title: RNCrps25∆72h rep1

city: Guangzhou

first: Xihao

last: Liao

state: Guangdong

address: No.382, Outer Ring East Road, Higher Education Mega Center

department: School of Biological and Bioegineering

institute: South China University of Technology

description: RNC-RNA

data_processing:
Illumina bcl2fastq2-v2.17 software used for basecalling.
After filtered out less than 50 bp reads with raw reads trimming adapter, the reads of all samples were mapped to transcript reference libraries Pichia pastoris GS115 with FANSe2.
Gene expression levels are quantified using RPKM (reads per kilobase per million reads) as unit.
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each Sample.

organism: Komagataella pastoris

extract_protocol:
After ribosome-nascent chain complexes (RNCs) extraction, total RNA and RNC-RNA was harvested using TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: fermentation stage


title: 4210B: Tumor of Patient 4210

status: Public on Dec 01 2018

type: RNA

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

department: DPDS

country: Belgium

institute: Janssen R&D

hyb_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

data_processing: Data were analyzed using Bioconductor 3.2 running on R 3.2.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient 4210

extract_protocol: Qiagen RNAeasy FFPE

tag: patient id

tag: age

tag: gender

value: Female

tag: tissue

value: Tumor

tag: adenomadiagnosis

value: Adenocarcinoma

tag: tnm

value: pT3, pN1, pMx

tag: uicc

value: IIIB


title: RNCrps25∆72h rep2

type: SRA

country: China

description: RNC-RNA

library_source: transcriptomic

tag: strain


title: CO1_390209M

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

country: USA

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 9.

source_name: tissue biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

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

treatment_protocol: Mucosal biopsies were collected 15 to 20 cm from the anal verge at screening during endoscopies from a subset of patients who participated in the PURSUIT (n=87) study.  Independent of the PURSUIT study , biopsies were also collected from 21 healthy normal subjects to serve as control.  Biopsies were immediately placed in RNAlater and subsequently stored at –80oC until RNA preparation.

tag: subject

tag: diseaseextent

tag: disease

value: Normal

value: Colon


title: 1020


title: IV7

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality trimming of raw reads was done with Sickle v1.33 with a threshold of 20.
Adapter trimming of raw reads was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 2.3.4 was used to map the reads to the appropriate references with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum ITAGv3.2 combined with either B. cinerea ASM83294v1, F. acuminatum (GGXD01000000), or R. stolonifer (GGWM01000000) transcriptomes for inoculated fruit samples.  Pathogen transcriptomes alone were used for in vitro samples.
Supplementary_files_format_and_content: Bcin_Raw_Read_Count_Matrix.csv, Facu_Raw_Read_Count_Matrix.csv, Rsto_Raw_Read_Count_Matrix.csv: comma-separated files determined by mapping trimmed sequencing reads

organism: Botrytis cinerea

source_name: In vitro fungal culture

extract_protocol:
Fungal RNA from the in vitro cultures was extracted using TRIzol (Invitrogen) and purified using the Quick-RNA MiniPrep Kit (Zymo Research).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

tag: ripening stage

tag: days post inoculation


title: RNCrps25∆48h rep2

description: RNC-RNA


title: 4210C: Adjacent Mucosa of Patient 4210

scan_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

value: Adjacent Mucosa

value: Benign


title: 1015


title: 1016


title: NATL2A_PVC leachate rep1

city: Sydney

first: Sasha

last: Tetu

state: NSW

address: Macquarie University

department: Molecular Sciences

country: Australia

institute: Macquarie University

description:
NAT_P1
processed data file : NATL2A_transcript_counts.csv

data_processing:
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) v 1.3.1 was used to align reads to genome sequences (Magoc et al 2013)
Subread featurecounts script was used to summarise reads to genomic features (Liao et al 2013)
Genome_build: NCBI accessions NC_007577.1 (MIT9312) and NC_007335.2 (NATL2A)
Supplementary_files_format_and_content: Tab delimted text file with the number of reads mapping to each ORF for all replicates, gene annotations are included alongside ORF names

organism: Prochlorococcus marinus str. NATL2A

source_name: Prochlorococcus in vitro culture

growth_protocol: Prochlorococcus marinus MIT9312 and NATL2A were cultured in acid washed glassware using AMP1 media at

extract_protocol:
Cells were collected by centrifugation for 7 mins, pellet resuspended immediately in Qiazol solution and further processed using the Qiagen MiRNeasy kit, according to the manufacturer's instructions
rRNA was depleted using Ribozero bacterial kit, RNA converted to cDNA and used to prepare TruSeq RNA-seq stranded libraries
TruSeq RNA-seq stranded libraries were prepared and sequenced using NextSeq500 75bp SR at the Ramaciotti Centre for Genomics

treatment_protocol: Three independent biological replicates were set up in 50mL volumes with control media (AMP1 only) or media containing a dilution of sterile leachate from plastic bags (HDPE, applied at 50% final volume) or plastic matting (PVC, applied at 2% final volume). PVC spiked cultures were harvested after 90 mins exposure, control and HDPE exposed cultures were harvested after 180 mins.

tag: exposed to

value: PVC leachate

tag: molecule subtype

value: rRNA depleted total RNA


title: E5524808-5

value: Extensive

value: Ulcerative Colitis (UC)


title: 4250A: Adenoma of Patient 4250

source_name: Patient 4250

label_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

value: Adenoma

value: Tubulovillous Adenoma with High Grade Dysplasia


title: RNCrps25∆24h rep2

description: RNC-RNA

tag: genotype


title: NATL2A_HDPE leachate rep3

description:
NAT_H6
processed data file : NATL2A_transcript_counts.csv

value: HDPE leachate


title: CO7_671221M


title: RNCrps25∆48h rep1

description: RNC-RNA

tag: fermentation stage


title: 1022


title: CO3_500130M


title: NATL2A_PVC leachate rep3

description:
NAT_P3
processed data file : NATL2A_transcript_counts.csv


title: NATL2A_HDPE leachate rep2

description:
NAT_H5
processed data file : NATL2A_transcript_counts.csv


title: RNCrps25∆24h rep1

description: RNC-RNA


title: NATL2A_HDPE leachate rep1

description:
NAT_H4
processed data file : NATL2A_transcript_counts.csv


title: 4250C: Adjacent Mucosa of Patient 4250

tag: patient id


title: 533B: Tumor of Patient 533

source_name: Patient 533

tag: age

value: pT1, pN0, pMx

value: I


title: Drought-stressed WT plants replicate 1

city: Wuhan

first: langlang

last: zhang

state: HuBei

address: Cross road of Jiufeng 1 and Guanggu 7 road

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

description:
WT-1D
 CL100012084_L02_4_1

data_processing:
The libraries were purified using the AMPure XP system (Beckman Coulter, Beverly, USA) and validated on the Agilent Technologies 2100 bioanalyzer. Then, the libraries were sequenced using BGISEQ-500 platform (BGI, Wuhan, China, http://www.seq500.com).
High quality reads were then mapped on the reference genome (TAIR10) of Arabidopsis with STAR (https://github.com/alexdobin/STAR). Based on the distribution of samples in a first PCA plot, the two most similar replicates per condition were considered for further statistical analyses.
Clean reads from each sample were mapped to the reference genome of vitis vinifera (Vitis_vinifera.IGGP_12x; http://plants.ensembl.org/Vitis_vinifera/Info/Index), using Hisat2 v.2.0.5 (https://ccb.jhu.edu/software/hisat2/index.shtml) with default parameters
Read summarization was then performed with featureCounts (http://bioinf.wehi.edu.au/featureCounts/) using only the reads with a mapping quality higher than 30. The statistical analysis was performed with R. Specifically, lowly expressed genes were removed with the package HTSFilter (http://www.bioconductor.org/packages/release/bioc/html/HTSFilter.html), selecting "TMM" as the normalization method
Then, the filtered genes were used to perform a differential analysis with EdgeR. Genes were considered statistically differentially expressed if the corrected p-value was lower than 0.05.
Genome_build: Arabidopsis thaliana Col-0 TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Arabidopsis thaliana

source_name: Drought-stressed WT plants

growth_protocol: Seeds of Arabidopsis thaliana (ecotype Columbia-0) were surface-sterilized with 6% sodium hypochlorite for 5 min followed by three washes with sterile water and then plated on 1/2 MS solid medium containing 0.7% agar. One-week-old seedlings were transferred from plates into pots filled with peat moss in a greenhouse under controlled environmental conditions, at 22 °C, under 50%–60% relative humidity, and under 130 µmol photons m−2 s−1 with a 16 h/8 h light/dark cycle.

extract_protocol:
Total RNA was extracted from collected samples using TIANDZ Column Plant RNAout 2.0 Kit (Tiandz, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA-Seq analysis was performed using 3-week-old transgenic Arabidopsis mixture and WT plants under normal and drought stress (without water for 5 days) conditions.

tag: ecotype background

tag: genotype/variation

value: Wild type

value: 3-week old

tag: treated with

value: Whole plants


title: RNCrps7∆72h rep2

description: RNC-RNA


title: CO2_550922M

tag: tissue


title: 533A: Adenoma of Patient 533

tag: gender

value: Female

tag: adenomadiagnosis

value: Tubulovillous Adenoma

tag: tnm

tag: uicc


title: NATL2A_Control rep3

description:
NAT_C6
processed data file : NATL2A_transcript_counts.csv

value: none (control)

tag: strain


title: 4250B: Tumor of Patient 4250

value: Tumor

value: Adenocarcinoma

value: pT3, pN1, pMx

value: IIIB


title: 1017

tag: subject

tag: diseaseextent

tag: disease

value: Normal

value: Colon


title: NATL2A_Control rep2

description:
NAT_C5
processed data file : NATL2A_transcript_counts.csv

tag: exposed to

tag: molecule subtype

value: rRNA depleted total RNA


title: RNCrps7∆48h rep2

description: RNC-RNA

tag: genotype

tag: fermentation stage


title: CO13_500128V

tag: age


title: RNCrps7∆48h rep1

description: RNC-RNA


title: 744A: Adenoma of Patient 744

source_name: Patient 744

tag: patient id

value: Adenoma


title: NATL2A_Control rep1

description:
NAT_C4
processed data file : NATL2A_transcript_counts.csv


title: CO16_300823M


title: CO8_360412M


title: 533C: Adjacent Mucosa of Patient 533

value: Adjacent Mucosa

value: Benign


title: RNCrps7∆24h rep2

description: RNC-RNA


title: 7479A: Adenoma of Patient 7479

source_name: Patient 7479

value: Male

value: Tubular Adenoma


title: 744B: Tumor of Patient 744

value: Colonic Adenocarcinoma


title: CO9_480129V


title: CO5_331020M


title: RNCrps7∆72h rep1

description: RNC-RNA


title: 744C: Adjacent Mucosa of Patient 744


title: 7479B: Tumor of Patient 7479

value: pT3, pN0, pMx

value: IIA


title: CO11_480308M


title: RNCrpl9a∆72h rep2

description: RNC-RNA


title: RNCrps7∆24h rep1

description: RNC-RNA


title: 1014


title: RNCrpl9a∆48h rep2

description: RNC-RNA


title: IV6

organism: Fusarium acuminatum

tag: ripening stage

tag: days post inoculation


title: IV5


title: RNCrpl9a∆48h rep1

description: RNC-RNA


title: RNCrpl9a∆24h rep2

description: RNC-RNA


title: IV3

organism: Rhizopus stolonifer


title: 833A: Adenoma of Patient 833

source_name: Patient 833

value: Female

tag: tissue


title: 7479C: Adjacent Mucosa of Patient 7479

tag: gender


title: RNCrpl9a∆24h rep1

description: RNC-RNA


title: Tangerine2 Mutant Breaker_rep 1_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression at Breaker stage of Tangerine2 Mutant

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Genotypic designed Tomato_GXP_8x60K (AMADID:65951). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2600D at 3 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software Version 11.5.1.1  and Normalization of the data was done in GeneSpring GX V 12.0

organism: Solanum lycopersicum

source_name: Tangerine2 Mutant Breaker stage of Fruit ripening

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Tangerine2 mutant and Wild type (Solanum lycopersicum) tomato plants were grown in a greenhouse with supplementary lighting providing an irradiance of 250–400 l mol m-2 s-1. Individual tomato plants were grown in pots (20 cm diameter) containing compost supplemented with appropriate fertilizers. Plants were watered daily and fruit were tagged at anthesis and harvested when they had reached the appropriate developmental stage. Individual fruit were removed from the plant, weighed, kept in RNA Later, and stored at -80 c until required.

extract_protocol: Isolation of RNA from Tomato fruit was carried out by using Ambion RNAaqueous Phenol free total RNA isolation Kit (Cat # AM1912) with Ambion plant RNA isolation Aid (P/N: AM9690) as per the manufacturer’s protocols.

treatment_protocol: Pericarp tissue was selected for microarray analysis. The tissue was collected at Mature Green (MG), Breaker (BR), Turning (TR), and Fully Ripen (FR) stages from Tangerine2 mutant and Wild type. Fruits were collected from green house and transfer immediately into thermocouple boxes. Sterile working area was prepared by wiping the working area surface with 1% hypochlorite bleach. Samples were dissected wearing new Nitrile gloves which were wiped with 1% hypochlorite. Pre labelled RNA free 2 ml tubes filled with 1.5 ml RNALater (RLT) solution were placed in working area for sample collection. The samples were kept in sterile petri plate and the tissue was sliced 3 mm or less in size and then transferred immediately in labelled vial containing RNALater (1.5 ml) and this step was finished within 90 seconds (Long time might degrade RNA). Each sample was prepared in triplicates containing 10-15 small pieces and the tissue was stored at -80 °C until to carry out the further experiment.

value: Fruit tissue

tag: genotype/variation

value: Tangerine2 Mutant

tag: Stage

value: Breaker


title: RNCrpl9a∆72h rep1

description: RNC-RNA


title: CO10_481222V


title: Tangerine2 Mutant Ripening_rep 1_4

description: Gene expression at Ripening stage of Tangerine2 Mutant

source_name: Tangerine2 Mutant Ripening stage of Fruit ripening

value: Ripening


title: 833C: Adjacent Mucosa of Patient 833

tag: adenomadiagnosis

tag: tnm

tag: uicc


title: Tangerine2 Mutant Turning_rep 1_3

description: Gene expression at Turning  stage of  Tangerine2 Mutant

source_name: Tangerine2 Mutant Turning stage of Fruit ripening

value: Fruit  tissue

value: Turning


title: IV2


title: RNCrpl38∆72h rep2

description: RNC-RNA

tag: strain


title: 1467C: Adjacent Mucosa of Patient 1467

source_name: Patient 1467


title: 1021

tag: subject

tag: diseaseextent

tag: disease

value: Normal

value: Colon


title: CO6_670606M


title: Z094865-23

treatment_protocol: Mucosal biopsies were collected from the distal sigmoid colon (less than 15 to 20 cm from the anal verge) at screening during endoscopies from a subset of patients who participated in the CNTO148UCO1001 (n=19) study. Biopsies were immediately placed in RNAlater and subsequently stored at –80oC until RNA preparation.

value: LIMITED UC

value: Ulcerative Colitis (UC)


title: 833B: Tumor of Patient 833

value: Tumor

value: Adenocarcinoma

value: pT4, pN2, pMx

value: IIIC


title: 1487B: Tumor of Patient 1487

source_name: Patient 1487

value: pT3, pN0, pMx


title: IV1


title: IV4


title: RNCrpl38∆72h rep1

description: RNC-RNA

tag: genotype


title: 1487C: Adjacent Mucosa of Patient 1487

value: Adjacent Mucosa

value: Benign


title: Tangerine2 Mutant Mature Green_rep 1_1

description: Gene expression at Mature green stage of Tangerine2 Mutant

source_name: Tangerine2 Mutant Mature Green stage of Fruit ripening

value: Mature green


title: I769897-23


title: RNCrpl38∆48h rep1

description: RNC-RNA

tag: fermentation stage


title: RNCrpl38∆24h rep2

description: RNC-RNA


title: RNCrpl38∆48h rep2

description: RNC-RNA


title: RNCrpl38∆24h rep1

description: RNC-RNA


title: RNCwt72h rep2

description: RNC-RNA

value: wt


title: RNCwt72h rep1

description: RNC-RNA


title: RNCwt48h rep2

description: RNC-RNA


title: 3492B: Tumor of Patient 3492

source_name: Patient 3492

tag: age

value: Female

value: Colonic Adenocarcinoma

value: pT2, pN1a, pMx

value: IIIA


title: RNCwt48h rep1

description: RNC-RNA


title: 3492C: Adjacent Mucosa of Patient 3492

tag: patient id


title: 2615A: SSA of Patient 2615

source_name: Patient 2615

value: SSA

value: Sessile Serrated Adenoma


title: I769929-23

source_name: tissue biopsy

value: LIMITED UC

value: Colon


title: W457453-23

value: EXTENSIVE

value: Ulcerative Colitis (UC)


title: 2615C: Adjacent Mucosa of Patient 2615


title: I769988-23


title: 2615B: Tumor of Patient 2615

value: Tumor

value: Adenocarcinoma

value: mpT2, pN0, pMx

value: I


title: I771787-23


title: 789A: Adenoma of Patient 789

source_name: Patient 789

value: Male

value: Adenoma

value: Tubular Adenoma


title: Y396209-23


title: W457483-23


title: RNCwt24h rep2

description: RNC-RNA

value: wt


title: RNCwt24h rep1

description: RNC-RNA


title: W457491-23


title: Y396214-23


title: Single Cell RNA-seq, BM-hMSC-TERT4 adipocyte diff 7d

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: SingleCell RNA

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
ATAC-seq reads were aligned to the hg19 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept. RNA-seq reads were aligned to hg19 genome using STAR aligner and default settings. Only one read per position and read length was kept.
Sequencing reads from donors of a tissue of origin were pooled to indentify regions enriched of open chromatin using HOMER. ATAC- regions for Human Primary Stromal Cells were merged using Homer with distance option -d given.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Donors and Time Points into the design matrix, excluding genes which were not detected in any sample. Log 2 fold changes and FDR values were calculated with respect to undifferentiated stromal cells.
Raw base calls of 10x libraries were demultiplexed into fastq files, aligned and filtered for intact cells using the Cell Ranger pipeline. Quality controls and library normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411) to yield a gene count matrix for all 13148 cells.
ATAC-seq signal was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -noadj. Normalization of sequencing reads was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Donors into the design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Zip compressed files contain the output of the Cell Ranger pipeline, that is a filtered matrix of putative cells with gene counts
I1 files (technical) contain the library index        R1 files (technical) have the cellular barcode at position 1:16, the UMI at 17:26        R2 files (biological) have the transcript read

source_name: BM-hMSC-TERT4 aipocyte diff 7d

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) or adipose tissue origin (AT-hMSC-TERT) as well as non-mesenchymal cells were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S). Primary stromal cells were gron in DMEM/F12 supplemented with 15 mM HEPES, 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S)

extract_protocol:
Single Cell RNA-seq: Cells have been trypsinized and spun down at 200 g and washed twice in culture media. Cells were separated using a 40 µm mesh, washed 3 times in PBS with 0.04% non-acetylated BSA, and cell numbers were adjusted to 0.7 million cells per ml followed by a final transfer through a 40 µm mesh.
Single Cell RNA-seq: Libraries were prepared according to manufactures instructions (10x Genomics) and sequencing reads were processed using the Cell Ranger pipeline

treatment_protocol:
Immortalized cells and non-mesenchymal cells: Two days post confluency cells were induced to undergo osteoblast or adipocyte differentiation by switched to α-MEM supplemented with 10% FCS, 10 mM dexamethasone, 10 nM vitamin D, 10 mM β-glycerolphosphate, and 50 µg/ml ascorbic acid or to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine. Media was replaced on day 2, 4, 7, 9 and 11.
Human primary stromal cells: Primary cells were expanded prior to the induction of differentiation with DMEM/F-12 supplemented with 10 % FCS, 1 % P/S, 15 mM HEPES and 1 nM FGF-1. Osteogenic induction was similar as for the immortalized cells while the adipogenic induction cocktail contained DMEM/F12 supplemented with 1 % P/S, 15 mM HEPES, 500 µM isobutylmethylxanthine, 100 nM dexamethasone, 10 µg/mL insulin and transferrin, 2 nM T3 and 200 mM rosiglitazone. Both induction cocktails were replaced every third day, while dexamethasone and isobutylmethylxanthine were withdrawn at day three and rosiglitazone at day 6 of adipogenic differentiation

tag: cell type

value: BM-hMSC-TERT4 aipocyte diff 7d


title: K412777-22


title: Y200913-23


title: Single Cell RNA-seq, BM-hMSC-TERT4 undifferentiated

description: SingleCell RNA

source_name: BM-hMSC-TERT4 undifferentiated

value: BM-hMSC-TERT4 undifferentiated


title: RNArps25∆72h rep2


title: 271C: Adjacent Mucosa of Patient 271

source_name: Patient 271

value: Adjacent Mucosa

value: Benign


title: K690175-22


title: 271B: Tumor of Patient 271

value: Colonic Adenocarcinoma

value: pT3, pN2a, pMx

value: IIIB


title: RNArps25∆72h rep1


title: 789B: Tumor of Patient 789

value: pT4b, pN0, pMx

value: IIB


title: 271A: Adenoma of Patient 271


title: Single Cell RNA-seq, BM-hMSC-TERT4 osteoblast diff 7d

description: SingleCell RNA

source_name: BM-hMSC-TERT4 osteoblast diff 7d

value: BM-hMSC-TERT4 osteoblast diff 7d


title: X399843-23

value: EXTENSIVE

value: Ulcerative Colitis (UC)

value: Colon


title: Y740511-23


title: RNArps25∆48h rep2


title: RNA-seq, SHSY5Y adipocyte diff 7d

description:
SH_SY5Y_Ad
RNA_NonMesenchymalCells.txt

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
RNA-seq reads were aligned to hg19 genome using STAR aligner and default settings. Only one read per position and read length was kept.
Genome_build: hg19
Supplementary_files_format_and_content: The txt file "RNA_NonMesenchymalCells.txt" contains only raw gene counts and normalized gene counts, but no log 2 fold changes or statistics due to lack of replicates.

source_name: SHSY5Y adipocyte diff 7d

extract_protocol:
RNA-seq: RNA was extracted from 6-well dishes using TRI Reagent (Sigma) follwed by chloroform extraction and purification of RNA using Econo Spin columns (Epoch Life Sciences).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 2 µg RNA for preparation of cDNA libraries.

tag: cell line

tag: differentiation status

value: adipocyte

tag: timepoint


title: L419087-22

tag: tissue


title: RNArps25∆48h rep1


title: RNA-seq, SHSY5Y undifferentiated

description:
SH_SY5Y_Msc
RNA_NonMesenchymalCells.txt

source_name: SHSY5Y undifferentiated

value: undifferentiated


title: W457462-23


title: RNArps25∆24h rep1


title: RNArps25∆24h rep2


title: RNA-seq, SHSY5Y osteoblast diff 7d

description:
SH_SY5Y_Ob
RNA_NonMesenchymalCells.txt

source_name: SHSY5Y osteoblast diff 7d

value: osteoblast


title: RNA-seq, PACF1 adipocyte diff 7d

description:
PACF1_Ad
RNA_NonMesenchymalCells.txt

source_name: PACF1 adipocyte diff 7d


title: RNA-seq, PACF1 undifferentiated

description:
PACF1_Msc
RNA_NonMesenchymalCells.txt

source_name: PACF1 undifferentiated


title: RNArps7∆72h rep2


title: RNArps7∆72h rep1


title: RNA-seq, PACF1 osteoblast diff 7d

description:
PACF1_Ob
RNA_NonMesenchymalCells.txt

source_name: PACF1 osteoblast diff 7d


title: RNArps7∆48h rep2


title: RNArps7∆24h rep2


title: RNA-seq, HEK293 osteoblast diff 7d

description:
HEK293_Ob
RNA_NonMesenchymalCells.txt

source_name: HEK293 osteoblast diff 7d


title: RNA-seq, HEK293 adipocyte diff 7d

description:
HEK293_Ad
RNA_NonMesenchymalCells.txt

source_name: HEK293 adipocyte diff 7d


title: Sample 12_300_N+S-_rep3

city: Clermont-Ferrand

first: Titouan

last: Bonnot

address: 5 chemin de Beaulieu

country: France

institute: INRA

description:
12_AGTCAA_L003
processed data file:
GEN150722_N+S-_R.profiling-table

data_processing:
For processing of raw data RTA version 1.18.61 and CASAVA 1.8.4 was used to generate FASTQ-files
Reads were mapped to the T. monococcum reference genome available at the MIPS genome database, using BWA-MEM (version 0.7.12-r1039, http://bio-bwa.sourceforge.net/) tool
Only reads with unique mapping position and a mapping quality score of at least 10 were considered for read counting. Paired-end reads that were mapped to the same reference with about the expected insert size were counted as one read. Paired-end reads that were mapped to different references or with an unexpected insert size were counted as two reads. If only one read of a pair was mapped, it was counted as one read. Single-end reads were used straightforwardly. Only reads overlapping exon-features were counted. All reads mapping to features with the same grouping-tag were summed.
A Trimmed Mean of M-values (TMM) normalization was performed using the ‘edgeR’ package (Robinson et al., 2010; Robinson and Oshlack, 2010) of the R software environment (R Core Team, 2017) to reconstruct transcripts and estimate transcript abundance in counts-per-million (CPM). Genes with a CPM > 1 were considered as expressed.
Genome_build: T. monococcum reference genome available at the MIPS genome database (Mewes, 2002)
ftp://ftpmips.helmholtz-muenchen.de/plants/wheat/IWGSC/IWGSC_genePredictions_of_other_wheat_species/Tm_IWGSC_MIPSv2.0_HighConf_CDS_2014Jul24.fa.gz
Supplementary_files_format_and_content: R.profiling-tables include raw counts and normalized CPM values for each gene and for each sample. Four tables are provided, which correspond to the four treatments used in our experiment. The table 'GEN150722_N-S-_R.profiling-table' contains values for samples corresponding to the N-S- treatment; the table 'GEN150722_N+S-_R.profiling-table' contains values for samples corresponding to the N+S- treatment; the table 'GEN150722-N-S+_R.profiling-table' contains values for samples corresponding to the N-S+ treatment; and the table 'GEN150722_N+S+_R.profiling-table' contains values for samples corresponding to the N+S+ treatment.

molecule: polyA RNA

organism: Triticum monococcum

growth_protocol: Seeds of Triticum monococcum ssp. monococcum (accession ERGE 35821) were germinated on filter paper in Petri dishes moistened with demineralized water, then seedlings were transplanted to 50 mL PVC columns (7.5 cm i.d. × 50 cm deep; 2 seedlings per column) filled with a 2:1 (v/v) mixture of washed perlite:river sand. Columns were placed in a greenhouse to obtain a homogenous plant stand with a density of 512 plant m-2. Air temperature in the greenhouse was controlled at 20°C/15°C (day/night) and an air relative humidity was controlled at 55%/75% (day/night) at the top of the plant stand, with a 16-h photoperiod.

extract_protocol:
RNA were extracted from einkorn grain according to the method used by (Pont et al., 2011). Three biological replicates were used. The 54 grain samples (three replicates at 100 and 200°Cd after anthesis and three replicates × four treatments [N-S-, N+S-, N-S+, N+S+] at 300, 400, 500 and 600°Cd after anthesis) were ground in liquid nitrogen and 4.5 mL of buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.1 M NaCl, 1% SDS) were added to approximately 0.5 g of flour. The supernatant was collected and 3 mL of a 25 : 24 : 1 phenol : chloroform : isoamyl alcohol mixture (v : v) were added to eliminate starch and proteins. Supernatant was collected, and nucleic acids were precipitated by adding 0.1 volume of 3M AcNA (pH5.2) and 2 volumes of 100% ethanol. The pellet was dried under ambient condition for 1 h and dissolved in RNase-free water. A DNAse treatment was then performed using a RNase-Free DNase set (Qiagen) and then a RNeasy MinElute Cleanup kit (Qiagen).
RNA strand-specific libraries were created using commercially available kits according to the manufacturer’s instructions. In brief, polyA-RNA was extracted from total RNA using an oligodT-bead based method. After fragmentation of the mRNA, first and dUTP based second strand synthesis was carried out, followed by end-repair, A-tailing, ligation of the indexed Illumina Adapter and digestion of the dUTP-strand. Size selection was done using a bead based method targeting an average insert size of 150-400 bp. After PCR amplification, the resulting fragments were cleaned up, pooled, quantified and used for cluster generation. For sequencing, pooled libraries were loaded on the cBot (Illumina) and cluster generation was performed using manufacturer’s instructions. Paired-end sequencing using 125 bp read length was performed on a HiSeq2500 machine (HiSeq Control Software 2.2.38) using HiSeq Flow Cell v4 and TruSeq SBS Kit v4.

treatment_protocol: From seedling transplantation to anthesis, each PVC column received 167 mL d-1 of demineralized water. Then four treatments that contained different combinations of N and S supply were applied from 200°Cd to 700°Cd after anthesis: a treatment corresponding to a nutrient solution with no N and S (treatment termed N-S-); a high N and low S treatment (6 mM N and no S, termed N+S-); a low N and high S treatment (0.5 mM N and 2 mM S, termed N-S+); and a high N and S treatment (6 mM N and 2 mM S, termed N+S+). Grains were collected every 100°Cd after anthesis from  100 to 600°Cd for transcriptome analysis.

value: grain

tag: grain developmental stage (°cd after anthesis)

tag: treatment

value: N+S-

tag: replicate


title: RNA-seq, HEK293 undifferentiated

description:
HEK293_Msc
RNA_NonMesenchymalCells.txt

source_name: HEK293 undifferentiated


title: Sample 10_300_N+S-_rep1

description:
10_GGCTAC_L003
processed data file:
GEN150722_N+S-_R.profiling-table


title: Sample 11_300_N+S-_rep2

description:
11_CTTGTA_L003
processed data file:
GEN150722_N+S-_R.profiling-table


title: RNA-seq, EAhy926 adipocyte diff 7d

description:
EAhy926_Ad
RNA_NonMesenchymalCells.txt

source_name: EAhy926 adipocyte diff 7d


title: RNArpl9a∆72h rep2


title: RNArps7∆24h rep1


title: Sample 8_300_N-S-_rep2

description:
8_ACTTGA_L003
processed data file:
GEN150722_N-S-_R.profiling-table

value: N-S-


title: Sample 9_300_N-S-_rep3

description:
9_TAGCTT_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: Z343899-23


title: RNA-seq, EAhy926 undifferentiated

description:
EAhy926_Msc
RNA_NonMesenchymalCells.txt

source_name: EAhy926 undifferentiated


title: Brain_WT_ischemia_Day14

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

hyb_protocol: Expression Hybridization Kit (Agilent)

scan_protocol: DNA Microarray Scanner (2505C, Agilent), Gene Expression Wash Pack (Agilent)

data_processing: Feature Extraction ver 10.7.1.1 (Agielnt)

organism: Mus musculus

source_name: Brain tissue from ischemic WT mice at day14 after stroke onset

label_protocol: One-Color RNA Spike-In Kit, Low Input Quick Amp Labeling Kit (Agilent)

extract_protocol: For brain tissue, total RNA was isolated using QIAzol Lysis Reagent (QIAGEN) from the day 14 post-ischemic or sham brains of WT or DEREG mice (slice 3 on the ischemic side). For CD4+ T cells, total RNA was isolated using a TRIzolTM LS reagent (Invitrogen) from the CD4+ T cells in WT ischemic mice brain or in untreated mice spleen.

value: Brain

tag: cell

value: whole tissue

tag: genotype/variation

value: wild type


title: Brain_WT_sham_Day14

source_name: Brain tissue from sham WT mice

treatment_protocol: For brain tissue, total RNA was isolated using QIAzol Lysis Reagent (QIAGEN) from the day 14 post-ischemic or sham brains of WT or DEREG mice (slice 3 on the ischemic side). For CD4+ T cells, total RNA was isolated using a TRIzolTM LS reagent (Invitrogen) from the CD4+ T cells in WT ischemic mice brain or in untreated mice spleen.


title: J369887-23

source_name: tissue biopsy

tag: subject


title: RNArpl9a∆72h rep1

tag: strain


title: RNA-seq, EAhy926 osteoblast diff 7d

description:
EAhy926_Ob
RNA_NonMesenchymalCells.txt

source_name: EAhy926 osteoblast diff 7d


title: Sample 7_300_N-S-_rep1

description:
7_CAGATC_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: RNArps7∆48h rep1


title: Sample 6_200_N-S-_rep3

description:
6_GCCAAT_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: RNArpl9a∆48h rep2


title: Brain_DEREG_ischemia_Day14

source_name: Brain tissue from ischemic DEREG mice at day14 after stroke onset

value: DEREG


title: RNA-seq, A549 adipocyte diff 7d

description:
A549_Ad
RNA_NonMesenchymalCells.txt

source_name: A549 adipocyte diff 7d


title: RNA-seq, A549 undifferentiated

description:
A549_Msc
RNA_NonMesenchymalCells.txt

source_name: A549 undifferentiated


title: RNArpl9a∆48h rep1


title: Sample 4_200_N-S-_rep1

description:
4_TGACCA_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: Sample 5_200_N-S-_rep2

description:
5_ACAGTG_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: RNArpl9a∆24h rep2


title: RNA-seq, A549 osteoblast diff 7d

description:
A549_Ob
RNA_NonMesenchymalCells.txt

source_name: A549 osteoblast diff 7d


title: Brain_DEREG_sham_Day14

source_name: Brain tissue from sham DEREG mice


title: Sample 3_100_N-S-_rep3

description:
3_TTAGGC_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: 48hr 27µM MP exposed_rep-2

description: 48hr 27µM MP exposed  L4, rep-2

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Custom C.elegans GXP_8X60k Array designed by Genotypic Technology Private Limited. (AMADID: 052672). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

organism: Caenorhabditis elegans

growth_protocol: Wild-type strain (Bristol strain N2), cultured on standard nematode growth medium (NGM) with E. coli OP50 as a food source was grown at 20-22˚C.

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: L4 stage C.elegans were exposed to 2.7µM and 27µMof LC50 of Methyl Parathion and incubated for  24 and 48hrs at 22 ºC in an incubator shaker, along with respective controls.

tag: developmental stage

value: L4 larval stage

value: Hermaphrodite bristol N2


title: RNArpl9a∆24h rep1

tag: genotype


title: ATAC-seq, AT-hMSC-TERT undifferentiated rep2

library_source: genomic

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
ATAC-seq reads were aligned to the hg19 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept.
Sequencing reads from donors of a tissue of origin were pooled to indentify regions enriched of open chromatin using HOMER. ATAC- regions for Human Primary Stromal Cells were merged using Homer with distance option -d given.
ATAC-seq signal was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -noadj. Normalization of sequencing reads was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Donors into the design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain genomic regions identified from ATAC-seq experiments in the immortalized cells and in human primary stromal cells. Peak column in bed files indicate with 1 if the peak was found in the specific samples, 0 indicates absence. Txt file contains non-adjusted gene expression values for eauch replicate and averaged normalized counts and standard deviation for each time point as well as FDR and Log2FC with respect to undifferentiated state for human primary stromal cells. Txt file contains non adjusted quantification of ATAC-seq libraries from human primary stromal cells for two individual donors, averaged normalized counts as well as standard deviations.

molecule: genomic DNA

source_name: AT-hMSC-TERT undifferentiated

extract_protocol:
ATAC-seq: Cells were scrabed off from 6-well dishes in ice cold PBS, centrifuged and permeabilised. Nuclei were rinsed through a cell strainer (10 micro m) and counted. 5.000 nuclei were exposed to 1 micro l transposase as described originally (Buenrostro J D, et. al 2015. Current Protocols in Molecular Biology 109: 1-9).
ATAC-seq libraries were constructed according to the manufacturer's instructions (Illumina).

value: AT-hMSC-TERT


title: 48hr 27µM MP exposed_rep-1

description: 48hr 27µM MP exposed  L4, rep-1


title: 48hr 2.7µM MP exposed_rep-1

description: 48hr 2.7µM MP exposed  L4, rep-1


title: ATAC-seq, BM-hMSC-TERT4 undifferentiated

source_name: BM-hMSC-TERT4 undifferentiated


title: RNArpl38∆72h rep1

tag: fermentation stage


title: 48hr Solvent control_rep-1

description: 48 hr Solvent control L4, rep-1


title: 48hr Solvent control_rep-2

description: 48 hr Solvent control L4, rep-2


title: 48hr 2.7µM MP exposed_rep-2

description: 48hr 2.7µM MP exposed  L4, rep-2


title: RNArpl38∆48h rep2


title: RNArpl38∆48h rep1


title: RNArpl38∆24h rep2


title: Sample 52_600_N+S+_rep1

description:
52_GAGTGG_L005
processed data file:
GEN150722_N+S+_R.profiling-table

value: N+S+


title: Sample 53_600_N+S+_rep2

description:
53_ACTGAT_L005
processed data file:
GEN150722_N+S+_R.profiling-table


title: FC18-1

source_name: Inoculated fruit

extract_protocol:
Two grams of tissue per sample were ground in liquid nitrogen and 10mL of the RNA extraction buffer (CTAB 2% v/v, PVP 2%v/v, 100mMTris pH 8, 2MNaCl, 25mM EDTA, 0.5 g/L spermidine, 10mM β-mercaptoethanol) were added. The samples were immediately incubated for 5min at 65◦C. Two extractions with one equal volume of chloro- form:isoamyl alchohol (24:1, v/v) followed by centrifugation at 4000 rpm for 45 min at 4◦C were performed. The supernatant was recovered and 1/10 volume of 1MKOAc was added followed by centrifugation at 4000 rpm for 20 min at 4◦C. The super- natant was collected and 1/4 volume of 10M LiCl was added. Samples were incubated overnight at−20◦C and then centrifuged at 4000 rpm for 45 min at 4◦C. The supernatant was discarded and the RNA pellet was further purified using the RNeasy Plant Mini Kit (Qiagen®). DNAse treatment (RNase-Free DNase Set,Qiagen®) was done in column during the purification step. The RNA was resuspended in 35µL of nuclease-free water. The RNA concentration and purity were measured using NanoDrop 2000c Spectrophotometer (Thermo Scientific, Inc.). The RNA integrity was checked by agarose gel electrophoresis.
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

tag: ripening stage

value: RR

tag: days post inoculation

tag: agent

value: Rhizopus stolonifer


title: Sample 54_600_N+S+_rep3

description:
54_ATTCCT_L005
processed data file:
GEN150722_N+S+_R.profiling-table


title: FC17-50


title: Sample 2_100_N-S-_rep2

description:
2_CGATGT_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: RNArpl38∆72h rep2


title: 24hr 27µM MP exposed_rep-1

description: 24hr 27µM MP exposed  L4, rep-1


title: RNArpl38∆24h rep1


title: Sample 1_100_N-S-_rep1

description:
1_ATCACG_L003
processed data file:
GEN150722_N-S-_R.profiling-table


title: Sample 50_600_N-S+_rep2

description:
50_GTTTCG_L005
processed data file:
GEN150722-N-S+_R.profiling-table

value: N-S+


title: 24hr 2.7µM MP exposed_rep-2

description: 24hr 2.7µM MP exposed  L4, rep-2


title: 24hr 27µM MP exposed_rep-2

description: 24hr 27µM MP exposed  L4, rep-2


title: ATAC-seq, AT-hMSC-TERT undifferentiated rep1

tag: cell line


title: RNAwt72h rep2

value: wt


title: FC17-26


title: 24 hr Solvent control_rep-1

description: 24 hr Solvent control L4, rep-1


title: Sample 51_600_N-S+_rep3

description:
51_CGTACG_L005
processed data file:
GEN150722-N-S+_R.profiling-table


title: RNAwt72h rep1


title: Sample 49_600_N-S+_rep1

description:
49_GTGGCC_L005
processed data file:
GEN150722-N-S+_R.profiling-table


title: 24 hr Solvent control_rep-2

description: 24 hr Solvent control L4, rep-2


title: DH-43

description: Gene expression after 48hrs 0.312 µM Methyl parathion

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent designed Drosophila_GXP_8x60K (AMADID: 039596) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

organism: Drosophila melanogaster

source_name: Test sample-2_48 hrs 0.312 µM Methyl parathion

growth_protocol: Drosophila was maintained on standard Drosophila food (maize powder, sugar, yeast, nipagin and propionic acid) at 23-25˚C.

treatment_protocol: Drosophila were exposed to 0.0312 & 0.312 µM Methyl parathion concentrations for 24 and 48hrs, along with DMSO(< 0.03%) controls.

tag: age

value: 1 day old flies

tag: gender

value: Male


title: 24hr 2.7µM MP exposed_rep-1

description: 24hr 2.7µM MP exposed  L4, rep-1


title: FC17-73

value: MG


title: RNAwt48h rep2


title: Sample 47_600_N+S-_rep2

description:
47_GTCCGC_L005
processed data file:
GEN150722_N+S-_R.profiling-table

tag: tissue

value: grain

value: N+S-


title: RNAwt48h rep1


title: FC17-49


title: RNAwt24h rep2


title: Sample 45_600_N-S-_rep3

description:
45_TAGCTT_L005
processed data file:
GEN150722_N-S-_R.profiling-table

tag: grain developmental stage (°cd after anthesis)

value: N-S-


title: Sample 46_600_N+S-_rep1

description:
46_GGCTAC_L005
processed data file:
GEN150722_N+S-_R.profiling-table

tag: treatment


title: FC17-25


title: RNAwt24h rep1


title: FC17-20


title: FC17-16


title: Sample 44_600_N-S-_rep2

description:
44_ACTTGA_L005
processed data file:
GEN150722_N-S-_R.profiling-table

tag: replicate


title: Sample 48_600_N+S-_rep3

description:
48_GTGAAA_L005
processed data file:
GEN150722_N+S-_R.profiling-table


title: FC17-12


title: DH 42


title: DG 42

description: Gene expression after 48hrs 0.0312 µM Methyl parathion

source_name: Test sample-1_48 hrs 0.0312 µM Methyl parathion


title: Sample 43_600_N-S-_rep1

description:
43_CAGATC_L005
processed data file:
GEN150722_N-S-_R.profiling-table


title: FC17-8


title: Sample 42_500_N+S+_rep3

description:
42_GCCAAT_L005
processed data file:
GEN150722_N+S+_R.profiling-table


title: FC17-4


title: 3492A: Adenoma of Patient 3492

source_name: Patient 3492

tag: patient id

value: Female

value: Adenoma

tag: adenomadiagnosis

value: Tubulovillous Adenoma

tag: tnm

tag: uicc


title: Sample 41_500_N+S+_rep2

description:
41_ACAGTG_L005
processed data file:
GEN150722_N+S+_R.profiling-table


title: FC17-15


title: Sample 40_500_N+S+_rep1

description:
40_TGACCA_L005
processed data file:
GEN150722_N+S+_R.profiling-table


title: FC17-7


title: FC17-3


title: DF 41

description: Gene expression after 48hrs 0 µM Methyl parathion

source_name: Test Control_ 48 hrs


title: DG 41


title: FC18-2

value: Fusarium acuminatum


title: Sample 38_500_N-S+_rep2

description:
38_CGATGT_L005
processed data file:
GEN150722-N-S+_R.profiling-table


title: Sample 39_500_N-S+_rep3

description:
39_TTAGGC_L005
processed data file:
GEN150722-N-S+_R.profiling-table


title: Sample 37_500_N-S+_rep1

description:
37_ATCACG_L005
processed data file:
GEN150722-N-S+_R.profiling-table


title: DD22

description: Gene expression after 24hrs 0.312 µM Methyl parathion

source_name: Test sample-2_24 hrs 0.312 µM Methyl parathion


title: DC 24

description: Gene expression after 24hrs 0.0312 µM Methyl parathion

source_name: Test sample-1_24 hrs 0.0312 µM Methyl parathion


title: 11197

type: protein

city: Salt Lake City

first: Sheri

last: Holmen

state: UT

address: 2000 Circle of Hope Dr.

department: Surgery

institute: University of Utah

description: quality control exclusion

hyb_protocol: Lysates were arrayed on nitrocellulose-coated slides, probed with 304 antibodies by tyramide-based signal amplification, and visualized by DAB colorimetric reaction

scan_protocol: Array-Pro Analyzer was used to quantify 16-bit TIFF images produced by slides scanned on a flatbed scanner

data_processing: Relative protein levels were determined by interpolation of each dilution curve from the standard curve of the slide. All data points were normalized for protein loading and transformed to a linear value.

molecule: protein

source_name: melanoma

label_protocol: Each slide was probed with a validated primary antibody plus a biotin-conjugated secondary antibody

growth_protocol: Dct::TVA model used to generate primary tumors used in analyses

extract_protocol: Protein extraction was performed using RPPA lysis buffer. Cellular proteins were denatured by 1% SDS (with Beta-mercaptoethanol) and diluted in five 2-fold serial dilutions in dilution lysis buffer.

treatment_protocol: Frozen primary tumor samples were embedded in optimal cutting temperature compound (OCT). A 5 µm H&E-stained slide was prepared from each sample and reviewed by a pathologist for regions containing 70% or more viable tumor. Marked H&E slides were then used to guide macrodissection of viable tumor from the OCT blocks.

tag: strain

value: sacrified day 49


title: 11192

description: quality control exclusion

tag: genotype

value: sacrified day 56


title: DC 21


title: CH79-2: whole plant tissues of CH79 at tillering stage, biological rep2

city: Kunming

first: Dongsun

last: Lee

state: Yunnan

address: Fengyuan

department: Rice Research Institute

institute: Yunnan Agricultural University

description: Gene expression data from whole plant tissues of F1 hybrids between CH7 and CH9 at tillering stage

hyb_protocol: Affymetrix expression GeneChip hybridization was conducted by CapitalBio Technology (Beijing, China).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000.

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

organism: Oryza sativa Japonica Group

label_protocol: Labelled cRNA synthesis was conducted by CapitalBio Technology (Beijing, China).

growth_protocol: The rice seeds employed for this study were germinated in distilled water and grown in a greenhouse under natural growth conditions.

extract_protocol: Total RNA extraction was conducted by CapitalBio Technology (Beijing, China).

treatment_protocol: Whole rice plants were sampled and cutted into small pieces, then samples were frozen by liquid nitrogen and stored under -80℃

value: whole plant

tag: developmental stage

value: tillering

tag: line

value: CH7/CH9 F1 hybrid


title: FC17-58

tag: ripening stage

value: RR

tag: days post inoculation


title: DF 42


title: CH78-2: whole plant tissues of CH78 at tillering stage, biological rep2

description: Gene expression data from whole plant tissues of F1 hybrids between CH7 and CH8 at tillering stage

value: CH7/CH8 F1 hybrid


title: DB22

description: Gene expression after 24hrs 0 µM Methyl parathion

source_name: Test Control_ 24 hrs

value: 1 day old flies


title: DD21

value: Male


title: CH89-2: whole plant tissues of CH89 at tillering stage, biological rep2

description: Gene expression data from whole plant tissues of F1 hybrids between CH8 and CH9 at tillering stage

value: CH8/CH9 F1 hybrid


title: DB21


title: CH78-1: whole plant tissues of CH78 at tillering stage, biological rep1


title: FC17-34

tag: agent


title: CH89-1: whole plant tissues of CH89 at tillering stage, biological rep1


title: CH9-1: whole plant tissues of CH9 at tillering stage, biological rep1

description: Gene expression data from whole plant tissues of CH9 at tillering stage


title: 11355

tag: age

value: sacrified day 46


title: Sample 35_500_N+S-_rep2

description:
35_CGTACG_L004
processed data file:
GEN150722_N+S-_R.profiling-table

value: grain

value: N+S-


title: CH9-2: whole plant tissues of CH9 at tillering stage, biological rep2


title: 11361

value: sacrified day 53


title: CH79-1: whole plant tissues of CH79 at tillering stage, biological rep1


title: CH8-2: whole plant tissues of CH8 at tillering stage, biological rep2

description: Gene expression data from whole plant tissues of CH8 at tillering stage


title: Sample 34_500_N+S-_rep1

description:
34_GTTTCG_L004
processed data file:
GEN150722_N+S-_R.profiling-table


title: FC17-57

value: MG


title: 11360


title: Sample 33_500_N-S-_rep3

description:
33_GTGGCC_L004
processed data file:
GEN150722_N-S-_R.profiling-table

value: N-S-


title: Sample 36_500_N+S-_rep3

description:
36_GAGTGG_L004
processed data file:
GEN150722_N+S-_R.profiling-table


title: FC17-33

value: Fusarium acuminatum


title: 11358


title: CH8-1: whole plant tissues of CH8 at tillering stage, biological rep1


title: Sample 32_500_N-S-_rep2

description:
32_GTGAAA_L004
processed data file:
GEN150722_N-S-_R.profiling-table


title: FC17-18


title: FC17-14


title: Sample 30_400_N+S+_rep3

description:
30_CCGTCC_L004
processed data file:
GEN150722_N+S+_R.profiling-table

value: N+S+


title: Sample 31_500_N-S-_rep1

description:
31_GTCCGC_L004
processed data file:
GEN150722_N-S-_R.profiling-table


title: FC17-10


title: 10819


title: 10996

value: sacrified day 58


title: FC17-81


title: 11017

description: quality control exclusion

value: sacrified day 44


title: 10995

value: sacrified day 88


title: FC17-6


title: Sample 28_400_N+S+_rep1

description:
28_AGTTCC_L004
processed data file:
GEN150722_N+S+_R.profiling-table


title: Sample 29_400_N+S+_rep2

description:
29_ATGTCA_L004
processed data file:
GEN150722_N+S+_R.profiling-table


title: CH7-2: whole plant tissues of CH7 at tillering stage, biological rep2

description: Gene expression data from whole plant tissues of CH7 at tillering stage

value: whole plant

value: tillering


title: FC17-13


title: Sample 27_400_N-S+_rep3

description:
27_AGTCAA_L004
processed data file:
GEN150722-N-S+_R.profiling-table

value: N-S+


title: CH7-1: whole plant tissues of CH7 at tillering stage, biological rep1


title: FC17-9


title: iPSC-NCCs (inflamed condition) 2

city: Kobe

first: Shota

last: Fujii

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: The Laboratory for Retinal Regeneration

institute: RIKEN Center for Developmental Biology

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.

source_name: coculture with a mix of PBMCs for 5 days

growth_protocol: We induced NCCs from human iPSCs according to the previously described method with some modifications for 3 weeks to complete.  After the differentiation, iPSC-NCCs were harvested in a 12-well culture plate. The medium was RPMI 1640 (Nacalai Tesque) containing 10% FBS supplemented with human recombinant interleulin-2 (BD).  iPSC-NCCs (normal condition, 1.0 x 10^6 cells/well) were incubated in the absence of the transwell membrane. On the other hand, iPSC-NCCs (inflamed condition, 1.0 x 10^6 cells/well) were incubated in the presence of the transwell membrane. A mix of the human peripheral blood mononuclear cells (PBMCs, 3.0 x 10^6 cells/well) from 5 healthy donors were added to the upper wells of a transwell plate. PBMCs were obtained Lymphoprep (Stemcell technologies) density gradient centrifugation in accordance with the manufacturer’s instructions.

extract_protocol: The total RNA of iPSC-NCCs (normal condition, n=2) and iPSC-NCCs (inflamed condition, n=2) were extracted by High Pure RNA Isolation Kit (Roche) after the cells were incubated for 5 days.

tag: cell line

tag: cell type

value: neural crest cell


title: FC17-5


title: 9868

description: quality control exclusion

value: sacrified day 48


title: 10932

value: sacrified day 49


title: FC17-1


title: Sample 25_400_N-S+_rep1

description:
25_GGCTAC_L004
processed data file:
GEN150722-N-S+_R.profiling-table

tag: tissue

tag: grain developmental stage (°cd after anthesis)


title: Sample 24_400_N+S-_rep3

description:
24_TAGCTT_L004
processed data file:
GEN150722_N+S-_R.profiling-table

tag: treatment

tag: replicate


title: FC18-3

value: RR

value: Botrytis cinerea


title: 8195

value: sacrified day 37


title: iPSC-NCCs 2

description: neural crest 2

source_name: iPSC-NCCs

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

growth_protocol: The iPSCs were cultured under the feeder-free and serum-free condition with AK03N medium (Ajinomoto) on the 6-well culture plate coated with iMatrix-511 (Nippi).  After the undifferentiated iPSCs reached confluence in culture, the iPSCs were dissociated with Accutase (Millipore) and seeded first on the 3-D culture plate (EZSPHERE®, AGC TECHNO GLASS) at a density of 2×10^5 cells/mL in embryoid body (EB) induction medium which composed from DMEM/F12 (Sigma-Aldrich) supplemented with 1% N-2 (GIBCO), 2% MACS® NeuroBrew-21 (Miltenyi Biotec), 2 mM L-glutamine (Sigma-Aldrich), 20 ng/ml recombinant human epidermal growth factor (EGF: PeproTech), 1% penicillin/streptomycin (GIBCO) and 10 μM Y-27632 (Wako). The spent medium was changed once on EB culture day 4 and uniformly sized EBs were formed in 7 days. Subsequently, the EBs were replated on non-coated 10 cm dish in NCCs induction medium, DMEM/F12 with 1% N-2, 2 mM L-glutamine, 1% penicillin/streptomycin, 20 ng/ml EGF, 20 ng/ml recombinant human fibroblast growth factor-basic (bFGF: Wako), and 5 μg/ml heparin (Sigma-Aldrich). To allow the EBs to attach the culture dish and induced NCCs to migrate from the attached EBs, the culture dish was stand for first 3 days and the spent medium was changed on days 4, 8, 11, 13, and 14 after re-plating of the EBs. NCCs induction was completed on day 14. .

extract_protocol: The total RNA of iPSCs (n=2) and iPSC-NCCs (n=2) were extracted by High Pure RNA Isolation Kit (Roche) after the cells were harvested.

value: iPSCs-derived neural crest cells (NCCs)

tag: time point

value: at the end of the induction


title: iPSC-NCCs (normal condition) 1

source_name: monoculture for 5 days


title: iPSC-NCCs (inflamed condition) 1


title: Sample 23_400_N+S-_rep2

description:
23_ACTTGA_L004
processed data file:
GEN150722_N+S-_R.profiling-table

value: grain

value: N+S-


title: 9819

value: sacrified day 34


title: FC17-90


title: iPSC-NCCs (normal condition) 2


title: iPSC-NCCs 1

description: neural crest 1


title: 10930

description: quality control exclusion

value: sacrified day 75


title: Sample 22_400_N+S-_rep1

description:
22_CAGATC_L004
processed data file:
GEN150722_N+S-_R.profiling-table


title: Sample 26_400_N-S+_rep2

description:
26_CTTGTA_L004
processed data file:
GEN150722-N-S+_R.profiling-table


title: 7873


title: FC17-42


title: Sample 21_400_N-S-_rep3

description:
21_GCCAAT_L004
processed data file:
GEN150722_N-S-_R.profiling-table

value: N-S-


title: Sample 20_400_N-S-_rep2

description:
20_ACAGTG_L004
processed data file:
GEN150722_N-S-_R.profiling-table


title: BB9

value: MG


title: BB8


title: 9389

description: quality control exclusion


title: iPSCs 1

description: iPS 1

source_name: iPSCs

tag: source cell type

value: adult skin fibroblast derived, passage 61

value: human induced pluripotent stem cells (iPSCs)


title: 4083

value: sacrified day 40


title: unripening Mutant 2  Turning_rep 2_3

description: Gene expression at Turning  stage of  unripeningMutant 2

source_name: Unripening Mutant 2  Turning stage of Fruit ripening

growth_protocol: Wild type (Solanum lycopersicum) and Unripening Mutant tomato plants were grown in a greenhouse with supplementary lighting providing an irradiance of 250–400 l mol m-2 s-1. Individual tomato plants were grown in pots (20 cm diameter) containing compost supplemented with appropriate fertilizers. Plants were watered daily and fruit were tagged at anthesis and harvested when they had reached the appropriate developmental stage. Individual fruit were removed from the plant, weighed, kept in RNA Later, and stored at -80 c until required.

treatment_protocol: Pericarp tissue was selected for microarray analysis. The tissue was collected at Mature Green (MG), Breaker (BR), Turning (TR), and Fully Ripen (FR) stages from unripening mutant and Wild type. Fruits were collected from green house and transfer immediately into thermocouple boxes. Sterile working area was prepared by wiping the working area surface with 1% hypochlorite bleach. Samples were dissected wearing new Nitrile gloves which were wiped with 1% hypochlorite. Pre labelled RNA free 2 ml tubes filled with 1.5 ml RNALater (RLT) solution were placed in working area for sample collection. The samples were kept in sterile petri plate and the tissue was sliced 3 mm or less in size and then transferred immediately in labelled vial containing RNALater (1.5 ml) and this step was finished within 90 seconds (Long time might degrade RNA). Each sample was prepared in triplicates containing 10-15 small pieces and the tissue was stored at -80 °C until to carry out the further experiment.

value: Fruit  tissue

value: Turning


title: Sample 19_400_N-S-_rep1

description:
19_TGACCA_L004
processed data file:
GEN150722_N-S-_R.profiling-table


title: 7788

value: sacrified day 42


title: 3125

value: sacrified day 41


title: Sample 18_300_N+S+_rep3

description:
18_GTGGCC_L003
processed data file:
GEN150722_N+S+_R.profiling-table

value: N+S+


title: BI16-118

value: RR

value: Botrytis cinerea


title: iPSCs 2

description: iPS 2


title: Sample 17_300_N+S+_rep2

description:
17_GTGAAA_L003
processed data file:
GEN150722_N+S+_R.profiling-table


title: unripening Mutant 2 Breaker_rep 2_2

description: Gene expression at Breaker stage of unripening Mutant 2

source_name: Unripening  Mutant 2 Breaker stage of Fruit ripening

value: Fruit tissue

value: Breaker


title: Sample 16_300_N+S+_rep1

description:
16_GTCCGC_L003
processed data file:
GEN150722_N+S+_R.profiling-table

value: grain


title: BI16-70


title: 3126

description: quality control exclusion

value: sacrified day 59


title: 3971

value: sacrified day 36


title: BI16-46


title: Sample 15_300_N-S+_rep3

description:
15_CCGTCC_L003
processed data file:
GEN150722-N-S+_R.profiling-table

value: N-S+


title: 3143

value: sacrified day 53


title: BI16-16


title: 4326

value: sacrified day 46


title: Sample 14_300_N-S+_rep2

description:
14_ATGTCA_L003
processed data file:
GEN150722-N-S+_R.profiling-table


title: BB7

value: MG


title: Sample 13_300_N-S+_rep1

description:
13_AGTTCC_L003
processed data file:
GEN150722-N-S+_R.profiling-table


title: 5477

description: quality control exclusion

value: sacrified day 65


title: Wild Type Turning_rep 1_3

description: Gene expression at Turning stage of Wild type

source_name: Wild type Turning stage of fruit ripening

value: Fruit  tissue


title: BI16-93


title: Wild Type Ripening_ rep 1-4

description: Gene expression at Ripening stage of Wild type

source_name: Wild type Ripening stage of Fruit ripening

value: Ripening


title: 5548


title: unripening Mutant 2 Ripening_rep 2_4

description: Gene expression at Ripening stage of unripening Mutant 2

source_name: Unripening Mutant 2 Ripening stage of Fruit ripening


title: Wild Type Breaker_rep 1_2

description: Gene expression at Breaker stage of Wild type

source_name: Wild type Breaker stage of fruit ripening


title: Deficient-rep1-cold

city: Beijing

first: wenxin

last: song

address: Hai Dian, Beijing

institute: Tsinghua university

data_processing:
BaseCall1.1.0 software was used for basecalling.
SOAPnuke 1.5.2 software was used for data filtering steps
HISAT2 v2.0.4 software was used for read alignment
RSEM v1.2.12 software was used for abundance measurement
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: inguinal white adipose tissue_Oct3 deficient_4C

extract_protocol:
WAT were removed, flash frozen on dry ice, and RNA was harvested using using the RNeasy Lipid Mini Kit (Qiagen, Hilden, Germany).
Quality of RNA was analyzed using the Agilent 2100 (Agilent Technologies, Palo Alto, Calif.). The poly-A-containing mRNA was purified by using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented into small pieces using divalent cations under elevated temperature. RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. A single 'A' base was added to cDNA fragments and the adapter was subsequently ligated. The products were then purified and enriched with PCR amplification. PCR yield was quantified by Qubit and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.  DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and had 50 bp of single end read through the BGISEQ-500 platform. The DNA nanoball-based nanoarrays and stepwise sequencing were combined using Combinational Probe-Anchor Synthesis Sequencing Method and analyzed.

value: inguinal white adipose tissue

value: Oct3 deficient


title: BI16-69

source_name: Inoculated fruit


title: Deficient-rep2-cold


title: BI16-45


title: 5611

value: sacrified day 37


title: BI16-117


title: 7472

value: sacrified day 71


title: Control-rep1-cold

value: Control


title: Wild Type Mature Green_ rep 1_1

description: Gene expression at Mature green stage of Wild type

source_name: Wild type Mature green stage of  fruit ripening

value: Mature green


title: WT H3 Input

status: Public on Nov 30 2018

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq reads were first trimmed for possible adapter contamination using cutadapt (v1.10), (Martin, 2011) with the recommended sequence for Illumina adapters as well as a minimum read length of 36 base pairs (bp). Low quality reads were then filtered with fastq_quality_filter, a function within the fastx-toolkit (v0.0.14), with command line options -p 90 and -q 20 to keep reads with at least a 20 Phred score at a minimum of 90% of the bases. Reads were then aligned to the sacCer3 genome using STAR (v2.5.2b), (Dobin et al., 2013) and the following options: --quantMode TranscriptomeSAM, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. A GTF file was given for the --sjdbGTFfile option that was generated in house combining the sacCer3 RefSeq and ERCC spike-in GTFs. Finally, the Salmon (v0.8.1), (Patro et al., 2017) function quant was used to quantify RNA counts over each gene, and DESeq2 (v1.14.1), (Love et al., 2014) was used to calculate differential genes.    Stranded RNA-seq allows us to map reads to specific strands, so all aligned reads were assigned sense or antisense based on whether they overlapped sacCer3 RefSeq genes in the same or opposite strand, respectively. Reads that didn’t overlap any gene were discarded for any stranded analyses as we couldn’t confidently assign them sense/antisense. Unfortunately, overlapping genes cause reads to be assigned to both sense and antisense, so regions of gene overlap plus 49bp on either side (to account for read length) were subtracted out using bedtools (v2.26), (Quinlan and Hall, 2010), and expression of the remaining regions was re-quantified. Antisense cryptic transcripts were identified using previously published methods with no changes except using a minimum of 0.5 RPKM versus their previous minimum of 4.0 FPKM (Dejean, 1970). File conversions were done with samtools (v1.3.1, (Li et al., 2009) and in-house scripts.  Reads were initially aligned and processed as paired end fragments, however signal tracks demonstrated an unusual pile-up of reads at specific and consistent locations across the gene that only occurred in the “R1” reads. To eliminate potential biases this may have added to downstream analyses, we only used the “R2” reads in this work. As no global transcriptional changes were observed using the ERCC spike-in, ERCC reads were removed from the dataset and not used for downstream analysis or quantification.
ChIP-seq reads were first trimmed for possible adapter contamination using cutadapt (v1.10), (Martin, 2011) with the recommended sequence for Illumina adapters as well as a minimum read length of 36 base pairs (bp). Low quality reads were then filtered with fastq_quality_filter, a function within the fastx-toolkit (v0.0.14), with command line options -p 90 and -q 20 to keep reads with at least a 20 Phred score at a minimum of 90% of the bases. To eliminate possible PCR artifacts from library preparation, we used in-house scripts to keep at most 5 reads that had the same sequence, where those above that threshold were filtered out. As this was paired end sequencing, we used in-house scripts to re-synchronize the reads that were kept into proper, ordered pairs between “R1” and “R2” fastqs for alignment. Reads were then aligned to the sacCer3 genome using STAR (v2.5.2b), (Dobin et al., 2013) and the following options: --outFilterMultimapNmax 1, --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. The sacCer3 RefSeq GTF file was given for the option --sjdbGTFfile. Samtools (v1.3.1) (Li et al., 2009) was used to eliminate alignments that did not contain properly paired reads or were not primary alignments. Bigwigs were then made using genomeCov within bedtools (v2.26), (Quinlan and Hall, 2010) as well as tool bedGrapthToBigWig (Kent et al., 2010).     To identify genes that had low 5’ levels of Spt6 ChIP-seq signal in spt6S8A8 relative to WT, we calculated the log2 ratio of average signal between the first and second half of each gene for both spt6S8A8 and WT. The variance of this score was calculated across three replicates, and genes with variance >0.01 for either spt6S8A8 or WT were removed to select genes with consistent signal across replicates. For the remaining genes, the difference of ratios between spt6S8A8 and WT were calculated (i.e., log2(avg(WT first half signal)/avg(WT second half signal) )- log2(avg(S8A first half signal)/avg(S8A second half signal) )). Those with a score of 0.15 or greater were selected for downstream analyses.
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig files for the stranded RNA-seq were provided, and represent read-depth normalized sense or antisense signal genome-wide.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: WT, spt6S8A, Spt6S8E and spt6-1004 alleles were grown in YPD. For RNAseq and ChiPseq experiemnts, Overnight saturated cultures were diluted back to an ON of 0.2 and were allowed to grow until  they reached an optical density of 1.  They were collected and flash frozen in liquid nitrogen for RNA extraction and fixed in 1% Formaldehyde for 15 minutes and quenched with glycine and sonicated uisng established conditions as described in the proocol.

extract_protocol:
Yeast cultures of the indicated genotypes were grown at 30C and in YPD conditions and used for RNA extraction using acid phenole method  as described in materials and methods. ChIPs were performed as described in materials and methods with anti-H3 antibody. Isolated ChiP DAN was quantified  and used for the generation of libraries using Kappa Hyper kit.
For RNA seq: RNA was extracted using acid-phenol method (Collart and Oliviero, 2001) and was quantified spectrophotometrically. 2.5g of total RNA was used to deplete rRNA using the Ribo-zero kit (Illumina). ERCC spike-in controls were added to the RNA samples after rRNA clean-up and before proceeding on to the library preparation. Stranded RNA-seq libraries were prepared using TruSeq Stranded Total RNA sample preparation according to manufacturer’s instructions.  The libraries were sequenced on Illumina HiSeq 2500, paired-end 50bp reads).  For ChiP-seq ChIP was performed as described in the text and libraraies were prepared using akppa hyprep kit using manufacturers instructions.

treatment_protocol: Yeast cells of the indicated genotypes were grown as described above. Other than fixing the cells for ChIPs no special treatments were followed.  For ChIP seq, clarified sonicated lysates were incubated with anti H3 antibody to assess nucleosome occupancy changes

tag: antibody

value: input

value: WT


title: 5613

tag: strain


title: spt6-S8E H3 ChIP Rep2

tag: genotype


title: 5474

value: sacrified day 51


title: unripening Mutant 2 Mature Green_rep 2_1

description: Gene expression at Mature green stage of unripening Mutant 2

source_name: Unripening Mutant 2  Mature Green stage of Fruit ripening

tag: developmental stage


title: Control-rep2-cold


title: tSBE2-Vp64 H3K27me3

type: genomic

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: H3K27me3 ChIP-chip

hyb_protocol: The labeled ChIP DNA was hybridized for 16-18 h at 42C, and then washed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html). A custom 3x720K mouse tiling array (NimbleGen, Roche) containing 179,493 unique probes from different genomic regions, with each probe represented by 4 replicates, was used.

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray scanner (Roche) using 100% laser power and 2μm resolution.

data_processing: Raw signal intensity values were averaged across replicate probes (4 replicated per unique probe sequence). Averaged signal intensities were subsequently corrected for dye bias between each pair of co-hybridised ChIP and input samples using loess normalisation. Corrected values were then transformed into log2 ChIP/Input ratios and scale normalised across all like-sample types (e.g. H3K27ac and H3K27me3 ChIP samples). For visualisation, normalised log2 intensity ratios were assigned to the mm9 location of the probe sequence. UCSC browser compatible visualisation parameters were added to the description track of each ‘.wig’ browser file.

source_name: H3K27me3 ChIP DNA from 46c ESC

label_protocol: One microgram of genomic DNA was amplified and labelled with Cy3 or Cy5 by random priming according to the Agilent ChIP-chip protocol (Roche).

growth_protocol: GMEM+ Supplement

extract_protocol: Nuclei from 3x10e6 mESCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012). Antibodies used for ChIP were H3K27ac (Millipore 07-360) and H3K27me3 (Millipore 07-449).

treatment_protocol: ESC transfected with tSBE2-Vp64 plasmid.

value: 46c ESCs

tag: transfection

tag: chip antibody

source_name: Input DNA from 46c ESCs


title: BI16-15

tag: ripening stage

tag: days post inoculation

value: Botrytis cinerea


title: spt6-S8E RNA Rep1

description:
spt6-S8E_allRepsMerged_senseReads_R2.bw
spt6-S8E_allRepsMerged_antisenseReads_R2.bw


title: spt6-S8A RNA Rep1

description:
spt6-S8A_allRepsMerged_senseReads_R2.bw
spt6-S8A_allRepsMerged_antisenseReads_R2.bw


title: WT RNA Rep2

description:
WT_allRepsMerged_senseReads_R2.bw
WT_allRepsMerged_antisenseReads_R2.bw


title: spt6-S8A H3 ChIP Rep2


title: WT H3 ChIP Rep2


title: spt6-S8E RNA Rep3


title: WT H3 ChIP Rep1


title: WT RNA Rep3


title: spt6-S8A H3 ChIP Rep1


title: spt6-S8E H3 ChIP Rep1


title: WT RNA Rep1


title: spt6-S8A RNA Rep3


title: Histone_6hoursSPhase

first: Christopher

last: Holmquist

address: 208 Fordham Hall

institute: UNC Chapel Hill

description: Sample 3

data_processing:
Basecalls performed using CASAVA v. 1.8.2
Reads were aligned to hg19 (including custom chromosome containing histone genes) using Bowtie2
The AppEnD algorithm was used to identify 3' tails
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing 3' tails generated using AppEnD

source_name: Hct116 Cells

growth_protocol: Hct116 cells were plated at 2X10^5 cells per well in 6 well plate and synchronized by double thymidine block.

extract_protocol:
Total RNA was extracted with Trizol.
Libraries were prepared with Illumina sequences using two limited rounds of PCR after ligation of a custom linker to the 3' end of the RNA; cDNA was synthesized with a primer to the custom linker. Histone specific primers were used to amplify all H2A and H2B transcripts.

treatment_protocol: For Sample 2, cells were treated with 5mM hydroxyurea for 20 minutes after 3 hours release into S-Phase.

tag: 3' linker

value: SOLID Reverse

value: colon cancer cell

tag: protocol

value: Samples taken 6 hours at the end of S-Phase


title: spt6-1004 RNA Rep1

description:
spt6-1004_allRepsMerged_senseReads_R2.bw
spt6-1004_allRepsMerged_antisenseReads_R2.bw


title: Histone_20minHU

description: Sample 2

tag: cell line

tag: cell type

value: Cells treated with 5mM Hydroxyurea for 20 minutes, 3 hours into S-Phase


title: spt6-S8A RNA Rep2


title: spt6-1004 RNA Rep2


title: Histone_3hoursSPhase

description: Sample 1

value: Samples taken 3 hours into S-Phase


title: spt6-S8E RNA Rep2


title: spt6-1004 RNA Rep3


title: tShh-Vp64 H3K27ac

description: H3K27ac ChIP-chip

source_name: H3K27ac ChIP DNA from 46c ESC

treatment_protocol: ESC transfected with tShh-Vp64 plasmid.


title: eGFP H3K27ac

description: H3K27ac ChIP-chip

treatment_protocol: ESC transfected with eGFP-N1 plasmid.


title: tShh-Vp64 H3K27me3

description: H3K27me3 ChIP-chip


title: eGFP H3K27me3

description: H3K27me3 ChIP-chip


title: tSBE6-Vp64 H3K27ac

description: H3K27ac ChIP-chip

treatment_protocol: ESC transfected with tSBE6-Vp64 plasmid.


title: Bru_H2O_DRB10m

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: IP of BrU-labeled nascent RNA

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7. Custom software was used to remove duplicates from NET-seq libraries: https://github.com/sheridar/TFIISdn_paper.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: BigWig

source_name: HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

extract_protocol:
After treatment, cells were scaped in trizol, BrU-labeled RNA was isolated by IP
20-100 ng of RNA was used with the KAPA RNA HyperPrep Kit (KR1350)

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min

tag: growth conditions

value: DMEM 10% FCS, +hygromycin, +blasticidin, +DRB

value: Mouse B44 anti-BrU

tag: molecule

value: Nascent RNA


title: Bru_H2O_DRB5m

description: IP of BrU-labeled nascent RNA

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 5 min


title: Bru_Dox_DRB10m

description: IP of BrU-labeled nascent RNA

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB


title: Bru_H2O_DMOG_r2

description: IP of BrU-labeled nascent RNA

treatment_protocol: Uninduced control cells were treated with 2 mM DMOG for 16 hrs

value: DMEM 10% FCS, +hygromycin, +blasticidin, +DMOG


title: Bru_H2O_r1

description: IP of BrU-labeled nascent RNA

treatment_protocol: Uninduced control cells

value: DMEM 10% FCS, +hygromycin, +blasticidin


title: Bru_Dox_r1

description: IP of BrU-labeled nascent RNA

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline


title: Bru_H2O_DRB20m

description: IP of BrU-labeled nascent RNA

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 20 min


title: Bru_Dox_r2

description: IP of BrU-labeled nascent RNA


title: tSBE2-Vp64 H3K27ac

description: H3K27ac ChIP-chip


title: Bru_Dox_DMOG_r1

description: IP of BrU-labeled nascent RNA

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 2 mM DMOG for 16 hrs

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DMOG


title: Bru_Dox_DRB5m

description: IP of BrU-labeled nascent RNA

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 5 min


title: Bru_Dox_DMOG_r2

description: IP of BrU-labeled nascent RNA


title: Bru_H2O_r2

description: IP of BrU-labeled nascent RNA


title: Bru_H2O_DMOG_r1

description: IP of BrU-labeled nascent RNA


title: Bru_Dox_DRB20m

description: IP of BrU-labeled nascent RNA

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 20 min


title: GRO-seq pro-B cell [12379]

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
BrdU-incorporated RNA
GRO-seq pro-B cell [12379] Rag2(–/–)

data_processing:
Library strategy: Gro-Seq
The database generation of RefSeq-annotated genes was performed as previously described (Wöhner et al., 2016). To refine the annotation of immunoglobulin genes, the immunoglobulin l light-chain segments were replaced with their corresponding converted GRCm38.p3 annotations (Ensembl version 79) (Yates et al., 2016). The resulting number of genes was 24,732.
In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 nucleotides and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al, 2009).
In case of ChIP-seq, GRO-Seq and ATAC-seq experiments, all sequence reads that passed the Illumina quality filtering were considered for alignment after adapter trimming. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program versions 0.12.1, 1.0.0 and 2.1.0, respectively [Langmead et al, 2009; 2014]. For GRO-Seq, additional four bases were trimmed after adapter trimming and filtered against the rDNA with Bowtie version 2.1.0 before mouse genome alignment. For ATAC-seq, additional alignment parameters were ‘-sensitive -X 5000’
The number of reads per gene was counted using featureCounts version 1.5.0 with default settings. TPM values were calculated as described in Liao et al., Bioinformatic (2014).
Peak calling:  Peaks were called using the MACS program version 2.1.0 (ref. (Zhang et al., 2008)) with default parameters, appropriate input for Pro-B and Mature B cell (Pro -B: GSM1145867, Schwickert et al., 2014; Mature B: GSM2058441, Wöhner et al., 2016) and a genome size of 2.654.911.517 bp (mm9). 889 peaks (Pro-B) and 14512 peaks (Mature B) had a signficant p-value (< 1e-05). Peaks were further filtered for P values of < 10-10, which resulted in 762 (Pro-B) and 9320 (Mature B), respectively.
Read coverage bigwig files were created using bedtools version 2.26.0 with MACS2 predicted fragment sizes.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million after extension to 150 base pairs (.density_150.rpm.bw); text tab delim = TPM values in ASCII text format tab delimited

source_name: Pro-B cell

extract_protocol: phenol-chloroform extraction

tag: cell preparation

value: Ex-vivo, CD19 enriched

tag: cell sorting strategy

value: CD19 enrichment MACS sort

value: anti-BrdU agarose beads (Santa Cruz IIB5)


title: WT Irf8VENUS+ resident DC1 [32672-17_180629_WT_pos_res]

city: St Louis

first: Theresa

last: Murphy

state: MO

address: 4940 Parkview Place

institute: washington university school of medicine

description: gene expression data from DC1 sorted from SDLN

hyb_protocol: Biotinylated cRNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner.

data_processing: Expression values were analyzed after RMA background correction and quantile normalization using ArrayStar software (DNASTAR)

source_name: sorted DC1

label_protocol: Target preparation was performed using the GeneChip WT Pico Kit (Affymetrix).

growth_protocol: Mice were bred and maintained in a specific pathogen-free animal facility according to institutional guidelines and under approved protocols.

extract_protocol: Total RNA was isolated from cells using an RNAqueous-Micro Kit (Ambion).

treatment_protocol: Inguinal, cervical and brachial lymph nodes (SDLN) were minced and digested with Collagenase B and DNAse 1. After ACK lysis, cells were labeled with antibodies and DC1 cells were sorted as B220- EpCam- CD11c+ MHCII+ CD24+ CD172-. Resident DCs were MHCIIint CD11chi and migratory DCs were MHCIIhi CD11cint.

tag: strain background

tag: tissue

value: resident DC1 SDLN

tag: genotype/variation

value: WT Irf8VENUS+


title: Batf3-/- Irf8VENUS+ migratory DC1 [32674-19_180629_3KO_pos_mig]

value: migratory DC1 SDLN

value: Batf3-/- Irf8VENUS+


title: Batf3-/- Irf8VENUS+ migratory DC1 [32667-8_180621_3KO_pos_mig]


title: WT Irf8VENUS+ resident DC1 [32668-11_180627_WT_pos_res]


title: GRO-seq pro-B cell [14540]

description:
BrdU-incorporated RNA
GRO-seq pro-B cell [14540] Rag2(–/–)

tag: strain

tag: genotype


title: Batf3-/- Irf8VENUS+ resident DC1 [32670-13_180627_3KO_pos_res]


title: GRO-seq mature B cell [14539]

description:
BrdU-incorporated RNA
GRO-seq mature B cell [14539] Ebf1(fl/–) CD23-cre

source_name: Mature B cell

value: Ebf1(fl/-) CD23-cre

value: Ex-vivo, CD23 enriched

value: CD23 enrichment MACS sort


title: polII_H2O_r1

description: Chromatin IP of RNA pol II

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

tag: antibody

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: Genomic DNA


title: polII_Dox_r3

description: Chromatin IP of RNA pol II


title: GRO-seq mature B cell [14538]

description:
BrdU-incorporated RNA
GRO-seq mature B cell [14538] Ebf1(fl/+) CD23-cre

value: Ebf1(fl/+) CD23-cre

tag: chip antibody


title: WT Irf8VENUS+ migratory DC1 [32669-12_180627_WT_pos_mig]


title: polII_Dox_r2

description: Chromatin IP of RNA pol II


title: polII_Dox_r1

description: Chromatin IP of RNA pol II


title: WT Irf8VENUS+ migratory DC1 [32665-6_180621_WT_pos_mig]


title: Batf3-/- Irf8VENUS+ resident DC1 [32675-20_180629_3KO_pos_res]


title: WT Irf8VENUS+ resident DC1 [32664-5_180621_WT_pos_res]


title: Batf3-/- Irf8VENUS+ resident DC1 [32666-7_180621_3KO_pos_res]


title: Batf3-/- Irf8VENUS+ migratory DC1 [32671-14_180627_3KO_pos_mig]


title: polII_H2O_r3

description: Chromatin IP of RNA pol II


title: polII_H2O_r2

description: Chromatin IP of RNA pol II


title: WY_E_L38_3

first: Jun

last: Wang

state: Beijing

address: No. 17 Tsinghua East Road, Beijing, 100083, China.

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2（http://genomes.cribi.unipd.it/grape/） using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: De novo assembled reference transcriptome generated from the mixture of all samples
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xls table files.

organism: Vitis vinifera

source_name: grape berry

growth_protocol: The experiment was conducted in 2014 on seven-year-old grapevines grafted onto unknown rootstock in southern China. The grape viticulture regime in this subtropical region was dominated by double cropping systems per year. The vines were planted in north-south rows under a rain-shelter treatment with an inter- and intra-row vine spacing of 3.0 m × 1.0 m and were managed in a closing Y-shaped training system with 2 × 4/5 shoots per meter and 1.0 m cordon above ground.

extract_protocol:
Three biological replicates were performed for each sample. A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNA was extracted from the frozen deseeded berries (whole pericarp) using a SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, CA, USA).  RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The vines are pruned twice and the grapes are harvested twice per year. To produce the first crop, the vines were pruned and enforced with 2.5%-3.0% hydrogen cyanamide in mid-February when the temperature was maintained above 10 °C. The terminal bud was not sprayed to avoid apical dominance. Then, the grapevines were in full bloom around mid-April, while the veraison stage around mid-June, followed by the harvest stage (summer grape). This whole period was termed as summer cropping cycle. Then, the vines were pruned and forced again in August, leading to the second crop (winter grape) in early January of the following year. In detail, the grapevines were pruned and manually defoliated at approximately 20th August, with an average of 5-10 buds left for each cane. Hydrogen cyanamide was smeared only at the terminal bud and in the vicinity of the pruning-wound surface. Then, the bud burst 5-8 days later and initiated the winter cropping cycle.

value: grape berry

tag: cultivar

value: Muscat Superior

tag: Stage

tag: crop

value: Winter


title: WY_E_L38_2


title: WY_E_L36_1


title: WY_E_L36_3


title: WY_E_L36_2


title: WY_E_L38_1


title: SY_E_L36_2

value: Summer


title: WY_E_L35_3


title: SY_E_L38_2


title: WY_E_L35_2


title: SY_E_L38_3


title: SY_E_L38_1


title: WY_E_L35_1


title: SY_E_L35_3


title: SY_E_L35_2


title: WV_E_L38_3

value: Victoria


title: WV_E_L38_1


title: WV_E_L36_3


title: WV_E_L38_2


title: WV_E_L36_2


title: WV_E_L35_2


title: WV_E_L35_3


title: SV_E_L38_2


title: SV_E_L38_1


title: SV_E_L38_3


title: SV_E_L36_3


title: WV_E_L35_1


title: SY_E_L36_3


title: SY_E_L36_1


title: SV_E_L36_2


title: SV_E_L35_3


title: SV_E_L35_1


title: SV_E_L35_2


title: SY_E_L35_1


title: WV_E_L36_1


title: RNA-seq pre-B cell [44076]

description: RNA-seq pre-B cell [44076] wildtype

data_processing:
The database generation of RefSeq-annotated genes was performed as previously described (Wöhner et al., 2016). To refine the annotation of immunoglobulin genes, the immunoglobulin l light-chain segments were replaced with their corresponding converted GRCm38.p3 annotations (Ensembl version 79) (Yates et al., 2016). The resulting number of genes was 24,732.
In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 nucleotides and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al, 2009).
In case of ChIP-seq, GRO-Seq and ATAC-seq experiments, all sequence reads that passed the Illumina quality filtering were considered for alignment after adapter trimming. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program versions 0.12.1, 1.0.0 and 2.1.0, respectively [Langmead et al, 2009; 2014]. For GRO-Seq, additional four bases were trimmed after adapter trimming and filtered against the rDNA with Bowtie version 2.1.0 before mouse genome alignment. For ATAC-seq, additional alignment parameters were ‘-sensitive -X 5000’
The number of reads per gene was counted using featureCounts version 1.5.0 with default settings. TPM values were calculated as described in Liao et al., Bioinformatic (2014).
Peak calling:  Peaks were called using the MACS program version 2.1.0 (ref. (Zhang et al., 2008)) with default parameters, appropriate input for Pro-B and Mature B cell (Pro -B: GSM1145867, Schwickert et al., 2014; Mature B: GSM2058441, Wöhner et al., 2016) and a genome size of 2.654.911.517 bp (mm9). 889 peaks (Pro-B) and 14512 peaks (Mature B) had a signficant p-value (< 1e-05). Peaks were further filtered for P values of < 10-10, which resulted in 762 (Pro-B) and 9320 (Mature B), respectively.
Read coverage bigwig files were created using bedtools version 2.26.0 with MACS2 predicted fragment sizes.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million after extension to 150 base pairs (.density_150.rpm.bw); text tab delim = TPM values in ASCII text format tab delimited

source_name: Pre-B cell

extract_protocol: Rneasy Plus Mini Kit, Dynabeads mRNA purification kit

value: wildtype

value: Ex-vivo, FACS-sorted


title: RNA-seq pro-B cell [44071]

description: RNA-seq pro-B cell [44071] wildtype

value: (CD19+ B220+ IgM- IgD- ckit+)


title: RNA-seq KI pro-B cell [44077]

description: RNA-seq KI pro-B cell [44077] Prdm1(IhCd2/+)


title: RNA-seq pre-B cell [44072]

description: RNA-seq pre-B cell [44072] wildtype


title: RNA-seq KI pro-B cell [44073]

description: RNA-seq KI pro-B cell [44073] Prdm1(IhCd2/+)


title: RNA-seq pro-B cell [44075]

description: RNA-seq pro-B cell [44075] wildtype


title: V5 ChIP-seq pro-B cell [58603]

description: V5 ChIP-seq pro-B cell [58603] Prdm1(IhCd2/+)

extract_protocol: ChIP DNA Clean & Concentrator - Zymo research

value: In-vitro, Pro-B cell culture

value: Anti-V5 agarose beads (Sigma-Aldrich V5-10)


title: RNA-seq KI pre-B cell [44074]

description: RNA-seq KI pre-B cell [44074] Prdm1(IhCd2/+)


title: RNA-seq KI pre-B cell [44078]

description: RNA-seq KI pre-B cell [44078] Prdm1(IhCd2/+)


title: RNA-seq follicular B cell [22432]

description: RNA-seq follicular B cell [22432] wildtype

source_name: Follicular B cell


title: RNA-seq follicular B cell [22431]

description: RNA-seq follicular B cell [22431] wildtype