title: bisulphite converted DNA from control placenta PL180

source_name: PL180 twin placenta

value: E

value: twins


title: MRA6 Empty Vector-2

status: Public on Feb 05 2019

type: SRA

city: MADISON

first: Vijayasaradhi

last: Setaluri

address: 1300 University Avenue

department: Dermatology

country: USA

institute: University of Wisconsin-Madison

description:
MRA6.data.EMPTY.D2.4
MRA6-EMPTY-D2-4_S4_L003_R1_001.fastq

library_source: transcriptomic

data_processing:
Raw FASTQ files were analyzed for quality using FASTQC, and low quality reads and adaptors were filtered and trimmed using cut-adapt. RSEM was used to map the reads to transcripts from human genome version hg19 and call isoform level expression.
Genome_build: hg19
Supplementary_files_format_and_content: Text File: Contains Reads per Million,  Differential expression and fold change for gene expression

molecule: total RNA

organism: Homo sapiens

source_name: Metastatic tumor

growth_protocol: Cells were maintained and passaged in DMEM, high glucose, pyruvate medium supplemented with 10% FBS and 1% penicillin-streptomycin. BRAF mutation was confirmed by genomic DNA PCR and western blotting for expression of BRAF(V600E) protein. The cell cultures were maintained in a CO2 (5%) incubator at 37oC.

extract_protocol:
RNA samples were extracted and purified using the miRNeasy Mini Kit (#217004, Qiagen, Germany). The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were plated on 6-well plates. After attachment, cells were transduced with equal amounts of either the NICD expression or control lentiviruses.  30 hours after transduction RNA was extracted.

tag: cell type

value: melanoma

tag: genotype

value: BRAF(V600E)/WT NRAS

tag: transduced with

value: empty vector

tag: phenotype

value: MAPKi Sensitive


title: MRA5 NICD-2

description:
MRA5.data.NICD.D2.10
MRA5-NICD-D2-10_S5_L004_R1_001.fastq

value: NICD

value: MAPKi intrinsically resistant


title: MRA5 NICD-1

description:
MRA5.data.NICD.D1.9
MRA5-NICD-D1-9_S1_L005_R1_001.fastq


title: Epi_P0.5_2 3'SAGE-seq

city: Noda, Chiba

first: Kazushige

last: Shiraishi

address: Yamasaki 2669

country: Japan

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by Trimommatic-0.33 and PRINSEQ-0.20.4. Trimmed reads were mapped to the Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Total tag number was adjusted to 1 million tags, and between-sample normalization was performed by using R-3.4.0 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Lung epithelial cells

extract_protocol:
Epithelial cells and fibroblasts from various developmental stages (E18.5, P0.5, P2, P7, P28, and P56) were isolated from C57BL/6 mice. Lungs were cut into small pieces and digested enzymatically using collagenase (Wako, Osaka, Japan), Dispase II (Roche, Basel, Switzerland), and DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Single-cell suspended lung cells were first stained with anti-mouse CD31, CD45, Ter119, CD146, and Epcam antibodies. Cells were next stained with Streptavidin-APC, followed by anti-APC microbeads (Miltenyi). Labeled cells were magnetically depleted. Finally, lineage (CD31, CD45, Ter119, and CD146)– propidium iodide– GFP– Epcam+ live epithelial cells and lineage (CD31, CD45, Ter119, and CD146)– propidium iodide– Epcam– GFP+ fibroblasts were sorted with a MoFlo Astrios flow cytometer (Beckman Coulter).
polyA RNAs were isolated and amplified from donor epithelial cells and fibroblasts according to the protocol described in (Huang H, Nucleic Actd Res, 2014) with some modifications. 3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

value: lineage (CD31, CD45, CD146 and Ter119) negative, Col1a2-GFP negative, Epcam positive epithelial cells

tag: strain

tag: tissue

value: lung

tag: developmental stage

value: Postnatal day 0.5

value: Col1a2-GFP Transgenic


title: bisulphite converted DNA from control placenta PL59

type: genomic

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridised to Illumina HumanMethylationEPIC and HumanMethylation450 Beadchips using standard Illumina protocol

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

data_processing: Minfi package for the R statistical software and in-house R scripts

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PL59 triplet placenta

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from placenta samples using standard phenol/chloroform extraction protocol

value: placenta

tag: gestation

value: D

tag: test

value: opposite sides / triplets


title: Epi_E18.5_2 3'SAGE-seq

value: lineage (CD31, CD45, CD146 and Ter119) negative, Epcam positive epithelial cells

value: Embryonic day 18.5


title: Epi_E18.5_1 3'SAGE-seq


title: MRA5 Empty Vector-2

description:
MRA5.data.EMPTY.D2.2
MRA5-EMPTY-D2-2_S1_L007_R1_001.fastq


title: MRA5 Empty Vector-1

description:
MRA5.data.EMPTY.1
MRA5-EMPTY-1_S1_L003_R1_001.fastq


title: Muscle_pre-diet_8

type: RNA

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

hyb_protocol: Hybridized to Affymetrix Human Gene Human Gene ST Array 2.1 according to manufacturer's protocols in a GeneChip Hybridization Oven 640 (Affymetrix). Arrays were washed and stained with a GeneChip Gluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Pre-processing of data was performed using Robust Multi-array Average (RMA) using oligo and(hugene21sttranscriptcluster.db

label: biotin

source_name: vastus lateralis pre-intervention

label_protocol: Sense strand cDNA was synthesized from total RNA with Ambion® WT Expression Kit (Life Techniologies) and biotin labeled with the Affymetrix® GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: mirVana mRNA extraction kit following manufacturer’s recommendations

value: vastus lateralis

tag: diet

value: pre-diet

tag: disease state

value: obese, non-diabetic


title: bisulphite converted DNA from control placenta PL4881886

source_name: term placenta PL4881886

value: B

value: 1st trimester vs term


title: bisulphite converted DNA from control placenta PL179

source_name: PL179 twin placenta

value: E

value: twins


title: bisulphite converted DNA from control placenta PL58

source_name: biopsy 1 PL58 triplet placenta


title: bisulphite converted DNA from control placenta BCA16172

source_name: 1st trimester BCA16172 CVS


title: bisulphite converted DNA from control placenta BC162905231

source_name: 1st trimester BC162905231 CVS

value: A


title: HONE1 SHROOM2 knockdown cells

city: Guangzhou

first: Xue-Kang

last: Qi

address: Dongfeng East Road 651

department: Department of Experimental Research

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: HONE1 SHROOM2 knockdown cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: The cell lines were cultured in RPMI-1640 medium (Invitrogen, CA) supplemented with 10% fetal bovine serum (Gibco) at 5% CO2, 37°C.

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

treatment_protocol: SHROOM2 knockdown with SHROOM2 shRNA

tag: cell line

tag: genotype/variation

value: SHROOM2 knockdown


title: Muscle_post-diet_6

source_name: vastus lateralis post-intervention

value: post-diet


title: HONE1 cell

source_name: HONE1 cell line

value: wildtype


title: BB1702

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

description: Gene expression data from primary diffuse large B-cell lymphoma

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

scan_protocol: Gene Chips HG-U133 Plus 2.0 were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: RMA normalized using R (v3.4.3), and the RMA Pre-processing function from hemaClass (v1.3.2), available at https://github.com/oncoclass/hemaClass.

label: Biotin

source_name: Primary diffuse large B-cell lymphoma tissue

label_protocol: Affymetrix GeneChip 3' IVT PLUS Reagent Kit (#P/N 902416)

extract_protocol: Total RNA was extracted using a modified protocol combining Trizol reagent (Invitrogen) and mirVana microRNA isolation kit (Ambion/ThermoFisher Scientific)

treatment_protocol: The tumor sample was after removal snap frozen and stored in OCT at -80ºC. From each OCT block, a small fraction of the sample was removed using a scalpel, washed twice in PBS, and homogenized using the TissueLyser II (Qiagen).

tag: abc/gcb/nc class

value: GCB

tag: bags class

value: Centrocyte

tag: probability of being sensitive to vincristine

tag: ipi status

tag: treatment


title: Muscle_pre-diet_4


title: Muscle_post-diet_7


title: Muscle_post-diet_8


title: Muscle_post-diet_4


title: BB1687

value: ABC

value: Centroblast


title: Muscle_post-diet_5


title: Muscle_pre-diet_2


title: Muscle_pre-diet_6


title: Muscle_post-diet_2


title: Muscle_post-diet_3


title: BB1684

value: Naïve


title: Muscle_pre-diet_5


title: internal control

city: Pittsburgh

first: Yuri

last: Bunimovich

state: PA

address: 580 S. Aiken Avenue, 2nd Floor

department: Department of Dermatology

institute: University of Pittsburgh

description:
UC_091316
normal human kidney sample lab standard

hyb_protocol: Fragmented 12 ug cRNAs were mixed in a hybridization buffer (Affymetrix) with water to a final volume of 200 μL. Aliquots of 130 µL of the hybridization cocktail were hybridized on each array at 45°C for 18 h

scan_protocol: Gene chips were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were processed with Bioconductor package affy's rma function using RMA background correction and quantil normalization, and summarided in RMA expression measure. Control probesets and probesets with small SDs (in the lower 30%) were filtered out. Internal control sample was only used for data processing.

source_name: Lab standard: normal kidney sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting from 100ng total RNA.

growth_protocol: Primary adult human Scwann cells, dervied from spinal nerve, were purchased from ScienCell, Inc. Schwann cells were cultured in Schwann cell media (ScienCell) to 90% confluence (ScienCell), and treated with either control medium (RPI-1640) or melanoma conditioned medium (RPMI-1640) for 48 hours at 20% (v/v).

treatment_protocol: Treated with 20% (v/v) of control RPMI-1640 or melanoma cell line-conditioned medium for 48 hours.

tag: cell type

value: normal kidney sample


title: bisulphite converted DNA from control placenta PL4853477_new

source_name: term placenta PL4853477_new

value: placenta


title: MRA6BR Empty Vector-1

description:
MRA6BR.data.EMPTY.D1.5
MRA6-BR-EMPTY-D1-5_S5_L003_R1_001.fastq

value: melanoma

tag: genotype

value: BRAF(V600E)/WT NRAS

tag: transduced with

value: empty vector

value: Acquired resistance to BRAF(V600E)i


title: BB1683

value: NC


title: Muscle_pre-diet_1

value: vastus lateralis

value: pre-diet

value: obese, non-diabetic


title: Muscle_post-diet_1

value: post-diet


title: cell line 2, biological rep3

description:
16_0378
Gene expression data from adult Schwann cells in 397-mel conditined medium

source_name: Schwann cell in 397-mel conditioned medium

value: primary Schwann cells from human spinal nerve

value: melanoma conditioned medium


title: cell line 2, biological rep2

description:
16_0377
Gene expression data from adult Schwann cells in 397-mel conditined medium


title: Muscle_pre-diet_3


title: H581

value: GCB

value: CHOP


title: cell line 3, biological rep3

description:
16_0381
Gene expression data from adult Schwann cells in 624-mel conditined medium

source_name: Schwann cell in 624-mel conditioned medium


title: LuPos_rep6

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: 2.5µg of labeled DNA were taken for the preparation of an hybridization cocktail according Affymetrix/Thermo recommendatations for the hybridization of a 24 array plate. Finally 2.25µg of labeled DNA were hybridized onto mouse gene array plate.

scan_protocol: Affymetrix array plate was hybridized, washed, stained and scanned using an Affymetrix Genetitan 4C device.

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

source_name: LuPos

label_protocol: 500pg of total RNA were amplified according Nugen Ovation protocol (SPIA method) to labell 5µg of sens DNA.

growth_protocol: Freshly isolated mammary luminal cells were pelleted and kept at -80°C before being processed.

extract_protocol: Total RNA was extracted from the cells using RNAeasy Microkit from Qiagen according to the manufacturer's instructions.

value: CD24+ ICAM1+


title: cell line 3, biological rep2

description:
16_0380
Gene expression data from adult Schwann cells in 624-mel conditined medium


title: cell line 2, biological rep1

description:
16_0376
Gene expression data from adult Schwann cells in 397-mel conditined medium


title: cell line 3, biological rep1

description:
16_0379
Gene expression data from adult Schwann cells in 624-mel conditined medium


title: cell line 1, biological rep2

description:
16_0374
Gene expression data from adult Schwann cells in 526-mel conditined medium

source_name: Schwann cell in 526-mel conditioned medium


title: H556

value: ABC

value: Plasmablast

value: Cyclophophamide


title: Muscle_pre-diet_7


title: cell line 1, biological rep1

description:
16_0373
Gene expression data from adult Schwann cells in 526-mel conditined medium


title: cell line 1, biological rep3

description:
16_0375
Gene expression data from adult Schwann cells in 526-mel conditined medium


title: control, biological rep2

description:
16_0371
Gene expression data from control adult human Schwann cells

source_name: Schwann cells treated with control medium

value: control medium


title: control, biological rep1

description:
16_0370
Gene expression data from control adult human Schwann cells


title: Epi_P2_1 3'SAGE-seq

source_name: Lung epithelial cells

value: lineage (CD31, CD45, CD146 and Ter119) negative, Col1a2-GFP negative, Epcam positive epithelial cells

tag: strain

value: lung

value: Postnatal day 2

value: Col1a2-GFP Transgenic


title: control, biological rep3

description:
16_0372
Gene expression data from control adult human Schwann cells


title: LuPos_rep5


title: LuPos_rep4


title: Normal colon tissue 5 replicate 2

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

description: Gene expression

hyb_protocol: Cy3 labeled cRNA was hybridized on 44K or 4x44K oligonucleotide-based Whole Human Genome Microarray (Agilent) according to the manufacturer’s protocol version 4.0.

scan_protocol: Microarrays were washed and processed using an Agilent G2565BA scanner.

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol.

source_name: Normal colon tissue 5

label_protocol: One mg each of cell line or normal human colon RNA (Ambion, Austin, TX) were amplified and labeled with Cy3, respectively, using a T7 RNA Polymerase (Low RNA Input Fluorescent Linear Amplification Kit, Agilent) according to the manufacturer’s protocols

growth_protocol: All of the cell lines were obtained from the ATCC (American Type Culture Collection) and cultured following their recommendations, except p53HCT116, a derivative of HCT116 with a homozygous disruption of TP53 (Bunz et al., 1998), which was kindly provided by Dr. Curtis C. Harris of the National Cancer Institute, NIH.

extract_protocol: DNA and RNA was extracted from the cell lines following standard procedures (http://www.riedlab.nci.nih.gov/protocols. asp). Nucleic acid quantification was determined using the Nanodrop ND-1000 UV-VIS spectrophotometer (Nanodrop, Rockland, DE) and RNA quality was assessed using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Normal colon RNA isolated postmortem from five different donors without a history of colorectal cancer was purchased from Ambion (Applied Biosystems, Foster City, CA).

value: colon tissue


title: LuPos_rep7


title: Normal colon tissue 5 replicate 3

description: Gene expression


title: Normal colon tissue 4 replicate 3

description: Gene expression

source_name: Normal colon tissue 4


title: LuPos_rep2


title: LuPos_rep1


title: LuPos_rep3


title: Normal colon tissue 3 replicate 3

description: Gene expression

source_name: Normal colon tissue 3


title: Normal colon tissue 4 replicate 2

description: Gene expression


title: Normal colon tissue 4 replicate 1

description: Gene expression


title: LuNeg_rep7

source_name: LuNeg

value: CD24+ ICAM1-


title: Normal colon tissue 2 replicate 2

description: Gene expression

source_name: Normal colon tissue 2


title: Normal colon tissue 2 replicate 3

description: Gene expression


title: Normal colon tissue 3 replicate 2

description: Gene expression


title: LuNeg_rep3


title: SW837 cell line replicate 3

description: Gene expression

source_name: SW837 cell line

value: cell line


title: T84 cell line replicate 3

description: Gene expression

source_name: T84 cell line


title: LuNeg_rep4


title: SW837 cell line replicate 2

description: Gene expression


title: Zm_nkd

city: Cambridge

first: Steven

middle: James

last: Burgess

state: Cambridgeshire

address: Department of Plant Sciences, Downing College

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description: DNAse I digestion on deproteinated DNA

library_source: genomic

data_processing:
Reads were mapped to genomes using bowtie2 (Langmead and Salzberg, 2012) and processed using samtools (Li et al., 2009) to remove those with a MAPQ score <42.
Genome_build: The following genome assemblies were used: Bdistachyon_283_assembly_v2.0; Sbicolor_255_v2.0; Sitalica_164_v2; Zmays_284_AGPv3.

organism: Zea mays

source_name: Whole leaf

growth_protocol: S. bicolor, S. italica and Z. mays were grown under controlled conditions at the University of Cambridge in a chamber set to 12 h/12 h light/dark; 28 ºC light/20 ºC dark; 400µmol m-2 s-1 photon flux density, 60% humidity. For germination, S. bicolor and Z. mays seeds were imbibed in H2O for 48 h, S. italica seeds were incubated on wet filter paper at 30 ºC overnight in the dark. Z. mays, S. bicolor and S. italica were grown on 3:1 (v/v) M3 compost to medium vermiculite mixture, with a thin covering of soil. Seedlings were hand-watered. For B. distachyon plants were grown under controlled conditions at the Sainsbury Laboratory Cambridge University, first under short day conditions 14 h/10 h, light/dark for 2 weeks and then shifted to long day 20 h/4 h, light/dark, for 1 week and harvested at ZT20. Temperature was set at 20 ºC, humidity 65% and light intensity 350 µmol m-2 s-1.

extract_protocol:
Deproteinated DNA was extracted using a QIAGEN DNeasy Plant Mini Kit (QIAGEN, UK) according to the manufacturer’s instructions.
The extracted DNA samples were quantified fluorometrically using Qubit 3.0 Fluorometer (Life technologies), and a total of 1 ng of digested DNA was used for library construction. Sequencing ready libraries were prepared using a KAPA Hyper Prep Kit (KAPA Biosystems, London UK) according to the manufacturer’s instructions.

tag: tissue

value: Leaf

value: Fully expanded


title: DonorZ_13_STCO1 A15L/A19L

city: La Jolla

first: Lars

last: Pache

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Kallisto (v0.43) was used to build an index using the GRCh38 Homo sapiens reference transcriptome.
Pseudo-alignment of RNAseq reads and quantification of transcript abundance was performed by Kallisto (v0.43).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated values containing transcript counts and TPM-normalized transcript quantification.

source_name: CD4+ T Cells

growth_protocol: PBMCs from healthy human donors were isolated using lymphocyte separation medium (Biocoll separating solution; Biochrom). CD4+ T cells were negatively isolated using the RosetteSep™ Human CD4+ T Cell Enrichment Cocktail (Stem Cell Technologies) according to the manufacturer’s instructions. Primary cells were cultured in RPMI-1640 medium containing 10% fetal calf serum (FCS) plus 2 mM glutamine, streptomycin (100 µg/ml), penicillin (100 U/ml) and 10 ng/ml interleukin 2 (IL-2) at 37 °C in a 5% CO2 atmosphere. Before infection, cells were stimulated for three days with phytohemagglutinin (PHA) (1 μg/ml).

extract_protocol:
Total RNA was isolated and purified from infected CD4+ T cells using the RNeasy Plus Mini Kit (QIAGEN).
RNA sequencing libraries were generated from 150 ng of RNA using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following manufacturer’s instructions, modifying the shear time to 5 minutes. RNA libraries were multiplexed and sequenced with 50 basepair (bp) single reads (SR50) to a depth of approximately 30 million reads per sample on an Illumina HiSeq4000.

treatment_protocol: CD4+ T cells were infected via spinoculation (2500 g) for 90 min at 37°C and subsequently incubated for 72 hrs at 37°C.

tag: donor id

value: Z

tag: virus

value: STCO1 A15L/A19L


title: LuNeg_rep2


title: Normal colon tissue 1 replicate 2

description: Gene expression

source_name: Normal colon tissue 1


title: DonorZ_12_STCO1 R45K

value: STCO1 R45K


title: Normal colon tissue 1 replicate 3

description: Gene expression


title: p53HCT-116 cell line replicate 3

description: Gene expression

source_name: p53HCT-116 cell line


title: LuNeg_rep6


title: SW.480 cell line replicate 3

description: Gene expression

source_name: SW.480 cell line


title: LuNeg_rep1


title: SW48 cell line replicate 3

description: Gene expression

source_name: SW48 cell line


title: NCI-Hs.716 cell line replicate 1

description: Gene expression

source_name: NCI-Hs.716 cell line


title: SW.480 cell line replicate 2

description: Gene expression


title: NCI-Hs.508 cell line replicate 1

description: Gene expression

source_name: NCI-Hs.508 cell line


title: LS411N cell line replicate 1

description: Gene expression

source_name: LS411N cell line


title: SW48 cell line replicate 2

description: Gene expression


title: SKCO-1 cell line replicate 1

description: Gene expression

source_name: SKCO-1 cell line


title: DonorZ_07_CH077 vpu stop

value: CH077 vpu stop


title: DonorZ_11_STCO1 vpu stop

value: STCO1 vpu stop


title: LuNeg_rep5


title: DLD1 cell line replicate 2

description: Gene expression

source_name: DLD1 cell line


title: ABC a1/g1 fl/fl-LysM-Cre+3

city: Heidelberg

first: Juan

last: Rodriguez-Vita

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Samples were prepared and were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays according to Affymetrix specifications

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.

source_name: Cell sorting by flow cytometry

label_protocol: end-labelling

extract_protocol: Tumor associated macrophages were isolated from tumor bearing mice. Cells were sorted with the following sorting strategy: CD45.2+, Lin- (NK1.1 Ly6G CD5 CD19), CD11b+, CD64+, Tim4+

value: Cre+

tag: tumor stage

value: 6 Weeks post tumor implantation


title: DonorZ_09_CH077 A15L/A19L


title: Colo201 cell line replicate 3

description: Gene expression

source_name: Colo201 cell line


title: DLD1 cell line replicate 3

description: Gene expression


title: ABC a1/g1 fl/fl-LysM-Cre+4


title: LoVo cell line replicate 3

description: Gene expression

source_name: LoVo cell line


title: DonorZ_08_CH077 R45K


title: COLO320DM cell line replicate 1

description: Gene expression

source_name: COLO320DM cell line


title: HCT116 cell line replicate 3

description: Gene expression

source_name: HCT116 cell line


title: HCT116 cell line replicate 2

description: Gene expression


title: HT29 cell line replicate 3

description: Gene expression

source_name: HT29 cell line


title: DonorZ_10_STCO1 wt

value: STCO1 wt


title: DonorZ_04_CH293 R50K


title: ABC a1/g1 fl/fl-LysM-Cre+1


title: ABC a1/g1 fl/fl-LysM-Cre+2


title: DonorZ_06_CH077 wt

value: CH077 wt


title: Colo201 cell line replicate 2

description: Gene expression


title: DonorZ_02_CH293 wt

value: CH293 wt


title: DonorY_13_STCO1 A15L/A19L

value: Y


title: ABC a1/g1 fl/fl-LysM-Cre-2

value: Cre-


title: ABC a1/g1 fl/fl-LysM-Cre-3


title: RockML7_6h_A

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from Y27632/ML7-treated MCF10ATk1 cells - replicate 1

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization on BeadChip Array HumanHT-12-v4

scan_protocol: Illumina hiscanSQ

data_processing: Microarray data underwent background correction, variance stabilization, and quantile normalization using the lumi package of Bioconductor.

source_name: MCF10ATk1 immortalized human mammary epithelial cells

label_protocol: Illumina TotalPrep RNA Amplification kit

growth_protocol: Cells were seeded at low confluence on day 1 in standard growth medium (MCF10ATk1: DMEM/F12 with 1mM Glutamine, 17.5mM D-glucose, antibiotics, 5% Horse Serum, Insulin, hEGF, Cholera Toxin and Hydrocortisone as in Debnath et al., Methods 2003 DOI:10.1016/S1046-2023(03)00032-X).

extract_protocol: Extraction of total RNA with commercial kits (Qiagen), followed by DNAseI digestion to reduce genomic DNA contaminations, was performed according to the manufacturer's instructions.

treatment_protocol: On day 2, cells were treated by supplementing hte medium with DMSO (control cells) or Y27632+ML7 (treated) for 6 hours and harvested for RNA extraction.

value: Y27632+ML7 20microM each


title: DonorZ_03_CH293 vpu stop

source_name: CD4+ T Cells

value: CH293 vpu stop


title: DonorY_10_STCO1 wt


title: ABC a1/g1 fl/fl-LysM-Cre-1


title: ABC a1/g1 fl/fl-LysM-Cre-4


title: RockML7_6h_B

description: Gene expression data from Y27632/ML7-treated MCF10ATk1 cells - replicate 2


title: RockML7_6h_C

description: Gene expression data from Y27632/ML7-treated MCF10ATk1 cells - replicate 3


title: Ctr_6h_B

description: Gene expression data from control-treated MCF10ATk1 cells - replicate 2

value: DMSO (vehicle)


title: Ctr_6h_C

description: Gene expression data from control-treated MCF10ATk1 cells - replicate 3


title: DonorY_08_CH077 R45K


title: DonorZ_01_mock

value: mock


title: DonorY_07_CH077 vpu stop


title: DonorY_06_CH077 wt


title: DonorY_11_STCO1 vpu stop


title: DonorY_09_CH077 A15L/A19L


title: αSMACreER;Foxf1 fl/fl (Knockout)

city: Cincinnati

first: Hannah

middle: M

last: Flood

state: OH

address: 3333 Burnet Ave

department: Department of Pediatrics

institute: CCHMC

description: RNA-seq analysis of isolated stromal cells from KO mouse livers

data_processing:
Allignment was perfomed using the Tophat/Cufflink pipeline. Cuffmerge tool was used to generate Binary Alignment/Map files (BAM files).
BAM files of RNA-seq data were analyzed using Avadis NGS Version 1.3.0 software. Reads were filtered to remove: 1) duplicate reads, 2) non-primary-matched reads, and 3) reads with alignment scores <95.
Quantification was performed on the filtered reads against the RefSeq annotation. Data normalization was performed with the DESeq package. The sequencing depth was estimated by the read count of the gene with the median read count ratio across all genes.
The method was based on the negative binomial distribution, which allows for less restrictive variance parameter assumptions than does the Poisson distribution. The false discovery rate was calculated according to the Benjamini and Hochberg algorithm.
Genes with expression altered by a factor of 1.5 and a false discovery rate of 0.05 in Foxf1fl/fl cells compared with αSMACreER;Foxf1-/- cells were selected for gene set enrichment analysis using ToppGene Suite. Hierarchical clustering was performed by Ward’s method using Euclidean distance metric.
Genome_build: mm10
Supplementary_files_format_and_content: Files are additionally provided for WT and KO mouse cells.

source_name: Knockout (KO)

growth_protocol: Adult, male WT and KO mice were treated with Carbon tetrachloride (CCl4).

extract_protocol:
Liver cell suspension from carbon tetrachloride-treated mice were plated on tissue culture dishes and incubated for 2 hours at 37°C. Supernatant and non-adherent cells were washed off and the adherent cell population was collected for experiments.
Samples were pooled to generate the libraries using the TruSeq RNA library preparation kit and were sequenced on an Illumina HiSeq 2000 sequencer, generating approximately 10 M high quality single end reads (75 base-long reads).

treatment_protocol: Mice were treated with CCl4 for 5 weeks to inuce hepatic fibrosis.

value: Liver

value: Stromal


title: WT_Th9_RA.input_r1

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
base calling was carried out using CASAVA1.8.2/bcl2fastq1.8.4
ATAC-seq, alignment: PE reads were mapped to the mouse genome (mm9 assembly) using Bowtie 1.1.1.
ATAC-seq, peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
RNA-seq, alignment: SE reads were mapped to the mouse genome mm9 using TopHat 2.1.0
RNA-seq, RPKM calculation RNA-seq: RPKMs were calculated using Partek6.6
ChIP-seq, alignment: SE reads were aligned to the mouse genome build mm9 with Bowtie 1.1.1
ChIP-seq, peak calling: Non-redundant and Uniquely mapped reads were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
Genome_build: mm9
Supplementary_files_format_and_content: peak bed files for ATAC-seq & ChIP-seq generated by MACS1.4.2; RPKM files for RNA-seq generated by Partek 6.6

source_name: WT Th9 cells treated with retinoic acid

extract_protocol:
Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody. Aliquots of genomic DNA (input) and immunoprecipitated samples were treated with proteinase K, heated to induce de-cross linking, and purified using columns (D4014, Zymo).
After recovering purified DNA, 5ng or more of DNA was used to generate libraries according to the vendor’s manual for the Illumina platform (Cat#0344; NuGEN).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq  2500 following the manufacturer's protocols.

value: Spleen and lymph nodes

tag: culture condition

value: in vitro culture for 72 hours with anti CD3/28, Th9-promoting cytokines/antibodies, and retinoic acid

tag: chip antibody


title: WT_Th9_RA.K4M3_r1

value: AbCam ab8580


title: DonorY_12_STCO1 R45K

value: STCO1 R45K


title: Foxf1 fl/fl (Wild-type)

description: RNA-seq analysis of isolated stromal cells from WT mouse livers

source_name: Wild Type (WT)


title: WT_Th9_RA.K4m1_r1

value: AbCam ab8895


title: WT_Th9_me3_r1

source_name: WT Th9 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th9-promoting cytokines/antibodies


title: DonorY_05_CH293 A20L/A24L


title: WT_Th9_RA.K27Ac_r1

value: AbCam ab4729


title: DonorY_04_CH293 R50K


title: Human aortic vascular smooth muscle cells-transfected with empty vector [Control1]

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

description: SAMPLE 1

hyb_protocol: Biotinylated cRNA (750 ng) was hybridized at 58 °C for 16 hrs to HumanHT-12 v4 expression BeadChip (Direct Hybridization Assay Kit, Illumina).

scan_protocol: BeadChip was washed, blocked, scanned using (Illumina BeadArray Reader), and Cy3 signal intensity was measured.

data_processing: The data were log2 transformed and normalised via quantile normalisation using lumi R package.

label_protocol: Total RNA (500 ng) was amplified and labelled with biotin using the Illumina Total Prep RNA Amplification Kit (Ambion).

growth_protocol: Cells were cultured in Medium 231 supplemented with smooth muscle growth supplement.

extract_protocol: Total RNA was isolated using High Pure RNA Isolation Kit (Roche Applied Science).

treatment_protocol: Cells were transfected with 2 µg pSUPERIOR.shTRPC1 and empty vector as negative control via electroporation (Neon, Invitrogen) with 2 pulses at 1350 volts for 20 milliseconds and incubated for 48 hours.

tag: cell line

value: Primary Aortic Smooth Muscle Cells; Normal, Human (ATCC® PCS-100-012™)


title: Human aortic vascular smooth muscle cells-transfected with empty vector [Control2]

description: SAMPLE 2


title: Human aortic vascular smooth muscle cells-transfected with silencing vector [Silencing3]

description: SAMPLE 9


title: WT_Th9_me1_r1


title: Human aortic vascular smooth muscle cells-transfected with empty vector [Control3]

description: SAMPLE 3


title: Human aortic vascular smooth muscle cells-transfected with empty vector [Control6]

description: SAMPLE 6


title: Human aortic vascular smooth muscle cells-transfected with silencing vector [Silencing6]

description: SAMPLE 12


title: Ctr_6h_A

description: Gene expression data from control-treated MCF10ATk1 cells - replicate 1


title: Human aortic vascular smooth muscle cells-transfected with silencing vector [Silencing1]

description: SAMPLE 7


title: WT_Th9_input_r1


title: Human aortic vascular smooth muscle cells-transfected with silencing vector [Silencing5]

description: SAMPLE 11


title: Human aortic vascular smooth muscle cells-transfected with silencing vector [Silencing2]

description: SAMPLE 8


title: Human aortic vascular smooth muscle cells-transfected with empty vector [Control5]

description: SAMPLE 5


title: Human aortic vascular smooth muscle cells-transfected with silencing vector [Silencing4]

description: SAMPLE 10


title: Human aortic vascular smooth muscle cells-transfected with empty vector [Control4]

description: SAMPLE 4


title: DonorZ_05_CH293 A20L/A24L

value: Z


title: DonorY_03_CH293 vpu stop

value: Y


title: DonorY_02_CH293 wt

value: CH293 wt


title: Foxp3Sf_Th17_r2

description:
150828_0385_c_s03
RNA-Seq_R23-R70_rpkm.xlsx
R61

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th17 cells

extract_protocol:
For in vitro polarized cells, total RNA was prepared from approximately 500,000 cells using an Ambion mirVana miRNA isolation kit following the manufacturer’s protocol (ThermoFisher AM1560). For in vivo IL-9 producing cells and other subsets, total RNA was prepared from approximately 2,000-10,000 cells using a Trizol-based extraction technique following the manufacturer’s protocol (ThermoFisher 15596026).
Total RNA was subsequently processed to mRNA-seq library using NEBNext Poly(A) mRNA Magnetic Isolation followed by either Ultra II Directional RNA Library Prep kit for Illumina (NEB E7490,  E7760, E7335); or Mondrian Ovation Ultralow according to the vendor’s manual for the Illumina platform (Cat#0344; NuGEN).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2500 following the manufacturer's protocols.

value: in vitro culture for 72 hours with anti CD3/28 and Th17-promoting cytokines/antibodies


title: WT_Th9_K27Ac_r1


title: Foxp3Sf_Th17+RA_r2

description:
150828_0385_c_s04
RNA-Seq_R23-R70_rpkm.xlsx
R62

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th17 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th17-promoting cytokines/antibodies, and retinoic acid


title: DonorY_01_mock


title: Foxp3Sf_iTr+RA_r2

description:
150428_0000_b_s31
RNA-Seq_R23-R70_rpkm.xlsx
R57

source_name: Rag2 OT-II Foxp3Sf (Scurfy) iTreg cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28,  iTreg-promoting cytokines/antibodies, and retinoic acid


title: Foxp3Sf_Th9+RA_r2

description:
150428_0000_b_s30
RNA-Seq_R23-R70_rpkm.xlsx
R56

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th9 cells treated with retinoic acid


title: DonorX_13_STCO1 A15L/A19L

value: X

value: STCO1 A15L/A19L


title: Foxp3WT_Th17_+RA_r2

description:
150828_0385_c_s02
RNA-Seq_R23-R70_rpkm.xlsx
R60

source_name: Rag2 OT-II (WT) Th17 cells treated with retinoic acid


title: Foxp3WT_Th17_r2

description:
150828_0385_c_s01
RNA-Seq_R23-R70_rpkm.xlsx
R59

source_name: Rag2 OT-II (WT) Th17 cells


title: Foxp3Sf_iTr-RA_r2

description:
150428_0000_b_s32
RNA-Seq_R23-R70_rpkm.xlsx
R58

source_name: Rag2 OT-II Foxp3Sf (Scurfy) iTreg cells

value: in vitro culture for 72 hours with anti CD3/28 and iTreg-promoting cytokines/antibodies


title: DonorX_12_STCO1 R45K


title: Foxp3Sf_Th9-RA_r2

description:
150428_0000_b_s29
RNA-Seq_R23-R70_rpkm.xlsx
R55

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th9 cells

value: Spleen and lymph nodes


title: DonorX_11_STCO1 vpu stop

value: STCO1 vpu stop


title: Foxp3Sf_Th2+RA_r2

description:
150428_0000_b_s28
RNA-Seq_R23-R70_rpkm.xlsx
R54

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th2 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th2-promoting cytokines/antibodies, and retinoic acid


title: slice 3, normal

data_processing:
Base-calling performed with Illumina Casava version 1.7
Sequenced reads were mapped to Ensembl homo sapiens GRCh38 assembly (release 90) using HISAT2 v2.1.0 with options -p 8 --dta --rna-strandness RF -t --un-conc
Using Ensembl homo sapines GRCh38 assembly (release 90) as annotation, number of read pairs aligned to each gene in was quantified using HTSeq-count 0.9.0 with options --format bam --order pos --stranded reverse --mode union --minaqual 10 --type exon --idattr gene_id.  Read pairs with more than one reported alignments were discarded and so were read pairs aligned but could not be assigned to any feature, read pairs mapped to more than one feature, and read pairs with mapping quality lower than 10.  Due to significant amount of snoRNA sequences in our data, only coding genes were included for gene expression quantification.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include un-normalized counts for each Sample

source_name: Section 3: tissue adjacent to tumor

growth_protocol: Tissue was obtained from formalin fixed frozen primary human melanoma samples

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy mini kit (Qiagen Inc.).
Samples were processed by the Illumina FFPe TruSeq RNA ACCESS library prep kit. A single adenine was added to 3’ blunt end fragments using an A-tailing Mix for ligation to adapters with a single thymine end. The 30 µl reaction comprised 1.5 µl of resuspension buffer for each sample (100 ng) plus 12.5µl of A-tailing mix followed by incubation (37°C, 1 h) and denaturation (70°C, 5 min). Adapters which serve as linkers to the flow cell surface were ligated to the ds cDNA fragments (P5: 5’ end; P7:3’ end). Unique bar code indices were added as discriminating sample identifiers. Resuspension buffer (2.5 µl), an RNA Adapter Index (2.5 µl) and Ligation Mix (2.5 µl) were added to each sample bringing the volume to 37.5 µl for incubation (30°C, 15 min). Stop Ligation Buffer (5 µl) was added followed by AmpXP beads (42 µl, 10 min, RT) and the cDNA eluted using the Dyna Mag 2 magnet (5 min, RT) as previously described. A 15 cycle PCR enrichment step was performed to select fragments with adapters on both ends by combining Primer Cocktail (5 µl) and PCR Master Mix (25 µl) with each sample (20 µl) followed by denaturation, selective annealing and extension in a thermocycler (30 sec @ 98°C; [15 X: 10 sec @ 98°C, 30sec @ 60°C, 30sec @ 72°C]; 5 min @ 72°C; 4°C Hold). The samples were transferred to 1.5 ml LoBind tubes, mixed with AMPure beads (50 µl XP beads, 10 min incubation) and separated using the Dyna-Mag 2 magnet (5 min). The supernatant from each sample was discarded and the cDNA subjected to two EtOH washes (200 µl of 80% EtOH, 30 sec, 2X) as described previously followed by elution in 17.5 µl Resuspension Buffer.

treatment_protocol: Tissue was formalin fixed and frozen prior to total RNA extraction

value: tissue adjacent to tumor

tag: slice


title: Foxp3Sf_Th2-RA_r2

description:
150428_0000_b_s27
RNA-Seq_R23-R70_rpkm.xlsx
R53

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th2 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th2-promoting cytokines/antibodies


title: slice 3, border

source_name: Section 3: tumor border

value: melanoma tumor border


title: DonorX_10_STCO1 wt

source_name: CD4+ T Cells

value: STCO1 wt


title: Foxp3Sf_Th0-RA_r2

description:
150428_0000_b_s25
RNA-Seq_R23-R70_rpkm.xlsx
R51

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th0 cells

value: in vitro culture for 72 hours with anti CD3/28


title: Foxp3WT_iTr+RA_r2

description:
150428_0000_b_s24
RNA-Seq_R23-R70_rpkm.xlsx
R50

source_name: Rag2 OT-II (WT) iTreg cells treated with retinoic acid


title: slice 3, tumor

source_name: Section 3: tumor center

value: melanoma tumor center


title: slice 2, normal

source_name: Section 2: tissue adjacent to tumor


title: Foxp3WT_Th9+RA_r2

description:
150428_0000_b_s22
RNA-Seq_R23-R70_rpkm.xlsx
R48

source_name: Rag2 OT-II (WT) Th9 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th9-promoting cytokines/antibodies, and retinoic acid


title: DonorX_08_CH077 R45K


title: Foxp3WT_Th9-RA_r2

description:
150428_0000_b_s21
RNA-Seq_R23-R70_rpkm.xlsx
R47

source_name: Rag2 OT-II (WT) Th9 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th9-promoting cytokines/antibodies


title: DonorX_09_CH077 A15L/A19L


title: slice 2, border

source_name: Section 2: tumor border


title: Foxp3WT_Th2+RA_r2

description:
150428_0000_b_s20
RNA-Seq_R23-R70_rpkm.xlsx
R46

source_name: Rag2 OT-II (WT) Th2 cells treated with retinoic acid


title: DonorX_07_CH077 vpu stop

value: CH077 vpu stop


title: slice 2, tumor

source_name: Section 2: tumor center


title: Foxp3WT_Th2-RA_r2

description:
150428_0000_b_s19
RNA-Seq_R23-R70_rpkm.xlsx
R45

source_name: Rag2 OT-II (WT) Th2 cells


title: Foxp3WT_Th0+RA_r2

description:
150428_0000_b_s18
RNA-Seq_R23-R70_rpkm.xlsx
R44

source_name: Rag2 OT-II (WT) Th0 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28 and retinoic acid


title: DonorX_06_CH077 wt

value: CH077 wt


title: Foxp3WT_Th0-RA_r2

description:
150428_0000_b_s17
RNA-Seq_R23-R70_rpkm.xlsx
R43

source_name: Rag2 OT-II (WT) Th0 cells


title: slice 1, normal

source_name: Section 1: tissue adjacent to tumor


title: Foxp3Sf_iTr+RA_r1

description:
150428_0000_b_s16
RNA-Seq_R23-R70_rpkm.xlsx
R42

source_name: Rag2 OT-II Foxp3Sf (Scurfy) iTreg cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28,  iTreg-promoting cytokines/antibodies, and retinoic acid


title: slice 1, border

source_name: Section 1: tumor border


title: DonorX_05_CH293 A20L/A24L

value: X


title: DonorX_04_CH293 R50K


title: Foxp3Sf_Th0+RA_r2

description:
150428_0000_b_s26
RNA-Seq_R23-R70_rpkm.xlsx
R52

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th0 cells treated with retinoic acid


title: Foxp3WT_iTr-RA_r2

description:
150428_0000_b_s23
RNA-Seq_R23-R70_rpkm.xlsx
R49

source_name: Rag2 OT-II (WT) iTreg cells

value: in vitro culture for 72 hours with anti CD3/28 and iTreg-promoting cytokines/antibodies


title: DonorX_03_CH293 vpu stop

source_name: CD4+ T Cells

value: CH293 vpu stop


title: Foxp3Sf_Th9+RA_r1

description:
150428_0000_b_s14
RNA-Seq_R23-R70_rpkm.xlsx
R40

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th9 cells treated with retinoic acid

value: Spleen and lymph nodes


title: Foxp3Sf_Th0+RA_r1

description:
150428_0000_b_s10
RNA-Seq_R23-R70_rpkm.xlsx
R36


title: nanoCAGE-seq H727

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter-trimmed with cutadapt. For nanoCAGE library, we also trimmed the first 17 bases from read 1 to remove adapter and index sequences.
RNA reads were aligned to hg19 genome using STAR. nanoCAGE reads were aligned to hg38.
WGBS reads were aligned to hg19 using bismark with standard parameters.
CAGE reads were trimmed to 100bp and aligned to hg19 using HISAT.
omniATAC reads were aligned to hg19 using bwa-mem.
Genome_build: hg19, hg38
Supplementary_files_format_and_content: RNA and omniATAC bam files were converted to bigWig format. nanoCAGE-seq and CAGE-seq CTSS bedgraphs were generated with CAGEr package. WGBS methylation values of CpGs from bismark analysis is available.

source_name: H727 lung cancer cell line

growth_protocol: H1299, H727 and H838 cells were grown in 10cm culture-treated plates in RPMI1640 + 10% FBS + 1x P/S media. Cells were collected by trypsinization with 0.05% Trypsin-EDTA.

extract_protocol:
RNA was collected using Trizol following manufacture's recommendation.  mRNA for nanoCAGE was extracted using Dynabeads mRNA DIRECT kit following manufacture's recommendation. DNA was extracted with Quick-DNA Miniprep Kit.
CAGE-seq was generated using CAGE Preparation Kit from DNAFORM. nanoCAGE-seq was generated following protocol designated in Poulain et al. 2017. WGBS-seq was generated using EZ DNA Methylation-Direct kit. RNA-seq was generated using TruSeq RNA Library Prep Kit v2. Published omniATAC-seq was followed to generate ATAC-seq data.

value: lung cancer cell line


title: Foxp3Sf_Th2-RA_r1

description:
150428_0000_b_s11
RNA-Seq_R23-R70_rpkm.xlsx
R37

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th2 cells


title: DonorX_02_CH293 wt

value: CH293 wt


title: Foxp3Sf_Th0-RA_r1

description:
150428_0000_b_s09
RNA-Seq_R23-R70_rpkm.xlsx
R35

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th0 cells


title: Foxp3WT_iTr+RA_r1

description:
150428_0000_b_s08
RNA-Seq_R23-R70_rpkm.xlsx
R34

source_name: Rag2 OT-II (WT) iTreg cells treated with retinoic acid


title: AlaRS_2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Embryonic kidney cells

growth_protocol: HEK293 cells were routinely passaged by re-plating culture vessel (normally 1 X 107 in 150 mm dish)

extract_protocol: The RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA). RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: derivation

value: Embryonic kidney 293 cells containing SV40 T-antigen

tag: molecular subtype

value: Immunoprecipitated RNA

tag: antibody

value: AlaRS (Santa Cruz Biotechnology, sc-98547)


title: DonorX_01_mock

value: mock


title: AlaRS_1


title: Foxp3WT_Th9+RA_r1

description:
150428_0000_b_s06
RNA-Seq_R23-R70_rpkm.xlsx
R32

source_name: Rag2 OT-II (WT) Th9 cells treated with retinoic acid


title: Foxp3WT_iTr-RA_r1

description:
150428_0000_b_s07
RNA-Seq_R23-R70_rpkm.xlsx
R33


title: Foxp3Sf_iTr-RA_r1

description:
150428_0000_b_s15
RNA-Seq_R23-R70_rpkm.xlsx
R41

source_name: Rag2 OT-II Foxp3Sf (Scurfy) iTreg cells


title: DonorA1_13_STCO1 A15L/A19L

value: STCO1 A15L/A19L


title: Foxp3WT_Th2+RA_r1

description:
150428_0000_b_s04
RNA-Seq_R23-R70_rpkm.xlsx
R30

source_name: Rag2 OT-II (WT) Th2 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th2-promoting cytokines/antibodies, and retinoic acid


title: Foxp3WT_Th9-RA_r1

description:
150428_0000_b_s05
RNA-Seq_R23-R70_rpkm.xlsx
R31

source_name: Rag2 OT-II (WT) Th9 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th9-promoting cytokines/antibodies


title: Foxp3WT_Th2-RA_r1

description:
150428_0000_b_s03
RNA-Seq_R23-R70_rpkm.xlsx
R29

source_name: Rag2 OT-II (WT) Th2 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th2-promoting cytokines/antibodies


title: TRS_2

value: TRS (Santa Cruz Biotechnology, sc-98543)


title: TRS_1


title: Foxp3Sf_Th9-RA_r1

description:
150428_0000_b_s13
RNA-Seq_R23-R70_rpkm.xlsx
R39

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th9 cells


title: IgG_2

value: IgG (Santa Cruz Biotechnology, sc-66931)


title: Foxp3Sf_Th2+RA_r1

description:
150428_0000_b_s12
RNA-Seq_R23-R70_rpkm.xlsx
R38

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th2 cells treated with retinoic acid


title: DonorA1_11_STCO1 vpu stop

value: STCO1 vpu stop


title: slice 1, tumor

source_name: Section 1: tumor center

value: melanoma tumor center


title: Foxp3Sf_Th17+RA_r1

description:
140722_0265_a_s32
RNA-Seq_R23-R70_rpkm.xlsx
R26

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th17 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th17-promoting cytokines/antibodies, and retinoic acid


title: Foxp3Foxp3WT_Th0+RA_r1

description:
150428_0000_b_s02
RNA-Seq_R23-R70_rpkm.xlsx
R28

source_name: Rag2 OT-II (WT) Th0 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28 and retinoic acid


title: DonorA1_12_STCO1 R45K

source_name: CD4+ T Cells

value: STCO1 R45K


title: DonorA1_10_STCO1 wt

value: STCO1 wt


title: IgG_1


title: Foxp3Sf_Th17_r1

description:
140722_0265_a_s31
RNA-Seq_R23-R70_rpkm.xlsx
R25

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th17 cells

value: Spleen and lymph nodes

value: in vitro culture for 72 hours with anti CD3/28 and Th17-promoting cytokines/antibodies


title: Foxp3Foxp3WT_Th0-RA_r1

description:
150428_0000_b_s01
RNA-Seq_R23-R70_rpkm.xlsx
R27

source_name: Rag2 OT-II (WT) Th0 cells

value: in vitro culture for 72 hours with anti CD3/28


title: Foxp3WT_Th17+RA_r1

description:
140722_0265_a_s27
RNA-Seq_R23-R70_rpkm.xlsx
R24

source_name: Rag2 OT-II (WT) Th17 cells treated with retinoic acid


title: Foxp3WT_Th17_r1

description:
140722_0265_a_s26
RNA-Seq_R23-R70_rpkm.xlsx
R23

source_name: Rag2 OT-II (WT) Th17 cells


title: DonorA1_08_CH077 R45K


title: DonorA1_07_CH077 vpu stop

value: CH077 vpu stop


title: DonorA1_09_CH077 A15L/A19L


title: CAGE-seq H838

source_name: H838 lung cancer cell line

value: lung cancer cell line


title: omniATAC-seq H1299

source_name: H1299 lung cancer cell line


title: DonorA1_05_CH293 A20L/A24L


title: WGBS-seq H838


title: DonorA1_03_CH293 vpu stop

value: CH293 vpu stop


title: DonorA1_04_CH293 R50K


title: Sb_nkd

description: DNAse I digestion on deproteinated DNA

organism: Sorghum bicolor

source_name: Whole leaf

value: Leaf

tag: developmental stage

value: Fully expanded


title: DonorA1_01_mock

value: mock


title: RNA-seq H838


title: HelatD3-HW1_mRNA-seq

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

description:
HelatD3-HW1
mRNA

data_processing:
Alignment to H. e. lativitta genome using tophat.
Read counts overlapping genes were calculated with bedtools.
Differential expression analysis was performed using DESeq2.
Genome_build: Heliconius erato lativitta genome version 1 (http://ensembl.lepbase.org/Heliconius_erato_lativitta_v1/Info/Index)
Supplementary_files_format_and_content: *.sorted.counts.txt: Tab-delimited text files; Read counts overlapping genes were calculated with bedtools.

organism: Heliconius erato lativitta

source_name: Whole wing tissue

growth_protocol: Caterpillars and pupae were raised at ~27C until 3 days post pupation.

extract_protocol:
RNA was isolated from whole wing tissue and poly-A selected using NEB poly-A selection beads.
Libraries were prepared using the NEB RNA library prep kit.

value: Whole wing

value: Day 3 Post-Pupation


title: HepetD3-HW2_mRNA-seq

description:
HepetD3-HW2
mRNA

organism: Heliconius erato petiverana


title: HelatD3-HW2_mRNA-seq

description:
HelatD3-HW2
mRNA


title: HepetD3-HW3_mRNA-seq

description:
HepetD3-HW3
mRNA


title: HelatD3-HW3_mRNA-seq

description:
HelatD3-HW3
mRNA


title: Gr mutant swimming (UOPT--) sample 3

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description:
Sample 15
UOPT--_versus_REST--_DiffExpr.txt
UOPT--_versus_UOPT++_DiffExpr.txt

data_processing:
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
Illumina reads were aligned against the zebrafish genome sequence (GRCz10.80) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9) (Anders and Huber, 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Danio_rerio.GRCz10.80
Supplementary_files_format_and_content: UOPT++_versus_REST++_DiffExpr.txt, UOPT--_versus_REST--_DiffExpr.txt, REST--_versus_REST++_DiffExpr.txt and UOPT--_versus_UOPT++_DiffExpr.txt: Microsoft Office Excel file (.txt) with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Danio rerio

source_name: Gr mutant swimming (UOPT--)

extract_protocol:
White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater (Ambion) at -20 ºC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer’s description (Qiagen Benelux BV, Venlo, the Netherlands). RNA was eluted in 50 μl and quantified by Nanodrop (Thermo Fisher Scientific, Amsterdam, the Netherlands). Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip (Agilent, Amstelveen, Netherlands).
Illumina RNAseq libraries were prepared from 1 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina, San Diego CA, USA).

value: white muscle

value: Gr mutant

tag: treatment

value: swimming


title: HelatD3-FW3_mRNA-seq

description:
HelatD3-FW3
mRNA


title: HepetD3-HW1_mRNA-seq

description:
HepetD3-HW1
mRNA


title: Gr mutant swimming (UOPT--) sample 2

description:
Sample 14
UOPT--_versus_REST--_DiffExpr.txt
UOPT--_versus_UOPT++_DiffExpr.txt


title: HepetD3-FW2_mRNA-seq

description:
HepetD3-FW2
mRNA


title: HelatD3-FW1_mRNA-seq

description:
HelatD3-FW1
mRNA


title: omniATAC-seq H838


title: Gr mutant swimming (UOPT--) sample 1

description:
Sample 11
UOPT--_versus_REST--_DiffExpr.txt
UOPT--_versus_UOPT++_DiffExpr.txt


title: HepetD3-FW1_mRNA-seq

description:
HepetD3-FW1
mRNA


title: HelatD3-FW2_mRNA-seq

description:
HelatD3-FW2
mRNA


title: DonorA1_06_CH077 wt

value: CH077 wt


title: HelatOM-HW-ATAC-seq, rep2

data_processing:
Alignment to H. e. lativitta genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20.
Peak calls were performed with F-seq.
Genome_build: Heliconius erato lativitta genome version 1 (http://ensembl.lepbase.org/Heliconius_erato_lativitta_v1/Info/Index)
Supplementary_files_format_and_content: *sorted.signal.bw: bedWig; RPM normalized files were produced using bedtools.

growth_protocol: Caterpillars and pupae were raised at ~27C until 3 days post pupation or ommochrome pigment deposition before sampling.

extract_protocol:
Nuclei from whole wing tissue were treated with hyperactive Tn5 as described in the ATAC-seq protocol.
Libraries were prepared as described in the ATAC-seq protocol.

value: Ommochrome pupal stage


title: HelatOM-FW-ATAC-seq, rep2


title: Wild-type swimming (UOPT++) sample 3

description:
Sample 13
UOPT++_versus_REST++_DiffExpr.txt
UOPT--_versus_UOPT++_DiffExpr.txt

source_name: Wild-type swimming (UOPT++)

value: Wild-type


title: Wild-type swimming (UOPT++) sample 2

description:
Sample 9
UOPT++_versus_REST++_DiffExpr.txt
UOPT--_versus_UOPT++_DiffExpr.txt


title: HepetOM-HW-ATAC-seq, rep2


title: HepetOM-FW-ATAC-seq, rep2


title: HelatD3-HW-ATAC-seq, rep2


title: Wild-type swimming (UOPT++) sample 1

description:
Sample 8
UOPT++_versus_REST++_DiffExpr.txt
UOPT--_versus_UOPT++_DiffExpr.txt


title: DonorA1_02_CH293 wt

value: CH293 wt


title: Gr mutant resting (REST--) sample 3

description:
Sample 6
UOPT--_versus_REST--_DiffExpr.txt
REST--_versus_REST++_DiffExpr.txt

source_name: Gr mutant resting (REST--)

value: resting


title: HelatD3-FW-ATAC-seq, rep2


title: Gr mutant resting (REST--) sample 2

description:
Sample 5
UOPT--_versus_REST--_DiffExpr.txt
REST--_versus_REST++_DiffExpr.txt


title: HepetOM-FW-ATAC-seq, rep1


title: HepetD3-FW-ATAC-seq, rep2


title: HelatOM-FW-ATAC-seq, rep1


title: HelatOM-HW-ATAC-seq, rep1


title: HelatD3-HW-ATAC-seq, rep1


title: Wild-type resting (REST++) sample 3

description:
Sample 3
UOPT++_versus_REST++_DiffExpr.txt
REST--_versus_REST++_DiffExpr.txt

source_name: Wild-type resting (REST++)


title: HepetOM-HW-ATAC-seq, rep1


title: HepetD3-FW-ATAC-seq, rep1


title: HelatD3-FW-ATAC-seq, rep1


title: Wild-type resting (REST++) sample 2

description:
Sample 2
UOPT++_versus_REST++_DiffExpr.txt
REST--_versus_REST++_DiffExpr.txt


title: HepetD3-FW3_mRNA-seq

description:
HepetD3-FW3
mRNA


title: SPL_CTR2

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description:
after 4 weeks of dox treatment
SPL_DT_TPM.txt

data_processing:
Reads were mapped to the mouse reference genome GRCm38 (mm10) using HISAT2 (v2.1.0).
Reads were assigned and counted using featureCount (v1.6.0).
Differential gene expression analysis was performed using edgeR (v3.24.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files including gene ID and TPM

source_name: spleen

extract_protocol:
Total RNA was isolated from DT and CTR spleens using the miRNeasy Mini Kit (Qiagen) including an on-column DNAse I digestion step.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced using the 75 bp single-read protocol on a NextSeq 500 platform (Illumina).

tag: Sex

value: female

tag: age

value: 16 weeks


title: SPL_CTR3

tag: genotype

value: wild-type

value: male


title: SPL_CTR4

tag: strain


title: HepetD3-HW-ATAC-seq, rep2

tag: tissue


title: SPL_CTR1


title: SPL_DT4


title: SPL_DT3


title: SPL_DT2


title: SPL_DT1


title: HepetD3-HW-ATAC-seq, rep1


title: Gr mutant resting (REST--) sample 1

description:
Sample 4
UOPT--_versus_REST--_DiffExpr.txt
REST--_versus_REST++_DiffExpr.txt


title: Wild-type resting (REST++) sample 1

description:
Sample 1
UOPT++_versus_REST++_DiffExpr.txt
REST--_versus_REST++_DiffExpr.txt


title: SPL_KO2

data_processing:
Quality assessment of the RNA-seq data was performed using NGS QC Toolkit (v2.3.3). Reads with more than 30% of nucleotides with a Phred quality score of less than 20 were removed from further analysis.
Quality-filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using Tophat2 (v2.0.12) with default settings.
Aligned reads were counted per gene using featureCount (v1.4.6).
Differential gene expression analysis was carried out using EdgeR (v3.8.6).
Fragments per kilobase million (FPKM) were obtained using Stringtie (v1.2.2).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files including gene ID and FPKM

extract_protocol:
Total RNA was isolated from Norad+/+ and Norad-/- brains and spleens using the miRNeasy Mini Kit (Qiagen) including an on-column DNAse I digestion step.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced using the 75 bp single-read protocol on a NextSeq 500 platform (Illumina).

value: Norad-/-

tag: strain, sex

value: C57BL/6, male

value: 10 weeks


title: SPL_WT3

value: Norad+/+


title: SPL_KO3


title: SPL_WT2


title: SPL_KO1


title: SPL_WT1


title: BRN_KO3

source_name: brain


title: BRN_KO2


title: SW48, normoxia

city: Tokyo

first: Masatoshi

last: Wakui

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Laboratory Medicine

institute: Keio University School of Medicine

description: gene expression after culture

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 or 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: normoxia

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: Total RNAs were extracted from cell cultures of myxoid liposarcoma cell line using the QIAzol reagent and the miRNeasy Mini Kit (QIAGEN) according to the manufacture’s instructions.

treatment_protocol: The cell lines were cultured under normoxic or hypoxic condition and subjected to transcriptomic profiling.

tag: origin

value: colon cancer


title: HT29, hypoxia

description: gene expression after culture

source_name: hypoxia


title: LCAI, hypoxia

description: gene expression after culture

value: LCAI

value: lung cancer


title: BRN_WT3


title: HT29, normoxia

description: gene expression after culture


title: Caco2, hypoxia

description: gene expression after culture


title: PC9, normoxia

description: gene expression after culture


title: MESO1, hypoxia

description: gene expression after culture

value: mesothelioma


title: MESO1, normoxia

description: gene expression after culture


title: LCAI, normoxia

description: gene expression after culture


title: PC9, hypoxia

description: gene expression after culture


title: SW48, hypoxia

description: gene expression after culture


title: HehimD3-HW3_mRNA-seq

description:
HehimD3-HW3
mRNA

organism: Heliconius himera

value: Whole wing

value: Day 3 Post-Pupation


title: A549, hypoxia

description: gene expression after culture


title: A549, normoxia

description: gene expression after culture


title: SK-BR-3, normal condition

description: gene expression after culture

source_name: normal condition

value: breast cancer


title: Caco2, normoxia

description: gene expression after culture


title: MDA-MB-468, normal condition

description: gene expression after culture


title: MCF7, normal condition

description: gene expression after culture


title: HehimD3-HW2_mRNA-seq

description:
HehimD3-HW2
mRNA


title: BRN_KO_IP_B

data_processing:
Adapters were trimmed using Cutadapt with an e-value set to 0.1.
All reads with a length of at least 18 nt were first aligned to Norad and then to GRCm38 (mm10) using Tophat2 (v2.0.12) with default settings.
Only uniquely mapped reads were retained. PCR duplicates were removed based on the information obtained from the unique molecular identifiers.
The read counts of each IP/input pair were obtained for every bin, requiring at least a 50% sequence overlap. The fold-changes for each IP/input pair were calculated. Bins with fold-changes greater than or equal to 4 were considered as clusters.
Finally, clusters were filtered for those that were detected in both biological replicates of either genotype. Clusters that overlapped with at least 30% of their length were merged.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files including genomic location, cluster ID, gene ID and annotation type.

extract_protocol:
Following immunoprecipitation of PUM2, interacting RNAs were isolated from input and IP samples according to a previously published protocol (Van Nostrand et al. 2016).
Sequencing libraries were similarly prepared as previously described (Van Nostrand et al. 2016). Single-read sequencing was performed on a NextSeq500 platform using a NextSeq 500/550 High Output v2 Kit (Illumina).

treatment_protocol: Fresh brain samples were first minced in ice-cold PBS and then UV crosslinked at 254nm. Two mice per genotpye were used as biological replicates (A and B).

value: C57BL/6, female

value: 3 months


title: MDA-MB-231, normal condition

description: gene expression after culture


title: BRN_KO1


title: BRN_KO_IP_A


title: Normal colon tissue 5 replicate 1

description: Gene expression

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol.

source_name: Normal colon tissue 5

extract_protocol: DNA and RNA was extracted from the cell lines following standard procedures (http://www.riedlab.nci.nih.gov/protocols. asp). Nucleic acid quantification was determined using the Nanodrop ND-1000 UV-VIS spectrophotometer (Nanodrop, Rockland, DE) and RNA quality was assessed using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Normal colon RNA isolated postmortem from five different donors without a history of colorectal cancer was purchased from Ambion (Applied Biosystems, Foster City, CA).

tag: cell type

value: colon tissue


title: BRN_WT1


title: HehimD3-FW3_mRNA-seq

description:
HehimD3-FW3
mRNA


title: BRN_KO_input_A


title: HehimD3-HW1_mRNA-seq

description:
HehimD3-HW1
mRNA


title: BRN_WT2


title: Normal colon tissue 1 replicate 1

description: Gene expression

source_name: Normal colon tissue 1


title: BRN_WT_IP_B


title: HehimD3-FW2_mRNA-seq

description:
HehimD3-FW2
mRNA


title: Normal colon tissue 2 replicate 1

description: Gene expression

source_name: Normal colon tissue 2


title: Normal colon tissue 3 replicate 1

description: Gene expression

source_name: Normal colon tissue 3


title: HehimD3-FW1_mRNA-seq

description:
HehimD3-FW1
mRNA


title: BRN_KO_input_B


title: BRN_WT_input_A


title: T84 cell line replicate 2

description: Gene expression

source_name: T84 cell line

value: cell line


title: ATACseq-Th2-Setdb1-KO

city: Toulouse

first: Veronique

last: Adoue

address: CHU Purpan

institute: CNRS

data_processing:
Trimming of adaptor sequences and removal of low-quality bases (−q value, <15) (Cutadapt).
BWA mem (alignment).
H3K4me1, H3K27ac and ATAC-seq peaks were detected by using the ‘broad’ option of MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include ChIP-seq peaks coordinates for each histone mark or ATAC-seq peaks.

source_name: Spleen CD4+ T cells

growth_protocol: Naïve CD4 T cells were cultured for three days in 96-well flat bottom plates coated with 10 ug/mL anti-CD3epsilon antibody (145-2C11, InVivoMabTM, BioXcell) in RPMI 1640 GlutamaxTM supplemented with 1 mM sodium pyruvate, non-essential amino acids, 10 mM HEPES, 100 units/mL penicillin, 100 ug/mL streptomycin, 50 mM 2beta-mercaptoethanol, 10% fetal calf serum (all from Thermo Fischer Scientific) and 1 ug/mL anti-CD28 antibody (37.51, InVivoMabTM, BioXcell). Th2 medium contained 50 ng/mL recombinant mouse IL-4 (R&D systems) and 10 ug/mL anti-IFNgamma neutralizing antibody (XMG1.2, InVivoMabTM, BioXcell). At day 3, the cells were re-plated in the same conditioning medium but without the anti-CD3epsilon and anti-CD28 antibodies and with 30 IU/mL recombinant IL-2 (Proleukin).

extract_protocol:
DNA purification was performed by column (MinElute PCR purification kit, Qiagen).
Libraries were prepared for sequencing using standard TruSeq Illumina protocols (ChIP-seq) and Nextera DNA Library Prep Kit Illumina (ATAC-seq).

value: Th2 T lymphocytes

tag: number of culture days

value: C57BL/6 Setdb1-/-


title: ATACseq-Th2-WT

value: C57BL/6 Setdb1+/+


title: HehimOM-FW-ATAC-seq, rep2

value: Ommochrome pupal stage


title: HehimOM-HW-ATAC-seq, rep2


title: HehimD3-FW-ATAC-seq, rep2


title: HehimD3-HW-ATAC-seq, rep2


title: T84 cell line replicate 1

description: Gene expression


title: BRN_WT_IP_A


title: BRN_WT_input_B


title: HehimOM-FW-ATAC-seq, rep1


title: SW837 cell line replicate 1

description: Gene expression

source_name: SW837 cell line


title: SW.480 cell line replicate 1

description: Gene expression

source_name: SW.480 cell line


title: HehimD3-HW-ATAC-seq, rep1

source_name: Whole wing tissue


title: HehimOM-HW-ATAC-seq, rep1


title: LoVo cell line replicate 2

description: Gene expression

source_name: LoVo cell line


title: HehimD3-FW-ATAC-seq, rep1


title: 161406A_D020

city: Beijing

first: Tianyu

last: Zhou

address: No.8 Xishiku Street

department: Respiratory and Critical Care

institute: Peking University First Hospital

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: healthy control_current-smoker_Male

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: PBMC were extracted from blood sample of stable COPD patients(n=6) and healthy adults (n=6) and then stored in TRIzol reagent at < -70 ℃ before RNA extaction.

tag: subject status

value: healthy control

tag: smoking status

value: current-smoker

tag: gender

value: Male

value: PBMC


title: HT29 cell line replicate 1

description: Gene expression

source_name: HT29 cell line


title: 161406A_D013

source_name: healthy control_ex-smoker_Male

value: ex-smoker


title: LoVo cell line replicate 1

description: Gene expression


title: p53HCT-116 cell line replicate 1

description: Gene expression

source_name: p53HCT-116 cell line


title: HT29 cell line replicate 2

description: Gene expression


title: 161406A_D011


title: SW48 cell line replicate 1

description: Gene expression

source_name: SW48 cell line


title: p53HCT-116 cell line replicate 2

description: Gene expression


title: 161406A_D003


title: 161406A_D010

source_name: healthy control_non-smoker_Female

value: non-smoker

value: Female


title: 161406A_B021

value: stable COPD patient


title: DLD1 cell line replicate 1

description: Gene expression

source_name: DLD1 cell line


title: 161406A_D004

source_name: healthy control_non-smoker_Male


title: 161406A_B020


title: Colo201 cell line replicate 1

description: Gene expression

source_name: Colo201 cell line


title: 161406A_B013


title: PS2_plus_TEX

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Read quality trimming, length filtering and mapping: READmeption v0.4.3 ; segemehl  0.2.0
Coverage Calculation: READmeption v0.4.3
Genome_build: NC_002976.3,NC_006663.1
Supplementary_files_format_and_content: wiggle format, nucleotide wise coverages

organism: Staphylococcus epidermidis

source_name: clinical isolate, septicemia

growth_protocol: An overnight culture of Staphylococcus epidermidis was diluted 1:1000  in prewarmed Trypticase™ Soy Broth (TSB; BD BBL™) and grown at 37°C to early-exponential growth stage (OD600 = 1) with a 1:5 medium to flask ratio.

extract_protocol:
Cells were disrupted mechanically using Lysing Matrix E glass bead tubes and the FastPrep® Instrument (MP Biomedicals) and total RNA was extracted using the hot phenol technique. In brief, the supernatant of the disrupted cells was mixed with SDS (1 %), sodium acetate (pH 5.5, 0.1 M) and phenol (1:1) and incubated at 64°C in a water bath for 10 min. The aqueous phase was then transferred to PLG tubes (phase-lock gel tubes, cat. no. 2302830, 5 Prime) and after chloroform extraction (1:1), the aqueous phase was again transferred to fresh tubes and the RNA precipitated with 4X vol. ethanol/3 M sodium acetate pH 6.5 (30:1 mix) at  20°C overnight. Pelleted RNA was washed with 70 % ethanol and finally solved in RNase-free water and remaining genomic DNA was eliminated by DNase I treatment.
For depletion of processed transcripts, equal amounts of RNA were incubated with Terminator 5'-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020). The transcripts were not fragmented in order to get mainly sequencing reads of the 5'-end of the transcripts. Libraries for Illumina sequencing of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/) as described previously (Berezikov et al.,2006), but omitting the RNA size-fractionation step prior to cDNA synthesis. Equal amounts of RNA samples were poly(A)-tailed using poly(A) polymerase. Then, the 5'-triphosphates were removed by applying tobacco acid pyrophosphatase (TAP) resulting in 5'-monophosphate. Afterwards, a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. The resulting cDNA libraries were sequenced using a HiSeq 2500 machine (Illumina) in single-read mode and running 100 cycles.

treatment_protocol: Samples from bacterial cultures were mixed with 0.2X vol. STOP mix solution (95 % (v/v) ethanol/ 5 % (v/v) aqua-phenol, cooled to  20°C) for immediate RNA stabilization.

tag: isolate

value: exponentially growing cells

value: TEX-treated

tag: isolation source

value: blood culture

tag: phenotype

value: Protein biofilm matrix producer


title: Pputida_KT2440_hfq-

city: Cantoblanco

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description: HFQ

data_processing:
Quality check: Quality of raw sequences in FASTQ format was checked with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Alignment: Reads were aligned against the P. putida KT2440 genome (NCBI reference sequence NC_002947.3) using Bowtie2 software (Langmead and Salzberg, 2012) employing the default parameters
Gene Quantification: Unique aligned reads were assigned to genes with htseq-count using parameters for stranded single-end reads
Differential Expression: the differential expression of genes between samples was quantified using the Bioconductor edgeR package (Robinson et al., 2010), employing the default parameters
Genome_build: NC_002947.3
Supplementary_files_format_and_content: tab-delimited text files include normalized gene expression values as calculated by edgeR (linear scale)

organism: Pseudomonas putida

source_name: bacterial culture

growth_protocol: P. putida strains KT2440, KT2440Δhfq, KTVC, and the double mutant KTHC, were cultured in M9 minimal salts medium containing succinate as the carbon source to a turbidity of 0.6.

extract_protocol:
Cells were collected by centrifugation at 4°C and total RNA purified using the RNeasy kit (QIAGEN). It was then treated with the RNase-free DNase Set Kit (QIAGEN) to completely eliminate all residual DNA. RNA quality was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Ribosomal RNA was eliminated using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). Directional (strand-specific) libraries were constructed using the Illumina mRNA Sequencing Sample Preparation Kit (TruSeq) and sequenced in single-end-read format (1x150) using the Illumina HiSeqTM 2000 system (Illumina).

value: delta hfq


title: 161406A_B011


title: Pputida_KT2440_crc-_hfq-

value: delta crc / delta hfq


title: 161406A_B012


title: 161406A_B009


title: Pputida_KT2440_crc-

description: CRC

value: delta crc


title: PS2_minus_TEX

value: TEX-untreated


title: HCT116 cell line replicate 1

city: Bethesda

first: Yue

last: Hu

address: 50 South Drive, Bldg. 50, Rm. 1408

institute: NCI

description: Gene expression

source_name: HCT116 cell line

value: cell line


title: WT rep3

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

data_processing:
FastQC was conducted for Quality control (QC) of RNA-seq reads
Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads
Trimmed reads were mapped to the Rattus norvegicus reference genome by the Hisat 2(version:2.0.4)
String Tie(version:1.3.0) was performed for each gene count from trimmed reads
Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

extract_protocol:
Cerebellar cortex tissues were removed, flash frozen and homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Sprague-Dawly (SD)

value: 10-week old age

tag: genotype/variation

value: wild type

value: Cerebellum cortex


title: WT rep2


title: WT rep1


title: bisulphite converted DNA from control placenta PL58_b

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

data_processing: Minfi package for the R statistical software and in-house R scripts

source_name: biopsy 2 PL58_b triplet placenta

extract_protocol: genomic DNA was extracted from placenta samples using standard phenol/chloroform extraction protocol

value: placenta

tag: gestation

value: D

tag: test

value: opposite sides / triplets


title: Si_nkd

city: Cambridge

first: Steven

last: Burgess

address: Department of Plant Sciences, Downing College

institute: University of Cambridge

description: DNAse I digestion on deproteinated DNA

data_processing:
Reads were mapped to genomes using bowtie2 (Langmead and Salzberg, 2012) and processed using samtools (Li et al., 2009) to remove those with a MAPQ score <42.
Genome_build: The following genome assemblies were used: Bdistachyon_283_assembly_v2.0; Sbicolor_255_v2.0; Sitalica_164_v2; Zmays_284_AGPv3.

organism: Setaria italica

source_name: Whole leaf

extract_protocol:
Deproteinated DNA was extracted using a QIAGEN DNeasy Plant Mini Kit (QIAGEN, UK) according to the manufacturer’s instructions.
The extracted DNA samples were quantified fluorometrically using Qubit 3.0 Fluorometer (Life technologies), and a total of 1 ng of digested DNA was used for library construction. Sequencing ready libraries were prepared using a KAPA Hyper Prep Kit (KAPA Biosystems, London UK) according to the manufacturer’s instructions.

value: Leaf

tag: developmental stage

value: Fully expanded


title: bisulphite converted DNA from control placenta PL55_b

source_name: biopsy 2 PL55_b placenta

value: C

value: opposite sides


title: PS10_plus_TEX

value: exponentially growing cells

tag: treatment

value: TEX-treated

value: blood culture

value: PIA biofilm matrix producer


title: CSB+/- rep2

tag: age

value: heterozygous mutant for CSB; CSBR571X/-

tag: tissue


title: CSB+/- rep1


title: Bd_nkd

description: DNAse I digestion on deproteinated DNA

organism: Brachypodium distachyon


title: bisulphite converted DNA from control placenta PL55

source_name: biopsy 1 PL55 placenta


title: Mature hepatocytes MH-2

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

institute: Sapporo Medical University School of Medicine

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction. Expression profiles were analyzed using an oligo microarray (SurePrint G3 Rat Gene Expression v2 G4853B).

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction

source_name: Mature hepatocytes isolated from fresh livers.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: LN111 were passaged and cultured cells on laminin111-coated dishes. LN511 were passaged and cultured cells on laminin511-coated dishes. Mat were passaged and cultured cells on matrigel-coated dishes.

extract_protocol: Total RNAs of prepared cells were extracted using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were suspended in serum-free Dulbecco’s modified Eagle’s medium/Nutrient Mixture Ham F-12 (DMEM/F12; Sigma-Aldrich Co., St.Louis, MO) supplemented with 20 mM HEPES (Dojindo Laboratories, Kumamoto, Japan), 25 mM NaHCO3 (Kanto Chemical Co. Inc., Tokyo, Japan), 30 mg/L L-proline (Sigma-Aldrich Co.), 0.1% bovine serum albumin (BSA; Serologicals Proteons Inc., Kankakee, IL), 10 mM nicotinamide (Sigma-Aldrich Co.), 1 mM ascorbic acid-2 phosphate (Asc2P; Wako Pure Chem. City, Japan), 10−7 M dexamethasone (Dex; Wako Pure Chem.), 0.5 mg/L insulin-transferrin-selenium (ITS-X; GIBCO-BRL Invitrogen, Grand Island, NY), 10 ng/mL epidermal growth factor (EGF; BD Biosciences, San Jose, CA) and antibiotics.

tag: strain

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]

value: Liver

value: mature heptocytes (MH)


title: bisulphite converted DNA from IUGR placenta 217

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

source_name: placenta 217 IUGR

tag: iugr

value: yes

tag: pre-eclampsia

value: no


title: bisulphite converted DNA from IUGR placenta 98

source_name: placenta 98 IUGR

value: placenta


title: G4

city: Leioa

first: Ander

middle: Hernández

last: Plágaro

state: Bizkaia

address: Barrio Sarriena S/N

department: Immunology, Microbiology and Parasitology

institute: University of the Basque Country

description:
6 d Stress, Replic 3
processed data file: counts.txt

data_processing:
Base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 2.7.6) and followed by generation of FASTQ sequence files by CASAVA.
The processed RNA-seq reads were mapped against Vibrio harveyi reference genome (Vibrio harveyi ATCC 43516) (accession number GCA_001558435.1) with STAR (Dobin et al., 2013) and were further quantified with RSEM (Li and Dewey, 2011). Information about some sRNAs initially absent in the annotation of V. harveyi ATCC 43516 genome were added to the annotation file by performing a highly restrictive BLAST search by using the sequences of V. campbellii ATCC BAA-116 sRNAs retrieved from RFAM and BSRD databases as queries.
Functional annotation of other genes was performed by blasting each assembled gene sequence to find homology to other V. harveyi genes already annotated in the NCBI database and the functional annotations of the best hits was used for the final annotations of transcripts revealed by RNAseq.
Calculation of expression values was performed with the assistance of DESeq2 R.
Genome_build: GCA_001558435.1
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file includes read counts.
Supplementary_files_format_and_content: modified_genome_with_sRNAs.gtf

organism: Vibrio harveyi

source_name: cell pellet

growth_protocol: The survival assays were performed in triplicate with Vibrio harveyi ATCC® 14126™ incubated in natural seawater, which was sampled in the Port of Armintza in the Bay of Biscay, 43°26’24’’N and 2°54’24’’W and then filter sterilized and autoclaved. The experiments were carried out in glass flasks beforehand cleaned with H2SO4 (97%, v/v), rinsed with deionized water and heated at 250°C for 24 h to avoid any presence of residual organic matter. For each experiment, V. harveyi was semi-aerobically grown overnight at 26°C (optimal temperature for V. harveyi growth) in marine broth (MB) (Panreac) and aliquots of the stationary phase cultures were used to inoculate sterile natural seawater to obtain a final density of 10^8 cells mL−1. The resulting inoculates of V. harveyi were incubated in dark with shaking (90 rpm) at 30°C.

extract_protocol:
Cell pellets were collected by centrifugation, total RNA was extracted with TRIzol reagent (Ambion) and PureLink RNA Mini Kit (Ambion) and treated with DNAseI (Invitrogen).
The libraries were prepared from total RNA by using ScriptSeq Complete kit (Illumina) optimized for bacterial RNA. The kit included the Ribo-Zero™ (Bacteria) rRNA removal kit and the ScriptSeq™ v2 Kit with ScriptSeq Index PCR Primers Set. The preparation of libraries was carried out following the manufacturer’s instructions.

tag: strain/background

value: 30C for 6d


title: bisulphite converted DNA from IUGR placenta 67

source_name: placenta 67 IUGR


title: G3

description:
6 d Stress, Replic 2
processed data file: counts.txt


title: CSBmut rep5

value: Sprague-Dawly (SD)

value: 10-week old age

value: homozygous mutant for CSB;  CSBR571X/R571X

value: Cerebellum cortex


title: Pputida_KT2440_WType

first: Juan

description: WTYPE

tag: genotype

value: Wild Type


title: G2

description:
6 d Stress, Replic 1
processed data file: counts.txt


title: bisulphite converted DNA from IUGR placenta 73

source_name: placenta 73 IUGR


title: bisulphite converted DNA from IUGR placenta 216

source_name: placenta 216 IUGR


title: bisulphite converted DNA from IUGR placenta 91

source_name: placenta 91 IUGR


title: bisulphite converted DNA from IUGR placenta 90

source_name: placenta 90 IUGR


title: F4

description:
3 d Stress, Replic 3
processed data file: counts.txt

value: 30C for 3d


title: CSBmut rep4


title: Mature hepatocytes MH-1

tag: cell type


title: Primary rat small hepatocytes Mat-3

source_name: Passaged and cultured cells on matrigel-coated dishes

value: small hepatocytes


title: IPO3

city: Changsha

first: Pengpeng

last: Zhang

state: Hunan

address: No.138 Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. When Data was extracted, Quantile normalization and subsequent data processing were conducted to use the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through fold change and p-value (fold change ≥2.0 and p-value <0.05)

source_name: liver

label_protocol: total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was extracted from 9 frozen mouse liver tissues (selected 3 samples from each group randomly) using TRIzol (Invitrogen, USA) according to manufacturer’s instructions.

value: after I/R , 3 cycles of 5 seconds ischemia followed by 5 seconds of reperfusion before reperfusion phase

value: liver

tag: gender

value: male

value: 8 week


title: bisulphite converted DNA from IUGR placenta 64

source_name: placenta 64 IUGR


title: CSBmut rep3


title: bisulphite converted DNA from IUGR placenta 109

source_name: placenta 109 IUGR


title: Primary rat small hepatocytes Mat-2

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]

value: Liver


title: bisulphite converted DNA from IUGR placenta 45

source_name: placenta 45 IUGR

value: yes


title: bisulphite converted DNA from IUGR placenta 55

source_name: placenta 55 IUGR

value: no


title: F3

description:
3 d Stress, Replic 2
processed data file: counts.txt


title: IPO2


title: bisulphite converted DNA from IUGR placenta 160

source_name: placenta 160 IUGR

value: placenta


title: F2

description:
3 d Stress, Replic 1
processed data file: counts.txt


title: Mature hepatocytes MH-3

value: mature heptocytes (MH)


title: CSBmut rep1

value: Sprague-Dawly (SD)


title: CSBmut rep2

value: 10-week old age


title: Primary rat small hepatocytes Mat-1


title: IPO1


title: E4

description:
12 h Stress, Replic 3
processed data file: counts.txt

value: 30C for 12h


title: bisulphite converted DNA from IUGR placenta 37

source_name: placenta 37 IUGR


title: gl2

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

data_processing:
Single-cell raw fastq files were processed by 10X Chromium cell ranger pipeline v2.1.1
only UMI count data was used for downstream analysis
Genome_build: TAIR10
Supplementary_files_format_and_content: 5way_merge_raw.tsv contains the raw count for all 5 samples; The  barcodes are included in the column header line in the format of 'sample_sample_cellBarcode'.
Supplementary_files_format_and_content: The tar archive on the series record contains Cell Ranger (Ver. 2.1.1) output from sequence reads, separated by batch (TSV, MTX).

organism: Arabidopsis thaliana

source_name: gl2_protoplasts from roots

growth_protocol: Plants grow on MS media for 5 DAG (day after germination).

extract_protocol:
After Isolating protoplasts from roots, load into 10X Genomics unit for single-cell cDNA library construction.
Libraries were prepared for sequencing using 10X Genomics protocols; R1 is technical and R2 contains the real biological information.

tag: ecotype background

value: Landsberg erecta background

tag: genotype/varaition

value: gl2 mutant

tag: development stage

value: 5 day after germination

value: root

value: protoplasts


title: IR3

value: ischemia 1h and reperfusion 4h

value: liver


title: bisulphite converted DNA from control placenta 9

source_name: placenta 9 control


title: CSBmut rep6

tag: strain background

tag: genotype/variation

value: homozygous mutant for CSB;  CSBR571X/R571X

value: Cerebellum cortex


title: bisulphite converted DNA from control placenta 35

source_name: placenta 35 control


title: rhd6-1

source_name: rhd6-1_protoplasts from roots

value: mixed Columbia/Ws background

value: rhd6 mutant


title: bisulphite converted DNA from control placenta 172

source_name: placenta 172 control

value: no


title: Primary rat small hepatocytes LN511-2

source_name: Passaged and cultured cells on LN511-coated dishes

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]

value: Liver

value: small hepatocytes


title: bisulphite converted DNA from control placenta 58

source_name: placenta 58 control

value: placenta


title: E2

description:
12 h Stress, Replic 1
processed data file: counts.txt

source_name: cell pellet

value: 30C for 12h


title: IR2

value: male

value: 8 week


title: PS10_minus_TEX

source_name: clinical isolate, septicemia

tag: isolate

value: exponentially growing cells

value: TEX-untreated

tag: isolation source

value: blood culture

tag: phenotype

value: PIA biofilm matrix producer


title: Primary rat small hepatocytes LN511-1


title: E3

description:
12 h Stress, Replic 2
processed data file: counts.txt

tag: treatment


title: WT_rep3

source_name: WT_protoplasts from roots

value: wild type

value: 5 day after germination

tag: tissue

value: root

value: protoplasts


title: C2

description:
Control, Replic 2
processed data file: counts.txt

value: 26C (control)


title: C4

description:
Control, Replic 3
processed data file: counts.txt


title: Primary rat small hepatocytes LN111-3

source_name: Passaged and cultured cells on LN111-coated dishes

tag: strain


title: WT_rep2


title: bisulphite converted DNA from control placenta 7

source_name: placenta 7 control

tag: iugr

value: no


title: bisulphite converted DNA from control placenta 3

source_name: placenta 3 control

tag: pre-eclampsia


title: bisulphite converted DNA from control placenta 34

source_name: placenta 34 control


title: IR1

source_name: liver

value: ischemia 1h and reperfusion 4h

value: liver

tag: age


title: C1

description:
Control, Replic 1
processed data file: counts.txt

tag: strain/background


title: bisulphite converted DNA from control placenta 1

source_name: placenta 1 control


title: Primary rat small hepatocytes LN111-1

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]

value: Liver

tag: cell type

value: small hepatocytes