title: Pregnant stromal cells [PS39]

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

data_processing:
The obtained sequence reads (Fastq files) were analyzed with a locally installed version of Galaxy
The adapter sequence was clipped (for shorter fragments where sequencing runs into the adapter) and 5 bp were removed from the start of the reads
Reads were filtered by CPM cutoff after removing the PCR duplicates with NUGEN nudup
The resulting read count table was used for statistical analysis in EdgeR to identify differentially expressed genes
note: R2 reads: UMI sequences to recognize PCR duplicates
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: tabular.gz; Before cpm filter
Supplementary_files_format_and_content: _filter.tabular.gz; After cpm filter

organism: Sus scrofa

source_name: endometria

extract_protocol:
PicoPure RNA Isolation Kit
Ovation SoLo Single Cell RNA-Seq System

value: stromal cells

tag: group

value: pregnant pig on Day 14 of gestation


title: TSS-Seq in hen2-2 cold - rep1

status: Public on Oct 29 2019

type: SRA

city: Frederiksberg C

first: Quentin

middle: Angelo Pierre

last: Thomas

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

description: TSS-Seq

library_source: transcriptomic

data_processing:
Adapter and UMI-trimmed with cutadaptv1.18
PolyA tails removed with cutadapt and filtered with AfterQC v0.9.7
Aligned using STAR v2.6.1c (--alignEndsType EndToEnd – alignMatesGapMax 15000)
Deduplicated with UMI-tools and filtered for multi-aligned reads with SAMtools
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files of TIF-Seq clusters calculated with a clustering custom script in relation with the method. Bedgraph for TSS-Seq files calculated with BEDTools genomecov

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Sterilized Arabidopsis thaliana seeds were grown on plates containing 1/2 Murashige and Skoog (MS) medium containing 1% sucrose and supplemented with 1% Microagar. Plates were grown in climate chambers with a long day photoperiod (16h light/8h dark cycle) at 22°C/18 °C for 14 days

extract_protocol:
total Arabidopsis RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (Thermo Fisher Scientific) according to manufacturers’ instructions
libraries were prepared according to the publication protocol for TIF-Seq. For TSS-Seq the protocol was as in Nielsen et al,2019

treatment_protocol: For cold treatment, seedlings were grown in control conditions for two weeks and subsequently transferred to a cold room (4 °C) for three hours before harvesting. For others seedling were frozen in liquid nitrogen immediately

tag: tissue

value: seedlings

tag: genotype

tag: treatment

value: 4C cold treatment for 3h

tag: developmental stage

value: 14 days seedlings


title: TSS-Seq in hen2-2 cold - rep2

description: TSS-Seq


title: TSS-Seq in hen2-2 - rep2

description: TSS-Seq


title: TSS-Seq in hen2-2 - rep1

description: TSS-Seq


title: TSS-Seq in WT cold - rep1

description: TSS-Seq

value: Col-0 wild type


title: g46: Pca_Sample46_Prognosis_good

type: genomic

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The methylation data was processed using the RnBeads R package (Assenov et al, 2014). Probes with SNPs (dbSNP 144) overlapping with the C nucleotide of the CG site and having MAF>0.01 (28722 probes) were excluded. Probes with high likelihood of false hybridization (28736 probes, as defined in RnBeads) were also removed. Quality filtering was performed using the Greedycut algorithm, which removed 21040 probes and 11 samples. Additional 969 non-CpG probes and 9229 probes located on the sex chromosomes were removed. No normalization or background correction was used. The top 10000 most variable CpG sites showing differences based on the souce of tissue (fresh frozen vs. formalin-fixed, paraffin embedded) were removed. These probes were identified using prinipal component analysis.

label: Standard Illumina labelling (Cy5, Cy3)

molecule: genomic DNA

organism: Homo sapiens

source_name: prostate tumor

label_protocol: Standard Illumina Protocol

extract_protocol: AllPrep® DNA/RNA FFPE kit (Qiagen)

tag: gender

value: male

tag: age

tag: diagnosis

value: prostate cancer

value: prostate tumor

tag: prognosis

value: good


title: g16: Pca_Sample16_Prognosis_good


title: TIF-Seq in spt16-1 - rep 1

description:
TIF-Seq
spt16-1.bed


title: TIF-Seq in spt16-1 - rep 2

description:
TIF-Seq
spt16-1.bed


title: Pregnant stromal cells [PS41]

country: Switzerland


title: Pregnant luminal epithelium [PL41]

value: luminal epithelium


title: agonist 8844

city: Gothenburg

first: Maria

middle: E

last: Johansson

address: Medicinaregatan 11

department: Physiology

country: Sweden

institute: University of Gothenburg

data_processing:
Base-calling, CASAVA 1.8.2
Data trimming, prinseq 0.20.3, parameters: -min_qual_mean 20 -ns_max_  p 10 -trim_qual_right 3 -min_len 30
Alignment, STAR 2.5.2b
Gene-counts, htseq 0.6.1p1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw gene counts containing all samples

organism: Mus musculus

source_name: Aorta

extract_protocol:
Thoracic aorta was dissected, snap frozen in liquid nitrogen and RNA was extracted by using the RNAeasy® Fibrous Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol.
TrueSeq stranded Total RNA Sample preparation with RiboZero Gold, following protocol 15031048 Rev E

treatment_protocol: Mice were treated with α7nAChR agonist AZ6983 (50 µmol kg-1 per day) or vehicel for 8 weeks using osmotic minipumps

tag: strain

value: apoe-/-

value: thoracic aorta

value: 18 weeks


title: TIF-Seq in ssrp1-2 - rep 2

description:
TIF-Seq
ssrp1-2.bed


title: Pregnant luminal epithelium [PL43]


title: Pregnant stromal cells [PS139]


title: Pregnant luminal epithelium [PL39]


title: agonist 7110


title: Pregnant stromal cells [PS43]


title: p53+/+ H3K27me3 ChIP-seq

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
For ChIP-seq: sequence reads were aligned to mouse reference genome mm10 using BWA with default settings. Mouse alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. H3K27me3 enriched regions were identified using the SICER algorithm with a MaxGap parameter setting of 600 bp. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
For RNA-seq:  sequence reads were aligned to mouse reference genome mm10 with STAR-2.5.2b. featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“–Q 10")
For RNA-seq: differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq: bigwig file; for RNA-seq: tab-delimited file includes raw counts, log2 fold change values, p-values and FDR for all samples

source_name: Wild-type p53+/+_Lin-Kit+ cells

extract_protocol:
Lin-Kit+ cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer..
For ChIP-seq, Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end). Clontech SMART-Seq v4 Ultra Low Input RNA Kit  was used for preparing the RNA-seq libraries.

tag: strain background

tag: genotype/variation

value: Wild-type p53+/+

tag: cell type

value: Hematopoietic stem and progenitor cells

tag: cell subtype

value: Lin-Kit+ cells

tag: chip antibody

value: H3K27me3 (clone:39155, Active Motif)


title: TIF-Seq in hen2-2 cold - rep 2

description:
TIF-Seq
hen2-2cold.bed


title: g17: Pca_Sample17_Prognosis_good


title: g07: Pca_Sample07_Prognosis_good


title: TIF-Seq in WT cold - rep 2

description:
TIF-Seq
Col-0cold.bed


title: agonist 5830


title: Pregnant luminal epithelium [PL139]

value: pregnant pig on Day 14 of gestation


title: TIF-Seq in hen2-2 - rep 2

description:
TIF-Seq
hen2-2.bed

value: seedlings


title: TIF-Seq in WT cold - rep 1

description:
TIF-Seq
Col-0cold.bed

value: 4C cold treatment for 3h


title: TIF-Seq in WT - rep 1

description:
TIF-Seq
Col-0.bed

value: 14 days seedlings


title: Pregnant glandular epithelium [PG43]

value: glandular epithelium


title: agonist 1683


title: TIF-Seq in hen2-2 - rep 1

description:
TIF-Seq
hen2-2.bed


title: agonist 3301


title: Pregnant glandular epithelium [PG41]

description: the PG41 sample was deleted in the process data.


title: agonist 4012


title: Pregnant glandular epithelium [PG39]


title: UCD-T2DM pre-diabetic Rep #3_small RNA

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
Prediabetic5199_S22_L003_R1_001

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

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA extraction protocol not provided.
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: liver


title: TIF-Seq in hen2-2 cold - rep 1

description:
TIF-Seq
hen2-2cold.bed


title: Pregnant glandular epithelium [PG139]


title: g13: Pca_Sample13_Prognosis_good

value: male

value: prostate cancer


title: g08: Pca_Sample08_Prognosis_good

value: prostate tumor

value: good


title: g05: Pca_Sample05_Prognosis_good


title: Control 9090

value: apoe-/-


title: Obese ZF rat Rep #5_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L8_Obese_S11_L002_R1_001

value: Zucker Fatty


title: TIF-Seq in WT - rep 2

description:
TIF-Seq
Col-0.bed

value: Col-0 wild type


title: Pregnant blood vessel [PB43]

value: blood vessel


title: UCD-T2DM pre-diabetic Rep #2_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
Prediabetic5189_S23_L003_R1_001


title: Control 8847

value: thoracic aorta

value: 18 weeks


title: g06: Pca_Sample06_Prognosis_good


title: Obese ZF rat Rep #2_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L5_Obese_S10_L002_R1_001


title: Obese ZF rat Rep #4_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L7_Obese_S4_L001_R1_001


title: Obese ZF rat Rep #3_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L6_Obese_S3_L001_R1_001


title: g04: Pca_Sample04_Prognosis_good


title: Control 6711


title: Pregnant blood vessel [PB41]


title: Pregnant blood vessel [PB139]


title: Pregnant blood vessel [PB39]


title: Lean ZF rat Rep #5_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L42_Lean_S9_L002_R1_001


title: g15: Pca_Sample15_Prognosis_good


title: Lean ZF rat Rep #3_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L37_Lean_S15_L003_R1_001


title: Control 3295


title: Lean ZF rat Rep #4_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L41_Lean_S8_L002_R1_001


title: Obese ZF rat Rep #1_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L2_Obese_S16_L003_R1_001


title: TIF-Seq in ssrp1-2 - rep 1

description:
TIF-Seq
ssrp1-2.bed


title: Control stromal cells [CS78]

value: stromal cells

value: nonpregnant pig on Day 14 after ovulation


title: Vehicle-control ZF rat Rep #5_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
D8_BT2_S13_L002_R1_001


title: Control stromal cells [CS42]


title: Vehicle-control ZF rat Rep #4_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
D6_Vehicle_S12_L002_R1_001


title: Control 521


title: Vehicle-control ZF rat Rep #3_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
D5_Vehicle_S19_L003_R1_001


title: p53R248W/+ #3 [R.3481.LSK]

source_name: p53R248W/+_Lin-Sca1+ Kit+ cells

value: Hematopoietic stem and progenitor cells

value: Lin-Sca1+ Kit+ cells


title: Control stromal cells [CS40]


title: Vehicle-control ZF rat Rep #2_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
D4_Vehicle_S5_L001_R1_001


title: p53R248W/+ #2 [R.2.LSK]


title: BT2-treated ZF rat Rep #4_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene; BT2 = 3,6- dichlorobenzo[b]thiophene-2-carboxylic acid
ZF_RPMMM_all.csv
Sample name:
B5_BT2_S14_L002_R1_001


title: Lean ZF rat Rep #2_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L32_Lean_S2_L001_R1_001


title: Control stromal cells [CS128]


title: p53R248W/+ #1 [R.001]


title: Control 1633


title: Lean ZF rat Rep #1_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
L31_Lean_S1_L001_R1_001


title: BT2-treated ZF rat Rep #3_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene; BT2 = 3,6- dichlorobenzo[b]thiophene-2-carboxylic acid
ZF_RPMMM_all.csv
Sample name:
B4_BT2_S6_L001_R1_001


title: BT2-treated ZF rat Rep #5_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene; BT2 = 3,6- dichlorobenzo[b]thiophene-2-carboxylic acid
ZF_RPMMM_all.csv
Sample name:
B7_BT2_S17_L003_R1_001


title: BT2-treated ZF rat Rep #2_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene; BT2 = 3,6- dichlorobenzo[b]thiophene-2-carboxylic acid
ZF_RPMMM_all.csv
Sample name:
B3_BT2_S20_L003_R1_001


title: Control luminal epithelium [CL42]

value: luminal epithelium


title: UCD-T2DM pre-diabetic Rep #1_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
4923_Prediabetic_S21_L003_R1_001

tag: duration of diabetic phenotype

value: n/a (Prediabetic)


title: p53-/- #3 [p53KO.3]

source_name: p53-/-_Lin-Sca1+ Kit+ cells


title: BT2-treated ZF rat Rep #1_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene; BT2 = 3,6- dichlorobenzo[b]thiophene-2-carboxylic acid
ZF_RPMMM_all.csv
Sample name:
B10_BT2_S21_L003_R1_001

value: liver


title: Control luminal epithelium [CL78]


title: UCD-T2DM 3-month Rep #2_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
3_months_5145_S26_L003_R1_001

value: 3 months


title: p53-/- #1 [p53KO.1]


title: Control luminal epithelium [CL128]


title: Control luminal epithelium [CL40]


title: Control glandular epithelium [CG78]

value: glandular epithelium


title: p53+/+ #3 [WT.3478.LSK]

source_name: Wild-type p53+/+_Lin-Sca1+ Kit+ cells

value: Wild-type p53+/+


title: UCD-T2DM 2-week Rep #6_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
2weeks_5113_S32_L003_R1_001

value: 2 weeks


title: p53+/+ #2 [WT.2.LSK]


title: UCD-T2DM 2-week Rep #5_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
2weeks_4915_S31_L003_R1_001


title: UCD-T2DM 2-week Rep #4_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
2weeks_4837_S29_L003_R1_001


title: UCD-T2DM 3-month Rep #1_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
3_months_4901_S25_L003_R1_001


title: UCD-T2DM 2-week Rep #3_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
2weeks_4813_S30_L003_R1_001


title: Control glandular epithelium [CG42]


title: UCD-T2DM 2-week Rep #1_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
2weeks_4603_S27_L003_R1_001


title: High dose PCB118 treatment

city: Nanjing

first: Wang

last: Haiquan

address: Hankou Road

country: China

institute: Nanjing University

data_processing:
Reads of RNA-seq were mapped to the mouse genome (mm10) with Hisat2
Mapped reads were subsequently assembled into transcripts guided by the reference annotation with Stringtie
Gene differential expression analysis using Ballgown
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: oocytes

extract_protocol:
Oocytes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: female

value: ICR

value: 8 weeks

tag: exposure

value: high


title: UCD-T2DM 2-week Rep #2_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
2weeks_4673_S28_L003_R1_001

tag: tissue


title: Control glandular epithelium [CG40]

tag: group


title: p53-/- #2 [p53KO.2]


title: Control glandular epithelium [CG128]


title: NAc_Cocaine_2_INO80_Input_2

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Cocaine_peaks.txt
7_CAGATC_L004

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIPseq: Raw sequencing reads were aligned to the rat genome (rn6) using default settings of HISATv0.1.7. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicated reads. Peak-calling–normalized to respective inputs–was performed using MACSv2.1.150 with default settings and filtered for FDR < 0.05 and fold change > 1.2; the window size was set as 300 bp.
Genome_build: rn6
Supplementary_files_format_and_content: Peaks from MACS in tab delimited text files

extract_protocol:
Brain tissues were crosslinked and quenched. Samples were washed thoroughly before being subjected to lysis and sonication. Samples were then incubated with INO80 antibodies (7.5 μg/sample) bound to M-280 Dynabeads on a rotator at 4°C overnight. The following day, immunoprecipitates were washed, eluted and reverse crosslinked. Following RNA and protein digestion, DNA fragments were purified using a Qiagen PCR purification kit.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats trained to SA cocaine were sacrificed 30d post-extended access to the drug (i.e., withdrawal)

tag: treatment

value: Cocaine

value: nucleus accumbens


title: NAc_Cocaine_2_INO80_ChIP_2

description:
Cocaine_peaks.txt
7_CAGATC_L002

value: INO80 Antibody (Bethyl Laboratories, Inc., catalog# A303-371A, lot# A303-371A-1)


title: Low dose PCB118 treatment

value: low


title: UCD-T2DM 3-month Rep #3_small RNA

description:
small RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_RPMMM_all.csv
Sample name:
3_months_5147_S24_L003_R1_001


title: Control


title: NAc_Cocaine_2_INO80_ChIP_1

description:
Cocaine_peaks.txt
7_CAGATC_L001


title: NAc_Cocaine_2_INO80_Input_1

description:
Cocaine_peaks.txt
7_CAGATC_L003


title: Control blood vessel [CB78]

value: blood vessel

value: nonpregnant pig on Day 14 after ovulation


title: NAc_Cocaine_1_INO80_Input_2

description:
Cocaine_peaks.txt
6_GCCAAT_L004


title: Control blood vessel [CB42]


title: SAQ_BITC3

city: DaLian

first: Xiaoning

last: Wang

address: NO.1 Light-Industry Garden, Ganjingzi Borough

institute: Dalian Polytechnic University

data_processing:
Illumina Casava 1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=staphylococcus+aureus
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Staphylococcus aureus

source_name: Food-borne microorganism

extract_protocol:
Extracting RNA from cultured bacteria under different conditions (presence and absence of BITC). A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1/4MIC BITC


title: Control blood vessel [CB128]


title: p53+/+ #1 [WT.001]

value: Hematopoietic stem and progenitor cells

value: Lin-Sca1+ Kit+ cells


title: NAc_Saline_3_INO80_Input_2

description:
Saline_peaks.txt
5_ACAGTG_L004

value: Saline


title: NAc_Cocaine_1_INO80_Input_1

description:
Cocaine_peaks.txt
6_GCCAAT_L003


title: NAc_Saline_3_INO80_Input_1

description:
Saline_peaks.txt
5_ACAGTG_L003


title: NAc_Saline_3_INO80_ChIP_2

description:
Saline_peaks.txt
5_ACAGTG_L002


title: NAc_Cocaine_1_INO80_ChIP_2

description:
Cocaine_peaks.txt
6_GCCAAT_L002


title: NAc_Saline_2_INO80_Input_1

description:
Saline_peaks.txt
4_TGACCA_L003


title: SAC3

value: Control


title: NAc_Saline_2_INO80_ChIP_2

description:
Saline_peaks.txt
4_TGACCA_L002


title: SAC2


title: NAc_Saline_2_INO80_ChIP_1

description:
Saline_peaks.txt
4_TGACCA_L001


title: SAC1


title: NAc_Saline_1_INO80_Input_2

description:
Saline_peaks.txt
2_CGATGT_L004


title: NAc_Saline_2_INO80_Input_2

description:
Saline_peaks.txt
4_TGACCA_L004


title: NAc_Saline_3_INO80_ChIP_1

description:
Saline_peaks.txt
5_ACAGTG_L001


title: NAc_Saline_1_INO80_ChIP_2

description:
Saline_peaks.txt
2_CGATGT_L002


title: Control blood vessel [CB40]


title: Fishoil control Rep #3_small RNA

description:
small RNA
Supplementation with fish oil or sunflower oil (control)
fishoil_RPMMM_all.csv
Sample name:
37496_S45_L006_R1_001

organism: Macaca mulatta

value: liver


title: NAc_Saline_1_INO80_Input_1

description:
Saline_peaks.txt
2_CGATGT_L003


title: SAQ_BITC1


title: Vehicle-control ZF rat Rep #1_small RNA

description:
small RNA
Zucker fatty rats that have mutation in leptin receptor gene
ZF_RPMMM_all.csv
Sample name:
D1_Vehicle_S18_L003_R1_001

value: Zucker Fatty


title: Fishoil treatment Rep #3_small RNA

description:
small RNA
Supplementation with fish oil or sunflower oil (control)
fishoil_RPMMM_all.csv
Sample name:
36422_S48_L006_R1_001


title: NAc_Saline_1_INO80_ChIP_1

description:
Saline_peaks.txt
2_CGATGT_L001


title: NAc_Cocaine_3_INO80_Input_2

description:
Cocaine_peaks.txt
12_CTTGTA_L004


title: NAc_Cocaine_3_INO80_Input_1

description:
Cocaine_peaks.txt
12_CTTGTA_L003


title: NAc_Cocaine_3_INO80_ChIP_2

description:
Cocaine_peaks.txt
12_CTTGTA_L002


title: NAc_Cocaine_3_INO80_ChIP_1

description:
Cocaine_peaks.txt
12_CTTGTA_L001


title: Fishoil treatment Rep #2_small RNA

description:
small RNA
Supplementation with fish oil or sunflower oil (control)
fishoil_RPMMM_all.csv
Sample name:
35494_S47_L006_R1_001


title: pPCL_N19

type: RNA

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

hyb_protocol: Hybridization  was performed on Affymetrix GeneChip HTA 2.0 Array as per the manufacturers protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Raw data were quantile normalized, background corrected and log2 transformed with the Robust Multi-array Average (RMA) algorithm using the oligo package (v.1.44.0) in R (v.3.5.0).  BrainArray custom CDF files (version 19 Ensembl) at  gene level were used as reference.
hta20hsensgcdf_19.0.0.cdf

label: biotin

source_name: Bone marrow plasma cells

label_protocol: As per manufacturer's instructions (Affymetrix)

growth_protocol: Not applicable

extract_protocol: RNA and DNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen). RNA integrity was assessed using Agilent 2100 Bioanalyzer.

treatment_protocol: Not applicable

tag: disease state

value: Primary plasma cell leukemia (pPCL)

value: Female

value: Yes

value: No

tag: status of the other p53 allele

value: Wild type


title: MM_N17

value: Multiple myeloma (MM)

tag: gender

value: Male

value: Mutated


title: Fishoil treatment Rep #1_small RNA

description:
small RNA
Supplementation with fish oil or sunflower oil (control)
fishoil_RPMMM_all.csv
Sample name:
33825_S46_L006_R1_001


title: pPCL_N16


title: MM_N18


title: Smore Seq Ribo depletion Replicate 3

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

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

organism: Saccharomyces cerevisiae

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

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

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

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

value: Wildtype

value: Ribo depletion


title: Fishoil control Rep #2_small RNA

description:
small RNA
Supplementation with fish oil or sunflower oil (control)
fishoil_RPMMM_all.csv
Sample name:
35537_S44_L006_R1_001


title: MM_N15


title: Htz1-Tap-Tag MNase Input Replicate 1

description: nucleosomal DNA

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


title: Htz1-Tap-Tag MNase ChIP Replicate 1

description: nucleosomal DNA


title: Fishoil control Rep #1_small RNA

description:
small RNA
Supplementation with fish oil or sunflower oil (control)
fishoil_RPMMM_all.csv
Sample name:
29386_S43_L006_R1_001


title: Combination (anti-HER2 + anti-CD47) [CM_298A]

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: 4000-6000 live sorted single cells used per sample

data_processing:
Fastq files for paired-end reads and the index file for each samples was procssed using 10X cellranger v 2.2.0 count program to generate an expressoin count matrix for each sample.  Alignment was done to the GRCH38 for human transcripts and mm10 for the mouse transcripts.
The raw counts were analzed with Seurat v 2.3.4
Using Seurat the raw counts were normalized and scaled for each sample
The normalized counts were then combined for all samples and clustered using the standard Seurat workflow.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Expresion Matrix

source_name: Breast tumor single cell suspensions

growth_protocol: HER2 expression was induced in mammary tissues of one month old mice, spontaneous breast tumor growth were monitored weekly

extract_protocol:
Breast tumors were removed and processed into single cell suspensions as described in manuscript, and live singlet cells were sorted.
10X Genomics gene expression libraries were generated using Chromium Single Cell 5’ Library Construction Kit (PN-1000020). A targeted cell recovery of 4000 cells were used for each sample.
scRNA seq (10X Genomics), Single Cell 5' Gene Expression Libraries, 26x8x98 single i7 index. Sequenced on NovaSeq S4 (sample 1-10) and Hi Seq X (sample 11-13)

treatment_protocol: Mice were put on weekly antibody treatment regimen as soon as palpable tumors (200 mm^3) were detected

value: Breast tumor and immune infiltrates

value: FVB/NJ

tag: library construction


title: anti-HER2 (4D5-IgG2A) [HR_696B]

value: Chromium Single Cell 5’ Library Construction Kit (PN-1000020)


title: anti-HER2 (4D5-IgG2A) [HR_696A]


title: T-ALL3_WGS

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
processed data file:
TALL_CNV.hg19.combined.sort.tsv
TALL_SV.hg19.combined.sort.tsv
TALL_SNV.hg19.combined.sort.tsv
TALL_INV.hg19.combined.sort.tsv
TALL_BND.hg19.combined.sort.tsv

data_processing:
library strategy: Whole Genome Sequencing
Read alignment: Paired-end reads were aligned against the reference genome sequence GRCh38/hg38 using iSAAC (version 03.16.02.19).
Copy number variants: CNVs were called using Canvas (version 1.3.1)
Structural variants: SVs (including indels, tandem-duplications and inversion) were called using Manta (version 0.28.0)
Single-nucleotide variants: SNVs were called using Starling variant caller (version 2.4.6). SNVs were filtered for a 1000genome project reported GMAF<1%
Translocations: Intra- and inter-chromosomal translocations were called with Manta (version 0.28.0) and delly (version XX) simultanously, and only results detected with both algorithms were kept.
Liftover: all results were lift-over to hg19 using UCSC liftOver
Genome_build: hg19
Supplementary_files_format_and_content: tsv - custom

source_name: Peripheral blood primary T-ALL cells

growth_protocol: Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft and when the tumor burden in pheripheral blood reached 80% the mice were the spleen was harvested and splenocytes were used for the Whole Genome Sequencing (WGS) analysis.

extract_protocol:
Nuclear extraction and DNA purification using QIAmp DNA extraction kit from Qiagen
Libraries were prepared by GeneWiz using NEBNext Ultra DNA library preparation kit for Illumina.

tag: tissue source

value: Peripheral blood

tag: subject status

value: T cell acute lymphoblastic leukemia patient

tag: xenografted cell type

value: Primary T-ALL cells

tag: host strain

value: splenocytes


title: T-ALL2_WGS

value: immunocompromised NOD SCID gamma mice (NSG)

tag: cell type


title: anti-HER2 (4D5-IgG2A) [HR_288B]

tag: strain


title: T-ALL1_WGS


title: MM_N14

value: Female


title: pPCL_N9

value: Primary plasma cell leukemia (pPCL)

value: Yes


title: MM_N11

value: No

value: Not applicable

value: Wild type


title: pPCL_N12

value: Male


title: pPCL_N13


title: anti-HER2 (4D5-IgG2A) [HR_288A]


title: SAQ_BITC2

value: 1/4MIC BITC


title: SH-METTL3 IP

city: Shanghai

first: Ben

last: Yue

address: 160 Pujian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Library strategy: m6A sequencing
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of all libraries were aligned to the reference genome (UCSC HG19)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
Genome_build: HG19
Supplementary_files_format_and_content: bed; m6A peak file

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum at 37 ℃ in an atmosphere of 5% CO2

extract_protocol: Total RNAs from the transfected gastric cancer cells were extracted with TRIzol (Invitrogen).

treatment_protocol: Stable knockdown of METTL3 in gastric cancer cell line BGC823

tag: cell line

value: gastric cancer cell line

tag: m6a antibody

value: Anti-N6-methyladenosine (m6A),  clone 17-3-4-1

tag: genotype

value: METTL3 knockdown


title: SH-NC IP

value: control


title: anti-CD47 (MIAP410) [CD_407A]

value: Breast tumor and immune infiltrates

value: FVB/NJ

value: Chromium Single Cell 5’ Library Construction Kit (PN-1000020)


title: SH-NC Input

value: no


title: anti-CD47 (MIAP410) [CD_407B]


title: Untreated [UN_698B]


title: SH-METTL3 Input


title: tissue- ulcerative colitis- 13.2 year old male

city: Boston

first: Jocelyn

middle: Anne

last: Silvester

state: Massachusetts

address: 300 Longwood Avenue

department: Gastroenterology

institute: Boston Children's Hospital

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

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

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

source_name: colon

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

growth_protocol: not applicable

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

treatment_protocol: not applicable

tag: age

tag: disease type

value: UC - L colitis

value: colon biopsy


title: tissue- control- 8.6 year old male

value: Control

tag: tissue


title: siYAP-2-lncRNAseq

city: Guangzhou

first: Wen

last: Ni

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

description: nc-vs-siYAP.mRNA.annot-PROCESSING DATA.xls

data_processing:
After total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs.
The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers.
Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer.
The cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000
Genome_build: The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample …

source_name: Colorector cancer cell

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

extract_protocol:
Total RNA was extracted using Trizol reagent (Takara, Dalian, China). Agilent 2100 Bioanalyzer (Agilent, CA, USA) and NanoDrop 2000 (Thermo Fisher, MA, USA) was used to analyze the total RNA quality and quantity.
The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000 (or other platforms) by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: The GAS5 plasmid or YAP-specific siRNA were transfected in CRC cells.

value: colon

tag: sirna

value: siYAP


title: tissue- ulcerative colitis- 14.9 year old male

value: UC - pancolitis


title: Isotype antibody [UN_241A]


title: tissue- ulcerative colitis- 11.6 year old male


title: siYAP-1-lncRNAseq


title: MM_N10

tag: disease state

value: Multiple myeloma (MM)

value: Female

value: No

value: Yes

value: Wild type


title: MM_N8

value: Male

tag: status of the other p53 allele


title: tissue- ulcerative colitis- 16.9 year old male

tag: gender


title: MM_N6


title: pPCL_N7

value: Primary plasma cell leukemia (pPCL)

value: Mutated


title: Untreated [UN_698A]

value: Breast tumor and immune infiltrates

value: FVB/NJ

tag: library construction


title: pPCL_N5


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

value: Crohn's Disease


title: pPCL_N4


title: GAS5-2-lncRNAseq

description: nc-vs-GAS5.mRNA.annot-PROCESSING DATA.xls


title: tissue- ulcerative colitis- 15.2 year old male


title: GAS5-1-lncRNAseq


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


title: d11178_2

first: Qing

address: No. 12 Xuefu Road, Pukou District

institute: Model Animal Research Center, Nanjing University

data_processing:
Illumina NovaSeq 6000 software used for basecalling.
The raw data after quality control, clean data(reads), is compared with the reference genome to obtain mapped data (reads) for subsequent transcript assembly, expression calculation, etc., and the alignment of the transcriptome is sequenced.
Based on the selected reference genome sequence, Mapped Reads are spliced using StringTie or Cufflinks software, and compared with the original genomic annotation information, to find the original unannotated transcribed region, to discover new transcripts and new genes of the species, thereby Supplement and improve the original genome annotation information.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: The excel table contains the Pvalue value of the gene expression difference of the tested experimental group.

source_name: cochlear

growth_protocol: postnatal day 3 cochlear culture in colleage in 2ml medium(B27,N2)and culture in five days in drug medium

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

treatment_protocol: RNA was harvested using Trizol reagent

value: cochlear

value: post natal day 3

tag: treatment


title: d11178_3


title: MM_N3


title: NAc_Cocaine_1_INO80_ChIP_1

description:
Cocaine_peaks.txt
6_GCCAAT_L001

value: Cocaine

tag: chip antibody

value: INO80 Antibody (Bethyl Laboratories, Inc., catalog# A303-371A, lot# A303-371A-1)

value: nucleus accumbens


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

value: colon biopsy


title: tissue- ulcerative colitis- 16.2 year old male

value: UC - pancolitis


title: tissue- ulcerative colitis- 11.3 year old female

value: Female


title: MM_N2

value: Multiple myeloma (MM)

value: No


title: NC-2-lncRNAseq

value: colon

value: NC


title: d1DAPT_2


title: d11178_1


title: IgG_RIPseq

data_processing:
After total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs.
The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers.
Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer.
The cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000
Genome_build: The rRNA removed reads of each sample were then mapped to reference genome by TopHat2   (version 2.1.1), respectively.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

extract_protocol:
Lysates were clarified from total RNA and protein-RNA complexes were isolated with antibody.
RIP experiment was performed according to the manuscript of the Magna RIP RNA Binding Protein Immunoprecipitation Kit (Millipore, MA, USA). Briefly, lysate preparation in lysis buffer containing protease inhibitor cocktail and RNase inhibitor. Then, preparation of protein A/G magnetic beads for incubation with 5 µg purified antibodies per immunoprecipitation. Incubate with rotation for 30 minutes at room temperature. Furtherly, immunoprecipitation of RNA-binding Protein-RNA complexes, and incubated all the mixture with rotating for 3 hours to overnight at 4°C. Finally, purification of RNA using proteinase K buffer, and Agilent 2100 Bioanalyzer (Agilent, CA, USA) and NanoDrop 2000 (Thermo Fisher, MA, USA) was used to analyze the total RNA quality and quantity. Further RNAs in an immunoprecipitation may be pursued by deep sequencing or qRT - PCR.

tag: rip antibody

value: IgG(Millipore, 12-370)


title: NC-1-lncRNAseq


title: d1DAPT_3


title: d1DAPT_1


title: YAP_RIPseq

value: YAP(CST, D8H1X)


title: d1CHIR_3


title: Left-atrium-PCM-1-adult-sample2

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were mapped to hg19 build of the human transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Atria-RNA-seq-counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).

source_name: atrial PCM-1 sorted nuclei

growth_protocol: Human adult and fetal atrial free wall tissue was obtained in strict accordance with the tissue regulation of the George Washington University and LUMC

extract_protocol:
Whole tissue: Total RNA was isolated from the atrial tissue using Trizol according to the manufacturer’s protocol (Sigma Aldrich), DNaseI treated and further purified using Nucleospin RNeasy MinElute Kit (Qiagen). PCM-1 samples: nuclei were extracted from snapfrozen samples, and stained with PCM-1 rabbit polyclonal antibody (Sigma) for FACS of specifically cardiomyocyte nuclei.
Adult tissue: NuGEN's Ovation RNA-seq V2 kit. Fetal: Truseq Stranded Total RNA Library Preparation Kit (Illumina, Part# 15031048 Rev. E)

value: Adult


title: d1CHIR_2


title: Right-atrium-fetal-22weeks

source_name: atrial free wall whole tissue

value: Fetal (22 weeks)


title: Left-atrium-PCM-1-adult-sample1


title: Right-atrium-fetal-14weeks

value: Fetal (14 weeks)


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

value: Male

value: Crohn's Disease


title: GLDT_trunc_2

city: Duesseldorf

first: Roxanne

last: van Rooijen

address: Universitaetsstrasse 1

institute: Heinrich Heine University

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia fused to a 5'truncated coding sequence of the NAC052 gene from Arabidopsis thaliana inserted randomly in the genome of Arabidopsis thaliana, biological rep2

data_processing:
Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, USA) with a read setup of 1x150 bp.
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.
The reads of all probes were adapter trimmed (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2).
Mapping was done against the Arabidopsis thaliana (TAIR10)
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file includes expression values for each Sample

source_name: complete rosette

growth_protocol: Plants were grown in soil (Floraton 1, Floragard, Oldenburg, Germany) for 28 days in a climate-controlled growth chamber (16h, 22°C, 110 μmol m-2 s-1 light; 8h, 20°C dark)

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini Kit including on column DNA digestion
The library preparation was performed according to the manufacturer's protocol using the Illumina¨ 'TruSeq Stranded mRNA Library Prep Kit'.

tag: ecotype

value: complete rosette


title: GLDT_trunc_3

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia fused to a 5'truncated coding sequence of the NAC052 gene from Arabidopsis thaliana inserted randomly in the genome of Arabidopsis thaliana, biological rep3


title: pPCL_N1

value: Primary plasma cell leukemia (pPCL)

value: Yes

value: gDNA not available


title: GLDT_30a_3

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia fused to the coding sequence of the NAC052 gene from Arabidopsis thaliana inserted randomly in the genome of Arabidopsis thaliana, biological rep3


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

value: colon biopsy


title: GLDT_trunc_1

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia fused to a 5'truncated coding sequence of the NAC052 gene from Arabidopsis thaliana inserted randomly in the genome of Arabidopsis thaliana, biological rep1


title: Left-atrium-fetal-22weeks


title: d1CHIR_1

value: cochlear

value: post natal day 3


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


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


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

value: Female


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


title: Quercetin3

city: JiNan

first: jiang

middle: yue

last: hua

state: Shandong

address: Jingshi Road

department: Department of Cardiovascular

institute: Shandong University of Traditional Chinese Medicine

description: HAECs treated with 50 μg/mL ox-LDL + 3 μmol/L quercetin

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent, 5190-2943, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US) for 17 hours, according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent, G2565CA, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

label_protocol: Total RNA was amplified and labeled using Low Input Quick Amp WT Labeling Kit (Agilent, 5190-2943, Santa Clara, CA, US). Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Human aortic endothelial cells (HAECs, ScienCell, 6100, USA) were cultured in a endothelial cell medium (ECM, ScienCell, 1001, USA) supplemented with 1% endothelial cell growth supplement (ECGS), 5% fetal bovine serum (FBS), and 1% penicillin/streptomycin (P/S) on culture dishes coated with human fibronectin at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA of HAECs was extracted by the TRIzol Reagent Kit (Life Technologies, 15596-018, Carlsbad, USA)

treatment_protocol: HAECs were cultured for 48 h in the presence of ox-LDL (50 μg/mL, Xiesheng Biotechnology, Beijing, China), or ox-LDL (50 μg/mL) + 3 μmol/L quercetin (Jiashi Yuhe Institute, 117-39-5, Beijing, China).

tag: cell type

value: Human aortic endothelial cells (HAECs)


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


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


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


title: tissue- IBD- 14 year old male

value: IBDU


title: GLDT_30a_2

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia fused to the coding sequence of the NAC052 gene from Arabidopsis thaliana inserted randomly in the genome of Arabidopsis thaliana, biological rep2


title: Mef2d Treg replicate 1

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

data_processing:
Base calling, aligment, filtering, peak calling, normalized ambunrance measurements, by Novogene company.
Genome_build: mm10
remove adapter, low quality, N reads
fq; BAM (mapping)STAR software to alignment for RNA-seq sequencing data analysis, using the MM10 genome
Htseq

source_name: Foxp3+ YFP-sorted regulatory T cell

growth_protocol: Floxed Mef2d, Mef2c, HDAC1, HDAC2 or Dyrk1 mice were mated with Foxp3YFPcre mice (Rubtsov et al. Immunity 2008) to generate conditional Rcor1-knockout mice lacking Rcor1 in Foxp3+ Treg. Foxp3YFPcre mice were used as control. We used male mice 6-8 weeks of age in this study.

extract_protocol:
RNA was isolated using RNeasy kits (QIAGEN), and RNA integrity and quantity were analyzed by NanoDrop ND-1000 and Nanochip 2100 Bioanalyzer (Agilent Technologies)
NEBNext® Ultra™ II RNA Library Prep was used according to the manufacturers instructions.

treatment_protocol: Foxp3+ regulatory T cells were isolated using FACS sorting via YFP (after CD4+ column enrichment).

value: Foxp3+ YFP-sorted regulatory T cell

tag: genotype/variation

value: Mef2d deletion


title: Mef2d Treg replicate 2


title: Ox-LDL1

description: HAECs treated with 50 μg/mL ox-LDL

source_name: HAECs treated with 50 μg/mL ox-LDL


title: Ox-LDL3

description: HAECs treated with 50 μg/mL ox-LDL

source_name: HAECs treated with 52 μg/mL ox-LDL


title: Quercetin2

source_name: HAECs treated with 50 μg/mL ox-LDL + 3 μmol/L quercetin


title: Mef2d Treg replicate 3


title: Quercetin1


title: Mef2c Treg replicate 3

value: Mef2c deletion


title: Right-atrium-adult-sample3

value: Adult


title: Ox-LDL2

description: HAECs treated with 50 μg/mL ox-LDL

source_name: HAECs treated with 51 μg/mL ox-LDL


title: HDAC2 Treg replicate 3

value: HDAC2 deletion


title: GLDT_30a_1

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia fused to the coding sequence of the NAC052 gene from Arabidopsis thaliana inserted randomly in the genome of Arabidopsis thaliana, biological rep1


title: CRISPR_30a_1

description: The reference line containing a CRISPR/Cas induced nucleotide insertion in the NAC052 gene from Arabidopsis thaliana, biological rep1


title: act_tagged_55_3

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia inserted in the coding sequene of the NAC052 gene from Arabidopsis thaliana, biological rep3


title: Mef2c Treg replicate 2


title: CRISPR_30a_3

description: The reference line containing a CRISPR/Cas induced nucleotide insertion in the NAC052 gene from Arabidopsis thaliana, biological rep3


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

value: Male


title: Right-atrium-adult-sample2


title: Left-atrium-adult-sample2


title: Left-atrium-fetal-14weeks

value: Fetal (14 weeks)


title: CRISPR_30a_2

description: The reference line containing a CRISPR/Cas induced nucleotide insertion in the NAC052 gene from Arabidopsis thaliana, biological rep2

value: complete rosette


title: HDAC2 Treg replicate 1


title: Right-atrium-adult-sample1


title: tissue- ulcerative colitis- 17 year old male

value: UC - pancolitis


title: Mef2c Treg replicate 1


title: tissue- ulcerative colitis- 14.4 year old male

value: UC - L colitis


title: tissue- crohn's disease16.4 year old female

value: Crohn's Disease


title: tissue- ulcerative colitis- 8.3 year old female

value: colon biopsy


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


title: HDAC2 Treg replicate 2


title: HDAC1 Treg replicate 2

value: HDAC1 deletion


title: act_tagged_55_2

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia inserted in the coding sequene of the NAC052 gene from Arabidopsis thaliana, biological rep2


title: Left-atrium-adult-sample1


title: Ref_2

description: An Arabidopsis thaliana bundle sheath reporter line containing a construct harbouring the promoter of the GLDPA gene from Flaveria trinervia (NCBI accession number Z99767), a chloroplast transit peptide (TP) of the Arabidopsis RbcS gene, and a synthetic GFP (sGFP), biological rep2


title: HDAC1 Treg replicate 3


title: act_tagged_55_1

description: The reference line containing the promoter of the GLDT gene from Flaveria trinervia inserted in the coding sequene of the NAC052 gene from Arabidopsis thaliana, biological rep1


title: Ref_1

description: An Arabidopsis thaliana bundle sheath reporter line containing a construct harbouring the promoter of the GLDPA gene from Flaveria trinervia (NCBI accession number Z99767), a chloroplast transit peptide (TP) of the Arabidopsis RbcS gene, and a synthetic GFP (sGFP), biological rep1


title: Left-atrium-adult-sample3


title: Dyrk1 Treg replicate 3

value: Dyrk1 deletion


title: Dyrk1 Treg replicate 2


title: AR2732_07: WT

city: Kyoto

first: Yoshihide

last: Matsumoto

state: Kyoto

address: Syogoinkawaramachi54 Sakyoku, Kyoto

country: Japan

institute: Kyoto University

description: gene expression of Villin-Cre colon tissue

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: Villin-Cre

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ug Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  Total pooled RNA isolated from 3 individual pools of colon tissues respectively was used for gene-expression analysis. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

value: Villin-Cre

value: colon


title: AR2732_08: EP4

description: gene expression of Villin-Cre; EP4flox/flox colon tissue

source_name: Villin-Cre; EP4flox/flox

value: Villin-Cre; EP4flox/flox


title: wild type Treg replicate 3

value: Foxp3+ YFP-sorted regulatory T cell

value: wild type


title: Ref_3

description: An Arabidopsis thaliana bundle sheath reporter line containing a construct harbouring the promoter of the GLDPA gene from Flaveria trinervia (NCBI accession number Z99767), a chloroplast transit peptide (TP) of the Arabidopsis RbcS gene, and a synthetic GFP (sGFP), biological rep3


title: wild type Treg replicate 2


title: RNASEQN7

city: Changsha

first: Liang

last: Zhang

address: Departments of Urology, Xiangya Hospital, Central South University, Changsha, China

institute: Central South University

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using HISAT2 v2.0.4 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4.
The circRNA were detected and identified using find_circ (Sebastian Memczak et al., 2013) and CIRI2 (Gao et al., 2017). Circos software was used to construct the circos figure.
The raw counts were first normalized using TPM .
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample.

source_name: Adrenal gland

extract_protocol:
Frozen samples and peripheral blood were taken out of the liquid nitrogen and immediately merged into TRIzol reagent (Ambion, USA). Tissues were homogenized and lyzed in TRIzol reagent, and the total RNAs were extracted by following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal adjacent adrenal gland

value: RET


title: tissue- IBD- 14.2 year old male

value: IBD w/ oral


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

value: Male


title: tissue- control- 8.5 year old male

value: Control


title: P3_RFP

city: Wroclaw

first: Artur

last: Tomal

address: Fryderyka Joliot-Curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wroclaw

data_processing:
Library strategy: Ribo-seq
RNA-Seq and Ribo-Seq reads were trimmed for 3' adaptor sequences and low quality reads using FastX-toolKit
All rRNA and tRNA sequences were filtered out by alignment reads to their sequences in three steps, with unaligned reads from each step used as an input for the next round of alignment. In the first step mitochondrial tRNAs and rRNAs were removed, then chloroplast tRNAs and rRNAs, and subsequently nuclear tRNAs and rRNAs.
The remaining reads were aligned to the A. thaliana mitochondrial genome with the split-aware aligner STAR (Spliced Transcripts Alignment to Reference) version 2.5.2b (Dobin et al., 2013) with default settings allowing for up to 5 mismatches.
The total reads mapped to the mitochondrial genome were sorted into two groups: one group with unique reads that mapped to a single location in the genome, and the other with reads that mapped to multiple locations in the genome
P-site offsets (i.e., the distances of the P-site from the 5' and 3' ends of the reads) were determined using riboWaltz v.1.0 (Lauria et al., 2018). For these results RiboTaper software was used to determine the 3-nt periodic pattern of analyzed sequences in all three possible frames assuming p-value < 0.05 (Calviello et al., 2016) using 5’ offsets of 12 - 21 for footprint lengths of, respectively, 25 - 34 nt.
To calculate transcriptional output of a gene RNA-Seq reads of all lengths aligned to CDS were used, whereas only 25-29 nt long Ribo-Seq reads, exhibiting a strong periodicity, were applied to estimate translational output. Both type of reads were counted by featureCounts (assuming fracOverlap=1) and then normalized  for sequencing depth and length as TPM unit, i.e., transcripts per million. Intron-containing genes were excluded from this analysis
Genome_build: (BK010421.1)
Supplementary_files_format_and_content: spreadsheet files include reads abundance and TPM measurements for each samples, and 3-nucleotide periodicity measurements for each frame of Ribo-Seq samples

source_name: Mitochondria

growth_protocol: Seeds of wild-type plants were germinated on half-strength Murashige and Skoog, supplemented with kanamycin (50 mg L−1) for the rps10 mutant. Seedlings were grown for 3 d at 4°C in the dark followed by 11 d in an 8-h-light/16-h-dark (short day) photoperiod at 22°C with light intensity of 100 μmol m−2 s−1. After that time, the wild-type and the kanamycin-resistant rps10 plants were transferred to the soil and grown in a growth chamber (short day, 22°C, 100 μmol m−2 s−1).

extract_protocol:
Mitochondria were isolated from leaves as described by Lister et al. (2007). Approximately 15 g (fresh weight) of leaves from rps10 and 30 g from wild-type plants were used per one isolation, yielded typically ~1 mg of mitochondrial proteins. Mitochondrial fractions were frozen in liquid nitrogen and stored at -800C.
Mitochondrial Ribo-Seq and RNA-Seq libraries were prepared using the ARTseq Ribosome Profiling Kit (Epicentre) dedicated for yeast, with slight modifications. Each library was prepared from fifteen independent mitochondrial preparations. Immediately after removing mitochondrial preparations from the -80°C freezer chloramphenicol was added to a final concentration of 100 μg/ml and thawed mitochondria were pooled, suspended in polysome extraction buffer (0.2 M sucrose, 0.2 M KCl, 10 mM MgCl2, 2% polyoxyethylene (10) tridecyl ether, 1 mM DTT, 1% Triton X-100, DNase I (0.01 U/μl), 100 μg/ml chloramphenicol, 40 mM Tris-acetate, pH 8.0), incubated on ice for 10 minutes and centrifuged for 10 minutes at 28,154 x g at 4°C to obtain clarified lysate. RNA concentration in the lysate was determined as OD260 and aliquots of 100 (mtRNA-seq library) and 200 μl (mtRibo-Seq library) were prepared. The 100-μl aliquot was supplemented with 10 μl of 10% SDS and total RNA was purified using the RNA Clean & Concentrator-25 kit according to the protocol for large RNAs >200 nt (Zymo Research). The 200-μl aliquot was treated with ARTseq nuclease (0.3 U nuclease per 1 OD260 of lysate) to degrade unprotected RNA following Epicentre instruction, and ribosome protected fragments (RPFs) were isolated using sucrose cushion ultracentrifugation at 4°C for 4 hours at 294,000 x g. The pellet was suspended in 100 μl nuclease-free water and 10 μl of 10% (w/v) SDS was added. Next, the RPFs were purified using RNA Clean & Concentrator-25 kit according to the protocol for small RNAs (17-200 nt). After purification the total RNA and RPFs preparations were depleted of rRNA using the Ribo-Zero rRNA Removal Plant Leaf kit (Illumina) and then were purified again using the RNA Clean & Concentrator-25 kit according to the protocol for large RNAs >200 nt for total RNA and the RNA Clean & Concentrator-5 kit according to the protocol for RNA >17 nt for RPFs. The total RNA preparation without ribosomal RNA was heat-fragmented. The RPFs without ribosomal RNA were purified by 15% TBE-urea PAGE (Thermo Fisher Scientific) and the gel fragment containing RNA of 25 to 35 nt was excised. The RPFs were recovered from the excised gel slices following overnight elution as specified in the ARTseq Ribosome Profiling Kit. The fragmented total RNA and RPFs were end-polished, purified by RNA Clean & Concentrator-5 kit according to protocol for >17 nt, ligated with 3’ adaptors, reverse-transcribed and purified as above. Purified cDNAs were separated on 10% TBE-urea PAGE, and gel fragments containing ssDNA of 80 to 100 nt for cDNA generated from total RNA fragments, and 70 to 80 nt for cDNA from RPFs, were excised. cDNA was recovered by overnight elution as specified in the ARTseq Ribosome Profiling Kit. The purified cDNA was then circularized and used for PCR with index PCR primers for 9 cycles. The libraries were purified by 8% Native TBE PAGE and AMPure XP beads (Beckman Coulter) and their quality and concentration was determined using an Agilent 2100 Bioanalyzer. High-throughput sequencing was performed on an Illumina Miseq 2500 sequencer in the single-end mode for 50 nucleotides at Wyzer Biosciences (Cambridge, MA, USA)

value: youngest leaves

value: 9-10 weeks


title: wild type Treg replicate 1


title: P2_Total

data_processing:
RNA-Seq and Ribo-Seq reads were trimmed for 3' adaptor sequences and low quality reads using FastX-toolKit
All rRNA and tRNA sequences were filtered out by alignment reads to their sequences in three steps, with unaligned reads from each step used as an input for the next round of alignment. In the first step mitochondrial tRNAs and rRNAs were removed, then chloroplast tRNAs and rRNAs, and subsequently nuclear tRNAs and rRNAs.
The remaining reads were aligned to the A. thaliana mitochondrial genome with the split-aware aligner STAR (Spliced Transcripts Alignment to Reference) version 2.5.2b (Dobin et al., 2013) with default settings allowing for up to 5 mismatches.
The total reads mapped to the mitochondrial genome were sorted into two groups: one group with unique reads that mapped to a single location in the genome, and the other with reads that mapped to multiple locations in the genome
P-site offsets (i.e., the distances of the P-site from the 5' and 3' ends of the reads) were determined using riboWaltz v.1.0 (Lauria et al., 2018). For these results RiboTaper software was used to determine the 3-nt periodic pattern of analyzed sequences in all three possible frames assuming p-value < 0.05 (Calviello et al., 2016) using 5’ offsets of 12 - 21 for footprint lengths of, respectively, 25 - 34 nt.
To calculate transcriptional output of a gene RNA-Seq reads of all lengths aligned to CDS were used, whereas only 25-29 nt long Ribo-Seq reads, exhibiting a strong periodicity, were applied to estimate translational output. Both type of reads were counted by featureCounts (assuming fracOverlap=1) and then normalized  for sequencing depth and length as TPM unit, i.e., transcripts per million. Intron-containing genes were excluded from this analysis
Genome_build: (BK010421.1)
Supplementary_files_format_and_content: spreadsheet files include reads abundance and TPM measurements for each samples, and 3-nucleotide periodicity measurements for each frame of Ribo-Seq samples


title: P3_Total


title: tissue- ulcerative colitis- 16.1 year old female

value: Female

value: UC - L colitis


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

value: Crohn's Disease

value: colon biopsy


title: RNASEQN5

value: SDHB


title: RNASEQN4

value: Mutation Not found


title: Combination (anti-HER2 + anti-CD47) [CM_796B]

description: 4000-6000 live sorted single cells used per sample

source_name: Breast tumor single cell suspensions

value: Breast tumor and immune infiltrates

value: FVB/NJ

value: Chromium Single Cell 5’ Library Construction Kit (PN-1000020)


title: P2_RFP


title: Combination (anti-HER2 + anti-CD47) [CM_796A]


title: Dyrk1 Treg replicate 1

value: Foxp3+ YFP-sorted regulatory T cell

value: Dyrk1 deletion


title: tissue- control- 11.5 year old female


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


title: RNASEQN3

value: Normal adjacent adrenal gland

value: HRAS


title: tissue- ulcerative colitis- 8.6 year old female

value: UC - pancolitis


title: RNASEQN6

value: VHL


title: RNASEQN2

value: RET


title: Combination (anti-HER2 + anti-CD47) [CM_298B]


title: WT_Total

value: youngest leaves

value: 9-10 weeks

value: wild type


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

value: Male

value: Crohn's Disease


title: WT_RFP


title: Mtss1 2

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Read quality were performed for all samples by using FastQC (version 0.11.2) (Andrews.2010) software with the default parameters.
Skewer (v0.2.2) (Bolger AM, el at. 2014) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed. Then the selected reads, named as Clean reads, were used for downstream analysis.
The alignment analysis can basically be divided into two steps: 1)genemeGenerate Build an index; 2) Sequence alignment. In this project, clean reads of each sample were align to reference genome by using STAR software with default parameters.
Expression estimation of gene and transcript was performed by using RSEM, TMM and CPM normalized read counts of genes were applied to compare between two samples in the downstream analysis.
Genes whose CPM and TMM value is greater than 1 in at least one sample were selected. The criteria for significantly differentially expressed genes was: padj <0.05 and |FC| >= 2.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were txt format.

growth_protocol: IMDM supplied with 10% fetal bovine serum.

extract_protocol:
Trizol reagent was used to extract RNA, then total RNA was subjected to Hiseq PE150 RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment.

value: mammary gland

tag: cell line

tag: cell phenotype

value: mesenchymal-like

value: Mtss1 overexpression


title: RNASEQN1

tag: genotype


title: RNASEQC7

value: Pheochromocytomas


title: Mtss1 1


title: RNASEQC6


title: hygro 2

value: control


title: MTAC-shLuciferace

first: Yuetong

address: 320 Yue Yang Road, Room 713

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

institute: Chinese Academy of Sciences

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 with Trim_galore. Then mapped to  whole genome using TopHat (Trapnellet al.,   2009) and cufflinks.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Mortazaviet al., 2008. 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: hg38
Supplementary_files_format_and_content: fpkm tracking files

source_name: human lung cancer cell line

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

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: EGFR-TKI resistant cell line derived from PC9

value: MTAC-P

tag: knockdown


title: MTAC-shBCAT1-2


title: MTAC-shBCAT1-1


title: tissue- control- 10.9 year old male

source_name: colon

tag: age

tag: disease type

value: Control

tag: tissue

value: colon biopsy


title: MTAC-P

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 with Trim_galore. Then mapped to  whole genome and differential gene and transcript expression analysis of RNA-seq experiments using TopHat and Cufflinks (Nature protocols, 2012, 7(3): 562-578).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Mortazaviet al., 2008. 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: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample


title: RNASEQC5

value: SDHB


title: RNASEQC4

value: Mutation Not found


title: tissue- control- 18.5 year old female

value: Female


title: HM86_UR

city: Ann Arbor

first: Harry

last: Mobley

state: Michigan

address: 1150 W. Medical Center Drive

department: Microbiology and Immunology

institute: University of Michigan

data_processing: Raw fastq files were processed with Trimmomatic  to remove adapter sequences and analyzed with FastQC to assess sequencing quality. Mapping was done with bowtie2 aligner  using default parameters. Read counts were calculated using HTseq htseq-count (union mode)

organism: Escherichia coli

source_name: in vitro urine culture

growth_protocol: Patient samples: Clean catch midstream urine samples from patients with UTIs were immediately stabilized with two volumes of RNAprotect (Qiagen) to preserve the in vivo transcriptional profileIn vitro conditions: Human urine was pooled from four age-matched healthy female volunteers. Overnight cultures of clinical isolates were washed once in human urine, then 250 μl of overnight culture was added to 25 ml of filter-sterilized human urine and cultured statically at 37C for 2 hours.

extract_protocol:
Samples were treated with proteinase K and total RNA was isolated using Qiagen RNAeasy minikit. Turbo DNase kit (Ambion) was used to remove contaminating DNA. Bacterial content of patient samples was enriched using MICROBenrich kit (Ambion)
Library preparation and sequencing was performed by University of Michigan sequencing core. Illumina ScriptSeq v2 library kit was used to construct rRNA-depleted stranded cDNA libraries.

value: Uropathogenic Escherichia coli (UPEC)


title: tissue- ulcerative colitis- 16.3 year old male

value: UC - pancolitis


title: RNASEQC3

value: HRAS


title: UCD-T2DM pre-diabetic RNA-seq Rep #5

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-6311

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

source_name: liver

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

value: liver

tag: duration of diabetic phenotype

value: n/a (Prediabetic)


title: HM68_UR


title: HDAC1 Treg replicate 1

value: Foxp3+ YFP-sorted regulatory T cell

value: HDAC1 deletion


title: RNASEQC2

value: RET


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

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

tag: gender

value: Crohn's Disease


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

value: Male


title: tissue- control- 15.3 year old male

value: Control--> CD


title: UCD-T2DM pre-diabetic RNA-seq Rep #4

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-6011


title: HM66_UR


title: hygro 1

value: mammary gland

value: mesenchymal-like

value: control


title: HM60_UR


title: RNASEQC1

value: Pheochromocytomas

value: VHL


title: UCD-T2DM 6-month RNA-seq Rep #6

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-5241

value: 6 months


title: patient4_normal

city: Los angeles

first: Xiangming

last: Ding

state: CA

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

description:
FPKM_normalized_expression.txt
s3B

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 UCSC trasncripts set using bowtie2. RSEM was uesd to estimated the gene expression and DCC was ued to circRNA prediction and circRNA expression calculation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples

source_name: gallbladder tissue

extract_protocol:
RNA was extracted from the tissue using the Qiagen RNA purificaction kit.
Libraries for RNA-Seq were prepared with Kapa hyper Prep Kits with RiboErase. The workflow consists of rRNA depletion, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: gallbladder

tag: disease state

value: normal


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

value: colon biopsy


title: PC9

last: Wang


title: HM57_UR

value: Uropathogenic Escherichia coli (UPEC)


title: patient4_tumor

description:
FPKM_normalized_expression.txt
s2A

value: tumor


title: UCD-T2DM 2-week RNA-seq Rep #4

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-5193

value: liver

value: 2 weeks


title: tissue- control- 16.9 year old female

value: Female

value: Control


title: patient3_normal

description:
FPKM_normalized_expression.txt
s1B


title: HM54_UR


title: UCD-T2DM pre-diabetic RNA-seq Rep #2

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-5189

value: n/a (Prediabetic)


title: patient3_tumor

description:
FPKM_normalized_expression.txt
s1A


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

value: Male

value: Crohn's Disease


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


title: UCD-T2DM 3-month RNA-seq Rep #5

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-5147

value: 3 months


title: patient2_normal

description:
FPKM_normalized_expression.txt
zhengchang


title: HM17_UR


title: tissue- control- 8.2 year old male


title: tissue- ulcerative colitis- 12.7 year old female

value: UC - pancolitis


title: UCD-T2DM pre-diabetic RNA-seq Rep #3

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-5199


title: tissue- control- 14.2 year old male


title: tissue- ulcerative colitis- 14.8 year old male


title: HM14_UR


title: HM56_UR


title: patient1_normal

description:
FPKM_normalized_expression.txt
aipangshen


title: UCD-T2DM 6-month RNA-seq Rep #3

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4961


title: patient1_tumor

description:
FPKM_normalized_expression.txt
ai


title: HM07_UR


title: tissue- control- 15.5 year old female


title: HM06_UR


title: UCD-T2DM 6-month RNA-seq Rep #5

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-5105


title: HM43_UR


title: UCD-T2DM 2-week RNA-seq Rep #3

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4933


title: HM03_UR


title: tissue- control- 15.1 year old male


title: tissue- control- 11.1 year old male


title: patient2_tumor

description:
FPKM_normalized_expression.txt
aishen


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


title: UCD-T2DM 6-month RNA-seq Rep #4

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4991


title: HM01_UR


title: HM86_UTI

description: human reads removed

source_name: UTI patient urine


title: HM68_UTI

description: human reads removed


title: UCD-T2DM 6-month RNA-seq Rep #2

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4865


title: tissue- control- 11.4 year old male


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


title: UCD-T2DM 3-month RNA-seq Rep #4

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4935


title: UCD-T2DM 2-week RNA-seq Rep #2

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4837


title: tissue- ulcerative colitis- 15.8 year old male

value: UC - proctitis


title: rWT CornOil rep3

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

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

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

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

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

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

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

value: rWT

tag: Sex

value: Liver

value: 12-15 weeks

tag: agent

value: corn oil vehicle

tag: dose

value: control

tag: time (exposure)

value: 19 hours


title: rWT CornOil rep4

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


title: HM60_UTI

description: human reads removed

value: Uropathogenic Escherichia coli (UPEC)


title: UCD-T2DM 3-month RNA-seq Rep #3

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4803

value: liver


title: tissue- control- 16.1 year old female

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

value: colon biopsy


title: UCD-T2DM pre-diabetic RNA-seq Rep #1

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4923


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


title: UCD-T2DM 6-month RNA-seq Rep #1

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4789

value: 6 months


title: tissue- control- 13.4 year old female

value: Female

value: Control


title: rWT CornOil rep2

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

value: Male


title: rWT CornOil rep1


title: rWT TCDD 500 μg/kg rep4

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

value: TCDD

value: 500 μg/kg


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

value: Crohn's Disease


title: UCD-T2DM 3-month RNA-seq Rep #2

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4783

value: 3 months


title: HM56_UTI

description: human reads removed


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


title: UCD-T2DM 3-month RNA-seq Rep #1

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4685


title: UCD-T2DM 2-week RNA-seq Rep #1

description:
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4813

value: 2 weeks


title: rWT TCDD 500 μg/kg rep2

value: rWT

value: Liver


title: HM54_UTI

description: human reads removed


title: rWT TCDD 500 μg/kg rep3

value: 12-15 weeks


title: HM17_UTI

description: human reads removed


title: rWT TCDD 500 μg/kg rep1


title: HM43_UTI

description: human reads removed


title: tissue- ulcerative colitis- 17.3 year old female

value: UC - pancolitis


title: rWT TCDD 5 μg/kg rep3

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

value: 5 μg/kg

value: 19 hours


title: rWT TCDD 5 μg/kg rep2


title: HM14_UTI

description: human reads removed

value: Uropathogenic Escherichia coli (UPEC)


title: tissue- control- 16.2 year old female

value: colon biopsy


title: HM57_UTI

description: human reads removed


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


title: HM07_UTI

description: human reads removed


title: tissue- control- 15.2 year old female

value: Control - infect


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

value: Female


title: DBA TCDD 500 μg/kg rep1

source_name: liver, male DBA/2, TCDD treated, 500 μg/kg


title: rWT TCDD 5 μg/kg rep1


title: DBA TCDD 500 μg/kg rep3


title: DBA TCDD 500 μg/kg rep4


title: tissue- control- 17.9 year old male

value: Control


title: HM06_UTI

description: human reads removed


title: HM03_UTI

description: human reads removed


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

value: Male


title: HM01_UTI

description: human reads removed


title: DBA TCDD 5 μg/kg rep4

source_name: liver, male DBA/2, TCDD treated, 5 μg/kg

value: TCDD


title: DBA TCDD 5 μg/kg rep3


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


title: DBA TCDD 500 μg/kg rep2

value: 500 μg/kg


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

value: Crohn's Disease


title: DBA TCDD 5 μg/kg rep2


title: MTAC-P-2

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

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

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

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

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

value: lung

value: resistant cell line established by mild-TKI treatment


title: tissue- control- 10.5 year old female


title: tissue- control- 16.2 year old male


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


title: DBA TCDD 5 μg/kg rep1


title: PC9-2


title: C57BL CornOil rep4

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

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

value: WT

tag: treatment

value: Corn Oil vehicle

tag: exposure time


title: C57BL CornOil rep3

tag: strain

value: Liver

value: 12-15 weeks


title: DBA CornOil rep3

source_name: liver, male DBA/2, corn oil treated

value: corn oil vehicle

value: control


title: HM66_UTI

description: human reads removed

value: Uropathogenic Escherichia coli (UPEC)


title: Ddc2: IP

city: Madrid

first: Rodrigo

last: Bermejo

address: Calle Ramiro de Maeztu 9

department: Center for Biological Research (CIB-CSIC)

institute: Spanish National Research Council (CSIC)

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

scan_protocol: Arrays were scanned on an Affymetrix Scanner

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

source_name: IP fraction of Ddc2-myc wt HU

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

growth_protocol: Cells were grown in YPD

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

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

tag: phase

value: S-phase

value: HU


title: Rev1-dde: SUP

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


title: Smore Seq PolyA-selected CIP-treated Tap-treated

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

institute: University of Texas at Austin

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

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

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

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

tag: genotype/variation

value: Wildtype

value: PolyA-selected CIP-treated Tap-treated


title: PC9-1

tag: cell line


title: C57BL CornOil rep2

tag: genotype

value: Male

value: 19 hours


title: DBA CornOil rep2

tag: age


title: C57BL TCDD 5 μg/kg rep4

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

value: 5 μg/kg TCDD


title: Smore Seq PolyA-selected Tap-treated

value: PolyA-selected Tap-treated


title: DBA CornOil rep1