title: control C5

value: control


title: UL16MODBC158

status: Public on Oct 22 2019

type: SRA

city: Cambridge

first: David

middle: Michael

last: Mauger

state: MA

address: 200 Technology Square

department: Platform Research

country: USA

institute: Moderna, Inc.

library_source: transcriptomic

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in SHAPEMapper pipeline version 1.2:
1. Reads from 'DEN', 'MOD', and 'NC' samples are mapped to the reference transcripts in Bowtie2
2. Mutation frequencies are calculated for each base in the samples
3. SHAPE reactivities are calculated form 'p', 'm', and 'd' mutational fre
Genome_build: Custom
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

molecule: total RNA

organism: synthetic construct

source_name: Luciferase mRNA L16 with U

extract_protocol:
Treated RNAs were purified with Ampure beads
SHAPE-MaP reverse transcript, NEBnext Ultra II RNA library prep kit for illumina

treatment_protocol: RNA were treated as described

tag: nucleotide chemistry

value: RNA contains Uracil

tag: treatment

value: Folded RNA treated with 1M6 in DMSO at 37C


title: ntp5-1 rep2

city: Nanchang

first: Jianbo

last: Song

state: Jiang Xi

address: Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China

country: China

institute: Jiang Xi Agricultural University

data_processing:
Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was applied for adapter trimming as well as quality control.
The remaining reads were mapped to the genome with hisat2 allowing 3’ soft clipping (Daehwan et al., 2015).
The reads that mapped to multiple loci were removed. Reads that mapped within 50 bp of annotated pre-miRNAs (miRBase release 21) (Ana and Sam, 2014) were retained.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/
Supplementary_files_format_and_content: The map file contains the pre-miRNA alignment information and the non-templated sequence information statistics.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under long day (16 h light/ 8 h darkness) conditions at 22°C

extract_protocol:
Arabidopsis seedlings were collected, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNAs from 14-day-old seedlings were resolved on a 15% denaturing polyacrylamide gel and RNAs of 40-400 nt were recovered from the gel. The size-fractionated RNAs were ligated to a 3’ adaptor using T4 RNA ligase 2, truncated (NEB). The 3’ adaptor-ligated RNAs were resolved on a 15% denature polyacrylamide gel and RNAs of 60-420 nt were recovered. The size-fractionated RNAs were reverse-transcribed with an RT primer that is complementary to the 3’ adaptor using SuperScript III (Life Technologies), followed by two-step PCR amplification. The cDNA was first amplified with the RT primer and a mixture of pre-miRNA-specific forward primers for 10 cycles and secondly amplified for 16 cycles with the 2nd PCR forward and reverse primers using Phusion DNA polymerase (NEB).  The PCR products were resolved on a 12% native polyacrylamide gel, and DNAs of 150-230 bp were recovered from the gel as the pre-miRNA 3’ RACE-seq library. The library was sequenced on Illumina HiSeq3000.

tag: ecotype background

tag: genotype

tag: age

value: 3 weeks

tag: tissue

value: Seeding


title: exposed to 100 ug/L of TCS 100_2

city: Namur

first: Elodie

last: Falisse

address: rue de Bruxelles 61

department: Biology

country: Belgium

institute: University of Namur

library_source: genomic

data_processing:
DNA from 12 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping ENCODE data) was used for further processing of data.
Genome_build: Zv9
Supplementary_files_format_and_content: Excel file contains variably methylated fragment details (excel)

molecule: genomic DNA

organism: Danio rerio

source_name: pool of 7dpf larvae

growth_protocol: zebrafish were maintained individually in 24-well microplates, at 26.5 °C under a 12:12 light/dark photoperiod cycle in a climate chamber during all the experiment.

extract_protocol:
Genomic DNA from each pooled larvae sample was extracted using DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer's protocol.
Reduced representation bisulfite sequencing libraries were prepared based on published protocols. Briefly, 12 RRBS libraries were prepared, 4 libraries per condition, each library containing a pool of 24 larvae. Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair, addition of 3′ A overhangs and addition of methylated adaptors (Illumina, San Diego, CA) to the digested fragments. Following adaptor ligation, DNA fragments ranging from 40–220 bp (pre-ligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulfite converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) with an extended incubation time of 18–20 h. Bisulfite converted libraries were amplified by PCR reactions and sequenced (100-bp single ended reads) by New Zealand Genomics Limited (University of Otago, New Zealand) on an Illumina HiSeq2000 sequencer.

treatment_protocol: zebrafsih were exposed to 2 sublethal concentrations of tCS: 50 and 100 µg/L. 50% of the solution were renewed every day.

tag: strain

value: AB strain

value: exposed to 100 ug/L of TCS


title: control C4


title: ntp4-1 rep2


title: control C3


title: HEK293 _H. Pylori_biological_rep3

type: RNA

city: Erlangen

first: Pachathundikandi

last: Suneesh Kumar

state: Bayern

address: Staudtstrasse 5

department: Chair of Microbiology

country: Germany

institute: FAU Erlangen-Nuremberg

hyb_protocol: 0.6 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K V2 using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

organism: Homo sapiens

source_name: Embryonic kidney_H.pylori-infected

label_protocol: Cyanine-3(Cy3) labelled cRNA was prepared by linear T7 based amplification step, 0.1 µg RNA (Nanodrop-1000 spectrophotometer/ND-1000) were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) following the protocol. cRNA yield and dye incorporation rate were quantified by ND-1000 spectrophotometer.

growth_protocol: Parental (HEK293 Blue Null) cells were maintained in DMEM medium with 1% sigma antibiotic-antimycotic solution and selected with 100  µg/ml Zeocin. TLR5+ (HEK293 Blue TLR5) cells were maintained in the same base medium and additionally selected using 100  µg/ml Blasticidin. Before experiment cells were grown in culture plates and washed with PBS for two times and maintained in antibiotics free media.

extract_protocol: RNA was prepared using Qiazol lysis reagent and miRNA easy kit (Qiagen, Germany) as per the manufacturer's protocol. The RNA quality was analyzed using Agilent 2100 Bioanalyzer and the samples had RIN value between 9.3 and 10.

treatment_protocol: Both cell lines in antibiotic free media were infected with H. pylori or mock infected for 6h at 37°C in a humidified CO2 incubator.

tag: cell line

value: HEK293 Blue Null

value: parental wildtype


title: UL16DENBC168

value: RNA heat denatured at 95C and treated with 1M6 in DMSO


title: control C2


title: UL15NCBC13

source_name: Luciferase mRNA L15 with U

value: RNA treated with DMSO


title: UL15DENBC15


title: R10LB 0.5ug/mL Nafcillin  Rep3a

city: San Diego

first: Akanksha

last: Rajput

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive La Jolla, CA 92093-0412  Contact Us  In Silico Lab:  858-822-1144

department: Bioengineering

institute: University of California San Diego

data_processing:
Sequenced reads were aligned to D712 genome (VFJD00000000.1 ) using bowtie-2 version 2.2.6 with parameters ’ -X 1000 -N 1 -3 3 ‘
Gene specific counts were generated from aligned reads with HTSeq version 0.9.1 using parameters ‘-s reverse -r pos’
Normalized TPM counts were generated with DESEq2 1.16.1
ComBat module in SVA package version 3.24.4 was used for batch correction of TPM data
Genome_build: VFJD00000000.1
Supplementary_files_format_and_content: Tab delimited file with read counts, normalized TPM counts and batch corrected TPM counts

organism: Staphylococcus aureus

source_name: R10LB 0.5ug/mL Nafcillin

growth_protocol: Overnight cultures of HA-VISA D712 were diluted to a starting OD600 of 0.01 into fresh media and grown at 37C with stirring to OD600 of 0.4. This preculture was then diluted back to OD600 0.01 into fresh media containing no drug or sub-inhibitory concentrations of nafcillin relative for each media type. Growth was monitored by obtaining OD600 readings every 45 min and sample for RNA sequencing was taken at 3 hours.

extract_protocol:
After 3 hours of growth, 3 mL samples were taken for RNA sequencing and added to tubes containing 6 mL RNAprotect. After incubation, they were centrifuged to remove the supernatant. RNA was extracted from the pelleted cells using a ‘Quick RNA Fungal/Bacterial Microprep’ kit developed by Zymo Research. The cells were mechanically lysed with a Roche MagNa Lyzer instrument and DNA was removed with DNase I during the  RNA purification. RNA quality was checked with an Agilent Bioanalyzer instrument and ribosomal RNA was removed using an Illumina Ribo-Zero kit.
The remaining RNA was used to build a cDNA library for sequencing using a KAPA Stranded RNA-seq Library Preparation Kit. The kit was used for RNA fragmentation, sequencing adapter ligation, and library amplification. The generated cDNA libraries were sent for Illumina  sequencing on a HiSeq 4000.

tag: media

tag: nafcillin concentration (ug/ml)


title: R10LB 0.5ug/mL Nafcillin  Rep2a


title: R10LB 0.5ug/mL Nafcillin  Rep3b


title: R10LB 0.5ug/mL Nafcillin  Rep1a


title: R10LB 0ug/mL Nafcillin  Rep3b

source_name: R10LB 0ug/mL Nafcillin


title: R10LB 0.5ug/mL Nafcillin  Rep1c


title: UL15MODBC14


title: R10LB 0.5ug/mL Nafcillin  Rep2b


title: ntp2-1 rep2


title: UL14NCBC119

source_name: Luciferase mRNA L14 with U


title: Col-0 rep5

source_name: wild type_seedilng

value: wild type


title: urt1-1 rep2


title: heso1-1 rep5


title: ntp2-1ntp6-1ntp7-1 rep1


title: R10LB 0ug/mL Nafcillin  Rep2b


title: R10LB 0ug/mL Nafcillin  Rep3a


title: UL14MODBC157


title: R10LB 0ug/mL Nafcillin  Rep2a


title: R10LB 0ug/mL Nafcillin  Rep1c


title: UL14DENBC167


title: R10LB 0ug/mL Nafcillin  Rep1a


title: ntp6-1ntp7-1 rep1


title: UL13NCBC118

source_name: Luciferase mRNA L13 with U


title: CAMHB 20ug/mL Nafcillin  Rep3b

source_name: CAMHB 20ug/mL Nafcillin

value: CAMHB


title: ntp10-1 rep1


title: R10LB 0ug/mL Nafcillin  Rep1b


title: R10LB 0.5ug/mL Nafcillin  Rep1b


title: ntp9-1 rep1


title: CAMHB 20ug/mL Nafcillin  Rep3a


title: ntp7-1 rep1


title: UL12NCBC117

source_name: Luciferase mRNA L12 with U


title: ntp8-1 rep1


title: UL13MODBC156


title: ntp6-1 rep1


title: CAMHB 20ug/mL Nafcillin  Rep1c


title: CAMHB 20ug/mL Nafcillin  Rep1a


title: CAMHB 20ug/mL Nafcillin  Rep1b


title: CAMHB 15ug/mL Nafcillin  Rep3a

source_name: CAMHB 15ug/mL Nafcillin


title: ntp5-1 rep1


title: CAMHB 15ug/mL Nafcillin  Rep2b


title: UL13DENBC166


title: CAMHB 15ug/mL Nafcillin  Rep2a


title: CAMHB 20ug/mL Nafcillin  Rep2a


title: CAMHB 15ug/mL Nafcillin  Rep3b


title: UL12MODBC155


title: ntp4-1 rep1


title: UL11NCBC80

source_name: Luciferase mRNA L11 with U


title: CAMHB 15ug/mL Nafcillin  Rep1c


title: urt1-1 rep1


title: ntp2-1 rep1


title: CAMHB 15ug/mL Nafcillin  Rep1a


title: CAMHB 0.5ug/mL Nafcillin  Rep3b

source_name: CAMHB 0.5ug/mL Nafcillin


title: CAMHB 15ug/mL Nafcillin  Rep1b


title: CAMHB 0.5ug/mL Nafcillin  Rep3a


title: CAMHB 20ug/mL Nafcillin  Rep2b


title: CAMHB 0.5ug/mL Nafcillin  Rep2b


title: CAMHB 0.5ug/mL Nafcillin  Rep1c


title: CAMHB 0.5ug/mL Nafcillin  Rep2a


title: CAMHB 0.5ug/mL Nafcillin  Rep1b


title: Col-0 rep4


title: UL10MODBC108

source_name: Luciferase mRNA L10 with U


title: UL12DENBC165


title: hen1-8 rep3


title: heso1-1 rep4


title: CAMHB 0.5ug/mL Nafcillin  Rep1a


title: CAMHB 0ug/mL Nafcillin  Rep3b

source_name: CAMHB 0ug/mL Nafcillin


title: CAMHB 0ug/mL Nafcillin  Rep2b


title: UL10DENBC127


title: CAMHB 0ug/mL Nafcillin  Rep3a


title: hen1-8 rep2


title: CAMHB 0ug/mL Nafcillin  Rep2a


title: hen1-8 rep1


title: UL11MODBC109


title: 12AjiaD2-1

city: Tianjin

first: Yueshan

last: Fan

address: 154 Anshan Road, Tianjin, China

institute: Tianjin Medical University General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Filter:1) Trim Smart-seq2 public primer sequence from the Reads (If the length of  trimmed Reads is lower than 30bp, reads should be discarded. If it is PE  sequence, both of the reads must be removed );  2) Remove the contaminated reads for adapters (The contaminated reads for  adapters was defined that the Read Bases contained more than 5bp of adapter  sequences. If either one of the PE Reads was polluted, we will remove both  ends of the reads);  3) Remove the low quality reads (The low quality reads was defined that the  number of Reads Bases whose phred Quality value was less than or equal to 19  accounted for more than 15% . If either one of the PE Reads defined as low  quality, we will remove both ends of the reads);  4) Remove the reads whose N base more than 5% for total bases (If either one of  the PE Reads had high Ns bases, we will remove both ends of the reads);
Alignment :HISAT2 2.1.0 is the software.--dta –t –p 4 is the parameter.And the mapping reads to genome.
Supplementary_files_format_and_content: FPKM

source_name: hCMEC/D3 cell lines

growth_protocol: hCMEC/D3 was obtained from Sigma-Aldrich , cultured in endothelial cell medium(ECM), and grown on 0.1% collagen type I-coated coverslips until a tight monolayer was formed. Medium was changed every other day.

extract_protocol:
The treated cells were removed, washing three times on dry ice, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols, NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: Hematoma was purchased from CSDH patients. The supernatant of the hematoma was collected after centrifugation at 3000 rpm for 15 min and stored at -80 ℃.  Subsequently, PBS, atorvastatin, dexamethasone, or a combination of atorvastatin and dexamethasone was added to the hematoma followed by co-culture with hCMEC/D3 for 1 h. The stimulated group of cells was transferred to normal medium containing no drugs.

value: brain vascular

tag: cell type

value: temporal lobe microvessels

tag: agent

value: combination


title: 12AjiaD2-2


title: prl1prl2


title: UL11DENBC128


title: CAMHB 0ug/mL Nafcillin  Rep1c


title: cdc5-2


title: UL10NCBC79


title: CAMHB 0ug/mL Nafcillin  Rep1b


title: 11D2-1

value: single dexamethasone


title: 10A2-2

value: single atorvastatin


title: tough

value: tough


title: CAMHB 0ug/mL Nafcillin  Rep1a


title: soe2


title: 8CA2

value: hematoma stimulation


title: 11D2-2


title: soe1

value: 3 weeks


title: mac-7

value: Seeding


title: 8CA1


title: hyl1-2 rep3


title: LEAF_rep3

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
Sequencing reads were cleaned with Trim Galore v0.5.0,  including removing bases with low quality score (<20)  and cutting sequencing adaptors followed by filtering short reads.
Cleaned reads of five tissues were fed to Trinity v2.8.4 separately for de novo assembly.
The resulting transcriptomes were filtered and combined using CD-HIT v4.6.8 with sequence identity threshold at 0.8 and sequence minimum length at 500 bp to reduce sequence redundancy and avoid short contigs
Paired-end reads were mapped to the Trinity transcriptome using Bowtie2 v2.3.4.3. RSEM v1.3.2 was used to quantify transcript abundance.
Genome_build: de novo assembly transcriptomes. FASTA file of transcript sequences is available on GSE134602.
Supplementary_files_format_and_content: tab-delimited text files include TPM for each Trinity transcript

organism: Ceratopteris richardii

source_name: Ceratopteris richardii leaf (without leaf tip)

growth_protocol: Ceratopteris richardii (wild type RNWT1) spores were cultured on 1/2 MS medium at 26 °C under a 16-h-light/8-h-dark photoperiod in a growth chamber.

extract_protocol:
The  root, leaf, root tip, leaf tip and shoot tip tissue were harvested and frozen in liquid nitrogen, RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 50-d growth, root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) tissue were separated from sporophyte seedings.

value: leaf (without leaf tip)

value: wild type RNWT1

value: 50 day after spore germination


title: ago1-27


title: 7S2-2

value: sham


title: 7S2-1


title: hyl1-2 rep2


title: 10A2-1


title: LEAF_rep2


title: CrpBfilmGlucose/933_A#

city: Chicago

first: Jeremy

middle: T

last: Ritzert

state: IL

address: 1032 W. Sheridan Road

institute: Loyola University Chicago

description: Y. pestis ∆crp grown in glucose in the biofilm state

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC
Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.
The cleaned reads were aligned to the Y. pestis genome (NC_003143.1) and plasmids pPCP1 (NC_003132.1) and pMT1 (NC_003134.1) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for Y. pestis
Read counts for sRNA were obtained using bedtools using the annotated locations
Genome_build: Y. pestis chromosome NC_003143.1, plasmid pPCP1 NC_003132.1, and pMT1 NC_003134.1
Supplementary_files_format_and_content: .xlsx file containing individual tabs comparing treatment conditions with GeneID, log2 fold change, and false discovery rate p values

organism: Yersinia pestis

growth_protocol: Y. pestis  and ∆crp were grown in defined, minimal TMH media in 0.2% glucose or 0.2% glycerol at 37ºC in 125 mL Erlenmeyer flasks. Adhering bioflm cells were scraped away and separated from planktonic cells after 18 hours of growth.

extract_protocol:
Bacteria were resuspended in RNA protect and extracted using RNA-whiz and precipitated in isoproponol. RNA was treated with Turbo Dnase
Total RNA was checked for quality and quantity on Agilent Bioanalyzer 2100 and Qubit fluorometer. The Illumina TruSeq Stranded Total RNA Library Preparation Kit was used to prepare sequencing libraries from 500 ng of total RNA samples according to manufacturer’s instructions without modifications. This procedure includes rRNA depletion with Ribo-Zero rRNA Removal Kit (Bacteria), remaining RNA purification and fragmentation, cDNA synthesis, 3’-end adenylation, Illumina adapter ligation, library PCR amplification and validation. Illumina NextSeq 500 Sequencer was used to sequence the libraries with the production of single-end, 75 bp reads.

tag: genotype/variation

value: pCD1-; {deta}crp

tag: carbon source

value: Glucose

tag: growth state

value: Biofilm


title: HDF Control 12h

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Array ID: 4675283075

hyb_protocol: Hybridization was performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals were developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays were dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction (Illumina BeadStudio Software).

source_name: HDF_Control medium

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Human dermal ﬁbroblasts (HDF) were derived from foreskin as previously described (König & Bruckner-Tuderman, 1994; Stark et al, 1999). HDF obtained from the outgrowth of explants culture and were grown in Dulbecco’s modiﬁed Eagle’s medium (DMEM) supplemented with 10% fetal calf serum (FCS), 1% L-glutamate, penicillin G and streptomycin (PAN-Biotech, Aidenbach, Germany). Cells were kept under a humidified environment with 5% CO2 and 3oC.  Fibroblasts at passages 2-8 and a density of 5-8 x 10^4 cells/cm^2 were used in all experiments.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Conditioned media from normal human keratinocytes (NHK) were used to stimulate cells. Sub-confluent monolayers of fibroblasts were grown in individual flasks, and conditioned medium (0.2-0.3 mL/cm2) was collected as follows: i. NHK conditioned medium (K): KSFM (supplemented with rhEGF and BPE) was added to keratinocyte culture flask and collected after 16h. The  After each conditioning treatment the collected media were centrifuged (200 xg/ 5 min) and then was used to stimulate other cells or tested. Time and volume was considered to have adequate soluble factors content and sufficient medium nutrients. RNA was collected fro expression profiling after 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 18 and 24h of  treatment.

tag: gender

value: male

value: skin

value: human dermal ﬁbroblasts (HDF)

tag: stimulated with

value: none (unstimulated control)

tag: time point

value: 12h after control-media treatment


title: hyl1-2 rep1


title: HDF Control 24h

description: Array ID: 4675283075

value: 24h after control-media treatment


title: HDF Control 8h

description: Array ID: 4675283075

value: 8h after control-media treatment


title: HDF Control 2h

description: Array ID: 4675283075

value: 2h after control-media treatment


title: LEAF_rep1


title: CrpPlankGlucose/933_P#

description: Y. pestis ∆crp grown in glucose in the planktonic state

value: Planktonic


title: HDF Control 0h

description: Array ID: 4675283075


title: heso1-1se-1

value: 3 weeks

value: Seeding


title: HDF Control 4h

description: Array ID: 4675283075

value: 4h after control-media treatment


title: ST_rep3

source_name: Ceratopteris richardii shoot tip

value: shoot tip

value: wild type RNWT1

value: 50 day after spore germination


title: HDF CondMed 18h

description: Array ID: 4675283074

source_name: HDF_NHK-conditioned medium

value: normal human keratinocytes (NHK)-conditioned medium

value: 18h after stimulation


title: KO PTEC 1

city: Carl Neuberg strasse

first: Roland

last: Schmitt

state: academic

address: M06 ebene-4

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2500ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml

organism: Mus musculus

source_name: primary tubular cells extracted from SerpinB2-/- B6.J  mice kidney  and treated with PMA 100ng/ml

label_protocol: Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies)

growth_protocol: primary tubular cells isolated from WT and Serpin B2 -/- mice kidney were grown and cultured in Promocell renal growth medium

extract_protocol: 150 ng of total RNA were used as input.

treatment_protocol: PMA 100ng/ml

tag: strain background

tag: Sex

value: male

tag: treatment

value: PMA 100ng/ml

value: primary kidney tubular cells


title: HDF CondMed 12h

description: Array ID: 4675283074

value: skin

value: human dermal ﬁbroblasts (HDF)

value: 12h after stimulation


title: WtBfilmGlycerol/259_AG#

description: Wild-type Y. pestis grown in glycerol in the biofilm state

value: Glycerol

value: Biofilm


title: WT PTEC 1

source_name: primary tubular cells extracted from wildtype B6.J mice kidney and treated with PMA 100ng/ml

value: wild type

tag: age


title: KO PTEC 2


title: HDF CondMed 24h

description: Array ID: 4675283075

tag: tissue

value: 24h after stimulation


title: se-1 rep3

tag: ecotype background

tag: genotype

value: 3 weeks

value: Seeding


title: WtBfilmGlucose/259_A#

description: Wild-type Y. pestis grown in glucose in the biofilm state

tag: strain

value: Glucose


title: WT PTEC 2


title: se-1 rep2


title: ST_rep1

value: shoot tip

value: wild type RNWT1


title: se-1 rep1


title: WtPlankGlycerol/259_PG#

source_name: Wild-type Y. pestis grown in glucose in the biofilm state

value: Planktonic


title: RT_rep3

source_name: Ceratopteris richardii root tip

value: root tip

value: 50 day after spore germination


title: RT_rep2


title: dcl1-7 rep3


title: WtPlankGlucose/259_P#

description: Wild-type Y. pestis grown in glucose in the planktonic state


title: HDF CondMed 6h

description: Array ID: 4675283074

value: male

value: normal human keratinocytes (NHK)-conditioned medium

value: 6h after stimulation


title: HDF CondMed_4h

description: Array ID: 4675283074

value: skin

value: human dermal ﬁbroblasts (HDF)

value: 4h after stimulation


title: HDF CondMed 8h

description: Array ID: 4675283074

value: 8h after stimulation


title: MS-275 treated repeat3

city: Hyderabad

first: PRASENJIT

last: MITRA

state: Telangana

address: University of Hyderabad Campus, Gachibowli

country: India

institute: Dr.Reddy’s Institute of Life Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with default parameter using Trimmomatic 0.36v
The reads that passed quality filters was mapped to the Rattus_norvegicus Rnor_6.0 using STAR 0.27v
Reads mapping to genes Rattus_norvegicus.Rnor_6.0 gene list [GTF] were counted using feature count module of sub reads package and were normalized in DESeq2v3.5
Differentially expressed genes were selected based on log2-ratio change with p-value <0.05 (Student‘s t test, unpaired).
Genome_build: Rnor_6.0 (GCA_000001895.4)
Supplementary_files_format_and_content: aligned bam files,tab-delimited text files include raw count values for each Sample, Differentially expressed genes list file

organism: Rattus norvegicus

source_name: BRIN-BD11 (ECACC 10033003) pancreatic beta cell line

growth_protocol: BRIN-BD11 pancreatic beta cells (ECACC cat.no: 10033003) were cultured at 37oC with 5% CO2 in RPMI medium 1640 GLUTAMAX supplemented with 10% heat inactivated Fetal Bovine Serum (FBS), 1mM Sodium pyruvate, 10µg/ml gentamycin, 100units/ml penicillin ,100µg/ml streptomycin and 50μM beta mercaptoethanol.

extract_protocol:
The cells were pelleted by centrifugation and flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit. 150 ng total RNA was used for preparing libraries for RNA sequencing.
The RNA was fragmented and then converted to cDNA according to the kit protocol (NEB #E7770S). The cDNA was end repaired and further purified using AMPure XP beads (A63880 AMPure XP).The cleaned cDNA was adapter ligated, purified and subjected to 12 PCR cycles of amplification using primers provided in the kit (NEB #E7770S). The PCR products were purified using AMPure XP beads. The quantification and size distribution of the prepared library was accomplished using Qubit fluorimeter and Agilent Tape station D1000 Kit (Agilent Technologies) following manufacturer’s instructions.

treatment_protocol: BRIN-BD11 pancreatic beta cells were seeded in 6-multiwell plates at a density of 500,000 cells/well. MS-275 (5µM, dissolved in 0.1%DMSO) was added 24h post seeding after cells were adhered and cultured for 16h in complete medium prior to RNA extraction

tag: cell line

value: A stable glucose-responsive insulin-secreting pancreatic beta-cell line established through electrofusion of RINm5F cells with New England Deaconess Hospital rat pancreatic islet cells

tag: passages

value: Passage 25

value: NEDH Rat

tag: hdac inhibitor

value: MS-275(Entinostat); Class1 HDAC inhibitor


title: RT_rep1


title: dcl1-7 rep2

value: 3 weeks

value: Seeding


title: dcl1-7 rep1


title: ST_rep2

value: shoot tip

value: wild type RNWT1


title: MS-275 treated repeat2

tag: cell type


title: HDF CondMed 2h

description: Array ID: 4675283074

value: 2h after stimulation


title: MS-275 treated repeat1


title: ROOT_rep3

source_name: Ceratopteris richardii root (without root tip)

value: root (without root tip)

value: 50 day after spore germination


title: ROOT_rep2


title: UT-SCC91_C1s siRNA

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: RNA sequencing data from cSCC

data_processing:
The samples were sequenced with the HiSeq3000 instrument using single-end sequencing with 50 bp read length.
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software and aligned against the human reference genome (GRCh38) using Star version 2.5.2b assembly.
The reads were then associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.1).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.0.1, Bioconductor version 2.12).
Genome_build: GRCh38
Supplementary_files_format_and_content: For statistical testing the data were further log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values.

source_name: Cutaneous squamous cell carcinoma 59A

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starved 24 hours before harvesting.

tag: source

value: Cutaneous SCC

value: Derived from cSCC tumors

value: Primary cSCC cells

value: C1s siRNA


title: WT repeat3


title: ago1-36 rep3


title: HDF CondMed 1h

description: Array ID: 4675283074

value: male

value: skin

value: human dermal ﬁbroblasts (HDF)

value: normal human keratinocytes (NHK)-conditioned medium

value: 1h after stimulation


title: UT-SCC91 negative control siRNA

description: RNA sequencing data from cSCC

value: Negative control siRNA


title: ago1-36 rep2

value: 3 weeks


title: WT repeat2

value: A stable glucose-responsive insulin-secreting pancreatic beta-cell line established through electrofusion of RINm5F cells with New England Deaconess Hospital rat pancreatic islet cells

value: Passage 25

value: NEDH Rat


title: ROOT_rep1

value: wild type RNWT1


title: UT-SCC12A_C1s siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 12A


title: HDF CondMed 3h

description: Array ID: 4675283074

value: 3h after stimulation


title: ago1-36 rep1

value: Seeding


title: UT-SCC59A_C1s siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 118

value: Cutaneous SCC

value: Metastatic cSCC cells


title: LT_rep3

source_name: Ceratopteris richardii leaf tip

value: leaf tip

value: 50 day after spore germination


title: UT-SCC12A negative control siRNA

description: RNA sequencing data from cSCC

value: Derived from cSCC tumors

value: Primary cSCC cells


title: UT-SCC59A negative control siRNA

description: RNA sequencing data from cSCC


title: LT_rep2


title: hopCascadeStem_2

city: Corvallis

first: John

last: Henning

state: OR

address: 3450 SW Campus Way

institute: USDA-ARS

data_processing:
Adaptor trimming of reads was done with Skewer (version 0.2.2).
RNA-seq reads were aligned to the hop Cascade assembly with hisat2 (version 2.1.0).
Exon counting was done with featureCounts (version 1.6.3).
RNA-seq alignments were assembled into transcripts with StringTie (v1.3.3b).
Transcript sequences were extracted with gffread.
Genome_build: PRJNA562558
Supplementary_files_format_and_content: Feature count files (*.txt) contain gene counts and were generated using featureCounts; FASTA files contain transcript sequences and were generated using gffread.

organism: Humulus lupulus

source_name: stem

growth_protocol: Cascade plants were grown in a glasshouse with active control of insects and plant pathogens.  Young tissue of leaves, stems actively growing and apical meristems were harvested and immediately immersed in liquid nitrogen, then transferred into -80 C freezer until RNA extraction.

extract_protocol:
RNA from hop tissues was extracted using RNeasy Plant Mini Kit (Qiagen), using glass hooks to remove RNA from tubes.
Three TruSeq RNA (Qiagen) libraries were developed from leaf, stem, and meristem tissues with each library sequenced on a single lane.

treatment_protocol: There were no treatments applied to different tissue other than chemical sprays controlling insects and fungal pathogens.

value: stem

tag: cultivar

value: Cascade


title: heso1-1 rep1

source_name: seedilng

tag: genotype/variation

value: heso1-1 mutant


title: hopCascadeMeristem_1

source_name: meristem

value: meristem


title: hopCascadeMeristem_2


title: Col-0 rep2

tag: ecotype

value: 3 weeks

value: Wild type


title: Col-0 rep3


title: Wild type cholinergic neurons adult replicate 1

city: La Jolla

first: Yishi

last: Jin

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Import fastq files to usegalaxy.org
Align reads with TopHat
measurement of abundance with Cufflinks
Counts by HTSEQ
Differential expression by DESEQ2
Genome_build: ce10
Supplementary_files_format_and_content: .tab, .xlsx

organism: Caenorhabditis elegans

source_name: Isolated C. elegans neurons

growth_protocol: Animals were synchronized by hypochlorite treatment. Eggs were isolated from wild type N2, CZ631, and CZ5808 gravid adults and allowed to hatch overnight and arrest at the L1-stage. Synchronized L1s were plated onto 15cm NGM plates seeded with OP50 bacteria. Approximately 8-10,000 L1s were plated to 15-20 plates for each strain. As N2 cells are only needed to control for the FACS sort, only 5 plates were prepared. These plates were incubated at 20°C for 72hr to reach adulthood prior to collection.

extract_protocol:
The entire process of cell preparation and sort was completed in a single day. Animals were washed off plates and spun down and the washed in M9 media to remove bacteria. Typically, pellets for each strain would be ~500µl in volume, and these would be split into two tubes. 750µl of lysis buffer (200µM DTT, 0.25% SDS, 20mM HEPES pH8.0, 3% sucrose) was added to each tube and samples were incubated for approximately 6-7 minutes. Worms were then rapidly washed in M9 five times. Next, 500µl of 20mg/ml freshly made pronase solution was added. Samples were incubated in pronase approximately 20 minutes. Every 2-3 minutes, each sample was disrupted by pipetting with a P200, and samples were monitored for dissociation with a dissection microscope. When large worm chunks were no longer visible under the dissection microscope, the reaction was stopped by adding 250µl ice cold PBS-FBS solution (1X PBS solution with 2% Fetal Bovine Serum). Samples were then centrifuged in the cold at top speed in a microcentrifuge for 10 minutes, and pelleted cells were resuspended in 500µl FBS. Cells were then syringe-filtered (5µm pore). Samples were spun again in the cold and resuspended in ½ the starting volume of FBS. 80,000-100,000 GFP+ cells were collected for each sample at the UCSD Flow Cytometric Core in Moore’s Cancer Center. Cells were sorted directly into Trizol LS and stored at -80°C until preparation. RNA was isolated using Qiagen RNAeasy kit.
RNA library preparation and sequencing were performed at the Institute for Genomic Medicine at UCSD. RNA libraries were prepared with Illumina TruSeq kit. Libraries were sequenced on an Illumina HiSeq4000.

value: young adult

value: cholinergic neurons


title: acr-2(gf) cholinergic neurons adult replicate 1


title: Wild type cholinergic neurons adult replicate 2


title: hopCascadeStem_1


title: WT repeat1

value: A stable glucose-responsive insulin-secreting pancreatic beta-cell line established through electrofusion of RINm5F cells with New England Deaconess Hospital rat pancreatic islet cells

value: Passage 25

value: NEDH Rat


title: hopCascadeLeaf_1

source_name: leaf

value: leaf


title: heso1-1 rep3

value: Seeding


title: hopCascadeLeaf_2


title: LT_rep1

value: leaf tip

value: wild type RNWT1


title: heso1-1 rep2


title: Rectum-2

status: Public on Oct 21 2019

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: cDNA library of single cell

data_processing:
Quality control and preprocessing of high throughput sequencing data were using SOAPnuke with parameters -n 0.1 -l 10 -A 0.25 -Q 2 -G --seqType 1
16 bp 10xTM Barcodes and 10bp UMIs were encoded at the start of Read 1 (R1).
Reads alignment, filtering, barcode counting, and UMI counting were performed using cellranger 2.1 with default parameters
Sample normalization and scaled gene expression data were calculated by Seurat2.3.2
Genome_build: GRCh38_Human
Supplementary_files_format_and_content: tab-delimited text files include raw UMIcounts and scaled data for each cell

source_name: adult human rectum epithelial cells

extract_protocol:
cDNA library establishment and sequencing: single cell suspensions were captured using the 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN-120237) according to the manufacturers protocol. (10XGenomics, Pleasanton). And libraries were sequenced on an illumine HiSeq EP151.
10X Genomics

treatment_protocol: Intestinal tissue was cut into small pieces and incubated in 5mM EDTA in HBSS for 30min at 4℃ to get epithelial tissues. Next, the tissue were incubated in 2mg/ml Collagenase I  for 15min at 37℃. Then the sediment was obtained through centrifugation and incubated in Tryple (Invitrogen) for 20 min at 37℃ to obtain single-cell suspension.

value: Epithelia cell

value: large intestine

tag: age of human


title: Rectum-1

description: cDNA library of single cell


title: acr-2(gf) cholinergic neurons adult replicate 2


title: Colon-1

description: cDNA library of single cell

source_name: adult human colon epithelial cells


title: Ileum-2

description: cDNA library of single cell

source_name: adult human ileum epithelial cells

value: small intestine


title: EPP control  sample 2

city: barcelona

first: roberta

last: antonelli

state: Cataluña

address: Passeig Vall d'Hebron 119-129 Collserola Building,, lab 207

country: Spain

institute: VHIR barcelona

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Three hundred nanograms of total RNA were hybridized to Human ClariomTM S assay (Affymetrix, Santa Clara, CA, USA) arrays with the GeneChip WT Terminal Labeling Hybridization Kit (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: transcription analysis console (Applied Biosystem, version 4.0.0.25)

label: biotin

source_name: Patient derived Tumor cell line

growth_protocol: EPN cells were grown in Neurocult medium supplemented with NeuroCult NS-A Proliferation Supplement (Human) (#05750 Stem Cell Technologies, Vancouver, BC, Canada), Epidermal Growth Factor (EGF; 20 ng/ml; #78006.1 Stem Cell Technologies), and basic Fibroblast Growth Factor

extract_protocol: RNA was then isolated using the miRNeasy mini kit (Qiagen, #509217004). RNA quality was evaluated using Agilent Bioanalyzer 2100 Eukaryote Total RNA Pico assay (Agilent Technologies, Santa Clara, CA). Three hundred nanograms of total RNA were hybridized to Human ClariomTM S assay (Affymetrix, Santa Clara, CA, USA) arrays with the GeneChip WT Terminal Labeling and

treatment_protocol: EPP cells (3 × 105 cells per well) were plated in 6-well plates and treated with 1 µM of C133 or DMSO for 5 h.

value: Patient derived ependymoma tumor cell line


title: EPP treated CN133 1uM 5h sample 1

label_protocol: GeneChip WT Terminal Labeling Hybridization Kit


title: EPP treated CN133 1uM 5h sample 2


title: EPP treated CN133 1uM 5h sample 3


title: EPP control  sample 3


title: EPP control  sample 1


title: Ileum-1

description: cDNA library of single cell


title: Col-0 rep1


title: UMRC2_shFTO#2 rep 1 IP

city: Stanford

first: Yiren

last: Xiao

state: CA

address: 1291 WELCH ROAD

institute: Stanford	University

data_processing:
TrimGalore v0.4.2
STAR
RSEM
Genome_build: hg38
Supplementary_files_format_and_content: TPM and fold changes

source_name: human ccRCC cell line

extract_protocol:
Qiagen RNeasy Mini Kit
For m6A sequecing, m6A-specific antibodies are used to immunoprecipitate RNA. Eluted RNA is reverse-transcribed to cDNA and deep sequenced
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1×106 cancer cells were growth in 100 mm plate 37 ℃, 5% CO2 overnight

tag: rna source

value: enriched with m6A-specific antibodies

value: tumor

tag: transfection


title: UMRC2_shFTO#2 rep 2 Input

value: input total RNA


title: UMRC2_shFTO#5 rep 2 Input


title: UMRC2_shFTO#5 rep 1 IP


title: UMRC2_shFTO#5 rep 1 Input


title: UMRC2-shControl rep 2 IP

value: shControl


title: UMRC2-shControl rep 2 Input


title: UMRC2_shFTO#5 rep 2 IP


title: UMRC2_shFTO#2 rep 1 Input


title: UMRC2-shControl rep 1 Input


title: Colon-2

description: cDNA library of single cell


title: HDF CondMed 10h

description: Array ID: 4675283074

source_name: HDF_NHK-conditioned medium

tag: gender

value: male

value: skin

value: human dermal ﬁbroblasts (HDF)

tag: stimulated with

value: normal human keratinocytes (NHK)-conditioned medium

tag: time point

value: 10h after stimulation


title: UMRC2_shFTO#2 rep 1

description: UMRC2_4_fpkm RNA-Seq dataset.xlsx

value: Total RNA


title: UMRC2_shFTO#5 rep 1

description: UMRC2_7_fpkm RNA-Seq dataset.xlsx


title: UMRC2_shFTO#2 rep 2

description: UMRC2_5_fpkm RNA-Seq dataset.xlsx


title: UMRC2_shFTO#5 rep 2

description: UMRC2_8_fpkm RNA-Seq dataset.xlsx


title: UMRC2-shControl rep 2

description: UMRC2_2_fpkm RNA-Seq dataset.xlsx


title: UMRC2_shFTO#2 rep 2 IP


title: UMRC2-shControl rep 1 IP


title: UMRC2-shControl rep 1

description: UMRC2_1_fpkm RNA-Seq dataset.xlsx


title: DH_1: DEX_ZT0 HFD REP1

city: Munich

first: Nina

middle: Henriette

last: Uhlenhaut

state: Bavaria

address: Ingolstädter Landstraße 1,  Neuherberg

department: Molecular Endocrinology

institute: HelmholtzZentrum München - IDC

data_processing:
Mapping against mm9 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1
IP efficiency normalization
Create normalized peak universe
Genome_build: mm9
Supplementary_files_format_and_content: broadpeak and  gappedPeak files were produced using macs2 representing GR peaks

source_name: Liver

extract_protocol:
ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 100 mg of frozen liver was minced and Dounce homogenated in 0.7 mg/mL DSG crosslinker and 1% Formaldheyde. Nuclei were isolated and chromatin sonicated to a 1-0.1 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies.
Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

tag: Sex

tag: tissue

value: liver

tag: treatment

value: 13 wk control Diet (Research Diet, D12329)

tag: chip antibody

value: GR (Santa Cruz, sc-1004X)


title: DH8pt: DEX_ZT12 HFD REP1

tag: strain

value: 12 wk control Diet (Research Diet, D12329)

value: GR ProteinTech


title: DH9pt: DEX_ZT12 HFD REP2


title: DL8sc: DEX_ZT12 control REP1


title: DL_2: DEX_ZT0 control REP2

value: 16 wk control Diet (Research Diet, D12329)


title: WT_LFD_Fasted Rep_4 [LR30]

city: Groningen

first: Sarah

last: Stolle

address: Antonius Deusinglaan 1

country: Netherlands

institute: University of Groningen

data_processing:
Trimmed sequencing reads (fastq files) were mapped to Mus Musculus reference genome using hisat/0.1.5-beta-goolf-1.7.20 with default settings.
SAMtools/1.2- goolf-1.7.20 was used to sort the aligned reads.
Quantification of gene read counts was performed by HTSeq-count HTSeq/0.6.1p1 using –mode=union
Genome_build: GRCm38 ensemble Release 82 (mm10)
Supplementary_files_format_and_content: readcounts values

extract_protocol:
Total RNA was isolated from crushed freeze-clamped liver with Trizol reagent. RNA integrity and concentration was measured with capillary electrophoris using PerkinElmer LabChipGC.
Lexogen QuantSeq 3'mRNA Library Prep Kit

tag: strain background

value: wild type

tag: age

tag: diet

value: Low-fat diet

tag: feeding state

value: fasted


title: DL8pt: DEX_ZT12 control REP1


title: KO_LFD_Fasted Rep_4 [LR28]

tag: genotype/variation

value: Acadm-knockout


title: DL9pt: DEX_ZT12 control REP2


title: WT_LFD_Fasted Rep_3 [LR26]


title: DH_2: DEX_ZT0 HFD REP2

value: 14 wk control Diet (Research Diet, D12329)


title: DL_1: DEX_ZT0 control REP1

value: male

value: 15 wk control Diet (Research Diet, D12329)


title: KO_HFD_Fasted Rep_4 [LR32]

value: High-fat diet


title: DL9sc: DEX_ZT12 control REP2


title: WT_HFD_Fed Rep_4 [LR27]

value: fed


title: WT_HFD_Fasted Rep_4 [LR29]


title: WT_LFD_Fed Rep_4 [LR25]


title: Pythium arrhenomanes infection replicate 3

city: Ghent

first: Ruben

last: Verbeek

address: Coupure links 653

department: Department of Biotechnology

institute: Ghent University

description: raw data file: US22502699_251784510140_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: Hybridization to custom-made 60-mer Agilent arrays was performed according to the manufacturer’s protocols (Agilent Technologies).

scan_protocol: Slide image files were generated using a DNA microarray scanner (G2505B; Agilent Technologies) and

data_processing:
Signal intensities were extracted and normalized within each array using Feature Extraction version 9.5 (Agilent Technologies).
Gene intensities of <100 in replicates were neglected, for these are not significant. Signal intensities among biological replicates per infection were normalized according to the quantile method for standardization (global scaling) using EXPANDER6.

organism: Oryza sativa

source_name: Pythium arrhenomanes infection_roots

label_protocol: A total of 850 ng of RNA was synthesized to cyanine 3- or cyanine 5-labeled cDNA using a low-input RNA labelling kit (Agilent Technologies) and hybridized to custom-made 60-mer Agilent arrays according to the manufacturer’s protocols (Agilent Technologies).

growth_protocol: Sterilized rice seeds were placed 2 cm apart on square Petri dishes (120 mm × 120 mm) filled with 50 mL of Gamborg B5 basal medium with 1% plant agar. Plants were grown at 26 °C under a 12-h/12-h light regime.

extract_protocol: Samples from mock-inoculated and Pythium-infected seedlings were collected 2 days post inoculation (dpi). Three biological replicates were sampled, where each biological replicate represents a pool from at least 20 individual plants, giving a total of six RNA samples (two treatments × three biological replicates). Total RNA was extracted from frozen root tissue using the spectrum plant total RNA kit (Sigma-Aldrich) and subsequently Turbo DNase treated according to the provided protocol (Ambion).

treatment_protocol: Three days post imbibition, when the primary roots were approximately 1 cm in length, the seeds were infected with P. arrhenomanes (PT60) using 0.6-cm PDA plugs of a 7-days-old culture of P. arrhenomanes or an sterile PDA plug.

tag: cultivar

value: Nipponbare

tag: sample group

value: 2 days after infection

value: roots


title: Pythium arrhenomanes infection replicate 1

description: raw data file: US22502699_251784510139_S01_GE2-v5_95_Feb07_1_3.txt


title: Mock infection replicate 3

source_name: Mock infection_roots

value: 2 days after (mock) infection


title: Pythium arrhenomanes infection replicate 2

description: raw data file: US22502699_251784510139_S01_GE2-v5_95_Feb07_1_4.txt


title: KO_HFD_Fasted Rep_3 [LR24]

value: liver


title: Mock infection replicate 2


title: Mock infection replicate 1


title: DH8sc: DEX_ZT12 HFD REP1

value: 12 wk control Diet (Research Diet, D12329)

value: GR (Santa Cruz, sc-1004X)


title: KO_LFD_Fed Rep_4 [LR31]


title: DH9sc: DEX_ZT12 HFD REP2


title: KO_LFD_Fed Rep_3 [LR22]


title: KO_HFD_Fed Rep_4 [LR23]


title: WT_HFD_Fasted Rep_3 [LR21]


title: WT_LFD_Fed Rep_2 [LR18]


title: KO_HFD_Fed Rep_3 [LR20]


title: KO_LFD_Fed Rep_2 [LR13]


title: KO_LFD_Fed Rep_1 [LR12]


title: KO_LFD_Fasted Rep_3 [LR15]


title: WT_HFD_Fasted Rep_1 [LR07]


title: KO_LFD_Fasted Rep_2 [LR08]


title: WT_LFD_Fed Rep_3 [LR19]


title: KO_HFD_Fed Rep_1 [LR10]


title: WT_HFD_Fed Rep_2 [LR05]


title: WT_LFD_Fasted Rep_2 [LR14]


title: WT_LFD_Fed Rep_1 [LR17]


title: KO_HFD_Fasted Rep_2 [LR03]


title: WT_HFD_Fasted Rep_2 [LR16]


title: KO_LFD_Fasted Rep_1 [LR04]


title: WT_LFD_Fasted Rep_1 [LR06]


title: KO_HFD_Fasted Rep_1 [LR01]


title: RNA-Seq_LFD Dex treated  at ZT12 and sac. at ZT16 REP 3

description:
LFD Dex treated  at ZT12 and sac. at ZT16 REP 3
sample code: GSE108690-DL_12
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt

data_processing:
Reads were aligned to the mm9 genome with STAR v2.4.2a and the output SAM files were converted to BAM using samtools v1.3.1
Feature counting: counting all reads which were located within an exon, do not overlap multiple features, are not chimeric, and have a minimum mapping quality of 4. Using featureCounts v1.4.6: featureCounts -p -C -F GTF -t exon -Q 4 -a gencode.vM1.annotation.gtf -g gene_id -o $output $input -T 16  However for further processing steps, the count matrix was filtered (0 count rows and those where the average was less then 50 were left out). These filtered tables were than the input tables for DESeq2 and for the normalization step.
Finding differentially expressed genes using DESeq2 v1.23.10
Finding oscillating genes with JTK from MetaCycle v1.2.0, period was set to 24 hours.
Genome_build: mm9
Supplementary_files_format_and_content: .txt tables. Those with the name table_featureCounts*.txt are the count matrices, where the rows are the genes and the columns the samples. A cell in the matrix contains the count number for gene i in sample j. Tables named table_filtered_*.txt are the prefiltered, normalized tables.
Supplementary_files_format_and_content: table_featureCounts_noBL41.txt: txt file which contains the count matrix
Supplementary_files_format_and_content: table_filtered_noBL41_rlog.txt: the rlog normalized count matrix
Supplementary_files_format_and_content: table_filtered_noBL41_VST.txt: the VST normalized count matrix
Supplementary_files_format_and_content: table_featureCounts_KO-WT_AlbCre.txt: txt file which contains the count matrix
Supplementary_files_format_and_content: table_filtered_KO-WT_AlbCre_rlog.txt: the rlog normalized count matrix
Supplementary_files_format_and_content: table_filtered_KO-WT_AlbCre_VST.txt: the VST normalized count matrix
Supplementary_files_format_and_content: table_featureCounts_ZT04.txt: txt file which contains the count matrix (mice were injected with Dex at ZT0 and sacrificed at ZT4)
Supplementary_files_format_and_content: table_featureCounts_ZT1216.txt: txt file which contains the count matrix (mice were injected with Dex at ZT12 and sacrificed at ZT16)
Supplementary_files_format_and_content: table_filtered_VST_ZT1216.txt: the VST normalized count matrix
Supplementary_files_format_and_content: table_filtered_VST_ZT04.txt: the VST normalized count matrix

extract_protocol:
Total RNA was isolated from >50mg of liver using QIAZOL (QIAGEN). Quality of the RNA was assayed using the Agilent RNA 6000 Nano Kit in a 2100 Bioanalyzer (Agilent).
Libraries were prepped from 1µg total RNA with the Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilent Bravo liquid handling platform). Libraries were run on Illumina sequencers.


title: RNA-Seq_LFD Dex treated at ZT0 and sac. at ZT4 REP 1

description:
LFD Dex treated at ZT0 and sac. at ZT4 REP 1
sample code: GSE108690-DL_4
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_LFD Dex treated at ZT0 and sac. at ZT4 REP 3

description:
LFD Dex treated at ZT0 and sac. at ZT4 REP 3
sample code: GSE108690-DL_6
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_LFD Dex treated at ZT0 and sac. at ZT4 REP 2

description:
LFD Dex treated at ZT0 and sac. at ZT4 REP 2
sample code: GSE108690-DL_5
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: WT_HFD_Fed Rep_1 [LR02]


title: RNA-Seq_LFD Dex treated at ZT12 and sac. at ZT16 REP 2

description:
LFD Dex treated at ZT12 and sac. at ZT16 REP 2
sample code: GSE108690-DL_11
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_HFD Dex treated at ZT0 and sac. at ZT4 REP 3

description:
HFD Dex treated at ZT0 and sac. at ZT4 REP 3
sample code: GSE108690-DH_6
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt

value: 12 wk High Fat Diet (Research Diet, D12331)


title: RNA-Seq_HFD Dex treated at ZT0 and sac. at ZT4 REP 1

description:
HFD Dex treated at ZT0 and sac. at ZT4 REP 1
sample code: GSE108690-DH_4
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_HFD Dex treated at ZT0 and sac. at ZT4 REP 2

description:
HFD Dex treated at ZT0 and sac. at ZT4 REP 2
sample code: GSE108690-DH_5
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_LFD Dex treated at ZT12 and sac. at ZT16 REP 1

description:
LFD Dex treated at ZT12 and sac. at ZT16 REP 1
sample code: GSE108690-DL_10
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_HFD Dex treated at ZT12 and sac. at ZT16 REP 3

description:
HFD Dex treated at ZT12 and sac. at ZT16 REP 3
sample code: GSE108690-DH_12
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: KO_HFD_Fed Rep_2 [LR11]


title: RNA-Seq_LFD control at ZT12 and sac. at ZT16 REP 2

description:
LFD control at ZT12 and sac. at ZT16 REP 2
sample code: BL5_3
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_LFD control at ZT12 and sac. at ZT16 REP 1

description:
LFD control at ZT12 and sac. at ZT16 REP 1
sample code: BL5_1
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_LFD control at ZT0 and sac. at ZT4 REP 1

description:
LFD control at ZT0 and sac. at ZT4 REP 1
sample code: BL2_1
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_HFD control at ZT12 and sac. at ZT16 REP 1

description:
HFD control at ZT12 and sac. at ZT16 REP 1
sample code: BH5_2
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_HFD control at ZT12 and sac. at ZT16 REP 2

description:
HFD control at ZT12 and sac. at ZT16 REP 2
sample code: BH5_3
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_HFD control at ZT0 and sac. at ZT4 REP 1

description:
HFD control at ZT0 and sac. at ZT4 REP 1
sample code: BH2_1
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_LFD control at ZT0 and sac. at ZT4 REP 2

description:
LFD control at ZT0 and sac. at ZT4 REP 2
sample code: BL2_3
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: RNA-Seq_ZT20 LFD WT REP 1

description:
ZT20 LFD WT REP 1
sample code: ZT20-LFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 LFD KO REP 3

description:
ZT20 LFD KO REP 3
sample code: ZT20-LFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_HFD Dex treated at ZT12 and sac. at ZT16 REP 1

description:
HFD Dex treated at ZT12 and sac. at ZT16 REP 1
sample code: GSE108690-DH_10
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_ZT20 LFD KO REP 2

description:
ZT20 LFD KO REP 2
sample code: ZT20-LFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 LFD WT REP 3

description:
ZT20 LFD WT REP 3
sample code: ZT20-LFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 LFD KO REP 1

description:
ZT20 LFD KO REP 1
sample code: ZT20-LFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 HFD WT REP 2

description:
ZT20 HFD WT REP 2
sample code: ZT20-HFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 HFD WT REP 1

description:
ZT20 HFD WT REP 1
sample code: ZT20-HFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 HFD KO REP 3

description:
ZT20 HFD KO REP 3
sample code: ZT20-HFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 HFD KO REP 2

description:
ZT20 HFD KO REP 2
sample code: ZT20-HFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 HFD KO REP 1

description:
ZT20 HFD KO REP 1
sample code: ZT20-HFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 LFD WT REP 2

description:
ZT16 LFD WT REP 2
sample code: ZT16-LFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 LFD WT REP 3

description:
ZT16 LFD WT REP 3
sample code: ZT16-LFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 LFD KO REP 2

description:
ZT16 LFD KO REP 2
sample code: ZT16-LFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 LFD WT REP 1

description:
ZT16 LFD WT REP 1
sample code: ZT16-LFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 HFD WT REP 2

description:
ZT16 HFD WT REP 2
sample code: ZT16-HFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 LFD KO REP 1

description:
ZT16 LFD KO REP 1
sample code: ZT16-LFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 HFD WT REP 3

description:
ZT16 HFD WT REP 3
sample code: ZT16-HFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_HFD Dex treated at ZT12 and sac. at ZT16 REP 2

description:
HFD Dex treated at ZT12 and sac. at ZT16 REP 2
sample code: GSE108690-DH_11
table_featureCounts_ZT1216.txt
table_filtered_VST_ZT1216.txt


title: RNA-Seq_HFD control at ZT0 and sac. at ZT4 REP 2

description:
HFD control at ZT0 and sac. at ZT4 REP 2
sample code: BH2_3
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.txt


title: WT_HFD_Fed Rep_3 [LR09]

value: wild type


title: RNA-Seq_ZT20 HFD WT REP 3

description:
ZT20 HFD WT REP 3
sample code: ZT20-HFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT20 LFD WT REP 2

description:
ZT20 LFD WT REP 2
sample code: ZT20-LFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 HFD WT REP 1

description:
ZT16 HFD WT REP 1
sample code: ZT16-HFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 HFD KO REP 3

description:
ZT16 HFD KO REP 3
sample code: ZT16-HFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT16 HFD KO REP 1

description:
ZT16 HFD KO REP 1
sample code: ZT16-HFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: Acinetobacter oleivorans DR1 aceA mutant

city: Seoul

first: Chulwoo

last: Park

address: Anam

country: South Korea

institute: Korea univ.

data_processing:
RNA sequencing was performed with two runs of the Illumina Genome Analyzer IIx to generate single-ended 100-bp reads
Quality-filtered reads were aligned to the reference genome sequence using CLC Genomics Workbench 6.5.1
Mapping was based on a minimal length of 100 bp with an allowance of up to two mismatches
Relative transcript abundance was measured in RPKM
Genome_build: NCBI genome accession no. CP002080
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Acinetobacter oleivorans

source_name: bacterial RNA

growth_protocol: Both WT and aceA knockout strains were grown to the exponential phase (WT OD600 ~0.5, ΔaceA OD600 ~0.15) in NaAc-amended MSB media.

extract_protocol:
Total RNA was isolated from 10 ml of cells using the RNeasy Mini Kit according to the manufacturer's instructions.
Libraries for Illumina sequencing were constructed with the TruSeq Stranded mRNA sample prep kit following the manufacturer's protocol.

tag: genotype

value: aceA mutant


title: RNA-Seq_ZT12 LFD WT REP 2

description:
ZT12 LFD WT REP 2
sample code: ZT12-LFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 LFD KO REP 1

description:
ZT12 LFD KO REP 1
sample code: ZT12-LFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 LFD KO REP 3

description:
ZT12 LFD KO REP 3
sample code: ZT12-LFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 LFD WT REP 1

description:
ZT12 LFD WT REP 1
sample code: ZT12-LFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: Acinetobacter oleivorans DR1 WT


title: RNA-Seq_ZT16 HFD KO REP 2

description:
ZT16 HFD KO REP 2
sample code: ZT16-HFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 LFD KO REP 2

description:
ZT12 LFD KO REP 2
sample code: ZT12-LFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 HFD WT REP 3

description:
ZT12 HFD WT REP 3
sample code: ZT12-HFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 HFD WT REP 2

description:
ZT12 HFD WT REP 2
sample code: ZT12-HFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 HFD WT REP 1

description:
ZT12 HFD WT REP 1
sample code: ZT12-HFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNAseq_RegionM_homo_rep2

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

data_processing:
Single end sequencing (51bp) was performed on the NextSeq550 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using  hisat2 (v2.1.0).
The read counts and Fragments Per Kilobase of exon per Megabase (FPKM) values for each gene were calculated using Cufflinks (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Blastocyst

extract_protocol:
In vivo-developed blastocyst-stage embryos were collected at 88 h after hCG, then incubated in M2 medium microdrops. Each blastocysts was picked up from the microdrops, and RNA from each blastocyst was extracted using Allprep DNA/RNA Micro kit (QIAGEN).
RNA libraries were prepared usig Ovation SoLo RNA-Seq Systems (NuGEN) for sequencing using standard Illumina protocols

treatment_protocol: Female mice were super-ovulated by an injection of 7.5 IU of PMSG, followed by 7.5 IU of hCG 48 h later. After the hCG injection, the mice were mated with fertile males of the same strain.

value: Blastocyst

value: embryo

value: homozygously deleted with Region M


title: RNAseq_RegionM_homo_rep4


title: RNAseq_RegionM_homo_rep3


title: RNA-Seq_ZT12 HFD KO REP 3

description:
ZT12 HFD KO REP 3
sample code: ZT12-HFD-KO-4
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNAseq_RegionM_homo_rep1


title: RNA-Seq_ZT12 HFD KO REP 2

description:
ZT12 HFD KO REP 2
sample code: ZT12-HFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT12 HFD KO REP 1

description:
ZT12 HFD KO REP 1
sample code: ZT12-HFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNAseq_RegionM_hetero_rep2

value: heterozygously deleted with Region M


title: RNAseq_RegionM_hetero_rep4


title: RNAseq_RegionM_hetero_rep3


title: RNA-Seq_ZT12 LFD WT REP 3

description:
ZT12 LFD WT REP 3
sample code: ZT12-LFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT08 LFD WT REP 1

description:
ZT08 LFD WT REP 1
sample code: ZT08-LFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT08 LFD WT REP 2

description:
ZT08 LFD WT REP 2
sample code: ZT08-LFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNAseq_RegionM_hetero_rep1


title: RNAseq_RegionM_WT_rep4


title: RNAseq_RegionM_WT_rep3


title: RNA-Seq_ZT08 HFD WT REP 2

description:
ZT08 HFD WT REP 2
sample code: ZT08-HFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT08 LFD KO REP 2

description:
ZT08 LFD KO REP 2
sample code: ZT08-LFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNAseq_RegionM_WT_rep2


title: RNA-Seq_ZT08 HFD WT REP 1

description:
ZT08 HFD WT REP 1
sample code: ZT08-HFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT08 HFD KO REP 2

description:
ZT08 HFD KO REP 2
sample code: ZT08-HFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT08 LFD KO REP 1

description:
ZT08 LFD KO REP 1
sample code: ZT08-LFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT08 HFD KO REP 1

description:
ZT08 HFD KO REP 1
sample code: ZT08-HFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT04 LFD WT REP 3

description:
ZT04 LFD WT REP 3
sample code: ZT04-LFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT04 LFD WT REP 2

description:
ZT04 LFD WT REP 2
sample code: ZT04-LFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: T-O-3

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
OTO3
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

molecule: polyA RNA

source_name: OSE-derived tumor

extract_protocol:
Normal ovary and fallopian tube (fimbriae) were embedded in FSC 22 Clear Frozen Section Compound and immediately frozen with liquid N2. The resultant blocks were cut at 5-8 μm and mounted on a PEN membrane frame (Leica), followed by air-drying the slides for 30 minutes at room temperature. Laser capture was performed with a Leica LMD6000 laser microdissection system, and excised pieces were harvested into 200 μl RNase-free tubes, which were carefully recovered from the microscope, centrifuged, and placed on ice. Ovarian tumors (T-O) were from LPT organoid implants, and fallopian tube tumors were (T-FT) from PTPT organoid implants, all at 6 months post-injection. RNA was extracted by using the miRNeasy mini Kit (Qiagen), following the manufacturer’s instruction.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit.

tag: strain/background

value: ovarian surface epithelium

tag: tissue type

value: tumor


title: RNA-Seq_ZT04 LFD WT REP 1

description:
ZT04 LFD WT REP 1
sample code: ZT04-LFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: Wild Type

city: Irvine

first: Kai

last: Kessenbrock

address: 839 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

data_processing:
Alignment of 3’ end counting libraries from scRNAseq analyses was completed utilizing 10× Genomics Cell Ranger 2.1.0. Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
“Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cell across the two libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each sample, Wild Type or PYMT, of this study

source_name: CD11b+, Gr1+ cells

extract_protocol:
The spleen was pushed through a 70-μm cell strainer and washed with RPMI to create a cell suspension of splenocytes. Cells were centrifuged at 500g at 4ºC for 5 min and then incubated for 5 min in 5 mL RBC lysis buffer at RT. Cells were quenched with 10 mL RPMI (Corning, 10-040-CV) with 5% FBS and centrifuged at 500g at 4ºC for 5 min. Cells were resuspended in 3 mL FACS buffer (1xPBS, 3% FBS), and total remaining live cells were counted by Countessä II and processed for FACS. Tissue samples were harvested from mice and mechanically dissociated to generate single cell suspensions as described above. Cells were blocked with anti-mouse FcγR (CD16/CD32) (BioLegend, 101301) on ice for at least 10 min. Cells were then centrifuged at 500g for 5 min at 4C and washed once with FACS buffer (1xPBS with 3%FBS). Cells were incubated for 30 min at 4ºC with pre-conjugated fluorescent labeled antibodies with the following combinations: CD45 (30-F11) (BioLegend, 103112 (APC) or 103115 (APC-cy7)), CD11b (M1/70) (BioLegend, 101206 (FITC) or 101212 (APC), Gr1 (Rb6-8C5) (BioLegend, 101206 (PE) or 108439 (BV605),  CD84 (mCD84.7) (BioLegend, 122805 (PE)), and Jaml (4e10) (BioLegend, 128503 (PE)). Sytox Blue dye (Life Technologies, S34857) was added to stained cells to assay for viability. Cells sorted by BD FACSAria™ Fusion
FACS-isolated CD11b+/Gr1+ cells from the spleens of control WT (5 mice pooled) and tumor-bearing PyMT mice (3 mice pooled) were washed once in PBS with 0.04% BSA, resuspended to a concentration of approximately 1,000 cell/µL and loaded onto the 10X Genomics Chromium platform for droplet-enabled scRNAseq according to the manufacturer’s instructions. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 User Guide: CG00052 Rev B. Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of 48,488 reads per cell

value: Spleen

value: FVB/n


title: PYMT

value: PYMT


title: T-FT-5

description:
FTO5
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv

source_name: FTE-derived tumor

value: fallopian tube epithelium


title: T-O-2

description:
OTO2
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: T-FT-4

description:
FTO4
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: T-O-1

description:
OTO1
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT04 LFD KO REP 2

description:
ZT04 LFD KO REP 2
sample code: ZT04-LFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: T-FT-3

description:
FTO3
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT04 LFD KO REP 1

description:
ZT04 LFD KO REP 1
sample code: ZT04-LFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT04 HFD WT REP 2

description:
ZT04 HFD WT REP 2
sample code: ZT04-HFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: T-FT-1

description:
FTO1
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT04 HFD WT REP 3

description:
ZT04 HFD WT REP 3
sample code: ZT04-HFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT04 HFD WT REP 1

description:
ZT04 HFD WT REP 1
sample code: ZT04-HFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNAseq_RegionM_WT_rep1


title: N-O-3

description:
ON3
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv

source_name: normal OSE

value: normal


title: N-O-2

description:
ON2
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT04 HFD KO REP 3

description:
ZT04 HFD KO REP 3
sample code: ZT04-HFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: N-O-1

description:
ON1
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT04 HFD KO REP 2

description:
ZT04 HFD KO REP 2
sample code: ZT04-HFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT04 HFD KO REP 1

description:
ZT04 HFD KO REP 1
sample code: ZT04-HFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: N-FT-3

description:
FN3
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv

source_name: normal FTE


title: RNA-Seq_ZT00 LFD WT REP 3

description:
ZT00 LFD WT REP 3
sample code: ZT00-LFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: N-FT-2

description:
FN2
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT00 LFD WT REP 2

description:
ZT00 LFD WT REP 2
sample code: ZT00-LFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: N-FT-1

description:
FN1
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: RNA-Seq_ZT04 LFD KO REP 3

description:
ZT04 LFD KO REP 3
sample code: ZT04-LFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT00 LFD WT REP 1

description:
ZT00 LFD WT REP 1
sample code: ZT00-LFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT00 LFD KO REP 3

description:
ZT00 LFD KO REP 3
sample code: ZT00-LFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: T-FT-2

description:
FTO2
processed data file: counts.raw.csv
processed data file: counts.normalized.csv
processed data file: counts.fpkm.csv


title: GR knockout REP1

data_processing:
Mapping against mm9 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1
IP efficiency normalization
Create normalized peak universe
Genome_build: mm9
Supplementary_files_format_and_content: narrowpeak files were produced using macs2 representing GR peaks

source_name: GR knockout_liver

extract_protocol:
ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 200 mg of frozen liver was minced and Dounce homogenated in 0.7 mg/mL DSG crosslinker and 1% Formaldheyde. Nuclei were isolated and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies.
Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

value: Liver


title: STAT5_ZT12 HFD REP2

source_name: STAT5_ZT12 HFD_liver


title: STAT5_ZT12 HFD REP1


title: RNA-Seq_ZT00 LFD KO REP 2

description:
ZT00 LFD KO REP 2
sample code: ZT00-LFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt

value: 12 wk control Diet (Research Diet, D12329)


title: RNA-Seq_ZT00 HFD WT REP 3

description:
ZT00 HFD WT REP 3
sample code: ZT00-HFD-WT-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: STAT5_ZT12 control REP1

source_name: STAT5_ZT12 control_liver


title: STAT5_ZT12 control REP2


title: PPARA_ZT12 HFD REP2

source_name: PPARA_ZT12 HFD_liver

value: PPARalpha (Santa Cruz, sc-9000X)


title: RNA-Seq_ZT00 HFD WT REP 2

description:
ZT00 HFD WT REP 2
sample code: ZT00-HFD-WT-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt

value: 12 wk High Fat Diet (Research Diet, D12331)


title: RNA-Seq_ZT00 HFD WT REP 1

description:
ZT00 HFD WT REP 1
sample code: ZT00-HFD-WT-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT00 HFD KO REP 3

description:
ZT00 HFD KO REP 3
sample code: ZT00-HFD-KO-3
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: GR_ZT20 HFD REP1

source_name: GR_ZT20 HFD_liver

value: GR (Santa Cruz, sc-1004X)


title: GR_ZT20 HFD REP2


title: RNA-Seq_ZT00 HFD KO REP 2

description:
ZT00 HFD KO REP 2
sample code: ZT00-HFD-KO-2
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: RNA-Seq_ZT00 HFD KO REP 1

description:
ZT00 HFD KO REP 1
sample code: ZT00-HFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt


title: GR_ZT16 HFD REP2

source_name: GR_ZT16 HFD_liver


title: PPARA_ZT12 control REP2

source_name: PPARA_ZT12 control_liver


title: B6TS_H3K27ac_Rep2

data_processing:
Single end sequencing (51bp or 101bp) was performed on the HiSeq2500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
For ChIP-seq data for TEAD4 and KLF5, single-end reads (51 bp) were mapped to the mm9 reference genome using the COBWeB Algorithm implemented in Avadis NGS (Agilent). Reads with average base quality below 30, PCR duplicate reads, non-primary multiply mapped reads were removed. The resultant mapped reads (.bam file) were subjected to the MACS peak detection algorithm implemented in Strand NGS (Agilent) to detect ChIP-seq peaks with the mapped reads from the matching IgG library as a control.
For ChIP-seq data for histone modifications, single-end reads (51 or 101 bp) from each sample were first trimmed by removing adapters and low quality bases at ends using Trimmomatic 0.22, and  were aligned to the mouse reference genome (mm9) using the Burrows-Wheeler Aligner 0.6.2. Uniquely mapped reads were selected by a custom script, converted from sam to bam using SAMtools 0.1.18. Reads with mapping quality < 20 were removed using SAMtools 0.1.18. The uniquely mapped reads (.bam files) were subjected the MACS peak detection algorithm (version 1.4.2 to identify ChIP-seq peaks with the matched input DNA reads as a control.
Genome_build: mm9
Supplementary_files_format_and_content: MACS peak calling output

source_name: TS cell line

growth_protocol: Mouse ES cells were cultured on feeder cells in knockout DMEM (Life Technologies) containing recombinant human leukemia inhibitory factor culture supernatant for mouse ES cell culture, GlutaMAX, 2-mercaptoethanol, non-essential amino acids, and 15% KSR (all from Life Technologies). Mouse TS cells were cultured on feeder cells in the presence FGF-4 (PeproTech, London, UK) and heparin (Sigma Chemical Company) to maintain their undifferentiated state.

extract_protocol:
Trypsinised feeder-free ES and TS cells (1×10^6) were collected and fixed with 1% formaldehyde at room temperature. Crosslinking reaction was quenched with 125 mM glycine for 5 min. The cells were resuspended in SDS lysis buffer (ChIP Reagent, Nippon Gene Co., Ltd.), and the lysate was sonicated to fragment chromatin using a Covaris S220 (Covaris, Woburn, MA, USA). The sonicated lysate was subjected to immunoprecipitation with a monoclonal antibody against TEDA4, KLF5, H3K4me1, or H3K27ac.
The immunoprecipitated and reverse-crosslinked DNA was purified using AMPure XP beads (Beckman Coulter, Inc., Pasadena, CA, USA) according to the manufacturer’s instructions. ChIP or input DNA (0.1 ~ 1 ng) was subjected to end repair, dA-tailing, and adaptor-ligation, and amplified by 6-13 cycles of PCR.

tag: cell type

value: TS cell line

value: anti-H3K27ac antibody (CMA309 provided by Dr. H. Kimura)


title: B6TS_input_Rep2


title: GR_ZT12 control REP2

source_name: GR_ZT12 control_liver


title: GR_ZT12 HFD REP1

source_name: GR_ZT12 HFD_liver


title: GR_ZT16 HFD REP1


title: B6TS_TEAD4_Rep2

value: anti-TEAD4 antibody (Abcam:ab58310)


title: B6TS_H3K4me1_Rep2

value: anti-H3K4me1 antibody (CMA302 provided by Dr. H. Kimura)


title: RNA-Seq_ZT00 LFD KO REP 1

description:
ZT00 LFD KO REP 1
sample code: ZT00-LFD-KO-1
table_featureCounts_KO-WT_AlbCre.txt
table_filtered_KO-WT_AlbCre_rlog.txt
table_filtered_KO-WT_AlbCre_VST.txt

source_name: Liver


title: B6TS_4C_Tead4-promoter_Rep2

data_processing:
Library strategy: 4C-seq
Paired-end sequencing (101bp x2) was performed on the HiSeq2500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Sequencing reads for each sample were demultiplexed and subjected to the trimming of the sequences within the bait region, a MspI-HindIII fragment corresponding to chr6:128,251,076-  128,251,379 (mm9). The exact nucleotide coordinates of the trimmed sequences are chr6:128,251,076-128,251,117 and chr6:128,251,328-128,251,379. The former region ranges from the base immediately after the MspI site to the 5' end of the target-specific sequence in  the Tead4_4C-Msp1R(-) primer, and the latter region ranges from the  5' end of the target-specific sequence in the  Tead4_4C-Hind3F(+) primer to the fifth base of the HindIII site.
Trimmed reads were mapped with the Burrows-Wheeler Aligner (BWA) and assgined to a specific HindIII fragment in the HindIII fragment database prepared from  the mouse reference genome sequence(mm9)
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read numbers counted for each of HindIII fragments are listed in bed format.

extract_protocol:
Cells (3x10^6) were cross-linked with 2% formaldehyde, lysed in the lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40), digested with HindIII, treated with Klenow fragment and dNTPs to fill in the HindIII digested overhangs, and ligated under a dilute condition. After reversing crosslinks, DNA was purified as a 3C library. The 3C library was digested wth MspI, ligated,  and amplified by PCR tp generate a 4C library.
4C library was amplified by PCR using  two sets of PCR primers. The fist set of primers, Tead4_4C-Hind3F(+)   "5'-TCTTTCCCTACACGACGCTCTTCCGATCTGCCTTCACTATTCCCCAAAA-3'" and Tead4_4C-Msp1R(-)   "5'-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAACCACTGCTGGGACCTAA-3'", contain a sequence specific to the mouse Tead4 promoter region at the 3' end and a partial sequence of illumina TruSeq adaptor at the 5' end.    The second primers are   "5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'" (TruSeq Universal Adapter sequence) and  "CAAGCAGAAGACGGCATACGAGAT[6bp_index]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'" (TruSeq Index Adapter sequence).

tag: restriction enzymes

value: HindIII, MspI


title: B6ES_4C_Tead4-promoter_Rep2

source_name: ES cell line

value: ES cell line


title: H3K27ac_ZT12 HFD REP1

data_processing:
Mapping against mm9 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1
IP efficiency normalization
Create normalized peak universe
Genome_build: mm9
Supplementary_files_format_and_content: broadpeak and gappedPeak files were produced using macs2 representing H3K27ac peaks

source_name: H3K27ac_ZT12 HFD

tag: time


title: PG.P18

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Department of Oral Biology

institute: State University of New York at Buffalo

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 2.1.0 mkoutput with Bcl2Fastq 2.19.1
Cellranger 2.1.0 Count against mm10 genome to produce count matrix
Seurat 2.3.0 used for marker gene analysis and visualization
Genome_build: mm10
Supplementary_files_format_and_content: CSV File containing UMI corrected read counts

source_name: Parotid Gland

extract_protocol:
Chromimum Single Cell 3' v2 (10x Genomics)
TruSeq Stranded RNA (illumina)

tag: tissue

value: Parotid Gland

tag: developmental stage

value: post natal day 18


title: D8_E3_S7

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description: cytotrophoblast (CTB)

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the human genome (hg38) by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference.
Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. DAVID (https://david.ncifcrf.gov) and IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively. Cells with more than 8,000 detected genes and for which genes with FPKM > 0.3 were kept in downstream analysis for lineage specification. Lineage specification was performed by Spearman correlation. Principle Component Analysis (PCA) and cluster analysis were performed using R
Genome_build: hg38
Supplementary_files_format_and_content: FASTQ

source_name: trophoblast cells

extract_protocol: The RNA-seq libraries were generated from individually cells using Smart-seq2 with minor modification. Briefly, individually cells were lysed and mRNA was captured and amplified by using Smart-seq2 v4 kit (Clontech). After pre-amplification and AMPure XP beads purification, amplified RNAs were quality checked using Agilent High Sensitivity D5000 kit (Agilent Technologies). High quality of amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The quality and quantity of sequencing libraries were determined using Qubit 3.0 assay (Life Technologies) and Agilent High Sensitivity kit at Tapestation 4200 system (Agilent), respectively. Pooled indexed libraries were then sequenced on Illumina HiSeq X platform with 125 bp pair-end reads.

value: trophoblast cells

value: Day 8 (Extended culture)


title: D8_E4_S1

description: cytotrophoblast (CTB)


title: D8_E3_S5

description: cytotrophoblast (CTB)


title: D8_E4_S2

description: cytotrophoblast (CTB)


title: D8_E3_S6

description: cytotrophoblast (CTB)


title: D8_E3_S8

description: cytotrophoblast (CTB)


title: H3K27ac_ZT12 control REP2

source_name: H3K27ac_ZT12 control

tag: treatment

tag: chip antibody


title: H3K27ac_ZT12 HFD REP2

tag: strain


title: D8_E3_S4

description: cytotrophoblast (CTB)


title: H3K27ac_ZT0 HFD REP2

source_name: H3K27ac_ZT0 HFD


title: H3K27ac_ZT12 control REP1


title: D8_E3_S2

description: cytotrophoblast (CTB)


title: D8_E3_S1

description: cytotrophoblast (CTB)


title: H3K27ac_ZT0 control REP2

source_name: H3K27ac_ZT0 control


title: B6TS_input_b_Rep2


title: D8_E3_S3

description: cytotrophoblast (CTB)


title: D8_E3_L4

description: multinucleated primitive syncytium (STB)


title: H3K27ac_ZT0 HFD REP1


title: D8_E4_S3

description: cytotrophoblast (CTB)


title: D8_E3_L2


title: D8_E3_L3


title: D8_E3_L1


title: H3K27ac-ControlClone2

city: Cambridge

first: Charles

last: Fulco

address: 415 Main Street

institute: Broad Institute

data_processing:
ChIP-seq reads were initially aligned to both the 129S1 and Castaneus genomes and reads were merged using pysuspenders as descibed in Engreitz et al. Nature (2016)
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)

source_name: F1 2-1 129/Castaneus Female mESCs

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).

extract_protocol: ChIP-Seq: We performed ChIP-Seq as described in Busby M et al. Epigenomics & Chromatin (2016)

treatment_protocol: Control clonal cell line isolated during genome engineering experiments (see Engreitz et al. Nature 2016)

tag: cell line

value: embryonic stem cell

tag: protocol

value: H3K27ac ChIP-seq


title: H3K27ac_ZT0 control REP1

value: Liver


title: D8_E2_S8

description: cytotrophoblast (CTB)


title: H3K27ac-ControlClone1

value: Control clonal cell line isolated during genome engineering experiments (see Engreitz et al. Nature 2016)


title: D8_E2_S5

description: cytotrophoblast (CTB)


title: D8_E2_S6

description: cytotrophoblast (CTB)


title: D8_E2_S4

description: cytotrophoblast (CTB)


title: D8_E2_S2

description: cytotrophoblast (CTB)


title: D8_E2_S3

description: cytotrophoblast (CTB)


title: KO-6

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

data_processing:
Illumina HiSeq 2500 sequencing, 50bp reads.
Adapter removal with cutadapt v1.16
Alignment to Mus musculus genome with hisat v2.1.0
Assignment of reads to gene features with Subread featureCounts v1.6.1
Signal detection via differential expression analysis between triplicate groups with DESeq2 1.18.1
Genome_build: mm10
Supplementary_files_format_and_content: Number of reads assigned to gene features, as computed by Subread featureCounts v1.6.1

source_name: testis

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P2 or P7 aged control and knockout mice.

extract_protocol:
Testes were isolated, total RNA was isolated using RNeasy Mini Kit and mRNA was purified by Dynabeads mRNA Purification Kit.
First strand cDNA was synthesized with SuperScript III Reverse Transcriptase. For second strand cDNA synthesis, the 100 μl reaction system included: 20 μl of first strand cDNA synthesis mix, 10 μl of 10x second strand buffer (500 mM Tris-HCl, pH 7.5; 50 mM MgCl2; 10 mM DTT), 3 μl of dNTP mix (10 mM), 1 μl of RNase H (2U/μl), 5 μl of DNA Pol I (10U/μl) and 61 μl water. The mixtures were incubated for 2 h at 16°C. The libraries were constructed with Nextera DNA Sample Preparation Kit (Illumina) per the manufacturer’s protocol. Generally, double-strand cDNA was fragmented, subjected to adapter ligation and amplified.

value: B6D2F1 inbred

value: testis

tag: age

value: post natal day 7


title: KO-5


title: Control-5


title: D8_E1_S8

description: cytotrophoblast (CTB)


title: D8_E2_S1

description: cytotrophoblast (CTB)


title: D8_E1_S7

description: cytotrophoblast (CTB)


title: Control-4


title: KO-3

value: post natal day 2


title: D8_E1_S5

description: cytotrophoblast (CTB)


title: D8_E1_S6

description: cytotrophoblast (CTB)


title: KO-1


title: D8_E1_S4

description: cytotrophoblast (CTB)


title: KO-2