title: NAT4

city: Guangzhou

first: Yuming

last: Luo

state: Guangdong

address: 107 Yanjiang West Avenue,Yuexiu district

department: General Surgery

country: China

institute: Sun yat-sen Memorial Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:hg38）using STAR（version:2.5）.
The circRNAs were identified using CIRI（version:2.0.5）and find_circ（version:1.2）.Quantity of gene-expression level was estimated by Reads Per Billion Mapped Reads (RPB).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPB values for each sample.

source_name: pancreas

extract_protocol:
PDAC or normal adjacent tissues were removed, flash frozen in liquid nitrogen and total RNA was extracted using Trizol reagent. The ribosomal RNA was removed using the Ribozero series kit and linear RNA was digested using RNaseR.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: normal pancreas


title: TG-KEO11_S11

status: Public on Aug 29 2019

type: SRA

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

country: USA

institute: University of Chicago

description:
sample name in processed data file:
BALBcJ 4
Ileum.tsv

library_source: transcriptomic

data_processing:
RNA-Seq reads were aligned to the Mus musculus reference with Ensembl gene annotation (GRCm38) by Kallisto (v0.44.0; default settings) for transcript quantification.
Technical replicates were pooled together and data is treated as additive for analysis purposes.
mRNA expression was quantified at transcript level (transcript per million; TPM) and then summarized into gene level (TPMs summed over all gene transcripts) measurements.
Gene level TPMs were log2 (n+1)-transformed for further analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file of Gene level TPMs for Colon, Ileum and Duodenum/Jejunum samples sequenced from BALB/cJ and C57BL/6J mice

molecule: total RNA

organism: Mus musculus

source_name: Ileum

extract_protocol:
RNA extraction was performed using PureLink RNA mini kit (Invitrogen, USA) according to the manufacturer’s instructions.
RNASeq libraries were prepared using Illumina TotalRNA TruSEQ kits (RiboZero 753 depletion).

tag: mouse-id

value: BALBcJ 4

tag: tissue

value: Ileum

tag: strain

value: BALB/cJ


title: transgenic line, anaerobiosis, replicate 2

type: RNA

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST was solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS. All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

scan_protocol: Scanning was performed on a Axon GenePix 4000A scanner. Laser was set at 33% power.

data_processing: Data extraction was carried out using the GenePix Pro 7 software. The normalization between arrays was performed using the quantile method.

organism: Citrus sinensis x Citrus trifoliata

source_name: root

label_protocol: Six µg of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions

growth_protocol: Three weeks old wild type (WT) and transgenic Carrizo citrange (TCC) plants were grown on MSC agar medium (Caruso et al. 2011) in a controlled growth chamber under a light intensity of 45 µmol m-2 s-1 with a 16/8 h (day/night) photoperiod (27°C, 60% relative humidity).

extract_protocol: Total RNA was extracted from WT and transgenic leaves using TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

treatment_protocol: For the anoxic and recovery experiments, plants were flushed for 24 h at 5 l h-1 with 100% N2 under sterile conditions. After the treatments, WT and TCC plants were transferred into tubes containing fresh MSC agar medium and allowed to recover for two weeks under normoxic conditions in a controlled growth chamber at 27°C.

value: Transgenic Line (Carrizo plus Mybleu)

tag: culture condition

value: anoxia

value: root

tag: age

value: 3 weeks


title: 12_DP4_1

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description: sample name: 22

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: PRJNA186477
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

organism: Panagrellus redivivus

source_name: embryo

extract_protocol:
Egg shells were removed from a Panagrellus redivivus embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.

tag: developmental stage

value: 12 cell

tag: cell type

value: embryonic cell


title: 12_r10_1

description: sample name: 21


title: transgenic line, anaerobiosis, replicate 1


title: Wild Type, anaerobiosis, replicate 1

value: Wild Type Carrizo


title: Wild Type, anaerobiosis, replicate 3


title: TG-KEO16_S16

description:
sample name in processed data file:
BALBcJ 6
Colon.tsv

source_name: Colon

value: BALBcJ 6

value: Colon


title: NAT3

organism: Homo sapiens


title: 12_r9_1

description: sample name: 20


title: NAT2


title: TG-KEO15_S15

description:
sample name in processed data file:
BALBcJ 5
Duodenum.tsv

source_name: Duodenum/Jejunum

value: BALBcJ 5

value: Duodenum/Jejunum


title: 12_r8_1

description: sample name: 19


title: 8_r1_1

description: sample name: 23

value: 8 cell


title: TEW6

city: Cincinnati

first: Sneha

last: Sitaraman

state: Ohio

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw image data file was transformed to sequenced reads by CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using STAR v2.5 with maximal mappable prefix method with parameter mismatch=2
HTSeq v0.6.1 was used to count the read numbers mapped of each gene with parameter -m union
Differential expression analysis was performed using the DESeq2 R package (2_1.6.3) with parameter padj<0.05
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes FPKM for each sample, gene name, chromosome, strand,  start, end, gene length, gene type and gene description

source_name: Alveolar type 2 epithelial cell RNA

growth_protocol: Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
Alveolar type 2 epithelial cells were isolated by magnetic activated cell sorting as desctibed in Rindler et al, doi: 10.1172/jci.insight.97381. Total RNA was extracted from freshly isolated cells using Rneasy mini prep kit (Qiagen). Total RNA was sent to Novogene for RNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed tamoxifen chow for 7 days prior to harvest on day 9

value: lung epithelial cells

value: 12 weeks

tag: genotype

value: SftpcWT/CreER (control)


title: TG-KEO1_S1

description:
sample name in processed data file:
BALBcJ 1
Colon.tsv

value: BALBcJ 1


title: PDAC5

value: pancreatic cancer


title: NAT5

value: normal pancreas


title: 12_r6_1

description: sample name: 18


title: NAT1


title: TEW5


title: 12_r5_1

description: sample name: 17


title: PDAC4


title: TEW4


title: 12_r4_1

description: sample name: 16


title: Wild Type, anaerobiosis, replicate 2

value: anoxia


title: 39plusstrand

city: Valencia

first: Manuel

last: Martín-Expósito

state: Valencia

address: Jaume Roig 11

department: Gene Expression and RNA Metabolism

country: Spain

institute: Instituto de Biomedicina de Valencia (IBV-CSIC)

description: 20 minutes under 39 ºC

data_processing:
Library strategy: PAR-CLIP
Sequencing data was demultiplexed as Jamonnak et al, 2011
Reads were trimmed of the 3’ adaptor using Sarah Wheelan wrapper (Schaughency et al, 2014)
Sequences were condensed to eliminate PCR artifacts and aligned to SacCer3 genome (R64-1-1) by using Bowtie 1.1.1.
In-house scripts and a Pysam python library were used to find PAR-CLIP specific mismatches.
Read coverage over gene body was calculated by using geneBody_coverage.py function from RSeqQC toolkit.
Genes models described in gtf file version 2.2 were used for gene coverage and binding level computation.  Binding levels per gene were computed by using HTSeq count tool.
RPKM and Trimmed Mean of M-values normalization approaches were applied.
Genome_build: R64
Supplementary_files_format_and_content: Tab-delimited text files include RPKM and TMM normalized values for each sample, and Wiggle track format

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells were grown overnight at 30 ºC in YPD. Cells at an OD600 of 0.1 were seeded into sterile cross-linking media (SC-URA supplemented with 2% glucose, 40 mg/L adenine, 60 µM uracil, and 1 µM biotin) and incubated until an OD600 of 0.6-0.8 was reached.

extract_protocol:
Cells lyses in SamplePrep 6870 freezer mill (SPEX SamplePrep) were performed. Lysates were sonicated and ultracentrifugated. Solutions were incubated in Ni-NTA agarose nickel beads (Qiagen). Incubation with streptavidin beads and treatment with RNase was accomplished. Lysates were treated with Thermosensitive Alkaline Phosphatase (Promega), T4 PNK (New England Biolabs) and 32P γ-ATP. Adaptors were bound to RNA and then incubated with Proteinase K (New England Biolabs). RNA obtained was purified by acid phenol/chloroform extraction/ethanol precipitation.
Reverse transcription, PCR amplification, cDNA multiplexing and gel extraction of cDNA libraries were accomplished.

treatment_protocol: Cells were incubated for 30 minutes at 30 ºC (non-stressed condition) or for 10 minutes at 30 ºC followed by 20 minutes at 39 ºC (heat-stressed condition). Both were incubated with 4-thiouracil for 45 minutes at 30 ºC or 25 minutes at 30 ºC and 20 minutes at 39 ºC. Irradiation with 365 nm UV from an LC-L5 LED UV lamp (Hamamatsu) was executed for 15 minutes with gentle stirring.

tag: growth conditions


title: PDAC3


title: Wild Type replicate 1

value: normoxia

value: root


title: Wild Type replicate 2

value: 3 weeks


title: PDAC1


title: 39minusstrand

description: 20 minutes under 39 ºC


title: TG-KEO10_S10

description:
sample name in processed data file:
BALBcJ 4
Colon.tsv

value: BALBcJ 4

value: BALB/cJ


title: 30minusstrand

description: 0 minutes under 39 ºC


title: Ddot1-CW-3

city: Jinan

first: Yanan

last: Li

address: Shanda south road 27

institute: Shandong University

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags. Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags. Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000
Supplementary_files_format_and_content: counts

organism: Penicillium oxalicum

source_name: Podot1 deletion strain in cellulose and wheat bran

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% microcrystalline cellulose and 1% wheat bran as carbon resources for 24h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.

value: Podot1 deletion strain

tag: medium

value: Modified Mendal’s medium with 1% microcrystalline cellulose and 1% wheat bran as carbon resource

tag: culture time

value: 24h after transferring washed mycelia to the new medium

value: Fungal mycelia


title: PDAC2


title: Ddot1-CW-1


title: TEW3

value: RPT3AT2delta/delta (Knockout)


title: Wild Type replicate 3

value: Wild Type Carrizo


title: 8_r7_1

description: sample name: 13

value: 8 cell

value: embryonic cell


title: EpCAM+_5hmC_DDC_d5_R1

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
5hmC profile from FACS sorted cells from tissue
SLX-15741.NEBNext05.HV3KVBBXX.CCGG.bed.txt.gz

library_source: genomic

data_processing:
Library strategy: 5hmC profiling
RRHP trimmed reads were then mapped to GRCm38 mouse genome using bowtie2. Details are available in the Methods. Bed files are provided.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPMs (tsv), peaks (bed), coverage (bedgraph), peaks (xlsx), calls (bed)

molecule: genomic DNA

source_name: FACS sorted cells from adult liver

growth_protocol: see Material and Methods

extract_protocol:
DNA extraction (see methods)
RRHP (see methods)

value: Adult DDC damaged liver

tag: gender

value: Male


title: 8_r5_1

description: sample name: 11


title: TEW1

value: lung epithelial cells

value: 12 weeks


title: 8_r8_1

description: sample name: 14


title: Uninf+Nutlin 3

city: London

first: Ryan

last: O'Shaughnessy

address: 4 Newark Street

institute: Queen Mary University of London

description:
Un Nut 3
processed data file: RNAseq_data.txt

data_processing:
Final libraries were pooled and sequenced across two runs on an Illumina NextSeq (75 cycle v2 high output kit).
Sequence read datasets were demultiplexed using bcl2fastq v2.17 under strict conditions (--barcode-mismatches 0), trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Aligned first against the human transcriptome (Homo sapiens (release 84) reference sequence (GRCh38)) and then against the VZV reference genome Dumas (GenBank accession number NC_001348.1) using Tophat2 (http://ccb.jhu.edu/software/tophat/index.shtml).
Transcript abundances were assessed using featureCounts and all data were normalised using TMM normalisation and followed by differential expression analysis using the edgeR package in Bioconductor.
FPKM values for each sample were then calculated from the edgeR output.
Genome_build: GRCh38
Supplementary_files_format_and_content: RNAseq_data.txt: Tab-delimited text file of normalised FPKM values.

source_name: MeWo (ATCC® HTB-65™)

growth_protocol: MeWo cells were cultured in MEM media (Sigma) supplemented with 10% FBS, 1% non-essential amino acid solution (Sigma) and 1% penicillin/streptomycin. MeWo cells infected with pOka at passage 24 at MOI of 0.01 were used for further analysis.

extract_protocol:
RNA was extracted from MeWo cells infected with pOka at passage 24 +/- Nutlin-3 treatment, normal MeWo cells and uninfected MeWo cells treated with Nutlin-3 using Tri Reagent (Zymo Research) followed by RNA extraction using the Direct-zol RNA MiniPrep kit (Direct-zol RNA MiniPrep, Zymo Research). The extracted RNA was further purified with the RNeasy Kit (Qiagen).
PolyA-selected stranded RNASeq libraries were generated using the Agilent SureSelect Strand Specific RNA Library Kit. 2µg of high quality total RNA was used per sample (RIN score >8), in accordance with manufacturer’s instructions.

treatment_protocol: Nutlin-3 treatment (10 mm) for the duration for 48 hours.

tag: cell line

value: MeWo

value: Melanoma cells

tag: vzv infection

value: Uninfected

tag: treatment

value: Nutlin-3 (10 um)


title: TEW2


title: Ddot1-CW-2


title: 8_r6_1

description: sample name: 12


title: EpCAM+_5hmC_DDC_d5_R2

description:
5hmC profile from FACS sorted cells from tissue
SLX-15741.NEBNext01.HV3KVBBXX.CCGG.bed.txt.gz

source_name: liver organoids


title: Ddot1-G-2

source_name: Podot1 deletion strain in glucose

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: Uninf+Nutlin 2

description:
Un Nut 2
processed data file: RNAseq_data.txt


title: 30plusstrand

description: 0 minutes under 39 ºC


title: EpCAM+_5hmC_DDC_d3_R1

description:
5hmC profile from FACS sorted cells from tissue
SLX-15741.NEBNext04.HV3KVBBXX.CCGG.bed.txt.gz


title: 12_r2_1

description: sample name: 10

value: 12 cell


title: 12_r3_1

description: sample name: 15


title: Ddot1-G-1

value: Podot1 deletion strain


title: 3_P1_2

description: sample name: 9

value: 3 cell


title: EpCAM+_5hmC_undamaged_R2

description:
5hmC profile from FACS sorted cells from tissue
SLX-15741.NEBNext09.HV3KVBBXX.CCGG.bed.txt.gz

value: Adult healthy liver


title: VZV+Nutlin 2

description:
pOka 24N 2
processed data file: RNAseq_data.txt

value: VZV (strain pOka) infected


title: 3_AB2_2

description: sample name: 8


title: Uninf+Nutlin 1

description:
Un Nut 1
processed data file: RNAseq_data.txt


title: VZV+Nutlin 1

description:
pOka 24N 1
processed data file: RNAseq_data.txt


title: VZV+Nutlin 3

description:
pOka 24N 3
processed data file: RNAseq_data.txt


title: 3_AB1_2

description: sample name: 7


title: Ddot1-G-3

value: 24h after transferring washed mycelia to the new medium

value: Fungal mycelia


title: 114-CW-3

source_name: 114-2 (wild type) in cellulose and wheat bran

value: 114-2 (wild type)

value: Modified Mendal’s medium with 1% microcrystalline cellulose and 1% wheat bran as carbon resource


title: EpCAM+_5hmC_undamaged_R1

description:
5hmC profile from FACS sorted cells from tissue
SLX-15741.NEBNext02.HV3KVBBXX.CCGG.bed.txt.gz

value: Male


title: VZV3

description:
pOka 24-3
processed data file: RNAseq_data.txt


title: 114-CW-2


title: EpCAM+_modifiedC_DDC_d5_R2

description:
WGBS from FACS sorted cells from tissue
allCG_D5_merge.tsv.gz

data_processing:
WGBS adaptor-trimmed paired reads were aligned to the mouse assembly GRCm38.p6 and to the lambda genome (used to determine bisulfite non-conversion rate) using Bismark. Details are available in the Methods. Bed files are provided.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPMs (tsv), peaks (bed), coverage (bedgraph), peaks (xlsx), calls (bed)

extract_protocol:
DNA extraction (see methods)
WGBS (see methods)

value: Adult DDC damaged liver


title: VZV2

description:
pOka 24-2
processed data file: RNAseq_data.txt


title: EpCAM+_5hmC_DDC_d3_R2

description:
5hmC profile from FACS sorted cells from tissue
SLX-15741.NEBNext06.HV3KVBBXX.CCGG.bed.txt.gz


title: EpCAM+_modifiedC_DDC_d5_R1


title: 114-CW-1


title: EpCAM+_modifiedC_DDC_d3_R2

description:
WGBS from FACS sorted cells from tissue
allCG_D3_merge.tsv.gz


title: 2_P1_1

description: sample name: 4

value: 2 cell

value: embryonic cell


title: Uninf 3

description:
Un 3
processed data file: RNAseq_data.txt

value: MeWo

value: Melanoma cells


title: 114-G-2

source_name: 114-2 (wild type) in glucose


title: 2_1_1

description: sample name: 6


title: 2_AB_1

description: sample name: 5


title: 114-G-3


title: VZV1

description:
pOka 24-1
processed data file: RNAseq_data.txt


title: EpCAM+_modifiedC_undamaged_R2

description:
WGBS from FACS sorted cells from tissue
allCG_T0merge.tsv.gz


title: 2_2_1

description: sample name: 3


title: EpCAM+_modifiedC_DDC_d3_R1


title: 114-G-1


title: 1_P0_2

description: sample name: 2

value: 1 cell


title: Uninf 1

description:
Un 1
processed data file: RNAseq_data.txt

value: Uninfected


title: 1_P0_1

description: sample name: 1


title: Patient 3 Bladder Homogenate

status: Public on Aug 28 2019

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger (version 2.2.0 for human data and version 3.0.0 for mouse data)
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat R package

Genome_build: GRCh38 for human data and mm10 for mouse data
Supplementary_files_format_and_content: the barcode, gene, expression matrix file of each sample

source_name: Bladder

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v2 user guide   to perform single cell suspension which were prepared before. Briefly, the  single-cell samples were passed through a 40μm cells strainer and counted using  a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to  recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the  oils onto the 10x Genomics single-cell-A chip and run this machine. After  droplet generation, samples were transferred onto a PCR tube and reverse  transcription was performed using T100 Thermal Cycler (BIO-RAD). After the  reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics  followed by a Silane DynaBead clean-up as outlined in the user guide. Purified  cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect  beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to  determine cDNA concentration.
10X Genomics Single Cell 3' v2 Reagent Kit

value: Total Bladder Homogenate


title: MAF1329

city: Beaverton

last: Keller

state: OR

address: 12655 SW Beaverdam Rd

institute: Children's Cancer Therapy Development Institute

data_processing:
Data filtering was performed using Sopanuke; -n 0.1 -l 10 -i -A 0.25
BGI Seq 500 instrumentation was used for high throughput sequencing
Supplementary_files_format_and_content: Tab delimited text files include TPM values

source_name: tumor

growth_protocol: Cells were expanded after surgical resection in T75 flasks and kept at a density of <90% confluence, in Optimem media with 15% FBS and 1% PenStrep.

extract_protocol:
Phenol-chloroform extraction with isopropanol precipitation was used to isolate RNA from a frozen cell pellet.
Library construction was peformed at BGI International and validated on a Agilent Technologies 2100 bioanalyzer.
Single end 50 (pair end 100/150) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

value: anaplastic ependymoma

tag: passage


title: Uninf 2

description:
Un 2
processed data file: RNAseq_data.txt


title: Patient 2 Bladder Homogenate


title: EpCAM+_modifiedC_undamaged_R1


title: MBDseq F4 male liver TBT rep 3

city: Santa Cruz

first: Carlos

last: Diaz-Castillo

state: California

address: 487 Physical Sciences Building

institute: University of California Santa Cruz

description: MBD-seq_processed data.txt

data_processing:
Statistical evaluation of TBT-dependent methylome and transcriptome variation in F3 and F4, female and male mesenchymal stem cells (MSCs) and F4 male liver was performed using R (version 3.4), and Bioconductor (version 3.8) packages MEDIPS (version 1.30), Rsubread (version 1.28), and edgeR (version 3.20). MEDIPS function MEDIPS.meth was used to estimate the statistical significance of MBD-seq reads differential coverage for GRCm38/mm10 mouse reference genomic 100-bp consecutive, non-overlapping windows with the following parameters: diff.method = edgeR, minRowSum = 10, and diffnorm = quantile. Rsubread function featureCounts was used to assigned uniquely mapped RNA-seq reads to GRCm38/mm10 mouse reference genome gene models and count reads with the following parameters: GTF.featureType = exon, GTF.attrType = gene_id, allowMultiOverlap = TRUE, nthreads = 24, and strandSpecific = 0. edgeR functions cpm and glmQLFTest were used to estimate the number of counts per million per gene model and the statistical significance of RNA-seq reads differential coverage between TBT and DMSO samples.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-seq_processed data.txt includes RNA-seq normalized counts per gene model for each sample, and results of the statistical analyses performed as described above.
Supplementary_files_format_and_content: MBD-seq_processed data.txt includes MBD-seq read counts, and rpkm for each sample, and results of the statistical analyses performed as described above for GRCm38/mm10 mouse reference genomic 100-bp consecutive, non-overlapping windows for which P value was lower than 0.001.

source_name: Liver

growth_protocol: Male (n=25) and female (n=50) C57BL/6J mice (7 weeks of age) were purchased from the Jackson Laboratory (Sacramento, CA). Mice were housed in micro-isolator cages in a temperature-controlled room (21–22°C) with a 12 hr light/dark cycle. Water and food was provided ad libitum unless otherwise indicated. Animals were treated humanely and with regard for alleviation of suffering. All procedures conducted in this study were approved by the Institutional Animal Care and Use Committee of the University of California, Irvine. All tissue harvesting was performed with the dissector blinded to which groups the animals belonged to.

extract_protocol:
Genomic DNA (gDNA) and RNA were isolated from mesenchymal stem cells from 8-week old F3 and F4, female and male mice and from livers from 33-week old F4 male using ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research). Nucleic acids from MSCs harvested from 3 non-sibling, non-cousin animals from the same treatment group and gender were pooled to generate each of the 5 biological replicates per treatment group and submitted for DNA methylome and transcriptome analyses. Nucleic acid samples from livers harvested from 4 randomly selected mice from control or TBT groups were submitted for DNA methylome and transcriptome analyses
Directional RNA-seq libraries were synthesized from ribosomal RNA-depleted samples using the TruSeq RNA-seq kit (Illumina).
Sonicated gDNA (100-200 bp, 500 ng) was subjected to methylated DNA enrichment using the MethylMiner kit (Life Technologies), followed by deep sequencing library construction using the NEBNext Ultra kit (New England Biolabs). Sonicated gDNA without methylation enrichment was used as input control. Following the ENCODE recommendation for ChIP-seq, we aimed for 20 million mapped reads (75 nt single) for each gDNA sample

treatment_protocol: Female C57BL/6J mice (25 females per treatment group) were randomly assigned to the different treatment groups and exposed via drinking water to 50 nM TBT or 0.1% DMSO vehicle (both diluted in 0.5% carboxymethyl cellulose in water to maximize solubility) for 7 days prior to mating. Chemicals were administered to the dams throughout pregnancy and lactation.We chose only 1 male and 2 females per litter for breeding. To randomize the breeding process as much as possible, we did not breed siblings and did not breed females from the same litter with the same male. Unexposed animals were bred to each other and TBT-exposed bred to each other. A similar approach was followed in generations F2-F4. Animals from F0-F4 were maintained on a standard diet (SD - Rodent Diet 20 5053*; PicoLab) throughout the experiment. F4 males and females (avoiding siblings within the same gender) were maintained on a higher fat diet (HFD - Mouse Diet 20 5058*; PicoLab) between weeks 19-25. Mice were subsequently returned to the SD for 8 more weeks prior to euthanasia at 33 weeks of age

value: 33 weeks

tag: generation

tag: Sex


title: MBDseq F4 male liver TBT rep 2

description: MBD-seq_processed data.txt


title: Patient 1 Bladder Homogenate

tag: tissue


title: MBDseq F4 male liver TBT rep 1

description: MBD-seq_processed data.txt

tag: strain


title: MBDseq F4 male MSCs TBT rep 1

description: MBD-seq_processed data.txt

source_name: Mesenchymal stem cells

value: 8 weeks


title: MBDseq F4 male liver DMSO rep 2

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs TBT rep 4

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs TBT rep 3

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs TBT rep 5

description: MBD-seq_processed data.txt


title: MBDseq F4 male liver DMSO rep 4

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs TBT rep 2

description: MBD-seq_processed data.txt


title: MBDseq F4 male liver DMSO rep 3

description: MBD-seq_processed data.txt


title: MBDseq F4 male liver DMSO rep 1

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs DMSO rep 3

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs DMSO rep 5

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs TBT rep 1

description: MBD-seq_processed data.txt

value: Female


title: MBDseq F4 male MSCs DMSO rep 1

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs TBT rep 2

description: MBD-seq_processed data.txt


title: MBDseq F4 male liver TBT rep 4

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs DMSO rep 5

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs TBT rep 3

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs TBT rep 5

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs DMSO rep 1

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs DMSO rep 2

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs TBT rep 5

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs DMSO rep 3

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs TBT rep 4

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs TBT rep 3

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs TBT rep 2

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs TBT rep 1

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs DMSO rep 4

description: MBD-seq_processed data.txt


title: MBDseq F4 male MSCs DMSO rep 2

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs TBT rep 4

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs DMSO rep 3

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs DMSO rep 4

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs DMSO rep 2

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs DMSO rep 5

description: MBD-seq_processed data.txt


title: MBDseq F4 female MSCs DMSO rep 4

description: MBD-seq_processed data.txt


title: MBDseq F3 male MSCs DMSO rep 1

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs DMSO rep 5

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs TBT rep 1

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs TBT rep 5

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs TBT rep 3

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs DMSO rep 2

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs TBT rep 4

description: MBD-seq_processed data.txt


title: RNAseq F4 male liver TBT rep 4

description: RNA-seq_processed data.txt


title: MBDseq F3 female MSCs DMSO rep 1

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs DMSO rep 4

description: MBD-seq_processed data.txt


title: RNAseq F4 male liver TBT rep 3

description: RNA-seq_processed data.txt


title: RNAseq F4 male liver TBT rep 1

description: RNA-seq_processed data.txt


title: RNAseq F4 male liver DMSO rep 3

description: RNA-seq_processed data.txt


title: RNAseq F4 male liver DMSO rep 2

description: RNA-seq_processed data.txt


title: RNAseq F4 male liver DMSO rep 4

description: RNA-seq_processed data.txt


title: RNAseq F4 male liver TBT rep 2

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs TBT rep 4

description: RNA-seq_processed data.txt


title: RNAseq F4 male liver DMSO rep 1

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs TBT rep 3

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs TBT rep 5

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs TBT rep 2

description: RNA-seq_processed data.txt


title: MBDseq F3 female MSCs TBT rep 2

description: MBD-seq_processed data.txt


title: MBDseq F3 female MSCs DMSO rep 3

description: MBD-seq_processed data.txt


title: RNAseq F4 male MSCs DMSO rep 4

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs DMSO rep 5

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs DMSO rep 3

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs DMSO rep 4

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs DMSO rep 1

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs TBT rep 1

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs TBT rep 2

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs DMSO rep 3

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs TBT rep 5

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs DMSO rep 2

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs DMSO rep 1

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs TBT rep 3

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs TBT rep 5

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs TBT rep 2

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs TBT rep 1

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs TBT rep 4

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs DMSO rep 1

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs DMSO rep 2

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs DMSO rep 4

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs DMSO rep 5

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs DMSO rep 3

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs TBT rep 4

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs DMSO rep 5

description: RNA-seq_processed data.txt


title: RNAseq F4 female MSCs TBT rep 4

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs TBT rep 3

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs TBT rep 2

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs TBT rep 5

description: RNA-seq_processed data.txt


title: RNAseq F3 male MSCs TBT rep 3

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs DMSO rep 4

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs TBT rep 1

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs DMSO rep 5

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs DMSO rep 2

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs DMSO rep 1

description: RNA-seq_processed data.txt


title: RNAseq F4 male MSCs DMSO rep 2

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs DMSO rep 3

description: RNA-seq_processed data.txt


title: RNAseq F3 female MSCs TBT rep 1

description: RNA-seq_processed data.txt


title: Tl4 normal_1 day RSV_biological rep1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression from HeOuJ mice exposed to 1 day RSV

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

label: biotin

source_name: Tlr4 normal mice, 1 day post RSV infection

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours.

extract_protocol: RNA was isolated from a portion of the left lung of each mouse (n = 3/group) using the RNeasy Mini kit

treatment_protocol: Age matched inbred mice were instranasally infected with 10^6 PFU RSV L19 or HepG2 vehicle in HBSS.  Mice were sacrificed 1 and 5 days post infection.

tag: genotype/variation

value: Tlr4 normal

value: left lung


title: Tl4 normal_vehicle_biological rep3

description: gene expression from HeOuJ vehicle control

source_name: Tlr4 normal mice, HepG2 vehicle control


title: Tlr4 mutant_5 day RSV_biological rep2

description: gene expression from HeJ mice exposed to 5 day RSV

source_name: Tlr4 mutant mice, 5 day post RSV infection

value: Tlr4 mutant


title: Tl4 normal_vehicle_biological rep2


title: Tlr4 mutant_1 day RSV_biological rep2

description: gene expression from HeJ mice exposed to 1 day RSV

source_name: Tlr4 mutant mice, 1 day post RSV infection


title: Tl4 normal_5 day RSV_biological rep3

description: gene expression from HeOuJ mice exposed to 5 day RSV

source_name: Tlr4 normal mice, 5 day post RSV infection


title: Tl4 normal_5 day RSV_biological rep2


title: Tl4 normal_vehicle_biological rep1


title: Tl4 normal_1 day RSV_biological rep2


title: Tl4 normal_1 day RSV_biological rep3


title: Tlr4 mutant_vehicle_biological rep3

description: gene expression from HeJ vehicle control

source_name: Tlr4 mutant mice, HepG2 vehicle control


title: Tl4 normal_5 day RSV_biological rep1


title: Tlr4 mutant_5 day RSV_biological rep1


title: Tlr4 mutant_5 day RSV_biological rep3


title: Tlr4 mutant_1 day RSV_biological rep1


title: Tlr4 mutant_vehicle_biological rep2


title: Tlr4 mutant_vehicle_biological rep1


title: whole_blood-unsupplemented-4hrs-donor_1b

city: Spring House

first: Matthew

middle: J

last: Loza

state: PA

address: 1400 McKean Rd

department: Immunology - Biomarkers

institute: Janssen R&D, LLC

description: replicate sample for donor 1

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data were quality controlled and pre-processed using OmicSoft ArrayStudio software with Robust Multichip Average (RMA) as normalization method. Data were normalized with additional CEL files from samples with different experimental conditions not included in this submission.

label: Biotin

label_protocol: Target was prepared from total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer's protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Whole blood from three healthy donors was drawn into EDTA vacutainer tubes.  Two aliquots of 1 ml blood were transferred to sterile 2 ml Eppendorf tubes.  Recombinant human CSF-1 (PeproTech) was added to one of the two replicate tubes to a final concentration of 50 ng/ml, with the second replicate tube retained as an unstimulated control sample.  Tubes were affixed to a tube rotator and incubated at 37 degrees C, 5% CO2.    Aliquots (100 uL) were collected from all tubes at 4 and 24 hr.

value: cultured whole blood

tag: stimulus

value: unsupplemented

tag: time

tag: donor


title: whole_blood-unsupplemented-4hrs-donor_3b

description: replicate sample for donor 3


title: whole_blood-unsupplemented-4hrs-donor_3


title: whole_blood-unsupplemented-4hrs-donor_2b

description: replicate sample for donor 2


title: whole_blood-unsupplemented-24hrs-donor_3b

description: replicate sample for donor 3


title: whole_blood-unsupplemented-24hrs-donor_1b

description: replicate sample for donor 1


title: whole_blood-unsupplemented-24hrs-donor_2b

description: replicate sample for donor 2


title: whole_blood-unsupplemented-24hrs-donor_1


title: whole_blood-unsupplemented-24hrs-donor_2


title: whole_blood-unsupplemented-4hrs-donor_1


title: whole_blood-unsupplemented-4hrs-donor_2


title: whole_blood-50 ng_ml _CSF1-24hrs-donor_2

value: 50 ng/ml CSF-1


title: whole_blood-50 ng_ml _CSF1-24hrs-donor_3


title: whole_blood-50 ng_ml _CSF1-4hrs-donor_1

source_name: whole_blood-50 ng_ml _CSF1-4hrs-donor_1


title: K562_TNF_24hr_5

data_processing: The data were quality controlled and pre-processed using OmicSoft ArrayStudio software with Robust Multichip Average (RMA) as normalization method. Samples that failed quality control assessments are indicated with Characteristic_QC: FAIL.

treatment_protocol: Three epithelial cell lines (A549, HT-29, 293) and K562 (mylegenous leukemia) cell line were cultured for 4 hrs with TNF-a or PBS, with 6 replicates per condition.

value: TNF

tag: replicate

tag: qc

value: PASS


title: K562_TNF_24hr_4


title: whole_blood-unsupplemented-24hrs-donor_3


title: whole_blood-50 ng_ml _CSF1-24hrs-donor_1


title: K562_PBS_24hr_2

value: PBS


title: K562_TNF_24hr_1


title: K562_TNF_4hr_5


title: K562_PBS_24hr_5


title: Tlr4 mutant_1 day RSV_biological rep3


title: K562_TNF_24hr_3


title: K562_TNF_24hr_2


title: K562_TNF_4hr_3


title: whole_blood-50 ng_ml _CSF1-4hrs-donor_3

source_name: whole_blood-50 ng_ml _CSF1-4hrs-donor_3


title: K562_PBS_24hr_3


title: K562_TNF_4hr_2


title: K562_PBS_24hr_4


title: K562_PBS_24hr_1


title: K562_TNF_4hr_4


title: whole_blood-50 ng_ml _CSF1-4hrs-donor_2

source_name: whole_blood-50 ng_ml _CSF1-4hrs-donor_2


title: K562_TNF_4hr_6


title: K562_TNF_4hr_1


title: K562_TNF_24hr_6


title: K562_PBS_4hr_5


title: HT29_PBS_24hr_6

value: FAIL


title: 293_PBS_24hr_6


title: K562_PBS_4hr_3


title: K562_PBS_4hr_1


title: K562_PBS_4hr_2


title: HT29_PBS_4hr_6


title: K562_PBS_4hr_6


title: HT29_PBS_4hr_4


title: HT29_TNF_4hr_6


title: HT29_PBS_24hr_4


title: HT29_PBS_4hr_2


title: HT29_TNF_24hr_6


title: HT29_TNF_4hr_2


title: 293_TNF_24hr_6


title: 293_TNF_24hr_5


title: K562_PBS_24hr_6


title: 293_PBS_24hr_4


title: K562_PBS_4hr_4


title: 293_TNF_24hr_1


title: A549_TNF_24hr_3


title: 293_TNF_4hr_6


title: 293_TNF_24hr_2


title: 293_TNF_24hr_4


title: 293_PBS_24hr_3


title: 293_TNF_4hr_5


title: 293_TNF_24hr_3


title: 293_PBS_4hr_3


title: 293_PBS_4hr_6


title: 293_TNF_4hr_1


title: 293_TNF_4hr_4


title: 293_TNF_4hr_3


title: 293_PBS_24hr_5


title: 293_PBS_4hr_5


title: 293_TNF_4hr_2


title: 293_PBS_4hr_2


title: 293_PBS_4hr_4


title: 293_PBS_4hr_1


title: A549_PBS_24hr_6


title: A549_TNF_24hr_4


title: A549_PBS_24hr_3


title: HT29_TNF_24hr_1


title: HT29_TNF_24hr_5


title: A549_PBS_24hr_4


title: HT29_TNF_24hr_3


title: A549_TNF_24hr_2


title: A549_PBS_24hr_5


title: A549_TNF_24hr_5


title: A549_TNF_24hr_1


title: A549_PBS_24hr_2


title: A549_TNF_24hr_6


title: HT29_PBS_24hr_5


title: HT29_PBS_24hr_1


title: HT29_PBS_24hr_3


title: HT29_TNF_4hr_4


title: HT29_TNF_24hr_2


title: A549_PBS_24hr_1


title: A549_TNF_4hr_2


title: A549_TNF_4hr_3


title: A549_TNF_4hr_1


title: A549_TNF_4hr_6


title: A549_TNF_4hr_5


title: HT29_TNF_4hr_5


title: HT29_TNF_24hr_4


title: A549_TNF_4hr_4


title: HT29_PBS_4hr_3


title: HT29_PBS_4hr_1


title: HT29_TNF_4hr_3


title: A549_PBS_4hr_6


title: A549_PBS_4hr_4


title: A549_PBS_4hr_5


title: HT29_TNF_4hr_1


title: zebrafish-5

city: BEIJING

first: Bo

last: Chen

state: BEIJING

address: TianTan XiLi No. 1, Dong-cheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Danio rerio

source_name: liver,BBR

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: AB strain zebrafish (Danio. rerio)  were kept under standard laboratory conditions with a 14-h light/10-h dark cycle at a temperature of 28.5±1°C. Embryos and larvae were maintained in embryo medium to 5 dpf without feeding. Zebrafish larvae were fed with control diet (AP100, 30mg/100 fish/day) or high cholesterol diet (HCD, 180mg AP100 plus 4% cholesterol/100fish/day) or HCD plus berberine (5μM) for 10 days.

value: AB

tag: developmental stage

value: larvae

tag: diet

value: HCD plus berberine (5μM) for 10 days

value: liver


title: A549_PBS_4hr_1


title: HT29_PBS_4hr_5


title: A549_PBS_4hr_2


title: ILC2 Sample 1

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted ILC2s

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

tag: cell type

tag: cell markers


title: zebrafish-2

source_name: liver,HCD

value: high cholesterol diet (HCD, 180mg AP100 plus 4% cholesterol/100fish/day)


title: Sample_pUltra-OE-3_count

city: Rehovot

first: Eran

last: Hornstein

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads for each sample were mapped independently using TopHat2 version (v2.0.10) against the mouse genome build mm9.
Only uniquely mapped reads were used to determine the number of reads falling into each gene with the HTSeq-count script (0.6.1p1).
Differentially expressed genes were calculated with the DESeq2 package (v1.4.5) .
Genes that were expressed at least on one sample were considered.
Differentially expressed genes, were determined by P-adj < 0.05 and an absolute fold change >1.5.
Hierarchical clustering using Pearson dissimilarity and complete linkage was performed in order to explore a pattern of gene expression.
Clustering analysis was performed with Matlab software (8.0.0.783).
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: primary motor neurons

extract_protocol:
Primary motor neurons were isolated and cultured as previously described (23). Briefly, time pregnant C57BL/6 mice at embryonic day 13.5 (E13.5) were sacrificed at rat embryonic day 14.5 (E14.5), and spinal cords were dissected and dissociated enzymatically with papain (2mg/ml, Sigma). Motor neurons were separated over a gradient of Optiprep (Sigma) and plated on 13mm coverslips (200,000 cells/ coverslip, Thermo scientific), pre-coated with 3µg/ml poly-ornithine (Sigma) and 3µg/ml laminin (Gibco). Motor neurons were cultured with Neurobasal medium (Gibco) supplemented with 2% B27 (Gibco) 2% horse serum (Sigma), X1 Glutamax (Gibco) and 1ng/ml CNTF and GDNF (Peprotech). To inhibit glial overgrowth, 200 μM fluorodeoxyuridine (Sigma) was added after 5 days of in vitro culture (DIV).
cDNAs were prepared following Lavin, Yonit, et al. "Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment." Cell 159.6 (2014): 1312-1326. and sequenced on one a single lane in a Hiseq2500 (Illumina) with 50bp single read. Fasta files for each sample were generated by the usage of Illumina CASAVA-1.8.2 software. Reads for each sample were mapped independently using TopHat2 version (v2.0.10) against the mouse genome build mm9. Approximately, 85-90% mapping rate was observed. Only uniquely mapped reads were used to determine the number of reads falling into each gene with the HTSeq-count script (0.6.1p1). Differentially expressed genes were calculated with the DESeq2 package (v1.4.5) . Genes that were expressed at least on one sample were considered. Differentially expressed genes, were determined by P-adj < 0.05 and an absolute fold change >1.5. Hierarchical clustering using Pearson dissimilarity and complete linkage was performed in order to explore a pattern of gene expression. Clustering analysis was performed with Matlab software (8.0.0.783).

value: primary embryonic motor neurons

tag: embryonic stage


title: ILC2 Sample 3


title: zebrafish-0

source_name: liver,con

value: control diet (AP100, 30mg/100 fish/day)


title: MSC co-cultured with CRC 3

city: seoul

first: In-Rok

last: Oh

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

country: South Korea

institute: korea university

hyb_protocol: 5.5 μg of labeled DNA targets were hybridized to Affymetrix GeneChip Human 2.0 ST arrays at 45 °C. for 16 hours.

scan_protocol: Hybridized arrays were washed and stained in GeneChip Fluidics Station 450 and scanned using a GCS3000 scanner (Affymetrix).

data_processing: Raw data were extracted in data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After using CEL files, the data were filterd and normalized with multi-average (RMA) implemented in Affymetrix® Expression Console™ Software (EC).

source_name: human amniotic membrane-derived mesenchymal stem cell

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.  Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour.

growth_protocol: MSCs were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco) with 10% fetal bovine serum (FBS, Gibco), penicillin and streptomycin (100 μg/ml, Gibco), and were incubated at 37°C with 5% CO2.

extract_protocol: After separating total RNA using TRIzol (Invitrogen),  RNA purity was assessed by the OD 260/280 ratio.

treatment_protocol: MSCs were co-cultured directly with colorectal cancer cells using Transwell.

value: human amniotic membrane

tag: condition

value: co-culture with colorectal cancer cells


title: MSC alone (control) 3

value: control


title: MSC alone (control) 1


title: MSC alone (control) 2


title: MSC co-cultured with CRC 2


title: A549_PBS_4hr_3

tag: cell line


title: MSC co-cultured with CRC 1


title: ILC2 Sample 2


title: ADRL 26m BAT Rep5

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

description:
Switched from fully-fed to dietary restricted
BAT_RNA-seq_Readcount_output.txt

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7,  parameters: --length 25). Trimmed sequences were aligned using Tophat2 (Kim et al., 2013) (v2.0.14, parameters: --no-mixed  --library-type=fr-firststrand -g 2 -p 15 -r 500 --mate-std-dev 525). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk  (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files including raw counts for each sample

source_name: BAT

extract_protocol:
We isolated RNA from liver and epididymal brown adipose tissue (BAT) of AL, DR, ALDR and DRAL mice at old age, as well as AL and ALDR mice at young age (three to five biological replicates each). RNA was isolated using Trizol Reagent (Thermo Fisher Scientific, Germany) according to the manufacturer’s protocol before treating samples with DNAse using the TURBO DNA-free Kit (Thermo Fisher Scientific, Germany). RNA quality was measured using the Agilent TapeStation System (Agilent Technologies, Germany). RNA-seq library preparation and sequencing was performed by the Max Planck-Genome-Centre Cologne, Germany (http://mpgc.mpipz.mpg.de/home/).
According to the facility’s procedure, stranded TruSeq RNA-seq libraries were prepared as described in (Sultan et al., 2012), using 3 μg of rRNA-depleted RNA as input. Multiplexed libraries were sequenced with 2x40 mio, 100 bp paired-end reads on an Illumina HiSeq2500 (Illumina, San Diego, California, USA). Liver RNA-seq data for young ALDR, young AL, old DR and old AL fed mice were previously published (Hahn et al., 2017) and is publically available under the Gene expression omnibus ID GSE92486.
Stranded, single-end,  mRNA-seq (polyA-enriched)

treatment_protocol: Animals were housed in groups of five females in individually ventilated cages under specific-pathogen-free conditions with constant temperature (21°C), 50-60% humidity and a 12-hour light/dark cycle. As enrichment mice had constant access to nesting material and chew sticks. All mice received commercially available rodent chow (ssniff R/M-H autoclavable, ssniff Spezialdiäten GmbH, Soest, Germany) and were provided with acidified water ad libitum. Food consumption of the AL group was measured weakly and DR animals received 60% of the food amounts consumed by AL animals. To avoid developmental effects, chronic DR treatment was started at 12 weeks of age. Late-life ALDR and DRAL diet switches were introduced when 20% of AL animals of the respective control cohort had died, corresponding to 24 months of age. DR was introduced stepwise by reducing the amount of given food by 10% per week over four consecutive weeks. DR animals were fed once per day and all animals were checked daily for their wellbeing and any deaths. Ten mice per diet group of the F3 cohort were sacrificed at the age of 5 and 27 months, corresponding to 2 months (short-term) and 24 months (long-term) DR treatment. All mice were killed within a period of three hours prior to the regular feeding time of DR mice. Mice were killed by cervical dislocation and tissues were rapidly collected and snap-frozen using liquid nitrogen.

value: Brown adipose tissue

tag: age

value: 26 months


title: Sample_pUltra-OE-2_count


title: DR 26m BAT Rep3

description:
Dietary restricted
BAT_RNA-seq_Readcount_output.txt


title: Sample_pUltra-KD-2_count


title: Sample_pUltra-OE-1_count


title: DRAL 26m BAT Rep3

description:
Switched from dietary restricted to fully-fed
BAT_RNA-seq_Readcount_output.txt


title: Sample_pUltra-ctrl-2_count


title: Sample_pUltra-ctrl-1_count


title: DRAL 26m BAT Rep2


title: HT29_PBS_24hr_2


title: DR 26m BAT Rep2


title: DR 26m BAT Rep1


title: ADRL 26m BAT Rep2


title: ADRL 26m BAT Rep4


title: DRAL 26m BAT Rep1


title: AL 26m BAT Rep1

description:
Fully-fed
BAT_RNA-seq_Readcount_output.txt


title: ADRL 26m BAT Rep3


title: ADRL 26m BAT Rep1


title: Sample_pUltra-KD-1_count


title: AL 5m BAT Rep2

description:
Fully-fed (at young age)
BAT_RNA-seq_Readcount_output.txt

value: 5 months


title: AL 26m BAT Rep3


title: ADRL 5m BAT Rep2

description:
Switched from fully-fed to dietary restricted (at young age)
BAT_RNA-seq_Readcount_output.txt


title: AL 26m BAT Rep2


title: AL 5m BAT Rep3


title: AL 5m BAT Rep1


title: DRAL 26m WAT Rep3

description:
Switched from dietary restricted to fully-fed
WAT_RNA-seq_Readcount_output.txt

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7,  parameters: --paired --length 25). Trimmed sequences were aligned using Tophat2 (Kim et al., 2013) (v2.0.14, parameters: --no-mixed  --library-type=fr-firststrand -g 2 -p 15 -r 500 --mate-std-dev 525). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk  (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files (one for liver, one for WAT) including raw counts for each sample

source_name: DRAL 26m WAT

extract_protocol:
We isolated RNA from liver and epididymal white adipose tissue (WAT) of AL, DR, ALDR and DRAL mice at old age, as well as AL and ALDR mice at young age (three to five biological replicates each). RNA was isolated using Trizol Reagent (Thermo Fisher Scientific, Germany) according to the manufacturer’s protocol before treating samples with DNAse using the TURBO DNA-free Kit (Thermo Fisher Scientific, Germany). RNA quality was measured using the Agilent TapeStation System (Agilent Technologies, Germany). RNA-seq library preparation and sequencing was performed by the Max Planck-Genome-Centre Cologne, Germany (http://mpgc.mpipz.mpg.de/home/).
According to the facility’s procedure, stranded TruSeq RNA-seq libraries were prepared as described in (Sultan et al., 2012), using 3 μg of rRNA-depleted RNA as input. Multiplexed libraries were sequenced with 2x40 mio, 100 bp paired-end reads on an Illumina HiSeq2500 (Illumina, San Diego, California, USA). Liver RNA-seq data for young ALDR, young AL, old DR and old AL fed mice were previously published (Hahn et al., 2017) and is publically available under the Gene expression omnibus ID GSE92486.
Stranded, paired-end, total RNA-seq

value: White adipose tissue

tag: treatment

value: DRAL


title: DRAL 26m WAT Rep1

tag: tissue


title: ADRL 5m BAT Rep1

tag: strain


title: ALDR 26m WAT Rep5

description:
Switched from fully-fed to dietary restricted
WAT_RNA-seq_Readcount_output.txt

source_name: ALDR 26m WAT

value: ALDR


title: DRAL 26m WAT Rep5


title: DRAL 26m WAT Rep4


title: DRAL 26m WAT Rep2


title: ALDR 26m WAT Rep4


title: ALDR 26m WAT Rep3


title: ALDR 26m WAT Rep2


title: ALDR 26m WAT Rep1


title: ADRL 5m BAT Rep3


title: KO sample 3

source_name: Sorted ILC3s from small intestine lamina propria

tag: genotype

value: Bmal1-flox, Rorc-cre


title: KO sample 2


title: Wild-type sample 2


title: KO sample 1


title: DR 26m WAT Rep3

description:
Dietary restricted
WAT_RNA-seq_Readcount_output.txt

source_name: DR 26m WAT

value: DR


title: DR 26m WAT Rep1


title: Pax9 wt-3

city: Newcastle upon Tyne

first: Simon

middle: D.

last: Bamforth

address: Central Parkway

department: Institute of Genetic Medicine

institute: Newcastle University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (version 0.32, default parameters).
Trimmed reads were then mapped to GRCm38.p5 whole genome using STAR  (version 2.5.1a) with default parameters for paired end reads.
featureCounts (version 1.5.1) was used to quantify the gene counts with default options for paired-end reads.
Genome_build: GRCm38.p5 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file were generated with featureCounts.

source_name: pharyngeal arch

growth_protocol: In vivo

extract_protocol:
Dissociated TECs were directly FACS-sorted into Smartseq-2 buffer.
Libraries were prepared according to Smartseq-2 protocol (Picelli et al, 2013). Libraries were sequenced on Illumina HiSeq4000 using 75bp paired end sequencing.

value: wild type


title: Wild-type sample 3


title: Pax9 wt-2


title: DR 26m WAT Rep2


title: Pax9 mt-3


title: Wild-type sample 1


title: AL 26m WAT Rep3

description:
Fully-fed
WAT_RNA-seq_Readcount_output.txt

source_name: AL 26m WAT

value: AL


title: AL 5m WAT Rep2

description:
Fully-fed (at young age)
WAT_RNA-seq_Readcount_output.txt

source_name: AL 5m WAT


title: AL 5m WAT Rep3


title: Pax9 mt-1


title: ALDR 5m WAT Rep1

description:
Switched from fully-fed to dietary restricted (at young age)
WAT_RNA-seq_Readcount_output.txt

source_name: ALDR 5m WAT


title: AL 5m WAT Rep1


title: ALDR 5m WAT Rep3


title: ALDR 5m WAT Rep2


title: AL 26m WAT Rep2


title: DRAL 26m Liver Rep3

description:
Switched from dietary restricted to fully-fed
Liver_RNA-seq_Readcount_output.txt

source_name: DRAL 26m Liver

value: Liver


title: DRAL 26m Liver Rep1


title: DRAL 26m Liver Rep2


title: ALDR 26m Liver Rep3

description:
Switched from fully-fed to dietary restricted
Liver_RNA-seq_Readcount_output.txt

source_name: ALDR 26m Liver


title: ALDR 26m Liver Rep2


title: ALDR 26m Liver Rep1


title: AL 26m WAT Rep1


title: AMI30

city: Detroit

first: Grace

middle: Michelle

last: Swanson

state: MI

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

data_processing:
Sequence reads were trimmed using Trimmomatic version 0.36 to clip adaptor sequence and remove reads smaller than 25 base pairs.
Sequences were aligned first to the human rRNA locus (U13369), then to the index of hg38 genome supplemented with 92 ERCCs and MS2 spike-in (for an additional 93 chromosomes). Reads aligning to both the rRNA locus and human genome were removed. Unmapped reads were then aligned to RepBase using HISAT2 for the purpose of indentifying reads aligning to repetitive elements.  The remaing unaligned reads were aligned to bacterial and viral genomes usign Kraken.  Duplicate removal was performed using the PicardTools MarkDuplicates.
Exonic and novel intronic, near exonic and orphan RNA elements were identified and quanitified as Reads Per Kilobase per Million (RPKM) using the protocol from Estill, MS et al., Nucleic Acids Research, 2018. Briefly, exonic RNA elements were identified using the Basic Gencode annotation with overlapping exons merged.  Novel RNA elements were assinged based on distance from the nearest genomic exon.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes the RPKM values for each sample

source_name: sperm

extract_protocol:
Total RNA was extracted using the protocol from Goodrich, R et al., Archives of Andrology, 2007. Briefly, gradient purification of spermatozoa from other cell-types was performed prior to isolation of total RNA based on the Qiagen RNAeasy protocol.
Library construction followed the protocol from Jodar, M et al., Human Reproduction Update, 2013.

tag: bmi classification

value: obese

value: sperm


city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

country: France

institute: Institut Curie

description: ChIPseq_H2AK119Ub_XistTetOP_delBC_D2_Dox_Rep2_B258C36_B265C18

data_processing:
Adapters and low quality bases (<Q20) have been removed from the sequencing data with TrimGalore (v0.4.0) {Krueger} and Cutadapt (1.8.2) (Martin et al., 2011).
Reads were then mapped to the mm10 genome with Bowtie2 (2.2.5) with options [--end-to-end -N1 -q] {Langmead, 2012}.
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES=true] {DePristo, 2011}, reads mapped with low quality (< q10) were removed using samtools (1.3) {Li, 2009} and reads mapped on blacklisted regions from Encode Consortium {ENCODE Consortium, 2012} were discarded.
Bigwig files were created with bedtools genomeCoverageBed (2.25.0) {Quinlan, 2010}, using a scale factor calculated on the total library (10.000.000/total reads) and loaded on UCSC genome browser {Kent, 2002}.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: All ESCs were grown at 37°C in 8% CO2 and medium was changed daily. Inducible expression of Xist driven by a TetO promoter was achieved by adding doxycycline (DOX) (1.5μg/ml) while differentiating the ESCs in LIF withdrawal medium - DMEM media containing 10% FBS, 10-4mM 2-mercaptoethanol and 50U/ml penicillin and 50μg/ml of streptomycin (Gibco), for 2 days.

extract_protocol:
Briefly, around 3.5 million cells were used per immunoprecipitation (IP) experiment. A fraction of these cells were always used to quantify levels of Xist induction by RNA FISH. Ten million cells was resuspended and lysed in 90µl of Lysis Buffer (50mM Tris-HCl, pH 7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 5mM CaCl2; Protease Inhibitor Cocktail; 5mM sodium butyrate) for 10min on ice. Lysis Buffer with MNase (62 µl) was then added for chromatin digestion and incubated at 37ºC for exactly 10min. Then, 20mM EGTA was added to stop the reaction, followed by centrifugation (13000rpm) for 5min  at 4ºC to sediment undigested debris. Supernatant was then transferred and equal amount of STOP buffer (50mM Tris-HCl, pH 7.5; 150mM NaCl ; 0.1% sodium deoxycholate; 1% Triton X-100; 30mM EGTA; 30mM EDTA; Protease Inhibitor Cocktail; 5mM sodium butyrate) was added to the samples, which were always kept on ice. Lysate (5µl) was mixed with 45µl of ProtK Digestion Buffer (20mM HEPES; 1mM EDTA; 0.5% SDS) and incubated at 56°C for 30min. AMPure XP beads (50µl) were mixed with the digested lysate with 60µl of 20% PEG8000 1.25M NaCl for 15min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30 seconds. DNA was eluted in 12µl of Low-EDTA TE and measured using Qubit DNA High-Sensitivity kit to normalise lysate concentration between samples. DNA isolated in this step was used for the input sample. The volume of each undigested lysate was adjusted for equal concentration to obtain 1ml per IP using a 1:1 mix of Lysis Buffer and STOP Buffer.  Protein-A Dynabeads (10µl/IP) were washed twice in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS) before being resuspended in Blocking buffer and coated with H3K27me3 [1µg/IP] (Cell Signalling, Cat#9733S) or H2AK119ub [0.4µg/IP] (Cell Signalling, Cat# 8240S) antibodies for 4 hours at 4°C. Once coated beads were magnet-separated and resuspended in 1ml of concentration-adjusted lysate. Samples were left rotating overnight at 4°C.   In the following day beads were magnet-separated and washed quickly with ice-cold washing buffers with Low Salt Buffer (0.1% SDS; 1% TritonX-100; 2mM EDTA; 20mM Tris-HCl, pH 8.1; 150mM NaCl; 0.1% sodium deoxycholate). IPs were then washed  four times with Low Salt Buffer, twice with High Salt Buffer (0.1% SDS; 1% TritonX-100; 2mM EDTA; 20mM Tris-HCl, pH 8.1; 360mM NaCl; 0.1% sodium deoxycholate) and twice with LiCl buffer (0.25M LiCl; 1% NP40; 1.1% sodium deoxycholate; 1mM EDTA; 10mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer by incubating at 56°C for 15min. Beads were separated and the supernatant was further digested for more 2 hours at 56°C. DNA was isolated using AMPure XP beads as described for the input sample.
DNA concentration was adjusted and used for library preparation using Ovation® Ultralow Library System V2 following suppliers protocol. Amplified libraries were size-selected for dinucleotide fraction (350-600 bp fragments) using agarose gel-separation and MinElute Gel Extraction Kit (Qiagen). Sample quality was inspected using D1000 tapestation. Samples were sequenced with HiSeq2500 using single-end 50bp mode.

value: D2 Dox

tag: assay

value: ChIP-seq

tag: target

tag: antibody


title: AMI31


title: AMI32


description: ChIPseq_Input_XistTetOP_delBC_D2_noDOX_Rep1_B258C03

value: D2 noDox

tag: replicate

value: Input


title: Pax9 mt-2


description: ChIPseq_H2AK119Ub_XistTetOP_delBC_D2_noDOX_Rep2_B258C35_B265C17


title: RNAseq_XistTetOP_FL_D2_Dox_Rep2

data_processing:
Reads were mapped on mm10 genome with Tophat (2.1.0) {Trapnell, 2009 #2336}, with options [-g 1 -x 1 -N 5 --read-edit-dist 5 --no-coverage-search], with refFlat annotation {Tyner, 2017 #2337}.
Reads covering exons of each gene were then counted with featureCounts (1.5.1) with options [-C -p] {Liao, 2014 #2329}.
Genome_build: mm10
Supplementary_files_format_and_content: count table

extract_protocol:
Total RNA was isolated using NYZol (NZYTech) and then DNAse I treated (Roche) to remove contaminating DNA following the manufacturer’s recommendations. Initial RNA quality were checked by electrophoresis and sent to NOVOGENE for sequencing. Quality of the samples were verified on a 2100 Agilent Bioanalyser system and only samples with RIN score above 9 were processed.
RNA (1 µg) was used for 250-300 bp insert cDNA library following manufacturer’s recommendations (except for Xist ΔB+C DOX#2, which only 100 ng of RNA was used for the library preparation using a low input method). Libraries were sequenced with NovaSeq 6000 platform using paired-end 150bp mode.

value: FL

value: RNA-seq


title: MEFs, Hypoxia 3

city: Cologne

first: Thomas

last: MacVicar

address: Joseph-Stelzmann Str 9B

country: Germany

institute: Max Planck Institute for Biology of Ageing

data_processing:
raw reads were mapped using HISAT version 2.1.0
transcripts were assembled using StringTie version 1.3.4d
differential gene expression was analyzed using cufflinks/cuffdiff version 2.2.1
Genome_build: BUILD_GRCm38_RELEASE_91
Supplementary_files_format_and_content: Tab-separated differential gene expression results

source_name: WT MEF

growth_protocol: 1x10e6 cells were incubated in normoxia or hypoxia for 16 h.

extract_protocol:
Cell pellets were frozen in LN2 prior to extraction. Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel)
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg  total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and Rnase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

value: SV40 immortalized mouse embryonic fibroblast

value: WT

value: 0.50% oxygen


description: ChIPseq_H3K27me3_XistTetOP_delBC_D2_Dox_Rep1_B265C24


title: MEFs, Hypoxia 2


title: RNAseq_XistTetOP_FL_D2_noDox_Rep2

description: RNAseq_XistTetOP_FL_D2_noDox_Rep2_WT_noDOX2

value: D2 noDOX


title: Pax9 wt-1


title: AMI29


title: RNAseq_XistTetOP_delA_D2_Dox_Rep2

description: RNAseq_XistTetOP_delA_D2_Dox_Rep2_delA_DOX2


description: ChIPseq_H2AK119Ub_XistTetOP_delBC_D2_Dox_Rep1_B265C30


title: RNAseq_XistTetOP_delA_D2_Dox_Rep1

description: RNAseq_XistTetOP_delA_D2_Dox_Rep1_ADOX_1


title: MEFs, Hypoxia 1


title: RNAseq_XistTetOP_delA_D2_noDox_Rep2

description: RNAseq_XistTetOP_delA_D2_noDox_Rep2_delA_noDOX2


title: AMI28


description: ChIPseq_H2AK119Ub_XistTetOP_delBC_D2_noDOX_Rep1_B265C29


description: ChIPseq_H3K27me3_XistTetOP_delBC_D2_noDOX_Rep1_B265C23


title: RNAseq_XistTetOP_delBC_D2_Dox_Rep2

description: RNAseq_XistTetOP_delBC_D2_Dox_Rep2_delBC_DOX2


title: AMI27


description: ChIPseq_H3K27me3_XistTetOP_delBC_D2_Dox_Rep2_B258C27_B265C10


title: RNAseq_XistTetOP_FL_D2_noDox_Rep1

description: RNAseq_XistTetOP_FL_D2_noDox_Rep1_Wt_DOX_1


title: RNAseq_XistTetOP_FL_D2_Dox_Rep1


title: RNAseq_XistTetOP_delBC_D2_Dox_Rep1

description: RNAseq_XistTetOP_delBC_D2_Dox_Rep1_BCDOX_1


title: AMI25


title: AMI24


title: AMI23


title: 10 days Cherry+ repl.2

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
The RSEM package (version 1.2.29) and Bowtie2 were used to aling reads to the mouse mm10 transcriptome, taken from known Gene reference table available at UCSC
The “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.12.4) within the R programming (version 3.3.1)
Genome_build: mm10 UCSC
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent UCSC mouse genes and columns represent individual samples.

extract_protocol:
Lungs were minced manually and then digested for 30 min at 37 degrees in a HBSS digestion solution containing DNase I (Sigma-Aldrich) and Liberase TM and TH (Roche Diagnostics). Samples were then washed, passed through a 100 um filter and incubated with Red Blood Cell Lysis buffer (Miltenyi Biotec) for 3-5 min. After a wash with MACS buffer (0.5% BSA and 250 mM EDTA in PBS), samples were passed through a 40 um filter and a 20 um strainer-capped flow cytometry tube to generate a single cell suspension to use for flow cytometric analysis or further purification. Samples were stained with a CD45 and a Ter119 antibody. Murine CD45-Ter119- cells were isolated via FACS.
Total RNA from sorted cell samples was isolated using the MagMax-96 Total RNA Isolation Kit (ThermoFIsher Scientific). The quality and concentration of total RNA for each sample was determined on Agilent 2100 Bioanalyzer using the Total RNA 6000 Pico Kit. RNA was amplified and libraries were prepared for sequencing using Illumina protocols.

treatment_protocol: Balb/c female mice 6-10 weeks old were injected intravenously with 4T1-labelling tumour cells and lungs were isolated at day 5 and day 10 after injection

value: Lung

value: CD45-Ter119- cells


title: RNAseq_XistTetOP_delA_D2_noDox_Rep1

description: RNAseq_XistTetOP_delA_D2_noDox_Rep1_A_DOX_1


title: RNAseq_XistTetOP_delBC_D2_noDox_Rep1

description: RNAseq_XistTetOP_delBC_D2_noDox_Rep1_BC_DOX_1


description: ChIPseq_H3K27me3_XistTetOP_delBC_D2_noDOX_Rep2_B258C26_B265C09


title: AMI21


title: AMI20


title: RNAseq_XistTetOP_delBC_D2_noDox_Rep2

description: RNAseq_XistTetOP_delBC_D2_noDox_Rep2_delBC_noDOX2


title: AMI22


title: 10 days Cherry- repl.2


title: 10 days Cherry+ repl.3


title: 10 days Cherry+ repl.1


title: GFP_CHX_DEX vs ERF#111_CHX_DEX Rep2

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

institute: University Bayreuth

description: transient overexpression

hyb_protocol: The hybridization experiments were performed as recommended in the Two-Color Microarray-Based Gene Expression Analysis protocol (manual G4140-90050, Agilent Technologies).

scan_protocol: Processed microarrays were scanned using a high-resolution microarray scanner (Agilent Technologies) and spot intensities were quantified using Agilent’s feature extraction software.

data_processing: Data were analyzed with the LIMMA package using the program R. Every array was background corrected and normalized with the Loess algorithm, between the arrays the Quantile method was used for normalization.

organism: Arabidopsis thaliana

source_name: rosette leaf protoplasts

label_protocol: 150 ng of total RNA of each sample were labelled using the Low Input Quick Amp Labeling Kit as recommended by the manufacturer (manual G4140-90050, Agilent Technologies).

growth_protocol: Seeds were surface-sterilized and sown on Murashige and Skoog (MS) medium (1 % (w/v) sucrose, 1 % (w/v) agar), stratified (3 d darkness, 4°C) and grown for 7 d under long-day (LD) conditions (23°C, 16 h/8 h light/dark cycle; 100 µmol photons m-2 s-1). For experiments with adult plants, 7-d-old seedlings were planted into soil (soil: vermiculite, 2:1) and grown for another 2 weeks under short-day (SD) conditions (23°C, 8 h/16 h light/dark cycle; 100 µmol photons m-2 s-1). For protoplast experiments, seeds were directly sown on soil and plants were grown for 4 weeks under SD conditions.

extract_protocol: Total RNA was isolated using the RNeasy® Plant Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: For the wounding experiments, all rosette leaves of 3-week-old plants grown on soil (8 leaf stage, 8 h photoperiod) were gently wounded with a needle, whereas non wounded control plants were kept in parallel. For the protoplast assay, 400 µl protoplast solution was transformed with 20 µg 35S:ERF#111-HBD or 35S:GFP-HBD, incubated over night for 18 h under LD conditions and then mixed with 50 µM CHX, or the same amount of the solvent DMSO. After 30 min incubation with CHX, 10 µM DEX was added to the suspension and incubated for additional 4 h under LD conditions. Afterwards, cells were frozen in liquid nitrogen.

value: 4 weeks

value: rosette leaf protoplasts

value: GFP OE + CHX + DEX

value: ERF#111 OE + CHX + DEX


title: 10 days Cherry- repl.3


title: 10 days Cherry- repl.1


title: Mice Bladder Homogenate Reaction 2

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger (version 2.2.0 for human data and version 3.0.0 for mouse data)
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat R package

Genome_build: GRCh38 for human data and mm10 for mouse data
Supplementary_files_format_and_content: the barcode, gene, expression matrix file of each sample

source_name: Bladder

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v2 user guide   to perform single cell suspension which were prepared before. Briefly, the  single-cell samples were passed through a 40μm cells strainer and counted using  a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to  recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the  oils onto the 10x Genomics single-cell-A chip and run this machine. After  droplet generation, samples were transferred onto a PCR tube and reverse  transcription was performed using T100 Thermal Cycler (BIO-RAD). After the  reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics  followed by a Silane DynaBead clean-up as outlined in the user guide. Purified  cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect  beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to  determine cDNA concentration.
10X Genomics Single Cell 3' v2 Reagent Kit

value: Total Bladder Homogenate


title: H3.3

city: Stanford

first: Graeme

last: Gowans

address: Gilbert Building, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
RNA-seq: Reads were aligned using bwa-aln and analysed using DESeq2 to generate differentially expressed genes and FPKM
ChIP-seq: Reads were aligned using bwa-aln. Peaks and signal tracks were generated using MACS2. Fold enrichment for acetyl and crotonyl signals were calculated vs histone H3 signal.
ChIP-seq: Deeptools2 (computeMatrix function, scale-regions) was used to generate counts across the transcriptional start/termination sites and the gene body from the signal tracks.
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: FPKM and log2 fold change in expressione (mutant vs wild-type) - RNA-seq/fold enrichment of H3K9acetyl and H3K9crotonyl over histone H3 across gene bodies, processed using Deeptools. Bin 1-10 = 200 bp upstream, bin 11-60 = gene bodies, bin 61-70 =200 bp downstream

source_name: yeast

growth_protocol: yeast grown in continuous culture to induce metabolic cycling

extract_protocol:
RNA: yeast were harvested and flash frozen. RNA was extracted using MasterPure RNA extraction kit (MPY03100). DNA: yeast cultures were collected and fixed in formaldehyde, quenched in glycine and flash frozen. Cells were lysed by beat-beating and the lysate sonicated. Lysates were incubated with the appropriate antibody for 2 hours. DNA was eluted and the crosslinks reversed. DNA was treated with RNaseA, proteinase K and purified.
RNA: 1 µg of RNA was used with the NEB Ultra Directional kit (E7420) using standard protocols. ChIP-seq: 0.5 ng of DNA was used with the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645)

treatment_protocol: Samples taken at different times across these metabolic cycles - samples A and B (RNA) are replicates. Based on the phase descriptions in Kuang et al 2014, timepoints 1 and 2 are OX phase (early/late), 3 and 4 are RB phase (early/late) and 5 is RC phase.


title: AMI19

value: overweight

value: sperm


title: 5 days Cherry+ repl.2

city: London


title: AMI16


title: AMI18


title: Mice Bladder Homogenate Reaction 1

city: Nanning

last: Yu

address: Shuangyong road 22

institute: Guangxi Medical University


title: AMI15


title: H3.4


title: ERF#111_CHX_DEX vs GFP_CHX_DEX Rep1

description: transient overexpression


title: 5 days Cherry+ repl.1


title: AMI17


title: ERF#111_DMSO_DEX vs GFP_DMSO_DEX Rep1

description: transient overexpression

value: ERF#111 OE + DMSO + DEX

value: GFP OE + DMSO + DEX


title: 5 days Cherry- repl.2


title: 5 days Cherry+ repl.3


title: erf#111_wound vs erf#111_control Rep2

description: knockout and stress

source_name: 3-week-old plant rosettes

value: 3 weeks

value: rosette leaves

value: 3 h after wounding

value: control


title: H3K9cr.4


title: WT_control vs WT_wound Rep1

description: knockout and stress


title: AMI12


title: WT_wound vs WT_control Rep2

description: knockout and stress


title: AMI11


title: ERF#111_leaf vs WT_leaf Rep1

description: stable overexpression

source_name: 7-day-old seedling shoots

value: 7 days

value: shoots


title: WT_root vs ERF#111_root Rep2

description: stable overexpression

source_name: 7-day-old seedling roots

value: roots


title: erf#111_control vs erf#111_wound Rep1

description: knockout and stress


title: AMI14


title: H3K9ac.4


title: H3K9cr.3


title: WT_leaf vs ERF#111_leaf Rep2

description: stable overexpression


title: mut3B.RNA

value: CEN.PK TAF14[W81A]


title: 5 days Cherry- repl.3

value: Lung

value: CD45-Ter119- cells


title: H3K9ac.3


title: AMI9


title: AMI13


title: mut1B.RNA


title: mut5B.RNA


title: Monocytes, Adult 3 - Unstimulated

city: São Paulo

first: Anna Cláudia

middle: Calvielli

last: Castelo Branco

state: São Paulo

address: Avenida Doutor Enéas de Carvalho Aguiar, 470. IMT prédio II, 3o andar

country: Brazil

institute: University of São Paulo

description:
Test
SAMPLE 16

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package.
For the normalization it uses the average of five housekeeping genes: ACTB (actin-beta), B2M (beta-2-microglobulin), GAPDH (glyceraldehyde 3-phosphate dehydrogenase) and HPRT1 (hypoxanthine phosphoribosyltransferase 1)
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: Monocytes

label_protocol: First-strand cDNA was synthesized based on the instructions of RT2 First-Strand and PreAMP Kit (Qiagen, Valencia, CA, USA), and the cDNA product was used for RT2 Profiler PCR Array using SYBR Green-based qPCR according to the manufacturer’s protocol (PAHS-018Z array, Qiagen). The array consisted of a panel of 84 genes related to the TLR signaling pathway

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: developmental stage

value: Adult

value: Monocyte

tag: activation agent

value: Unstimulated

tag: time


title: 5 days Cherry- repl.1


title: AMI7

value: healthy


title: AMI6

value: sperm


title: AMI10

value: overweight


title: mut4A.RNA


title: GFP_DMSO_DEX vs ERF#111_DMSO_DEX Rep2

description: transient overexpression

value: 4 weeks

value: rosette leaf protoplasts

value: GFP OE + DMSO + DEX

value: ERF#111 OE + DMSO + DEX


title: ERF#111_root vs WT_root Rep1

description: stable overexpression


title: AMI26

value: obese


title: mut2B.RNA


title: Transformed ductal cells (YFP+, CD44+)

first: Richard

middle: James

last: Mitter

state: LONDON

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

hyb_protocol: Following labelling samples were hybridized for 18 hr at 45C on Affymetrix Mouse Gene 1.0 ST GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 running GCOS software.

data_processing: Data were processed using R.  The oligo package's read.celfiles function was used import the raw CEL files with annotation package pd.mogene.1.0.st.v1 .  Data were further background corrected, normalized and summarized at the core gene level using oligo's rma function with default settings.

source_name: Pooled cells after sorting of YFP+ CD44+ cells from fifteen LSL-KRasG12D, Fbw7 F/F, R26-LSL-YFP, CK19-CreER pancreases two weeks after tamoxifen treatment

label_protocol: After fragmentation, labelling was performed using the NuGEN FL-Ovation cDNA Biotin module v2.

growth_protocol: KFCkY mice were allowed to grow to 8 weeks.

extract_protocol: RNA was extracted from the pooled, sorted samples using the MagMAX-96 Total RNA Isolation kit (Ambion) according to manufacturer's instructions.

treatment_protocol: These mice were then injected with two doses of intraperitoneal tamoxifen and then sacrificed two weeks later.

value: pancreas

tag: genotype/variation

value: transformed


title: Monocytes, Adult 2 - Unstimulated

description:
Test
SAMPLE 13

tag: cell type


title: AMI5


title: AMI8


title: AMI4


title: mut4B.RNA


title: Monocytes, Adult 3 - LPS

description:
Test
SAMPLE 17

value: LPS


title: mut2A.RNA

value: CEN.PK TAF14[W81A]


title: Monocytes, Adult 1- LPS+Histamine

description:
Test
SAMPLE 12

value: LPS and Histamine


title: DMSO-2

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile R20291 whole genome sequence using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied to compare Deoxycholate to DMSO, Cholate to DMSO and Deoxycholate to Cholate
Genome_build: Peptoclostridium difficile R20291 (FN545816.1)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts, Normalized Counts, Statistics (FC, pvalue, significant)

organism: Clostridioides difficile

source_name: strain R20291 Grown with DMSO

growth_protocol: Strains were grown anerobically in TY 10h at 37°C

extract_protocol:
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (MicrobExpress rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq non stranded RNA seq kit

tag: subsp.

value: strain

value: Wild type


title: AMI3


title: Monocytes, Adult 1 - LPS

description:
Test
SAMPLE 11

value: Adult

value: Monocyte


title: mut5A.RNA


title: DMSO-1


title: Control or non-transformed ductal cells (YFP+, CD44-)

source_name: Pooled cells after sorting of YFP+ CD44- cells from fifteen LSL-KRasG12D, Fbw7 F/F, R26-LSL-YFP, CK19-CreER pancreases two weeks after tamoxifen treatment

value: control


title: wt5B.RNA


title: AMI2

value: healthy

value: sperm


title: Monocytes, Adult 3 - LPS+Histamine

description:
Test
SAMPLE 18


title: Monocytes, Adult 2 - LPS+Histamine

description:
Test
SAMPLE 15


title: OH43_tassel_rep1

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

data_processing:
Illumina GAII software used for base calling
Supplementary_files_format_and_content: Processed data files not provided because differential expression was not performed on this data. Mapped data (i.e. bam files) was used to examine reads within a small genetic mapping window on a genome browser.

organism: Zea mays

source_name: 5-10mm maize greenhouse-grown wildtype tassels

growth_protocol: greenhouse-grown maize plants

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Illumina mRNA sequencing libraries were generated using TruSeq (Illumina)

treatment_protocol: greenhouse-grown plants from an F2 segregating population (ndl1 mutant X B73) and from inbred background OH43 were dissected and flash-frozen

tag: background

value: wildtype

value: tassel


title: ndl1_tassel_rep1

source_name: 5-10mm maize greenhouse-grown ndl1 mutant tassels

value: B73 and Oh43

value: ndl1 mutant


title: mut3A.RNA


title: wildtype_sibling_tassel_rep1

source_name: 5-10mm maize greenhouse-grown wildtype looking tassels


title: DMSO-3


title: Monocytes, Adult 2 - LPS

description:
Test
SAMPLE 14


title: Clinical_Sample

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
HC
Stranded RNA-Seq

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Post deplexing, fastq files were processed via Path-Seq software (http://software.broadinstitute.org/pathseq/); resulting in a tab-delimited text file being produced detailing read counts for microbes detected present.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Microbes_Detected_by_PathSeq.txt: Tab-delimited text file detailing read counts for microbes detected present by the Path-Seq tool (GATK).

source_name: Postmortem cortex

extract_protocol:
Single piece of postmortem human cortex (<10mg) was lysed through flash freezing, grinding and syringe homogenization. Total RNA was extracted from the homogenate using the EZ1 RNA Tissue mini kit with no modification to manufacturer instructions (Qiagen Cat No: 959034).
For library construction, the NEB Ultra II RNA Library Prep Kit for Illumina was used. Specifically, for first-strand synthesis, the NEBNext RNA First Strand Synthesis Module was used (E7525) with no modification to manufacturer instructions. For second-strand-synthesis, the NEBNext Ultra Directional RNA Second Strand Synthesis Module was used (E7550) with no modification to manufacturer instructions. Purification post second-strand synthesis was accomplished using SPRIselect beads (Beckman Coulter B23317) with no modification to manufacturer instructions.

value: Brain cortex

tag: sample group

value: HC

tag: technical replicate

value: No

tag: biological replicate

tag: longitudinal replicate

tag: gender

value: Male

tag: race

value: African-American

tag: age


title: wt3B.RNA

tag: genotype


title: AMI1

tag: bmi classification

tag: tissue


title: Monocytes, Newborn 3 - LPS+Histamine

description:
Test
SAMPLE 9

tag: developmental stage

value: Newborn

value: LPS and Histamine


title: Monocytes, Newborn 3 - LPS

description:
Test
SAMPLE 8

tag: activation agent

value: LPS


title: mut1A.RNA

value: CEN.PK TAF14[W81A]


title: scramble control for miR-574-3p [3p_control-2]

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Gene expression levels were expected of fragments per kilobase of transcript sequence per millions base pairs mapped (FPKM) using Cufflinks v2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for  mRNA genes in each sample

source_name: MGC-803_scramble control for miR-574-3p

growth_protocol: gastric cancer cells MGC-803 were grown in DMEM with 10% FCS

extract_protocol:
MGC-803 cells were transfected with miR-574-5p/-3p mimics or scramble controls, 48 hours later, MGC-803 cells were collected,total RNA was extracted from the cells with TRIzol reagent
The cDNA libraries were generated in as described previously. Zhao H, et al. Nat Commun. 2017 Nov 10;8(1):1428.
rRNA depletion

tag: cell line

value: gastric cancer cell line

value: scramble control for miR-574-3p


title: wt4B.RNA


title: Chol-3

source_name: strain R20291 Grown with 5 mM Cholate

value: strain

tag: strain

value: Wild type


title: scramble control for miR-574-3p [3p_control-1]

treatment_protocol: MGC-803 cells were transfected with miR-574-5p/-3p mimics or scramble controls

tag: cell type

tag: genotype/variation


title: Monocytes, Newborn 3 - Unstimulated

description:
Test
SAMPLE 7

value: Monocyte

value: Unstimulated

tag: time


title: Monocytes, Adult 1 - Unstimulated

description:
Test
SAMPLE 10

value: Adult


title: miR-574-3p overexpression [s3p-1]

source_name: MGC-803_miR-574-3p overexpression

value: miR-574-3p overexpression


title: Chol-2

tag: subsp.


title: Chol-0


title: DMSO-0


title: wt1B.RNA


title: scramble control for miR-574-5p [574_minmi_2]

description: 574_minmi_2_803_20160726_GTCCGC_L005_R1_001_val

source_name: MGC-803_scramble control for miR-574-5p

value: scramble control for miR-574-5p


title: wt5A.RNA


title: wt2B.RNA


title: wt4A.RNA


title: Monocytes, Newborn 2 - LPS+Histamine

description:
Test
SAMPLE 6


title: Deox-3

source_name: strain R20291 Grown with 0.5 mM Deoxycholate


title: Deox-2


title: Monocytes, Newborn 2 - Unstimulated

description:
Test
SAMPLE 4


title: Monocytes, Newborn 1 - LPS+Histamine

description:
Test
SAMPLE 3


title: scramble control for miR-574-5p [574_minmi_1]

description: 574_minmi_1_803_20160726_CCGTCC_L005_R1_001_val


title: wt3A.RNA

source_name: yeast


title: Deox-1


title: Monocytes, Newborn 1 - LPS

description:
Test
SAMPLE 2


title: miR-574-3p overexpression [s3p-2]


title: miR-574-5p overexpression [574_5p_2]

description: 574_5p_2_803_20160726_TAGCTT_L005_R1_001_val

source_name: MGC-803_miR-574-5p overexpression

value: miR-574-5p overexpression


title: Chol-1


title: miR-574-5p overexpression [574_5p_1]

description: 574_5p_1_803_20160726_GATAGA_L005_R1_001_val


title: Deox-0


title: Monocytes, Newborn 1 - Unstimulated

description:
Test
SAMPLE 1


title: Monocytes, Newborn 2 - LPS

description:
Test
SAMPLE 5


title: wt1A.RNA


title: wt2A.RNA