title: Rumen_epithelium_Early_Stage (14 months of age) 8

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.8 during the Early stage

value: Rumen epithelium

value: In vivo


title: Adjuvant paste 5 days, biological rep2

status: Public on Jun 22 2019

type: SRA

city: Porto Alegre

first: Arthur

last: Fett-Neto

state: Rio Grande do Sul

address: Av. Paulo Gama, 110 - Bairro Farroupilha

department: Center for Biotechnology

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: Gene expression data from vascular cambium of slash pine plants with stimulant paste - 5 days

library_source: transcriptomic

data_processing:
llumina HiSeq High-Output
Raw reads were filtered before data analysis. Identification of low-quality sequences, empty sequences and sequences with only one copy was done using FastQC software.
Based on these data, the Trimmomatic software version 0.32 (Bolger et al., 2014) was used to eliminate sequences of reads with a Phred quality score below 30, as well as the adapters.
Transcript abundance estimation in RPKM values and subsequent differential expression analysis were performed using the Cufflinks program version 2.1.1.
Genome_build: The filtered reads were then anchored to the reference genome of Pinus taeda (https://treegenesdb.org/Drupal) with HISAT2 2.0.4.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Pinus elliottii

source_name: Pine trees with the bark stripped and with stimulant paste (Ethrel) - 5 days

growth_protocol: In this study we used 16-year-old trees of slash pine with circumference at breast height between 65 and 90 cm. Trials were carried out at Irani Celulose forest installations at Balneário Pinhal, RS, Brazil (30◦14′S and 50◦14′W). Resin tapping and stimulant paste application followed standard commercial practices. Trees had previously been tapped for resin fortnightly during one year with conventional stimulant paste.

extract_protocol:
Total RNA of the sixteen libraries was extracted from vascular cambium of slash pine plants using Concert plant RNA reagent157 (Life Technologies). Nanodrop spectrophotometer (Thermo Scientific) was used to quantify RNA concentration. Samples were precipitated with 3 M sodium acetate, 5 mg.ml-1 glycogen and ethanol. Pellets were kept in 70 % ethanol for shipping.
Library preparation and RNA sequencing were performed with Fasteris S.A. standard protocols (single-end 1x 125 bp Illumina HiSeq High- Output) after depletion of rRNA with RiboZero kit.

treatment_protocol: Four randomly chosen trees of the internal zone of the stand were used. On the bark wound, stimulant paste (3 % of 2-chloroethylphosphonic acid (v/v) (Ethrel), a synthetic precursor of ethylene, and 20 % of sulfuric acid (v/v) was streaked right after injury. Inert components of stimulant paste included rice husk powder to promote adhesion to the wound line. In the present experiments, paste treated trees (hereafter referred to as Et) received a streak of the stimulant paste described above right after the bark stripping. Control trees (from now on referred to as C) had the bark stripped and did not receive any paste. Gene expression analyses were done with samples harvested after 5 and 15 days, obtained slightly above the wound zone, since the wound line produces poor quality RNA.

tag: tissue

value: Vascular cambium

tag: treatment

value: Adjuvant paste 5 days - Et5d


title: Adjuvant paste 5 days, biological rep1


title: Control 5 days, biological rep4

description: Gene expression data from vascular cambium of slash pine plants without stimulant paste - 5 days

source_name: Pine trees with the bark stripped and without stimulant paste - 5 days

value: Control 5 days - C5d


title: Rumen_epithelium_Early_Stage (14 months of age) 9

type: RNA

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.9 during the Early stage

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Sure Scan) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_1100_Jul11) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 200 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the peripheral neutrophil and liver tissue using Trizol reagent (Invitrogen) according to the manufacturer's instructions.

tag: experiment type


title: Control 15 days, biological rep4

description: Gene expression data from vascular cambium of slash pine plants without stimulant paste - 15 days

source_name: Pine trees with the bark stripped and without stimulant paste - 15 days

value: Control 15 days - C15d


title: 0h TNFα 2h ICRF193

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
trimmomatic SE /path/to/fastq/files.fastq -threads 8 HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
STAR --runThreadN 8 --genomeDir /path/to/starindex --readFilesIn /path/to/fastq/files.fastq --outFileNamePrefix out.fastq --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
featureCounts -t exon -T 8 -g gene_id -a /path/to/gtf/file.gtf -o /path/to/output path/to/bam/input/file.bam
bamCoverage -b /path/to/bam/files.bam -o /path/to/output.bigwig -of bigwig --binSize 10 -p 8 --normalizeUsingRPKM --smoothLength 100
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamCoverage

organism: Homo sapiens

growth_protocol: Human KB and diploid HCT116 cells were maintained in DMEM GlutaMAX(TM) (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal calf serum and 100 U/ml penicillin/streptomycin at 37 ºC in a humidiﬁed atmosphere containing 5% CO2

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany) according to the procedure described by the manufacturer.
RNA-Seq libraries were prepared from total RNA using the TruSeq Stranded total RNA LT kit (Illumina) and the further analysis was performed as published (Riedlinger FASEB; PMID: 30526044)

treatment_protocol: Cells were pre-incubated with 5 µM CPT or ICRF193 for 2h, 20 ng/ml TNFa were added additionally for 1h

tag: cell line

value: 0h TNFα 2h ICRF193


title: 0h TNFα 2h CPT

value: 0h TNFα 2h CPT


title: Control 5 days, biological rep2


title: Control 5 days, biological rep3


title: Rumen_epithelium_Early_Stage (14 months of age) 6

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.6 during the Early stage


title: LIX1L siRNA2

city: 南京

first: xiaoyun

last: zhu

address: 江苏省南京市中国药科大学

country: China

institute: China Pharmaceutical University

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

source_name: LIX1L siRNA2

extract_protocol:
LX2 cells were transfected with siControl or siLIX1L, and subsequently cultured for 48h. The total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Human hepatic stellate cell

tag: sirna


title: Rumen_epithelium_Early_Stage (14 months of age) 5

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.5 during the Early stage


title: Adjuvant paste 5 days, biological rep4


title: 0h TNFα

value: 0h TNFα


title: Control 5 days, biological rep1


title: Heart__Male__WT__rep2

city: Cambridge

first: Jordan

last: Lewandowski

state: MA

address: 7 Divinity Ave

country: USA

institute: Harvard University

description: E11.5 male heart, wildtype

data_processing:
Reads were mapped to the mm10 reference genome using TopHat v2.1.1 with Bowtie v2.2.8 and the following options: --no-coverage-search; --transcriptome-index with an index built from Gencode vM9.
Gene expression levels were estimated using Cuffdiff v2.2.1 with default options, using a reference transcriptome based on Gencode vM9.
Genome_build: mm10
Supplementary_files_format_and_content: gene_expression.txt contains per-replicate gene expression levels (FPKM). gene_exp.diff contains raw Cuffdiff output, including: gene-level expression estimates (average FPKM across replicates), log2 fold change between relevant conditions, and associated FDR values.

molecule: polyA RNA

organism: Mus musculus

source_name: Heart [male]

extract_protocol:
Tissues were harvested and immediately homogenized in TRIzol. Total RNA was isolated according to the manufacturer's protocol (RNeasy Mini, Qiagen).
Libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina). For each tissue, 500ng of total RNA was used as input, with the exception of lung (200ng) and pre-somitic mesoderm (80ng). Libraries were individually barcoded, amplified for only 10 PCR cycles to minimize artifacts, pooled into groups of six with a mix of wildtype and knockout samples, and then sequenced on an Illumina HiSeq 2500.

tag: strain

value: Heart

tag: age

tag: Sex

value: Male

tag: genotype/variation

value: wildtype


title: Heart__Male__KO__rep3

description: E11.5 male heart, Firre knockout

value: Firre knockout


title: Rumen_epithelium_Early_Stage (14 months of age) 2

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.2 during the Early stage


title: MT2

status: Public on Jun 21 2019

city: Lembah Pantai

first: Chung Kiat

last: Ng

address: Jalan Universiti

country: Malaysia

institute: University of Malaya

data_processing:
CLC Genomics Workbench version 7.5 (Assembly)
HTSeq-count (Raw count generation)
DESeq2 (Differential expression analysis)
Supplementary_files_format_and_content: tab-delimited text files include raw counts, normalized counts and expression for each sample. Differential expression file includes gene accessions and statistics.

organism: Acinetobacter baumannii

source_name: Sputum

growth_protocol: LBB, 37 °C, OD 2.75(wild type), OD 2.25(ΔabaI::Km)

extract_protocol:
Bacterial cells were harvested and RNA was stabilised with RNAprotect Bacteria Reagent. RNA was then extracted using Nucleospin RNA extraction kit
Library was constructed using ScriptSeq v2 RNA-Seq Library Prep Kit according to manufacturer's protocol

treatment_protocol: Replacement knockout of N-acylhomoserine lactone synthase gene, abaI

tag: genotype


title: WT3

value: Wild type


title: WT2


title: MT1


title: RNA-seq of test group IV E-1 of breast muscle

city: Zhengzhou

first: Donghua

last: Li

state: China

address: Wenhua Road 95, Zhengzhou City

institute: Henan Agricultural University

data_processing:
Raw reads was stored in the FastQC format. Raw reads were processed to remove adaptor sequences, low-quality reads and reads containing ploy-N from raw data by Seqtk (https://github.com/lh3/seqtk)
Genome mapping of clean reads using the spliced mapping algorithm of TopHat (version: 2.0.9), mapped to the reference genome based on the Ensemble (Galgal5)
Counting the number of Fragments per gene after Hisat2 alignment using Stringtie(version:1.3.0)
the FPKM（Fragments Per Kilobase of exon model per Million mapped reads）value of each gene was calculated using the perl script
Genome_build: (Galgal5)
Supplementary_files_format_and_content: normalized by TMM (trimmed mean of M values)

organism: Gallus gallus

source_name: breast muscle

extract_protocol:
a total of 1-2g the breast meat were frozen immediately in liquid nitrogen and stored at −80°C until for RNA-seq
The sequencing process is controlled by data collection software provided by Illumina HiSeq 2000 platform.

value: breast muscle

tag: Stage

value: 12 weeks

value: Xichuan black-bone

tag: diet

value: Tyrosine was added to basal diet by  0.8%  in test group IV


title: WT1


title: RNA-seq of control group A  of breast muscle

value: control group was fed with basal diet


title: NAc, H2O (VEH), RNA170119AO_40_S40

city: Portland

first: Angela

middle: Renee

last: Ozburn

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: OHSU

data_processing:
Real-time Basecalling was executed via an Illumina HiSeq 2500 Sequencer (Illumina, San Diego, CA, USA) with poly(A)+ stranded selection and paired-end reads at 50 cycles.
Raw FASTA files generated from sequencing were aligned to the Genome Reference Consortium Mouse Reference 38, based on the Mus musculus strain C57BL/6J (GRCm38). Base call quality was assessed using FastQC (Andrews S., 2010) and alignment was run using STAR: ultrafast universal RNA-seq aligner (Dobin et al., 2013) (version: 2.6.0) where paired-end reads were specified, the maximum number of mismatches per pair was indicated as 3 and maximum number of multiple alignments allowed per read was indicated as 1.
Processed Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were generated using HTSeq (version 0.9.1) (S Anders, T P Pyl, W Huber et al., 2014) against the Encode vM4 annotation with paired-end read order specification.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample generated via HTSeq.

source_name: brain tissue

extract_protocol:
NAc tissue punches were mechanically homogenized in PureZol and the RNA was isolated using the Aurum Total RNA Fatty and Fibrous Tissue kit (Bio-Rad Laboratories, Inc., Hercules, CA).
RNA samples (500 ng) were sent to the Massively Parallel Sequencing Shared Resource (MPSSR) at OHSU for quality assessment (via 2100 BioAnalyzer, Agilent Technologies, Palo Alto, CA). The library was prepared using the Illumina TruSeq RNA-Seq Library Protocol and quality checks were performed.

treatment_protocol: Female HDID-1 mice (S35.G37) were stereotaxically injected with 0.5uL rAAV2/5-CMV-Cre-GFP and 0.5uL rAAV2-hSyn-DIO-hM3Dq-mCherry bilaterally into the NAc (from bregma, in mm: angle 10°, AP +1.34, Lat +1.5, DV -4.5). AAV titers were 4-8x10^12 vg and were purchased from the University of North Carolina Viral Vector Core (Cre) and Add Gene (DIO constructs). Mice were individually housed and habituated to novel sipper tubes one week prior to DID. The DID experiment was carried out daily for 6 weeks. Mice were serially treated with vehicle prior to DID during week 1 to establish baseline drinking, CNO (1mg/kg) during weeks 2-5 to measure the effects of chronic treatment, and then mice were treated with vehicle again during week 6 to determine if there were any lasting effects of chronic CNO treatment. In this experiment, there were 2 fluid groups (water or ethanol) and 2 treatment groups (VEH/VEH/VEH or VEH/CNO/VEH).

tag: mouse number

value: female

tag: selection generation

value: nucleus accumbens

tag: fluid(treatment)

value: H2O (VEH)


title: Rumen_epithelium_Early_Stage (14 months of age) 1

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.1 during the Early stage

source_name: Rumen_epithelium_Early_Stage (14 months of age) (14 months of age)

value: Rumen epithelium

value: In vivo


title: NAc, H2O (VEH), RNA170119AO_41_S45


title: NAc, H2O (VEH), RNA170119AO_44_S18


title: NAc, H2O (VEH), RNA170119AO_39_S35


title: NAc, H2O (VEH), RNA170119AO_29_S11


title: MT3


title: NAc, H2O (VEH), RNA170119AO_28_S5


title: NAc, H2O (VEH), RNA170119AO_34_S23


title: NAc, H2O (VEH), RNA170119AO_30_S17


title: NAc, H2O (VEH), RNA170119AO_45_S24


title: NAc, H2O (VEH), RNA170119AO_35_S29


title: NAc, H2O (CNO), RNA170119AO_42_S6

value: H2O (CNO)


title: Rumen_epithelium_Early_Stage (14 months of age) 3

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.3 during the Early stage


title: NAc, H2O (CNO), RNA170119AO_43_S12


title: NAc, H2O (CNO), RNA170119AO_38_S44


title: NAc, H2O (CNO), RNA170119AO_36_S39


title: NAc, H2O (CNO), RNA170119AO_33_S34


title: NAc, H2O (VEH), RNA170119AO_46_S30


title: Rumen_epithelium_Early_Stage (14 months of age) 4

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.4 during the Early stage


title: NAc, H2O (CNO), RNA170119AO_26_S10


title: NAc, H2O (CNO), RNA170119AO_25_S4


title: NAc, H2O (CNO), RNA170119AO_31_S22


title: NAc, EtOH (VEH), RNA170119AO_4_S2

value: EtOH (VEH)


title: NAc, EtOH (VEH), RNA170119AO_5_S8


title: NAc, EtOH (VEH), RNA170119AO_6_S14


title: NAc, EtOH (VEH), RNA170119AO_24_S38


title: NAc, H2O (CNO), RNA170119AO_27_S16


title: NAc, EtOH (VEH), RNA170119AO_16_S37


title: NAc, EtOH (VEH), RNA170119AO_11_S26


title: NAc, EtOH (VEH), RNA170119AO_12_S32


title: NAc, H2O (CNO), RNA170119AO_37_S43


title: NAc, EtOH (CNO), RNA170119AO_8_S25

value: EtOH (CNO)


title: NAc, EtOH (CNO), RNA170119AO_9_S31


title: NAc, EtOH (CNO), RNA170119AO_7_S19


title: NAc, EtOH (CNO), RNA170119AO_3_S13


title: NAc, EtOH (CNO), RNA170119AO_20_S21


title: NAc, EtOH (VEH), RNA170119AO_10_S20


title: NAc, EtOH (CNO), RNA170119AO_2_S7


title: NAc, EtOH (CNO), RNA170119AO_19_S15


title: Adjuvant paste 15 days, biological rep2

description: Gene expression data from vascular cambium of slash pine plants with stimulant paste - 15 days

source_name: Pine trees with the bark stripped and with stimulant paste (Ethrel) - 15 days

value: Vascular cambium

value: Adjuvant paste 15 days - Et15d


title: NAc, EtOH (CNO), RNA170119AO_21_S27


title: NAc, EtOH (CNO), RNA170119AO_15_S3


title: NAc, H2O (CNO), RNA170119AO_32_S28


title: NAc, EtOH (CNO), RNA170119AO_14_S41


title: NAc, EtOH (CNO), RNA170119AO_13_S36


title: NAc, EtOH (CNO), RNA170119AO_1_S1


title: NAc, EtOH (VEH), RNA170119AO_18_S9


title: NAc, EtOH (VEH), RNA170119AO_17_S42


title: NAc, EtOH (VEH), RNA170119AO_22_S33


title: WT_Ar_rep2

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Align to mm10 reference genome using bowtie 2.3.4
Peak calling to generate signal tracks on individual repicates using MACS2 2.1.0.20151222 with options -B -p 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Coverage track in bigWig format

molecule: genomic DNA

source_name: primary mouse prostate organoid culture

growth_protocol: Freshly sorted cells carrying pCW constructs (dsRED+) were seeded in duplicate per infected construct at the start of the assay, and moving forward, replicates were processed independently, collected following 5 days of doxycycline treatment.

extract_protocol:
At time of collection, cells were trypsinzed, and 70,000 cells (counted by using trypan blue exclusion) were processed for ChIP-sequencing as follows.  Cells were fixed with formaldehyde (1%) and reaction was quenched with Glycine 1.25M and Tris 1M pH8.  Fixed cells were lysed with SDS lysis solution containing protease inhibitors. Re-suspended pellets were sonicated, precipitated with antibodies (anti-FoxA1 Novus, AR and FLAG) and protein A/G bead complex. The chromatin and immune-complex were sequentially washed with a low-salt solution, high-salt solution, LiCl solution and Tris-NaCl solution. Chromatin was eluted from the complex with a solution containing 1% of SDS and 0.1 mol/l of NaHCO3. Cross-linking between DNA and protein was reversed by adding NaCl solution and incubating at 65°C over-night.
Libraries were made using NEBNext Ultra II DNA library prep kit for Illumina (NEB E7645L).  Quality control was performed with Bioanalyzer 2200 (Agilent technologies, D1000 screentapes & reagents, cat# 5067-5582) to assess size range of amplified DNA fragments, and with Quant-iT™ PicoGreen™ dsDNA Assay Kit (Thermofisher cat# P11496) to quantify the DNA fragments generated. ChIP Libraries were then pooled at equimolar concentration and were sequenced multiplexed on the Illumina HiSeq with 50bp paired-end sequencing.

treatment_protocol: Organoids treated with doxycycline (dox) (500ng/mL) to induce expression of the FOXA1-2A-DsRED fusion

value: primary mouse prostate organoid culture

value: overexpression of Foxa1 WT

tag: chip antibody

value: AR Antibody (ER179(2), Abcam)


title: WT_Foxa1_rep1

tag: tissue

value: HNF-3 alpha/FoxA1 Antibody (3B3NB) (Novus Biologicals)


title: WT_Input


title: R219S_Ar_rep2

value: overexpression of Foxa1 R219S


title: FE255del_Input

value: overexpression of Foxa1 FE255del


title: R219S_Foxa1_rep1


title: R219S_Input


title: WT_Ar_rep1


title: EV_Input

value: empty vehicle


title: FE255del_Ar_rep2


title: EV_Foxa1_rep2


title: FE255del_Ar_rep1


title: R219S_Ar_rep1


title: EV_Ar_rep2


title: FE255del_Foxa1_rep2


title: EV_Foxa1_rep1


title: RNA-Seq Day11_R219S_rep3

data_processing:
Align to mm10 and GENCODE vM2 using STAR v2.4.2a
Gene quantification by featureCounts v1.4.3
Genome_build: mm10
Supplementary_files_format_and_content: Gene quantification count in txt format

growth_protocol: Freshly sorted cells carrying pCW constructs (dsRED+) were seeded in triplicate per infected construct at the start of the assay, and moving forward, replicates were processed independently, collected at the appropriate time points.

extract_protocol:
RNA was extracted from organoids using an RNeasy Kit (Qiagen). Freshly sorted dsRED+ cells were seeded in triplicate per infected construct at the start of the assay, and moving forward, replicates were processed independently, collected at the appropriate time points.
RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit in accordance with the manufacturer’s instructions.

tag: time point

value: Day 11

value: Foxa1 R219S


title: RNA-Seq Day11_FE255del_rep2

value: Foxa1 FE255del


title: RNA-Seq Day11_FE255del_rep3


title: RNA-Seq Day11_R219S_rep1


title: RNA-Seq Day11_R219S_rep2


title: WT_Foxa1_rep2


title: RNA-Seq Day11_WT_rep3

value: wild type


title: R219S_Foxa1_rep2


title: RNA-Seq Day11_EV_rep3


title: RNA-Seq Day11_WT_rep1


title: RNA-Seq Day11_WT_rep2


title: RNA-Seq Day11_FE255del_rep1


title: RNA-Seq Day11_EV_rep2


title: RNA-Seq Day11_EV_rep1


title: EV_Ar_rep1


title: RNA-Seq Day1_R219S_rep3

value: Day 1


title: RNA-Seq Day1_R219S_rep2


title: RNA-Seq Day1_FE255del_rep3


title: RNA-Seq Day1_R219S_rep1


title: RNA-Seq Day1_WT_rep1


title: RNA-Seq Day1_EV_rep3


title: RNA-Seq Day1_EV_rep2


title: RNA-Seq Day1_FE255del_rep2


title: RNA-Seq Day1_EV_rep1


title: RNA-Seq Day0_R219S_rep3

value: Day 0


title: RNA-Seq Day1_WT_rep2


title: RNA-Seq Day1_WT_rep3


title: RNA-Seq Day0_R219S_rep2


title: FE255del_Foxa1_rep1


title: RNA-Seq Day0_R219S_rep1


title: RNA-Seq Day0_WT_rep3


title: RNA-Seq Day0_FE255del_rep2


title: RNA-Seq Day0_FE255del_rep1


title: RNA-Seq Day0_WT_rep1


title: RNA-Seq Day0_WT_rep2


title: RNA-Seq Day0_EV_rep3


title: RNA-Seq Day0_EV_rep1


title: RNA-Seq Day0_EV_rep2


title: RNA-Seq Day1_FE255del_rep1


title: RNA-Seq Day0_FE255del_rep3


title: Day5_WT_rep1

data_processing:
Align to mm10 reference genome using bowtie 2.3.4.1
Peak calling to generate signal tracks on individual replicates using macs2 2.1.1.20160309 with options -p 1e-2 --shift 0 --extsize 76
Genome_build: mm10
Supplementary_files_format_and_content: Coverage track in bigWig format

extract_protocol:
At time of collection, cells were trypsinzed, and 50,000 cells (counted by using trypan blue exclusion) were processed for ATAC-sequencing as follows.  After a wash step in cold Cell Wash Buffer (CWB= 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2), outer membranes were disrupted in lysis buffer (CWB + 0.1% NP40) for 2min on ice. Lysis reaction was stopped with the addition of 1ml of CWB. After a centrifugation step 1,500g for 10min, pelleted nuclei are kept for the next step.
In a 50μl final volume, tagmentation was performed for 30min at 37C, using the kit Nextera DNA library prep kit (Illumina cat# FC-121-1030). After addition of SDS 0.2% final concentration, DNA is purified in AMPure XP beads (Beckman Coulter cat# A63881) using a ratio 2:1 (V/V) beads:tagmented DNA.Freshly eluted DNA was barcoded and amplified in 110μl PCR volume (NEB Next Q5 Hot Start HiFi PCR, cat# M0543L) to generate library with the following PCR program: 65C, 5min, 98C, 30sec, (98C, 10sec – 65C, 30sec) *11cycles, 4C hold.

value: Day 5

tag: sgrna


title: Day5_EV_rep3


title: Day5_R219S_rep3


title: Day5_R219S_rep2


title: Day5_R219S_rep1


title: Day5_FE255del_rep1


title: Day5_FE255del_rep3


title: Day5_EV_rep2


title: Day5_FE255del_rep2


title: Day5_WT_rep3


title: Day5_EV_rep1


title: Day5_sgFOXA1_2_rep3

value: sgRNA_FOXA1 2


title: Day5_WT_rep2


title: Day5_sgFOXA1_1_rep3

value: sgRNA_FOXA1 1


title: Day5_sgFOXA1_2_rep2


title: Day5_sgFOXA1_2_rep1


title: Day5_sgFOXA1_1_rep2


title: Day5_sgNT_rep3


title: Day1_FE255del_rep3


title: Day1_WT_rep3


title: Day1_R219S_rep1


title: Day5_sgNT_rep1


title: Day5_sgNT_rep2


title: Day1_R219S_rep2


title: Day5_sgFOXA1_1_rep1


title: Day1_WT_rep2


title: Day1_R219S_rep3


title: Day1_EV_rep3


title: Day1_EV_rep2


title: Day0_R219S_rep1


title: Day0_WT_rep1


title: Day0_FE255del_rep1


title: Day0_EV_rep3


title: Day0_EV_rep2


title: Day0_FE255del_rep3


title: Day1_FE255del_rep1


title: Day1_EV_rep1


title: Day0_R219S_rep3


title: Day0_R219S_rep2


title: Day0_FE255del_rep2


title: Day1_FE255del_rep2


title: Day0_EV_rep1


title: UL_P5_1 [RNA-Seq]

city: Bethesda

first: Whitney

middle: E

last: Heavner

state: MD

address: Building 35 Rm 2B-203

department: NINDS

institute: National Institutes of Health

data_processing:
100bp paired-end sequencing was performed on an Illumina Hi-Seq 2500
Sequenced reads were psuedo-aligned to mm9 using Kallisto version 0.43.1 (Bray et al. 2016)
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated values files contain the Ensembl transcript (target_id), the length of the transcript, a corrected length that accounts for sequencing bias (eff_length), the number of reads that align to the transcript (est_counts), and the proportion of the transcript in the library represented as transcripts per million (TPM)

source_name: Neocortex

extract_protocol:
For deep layer neurons, mice expressing the Golli-GFP transgene were used. For upper layer neurons, a birth-dating plasmid expressing Cdk5r promoter-GFP was introduced into the neocortex using in utero electroporation at E15.5, during the peak of upper layer neurogenesis. Neocortex was micro-dissected from the embryonic brain and kept on ice. A total of 2-8 embryos were used per replicate. Cells were dissociated in papain, and GFP-positive cells were purified using FACS. Cells were sorted into micro-centrifuge tubes containing neurobasal/DMEM-based cell culture medium and kept cold. Total RNA was extracted using a Qiagen RNeasy Micro kit. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2101) was used with a minimum of 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neocortex

tag: developmental stage

value: Postnatal day 5

tag: reporter

value: Cdk5r-GFP electroporated at E15.5


title: Day0_WT_rep2

value: primary mouse prostate organoid culture


title: UL_P1_3 [RNA-Seq]

value: Postnatal day 1


title: WT-Saline rep2

city: Dresden

first: Lan-Sun

last: Chen

address: Fetscherstraße 74

institute: TU Dresden

data_processing:
Raw reads in fastq format were trimmed using trim-galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the mouse genome, mm10, using HISAT2 (Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements.) with default parameters. htseq-count (Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data.) was used to assign reads to exons thus eventually getting counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read counts and log2foldchange

source_name: Adrenal gland

extract_protocol:
Adrenal gland were collected from WT mice after 3 hours of saline or LPS administration. Assoaciated fat or connective tissues were removed and total RNA were isolated with Rneasy Plus Mini Kit (QIAGEN; Hilden, Germany), according to manufacturer's instruction.
After verification of RNA integrity by 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany), RNA was subjected to the amplification workflow of the SMARTer Ultra HV v2 kit (Takara Bio Europe SAS, Saint-Germain-en-Laye, France). Amplified cDNA was successively converted into short read sequencing libraries using the NEBnext Ultra DNA library preparation chemistry (New England Biolabs, Frankfurt am Main, Germany). Libraries were equimolarly pooled and sequenced on an Illumina HiSeq 2500, resulting in ∼30 million single end reads per library in the Deep Sequencing Group, BIOTEC/Center for Regenerative Therapies Dresden.

value: Adrenal gland

value: 8 weeks

value: WT

tag: agent

value: saline


title: UL_P5_2 [RNA-Seq]

tag: strain


title: WT-Saline rep1

tag: age


title: Day1_WT_rep1


title: Day0_WT_rep3


title: WT-LPS rep1

value: LPS


title: WT-Saline rep3


title: UL_P1_1 [RNA-Seq]


title: UL_E17_2 [RNA-Seq]

value: Embryonic day 17.5


title: UL_E17_1 [RNA-Seq]


title: DL_E18_2 [RNA-Seq]

value: Embryonic day 18.5

value: Golli-GFP


title: DL_E16_1 [RNA-Seq]

value: Embryonic day 16.5


title: DL_E13_2 [RNA-Seq]

value: Embryonic day 13.5


title: DL_E13_1 [RNA-Seq]


title: DL_E16_2 [RNA-Seq]


title: DL_E18_1 [RNA-Seq]


title: UL_P5_2

data_processing:
100bp paired-end sequencing was performed on an Illumina Hi-Seq 2500
Sequenced reads were processed as follows: Adapters were trimmed using cutadapt and aligned to mm9 using Bowtie2. Duplicate reads were removed using the Picard (version 1.14.0) MarkDuplicates tool. Peaks were called using macs2 version 2.1.0 with the following subcommands: -p 1e-2 (p-value threshold of 1e-2), —nomodel —shift 75 (shift ends 75 bp in the 5’ direction), —keep-dup all (keep all tags at the same location), —call-summits (deconvolve subpeaks representing adjacent binding events)
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing four columns: chromosome number, peak start location, peak end location, peak name

extract_protocol:
For deep layer neurons, mice expressing the Golli-GFP transgene were used. For upper layer neurons, a birth-dating plasmid expressing Cdk5r promoter-GFP was introduced into the neocortex by in utero electroporation at E15.5, during the peak of upper layer neurogenesis. Neocortex was micro-dissected from the embryonic brain and kept on ice. A total of 2-8 embryos were used per replicate. Cells were dissociated in papain, and GFP-positive cells were purified using FACS. 2.5 x 10^5 - 5 x 10^5 cells per sample were sorted into micro-centrifuge tubes containing neurobasal/DMEM-based cell culture medium and kept cold. Cells were then washed once in PBS and resuspended in cold lysis buffer. Nuclei were then pelleted by centrifugation for 10 minutes at 4 degrees C. Nuclei were washed again in PBS, then incubated in Tn5 transposition reaction mix for 30 minutes at 37 degrees C. DNA was purified using a Qiagen MinElute kit.
ATACseq libraries were prepared for sequencing using standard protocols (Buenrostro et al. 2013). Briefly, transposed and purified DNA was amplified over 12 cycles of PCR using NEBNext High Fidelity PCR Master Mix (New England Biolabs M0451S). Libraries were then purified using a Qiagen PCR purification kit, and residual primers were removed using AMPure XP Beads (Beckman Coulter/Fisher NC9959336).


title: UL_P1_3


title: WT-LPS rep2


title: UL_P1_1


title: UL_E17_2


title: UL_P5_1


title: NTO, control, Rep 4

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  Samples from the five exposure replicates were hybridized to microarrays in a completely randomized design using a random number generator.  The microarray experiments included the following exposure concentrations of NTO (control (0), 192, 383, 720 mg/L).   Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software, version 10.7.3.1 (Agilent Technologies).  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.9 (Agilent Technologies). GeneSpring was also used to conduct statistical analyses to identify differentially expressed transcripts (DET) among treatments.  Specifically, one-way ANOVA (p = 0.01) was conducted for the NTO exposure to identify transcripts having significant differential expression where SNK pairwise comparisons with fold change cutoff of ≥ 1.5 was used to discern differences relative to the control.

organism: Pimephales promelas

source_name: whole testes

label_protocol: The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 80 ng of total RNA was used as the starting material for each exposure replicate.

growth_protocol: Exposures were performed in 7.6 L glass fish tanks with a test solution volume of 6.0 L following ASTM general guidance (ASTM 2014).  Partial water renewals were conducted thrice weekly on Mondays, Wednesdays and Fridays by removing and replacing 3.0 L of exposure solution.  Fish were fed Tetramin (Tetra U.S., Blacksburg, VA) fish food daily.  On water renewal days, food was added after renewals were performed.

extract_protocol: Each testis was homogenized in lysis buffer using a Kimble™ Kontes™ Pellet Pestle™ (DWK Life Sciences, Rockwood, TN)  before RNA isolation with RNeasy kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number > 8.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0.  If two samples were available that met RNA integrity standards within each exposure replicate, the samples were pooled.  Otherwise, RNA from a single fish contributed to the exposure replicate.  Overall, 24 of the 31 exposure replicates contained RNA from two individual testes samples, the rest contained RNA from a single testis sample.

treatment_protocol: Two fish were exposed in each tank to NTO at 0 (control), 94, 192, 383, 720 mg/L (measured concentrations) where each experimental treatment included 5 replicate tanks.  All fish surviving until the conclusion of the 21d assay were euthanized by immersion in an overdose solution of MS-222 (300 mg/L) for at least 10 minutes after cessation of movement.  After euthanasia, each fish was weighed (g) and then necropsied where one testis was fixed in 10% neutral-buffered formalin for histopathological evaluation and the other fixed for transcriptomics by flash freezing in liquid nitrogen.

value: adult

tag: gender

value: male


title: NTO, 720 mg/l, Rep 5


title: NTO, control, Rep 2


title: DL_E18_1

value: Neocortex


title: NTO, control, Rep 1


title: NTO, control, Rep 3


title: DL_E18_2


title: UL_E17_1


title: DL_E16_2


title: DL_E16_1


title: DL_E13_1


title: DL_E13_2


title: NTO, control, Rep 5


title: WT-LPS rep3

tag: genotype/variation


title: RNA_siP_2

city: Galveston

first: Rafael

last: Kroon Campos

state: TX

address: 11th street and mechanic

institute: UTMB

description: Total RNA

data_processing:
RNA-seq and footprinting reads were jointly mapped to the human transcriptome and DENV genome using the riboviz pipeline.
Sequencing adapters were trimmed from reads using Cutadapt 1.10 using parameters ‐‐trim-n -O 1 ‐‐minimum-length 5.
Trimmed reads that aligned to human/mouse rRNA were removed using HISAT2 version 2.1.0. Remaining reads were mapped to a set of 19,192 principal transcripts for each gene in the APPRIS database using HISAT2. Only reads that mapped uniquely were used for all downstream analyses. For genes with multiple principal transcripts, the first one in the list was chosen. Codes for selecting these transcripts were obtained from the riboviz package (https://github.com/shahpr/riboviz). We restricted analyses to genes with at least one data set (RNA-seq or footprinting across conditions) with 64 mapped reads, and genes with 0 read counts in any data set were ignored unless the mean read counts across all twelve data sets were >64.
Genome_build: Human transcriptome and Dengue 2 (New Guinea C) genome
Supplementary_files_format_and_content: Excel file containing the TPM values for viral RNA and each cellular mRNA.

source_name: RPLP1 and RPLP2 depleted A549 cells infected with DENV.

growth_protocol: Cells were grown in DMEM supplemented with 10% fetal bovine serum, non-essential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
A549 cells were plated at 1.5 x 106 cells per 10 cm dish. Three 10cm dishes were transfected with NSC siRNA whereas three other dishes were transfected with either siP1_1, siP2_1 or siP2_4 siRNAs as described in the transfections section. 48 h later cells were infected as described previously with DENV-2 (NGC strain) at MOI of 10 in a total volume of 10 ml, rocked every 15 minutes for 1 h and the infection was allowed to proceed for more 1.5 h (2.5 h total time). Cells were then flash frozen in liquid nitrogen without cycloheximide pretreatment and cold lysis buffer containing CHX was used to lyse the cells on ice. The RIBOseq strategy was adapted from Ingolia and colleagues with a few modifications described next. After nuclease digestion, samples were run in a polysome gradient and the ribosome fractions were collected. As described by Reid and colleagues, fractions were extracted using Trizol LS (Thermo Fisher Scientific), and rRNAs were removed using the Ribo-Zero gold rRNA removal kit (Illumina, San Diego CA) according to the manufacturer's protocol.
For adapter ligation and library building we used NEBNext Small RNA Library Prep Set (Illumina).

tag: cell type

tag: sirna

tag: viral strain

value: Dengue 2, strain New Guinea C

tag: sample treatment

value: RNA seq


title: RNA_siP_3

description: Total RNA


title: NTO, 383 mg/l, Rep 3


title: NTO, 383 mg/l, Rep 2


title: NTO, 383 mg/l, Rep 1


title: RNA_NSC_1

description: Total RNA

value: Control


title: RNA_NSC_2

description: Total RNA


title: NTO, 383 mg/l, Rep 5


title: NTO, 720 mg/l, Rep 3


title: NTO, 720 mg/l, Rep 1


title: NTO, 720 mg/l, Rep 4


title: NTO, 192mg/l, Rep 4


title: myc_3

first: Erika

last: Bach

department: Biochemistry and Molecular Pharmacology

institute: NYU Grossman School of Medicine

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software
Sequencing reads were mapped to the reference genome (dm6/BDGP6) using the splice-aware STAR aligner
PCR duplicates were removed using the Picard toolkit
HTSeq package was used to generate counts for each gene based on how many aligned reads overlap its exon
The DESeq2 package in the R statistical programming environment was utilized to differential expression using negative binomial generalized linear models
The mean read insert sizes and their standard deviations were calculated using Picard tools
Genome_build: dm6/BDGP6
Supplementary_files_format_and_content: CSV file containing normalized matrix of read counts which includes values for all features and all samples

organism: Drosophila melanogaster

source_name: wing imaginal discs

growth_protocol: We crossed dpp-gal4, UAS-gfp/TM6B, Tb to UAS-hop or to UAS-myc. We dissect from non-Tb larvae at least 60 third instar wing discs per genotype in triplicates.

extract_protocol:
The cells were dissociated and the GFP-positive cells were sorted by the Cytometry and Cell Sorting Core at NYU Langone Medical Center using a Sony SY3200 cell sorter per the protocol described in (de la Cruz and Edgar 2008). The sorted cells represent GFP-positive control cells from the dpp domain (referred to as “GFP” samples), GFP-positive cells from the dpp domain that had ectopic JAK/STAT signaling as a result of mis-expressing Hop (referred to as “Hop” samples) or GFP-positive cells from the dpp domain that had elevated Myc levels as a result of mis-expressing Myc (referred to as “Myc” samples). RNA was isolated from the sorted cells using TRIzol reagent (Ambion) and then purified using RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.
The RNA sequencing was performed by the Genome Technology Center at the NYU Langone Medical Center using Illumina HiSeq2500 Paired-End 50 Cycle Flow Cell.

tag: expression domain

value: FACS-sorted cells from the dpp expression domain

value: wandering third instar

tag: genotype

value: w/+; +/+; dpp-gal4, uas-gfp/uas-myc


title: RNA_siP_1

description: Total RNA


title: myc_2


title: Ribo_siP_2

description: RNA (footprint)

value: Ribo seq


title: Ribo_NSC_3

description: RNA (footprint)


title: NTO, 192mg/l, Rep 5


title: NTO, 720 mg/l, Rep 2


title: hop_2

value: w/+; +/+; dpp-gal4, uas-gfp/uas-hop


title: NTO, 383 mg/l, Rep 4


title: NTO, 192mg/l, Rep 2


title: hop_1


title: NTO, 192mg/l, Rep 3


title: hop_3


title: Ribo_siP_1

description: RNA (footprint)


title: myc_1


title: Ribo_siP_3

description: RNA (footprint)


title: gfp_3

value: w/+; +/+; dpp-gal4, uas-gfp/+


title: Ribo_NSC_2

description: RNA (footprint)


title: Ribo_NSC_1

description: RNA (footprint)


title: RNA_NSC_3

description: Total RNA


title: gfp_2


title: NTO, 192mg/l, Rep 1


title: DC32RnosgnoIFN-121418_S13

city: Worcester

first: Pranitha

last: Vangala

address: 55 Lake Avenue North

institute: University of Massachussets Medical School

description:
DC32RnosgnoIFN-rep2_S13
processed data file: rsem.all.TPM.tsv

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rsem.all.TPM.tsv: Tab-delimited text file includes TPM values for each Sample.

source_name: DC3.2 dendritic cell line

extract_protocol:
RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: DC3.2 lines harvested after 2 hours of stimulating with 5,000U/mL IFNα, 2ng/mL IFNγ, or media alone.

tag: cell line

value: Dendritic cell line


title: CEL245

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

description:
treatment to delivery interval: 5 days
run0164_lane91_read_indexD708-D508=Rh24517Hippocampus

data_processing:
Alignment to the MMUL8.01 done with Bowtie2
Read counts was done using FeatureCounts
Differential expression analysis was performed with EdgeR
Genome_build: MMUL8.01
Supplementary_files_format_and_content: counts

organism: Macaca mulatta

extract_protocol:
total RNA was extracted with Trizol per manufacturer's guidelines.
Afer polyA selection, paired-end RNA-sequencing with 75bp was done with a depth of 30M reads.

tag: gestational age

value: 131 days

tag: treatment

value: Betamethasone-acetate

tag: dose

tag: tissue

value: Hippocampus


title: CEL238

description:
treatment to delivery interval: 5 days
run0164_lane91_read_indexD704-D501=Rh23817Hippocampus

value: 132 days


title: DC32RnosgnoIFN-121118_S1

description:
DC32RnosgnoIFN-rep1_S1
processed data file: rsem.all.TPM.tsv


title: DC32RnosgIFNa-121418_S17

description:
DC32RnosgIFNa-rep2_S17
processed data file: rsem.all.TPM.tsv


title: CEL120

description:
treatment to delivery interval: 5 days
run1630_lane12_read_indexD703-D505=Hip16-120

value: 133 days


title: DC32RnosgIFNy-121418_S21

description:
DC32RnosgIFNy-rep2_S21
processed data file: rsem.all.TPM.tsv


title: CEL126

description:
treatment to delivery interval: 5 days
run1630_lane12_read_indexD704-D504=Hip16-126


title: CEL115

description:
treatment to delivery interval: 5 days
run1630_lane12_read_indexD702-D506=Hip16-115

value: 136 days


title: DC32RIRF2sgnoIFN-121418_S15

description:
DC32RIRF2sgnoIFN-rep2_S15
processed data file: rsem.all.TPM.tsv


title: BAC237

description:
treatment to delivery interval: 5 days
run0164_lane91_read_indexD703-D502=Rh23717Hippocampus


title: BAC136

description:
treatment to delivery interval: 5 days
run1630_lane12_read_indexD707-D501=Hip16-136


title: DC32RIRF2sgIFNy-121418_S23

description:
DC32RIRF2sgIFNy-rep2_S23
processed data file: rsem.all.TPM.tsv


title: DC32RIRF2sgIFNy-121118_S11

description:
DC32RIRF2sgIFNy-rep1_S11
processed data file: rsem.all.TPM.tsv


title: BAC130

description:
treatment to delivery interval: 5 days
run1630_lane12_read_indexD706-D502=Hip16-130


title: DC32RIRF2sgnoIFN-121118_S3

description:
DC32RIRF2sgnoIFN-rep1_S3
processed data file: rsem.all.TPM.tsv


title: DC32RnosgIFNa-121118_S5

description:
DC32RnosgIFNa-rep1_S5
processed data file: rsem.all.TPM.tsv


title: BAC128

description:
treatment to delivery interval: 5 days
run1630_lane12_read_indexD705-D503=Hip16-128


title: CTL212

description:
treatment to delivery interval: 5 days
run0164_lane91_read_indexD710-D507=Rh21217Hippocampus

value: 130 days

value: Saline


title: CTL209

description:
treatment to delivery interval: 5 days
run0162_lane91_read_indexD705-D501=Rh20917Hippocampus

value: 135 days


title: DC32RIRF1sgnoIFN-121418_S14

description:
DC32RIRF1sgnoIFN-rep2_S14
processed data file: rsem.all.TPM.tsv


title: CTL113

description:
treatment to delivery interval: 5 days
run1630_lane12_read2_indexD701-D507=Hip16-113


title: DC32RIRF2sgIFNa-121118_S7

description:
DC32RIRF2sgIFNa-rep1_S7
processed data file: rsem.all.TPM.tsv


title: DC32RIRF1sgnoIFN-121118_S2

description:
DC32RIRF1sgnoIFN-rep1_S2
processed data file: rsem.all.TPM.tsv


title: gfp_1

tag: developmental stage


title: CTL101

description:
treatment to delivery interval: 5 days
run0024_lane92_read_indexD710-D503=Hip-15-101


title: DC32RnosgIFNy-121118_S9

description:
DC32RnosgIFNy-rep1_S9
processed data file: rsem.all.TPM.tsv


title: DC32RIRF1sgIFNy-121118_S10

description:
DC32RIRF1sgIFNy-rep1_S10
processed data file: rsem.all.TPM.tsv


title: BAC235

description:
treatment to delivery interval: 5 days
run0164_lane91_read_indexD702-D503=Rh23517Hippocampus


title: CTL092

description:
treatment to delivery interval: 5 days
run0024_lane92_read_indexD710-D506=Hip-15-92


title: DC32RDKOnoIFN-121118_S4

description:
DC32RDKOnoIFN-rep1_S4
processed data file: rsem.all.TPM.tsv


title: DC32RDKOnoIFN-121418_S16

description:
DC32RDKOnoIFN-rep2_S16
processed data file: rsem.all.TPM.tsv


title: DC32RIRF1sgIFNa-121118_S6

description:
DC32RIRF1sgIFNa-rep1_S6
processed data file: rsem.all.TPM.tsv


title: DC32RIRF2sgIFNa-121418_S19

description:
DC32RIRF2sgIFNa-rep2_S19
processed data file: rsem.all.TPM.tsv


title: DC32RIRF1sgIFNa-121418_S18

description:
DC32RIRF1sgIFNa-rep2_S18
processed data file: rsem.all.TPM.tsv


title: 16-136

description:
IM Betamethasone-acetate 0.125mg/kg - delivery after 5d
processed data file: counts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mmul1.0 whole genome using bowtie v1.2.1.1.
Read counts were calculated using featurecounts v1.5.1, using the following parameters -pBC -T 4 -a.
Genome_build: mmul1.0
Supplementary_files_format_and_content: counts.csv: Comma-separated values with count number per genes was generated for each sample.

source_name: Lung

growth_protocol: Time-dated pregnant rhesus macaques.

extract_protocol:
Lungs were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Intramuscular injection with saline or corticosteroids.

value: wild type

value: lung

value: gestational day 124-130

value: IM Betamethasone-acetate 0.125mg/kg

tag: time point


title: 16-126

description:
IM Celestone 0.25mg/kg - delivery after 5d
processed data file: counts.csv

value: IM Celestone 0.25mg/kg


title: 16-130


title: 16-128


title: DC32RDKOIFNa-121118_S8

description:
DC32RDKOIFNa-rep1_S8
processed data file: rsem.all.TPM.tsv


title: 16-120


title: DC32RDKOIFNy-121118_S12

description:
DC32RDKOIFNy-rep1_S12
processed data file: rsem.all.TPM.tsv


title: 16-123

description:
IM Betamethasone-acetate 0.125mg/kg - delivery after 6h
processed data file: counts.csv


title: Dc3.2_Irf2KO_2h_LPS

description:
Dc3.2_Irf2KO_2h_LPS
processed data file: rsem.all.TPM.tsv


title: DC32RDKOIFNa-121418_S20

description:
DC32RDKOIFNa-rep2_S20
processed data file: rsem.all.TPM.tsv


title: Dc3.2_Irf2KO_2h_IFNa

description:
Dc3.2_Irf2KO_2h_IFNa
processed data file: rsem.all.TPM.tsv


title: 16-115


title: Dc3.2_Irf2KO_0h

description:
Dc3.2_Irf2KO_0h
processed data file: rsem.all.TPM.tsv


title: DC32RIRF1sgIFNy-121418_S22

description:
DC32RIRF1sgIFNy-rep2_S22
processed data file: rsem.all.TPM.tsv


title: DC32RDKOIFNy-121418_S24

description:
DC32RDKOIFNy-rep2_S24
processed data file: rsem.all.TPM.tsv


title: 15-101

description:
IM Saline treatment
processed data file: counts.csv

value: IM Saline


title: 16-113


title: 15-97

description:
IM Celestone 0.25mg/kg - delivery after 4h
processed data file: counts.csv


title: Dc3.2_2h_LPS

description:
Dc3.2_2h_LPS
processed data file: rsem.all.TPM.tsv


title: Dc3.2_2h_IFNa

description:
Dc3.2_2h_IFNa
processed data file: rsem.all.TPM.tsv


title: 17-254


title: 15-92


title: 16-131


title: Dc3.2_0h

description:
Dc3.2_0h
processed data file: rsem.all.TPM.tsv


title: 15-85


title: 15-81


title: HeLa_EmptyVector_rep2

city: PARMA

first: Giorgio

last: Dieci

state: PR

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

data_processing:
Reads alignment to GRCh38; STAR v. 2.5.3a: STAR --genomeDir GRCh38  --sjdbGTFfile gencode.v27.annotation.gtf --readFilesIn sample.fastq.gz --runThreadN 8 --readFilesCommand zcat --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2 --alignSJDBoverhangMin 1 --genomeLoad NoSharedMemory --limitBAMsortRAM 0 --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --sjdbOverhang 49 --seedSearchStartLmax 30 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Read counts; htseq-count  from HTSeq v. 0.11.2: htseq-count -f bam -r pos -s reverse sample.bam gencode.v27.annotation.gtf
Genome_build: GRCh38

source_name: HeLa

growth_protocol: IMR90 and HeLa cells were grown in DMEM medium supplemented with 10% FBS and 100U/ml penicillin/streptomycin. Subconfluent IMR90 were passaged at a 1:4 ratio, while subconfluent HeLa cells were passaged at a 1:6 ratio. The medium was changed every 3-4 days. Subconfluent HeLa

extract_protocol:
Proliferating cells in a 60mm plate were lysed with 2ml of Trizol (passage 9 for IMR90 cells) and total RNA was extracted using Zymo Research Direct-zol RNA MiniPrep Plus kit
RNA libraries were prepared using the Illumina TruSeq stranded mRNA library Preparation kit

value: HeLa

tag: disease

value: adenocarcinoma

value: cervix

value: epithelial

tag: passage


title: Irf8KO-Pristane 1

city: Boston

first: Pui

last: Lee

address: 60 Fenwood Rd.

institute: Brigham and Womens Hospital

data_processing:
base calling by bustard
Alignment using BWA to mouse assembly 9 (UCSC 2009).
The processed data is separated by sample barcode and aligned using Tophat version 2.0.10 (Kim et. al. 2013) with default settings.
Transcripts are quantified using the Cufflinks suite version 2.2.1 (Trapnell et. al. 2012).
Data are processed through CuffNorm if 50% of the reads align and there are at least 100,000 aligned pairs per sample. This filtering is done to ensure the quality of the normalization step.
Genome_build: Mouse assembly 9 (UCSC 2009)
Supplementary_files_format_and_content: txt file with gene count from CuffNorm

source_name: Peritoneal exudate cells

extract_protocol:
Peritoneal cells were collected by lavage with PBS.  1x10E6 cells were dissolved in RLT buffer (Qiagen).  Total RNA was isolated by Qiagen RNAeasy Micro kit.
Illumina SmartSeq2 low-input RNA-seq

treatment_protocol: Cells were extracted from 8 week-old C57BL/6 or Irf8-deficient mice by peritoneal lavage

value: Peritoneal lavage

tag: agent

value: Pristane


title: HeLa_EmptyVector_rep1


title: Irf8KO-Pristane 2


title: WT-PBS

value: Wildtype

value: PBS


title: WT-Pristane 1


title: HeLa_ControlRNA_rep1


title: HeLa_ControlRNA_rep2


title: HeLa_AluSx_rep1


title: WT-Pristane 2


title: HeLa_AluSq2_rep2


title: HeLa_AluSx_rep2


title: IMR90_EmptyVector_rep2

value: normal

value: fibroblasts


title: IMR90_EmptyVector_rep1


title: HeLa_AluSq2_rep1


title: ESC_H3K27me1_(50:50 L:H)

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: contains data from two replicates with different barcodes provided as raw files. Data was generated at low sequencing depth for global quantification only and no track file was generated

data_processing:
Demultiplexing and deduplication: Sequencing was performed using 50:8:34 cycles (Read1:Index1:Read2) Illumina bcl2fastq was used to demultiplex paired-end sequencing reads by 8nt index1 read (PCR barcode). NextSeq lanes were merged into single fastq files, creating the primary fastq files. Read1 starts with 6nt UMI and 8nt barcode in the format NNNNNNABCDEFGH. A sample sheet was used with four columns corresponding to sample name, replicate name, barcode sequence, primary fastq name. For each line in the sample sheet, reads matching the barcode sequence were extracted from the primary fastq file, allowing up to two mismatches. Duplicate reads identified by identical first 24nt of read1 were discarded. Read pairs matching parts of the adaptor sequence (SBS3 or T7 promoter) in either read1 or read2 were removed. Demultiplexed and deduplicated reads were written into sample-specific fastq file used for subsequent mapping.
Mapping: Sample-specific paired fastq files were mapped using botwie2 (v2.3.4.3) using --fast parameter to the mouse genome (mm9). Alignments were processed into sorted BAM files with samtools (v1.9). Blacklisted regions were removed from BAM file using BEDTools (v2.27.1). Reads were also mapped to a metagenome of RepBase murine repetitive sequences using botwie2.
Scaling: Input coverage tracks with 1bp resolution in BigWig format were generated from BAM files using deepTools (v3.1.0) bamCoverage and scaled to a reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using mm9 genome size 2654895218. ChIP coverage tracks were generated from BAM files using deepTools (v3.1.0) bamCoverage. Quantitative scaling amongst samples within each pool was based on their total mapped read counts, as well as the total mapped read counts of the respective input data. One condition in the pool served as a reference (Serum condition, no treatment), which was scaled to 1xRPGC. All other samples were scaled relative to the reference using an explicit scaling factor. The RPGC was calculate by the following formula: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files are scaled according to MINUTE quantification with respect to the reference of each pool (Serum condition, 1xRPGC)

source_name: Embryonic Stem Cell

growth_protocol: Murine embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated dishes.  "Serum" condition: Knockout DMEM (Life Technologies), 2 mM Glutamax (Gibco), 0.1 mM non-essential amino acids (Gibco), 15% ESC-grade fetal bovine serum (FBS) (Gibco), 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor (LIF) (Millipore); "2i" condition: serum free ESGRO Complete Basal medium (Millipore) with 0.1mM LIF and 2i as described above. For all conditions cells were passaged in 48 h intervals, using accutase (Sigma) for detachment. Cell line was tested for mycoplasma contamination.

extract_protocol:
MINUTE-ChIP and library preparation protocol is based on the Mint-ChIP protocol developed by the Bernstein lab (van Galen et al., 2016), with modifications as follows:  1x106  cells were harvested for each growth condition, washed twice with PBS and cell pellets were flash frozen at -80°C prior to use. Cells were resuspended in 50 μl PBS, lysed and digested to mono- to tri-nucleosomes fragments by adding 50 μl of 2x Lysis buffer (100 mM Tris-HCL [pH 8.0], 0.2% Triton X-100, 0.1% sodium deoxycholate, 10 mM CaCl2 and 1x PIC) containing 2U/μl of micrococcal nuclease (New England BioLabs, M0247S) and incubating on ice for 20 min and then 37°C for 10 min. Double-stranded DNA adaptors for barcoding and T7 amplification were generated by slow annealing of complementary single-stranded oligos (for sequences refer to Supplementary Table 1), where the UMI bases were randomized. While resulting dsDNA adaptors may contain mismatched bases within the UMI, only the bottom strand UMI is amplified and sequenced. For each sample, 40 μl of the whole cell lysate containing the digested chromatin was taken forward into an overnight blunt end ligation reaction (End-It DNA repair kit and Fast-Link DNA ligation kit, Epicentre) with double stranded DNA adapters at 16°C.  As in the original Mint-ChIP design, adaptors carried a partial SBS3 for Illumina sequencing flanked by a T7 RNA Polymerase for linear amplification. Between the SBS3 sequence and a 8bp sample barcode at the 3’ end, a 6bp randomized sequence was introduced, serving as a unique molecular identifier (UMI) (Figure 1a). UMI and sample barcode are ligated 5’ to the chromatin fragment and constitute the first 14 bases of read 1. The 4096 possible UMIs provide sufficient diversity to distinguish if two reads mapping to the exact same genomic location arose from a PCR amplification artifact or are indeed unique molecule. The adapter concentration was optimized to 2.5 μM / reaction to reduce adapter dimers. The ligation reaction was terminated with a lysis dilution buffer (50 mM Tris-HCl [pH 8.0], 150 mM NaCl, 1% Triton X-100, 50 mM EGTA, 50 mM EDTA, 0.1% sodium deoxycholate and 1x PIC) and barcoded samples were combined into a single pool, spun down at 24,000 r.p.m. for 10 min at 4°C. 50μl Protein A/G magnetic beads (BioRad) were washed twice with PBS-T (PBS+ 0.1% Tween 20) and coupled to one of the following antibodies in the same buffer for 1 hr at room temperature with rotation: 3 μl H3 (Active motif 39763), 5 μl H3K4me3 (Millipore 04-745), 5 μl H3K27me1 (Cell signaling 5326S),  5 μl H3K27me2 (Cell signalling D18C8), 5 μl H3K27me3 (Cell signaling 9733 (rab mAb) or Diagenode C15410195 (rab pAb) or Millipore 07-449 (rab pAb)). Beads were then washed quickly with RIPA buffer. 200-400 μl of the cleared lysate pool was added to the pre-coupled magnetic beads and parallel ChIP assays were incubated further for 4 h at 4°C with rotation. 5% of the above volume was saved as the input pool and processed through the remaining protocol in a manner similar to the IPs. Next, the beads were washed (RIPA, RIPA high salt, LiCl and TE buffer) resuspended in ChIP elution buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.1% SDS, and 300 mM NaCl) containing 0.25 mg/mL Proteinase K and eluted at 63°C for 1 h.
The native ChIP DNA was isolated using 1x SPRI beads (Beckman Coulter), retaining predominantly fragments > 100bp, and set up in an overnight in vitro transcription reaction (HiScribe T7 Quick High Yield RNA Synthesis kit, New England BioLabs).  The resulting RNA was purified using Silane beads (Life Technologies) and an RNA 3’ adapter was ligated onto it using T4 RNA ligase, truncated (New England BioLabs) for 1 h at 25°C. The mixture was subsequently supplemented with components of the reverse transcription reaction (SuperScript III First-Strand Synthesis SuperMix, Life Technologies) to produce cDNA, primed using the ligated 3’ adapter. Final libraries for each ChIP were produced using 150-200 ng of purified cDNA in a PCR reaction (High-Fidelity 2x master mix, New England BioLabs) for 8 cycles with 0.2 μM primers that carried a second 8bp barcode sequence. Quality assessment and concentration estimation of the purified DNA was done using the Qubit (Life Technologies) and BioAnalyzer (Agilent). Each library was then diluted to 4 nM and combined into a single pool before sequencing on the Illumina NextSeq500 platform.

treatment_protocol: Medium was supplemented with 10 μM GSK-J4 (Sigma) for 48 h or 10 μM EPZ-6438 (BioVision) for 7 days.

tag: background

tag: condition

value: Serum

tag: antibody

value: Cell signaling 5326S

tag: mixing ratio l

tag: supplementary file scaling


title: ESC_H3K27me1_(75:25 L:H)


title: ESC_H3K27me1_(25:75 L:H)


title: ESC_H3K27me1_(0:100 L:H)


title: ESC_H3K27me1_2i


title: ESC_H3K27me1_(5:95 L:H)


title: IMR90_ControlRNA_rep2

value: lung

tag: cell type


title: ESC_H3K27me1_(95:5 L:H)


title: ESC_H3K27me1_(100:0 L:H)


title: IMR90_ControlRNA_rep1


title: ESC_H3K27me2_2i

value: Cell signaling D18C8


title: IMR90_AluSx_rep2


title: ESC_H3K27me2_(0:100 L:H)


title: ESC_H3K27me2_(5:95 L:H)


title: IMR90_AluSx_rep1


title: ESC_H3K27me2_(25:75 L:H)


title: IMR90_AluSq2_rep1


title: IMR90_AluSq2_rep2


title: ESC_H3K27me2_(50:50 L:H)


title: ESC_H3K27me2_(95:5 L:H)


title: ESC_H3K27me2_(75:25 L:H)


title: ESC_H3K27me2_(100:0 L:H)


title: High BMI Gastroparesis [G42]

city: Indianapolis

first: Brian

middle: Paul

last: Herring

state: IN

address: 635 Barnhill Drive, MS309

department: Cellular and Integrated Physiology

institute: Indiana University School of Medicine

description:
G42
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx

data_processing:
Sequence reads were aligned to the reference genome with STAR-2.5.2b.
featureCounts (subread-1.5.1) was used to quantify gene expression.
Differential expression analysis was performed using edgeR v3.12.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: gastric_muscularis_processed.xlsx: EXCEL file with log2 transformed RPKM and raw counts.

source_name: Stomach muscularis

extract_protocol:
RNA was extracted with Trizol and purified using a Purelink micro RNA isolation kit.
KAPA mRNA Hyperprep Kit (KK8581).

value: Stomach muscularis

tag: bmi

value: High

tag: gastric motility

value: Gastroparesis


title: High BMI Gastroparesis [G106]

description:
G106
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: High BMI Gastroparesis [G80]

description:
G80
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: High BMI Gastroparesis [G30]

description:
G30
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: Low BMI Gastroparesis [G67]

description:
G67
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx

value: Low


title: ESC_H3_(0:100 L:H)

description: contains data from two replicates with different barcodes provided as raw files

value: Active motif 39763

value: relative to 100H sample


title: Low BMI Gastroparesis [G18]

description:
G18
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3_(5:95 L:H)


title: Low BMI Gastroparesis [G8]

description:
G8
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3_(25:75 L:H)


title: High BMI Control [C71]

description:
C71
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx

value: Normal


title: ESC_H3_(75:25 L:H)


title: ESC_H3_(95:5 L:H)


title: ESC_H3_(100:0 L:H)


title: Low BMI Gastroparesis [G7]

description:
G7
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: High BMI Control [C70]

description:
C70
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3K27me3_2i

value: Millipore 07-449


title: High BMI Control [C65]

description:
C65
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3K27me3_(0:100 L:H)


title: ESC_H3_2i


title: Low BMI Gastroparesis [G77]

description:
G77
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: High BMI Control [C27]

description:
C27
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3K27me3_(50:50 L:H)


title: ESC_H3K27me3_(25:75 L:H)


title: High BMI Control [C26]

description:
C26
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: Low BMI Control [104a]

description:
104a
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: Low BMI Gastroparesis [G9]

description:
G9
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3K27me3_(75:25 L:H)


title: Low BMI Control [103a]

description:
103a
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_H3K27me3_(95:5 L:H)


title: ESC_H3_(50:50 L:H)


title: Low BMI Control [C91b]

description:
C91b
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: Low BMI Control [C88]

description:
C88
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_IN_(0:100 L:H)

value: Input

value: 1x genome coverage


title: m138

city: Utrecht

first: Andrea

last: Kodde

address: Uppsalalaan 12

country: Netherlands

institute: Danone Nutricia Research

description:
processed data file: Changes_in_mito_function-RNA_seq_data_table.txt
processed data file: contrasts_98d_vs_21d_p0.05_5040transcripts_12may2017.txt

data_processing:
BaseCalling: Illumina Casava Pipeline 1.8.2.
Sequence Quality control: FASTQC quality control tool version 0.10.0.
Mapping: STAR Aligner 2.3.0.
Expression Analyses: Cufflinks v2.1.1.
Genome_build: Reference Genome Assembly: mouse reference genome mm10 (GRCm38)
Supplementary_files_format_and_content: Changes_in_mito_function-RNA_seq_data_table.txt: Tab-delimited text file containing FPKM (fragments per kilobase million) of all samples in adjacent cells.
Supplementary_files_format_and_content: contrasts_98d_vs_21d_p0.05_5040transcripts_12may2017.txt: Tab-delimited text file containing results contrast analyses between PN98 and PN21 data.

source_name: Inguinal depot

extract_protocol:
Inguinal depots were removed, fast frozen in liquid nitrogen and RNA was isolated using Trizol® (Thermo Fisher Scientific, Landsmeer, The Netherlands) and purified with a RNeasy Mini Kit (Qiagen Benelux b.v., Zwijndrecht, The Netherlands) including a DNase treatment with a RNase-free DNase Set (Qiagen Benelux b.v.). The NEBNext poly(A) mRNA magnetic isolation was used for sample preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Inguinal white adipose tissue

tag: age

value: Postnatal day 21


title: Low BMI Control [C86b]

description:
C86b
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: m145


title: ESC_IN_2i

description: contains data from two replicates with different barcodes provided as raw files


title: m125

value: Postnatal day 98


title: ESC_IN_(25:75 L:H)

value: Serum


title: ESC_IN_(5:95 L:H)


title: ESC_IN_(75:25 L:H)


title: ESC_IN_(50:50 L:H)


title: m114


title: ESC_H3K27me3_(5:95 L:H)


title: High BMI Control [C57]

description:
C57
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: ESC_IN_(95:5 L:H)


title: m106


title: m49


title: m35


title: Low BMI Control [C92]

description:
C92
PolyA enriched RNA
processed data file: gastric_muscularis_processed.xlsx


title: m1


title: ESC_H3K27me3_(100:0 L:H)


title: ESC_IN_(100:0 L:H)


title: LX1738

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
Proximal Basal#1
LX1738_TAAGGCGACTCTCTAT

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 100.  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse prostate cells_Proximal Basal

growth_protocol: 8~12-week-old C57BL/6 mouse prostate tissues were digested and dissociated into single cells. Dissociated single cells were cultured in Biocoat Collage I-coated plates (Corning, Corning, NY) in Bfs medium (5% Nu-Serum, 5% FBS, 1×Insulin/Selenium, 1×L-Glutamine, 1×Penicillin/Streptomycin, and 1×10-10M DHT in DMEM medium) at 37°C with 5% CO2. When the cell confluency reached around 90%, cells were trypsinized into single cells with 0.25% Trypsin-EDTA (Invitrogen, Carlsbad, CA). Cells were replated in Biocoat Collage I-coated plates (Corning, Corning, NY) for 30 min at 37°C/5% CO2. Unattached cells were discarded and remaining cells were cultured in Bfs at 37°C/5% CO2 till 80-90% confluency. All the experiments in this study used fresh primary stromal cells within 3 weeks after single cell dissociation from prostates.

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

treatment_protocol: Dissociated single murine and human prostate cells were incubated with florescence conjugated antibodies at 4 deg C for 30 minutes. FACS analyses and sorting were performed by using the BD LSR II, BD LSR Fortessa, Aria I or Aria III (BD Biosciences, San Jose, CA) and gating was confirmed using fluorescence minus one.

tag: strain

value: proximal ducts

value: prostate basal cells


title: LX1739

description:
Proximal Basal#2
LX1739_CGTACTAGCTCTCTAT

tag: tissue


title: LX1736

description:
Distal Basal#2
LX1736_GGACTCCTCTCTCTAT

source_name: mouse prostate cells_Distal Basal

value: distal ducts


title: S37A#3

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse prostate stroma cells

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (using both random priming and poly d(T) priming). cDNA from the SMART kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

treatment_protocol: cDNAs for S37A β-Catenin, dominant negative β-Catenin were gifts from Dr. Roger Lo at UCLA and Dr. Pierre Mccrea at MD Anderson Cancer Center, respectively. cDNA was cloned into the FU-CGW lentiviral vector at the EcoRI site. Lentivirus preparation, titering, and infection of UGSM cells or dissociated prostate cells were performed.

tag: genotype/variation


title: Vec#2

value: vec


title: Vec#3


title: LX1737

description:
Distal Basal #3
LX1737_TAGGCATGCTCTCTAT


title: S37A#2


title: LX1740

description:
Proximal Basal#3
LX1740_AGGCAGAACTCTCTAT


title: LX1735

description:
Distal Basal#1
LX1735_TCCTGAGCCTCTCTAT


title: S37A#1


title: PS2_RNA-Seq

description: fluorescence-activated cell sorting(FACS)-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse proximal prostatic duct  (sample PS2)

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat2 (version 0.6) with parameters -r 300. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (version 0.0.6).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: fluorescence-activated cell sorting(FACS)-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse proximal prostatic ducts  (sample PS2)

value: prostate stroma cells


title: PS3_RNA-Seq

description: fluorescence-activated cell sorting(FACS)-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse proximal prostatic ducts  (sample PS3)


title: Vec#1


title: DS2_RNA-Seq

description: fluorescence-activated cell sorting(FACS)-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse distal prostatic ducts (sample DS2)


title: Knockout cold 1 [KC1]

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Reads corresponding to individual samples were aligned to reference genome using STAR
Uniquely mapped reads were assigned to genes using HT-seq-Count
Genome_build: mm10/GRCm38p6
Supplementary_files_format_and_content: tab-delimited text file with rows as genes, columns as samples containing raw Counts and RPKM values.

source_name: Knockout cold_BAT

extract_protocol:
Total RNA was extracted from BAT tissue by Trizol (Invitrogen) using a dounce homogenizer (Wheaton).
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. mRNA-seq libraries were prepared as previously described (Takahashi et al., 2015)

tag: strain background

value: Noc-/-

tag: gender

value: F

tag: treatment

value: after a 4-hour cold exposure

value: Brown adipose tissue (BAT)


title: Wild type cold 4 [WC4]

source_name: Wild type cold_BAT

value: Noc+/+


title: Knockout room temperature 4 [KR4]

source_name: Knockout room temperature_BAT

value: M

value: room temperature exposure


title: Wild type room temperature 3 [WR3]

source_name: Wild type room temperature_BAT


title: Wild type room temperature 4 [WR4]


title: Wild type cold 3 [WC3]


title: Wild type cold 5 [WC5]


title: Knockout cold 2 [KC2]


title: Knockout cold 4 [KC4]


title: Wild type room temperature 2 [WR2]


title: Knockout room temperature 1 [KR1]


title: Knockout cold 3 [KC3]


title: Wild type cold 1 [WC1]


title: Knockout room temperature 2 [KR2]


title: 6 h nlp20_1

city: Oxford

first: Maricris

last: Zaidem

state: Oxfordshire

address: South Parks Rd

department: Department of Biology

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-seq reads were aligned to the CD-HIT optimized TAIR10 Col-0 reference transcripts using Bowtie 2.
Uniquely mapped reads were quantified per representative gene model using eXpress.
Supplementary_files_format_and_content: uniq_counts

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on half-strength MS medium under short-day conditions (8 h light/16 h darkness, 150 μmol/cm2s white fluorescent light, 40-60 % humidity, 22 °C).

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN), and DNA contamination was removed with the RNase-Free DNase Set (QIAGEN). RNA quantity and quality were checked with an ABI 3730xl DNA Analyzer (Applied Biosystems) and a Qubit® 2.0 Fluorometer (Invitrogen). Standard protocols provided by the kits were used for extraction.
The cDNA library was prepared from 2 μg RNA using Illumina® TruSeq® RNA Sample Preparation Kits (Illumina).  Standard protocol provided by the kits is used. For library construction.

treatment_protocol: Seedlings were moved from MS medium plate to water and soak in water overnight. Water was replace with water with/without elicitor (flg22, nlp20 or C6). Samples were harvested after 1, 6, and 24 hours.

tag: ecotype

tag: genotype

value: wild-type

tag: time point

value: 6 h

tag: agent


title: 1 h H2O_1

value: 1 h


title: 24 h C6_1


title: 0 h H2O_1

value: 0 h


title: 6 h C6_1


title: Wild type cold 2 [WC2]


title: Wild type room temperature 1 [WR1]


title: Knockout room temperature 3 [KR3]


title: DS3_RNA-Seq

description: fluorescence-activated cell sorting(FACS)-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse distal prostatic ducts  (sample DS3)


title: 0 h H2O_4


title: 24 h flg22_4


title: pancreas-Lats12null-1

first: Ondine

last: Cleaver

address: 6000 Harry Hines Boulevard, MC9148

department: Molecular Biology

description:
Lats1/2-null replicate 1
417_7-38440424

data_processing:
Analysis was performed by DNA Link USA, Inc
Sequence quality was assessed using FASTQC
Trimmed adapters using Cutadapt v 1.12
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Pairwise differential expression analysis was performed using Cuffdiff v2.2.1
Genome_build: Mus musculus (UCSC mm10)
Supplementary_files_format_and_content: tab-delimited w/ the following columns:tracking_id,gene_id,gene_short_name,locus,FPKM,FPKM_status
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pdx1Creearly;Lats1f/f;Lats2f/f pancreas

extract_protocol:
35 ng total RNA was isolated from each pancreas bud using RNeasy Microkit (Qiagen), per manufacturer's instructions.
RNA libraries were prepared for sequencing using standard KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Kapa Biosystems, Inc., KR1151-v3.15)

treatment_protocol: Pancreatic mesenchyme was manually removed using forceps to isolate pancreatic epithelial bud.

tag: developmental stage


title: pancreas-Lats12null-2

description:
Lats1/2-null replicate 2
417_8-38416754


title: pancreas-Lats12null-3

description:
Lats1/2-null replicate 3
417_9-38433478


title: Vcap-shBTF3

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

description: This sample is of Vcap transfected with lentivirus of shBTF3.

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 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 centrifμgation.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Ageilent DNA Microarray Scanner and uploaded into Agilent Feature Extraction (v11.0.0.1), and Cy3 label intensities determined.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the Agilent GeneSpring GX software package, version 12.1 .

label_protocol: cDNA samples were amplified, Cy3-labeled with Agilent Quick Amp labeling kit following manufacturer’s protocol.

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Vcap cells transfected with lentivirus are referred as Vcap-Scr and Vcap-shBTF3.

value: prostate cancer cell line Vcap

value: BTF3 knocked down


title: Vcap-Scr

description: This sample is of Vcap transfected with lentivirus of negtive control.

source_name: Vcap-Scr

value: negative control


title: pancreas-WT-4

description:
WT replicate 4
417_4-38435456

source_name: WT pancreas

value: WT


title: 1 h C6_4


title: 1 h nlp20_4


title: 6 h nlp20_4


title: pancreas-WT-3

description:
WT replicate 3
417_3-38440421


title: 6 h C6_4


title: pancreas-WT-5

description:
WT replicate 5
417_6-38421755


title: 24 h H2O_4


title: 24 h C6_4


title: hSATu2

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

description: processed data file header: DR72-3TU2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads were filtered and trimmed with BBDuk v38.82 (https://sourceforge.net/bbmap) first using the paramteres "ktrim=r k=28 mink=13 hdist=1 minlen=25 tbo tpe" followed by a sequential run using the parameters "qtrim=rl trimq=15 ktrim=r k=22 hdist=0 mink=9 minlen=25 ow"
paired files were aligned using STAR v2.5.0c using the parameters "--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNMax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1"
Isoforms were collapsed to single genes and quantified using RSEM v1.2.25 to yield transcripts per million at the gene level using the paramters "--estimate-rspd --calc-ci --no-bam-output --seed 12345 --paried-end --forward-prob 0.0"
Transcripts per million (TPM) were normalized across samples using the upper quartile strategy
Genome_build: GRCm38/mm10 and Gencode M9 annotations
Supplementary_files_format_and_content: tab-deliminated text file of Transcripts Per Million calculated by RSEM (TPM) after normalization using upper quartile.

source_name: Breast Tumor

extract_protocol:
Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific) according to manufacturer’s instructions
TruSeq Stranded Total RNA Library Prep Kit with Rib-Zero (Illumina) according to manufacturer's provided protocol

tag: age at injection

value: 6-8 weeks

value: wildtype

tag: injected with

value: human alpha satellite and shTP53

tag: site of injection

value: Breast

value: Breast Tumor


title: pancreas-WT-1

description:
WT replicate 1
417_1-38440423


title: hSATu1

description: processed data file header: KA6284Tu


title: 6 h H2O_4


title: MajTu3

description: processed data file header: KM461Tu

value: murine Major Satellite and shTP53


title: pancreas-WT-2

description:
WT replicate 2
417_2-38416753


title: KC_wt2_14w

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

description:
KC_wt2_14w_S2_L005_R1_001
fpkm_14w.txt

data_processing:
Signal intensities were converted to individual base calls during the sequence run using the system’s real time analysis (RTA) software. Sample de-multiplexing and conversion to fastq-files was performed using Illumina’s bcl2fastq software with default options.
Adaptor sequence were removed from sequenced reads by cutadapt and then mapped to mm10 mouse genome using STAR aligner. Fragments Per Kilobase of exon per Million reads (FPKM) were calculated using the Cufflinks pipeline based on Gencode M14 annotation for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Liver macrophages

extract_protocol:
Total RNA extraction and purification was performed using the TRIzol Reagent (ThermoFisher Scientific; 15596018) following the manufacturers’ protocol.
RNA integrity was determined using an Agilent Bioanalyzer. Libraries from mouse RNA were prepared using TruSeq Stranded mRNA kit (Illumina; RS-122-2201). The concentration of indexed libraries was quantified by RT–qPCR using the Universal Kapa Library Quantification Kit (KAPA Biosystems). Final libraries were normalized and sequenced on an Illumina HiSeq 3000 sequencer.

tag: cell type

value: Kupffer cells

value: 14 weeks


title: KC_wt4_9w

description:
KC_wt4_9w_S4_L007_R1_001
fpkm_9w.txt

value: 9 weeks


title: KC_wt3_14w

description:
KC_wt3_14w_S3_L005_R1_001
fpkm_14w.txt


title: KC_wt1_14w

description:
KC_wt1_14w_S1_L005_R1_001
fpkm_14w.txt


title: KC_ob2_14w

description:
KC_ob2_14w_S2_L006_R1_001
fpkm_14w.txt

value: ob/ob


title: KC_wt4_14w

description:
KC_wt4_14w_S4_L005_R1_001
fpkm_14w.txt


title: KC_ob3_14w

description:
KC_ob3_14w_S3_L006_R1_001
fpkm_14w.txt


title: KC_wt3_9w

description:
KC_wt3_9w_S3_L007_R1_001
fpkm_9w.txt


title: KC_ob4_14w

description:
KC_ob4_14w_S4_L006_R1_001
fpkm_14w.txt


title: KC_ob1_14w

description:
KC_ob1_14w_S1_L006_R1_001
fpkm_14w.txt


title: KC_ob4_9w

description:
KC_ob4_9w_S4_L008_R1_001
fpkm_9w.txt


title: KC_wt2_9w

description:
KC_wt2_9w_S2_L007_R1_001
fpkm_9w.txt


title: KC_ob3_9w

description:
KC_ob3_9w_S3_L008_R1_001
fpkm_9w.txt


title: KC_ob1_9w

description:
KC_ob1_9w_S1_L008_R1_001
fpkm_9w.txt


title: MajTu2

description: processed data file header: KM161Tu


title: 1 h flg22_4

value: wild-type


title: ob4_14w

description:
SS16_S4_L002_R1_001
mirna_expr_14w.txt

data_processing:
Signal intensities were converted to individual base calls during the sequence run using the system’s real time analysis (RTA) software. Sample de-multiplexing and conversion to fastq-files was performed using Illumina’s bcl2fastq software with default options.
Adaptor sequences were removed fom the raw reads by Cutadapt. ShortStack was used to align the small RNA reads against GENCODE mouse primary assembly (release M14, GRCm38.p5) and further identify the miRNA clusters in de-novo mode. Post-processing was performed to also quantify the less abundant RNAs (MinorRNAs) in addition to the most abundant RNAs (MajorRNAs) produced by ShortStack. The expression of both MajorRNAs and MinorRNAs were quantified at reads per million (RPM) to normalize the library sizes. All quantified miRNAs were then annotated into miRBase by aligning the sequences against miRBase mature miRNA sequence database using BLAST. All the miRNAs quantified from each sample were then pulled together into an expression matrix for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

extract_protocol:
small-RNA extraction and purification was performed using the miRNeasy mini kit (Qiagen; 217004) following the manufacturers’ protocol.
Libraries for small-RNA sequencing were prepared using TruSeq Small RNA kit (Illumina; RS-930-1012) The concentration of indexed libraries was quantified by RT–qPCR using the Universal Kapa Library Quantification Kit (KAPA Biosystems). Final libraries were normalized and sequenced on an Illumina HiSeq 3000 sequencer.


title: ob3_14w

description:
SS15_S3_L002_R1_001
mirna_expr_14w.txt


title: ob2_14w

description:
SS14_S12_L001_R1_001
mirna_expr_14w.txt


title: 6 h flg22_4

value: 6 h


title: ob1_14w

description:
SS13_S11_L001_R1_001
mirna_expr_14w.txt


title: MajTu1

description: processed data file header: DR66-4MGT


title: wt4_14w

description:
SS12_S2_L002_R1_001
mirna_expr_14w.txt


title: 1 h H2O_4

value: 1 h


title: KC_wt1_9w

description:
KC_wt1_9w_S1_L007_R1_001
fpkm_9w.txt


title: 6 h flg22_3


title: wt3_14w

description:
SS11_S1_L002_R1_001
mirna_expr_14w.txt


title: wt2_14w

description:
SS10_S10_L001_R1_001
mirna_expr_14w.txt


title: 1 h H2O_3


title: MG2

description: processed data file header: Dr712

source_name: Normal Mammary Gland

value: luciferase fragment and shTP53

value: Normal Mammary Gland


title: MG1

description: processed data file header: Dr721


title: wt1_14w

description:
SS9_S9_L001_R1_001
mirna_expr_14w.txt


title: 1 h nlp20_3


title: wt3_9w

description:
SS19_S7_L002_R1_001
mirna_expr_9w.txt


title: 0 h H2O_3

value: 0 h


title: wt4_9w

description:
SS20_S8_L002_R1_001
mirna_expr_9w.txt


title: ChIPSeq_Flag_MBD9-3xFlag

city: Los Angeles

first: magdalena

middle: ewelina

last: potok

state: CA

address: 4045 Terasaki Life Sciences Building

department: MCDB

institute: UCLA

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie57 using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized read coverage tracks were generated using the USeq package Sam2Useq application
ChIP-Seq peaks were called using callpeak function in MACS2 (v2.1.1.)
ChIP-seq data metaplots and k-means clustering were generated by  NGSPLOT (v4.02.48)59
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using bioloobox bam2wig.pl application

growth_protocol: About 5 g of 13 DAG T4 MBD9-3XFLAG and Col-0 seedlings grown on 1% MS were fixed in vivo and flash frozen.

extract_protocol:
Isolated nuclei were sonicate, cell lysates were cleared and  histone-DNA complexes were isolated with  antibody.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

value: 13 DAG shoots

tag: chip antibody

value: Flag (Sigma-Aldrich, F1804)


title: ChIPSeq_Flag_WT

value: wildtype


title: ob1_9w

description:
SS21_S9_L002_R1_001
mirna_expr_9w.txt

tag: age


title: wt2_9w

description:
SS18_S6_L002_R1_001
mirna_expr_9w.txt

tag: strain


title: ob3_9w

description:
SS24_S12_L002_R1_001
mirna_expr_9w.txt


title: 6 h C6_3


title: MG3

description: processed data file header: DR66-2MG

value: 6-8 weeks

tag: tissue


title: 24 h nlp20_3


title: wt1_9w

description:
SS17_S5_L002_R1_001
mirna_expr_9w.txt


title: top-2 nmad-1 deletion flag L4 IP rep2

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
Real-Time Analysis (RTA) software
The raw fastq files were quality checked through Fastqc(0.11.5) and the adaptors were trimmed through Trimmomatic(0.36).
The trimmed reads were mapped to Bowtie2(2.2.9) with ce10 build indexes. The sorted bam files were deduplicated and peaks were called with Picard (2.8.0) and Macs2(2.7.12) respectively.
Genome_build: ce10
Supplementary_files_format_and_content: Bigwig files are indexed binary format were generated from bam files

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
L4 stage worms were collected at 20°C. The worms were crosslinked with 1x linking buffer (11 mM HEPES-NaOH, 110 mM NaCl, 1.1 mM EDTA and 1.1 mM EGTA) with 1% formaldehyde for 10 minutes at RT. The reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at RT. Samples were washed with cold PBS twice. The samples were next dissociated with lysis buffer and sonicated by biorupter for 25 cycles in the cold room with 30 seconds on and 30 seconds off per cycle. Protein G beads were coupled to the flag antibody (F3165 Sigma) for 2 hours. Uncoupled Protein G beads were incubated with the sonicated samples to pull down non-specific binding chromatin. The precleared chromatin samples were incubated with antibody-coupled bead slurries and rotated at 4°C overnight. The bound DNA was eluted from the beads by 200  µl TE with 1% SDS after washing with low salt (0.2% SDS, 2% Triton X-100, 4 mM EDTA, 40 mM Tris-HCl), high salt (0.2% SDS, 2% Triton X-100, 4 mM EDTA, 40 mM Tris-HCl, and 1 M NaCl) and LiCl buffers (0.5 M LiCl, 2% NP-40, 1% Na deoxycholate, 2 mM EDTA, and 20 mM and Tris-HCl). The eluted DNA was next purified by phenol-chloroform.
NEBNext DNA library prep master mix set for Illumina (E6040L) was used follow the companies instructions.

value: Transgenic top-2 flag with nmad-1 deletion


title: 6 h H2O_3


title: 24 h nlp20_4


title: top-2  flag L4 IP rep2

value: Transgenic top-2 flag strain


title: top-2  flag L4 IP rep1


title: top-2 nmad-1 deletion flag L4 IP rep1


title: ob2_9w

description:
SS23_S11_L002_R1_001
mirna_expr_9w.txt


title: nmad-1 flag L4 IP  rep2

value: Transgenic nmad-1 flag strain


title: 24 h H2O_3


title: nmad-1 flag L4 IP  rep1


title: 24 h flg22_3


title: n2 L4 flag IP

value: Wild type


title: top-2-flag nmad-1 deletion L4 input


title: 1 h flg22_3


title: TRIM28-2 shRNA replicate 1

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

description:
shT28-2_1
Gene expression data from A375 cells transduced with a TRIM28-specific shRNA.

hyb_protocol: Hybridization was performed using the Affymetrix hybridization kit. Heat cocktails at 99° for 5 minutes, followed by 42° for 5 minutes. Centrifuge at max speed for 1 minute. Transfer 200μl of hybridization solution to each array. Hybridize 16 hours at 45° at 60rpm. The fluidics protocol was FS450_0001.

scan_protocol: HTA 2.0 chips were scanned using a GeneChip Scanner 3000 7G.

data_processing: CEL files were pre-processed using the R package oligo using the robust multichip average (RMA) preprocessing methodology.

label: Biotin

source_name: A375 melanoma cells transduced with shRNA targeting TRIM28

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: A375 cells were routinely tested for mycoplasma contamination. A375 cells were cultured in high-glucose DMEM (Sigma Aldrich) supplemented with fetal calf serum (10%), streptomycin (0.1 mg/ml), penicillin (100 U/ml), Sodium pyruvate (1 mM) (Sigma Aldrich), HEPES (10 mM) (Sigma Aldrich) and L-glutamine (2 mM) (Sigma Aldrich).

extract_protocol: Total RNA was isolated using RNeasy Mini Kit according to the recommended protocol (Qiagen).

treatment_protocol: For shRNA mediated knockdown, A375 cells were transduced with lentiviruses (LKO.1) that expressed non-targeting control (shSCR or shLuc) or shRNAs specific for TRIM28 (shT28-1 or shT28-2). After selection in puromycin (1 mg/ml), knockdown efficiency was validated by quantitative RT-PCR and immunoblotting.

tag: cell line

value: melanoma cells

tag: shRNA


title: TRIM28-2 shRNA replicate 2

description:
shT28-2_2
Gene expression data from A375 cells transduced with a TRIM28-specific shRNA.


title: TRIM28-1 shRNA replicate 2

description:
shT28-1_2
Gene expression data from A375 cells transduced with a TRIM28-specific shRNA.


title: nmad L4 input


title: top-2 L4 input