059872 B H3K27ac

data_processing:
Trimmomatic-0.32: trim adapter sequences
Bowtie2: read alignment to hg19+dm3
samtools: filter out low quality alignments and remove duplicate reads
samtools: divide hg19 reads and dm3 reads into separate files
MACS2: call peaks (q-value 0.001)
Genome_build: combined genome: hg19 + dm3
Supplementary_files_format_and_content: Processed data files are in bedgraph format with input signal subtracted from ChIP signal.

source_name: THP-1 cell line

extract_protocol:
Cells were resuspended in Buffer 1 (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 0.2% aprotinin, 1 mM PMSF) and rocked at 4°C for 10 min. Samples were centrifuged and resuspended in Buffer 2 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.2% aprotinin, 1 mM PMSF) then rocked at 4°C for 5 min. Samples were centrifuged then resuspended in Buffer 3 (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% sarkosyl, 0.2% aprotinin, 1 mM PMSF, Complete mini protease inhibitor cocktail). Samples were sonicated using a Bioruptor (Diagenode) on high setting for 25 cycles (30 sec on, 30 sec off). Next, 1% Triton X-100 was added, and samples were vortexed for 10 sec. Debris was pelleted by centrifuging at 20,000 xg for 10 min, and cleared lysates were transferred to new tubes. At this point, aliquots of chromatin were removed to serve as input controls. One quarter of each sample volume (corresponding to ~10 million cells equivalent) was used for immunoprecipitation. Samples were incubated overnight with 10 μg anti-H3K27ac. Protein A and Protein G Dynabeads were mixed at 1:1 ratio and washed with equilibration buffer (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 1% Triton X-100). Samples were rotated at 4°C for 1 hour after adding 60 μl Dynabeads mix per sample. Beads were washed four times (once in each buffer) by rotating for 5 min at 4°C in the following buffers: low salt wash (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), high salt wash (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100), LiCl wash (10 mM Tris pH 8.0, 25 mM LiCl, 1 mM EDTA, 1% Triton X-100), TE. Beads were washed a second time in TE by rotating for 5 min at room temperature. Beads were resuspended in 50 μl elution buffer (TE with 0.1% SDS, 200 mM NaCl, 0.8 μg/μl Proteinase K).
Agencourt AMPure XP Beads were used at 1.8X volume according to manufacturer’s instructions for size selection. Libraries were preparing by following manufacturer’s instructions for NEBNext Ultra II DNA Library Prep Kit for Illumina.
Immediately prior to crosslinking, drosophila S2 cells were added to treated THP-1 cells to serve as spike-in control (~1:27 ratio of drosophila:human cells). Cells were crosslinked with 1% formaldehyde, quenched with glycine, and washed with cold PBS. See "ChIP protocol" column above for experiment-specific protocols.

value: anti-H3K27ac (Abcam, ab4729)


title: INCB059872 A


title: WT-flu_rep1


title: WT-flu_rep2


title: 24hr INCB059872 A H3K27ac


title: CAD FMR1KO Fmr1 rescue Soma C


title: 24hr DMSO B H3K27ac


title: 24hr DMSO A H3K27ac


title: daf1_3_b3

city: Birmignham

first: Muhan

last: Hu

address: 1900 University BLVD

department: CDIB

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 1.8.4 was used for basecalling
Fastq files were trimmed using Trim Galore! version 0.4.0 with parameters --paired --trim1
Trimmed fastq files were aligned to the reference genome using TopHat version 2.0.12 with parameters -r 150 --library-type fr-firststrand --keep-fasta-order
Transcript abundances were calculated from the alignments using Cufflinks version 2.21 with parameters --library-type fr-firststrand -g -L
Cuffmerge, Cuffquant and Cuffdiff were then used and differentially expressed genes were further analyzed
Genome_build: Ensembl WBcel235 ceWS240 Release 76
Supplementary_files_format_and_content: tab delimited Excel file containing the FPKM values for each gene for each sample

growth_protocol: Worms were synchronized at the L1 stage using the bleaching technique. L1 larva were grown on 15 cm NGM plates with extra NA 22 E. coli. Worms were grown at 16C until L4, and switched to 25C for 25hrs. Worms were washed with M9 buffer into 50mL tubes. The worms were washed with M9 until the supernatent is clear of bacteria.

extract_protocol: 250 mg of worms were extracted using Trizol

value: whole worm


title: DMSO A


title: CAD FMR1KO Fmr1 rescue Soma B


title: 24hr INCB059872 B input


title: CAD FMR1KO Fmr1 rescue Neurite B


title: CAD FMR1KO Fmr1 rescue Soma A


title: P8AT1

value: olfactory epithelium


title: daf1_3_b1


title: P8CT42

source_name: Young nasal mucosa in smoking group

value: 8 weeks


title: CAD FMR1KO Fmr1-RGG rescue Neurite C

value: FMR1 KO, Fmr1-RGG rescue


title: P8AT7


title: daf1_3_b2


title: 24hr DMSO B input


title: 24hr DMSO A input


title: CAD FMR1KO Fmr1-RGG rescue Neurite B


title: daf1_b2


title: CAD FMR1KO Fmr1-RGG rescue Soma C

value: soma


title: P8CT14


title: daf1_b3


title: CAD FMR1KO Fmr1-RGG rescue Neurite A


title: P8CT7