title: PASE8_Lib4_scMAT-seq_20hr-PASE

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

description: scMAT-seq. 20 hr post BMP4 induction in 3D gastruloid model

data_processing:
Library strategy: scMAT-seq
Illumina bcl2fastq2 v 2.20 software used for basecalling
A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify genomic based epigenetic marks.
For genomic based reads, read 1 sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11
For genomic based reads, a custom Perl script was used to demultiplex cell barcodes and identify 5mCpG sites from the sam files. Processed text files were then created using another custom Perl script that by parsed 5mCpG sites based on their genomic context (GCH vs WCG).  This code is available on request.
For RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq hg19 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: DNA accessibility files (noted in the naming of the file) list detected methylated GCH sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Endogenous 5mC files (noted in the naming of the file) list detected methylated WCG sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Transcript count files (noted in the naming of the file) is a matrix with the columns indicating cell number, and each row indicating the number of transcripts detected for a given gene.

source_name: AICS-0024 (20 hr 3D gastruloid induction)

growth_protocol: All mammalian cells were culture at 37 C with 5% CO2. HEK293T cells were cultured on tissue culture treated plastic in high glucose DMEM (Gibco cat. No. 10569044) containing L-Glutamine and sodium pyruvate, supplemented with 10% FBS and 1x Penicillin-Streptomycin. H9 cells were grown feeder-free on Matrigel coated plates in mTeSR1 medium. Cells were routinely passaged 1:6 once they reached 75% confluency using 0.25% trypsin-EDTA or Versene solution for HEK293T or H9 cells respectfully. For FACS sorting, a single-cell suspension was created using 0.25% trypsin-EDTA. The trypsin was then neutralized using a serum containing medium. Afterwards, the cells were washed with 1x PBS before being passed through a cell strainer and sorted for single cells into 384 well plates. hiPSCs (Allen Cell line AICS-0024) were grown feeder-free on Matrigel coated plates in mTeSR1 medium. Cells were routinely passaged as clumps 1:6 once they reached 75% confluency using non-enzymatic agitation following manufacturer’s instructions (ReleSR, STEMCELL Tech.).

extract_protocol:
For single cell experiments, cells were sorted via FACs directly into lysis buffer.  For bulk experiments, genomic DNA was extracted using a Dneasy Blood & Tissue Kit from Qiagen.
scMAT-seq  4 µL of Vapor-Lock (QIAGEN) was manually dispensed into each well of a 384-well plate using a 12-channel pipet. All additional dispenses into the 384-well plate were added using the Nanodrop II liquid handling robot (BioNex Solutions). To each well 100 nL of uniquely barcoded 7.5 ng/uL CEL-seq primer containing 4 UMIs was added. The CEL-seq type primers used here were described previously in detail (2). Then 100 nL of lysis buffer (0.175% IGEPAL CA-630, 1.75 mM dNTPs, 1:1,250,000 ERCC RNA spike-in mix (Ambion, 4456740), and 0.19 U RNase inhibitor (Clontech, 2313A)) was added. A single cell was isolated per reaction well using FACS. Unless cryopreserved, after sorting, plates were heated to 65 C for 3 min and returned to ice to lyse the cells. Next, 150 nL of reverse transcription GC tagging mix (0.7 U RNAseOUT (Invitrogen, 10777-019), 1.17x first strand buffer, 11.67 mM DTT, 3.5 U Superscript II (Invitrogen, 18064-071), 0.19 mM SAM, 1.17x GC reaction buffer, 0.1 U M.CviPI (NEB, M0227S)) was added and the plate was heated to 37°C for 1 hr, 4°C for 5 min, 65°C for 10 min, and 70°C for 10 min. Next, 1.75 µL of second strand synthesis mix (1.74x second strand buffer (Invitrogen, 10812-014), 0.35 mM dNTP, 0.14 U E.coli DNA Ligase (Invitrogen, 18052-019), 0.56 U E.coli DNA Polymerase I (Invitrogen, 18010-025), 0.03 U RNase H (Invitrogen, 18021-071)) was added and the plate was cooled to 16°C for 2hr. Afterwards, protease mix (6 µg Protease (Qiagen, 19155), 6.25x buffer 4) was added, and the plate was heated to 50°C for 15 hrs, 70°C for 20 mins, and 80°C for 5 mins. Next, 5hmCs were blocked by adding the following mix (1 U T4-BGT (NEB, M0357L), 6x UDP-glucose, 1x buffer 4) to each well and the plate was heated to 37°C for 16 hrs. Afterwards, protease mix (2 µg Protease, 1x buffer 4) was added, and the plate was heated to 50°C for 3 hrs, 70°C for 20 mins, and 80°C for 5 mins. Next MspJI digestion mix (1x buffer 4, 8x enzyme activator solution, 0.1 U MspJI (NEB, R0661L)) was added and the plate was heated to 37°C for 4.5 hrs, and 65°C for 25 mins. Unless otherwise stated, to each well 320 uL of uniquely barcoded 125 nM MspJI double stranded adapter was added. The MspJI adapters have been described in detail previously (3). Next 680 nL of ligation mix (1.47x T4 ligase reaction buffer, 5.88 mM ATP (NEB, P0756L), 140 U T4 DNA ligase (NEB, M0202M)) was then added, and the plate was cooled to 16°C for 16 hrs. After ligation, reaction wells receiving different barcodes were pooled using a multichannel pipette, and the oil phase was discarded. This was then incubated for 30 mins with 1x AMPure XP beads (Beckman Coulter, A63881), washing twice with 80% ethanol and resuspending in 30 µL of nuclease free water. Afterwards, this was evaporated down to 6.4 µL. Following this step, library preparation was performed as previously described in the scAba-seq and scMspJI-seq protocols (3, 4). Libraries were sequenced on an Illumina NextSeq 500 or an Illumina Hiseq 4000, sequencing a minimum of 75-bp on read 1 to detect 5mC. To detect RNA transcripts, a minimum sequencing length of 25-bp on read 1 and 50-bp on read 2 was utilized. Additionally, unless otherwise stated, transcript detection as only performed on RNA enriched samples and 5mC detection was only performed on unenriched samples.

treatment_protocol: For mesodermal differentiation, the media was replaced with mTeSR1 supplemented with 5 uM of CHIR99021 (STEMCELL Tech.) for 24 hours. For gastrulating 3D stem-cell cultures, on Day 1: hiPSCs (Allen Cell line  AICS-0024) are released from well-plate surfaces using non-enzymatic agitation following manufacturer’s instructions (ReleSR, STEMCELL Tech.). Cells are resuspended as a single-cell suspension at densities of 750K-1M cells/mL in mTeSR1 containing 10μM ROCK inhibitor Y27632 (Abcam). 200μL of cell suspension is then pipetted onto prepatterned dishes (circular features 250 uM in diameter) and allowed to settle for 15 minutes before adding 1mL of mTeSR1 and allowing cells to settle for 10 additional minutes. Excess media is aspirated, leaving enough liquid to cover patterns and is replaced with fresh 2mL of mTeSR until the following day. On day 2: mTESR1 media is exchanged with mTESR1 media containing Matrigel (4%, v/v). This triggers lumen formation over 24hrs. On Day 3: micropatterned colonies have formed a lumen. mTESR1 is exchanged with the addition of 5ng/ml Recombinant Human BMP4 (Fisher Scientific 314BP010). Exposure to BMP4 triggers differentiation of cells and is considered 0 hours for experimental purposes. On Day 4 or 5: Samples were collected for single-cell sequencing at either 20, 36, or 48 hrs post BMP4 supplementation. Samples were dissociated into a single cell suspension using TrypLE reagent (Gibco), and gentle pipetting. The TrypLE reagent was then neutralized using a serum containing medium. Afterwards, the cells were washed with 1x PBS before being passed through a cell strainer and sorted for single cells into 384 well plates.

tag: single-cell

tag: cryopreservation

value: Fresh

tag: differentiation

value: 3D gastruloid

tag: molecule

value: genomic DNA & polyA RNA


title: MR-5-LB miRNA miRNA

status: Public on Dec 31 2022

type: SRA

city: Chiba-City

first: Ariki

last: Nagashima

address: Inohana 1-8-1

department: Department of gastroenterology

country: Japan

institute: Graduate School of Medicine, Chiba University.

library_source: transcriptomic

data_processing: The Deseq2 package version 1.34.0 was used for expression analysis.

molecule: total RNA

organism: Homo sapiens

source_name: MR group patient 5

extract_protocol:
After the biopsy, samples were placed in a microtube containing All Protect Tissue Reagent (QIAGEN), stabilized, and stored at -80 °C. Total RNA was extracted using the miRNeasy Micro Kit (Qiagen).
RNA concentration and RNA integrity number (RIN) were measured, and micro RNA (miRNA)/messenger RNA (mRNA) sequences were performed on samples that met the criteria (total RNA >3 μg, RIN >8) for the following analysis. The extracted total RNA was sequenced for miRNA and mRNA using the Novaseq (Illumina) by GENEWIZ Japan (Tokyo, JP).

tag: phenotype

value: MR

tag: patient id

tag: biopsy site

value: LB


title: MR-5-GB miRNA miRNA

value: GB


title: MR-5-LA miRNA

value: LA


title: C-3-GB miRNA miRNA

source_name: Control patient 3

value: Control


title: PASE8_Lib3_scMAT-seq_20hr-PASE

country: USA

library_source: genomic

molecule: genomic DNA


title: C-1-GB miRNA miRNA

source_name: Control patient 1


title: Pinot noir berry sample collected at time point 8.5 (replicate 2) over ripening season 2014 - Crop thinned 75%

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024;
https://www.ncbi.nlm.nih.gov/assembly/GCF_000003745.3
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

organism: Vitis vinifera

source_name: grape berry pericarp_time point 8.5_2014_Crop thinned 75%

growth_protocol: Vineyard Features: Vitis vinifera cultivar Pinot noir (clone FPS 23 grafted on rootstock Freedom and planted in 2001) was grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
165 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

treatment_protocol: Cluster thinning treatments: Moderate thinning (50% crop load reduction) was achieved removing clusters to maintain one cluster per shoot; severe thinning (75% crop load reduction) consisted in mantaining one cluster every other shoot; control (0% crop load reduction) was unthinned vines.

tag: cultivar

value: cv Pinot noir

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 75%

tag: tissue

value: grape berry pericarp


title: PASE8_Lib1_scMAT-seq_20hr-PASE


title: C-1-LB miRNA miRNA


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 8_2014_Crop thinned 50%

value: Crop thinned 50%


title: C-1-GA miRNA

value: GA


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: H1299-sictr

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

country: China

institute: beijing cancer hospital

data_processing:
Total RNA was extracted from cell/tissues using the Trizol (TsingKe) according to the manufacturer’s protocol.
Using the 3'-end polyA structure of messenger RNA and related molecular biology technology, mRNA separation, fragmentation, double-stranded cDNA synthesis, cDNA fragmentation modification, magnetic bead purification and fragmentation sorting were performed on the complete total RNA of the 4 RNA samples of this project. Library amplification and other processing. After testing and quality control, a sequencing library that can be used on the Illumina platform is finally obtained.
Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: The whole samples expression levels were presented as TPM

source_name: lung cancer cell line

extract_protocol:
RNA was extract though TsingKe Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: lung

tag: treatment

value: treated with siCTR for 48 hours


title: MR-4-GB miRNA miRNA

source_name: MR group patient 4


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 7_2014_Crop thinned 75%


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: MGC803_NC_1

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first trimmed to remove reads with adapter contaminants and low-quality bases (N>10%).
Second, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009).
Third, uniquely mapped reads were counted using htseq-count of the HTSeq package (Anders et al., 2014).
Finally, the expression levels FPKM was claculated by Cufflink.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the FPKM values of RefSeq genes.

source_name: Gastric cancer MGC803 cellline

growth_protocol: The AGS cell line was obtained from the Chinese National Infrastructure of Cell Line Resource and maintained in RPMI 1640 medium containing 10% FBS, GlutaMAX™ supplement, and streptomycin/penicillin at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
We performed mRNA isolation using the NEB Poly (A) mRNA Magnetic Isolation Module (NEB) and constructed an RNA library using the KAPA Hyper Prep Kit (KAPA Biosystems). The RNA library was sequenced on an Illumina HiSeq 4000 platform using 150-bp paired-end sequencing.

tag: cell type

value: Gastric cancer


title: MGC803_FABP5_2

description: polyA RNA


title: MR-4-LA miRNA


title: MR-3-GB miRNA miRNA

source_name: MR group patient 3


title: MGC803_FABP5_1

description: polyA RNA


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: MR-5-GA miRNA


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 7_2014_Crop thinned 50%


title: MR-3-LB miRNA miRNA


title: AGS_NC_2

description: polyA RNA

source_name: Gastric cancer AGS cellline

value: AGS


title: MR-3-GA miRNA


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: MR-3-LA miRNA


title: MGC803_NC_2

description: polyA RNA


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: C-1-LA miRNA


title: MR-2-GA miRNA

source_name: MR group patient 2


title: 14_Donor 2_Th0__plus__G9ai

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: 14_Donor_2_Th0__plus__G9ai.FCHG3YCBBXY_L8_R*_IACTTGA

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR 2.6.1c
Gene counts were generated using subread featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with FPKM values for each gene per sample

source_name: G9a inhibitor Treatment Th0

growth_protocol: 24 hour differentiation with cell media containing stimulating cytokines and antibodies.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat#74104)
Illumina TruSeq Stranded mRNA prep (Cat #20020594).

treatment_protocol:
Naive T cells treated with anti-CD3 and CD28 stimulation for 24 hours with drug (UNC0642)
Plates coated with Anti-CD3. Media Contained anti-CD28 with ant without IL2 and TGFb in addiiton or not to vehicle and UNC0642

value: peripheral blood

value: Naive T cells

tag: treatment 1

value: Anti-CD3 treatment

tag: treatment 2

value: Anti-CD28 treatment

tag: treatment 3

value: DMSO


title: MR-2-LB miRNA miRNA

tag: phenotype

value: MR

value: LB


title: AGS_FABP5_2

description: polyA RNA


title: AGS_NC_1

description: polyA RNA


title: MR-2-GB miRNA miRNA

tag: patient id

value: GB


title: MR-2-LA miRNA

tag: biopsy site

value: LA


title: MR-4-GA miRNA


title: MR-1-LB miRNA miRNA

source_name: MR group patient 1


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 6_2014_Crop thinned 75%

tag: cultivar

value: cv Pinot noir

value: Crop thinned 75%


title: MR-4-LB miRNA miRNA


title: MR-1-GB miRNA miRNA


title: All_Stage

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

data_processing:
First, the raw sequence data were demultiplexed by mkfastq software (Cell Ranger v1.3.1). Then, the cellranger count, alignment, filtering, cell barcode and UMI counting functions were run on the FASTQ files. Finally, we used the cellranger aggr function to aggregate the outputs from multiple runs of cellranger count by normalizing those runs to the same sequencing depth. The combined cell count matrix was used for subsequent analysis.
Genome_build: hg19,download from 10X website
Supplementary_files_format_and_content: 10x output count matrix

extract_protocol:
The gonadal biopsies were isolated and washed twice with L15 medium with 10% FBS. Then, the samples were cut into small pieces under controlled cooling conditions and digested with 600 µl of Accutase Cell Detachment Solution (Millipore #SCR005) at 37°C and 850 rpm for 15 min. To ensure that the digestion was as thorough as possible, we pipetted the digestion mixture for at least 20 times. Then 500 µl of L15 medium with 10% PBS was added, and single gonadal cells were obtained by filtering through 50 mm Pre-Separation Filters (Miltenyi Biotec #130-041-407). Then, the cells were pelleted by centrifugation at 300 × g for 8 min and were resuspended in 500 µl of L15 medium with 10% PBS, at which point they were prepared for scRNA-seq. The cells were counted with a hemocytometer.
In this study, scRNA-seq was performed with a 10x Genomics system. Cell capture and library preparation were performed according to the kit instructions (Single Cell 3’ Reagent Kits v2). In brief, cells were first diluted following manufacturer recommendations, and then mixed with a single cell master mix buffer before being loaded into a 10x ChromiumTM controller. Then, the RNA was reverse transcribed at 53°C for 45 min and 85 °C for 5min. After purifying the reverse transcription products, a sequencing library was prepared with 14 cycles of PCR for cDNA amplification. Then, the purified cDNA was used for library amplification, and the resulting library was sequenced on an Illumina HiSeq 4000 instrument.

value: human embryo gonad

tag: developemental stage

value: 6 week - 23 week

tag: experiment type

value: 10X single-cell RNA-Seq


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2014 - Crop thinned 75%

tag: year

tag: time point

tag: time point replicate

value: grape berry pericarp


title: MR-1-LA miRNA


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 6_2014_Crop thinned 50%

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 50%


title: SH2_ReD

city: Guangzhou

first: Ma

last: Jieyi

address: Zhongshan II road

institute: SYSU

description: TRAC-seq

data_processing:
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: txt

source_name: lung

growth_protocol: A549 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to the NEBNext® Small RNA Library Prep Set.

treatment_protocol: A549 cells were  transfected with shRNA for stable knockdown of METTL1. A549 cells transfected with shGFP were used as negative control.

value: lung epithelial

tag: treatment

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage

tag: genotype


title: SH2_DeM

description: TRAC-seq

tag: cell type

value: demethylated by ALKB


title: SH1_DeM

description: TRAC-seq


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2014 - Crop thinned 50%

tag: tissue


title: WT SETMAR 4

city: Indianapolis

first: Millie

last: Georgiadis

state: Indiana

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description:
HEK293T cells transfected with vector containing full length wild type SETMAR
Georgiadis_RNAseq_STAR_featureCoutns_edgeR_20170418_WTvsVoid.xlxs

data_processing:
All sequenced libraries were then mapped to the human genome (UCSC hg19) using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
The reads distribution across the genome was assessed using bamutils (from ngsutils). Uniquely mapped sequencing reads were assigned to hg19 refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10”.
Quality control of sequencing and mapping results were summarized using MultiQC. Genes with read count per million (CPM) < 1 in more than 4 of the samples were removed. The data were normalized using the TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR.
False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel spreadsheet of differential expression analysis from edgeR listing all expressed genes with false discovery rate, p-value, log2fold change, log2(CountsPerMillion) for each replicate, and raw counts for each replicate

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in an incubator at 37°C and 5% CO2.

extract_protocol:
Cells were harvested 48 hours post-transfection and RNA was isolated using the QIAGEN RNeasy Mini Kit. DNaseI digestion was performed immediately following RNA isolation using PureLink DNase according to manufacturer instructions, and samples were purified using the QIAGEN RNeasy Mini Kit.
500 nanograms of RNA per sample were then used to prepare a single-indexed strand-specific cDNA library using the TruSeq Stranded mRNA Library Prep Kit (Illumina). The resulting libraries were assessed for quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer.
200 pM pooled libraries were utilized per flowcell for clustering amplification on cBot using HiSeq 3000/4000 PE Cluster Kit and sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy). Sequencing data were first assessed using FastQC for quality control.

treatment_protocol: Cells were seeded into 6-well plates, 500,000 cells per well, and grown to ≈60% confluency and were then transiently transfected with either empty vector plasmid or plasmid containing wild type SETMAR. DNA (2 µg) was transfected with 2 µl of 2 µg/ml polyethyleneimine per well.

tag: vector

tag: cell line


title: NC_ReD

description: TRAC-seq

value: negative control


title: WT SETMAR 3


title: WT SETMAR 2


title: NC_DeM

description: TRAC-seq


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: AGS_FABP5_1

description: polyA RNA

value: Gastric cancer

value: AGS


title: A549_RNC_NC_2

description: Ribosome nascent-chain complex-bound mRNAs seq

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as TPM (Transcripts Per Kilobase of exon model per Million mapped reads) using edegR.
Genome_build: hg38
Supplementary_files_format_and_content: txt

molecule: polyA RNA

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit

value: Negative control


title: A549_RNC_shM1_1

value: Ribosome nascent-chain complex-bound mRNAs


title: A549_RNC_shM1_2


title: WT SETMAR 1


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: MR-1-GA miRNA

tag: phenotype

value: MR

tag: patient id

value: GA


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 5_2014_Crop thinned 75%

tag: cultivar

value: cv Pinot noir


title: A549_RNC_NC_1


title: A549_input_shM1_2


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2014 - Crop thinned 75%

value: Crop thinned 75%


title: Void 4

description:
HEK293T cells transfected with empty vector backbone
Georgiadis_RNAseq_STAR_featureCoutns_edgeR_20170418_WTvsVoid.xlxs


title: A549_input_shM1_1


title: A549_input_NC_2


title: A549_input_NC_1


title: Void 1


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 5_2014_Crop thinned 50%


title: 30kan_t-1440_rep2

city: Boulder

first: Christian

middle: Thomas

last: Meyer

state: CO

address: 3415 Colorado Ave, JSC Biotech; UCB 596

department: BioFrontiers

institute: University of Colorado Boulder

data_processing:
Rockhopper was used to get RNA counts from FASTQ files.  See Tjaden B. Methods. 176:62-70, 2020.
Supplementary_files_format_and_content: xls spread sheet with raw transcript counts.

organism: Escherichia coli BW25113

source_name: Bacterial cells

growth_protocol: From overnight growth in LB, outgrowth (1:100 dilution) In 37C shaker (180RPM) in 5mL minimal media for 2 hours.

extract_protocol:
Modified RNASnap (see Methods of associated paper)
Illumina single stranded total RNA prep with ribozero depletion of rRNA
Sequencing on Illumina NextSeq500 with a total >10M reads per sample

treatment_protocol: Kanamycin added (30ug/mL) for designated time.

value: Kanamycin (30ug/mL)


title: 30kan_t-1440_rep3


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: Void 2


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: 30kan_t-1440_rep1


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: 30kan_t-0360_rep3


title: Void 3


title: 30kan_t-0360_rep1


title: exp2, ChIP

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

description: Pulldown sample for experiment 2

data_processing:
ChIP-seq SE50 reads were mapped to the C. elegans genome (ce10) using the R function qAlign (splicedAlignment=TRUE, Rbowtie) from the QuasR package (Au et al., 2010; Gaidatzis et al., 2015)
Peaks were identified using the callpeak command from MACS2 (version 2.1.3.3) (Zhang, 2008) on pulldown sample versus corresponding control sample, with thresholding option "-m 2 50", effective genome size option "-g ce", and otherwise default parameters, for each sample pair independently.
Motifs were identified using HOMER (version 4.11) (Heinz, 2010), using segment size option "-size given", background segment count option "-N 180000", for motifs lengths "-len 8,10,12", autonormalisation "-nlen 3", and parallelisation options.
Putative binding sites were predicted on the non-mitochondrial mappable segments of the ce10 genome (established using function getMappableRegions() from FMI-developped R package swissknife), using the wrapper function findMotifHits() from R package monaLisa (Machlab, 2022), using a minimum score of 6, method "matchPWM", and parallelisation options.
Assembly: ce10
Supplementary files format and content: BED file of MACS2 peaks, filtering out peaks overlapping overmapped genomic regions, and filtering out the 10% least enriched peaks.
Supplementary files format and content: Gzipped BED file of predicted binding sites with scores above 6.

organism: Caenorhabditis elegans

source_name: Bulk whole organism extract

growth_protocol: HW2603 worms (grh-1(syb616(grh-1::GFP::3xFLAG)) I) were synchronised by hatching in the absence of food followed by synchronised plating on NA22-containing and peptone rich XL plates at 25°C.

extract_protocol:
5 million animals were collected in PBS + PI + PMSF 1mM at 15 hours and 19 hours after plating (ie 2 timepoints within L2) and popcorn was created from resuspended larvae mix. Popcorn from both time points were pooled and lysate was prepared by grinding the popcorn, crosslinking with 1.1% formaldehyde and sonication with a Diagnode Biorupter Pico. For the chromatin immuno-precipitation, 50 uL of protein G Dynabeads (10003D, ThermoFisher Scientific) were incubated with 5 ug of anti-GFP antibody (ab290, Abcam) for 4 hours rotating at 4°C. 100 ug of chromatin was added, and incubated over night at 4°C rotating. Beads were washed and the elute was treated with proteinase K and RNaseA, and DNA was purified using Zymo ChIP Concentrator Kit.
Libraries were prepared using the ChIP-seq NEB Ultra protocol, and sequenced using the Illumina 50-Cycle Single-End reads protocol on the HiSeq2500.

value: Bulk whole organism extract

tag: Sex

value: pooled male and female

tag: developmental stage

tag: chip target


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 4_2014_Crop thinned 75%

tag: year

tag: time point

value: grape berry pericarp


title: exp2, resequenced exp1 500mM ChIP

description: Pulldown sample for experiment 1 using 500mM of salt, with new extraction, library preparation, and sequencing.


title: SH1_ReD

description: TRAC-seq


title: 30kan_t-0360_rep2


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2014 - Crop thinned 75%

tag: time point replicate

tag: day after veraison


title: exp2, input

description: Control "input" sample for experiment 2


title: 30kan_t-0240_rep3


title: exp2, resequenced exp1 input

description: Control "input" sample from experiment 1, with new extraction, library preparation, and sequencing.


title: exp1, 1M ChIP

description: Pulldown sample using 1M salt

data_processing:
ChIP-seq SE50 reads were mapped to the C. elegans genome (ce10) using the R function qAlign (splicedAlignment=TRUE, Rbowtie) from the QuasR package (Au et al., 2010; Gaidatzis et al., 2015)
Peaks were identified using the callpeak command from MACS2 (version 2.1.3.3) (Zhang, 2008) on pulldown sample versus corresponding control sample, with thresholding option "-m 2 50", effective genome size option "-g ce", and otherwise default parameters, for each salt concentration independently.
Motifs were identified using HOMER (version 4.11) (Heinz, 2010), using segment size option "-size given", background segment count option "-N 180000", for motifs lengths "-len 8,10,12", autonormalisation "-nlen 3", and parallelisation options.
Putative binding sites were predicted on the non-mitochondrial mappable segments of the ce10 genome (established using function getMappableRegions() from FMI-developped R package swissknife), using the wrapper function findMotifHits() from R package monaLisa (Machlab, 2022), using a minimum score of 6, method "matchPWM", and parallelisation options.
Assembly: ce10
Supplementary files format and content: BED file of MACS2 peaks, filtering out peaks overlapping overmapped genomic regions, and filtering out the 10% least enriched peaks.
Supplementary files format and content: Gzipped BED file of predicted binding sites with scores above 6.


title: 30kan_t-0240_rep1


title: 30kan_t-0240_rep2


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2014 - Crop thinned 75%

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 4_2014_Crop thinned 50%

value: Crop thinned 50%


title: 30kan_t-0090_rep2

tag: treatment


title: 30kan_t-0090_rep1


title: 30kan_t-0090_rep3


title: exp1, 500mM ChIP

description: Pulldown sample using 500mM salt

tag: genotype


title: 30kan_t-0030_rep3


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2014 - Crop thinned 50%

tag: tissue


title: 30kan_t-0030_rep1


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: 30kan_t-0030_rep2


title: exp1, 350mM ChIP

description: Pulldown sample using 350mM salt


title: exp1, input

description: Control "input" sample

value: none (input)


title: 30kan_t-0000_rep3


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 3_2014_Crop thinned 75%


title: prp-19+atp-2 rep3

first: Xia

last: Peixue

address: No.5 Yiheyuan Road Haidian District

data_processing:
Raw sequencing data quality evaluation was performed using  FastQC
For differencial alternative splicing analysis,the sequencing reads were mapped using STAR (Version: 2.7.5c). Genome version ce11 and gene annotation from Ensembl Release 87 (WBcel235.87) was used.Differential AS (alternative splicing) events were analyzed with rMATS tool (Version: 3.2.5. Parameters: -t paired -len 101 -a 8 -c 0.05 -analysis U)
For For differential expression analysis, raw sequencing data was aligned to the ce11 reference genome using HISAT2 (version 2.1.0). Gene expression levels were quantified by feature Count (version 1.6.3) with the genomic annotation from UCSC。Downstream analysis was performed using R (version 4.0.5). Differential gene expression analysis was performed by DESeq2, genes with log2(fold change) > 1 and adjusted p-value < 0.05 were considered as differentially expressed genes.
Genome_build: WBcel235
Supplementary_files_format_and_content: Raw gene counts for each Sample.

source_name: whole worm

growth_protocol: Worms were grown on RNAi plates seeded with control RNAi or prp-19 RNAi

extract_protocol:
Day1 adulthood worms were collected and resuspended with 1mL TRI-zol reagent.Total RNA was isolated by chloroform extraction, followed by isopropanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols. PolyA RNA was selected.

treatment_protocol: Worms raised on control RNAi or prp-19 RNAi were untreated or treated with atp-2 RNAi

tag: strain

value: day1 adulthood


title: 30kan_t-0000_rep2


title: 30kan_t-0000_rep1


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 3_2014_Crop thinned 50%


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: prp-19+atp-2 rep2


title: Tet2_KO MPP3, replicate 2, scRNAseq

city: Los Angeles

first: Jiya

last: Eerdeng

address: 1425 San Pablo St

department: DSR

institute: University of Southern California

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and were made using the Cell Ranger software v6
Assembly: mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
FACS sorted HSPCs  from mice. Donor cells were sorted based on the CD45.2 marker and barcoded cells were sorted based on GFP.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, Bone marrow cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with beads, amplified by PCR and the apropiated sized fragments were selected with SPRI select reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Mice were treated with tamoxifien one-month post transplantation to indudce Cre-mediated exision of Tet2.

value: Bone Marrow

tag: cell type


title: prp-19+atp-2 rep1


title: Tet2_KO HSC, replicate 1, scRNAseq

value: HSC


title: Tet2_KO MPP3, replicate 1, scRNAseq


title: Ctrl MPP3, replicate 2, scRNAseq

value: Control


title: Tet2_KO HSC, replicate 2, scRNAseq


title: Ctrl MPP3, replicate 1, scRNAseq


title: Ctrl HSC, replicate 2, scRNAseq


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: Ctrl HSC, replicate 1, scRNAseq


title: prp-19 rep3


title: prp-19 rep2


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 2_2014_Crop thinned 75%


title: L4440+atp-2 rep3


title: prp-19 rep1


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: High fat diet group

city: Shenzhen

first: Rongsong

last: Ling

state: Guangdong

address: 3688 Nanhai Avenue, Nanshan District

institute: Shenzhen University

description: 10x Genomics

data_processing:
The Cell Ranger Single-cell Software Suite was used to demultiplexed the experimental data, Illumina’s bcl2fastq was wrapped around by mkfastq command.
The calculations based on UMI-tools was used to control quality of the RNA sequencing.Sample libraries balancing were carried out for the number of estimated reads per cell and then ran on the illumine-HiSeq300.
According to the 10x Genomics documentation, (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cellranger) demultiplexing, alignment filtering, barcode counting, UMI counting, and gene expression estimation were performed by Cell Ranger software on each sample. The LogNormalize algorithm worked in normalization. To compare experimental groups with normalized sequencing-depth and expression data, the IntegrateData (Seurat) was used to aggregate the gene expression estimates from each sample. Seurat (version 3.2.0) and R (version 4.0.0) package were used in downstream analysis. Cells with less than 200 genes detected and more than 30% mitochondrial gene count percentage were filtered out as low quality or dying cells. Dimension reduction was then performed on normalized and logarithmized data by three stages of analysis, including the selection of variable genes, principle component analysis (nPCs=50), and t-Distributed Stochastic Neighbor Embedding (t-SNE) with RunTSNE:dims=1-30. Then the cell clustering was performed using the original Louvain algorithm (resolution=0.9). We used the FindAllMarkers function to perform Wilcoxon rank-sum test based on the normalized data to identify gene markers in each cluster.
The Seurat package-FindAllMarkers was used to analyze the DEGs (differentially expressed genes) between the two groups. The cowplot (version 1.1.1) and ggplot2 (version 3.3.5) were used for graphing. Following sorting of endothelial cells can be performed with canonical markers Pecam1 and Cdh5 based on the estimated ration of EC in the total sample with resolution 0.4.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: aorta

extract_protocol:
This study used the Lung Dissociated Kit (Miltenyi Biotec) to make up enzyme mix used in dissociation and Dulbecco's modified Eagle's medium to maintain the activity of dissociated cells. Put aorta inside the tube with enzyme mix as soon as possible after dissection. Cut the aortic arch into pieces, the more shredded the pieces are, the better the dissociation effect. Digest the arch with enzyme remix at 37℃ for 40 minutes, filter mixture through the 70um strainer and wash the strainer three times with DMEM. Centrifuge the cell suspension for 5minutes at 500×g, 25℃. Pour off the supernatants and resuspend cells with DMEM again to proceed the final suspension.
Single cell suspension of the two aortas from each group was pooled together as one sample. Single cell RNA sequencing, library construction and quality control were executed using the illumina-HiSeq3000 platform by Genergy Bio-technology (Shanghai) Co., Ltd. Dying cells with mitochondrial RNA above 30% and cells lacking information with UMI<200 were eliminated during the quality control and 8155 dissociated cells, with 5416 cells from control group and 2739 from HFD one, were filtered out then. The median reads per cell were 3955 for control group and 3421 for HFD group, transcripts detected per cell in the two groups were 1364 and 1069 respectively.

value: aortic cells

value: aorta

tag: age

value: 16 weeks

value: High fat diet group


title: Normal diet group

description: 10x Genomics

value: Normal diet group


title: L4440+atp-2 rep2


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2014 - Crop thinned 75%

value: cv Pinot noir


title: L4440+atp-2 rep1


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 2_2014_Crop thinned 50%


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: L4440 rep2


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: C1

type: RNA

city: Thiruvananthapuram

first: Malini

last: Laloraya

state: Kerala

address: Thycaud PO, Poojappura

department: Department of Molecular Reproduction,

country: India

institute: Rajiv Gandhi Centre for Biotechnology,

description:
C1
MIN6 pancreatic beta cell line, control siRNA treated, replicate 1
Control siRNA treated MIN6 cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was quantile normalized and baseline transformation to median of all samples was done using GeneSpring Gx 13.0

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the TargetAmp™-Nano Labeling Kit for Illumina arrays

growth_protocol: MIN6 cells were maintained in DMEM containing 15% FBS, 2mM L-Glutamine, 0.1mM β-mercaptoethanol, 100U/mL penicillin and 100µg/mL streptomycin

extract_protocol: Total RNA was extracted with  Qiagen miRNeasy mini kit according to the prescribed protocol.

treatment_protocol: MIN6 cells were treated with control siRNA (C1, C2) and Stat5b siRNA followed by 30 minute stimulation with prolactin.

tag: cell line

value: MIN6 pancreatic beta cell line

tag: genotype/variation


title: L4440 rep1


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2014 - Crop thinned 75%

source_name: grape berry pericarp_time point 1_2014_Crop thinned 75%

tag: cultivar

value: Crop thinned 75%


title: 8_LXR-bKO_CTRL_(LXRa)_rep3

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

data_processing:
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Assembly: mm10
Supplementary files format and content: Processed files include bed files.

source_name: Bone marrow

growth_protocol: For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRβ-/- mice were isolated and cultured for 7 days in RPMI supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin). To analyze LXRα-dependent response, cells were cultured in RPMI supplemented with 10% FBS, 1% antibiotics (penicillin and streptomycin) and 100 nM of Lipopolysachaaride (LPS). Genome-wide locations of LXRα and H3K27ac acetylation mark were analized in response to treatment with  LPS.

extract_protocol:
Cells were fixed with DSG (2 mM) for 30 minutes and 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorruptor plus (Diagenode) and LXR-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
to create the sequencing library, DNA was end-repaired and ligated to stem-loop adaptors (DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions). Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

value: Bone marrow

value: Bmdm

value: bone marrow-derived macrophage

value: LXR-bKO

tag: chip antibody

value: A polyclonal antibody raised against LXRα and LXRβ was obtained from their original creators (Pehkonen 2012)

value: Vehicle


title: 33h ChIP

data_processing:
Sequencing reads were aligned to the ce10 C. elegans genome  using the qAlign function (default parameters) from the QuasR package in R
ChIP-seq counts within 1-kb windows, i.e. -500 bp to +500 bp around the annotated TSS (using WS220/ce10 annotations), were scaled by total mapped library size per sample and log2-transformed after adding a pseudocount of 8. Genes with a mean scaled TSS window count of less than 8 across all samples were excluded
Log2-transformed counts were then quantile-normalized using the normalize.quantiles function from the preprocessCore library in R (Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2) ,pp 185-193). Finally, quantile-normalized values were row-centered.
Genome_build: ce10
Supplementary_files_format_and_content: table with gene counts

source_name: C. elegans

growth_protocol: synchronized L1 wild-type worms were grown at 25°C. Worms were collected hourly from 22 hours until 33 hours developmental time

extract_protocol:
worms were incubated in M9 with 2% Formaldehyde for 30 minutes at room temperature with gentle agitation to allow protein-DNA crosslinking. Worms were lysed with beads using the FastPrep-24 5G machine (MP Biomedicals, settings: 8 m/sec, 30 sec on, 90 sec off, 5 cycles). Lysates were sonicated using the Bioruptor Plus Sonication system (Diagenode, settings: 30 sec on, 30 sec off, 20 cycles). 250 μg sonicated chromatin was incubated with 10 μg mouse anti-RNA polymerase II CTD antibody (8WG16, Abcam) at 4°C for 2 hours with gentle agitation and subsequently with 45 μL Dynabeads Protein G (Thermo Fisher Scientific) at 4°C overnight with gentle agitation. Elute was treated with 0.13 ug/uL RNase and 1 ug/uL Proteinase K.
ChIP-seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs)

tag: input/chip

value: anti-RNA polymerase II CTD antibody

value: wild-type


title: 32h ChIP


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2014 - Crop thinned 75%

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024;
https://www.ncbi.nlm.nih.gov/assembly/GCF_000003745.3
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

tag: year

value: grape berry pericarp


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2014 - Crop thinned 75%

tag: time point


title: 7_LXR-bKO_CTRL_(LXRa)_rep2


title: 3_LXR-DKO_CTRL_(LXRa)_rep2

value: LXR-DKO


title: 31h ChIP


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2014 - Crop thinned 50%

source_name: grape berry pericarp_time point 1_2014_Crop thinned 50%

tag: time point replicate

value: Crop thinned 50%


title: L4440 rep3

tag: developmental stage

value: day1 adulthood


title: 2_LXR-DKO_CTRL_(LXRa)_rep1


title: 1_Input_(LXRa)


title: T1

description:
T1
MIN6 pancreatic beta cell line, Stat5b siRNA treated, replicate 1
Stat5b siRNA treated MIN6 cells

value: Stat5b knockdown


title: PCOS Patient 1

data_processing: The data were normalised using quantile normalisation with GeneSpring GX v 10.0.2

label: biotin

source_name: PCOS Patient

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

extract_protocol: No specific treatment was performed as the study group included  blood samples collected from control and PCOS subjects.

treatment_protocol: Total RNA  with small RNAs was extracted with  QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Female

tag: diagnosis

value: Polycystic Ovarian Syndrome (PCOS)

value: Peripheral Blood


title: C2

description:
C2
MIN6 pancreatic beta cell line, control siRNA treated, replicate 2
Control siRNA treated MIN6 cells

value: MIN6 pancreatic beta cell line

value: Control


title: PCOS Patient 2


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2014 - Crop thinned 50%

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
165 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

value: cv Pinot noir

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: PCOS Patient 4

tag: tissue


title: PCOS Patient 3


title: T2

description:
T2
MIN6 pancreatic beta cell line, Stat5b siRNA treated, replicate 2
Stat5b siRNA treated MIN6 cells


title: Healthy Individual 2

source_name: Healthy Individual

value: Healthy


title: Healthy Individual 1


title: Healthy Individual 4


title: Healthy Individual 3


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: 29h ChIP

tag: strain

tag: genotype


title: 30h ChIP


title: 28h ChIP


title: 27h ChIP


title: TJ2_1c_2_model_T_cell_2_tissue_Colon_day_28_NA [TT180]

city: New York city

first: Zhi

last: Chai

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNA-seq reads were aligned against the mm10 reference genome using STAR (version 2.4.0g1)
and gene- and exon-level read summarizations were performed with the featureCounts program in subRead
Ensembl annotations were used for both the alignment and the read summarization.
For the exon-level read summarization, a collapsed version of the annotations file where gene designs are described based on non-overlapping “counting- bins” was used to avoid over- or under-counting of reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Raw Count values for each gene in each sample

source_name: Colon

extract_protocol:
The colons from 15 mice per group at each time point were collected for RNA analysis. 1 cm distal adjacent to rectum was used for histology and the remaining tissue was used for RNA. The remaining colon tissues were frozen in RNAlater at -80C for RNA extraction. Blood was collected by cardiac puncture from mice from every group at termination. Approximately 250ul of whole blood was collected into PAXgene tubes. Whole blood was assessed for RNA.  Colons from all groups were measured for length and weight. RNA was isolated with Qiagen RNeasy kits according to manufacturer’s instructions.
RNA TruSeq Kit by Illumina

treatment_protocol: DSS model. On Day 0, female C57Bl/6 mice were weighed and divided into 2 groups of 90 mice per group such that the average weight of each group is similar. Mice were enrolled onto study at body weight of 16-18 grams. Enrolling mice at a range of 16-18 grams ensures consistent disease across the groups while minimizing losses due to death. Mice in Group 1 received 2.5% DSS in drinking water at times shown below while mice in group 2 received plain drinking water at all times. Food was provided ad libitum.  At various times during the study (Day 5, 12, 17, 23, 27, and 34) 15 mice from each group were chosen randomly and sacrificed after an overnight fast; Adoptive Transfer model. CD45RBhigh CD4+T cells from C57Bl/6J mice were transferred to RAG1-/- mice which lack T and B cells. Induction. On study day 0, spleens for CD45RBhigh CD4+ T cell isolation were obtained from female C57Bl/6J mice using the RAG1-/- mice as recipient mice. After cells had been obtained and sorted, each female RAG1-/- mouse received an IP injection of 5X105 cells/ml (100μl/mouse injection). Control RAG1-/- mice served as a control.

value: wildtype

tag: model

value: Colon

tag: bio region

value: PMC

tag: ctrl disease

value: C

tag: day

tag: hit rest


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 9_2013_Crop thinned 75%

tag: cultivar

tag: year

value: Crop thinned 75%


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2013 - Crop thinned 75%

tag: time point

tag: time point replicate

value: grape berry pericarp


title: TJ2_1e_2_model_T_cell_2_tissue_Colon_day_42_NA [TT176]

value: DMC


title: 26h ChIP

tag: input/chip

value: anti-RNA polymerase II CTD antibody

value: wild-type


title: TJ2_2d_4_model_T_cell_2_tissue_Colon_day_35_NA [TT177]

value: D


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: TJ2_1a_5_model_T_cell_2_tissue_Colon_day_14_NA [TT174]


title: TJ2_2a_5_model_T_cell_2_tissue_Colon_day_14_NA [TT175]


title: TJ2_2c_3_model_T_cell_2_tissue_Colon_day_28_NA [TT179]


title: TJ2_2e_1_model_T_cell_2_tissue_Colon_day_42_NA [TT173]


title: 25h ChIP


title: Pinot noir berry sample collected at time point 9 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 9_2013_Crop thinned 50%

value: Crop thinned 50%


title: TJ2_2d_3_model_T_cell_2_tissue_Colon_day_35_NA [TT172]


title: TJ2_1a_1_model_T_cell_2_tissue_Colon_day_14_NA [TT171]


title: TJ2_1c_1_model_T_cell_2_tissue_Colon_day_28_NA [TT170]


title: TJ2_2d_2_model_T_cell_2_tissue_Colon_day_35_NA [TT168]


title: 24h ChIP


title: Pinot noir berry sample collected at time point 9 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: TJ2_2e_1_model_T_cell_2_tissue_Colon_day_42_NA [TT169]


title: TJ2_2c_1_model_T_cell_2_tissue_Colon_day_28_NA [TT166]


title: 22h ChIP


title: TJ2_2a_2_model_T_cell_2_tissue_Colon_day_14_NA [TT165]


title: 23h ChIP


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 8_2013_Crop thinned 75%


title: Pinot noir berry sample collected at time point 9 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: 33h input

value: input


title: TJ2_1d_3_model_T_cell_2_tissue_Colon_day_35_NA [TT167]


title: 32h input


title: TJ2_1d_2_model_T_cell_2_tissue_Colon_day_35_NA [TT162]


title: TJ2_1e_5_model_T_cell_2_tissue_Colon_day_42_NA [TT161]


title: TJ2_2c_4_model_T_cell_2_tissue_Colon_day_28_NA [TT163]


title: TJ2_2a_4_model_T_cell_2_tissue_Colon_day_14_NA [TT164]


title: TJ2_2d_3_model_T_cell_2_tissue_Colon_day_35_NA [TT160]


title: 31h input


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 8_2013_Crop thinned 50%


title: 30h input


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: TJ2_1a_3_model_T_cell_2_tissue_Colon_day_14_NA [TT158]


title: TJ2_2d_5_model_T_cell_2_tissue_Colon_day_35_NA [TT156]


title: TJ2_1e_1_model_T_cell_2_tissue_Colon_day_42_NA [TT157]


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: TJ2_2c_5_model_T_cell_2_tissue_Colon_day_28_NA [TT155]


title: TJ2_1e_5_model_T_cell_2_tissue_Colon_day_42_NA [TT154]


title: TJ2_2a_1_model_T_cell_2_tissue_Colon_day_14_NA [TT153]


title: 28h input


title: TJ2_1d_2_model_T_cell_2_tissue_Colon_day_35_NA [TT159]


title: TJ2_2e_4_model_T_cell_2_tissue_Colon_day_42_NA [TT152]


title: TJ2_1e_4_model_T_cell_2_tissue_Colon_day_42_NA [TT178]


title: TJ2_1d_4_model_T_cell_2_tissue_Colon_day_35_NA [TT151]


title: 27h input


title: 26h input


title: TJ2_1c_4_model_T_cell_2_tissue_Colon_day_28_NA [TT149]


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 7_2013_Crop thinned 75%


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: TJ2_2a_4_model_T_cell_2_tissue_Colon_day_14_NA [TT147]


title: 29h input


title: TJ2_1c_3_model_T_cell_2_tissue_Colon_day_28_NA [TT148]


title: 25h input


title: 24h input


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 7_2013_Crop thinned 50%


title: TJ2_1e_3_model_T_cell_2_tissue_Colon_day_42_NA [TT144]


title: 23h input


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: TJ2_2c_3_model_T_cell_2_tissue_Colon_day_28_NA [TT145]


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: 22h input


title: TJ2_1d_1_model_T_cell_2_tissue_Colon_day_35_NA [TT141]


title: TJ2_2c_2_model_T_cell_2_tissue_Colon_day_28_NA [TT143]


title: TJ2_1d_4_model_T_cell_2_tissue_Colon_day_35_NA [TT142]


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 6_2013_Crop thinned 75%


title: TJ2_2c_4_model_T_cell_2_tissue_Colon_day_28_NA [TT150]


title: TJ2_2d_1_model_T_cell_2_tissue_Colon_day_35_NA [TT140]


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: TJ2_1e_3_model_T_cell_2_tissue_Colon_day_42_NA [TT139]


title: TJ2_2e_3_model_T_cell_2_tissue_Colon_day_42_NA [TT138]


title: TJ2_2e_5_model_T_cell_2_tissue_Colon_day_42_NA [TT137]


title: TJ2_2a_3_model_T_cell_2_tissue_Colon_day_14_NA [TT136]


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: 32h

data_processing:
RNA-seq data were mapped to the C. elegans genome (ce10) using the qAlign function (splicedAlignment=TRUE, Rbowtie aligner version 1.16.0) from the QuasR package in R (Au et al., 2010; Gaidatzis et al., 2015; Kim et al., 2015; Langmead et al., 2009)
ChIP-seq counts within 1-kb windows, i.e. -500 bp to +500 bp around the annotated TSS (using WS220/ce10 annotations), were scaled by total mapped library size per sample and log2-transformed after adding a pseudocount of 8. Genes with a mean scaled TSS window count of less than 8 across all samples were excluded
Log2-transformed counts were then quantile-normalized using the normalize.quantiles function from the preprocessCore library in R (Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2) ,pp 185-193). Finally, quantile-normalized values were row-centered.
Exonic and intronic expression was quantified using qCount function from the QuasR package in R. For exonic expression, the exon annotation of the ce10 assembly (version WS220) was used. Genomic positions of introns were determined by gene body position (start of the first exon until end of the last exon) minus position of exons, which were extended with 10 nucleotides to ensure that reads close to the boundaries were not included in intronic counts.
Counts were scaled by total mapped library size for each sample. A pseudocount of 8 was added and counts were log2-transformed. Lowly expressed genes were excluded (maximum log2-transformed exonic expression - (log2(gene width) - mean(log2(gene width))) ≤ 6)
Genome_build: ce10
Supplementary_files_format_and_content: table with gene counts

extract_protocol:
RNA was extracted in Tri Reagent and DNase treated as described previously (Hendriks et al., 2014)
Total RNA-seq libraries were prepared using Total RNA-seq ScriptSeq Library Prep Kit for Illumina (New England Biolabs)


title: 31h


title: TJ2_2d_5_model_T_cell_2_tissue_Colon_day_35_NA [TT146]


title: 33h


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 6_2013_Crop thinned 50%


title: 30h


title: TJ2_1d_5_model_T_cell_2_tissue_Colon_day_35_NA [TT135]


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: 28h


title: 29h


title: TJ2_1c_4_model_T_cell_2_tissue_Colon_day_28_NA [TT129]


title: TJ2_1a_2_model_T_cell_2_tissue_Colon_day_14_NA [TT130]


title: TJ2_2e_4_model_T_cell_2_tissue_Colon_day_42_NA [TT128]


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 5_2013_Crop thinned 75%


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: TJ2_2d_1_model_T_cell_2_tissue_Colon_day_35_NA [TT126]


title: 26h


title: TJ2_1a_2_model_T_cell_2_tissue_Colon_day_14_NA [TT127]


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 5_2013_Crop thinned 50%


title: TJ2_1d_5_model_T_cell_2_tissue_Colon_day_35_NA [TT124]


title: TJ2_1d_3_model_T_cell_2_tissue_Colon_day_35_NA [TT134]


title: TJ2_1c_5_model_T_cell_2_tissue_Colon_day_28_NA [TT122]


title: TJ2_1a_1_model_T_cell_2_tissue_Colon_day_14_NA [TT121]


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: 24h


title: TJ2_1e_4_model_T_cell_2_tissue_Colon_day_42_NA [TT132]


title: TJ2_1e_2_model_T_cell_2_tissue_Colon_day_42_NA [TT133]


title: 25h


title: TJ2_1e_1_model_T_cell_2_tissue_Colon_day_42_NA [TT131]


title: 23h


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: TJ2_1a_4_model_T_cell_2_tissue_Colon_day_14_NA [TT120]


title: 27h


title: TJ2_1a_3_model_T_cell_2_tissue_Colon_day_14_NA [TT119]


title: 22h


title: TJ2_1d_1_model_T_cell_2_tissue_Colon_day_35_NA [TT118]


title: TJ2_1c_2_model_T_cell_2_tissue_Colon_day_28_NA [TT117]


title: TJ2_2e_2_model_T_cell_2_tissue_Colon_day_42_NA [TT116]


title: TJ2_1c_3_model_T_cell_2_tissue_Colon_day_28_NA [TT115]


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 4_2013_Crop thinned 75%


title: DSP-1001660008975-G-A01

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

library_source: other

data_processing:
The raw counts were processed in the NanoString’s GeoMx NGS pipeline v.2.1 where they were converted to the digital count conversion (DCC) files
The GeomxTools was used for quality control (QC) and downstream analysis of the DCC files in R
Assembly: hg38
Supplementary files format and content: GeoMx pipeline readable digital counts (DCC)
Library strategy: GeoMx NGS readout

molecule: other

organism: synthetic construct

source_name: No Template Control

extract_protocol:
Briefly, once the slides were deparaffinised and subjected to antigen retrieval procedures, samples were co-incubated with fluorescent-labeled visualization antibodies to detect tumor cells (pan-cytokeratin [CK]), all immune cells (CD45), together with DAPI for nuclei detection. Customizable fluorescent morphology markers, conjugated to unique oligonucleotide tags with an ultraviolet (UV) photocleavable linker, helped visualizing the tissue architecture. The samples were imaged and regions of interest (ROIs) were exposed to UV light that cleaved the linker and released the barcoded oligos for capture by microfluidics and GeoMx DSP then were coupled to next generation sequencing (NGS) readout to profile RNA expression for identifying over 1,800 genes in colon and rectal cancers. The 97 areas of illumination (AOIs) across all slides in mixed stroma/tumor regions was selected
After UV illumination, the barcodes were collected in 96-well plates and were used in the NGS readout library preparation procedure protocol. The resulted libraries were sequenced by the Illumina NextSeq 500 platform using 2 x 27 base paired reads

value: No Template Control

tag: disease state

tag: patient

tag: treatment

tag: segment

tag: tissue site

tag: slide

tag: roi number

tag: roi x_coordinate

tag: roi y_coordinate


title: TJ2_2c_1_model_T_cell_2_tissue_Colon_day_28_NA [TT125]

tag: strain

tag: genotype

tag: model

tag: tissue

tag: bio region

tag: ctrl disease


title: TJ2_2e_5_model_T_cell_2_tissue_Colon_day_42_NA [TT114]

tag: day

tag: hit rest


title: TJ2_2e_3_model_T_cell_2_tissue_Colon_day_42_NA [TT113]


title: TJ2_2a_1_model_T_cell_2_tissue_Colon_day_14_NA [TT123]


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2013 - Crop thinned 75%

tag: cultivar

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: TJ2_2c_5_model_T_cell_2_tissue_Colon_day_28_NA [TT111]


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 4_2013_Crop thinned 50%


title: TJ2_1c_5_model_T_cell_2_tissue_Colon_day_28_NA [TT110]


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: TJ2_1a_4_model_T_cell_2_tissue_Colon_day_14_NA [TT109]


title: Rice_OsC3'H1-KO-a-rep2

city: Tsuruoka

first: Yuri

last: Takeda-Kimura

state: Yamagata

address: 1-23 Wakabamachi

department: Faculty of Agriculture

institute: Yamagata University

data_processing:
All data analysis were performed using the public Galaxy server, which contains Trimmomatic, HISAT2, Cufflinks and Cuffdiff programs (http://usegalaxy.org/).
Base-calling and quality control was performed using the FastQC program.
Low-quality bases from reads were trimmed using the Trimmomatic program.
Read mapping was performed using the HISAT2 alignment program.
Transcript assembly was performed on the cufflinks program and gene expressions were normalized using cuffdiff program.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0  (https://rapdb.dna.affrc.go.jp/)
Supplementary_files_format_and_content: Tab-delimited text files include normalized RPKM values generated by cuffdiff program.

organism: Oryza sativa

source_name: 12-days-old OsC3'H1-knockout rice (line: b), biological replicate 2

growth_protocol: Rice plants were grown in sterile magenta boxes containing 1/2 diluted Murasige and Skoog medium and 0.4% agar in growth chamber at 27℃ with a 12h daily photoperiod. On 7 days after seeding, wild-type control plants were transplanted to a plastic container containing a hypotonic solution prepared with tap water.

extract_protocol:
RNA was prepared using the RNeasy plant mini kit (Qiagen) following the manufacturer's recommendations.
Library construction and sequencing were performed by Eurofins.

value: Nipponbare

value: whole aerial parts

tag: Stage

value: 12 days after seedling

tag: generation


title: TJ2_2a_3_model_T_cell_2_tissue_Colon_day_14_NA [TT108]

tag: strain


title: Rice_OsC3'H1-KO-b-rep3

source_name: 12-days-old OsC3'H1-knockout rice (line: a), biological replicate 3

tag: genotype


title: Rice_OsC3'H1-KO-a-rep3

source_name: 12-days-old OsC3'H1-knockout rice (line: b), biological replicate 3


title: TJ2_2e_2_model_T_cell_2_tissue_Colon_day_42_NA [TT105]

source_name: Colon

tag: model


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2013 - Crop thinned 50%

first: Marianna

last: Fasoli

address: Via della Pieve 70

value: cv Pinot noir

tag: tissue


title: TJ2_1c_1_model_T_cell_2_tissue_Colon_day_28_NA [TT106]

value: wildtype

tag: bio region


title: DSP-1001660008972-H-A01

tag: disease state

tag: patient

tag: treatment

tag: segment

tag: tissue site

tag: slide

tag: roi number

tag: roi x_coordinate

tag: roi y_coordinate


title: TJ2_2a_2_model_T_cell_2_tissue_Colon_day_14_NA [TT101]

value: Colon

tag: ctrl disease

tag: day

tag: hit rest


title: TJ2_1a_5_model_T_cell_2_tissue_Colon_day_14_NA [TT102]

tag: strain

value: PMC


title: TJ2_2d_4_model_T_cell_2_tissue_Colon_day_35_NA [TT107]

tag: genotype


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 3_2013_Crop thinned 75%

tag: cultivar

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: TJ2_2d_2_model_T_cell_2_tissue_Colon_day_35_NA [TT103]

tag: model

tag: tissue

tag: bio region


title: TJ2_2a_5_model_T_cell_2_tissue_Colon_day_14_NA [TT112]


title: Rice_OsC3'H1-KO-b-rep2

source_name: 12-days-old OsC3'H1-knockout rice (line: a), biological replicate 2

tag: Stage

tag: generation


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: TJ2_2c_2_model_T_cell_2_tissue_Colon_day_28_NA [TT104]

tag: ctrl disease


title: Rice_OsC3'H1-KO-a-rep1

source_name: 12-days-old OsC3'H1-knockout rice (line: b), biological replicate 1


title: TJ1_2e_6_model_T_cell_1_tissue_Blood_day_42_NA [TJ_2e_6_B]

source_name: Blood

value: Blood

value: B

tag: day


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2013 - Crop thinned 75%

value: Crop thinned 75%

value: grape berry pericarp


title: TJ1_2e_3_model_T_cell_1_tissue_Colon_day_42_NA [TJ_2e_3_PMC]

tag: hit rest


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: Rice_WT_12days_rep3

source_name: 12-days-old wild-type rice, biological replicate 3

value: wild type


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 3_2013_Crop thinned 50%


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: Rice_WT_5days_rep3

source_name: 5-days-old wild-type rice, biological replicate 3

value: 5 days after seedling


title: Rice_WT_12days_rep1

source_name: 12-days-old wild-type rice, biological replicate 1


title: TJ1_2e_4_model_T_cell_1_tissue_Colon_day_42_NA [TJ_2e_4_DMC]

tag: strain

value: DMC

value: D


title: TJ1_2e_2_model_T_cell_1_tissue_Blood_day_42_NA [TJ_2e_2_B]

tag: genotype


title: Rice_OsC3'H1-KO-b-rep1

source_name: 12-days-old OsC3'H1-knockout rice (line: a), biological replicate 1

tag: cultivar


title: TJ1_2e_4_model_T_cell_1_tissue_Colon_day_42_NA [TJ_2e_4_PMC]


title: TJ1_2e_4_model_T_cell_1_tissue_Blood_day_42_NA [TJ_2e_4_B]


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 2_2013_Crop thinned 75%

tag: year


title: TJ1_2d_5_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_5_PMC]


title: TJ1_2e_1_model_T_cell_1_tissue_Colon_day_42_NA [TJ_2e_1_PMC]


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2013 - Crop thinned 50%

tag: time point

value: Crop thinned 50%


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2013 - Crop thinned 75%

tag: time point replicate


title: TJ1_2e_5_model_T_cell_1_tissue_Colon_day_42_NA [TJ_2e_5_DMC]


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2013 - Crop thinned 75%

tag: day after veraison


title: TJ1_2e_1_model_T_cell_1_tissue_Colon_day_42_NA [TJ_2e_1_DMC]


title: Rice_WT_5days_rep1

source_name: 5-days-old wild-type rice, biological replicate 1


title: Rice_WT_12days_rep2

source_name: 12-days-old wild-type rice, biological replicate 2


title: TJ1_2d_5_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_5_DMC]


title: TJ1_2d_4_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_4_PMC]


title: TJ1_2e_1_model_T_cell_1_tissue_Blood_day_42_NA [TJ_2e_1_B]


title: TJ1_2d_5_model_T_cell_1_tissue_Blood_day_35_NA [TJ_2d_5_B]


title: TJ1_2d_4_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_4_DMC]


title: TJ1_2e_3_model_T_cell_1_tissue_Blood_day_42_NA [TJ_2e_3_B]


title: Wild-type Drosophila late-ovary sample, biological replicate 1 [RNA-seq]

city: Princeton

first: Elizabeth

last: Gavis

state: NJ

address: 401 Schultz Lab

institute: Princeton University

data_processing:
Adaptor trimming by Trim Galore! (default parameters).
rRNA subtraction by Bowtie (--best -m1 -v2).
Read alignment by Bowtie2 (default parameters).
Uniquely mapped reads counted by BAM to Wiggle.
Assembly: dm6
Supplementary files format and content: Aligned reads in un-normalized WIG files.

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: To obtain late-stage-oocyte-enriched ovaries (late-ovaries), female flies were fed for 4 days at 25°C in bottles of corn meal agar food supplemented with yeast paste and then starved in bottles with only wet Kimwipes (Kimtech) for 18 h at 25°C. Ovaries were hand-dissected on ice in PBS and used immediately to prepare extract.

extract_protocol:
~500 µL of ovaries were hand-dissected in Schneider’s Drosophila Medium (ThermoFisher), mixed with 3 mL of lysis buffer (0.5% Triton X-100, 150 mM NaCl, 5 mM MgCl2, 50 mM Tris-HCl pH 7.5, 1 mM DTT, 50 µM GMP-PNP, 2 µg/mL emetine, and 20 U/mL Superase·In RNase Inhibitor (Ambion)), and flash frozen in liquid N2. Ovaries were lysed using a Cellcrusher tissue pulverizer (Cellcrusher), allowed to thaw on ice, and centrifuged first at 10,000 rpm for 10 min and then at 13,200 rpm for 10 min. 300 µL of supernatant was used for footprint library preparation, another 300 µL were used for poly(A)-selected mRNA-Seq library preparation, and the rest was flash frozen in liquid N2 and stored at -80° C. Ribosome footprints were generated by incubating the lysate with 3 U/µg of RNA Micrococcal Nuclease (NEB) for 40 min at 25° C followed by quenching with added EGTA to a final concentration of 6.25 mM. Ribosomes were sedimented through a 34% sucrose cushion for 2.5 hr at 33,000 rpm in a Beckman SW50 rotor, and the pellet was re-suspended in 10mM Tris pH 7.0. RNA was extracted using TRIzol LS (Invitrogen) and size-selected (28-34 nt) on a 15% TBE-urea gel. For RNA-Seq libraries, total RNA was extracted from 300 µL of lysate with TRIzol LS, precipitated with isopropanol, washed in ice-cold 80% ethanol, and re-suspended in 10 mM Tris-HCl pH 7.0. mRNAs were then enriched by poly(A) selection.
All libraries were generated using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's protocols.

value: Ovary

tag: cell type

value: Late-stage oocytes

value: WT

tag: Sex

value: Female


title: Wild-type Drosophila late-ovary sample, biological replicate 2 [RNA-seq]


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 1_2013_Crop thinned 75%

value: cv Pinot noir

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 2_2013_Crop thinned 50%

tag: tissue


title: Rice_WT_5days_rep2

source_name: 5-days-old wild-type rice, biological replicate 2

value: Nipponbare

value: whole aerial parts

tag: Stage


title: TJ1_2d_1_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_1_DMC]

source_name: Colon

value: wildtype

tag: model

value: Colon

tag: bio region


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: TJ1_2d_4_model_T_cell_1_tissue_Blood_day_35_NA [TJ_2d_4_B]

value: Blood

value: B

tag: ctrl disease

tag: day


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2013 - Crop thinned 50%

value: grape berry pericarp


title: TJ1_2d_1_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_1_PMC]

tag: strain

value: PMC

tag: hit rest


title: TJ1_2d_3_model_T_cell_1_tissue_Blood_day_35_NA [TJ_2d_3_B]

tag: genotype


title: Set2_RNA_3

city: West Lafayette

first: Vikki

middle: M

last: Weake

address: 175 S University St

department: Biochemistry

institute: Purdue University

data_processing:
Sanger/Illumina 1.9 used for base calling.
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: "HEADCROP:15 CROP:35" for ATAC and "HEADCROP:8 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:30 MINLEN:75" for RNA. Cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 (ATAC) or STAR (RNA) producing SAM, BAM, and/or count files.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
BAM files are normalized to GC content using deepTools computeGCBias and correctGCBias packages, then bigwig files are obtained using bamCoverage package. For RNA-seq, Differential gene expression analysis was performed with DESeq2 using STAR-produced counts as input.
Assembly: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
Supplementary files format and content: Processed file is a bigwig file for each sample, and table with STAR-generated counts for RNA-seq

source_name: Retina

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506];UAS-siSet2 or UAS-siSet2) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10 days (D1 or D10) and transfered to new food every other day.  Flies were collected at relative Zeitgeber Time ZT6

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. Purified nuclei were obtained using an immunoenrichment protocol (Jauregui-Lozano, et al. 2021. Genetics)
Omni-ATAC libraries were made with Illumina Tagment DNA TDE1 Enzyme and Buffer kit and "IDT for Illumina" Nextera DNA UD Indexes Set A. RNA-seq libraries were constructed with Ovation® SoLo RNA-Seq Library Preparation Kit (Nugen-Tecan) using 10 ng of RNA as starting material

value: Photoreceptor neuron

tag: RNAi

tag: age

value: 10 days after eclosion


title: TJ1_2d_2_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_2_PMC]

value: D


title: Wild-type Drosophila late-ovary sample, biological replicate 3 [RNA-seq]


title: TJ1_2d_2_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_2_DMC]

value: DMC


title: TJ1_2b_5_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_5_PMC]


title: TJ1_2b_5_model_T_cell_1_tissue_Blood_day_21_NA [TJ_2b_5_B]


title: Wild-type Drosophila late-ovary sample, biological replicate 3 [Ribo-seq]

data_processing:
Library strategy: Ribo-seq
Adaptor trimming by Trim Galore! (default parameters).
rRNA subtraction by Bowtie (--best -m1 -v2).
Read alignment by Bowtie2 (default parameters).
Uniquely mapped reads counted by BAM to Wiggle.
Assembly: dm6
Supplementary files format and content: Aligned reads in un-normalized WIG files.

value: Ovary


title: Set2_RNA_2


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2013 - Crop thinned 75%

city: San Pietro in Cariano

institute: University of Verona

tag: cultivar

tag: year

tag: time point

tag: time point replicate

value: Crop thinned 75%


title: TJ1_2b_5_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_5_DMC]


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2013 - Crop thinned 50%

source_name: grape berry pericarp_time point 1_2013_Crop thinned 50%

tag: day after veraison

tag: sugar content (g/100ml)

value: Crop thinned 50%


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2013 - Crop thinned 50%

tag: treatment (cluster thinning)

tag: tissue


title: Wild-type Drosophila late-ovary sample, biological replicate 2 [Ribo-seq]

tag: cell type

value: Late-stage oocytes

value: WT

tag: Sex

value: Female


title: TJ1_2b_4_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_4_PMC]

tag: model

tag: bio region

tag: ctrl disease


title: TJ1_2d_2_model_T_cell_1_tissue_Blood_day_35_NA [TJ_2d_2_B]

tag: strain

tag: day

tag: hit rest


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2013 - Crop thinned 50%

value: cv Pinot noir


title: TJ1_2b_4_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_4_DMC]

tag: genotype

value: wildtype


title: Set2_RNA_1

tag: RNAi

tag: age


title: mCherry_ATAC_3

description: Accessible chromatin

value: mCherry


title: TJ1_2b_3_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_3_PMC]

value: Colon


title: TJ1_2d_1_model_T_cell_1_tissue_Blood_day_35_NA [TJ_2d_1_B]

value: Blood

value: B


title: TJ1_2b_3_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_3_DMC]


title: TJ1_2b_3_model_T_cell_1_tissue_Blood_day_21_NA [TJ_2b_3_B]


title: TJ1_2b_4_model_T_cell_1_tissue_Blood_day_21_NA [TJ_2b_4_B]


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 8_2012_Crop thinned 75%

tag: cultivar

tag: year

tag: time point

value: grape berry pericarp


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2012 - Crop thinned 75%

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)


title: TJ1_2b_2_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_2_PMC]

tag: tissue

value: PMC


title: mCherry_ATAC_2

description: Accessible chromatin

tag: cell type

value: Photoreceptor neuron

value: 10 days after eclosion


title: mCherry_ATAC_1

description: Accessible chromatin


title: TJ1_2b_2_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_2_DMC]

tag: model

value: DMC

value: D


title: TJ1_2b_2_model_T_cell_1_tissue_Blood_day_21_NA [TJ_2b_2_B]

source_name: Blood

tag: bio region


title: TJ1_2b_1_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_1_PMC]

tag: ctrl disease


title: Set2_ATAC_3

description: Accessible chromatin


title: Pinot noir berry sample collected at time point 8 (replicate 2) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 8_2012_Crop thinned 50%

tag: treatment (cluster thinning)


title: Pinot noir berry sample collected at time point 8 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: TJ1_2b_1_model_T_cell_1_tissue_Colon_day_21_NA [TJ_2b_1_DMC]

tag: strain

tag: day


title: Set2_ATAC_2

description: Accessible chromatin


title: TJ1_2b_1_model_T_cell_1_tissue_Blood_day_21_NA [TJ_2b_1_B]

tag: genotype

tag: hit rest


title: TJ1_2a_5_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_5_PMC]


title: Set2_ATAC_1

description: Accessible chromatin

tag: RNAi

tag: age


title: TJ1_2a_5_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_5_DMC]


title: TJ1_2a_5_model_T_cell_1_tissue_Blood_day_14_NA [TJ_2a_5_B]


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: cultivar

tag: year


title: TJ1_2a_4_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_4_PMC]


title: TJ1_2a_4_model_T_cell_1_tissue_Blood_day_14_NA [TJ_2a_4_B]


title: D40_H3K36me3_4

data_processing:
Sanger/Illumina 1.9 used for base calling.
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:23 MINLEN:75.  Cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 with settings: --sensitive.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Bigwig files were generated using deepTools subpackage bamCoverage, and bigwig files were analyzed using multiBigwigSummary, computeMatrix, plotCorrelation, plotProfile and plotHeatmap. Dm6 refGene GTF file was used for all analysis, available at UCSC.
Assembly: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
Supplementary files format and content: All processed files are bigwig files containing CPM-normalized tracks

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 40 days with transfer to new food every other day.  Flies were collected at ZT 6

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. Nuclei isolation, chromatin extraction, immunoprecipitation and library preparation was performed as previously described (Jauregui-Lozano, et al. 2021. Genetics).
ChIP-seq libraries were constructed with Ovation® V2 UltraLow Library Preparation Kit (Nugen-Tecan) using 2 ng of purified DNA as starting material

tag: Sex

value: male

value: day 40

tag: chip antibody


title: TJ1_2a_4_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_4_DMC]


title: D40_H3K36me3_3


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 7_2012_Crop thinned 75%

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

value: Crop thinned 75%


title: TJ1_2a_3_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_3_DMC]

tag: model

tag: tissue

tag: bio region


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: treatment (cluster thinning)


title: TJ1_2a_3_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_3_PMC]

tag: strain

tag: ctrl disease

tag: day


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: D40_H3K36me3_1

tag: cell type

tag: genotype


title: TJ1_2a_3_model_T_cell_1_tissue_Blood_day_14_NA [TJ_2a_3_B]

tag: hit rest


title: D40_H3K36me3_2

tag: age


title: Pinot noir berry sample collected at time point 8 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: cultivar

tag: year


title: Wild-type Drosophila late-ovary sample, biological replicate 1 [Ribo-seq]

value: Ovary

value: Late-stage oocytes

value: WT

tag: Sex


title: Pinot noir berry sample collected at time point 7 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 7_2012_Crop thinned 50%

value: cv Pinot noir

tag: time point

tag: time point replicate

value: Crop thinned 50%


title: TJ1_2a_2_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_2_PMC]

value: wildtype

value: Colon


title: TJ1_2a_2_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_2_DMC]


title: Pinot noir berry sample collected at time point 7 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: day after veraison

tag: sugar content (g/100ml)


title: TJ1_2a_2_model_T_cell_1_tissue_Blood_day_14_NA [TJ_2a_2_B]

tag: model

tag: tissue

value: Blood

value: B


title: TJ1_2a_1_model_T_cell_1_tissue_Colon_day_14_NA [TJ_2a_1_PMC]

tag: bio region

value: PMC


title: D40_H3K4me3_4

value: Photoreceptor neuron

tag: chip antibody


title: D40_H3K4me3_3


title: TJ1_2a_1_model_T_cell_1_tissue_Blood_day_14_NA [TJ_2a_1_B]

tag: strain

tag: ctrl disease


title: Pinot noir berry sample collected at time point 7 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: treatment (cluster thinning)

value: grape berry pericarp


title: TJ1_1e_5_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_5_PMC]

tag: genotype

value: C

tag: day


title: TJ1_1e_5_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_5_DMC]

value: DMC

tag: hit rest


title: D40_H3K4me3_2

tag: cell type

value: male

tag: age


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 6_2012_Crop thinned 75%

tag: cultivar

tag: year


title: D40_H3K4me3_1

tag: Sex

value: day 40


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2012 - Crop thinned 75%

tag: time point

tag: time point replicate

tag: day after veraison

value: Crop thinned 75%


title: TJ1_1e_4_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_4_PMC]

tag: model

tag: tissue


title: TJ1_1e_5_model_T_cell_1_tissue_Blood_day_42_NA [TJ_1e_5_B]

tag: bio region


title: TJ1_1e_4_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_4_DMC]

tag: strain


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: sugar content (g/100ml)


title: TJ1_1e_4_model_T_cell_1_tissue_Blood_day_42_NA [TJ_1e_4_B]

tag: ctrl disease


title: D40_H3_3

tag: genotype

tag: chip antibody


title: Pinot noir berry sample collected at time point 6 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 6_2012_Crop thinned 50%

tag: treatment (cluster thinning)


title: TJ1_1e_2_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_2_DMC]

tag: day

tag: hit rest


title: TJ1_1e_2_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_2_PMC]


title: TJ1_1e_1_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_1_PMC]


title: TJ1_1e_2_model_T_cell_1_tissue_Blood_day_42_NA [TJ_1e_2_B]


title: D40_H3_1

tag: cell type

tag: age


title: Pinot noir berry sample collected at time point 6 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: cultivar

tag: year


title: D40_H3_2

tag: Sex


title: Pinot noir berry sample collected at time point 6 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: time point

tag: time point replicate

tag: day after veraison


title: TJ1_1e_1_model_T_cell_1_tissue_Colon_day_42_NA [TJ_1e_1_DMC]

tag: model

tag: tissue

tag: bio region


title: D40_IN_4

value: none (input)


title: TJ1_1e_1_model_T_cell_1_tissue_Blood_day_42_NA [TJ_1e_1_B]

tag: strain

tag: ctrl disease


title: TJ1_1d_5_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_5_DMC]

tag: genotype


title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 5_2012_Crop thinned 75%

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: TJ1_1d_5_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_5_PMC]

tag: day

tag: hit rest


title: D40_IN_3

tag: cell type

tag: age

tag: chip antibody


title: TJ1_1d_5_model_T_cell_1_tissue_Blood_day_35_NA [TJ_1d_5_B]


title: D40_IN_2

tag: Sex


title: D40_H3_4


title: TJ1_1d_3_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_3_PMC]


title: TJ1_1d_4_model_T_cell_1_tissue_Blood_day_35_NA [TJ_1d_4_B]


title: TJ1_1d_3_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_3_DMC]


title: D40_IN_1