title: HIV low_ANA_2- 0w

description: Gene expression data from low ANA


title: WT_LS27_methylation

status: Public on Oct 01 2018

type: genomic

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

country: USA

institute: Rutgers Cancer Institute of New Jersey

description: DNA CpG Methylation profile for Human PanNETs

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
All IDAT files were processed in R using ChAMP package with QC,  normalization (FunctionNormalization) and Differentially methylated probes
Normalized data using FunctionNormalization method within ChAMP package and obtained Beta values for all quality passed probe

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: WT PanNET for ATRX / DAXX and MEN1

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from PanNET samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: Pancreatic neuroendocrine tumors (PanNETs)

tag: genotype

value: WT for ATRX/DAXX/MEN1

tag: pannet subtype

value: A-D-M WT PanNETs


title: WT_LS39_methylation


title: NHDF, 42 h_Rep1 (set1)

type: RNA

city: Edinburgh

first: Tom

middle: C

last: Freeman

address: Easter Bush Campus, Midlothian

department: Genetics and Genomics

country: United Kingdom

institute: Roslin Institute

description:
NHDF, 42 h, technical replica 1
Gene expression data of NHDF in synchronous post-mitotic proliferation

hyb_protocol: Samples were hybridized to Affymetrix Human Gene 1.1-ST Array Plate. Hybridization, wash and staining was done using the GeneTitan System (Affymetrix) with the Gene Titan Hybridization, Wash, and Stain Kit for WT Array Plates (Thermo Fisher)

scan_protocol: Arrays were scanned using the imaging station as part of the GeneTitan system (Affymetrix).

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised. This dataset was combined with Data Set 2 before downstream analysis. After merging the datasets, average intensities differences were adjusted with the batch correction algorithm ComBat.

label: biotin

molecule: total RNA

source_name: NHDF post-mitotic proliferation

label_protocol: fragmented cDNA was labeled  by TdT DNA labelling reagent using GeneChip® WT Terminal Labelling Kit (Affymetrix, Buckinghamshire, UK) according to manufacturer’s instructions

growth_protocol: Primary human dermal fibroblasts (NHDF) isolated from neonate foreskins (gifted by Dr Finn Grey, University of Edinburgh, UK) were plated on 175 cm2 tissue culture flasks (Thermo Fisher, Perth, UK) at density of 6x103 cells/cm2. Cells were cultured in DMEM (Sigma-Aldrich, Missouri, US) with 10% (v/v) foetal calf serum (FCS) (GE Healthcare, Little Chalfont, UK) and antibiotics (25 U/ml penicillin and 25 µg/ml streptomycin (Life technologies, Paisley, UK).

extract_protocol: total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Manchester, UK) according to manufacturer’s instructions

treatment_protocol: Starvation-induced synchronisation was achieved by replacing full medium with DMEM containing 0.5% FCS for 48 h. After this time, medium was replaced with DMEM containing 10% FCS promoting the synchronised entry of the NHDF back into the cell cycle.

value: Primary human fibroblasts (NHDF)

tag: age

value: early passage NHDF


title: DM1_mk52_methylation

source_name: DAXX and MEN1 mutated PanNET

value: DAXX and MEN1

value: A-D-M Mutant PanNETs


title: M1_LS1_methylation

source_name: MEN1 mutated PanNETs


title: HIV low_ANA_1- 0w

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

description: Gene expression data from low ANA

hyb_protocol: Affymetrix Human GeneChip U133 Plus 2.0 Array was used for RNA hybridization and labeling assay

scan_protocol: not provided.

data_processing: Biological profiles of distinct genes were analyzed and clustered using iPathway

source_name: Purified human B cells

label_protocol: total RNA were sent to do the gene expression microarray

growth_protocol: B cells were purified from fresh isolated PBMC

extract_protocol: RNeasy Micro kit

tag: diagnosis

value: HIV+

value: blood

tag: cell type

value: Purified human B cells

tag: gender

value: Female

tag: ana level

value: low

tag: weeks after influenza vaccination


title: DM1_mk44_methylation


title: HIV low_ANA_1- 1w

description: Gene expression data from low ANA


title: NHDF, 42 h_Rep2 (set1)

description:
NHDF, 42 h, technical replica 2
Gene expression data of NHDF in synchronous post-mitotic proliferation


title: NHDF, 36 h_Rep2 (set1)

description:
NHDF, 36 h, technical replica 2
Gene expression data of NHDF in synchronous post-mitotic proliferation


title: NHDF, 30 h_Rep3 (set1)

description:
NHDF, 30 h, technical replica 3
Gene expression data of NHDF in synchronous late proliferation

source_name: NHDF late proliferation


title: NHDF, 48 h_Rep1 (set1)

description:
NHDF, 48 h, technical replica 1
Gene expression data of NHDF in synchronous post-mitotic proliferation


title: NHDF, 48 h_Rep2 (set1)

description:
NHDF, 48 h, technical replica 2
Gene expression data of NHDF in synchronous post-mitotic proliferation


title: KO_12hpi_Rep3

type: SRA

city: Davis

first: Huaijun

last: Zhou

state: CA

address: Meyer 3307, One shields Ave.

institute: UC Davis

description:
12hKO3
TwelveKO3

library_source: transcriptomic

data_processing:
Trimming raw reads (Trim Galore! V0.4.5, default setting)
Alignment (STAR_2.5.2b) against reference chicken genome
Raw read count (HTSeq 0.10.0, htseq-count) extracted from each aligned bam file
Genome_build: Galgal5
Supplementary_files_format_and_content: csv, raw read counts from alignment bam files

organism: Gallus gallus

source_name: Modified DF-1 cell

extract_protocol:
TRI-zol
Directional RNA Library Prep

tag: cell line

value: UMNSAH/DF-1 (ATCC CRL-12203)

tag: genotype/variation

value: IRF7 knockout

tag: h6n2 infection


title: HIV high_ANA_5- 0w

description: Gene expression data from high ANA

value: high


title: HIV high_ANA_4- 0w

description: Gene expression data from high ANA


title: KO_12hpi_Rep2

description:
12hKO2
TwelveKO2


title: DM1_mk45_methylation


title: NHDF, 30 h_Rep2 (set1)

description:
NHDF, 30 h, technical replica 2
Gene expression data of NHDF in synchronous late proliferation


title: KO_12hpi_Rep1

description:
12hKO1
TwelveKO1


title: NHDF, 36 h_Rep1 (set1)

description:
NHDF, 36 h, technical replica 1
Gene expression data of NHDF in synchronous post-mitotic proliferation


title: HIV high_ANA_4- 1w

description: Gene expression data from high ANA


title: NHDF, 30 h_Rep1 (set1)

description:
NHDF, 30 h, technical replica 1
Gene expression data of NHDF in synchronous late proliferation


title: HIV high_ANA_3- 0w

description: Gene expression data from high ANA

value: Male


title: WT_12hpi_Rep3

description:
12hC3
TwelveC3

value: wild type


title: WT_12hpi_Rep2

description:
12hC2
TwelveC2


title: NHDF, 24 h_Rep3 (set1)

description:
NHDF, 24 h, technical replica 3
Gene expression data of NHDF in synchronous late proliferation

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised. This dataset was combined with another one before downstream analysis. After merging the datasets, average intensities differences were adjusted with the batch correction algorithm ComBat.


title: HIV high_ANA_2- 1w

description: Gene expression data from high ANA


title: WT_12hpi_Rep1

description:
12hC1
TwelveC1


title: D_mk9_methylation

source_name: DAXX mutated PanNET

value: Pancreatic neuroendocrine tumors (PanNETs)

value: DAXX


title: HIV high_ANA_1- 1w

description: Gene expression data from high ANA


title: DM1_mk17_methylation


title: NHDF, 24 h_Rep1 (set1)

description:
NHDF, 24 h, technical replica 1
Gene expression data of NHDF in synchronous late proliferation

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised. This dataset was combined with with Data Set 2 before downstream analysis. After merging the datasets, average intensities differences were adjusted with the batch correction algorithm ComBat.


title: NHDF, 24 h_Rep2 (set1)

description:
NHDF, 24 h, technical replica 2
Gene expression data of NHDF in synchronous late proliferation


title: HIV high_ANA_2- 0w

description: Gene expression data from high ANA


title: NHDF, 18 h_Rep2 (set1)

description:
NHDF, 18 h, technical replica 2
Gene expression data of NHDF in synchronous late proliferation

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised. This dataset was combined with Data Set 2 before before downstream analysis. After merging the datasets, average intensities differences were adjusted with the batch correction algorithm ComBat.


title: HIV high_ANA_3- 1w

description: Gene expression data from high ANA


title: HIV high_ANA_1- 0w

description: Gene expression data from high ANA


title: D_mk51_methylation


title: D_mk42_methylation


title: NHDF, 12 h_Rep2 (set1)

description:
NHDF, 12 h, technical replica 2
Gene expression data of NHDF in synchronous mid proliferation

source_name: NHDF mid proliferation


title: SETMAR-FLAG R2

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

description: Processed data combined for the two ChIP-seq replicates. Processed data avalable on GSM2913115.

library_source: genomic

data_processing:
Adapters trimmed with Sythe and Sickle (RNA-seq)
Alignment was done with Tophat2 v. 2.1.0 (RNA-seq) or BWA v. 0.7.5a (ChIP-exo) with default options
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.3.1
Mapped reads were de-duplicated with Picard (ChIP-exo)
Peak calling was performed with MACS v. 1.3.7.1 (ChIP-exo)
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: ChIP-exo of Flag-SETMAR in U2OS-SMF cell line

growth_protocol: U2OS cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.

extract_protocol:
RNA extracted with the High Pure RNA isolation kit (Roche Applied Science), following manufacturer's instructions
Libraries were prepared using Illumina's TruSeq RNA Sample Preparation V2 according to manufacturer's instructions

tag: chip antibody

value: Flag M2, F1804


title: NHDF, 18 h_Rep1 (set1)

description:
NHDF, 18 h, technical replica 1
Gene expression data of NHDF in synchronous late proliferation

value: Primary human fibroblasts (NHDF)


title: DM1_LS7_methylation

description: DNA CpG Methylation profile for Human PanNETs


title: KO_6hpi_Rep2

description:
6hKO2
SixKO2


title: KO_6hpi_Rep3

description:
6hKO3
SixKO3


title: D_mk34_methylation


title: Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 3

city: Pozuelo de Alarcon

first: Emilia

last: López Solanilla

state: Madrid

address: Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38

country: Spain

institute: CBGP-Universidad Politécnica de Madrid (UPM)

description:
White Rep 3
Gene expression after 10 min white light treatment.

hyb_protocol: 600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).

scan_protocol: Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Wild type 10 min under White light

label_protocol: cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).

growth_protocol: Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.

extract_protocol: Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).

value: Wild type

tag: culture type

value: Liquid

tag: treatment

value: White light

tag: treatment duration

value: 10 min


title: Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 4

description:
White Rep 4
Gene expression after 10 min white light treatment.


title: SETMAR-FLAG R1

description: Processed data combined for the two ChIP-seq replicates. Processed data avalable at the foot of this page.


title: KO_6hpi_Rep1

description:
6hKO1
SixKO1


title: D_mk26_methylation

value: A-D-M Mutant PanNETs


title: D_mk18_methylation


title: NHDF, 12 h_Rep1 (set1)

description:
NHDF, 12h, technical replica 1
Gene expression data of NHDF in synchronous mid proliferation

value: early passage NHDF


title: NHDF, 6 h_Rep2 (set1)

description:
NHDF, 6 h, technical replica 2
Gene expression data of NHDF in synchronous early proliferation

source_name: NHDF early proliferation


title: D_LS21_methylation


title: WT_6hpi_Rep3

description:
6hC3
SixC3


title: Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 2

description:
White Rep 2
Gene expression after 10 min white light treatment.


title: Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 1

description:
White Rep 1
Gene expression after 10 min white light treatment.


title: NHDF, 6 h_Rep1 (set1)

description:
NHDF, 6 h, technical replica 1
Gene expression data of NHDF in synchronous early proliferation


title: WT_6hpi_Rep2

description:
6hC2
SixC2


title: KO_2hpi_Rep3

description:
2hKO3
TwoKO3


title: KO_2hpi_Rep2

description:
2hKO2
TwoKO2


title: AM1_mk53_methylation

source_name: ATRX and MEN1 mutated PanNET

value: ATRX and MEN1


title: WT_6hpi_Rep1

description:
6hC1
SixC1


title: NHDF, 0 h_Rep3 (set1)

description:
NHDF, 0 h, technical replica 3
Gene expression data of NHDF in a quiescent state

source_name: NHDF quiescent


title: Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 1

description:
Red Rep 1
Gene expression after 10 min red light treatment.

source_name: Wild type 10 min under Red light

value: Red light


title: Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 4

description:
Red Rep 4
Gene expression after 10 min red light treatment.


title: KO_2hpi_Rep1

description:
2hKO1
TwoKO1

value: UMNSAH/DF-1 (ATCC CRL-12203)


title: Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 2

description:
Red Rep 2
Gene expression after 10 min red light treatment.


title: A_mk47_methylation

source_name: ATRX mutated PanNET

value: ATRX


title: NHDF, 0 h_Rep2 (set1)

description:
NHDF, 0 h, technical replica 2
Gene expression data of NHDF in a quiescent state


title: NHDF, unsynch_Rep2 (set1)

description:
NHDF, unsynchronised, technical replica 2
Gene expression data of NHDF unsynchronised

source_name: NHDF unsynchronised


title: MI-FTC_tumor_rep3

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

country: Japan

institute: Osaka Prefecture University

description: RNA from FFPE specimens

hyb_protocol: Fifteen ug of cRNA were subjected to fragmentation using the 3' fragmentation buffer hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis Console® using RMA as a summerization algorithm.

source_name: Tumorous region, MI-FTC, FFPE

label_protocol: Biotinylated cRNA were prepared usibg the GeneChip® WT Pico Reagent Kit from 100 ng total RNA (GeneChip® WT Pico Reagent Kit User Manual, Affymetrix).

extract_protocol: Total RNA was isolated using the NucleoSpin® totalRNA FFPE XS Kit (MACHEREY-NAGEL, Düren, Germany) according to the manufacturer's instructions. On-column DNaseI digestion was performed to avoid genomic DNA contamination.

value: Thyroid

value: female


title: MI-FTC_normal_rep3

description: RNA from FFPE specimens

source_name: Non-tumorous region, MI-FTC, FFPE


title: Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 4

description:
Blue Rep 4
Gene expression after 10 min blue light treatment.

source_name: Wild type 10 min under Blue light

value: Blue light


title: NHDF, 0 h_Rep1 (set1)

description:
NHDF, 0 h, technical replica 1
Gene expression data of NHDF in a quiescent state


title: Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 3

description:
Blue Rep 3
Gene expression after 10 min blue light treatment.


title: MI-FTC_tumor_rep2

description: RNA from FFPE specimens


title: Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 3

description:
Red Rep 3
Gene expression after 10 min red light treatment.


title: WT_2hpi_Rep2

description:
2hC2
TwoC2

value: wild type


title: MI-FTC_normal_rep2

description: RNA from FFPE specimens


title: MI-FTC_tumor_rep1

description: RNA from FFPE specimens

value: male


title: NHDF, unsynch_Rep1 (set1)

description:
NHDF, unsynchronised, technical replica 1
Gene expression data of NHDF unsynchronised

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised. This dataset was combined with Data Set 2. After merging the datasets, average intensities differences were adjusted with the batch correction algorithm ComBat.


title: QR-110 treated 2

city: Leiden

first: kalyan

last: dulla

address: Zernikedreef 9

country: Netherlands

institute: ProQR Therapeutics

data_processing:
Bowtie2  was used to map clean reads to reference gene and HISAT was used to map to reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma delimited text file includes FPKM values for all samples

source_name: iPSC derived retinal organoids

growth_protocol: Directed differentiation of iPSCs into three-dimensional retinal organoids was based on the protocol by Nakano et al.2012 Cell Stem Cell 10: 771-785 and Parfitt et al. 2016 Cell Stem Cell 18: 769-781. treatment started from day 96

extract_protocol:
RNA was extracted from the organoids using RNeasy Mini Kit (Qiagen)
Libraries were prepared by BGI Europe. Either oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. Perform sequencing on prepared library.

treatment_protocol: treated twice a week for 4 weeks

value: iPSC derived retinal organoids

tag: cell line/genotype

value: 1 µM QR-110 for 28 days


title: QR-110 treated 1


title: Untreated 2

value: untreated


title: AM1_mk36_methylation

description: DNA CpG Methylation profile for Human PanNETs

tag: tissue

value: Pancreatic neuroendocrine tumors (PanNETs)


title: A_mk11_methylation

tag: genotype


title: A_mk4_methylation

tag: pannet subtype


title: Untreated 1


title: WT_2hpi_Rep1

description:
2hC1
TwoC1


title: WT_2hpi_Rep3

description:
2hC3
TwoC3


title: MI-FTC_normal_rep1

description: RNA from FFPE specimens

tag: age


title: A_mk12_methylation


title: KO_0hpi_Rep3

description:
0hKO3
ZeroKO3

value: IRF7 knockout


title: KO_0hpi_Rep1

description:
0hKO1
ZeroKO1


title: Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 1

description:
Blue Rep 1
Gene expression after 10 min blue light treatment.

value: Wild type

value: Liquid

value: 10 min


title: WT_0hpi_Rep3

description:
0hC3
ZeroC3


title: KO_0hpi_Rep2

description:
0hKO2
ZeroKO2


title: NHDF, unsynch_Rep3 (set1)

description:
NHDF, unsynchronised, technical replica 3
Gene expression data of NHDF unsynchronised

value: Primary human fibroblasts (NHDF)

value: early passage NHDF


title: Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep2

description:
Dark Rep 2
Gene expression after 10 min darkness treatment.

source_name: Wild type 10 min Dark

value: Darkness


title: Lim3_control

city: Moscow

first: Olga

last: Rybina

state: Moskva

address: Kurchatov sq.,2

country: Russia

institute: IMG RAS

data_processing:
Basecalling by Illumina Casava1.8 software. Sequencing reads were aligned to annotated Drosophila transcripts (Dmel Release 5.57) using TopHat 0.6 with zero mismatch. The differentially expressed genes were identiied by the tool Cuffdiff (Galaxy Tool Version 0.0.7). Total expression level for each transcript, measured in FPKM (Fragments Per Kilobase-pair of exon Model), was calculated based on mapped reads. Genes with values under 0.6 FPKM and expression alteration under 1.7-fold were discarded and the remaining genes were taking into further analysis.
Genome_build: Dmel Release 5.57
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each transcript

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were kept at 25°C on a standard medium of semolina, sugar, raisins, yeast and agar with nipagin, propionic acid and streptomycin.

extract_protocol:
Total RNA was extracted from embryos of 0- to 16-hour (100–200 mkg)  using ExtractRNA (Evrogen). The poly-A containing mRNA fraction was isolated from total RNA samples using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s protocol.
The sequencing libraries were constructed from the poly-A containing mRNA fraction using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB) following the manufacturer's protocol with some modifications, namely fragmentation time was 94°C for 15 m; Agencourt Ampure XP beads (Beckman Coulter, Inc.) were used to purify ds cDNA >200bp after adapter ligation.  The obtained sequencing libraries of fragment size between 250 and 400bp were purified by gel extraction using Qiagen Gel Extraction (Qiagen).

treatment_protocol: The collected embryos were washed with Phosphate-buffered saline solution  (1×, pH 7.4)

value: embryos

value: 0- to 16-hour

tag: developmental stage

value: embryonic


title: Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep1

description:
Dark Rep 1
Gene expression after 10 min darkness treatment.


title: INS1_cells_6h_Giv_Cyt_replicate_2

city: Gentofte

first: Flemming

last: Pociot

address: Niels Steensens Vej 2

department: T1D Biology

country: Denmark

institute: Steno Diabetes Center Copenhagen

description: miRNA expression data from INS1 cells in 6h_Giv_Cyt group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint  8x15k Rat miRNA Agilent microarrays (G4473C) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: INS1 cells, treated with Givinostat + cytokines, 6h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: MiR-enriched total RNA was purified with the miRCURY™ RNA Isolation Cell and Plant Kit (Exiqon)

treatment_protocol: INS1 cells were incubated for 48h prior to exposure with or without 125 nM Givinostat (ITF2357) for 1 h, prior to addition of 150 pg/ml IL-1-β and 0.1 ng/ml IFN-γ for 6-24 h

tag: cell-line

value: Rat pancreatic INS1 cells

tag: group


title: INS1_cells_6h_Giv_Cyt_replicate_1


title: INS1_cells_6h_Cyt_replicate_3

description: miRNA expression data from INS1 cells in 6h_Cyt group

source_name: INS1 cells, treated with IL-1β and IFNγ, 6h


title: INS1_cells_6h_Giv_Cyt_replicate_3


title: Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep4

description:
Dark Rep 4
Gene expression after 10 min darkness treatment.


title: WT_0hpi_Rep2

description:
0hC2
ZeroC2

source_name: Modified DF-1 cell

value: UMNSAH/DF-1 (ATCC CRL-12203)

value: wild type


title: WT_0hpi_Rep1

description:
0hC1
ZeroC1


title: InVitro_24hr_FLAM76_IL-6

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description:
FLAM-76_004
Gene expression in FLAM-76 cells following 24 h of IL-6 treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The MM cell lines were incubated in a RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum in the absense of IL-6. The cells were then treated with IL-6 (10 ng/mL) for the indicated times at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: human multiple myeloma (MM) cell line, IL-6-dependent

tag: cell line source gender

value: male

tag: cell line source age

value: 77 years

tag: treated with

value: 10ng/ml IL-6 for 24hrs


title: InVitro_12hr_FLAM76_IL-6

description:
FLAM-76_003
Gene expression in FLAM-76 cells following 12 h of IL-6 treatment

tag: cell line

value: 10ng/ml IL-6 for 12hrs


title: InVitro_0hr_FLAM76_none

description:
FLAM-76_001
Gene expression  in non-treated FLAM-76 cells

source_name: FLAM-76, no treatment

value: none (no treatment control)


title: Lim3_knockdown


title: InVitro_6hr_FLAM76_IL-6

description:
FLAM-76_002
Gene expression in FLAM-76 cells following 6 h of IL-6 treatment

source_name: FLAM-76, 6hr,  IL-6, 10 ng/mL

value: 10ng/ml IL-6 for 6hrs


title: Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep3

description:
Dark Rep 3
Gene expression after 10 min darkness treatment.

tag: genotype/variation

value: Wild type

value: Liquid

value: 10 min


title: InVitro_24hr_ANBL-6_IL-6

description:
ANBL-6_004
Gene expression in ANBL-6 cells following 24 h of IL-6 treatment

source_name: ANBL-6, 24hr,  IL-6, 10 ng/mL

value: female

value: 67 years


title: InVitro_0hr_ANBL-6_none

description:
ANBL-6_001
Gene expression  in non-treated ANBL-6 cells

source_name: ANBL-6, no treatment


title: INS1_cells_6h_Cyt_replicate_2


title: PCC6803_drpaA_dark_rep1

city: Freiburg

first: Christin

last: Koebler

address: Schaenzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 600 ng of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. After background correction the median signal intensity was cyclic loess normalized.

organism: Synechocystis sp. PCC 6803

source_name: ∆rpaA cells from liquid culture grown in light-dark cylces, 5.5h after onset of dark

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Wild-type and ∆rpaA strain were grown in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) within Erlenmeyer flasks under continuous illumination with 50 µmol photons m-2s-1 at 30°C.

extract_protocol: 25 ml cell culture was harvested on Supor 800 0.8 mm membrane filters and directly transfered in a falcon with PGTX (Pinto et al., 2009; BMC Mol Biol 10: 79). After vortexing for 30 s, samples were snap frozen in liquid nitrogen and stored at  -80 °C. Samples were thawed on ice, followed by incubation for 5 min at 95 °C in a water bath. During incubation, samples were vortexed several times. Afterwards samples were cooled down on ice for 5 min and stored at room temperature for 10 min.  Phenol was extracted twice with 1-bromo-3-chloropropane and RNA was precipitated with 2-propanol at -20°C, followed by centrifugation at 4°C. The RNA pellet was washed with 75% ethanol and resuspended in RNase-free A. dest.

treatment_protocol: Cultures were diluted to OD750 = 0.8 and transfered to a light-dark (12h-12h) cycle. Samples were taken after 17.5 h (dark) or 29.5h (= 5.5 h light).

value: rpaA deletion mutant

tag: culture condition


title: PCC6803_drpaA_light_rep2

source_name: ∆rpaA cells from liquid culture grown in light-dark cylces, 5.5h after onset of light


title: PCC6803_Wildtype_dark_rep2

source_name: WT cells from liquid culture grown in light-dark cylces, 5.5h after onset of dark

value: WT


title: InVitro_6hr_ANBL-6_IL-6

description:
ANBL-6_002
Gene expression in ANBL-6 cells following 6 h of IL-6 treatment

source_name: ANBL-6, 6hr,  IL-6, 10 ng/mL


title: PCC6803_drpaA_light_rep1

value: liquid culture grown in light-dark cylces, 5.5h after onset of light


title: PCC6803_drpaA_dark_rep2

value: liquid culture grown in light-dark cylces, 5.5h after onset of dark


title: InVitro_12hr_ANBL-6_IL-6

description:
ANBL-6_003
Gene expression in ANBL-6 cells following 12 h of IL-6 treatment

source_name: ANBL-6, 12hr,  IL-6, 10 ng/mL


title: PCC6803_Wildtype_light_rep1

source_name: WT cells from liquid culture grown in light-dark cylces, 5.5h after onset of light


title: PCC6803_Wildtype_light_rep2


title: PCC6803_Wildtype_dark_rep1


title: INS1_cells_24h_Giv_Cyt_replicate_3

description: miRNA expression data from INS1 cells in 24h_Giv_Cyt group

source_name: INS1 cells, treated with Givinostat + cytokines, 24h

value: Rat pancreatic INS1 cells


title: INS1_cells_6h_Ctrl_replicate_2

description: miRNA expression data from INS1 cells in 6h_Ctrl group

source_name: INS1 cells, no treatment, 6h


title: INS1_cells_6h_Ctrl_replicate_3


title: INS1_cells_6h_Giv_Ctrl_replicate_3

description: miRNA expression data from INS1 cells in 6h_Giv_Ctrl group

source_name: INS1 cells, treated with Givinostat, 6h


title: INS1_cells_6h_Ctrl_replicate_1


title: INS1_cells_6h_Giv_Ctrl_replicate_2


title: INS1_cells_6h_Giv_Ctrl_replicate_1


title: INS1_cells_24h_Cyt_replicate_3

description: miRNA expression data from INS1 cells in 24h_Cyt group

source_name: INS1 cells, treated with IL-1β and IFNγ, 24h


title: INS1_cells_24h_Giv_Cyt_replicate_1


title: INS1_cells_24h_Giv_Cyt_replicate_2


title: INS1_cells_6h_Cyt_replicate_1


title: INS1_cells_24h_Cyt_replicate_2


title: INS1_cells_24h_Giv_Ctrl_replicate_3

description: miRNA expression data from INS1 cells in 24h_Giv_Ctrl group

source_name: INS1 cells, treated with Givinostat, 24h


title: INS1_cells_24h_Cyt_replicate_1


title: INS1_cells_24h_Giv_Ctrl_replicate_1


title: INS1_cells_24h_Ctrl_replicate_3

description: miRNA expression data from INS1 cells in 24h_Ctrl group

source_name: INS1 cells, no treatment, 24h


title: INS1_cells_24h_Giv_Ctrl_replicate_2


title: 983-LW-12

city: Nashville

first: Lauren

middle: Katie

last: Wareham

state: Tennessee

address: 2213 Garland Avenue, MRBIV 11435a

department: Vanderbilt Eye Institute

institute: Vanderbilt University Medical Center

data_processing:
DNase-treated total RNA quality was assessed using the 2100 Bioanalyzer (Agilent). Samples with a RNA integrity number greater than 6 were used to generate polyA (mRNA) enriched libraries using stranded mRNA sample kits with indexed adaptors (New England BioLabs).
Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems).
Pooled libraries were subjected to 100 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000).
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
Reads were aligned to the GENCODE GRCm38.p5 genome using STAR v2.5.3a.
GENCODE vM12 gene annotations were provided to STAR to improve the accuracy of mapping. Quality control on raw reads was performed using FastQC.
featureCounts v1.15.2 was used to count the number of mapped reads to each gene.
Significantly differential expressed genes with adjusted p-value < 0.05 and absolute fold change > 2 were detected by DESeq2 v1.14.
Genome_build: GENCODE GRCm38.p5
Supplementary_files_format_and_content: counts

organism: Mus musculus

source_name: interleukin-6 knockout_retina

growth_protocol: Tissue extracted from animals.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naïve mice aged 3 months with no additional treatment.

tag: strain background

value: 3 months old

tag: treatment

value: naïve

value: retina


title: 983-LW-13


title: myogenic precursors originating from non-hyperplasic muscle of fasted juvenile trout (FJT) [14-FJT 105-5]

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization  was performed using GeneSpring software (Agilent).

organism: Oncorhynchus mykiss

source_name: tissue:non-hyperplasic muscle of fasted juvenile trout (FJT)

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Rainbow trout (Oncorhynchus mykiss) weighting from 2g to 2kg were raised to a 12 h light:12 h dark photoperiod and 12 ± 1 °C in a closed circuit flow system located in the Laboratory of Physiology and Genomics of Fish. Fish were fed daily ad libitum on a commercial diet or starved during 3 or 4 weeks.

extract_protocol: Using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), total RNA samples were extracted from cells according to the manufacturer's recommendations

treatment_protocol: Myogenic precursors were isolated from juvenile trout (5g, JT), from 3-4 weeks fasted juvenile rainbow trout (5g, FJT) and from adult rainbow trout (1.5-2kg, AT) as previously described (Gabillard et al. 2010). Isolated myogenic precursors were plated on poly-L-lysine and laminin-coated plates at 80,000 cells per cm2 for every analysis except to proliferation measurement which were 60,000 cells per cm².

tag: origine of myogenic precursors

value: FJT


title: 983-LW-8

value: wild type

tag: tissue


title: 983-LW-11


title: myogenic precursors originating from non-hyperplasic muscle of fasted juvenile trout (FJT) [15-FJT 102-1]


title: myogenic precursors originating from non-hyperplasic muscle of fasted juvenile trout (FJT) [16-FJT 102-5]


title: 983-LW-9


title: 983-LW-7


title: myogenic precursors originating from non-hyperplasic muscle of fasted juvenile trout (FJT) [13-FJT 105-2]


title: INS1_cells_24h_Ctrl_replicate_2


title: 983-LW-6


title: 983-LW-5


title: INS1_cells_24h_Ctrl_replicate_1


title: 983-LW-4


title: Peak3 [Trypanosoma congolense]

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw sequence files are QC assessed using FASTQC
Paired sequences were aligned to a flattened version of the T. congolense genome using bowtie2 (version version 2.2.7; parameters: --very-sensitive -p 12 –no-unal –trim5 10)
Data were obtained for two lanes of sequence data per sample; BAM files for the two lanes were merged, sorted and reindexed using samtools (v 1.3), thus generating 1 BAM file per sample
Read counts were extracted from gene regions using bedtools (version v2.23.0; parameters: multicov)
All subsequent processing was undertaken in R using Bioconductor packages
Genome_build: Genome obtained from ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT/ Jan 2015
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts

organism: Trypanosoma congolense

source_name: mouse blood

growth_protocol: Samples were obtained 5 days (“ascend”) or 6/7 days (“peak”) post-infection with the Trypanosoma congolense IL3000 parasite.

extract_protocol:
Trypanosomes were purified from whole blood by passage through a DE52 column, and RNA samples were prepared using the Qiagen RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions.
RNA-Seq was carried out by BGI Hong Kong.

tag: strain

tag: condition

value: peak


title: 983-LW-10

tag: age


title: Peak2 [Trypanosoma congolense]


title: myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) [4-JT 101-4]

source_name: tissue:hyperplasic muscle of juvenile trout (JT)

value: JT


title: myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) [1-JT 101-1]


title: myogenic precursors originating from non-hyperplasic muscle of adult trout (AT) [10-AT 103-3 and 4]

source_name: tissue:non-hyperplasic muscle of adult trout (AT)

value: AT


title: myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) [5-JT 101-5]


title: myogenic precursors originating from non-hyperplasic muscle of adult trout (AT) [7-AT 104-2 and 4]


title: C604 Tag#991

growth_protocol: Tissue extracted from animal.

treatment_protocol: Mice aged 1 month received 1uL intracameral injections of either saline or 15-um-diameter microbeads causing elevated intraocular pressure for 4 weeks before tissue was harvested.

value: 2 months old

value: microbead-injected


title: C603 Tag#990


title: Peak1 [Trypanosoma congolense]


title: BA_3

city: Berlin

first: Henrik

last: Johansson

address: Albrecht-Thaer-Weg 6

institute: Freie Universität Berlin

description: Dark grown/etilated

data_processing:
HCS3.3.20, RTA 2.5.2 and bcl2fastq2-v2.16 were used for basecalling.
After removal of adaptors and low quality reads, the obtained clean reads (approximately 21 million) were stored as FASTQ format
Sequences were mapped to reference gene using Bowtie2 with the following parameters: -q--phred64--sensitive--dpad 0--gbar99999999--mp1,1--np 1--score-min L,0,-0.1-p16-k200 and reference genome using BWA with the parameters:  -o 1 -e 50 -i 50 -L -k 2 -l 31 -t 4 -q 10.
Gene expression levels based on the FPKM method were quantified using RSEM and differentially expressed genes (DEGs) were analyzed using the NOISeq method  with the following default criteria: fold change ≥2 and diverge probability ≥ 0,8.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Seeds were surface sterilized, sown on half MS medium without sucrose and stratified in darkness for 3 days at 4°C before given a two hours white light pulse (75 µmol m-2 s-1). The half MS medium was supplemented with either 3 µM BA and/or 10 µM AgNO3. Seedlings were grown for 4 days in complete darkness in a growth cabinet (Percival AR66L; Percival Scientific, Perry, IA, USA) at 22 °C.

extract_protocol:
Total RNA was extracted from seedlings flash-frozen in liquid nitrogen using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) as described in the user’s manual including an on-column DNAse treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: 4 days after germination

value: 10 µM AgNO3 + 3 µM BA

value: whole seedling


title: Raw264_Gpr137B-KO_IL4plus_rep2

hyb_protocol: Labeled cRNA was hybridized for 17 hr on Clariom S Array (mouse) using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

data_processing: The data were analyzed with Affymetrix® GeneChip Command Console using SST-RMA as a summarization algorithm.

source_name: Raw264 cells_Gpr137B-KO_IL4plus

label_protocol: The total RNA was subjected to cRNA synthesis followed by ssDNA synthesis using GeneChip WT Plus Reagent Kit (Affymetrix). The ssDNA (5.5 micrograms) was then fragmentated and biotin-labeled using GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer's manual.

growth_protocol: Raw264  cells were cultured in Eagle's MEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from Raw264 cells using RNAiso (Takara-bio, Kusatsu, Japan) according to the manufacturer's instructions.

treatment_protocol: Raw264 cells were treated with mouse IL-4 to induce M2 macrophage polarization.

value: Mouse macrophage cell line


title: myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) [3-JT 101-3]


title: myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) [2-JT 101-2]


title: Ascend3 [Trypanosoma congolense]

value: ascending


title: myogenic precursors originating from non-hyperplasic muscle of adult trout (AT) [8-AT 104-5]


title: C601 Tag#988


title: myogenic precursors originating from non-hyperplasic muscle of adult trout (AT) [11-AT 103-2]


title: myogenic precursors originating from non-hyperplasic muscle of fasted juvenile trout (FJT) [12-FJT 105-1]


title: BA_2

description: Dark grown/etilated


title: myogenic precursors originating from non-hyperplasic muscle of adult trout (AT) [9-AT 103-1]


title: BA_1

description: Dark grown/etilated


title: C600 Tag#987

value: saline-injected


title: Raw264_Gpr137B-KO_IL4minus_rep2

source_name: Raw264 cells_Gpr137B-KO_IL4minus


title: Ascend1 [Trypanosoma congolense]


title: Control_3

description: Dark grown/etilated

value: 10 µM AgNO3


title: C598 Tag#985


title: Ascend2 [Trypanosoma congolense]


title: Vector gRNA 2

city: Rome

first: Jamie

last: Hackett

address: via Ramarini 32

department: Epigenetics & Neurobiology

country: Italy

institute: European Molecular Biology Laboratory (EMBL)

description: CRISPR screen reference library; replicate 2

data_processing:
Library strategy: Amplicon-seq
RNA-seq reads were quality-trimmed and aligned to mm10 with TopHat2 version: 2.0.13
Differentially expressed genes were called using DESeq2
Datastore analysis was performed with SeqMonk version: 1.36
CRISPR libraries were processed using MaGECK software version 1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: Fastq raw read files

molecule: other

organism: unidentified plasmid

source_name: plasmid library

growth_protocol: Stella-GFP; Esg1-tdTomato (SGET) embryonic stem cells (ESC) were maintained and differentiated into epiblast-like cells (EpiLC) and primordial germ cell-like cells (PGCLC). For EpiLC, ESC were transferred to a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore; 16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml), bFGF (12 ng/ml) and knockout serum replacement (KSR; 1 %) for 42hrs. Purified EpiLC were seeded in ultra-low cell binding U-bottom 96-well plates (Nunc; 3x10e3 cells per well) in GK15 medium (GMEM, 15% KSR, NEAA, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine) supplemented with cytokines: BMP4 (500 ng/ml), LIF (1000 U/ml), SCF (100 ng/ml), BMP8a (500 ng/ml), and EGF (50 ng/ml) and collected on day2 or day6 of differentiation.

extract_protocol:
For fluorescence-activated cell sorting (FACS), cultured cells or embryoids were dissociated into single cells with TrypLE, and suspended in phosphate buffered saline (PBS) with 0.5% BSA or 3% FBS. Filtered cell suspensions were subsequently sorted using a Sony SH800Z or a MoFlow high-speed cell sorter (Beckman Coulter) or analysed with BD LSRFortessa X-20 (BD Biosciences). For exit from pluripotency analyses, cells were sorted/analysed based on absence or presence of Stella-GFP expression, whilst maintaining Esg1-tdTomato activitaion (SG+/-ET+). For PGCLC, cells were sorted/analysed based on Stella-GFP re-activation coupled with low Esg1-tdTomato. The threshold(s) levels for sorting was set and normalised based on expression levels in pre-optimised SGET ESC. A negative population of ESC without any fluorescence was used to set absolute thresholds. Forward and side scatters were used to gate for the cell population and doublets. For each sort the maximum number of cells was collected.
Sample1-36: For RNA-seq of Nr5a2-/-, Zfp296-/- and matched WT control cell lines, 100 ng of total RNA from triplicate biological independent experiments was used as inputs for the NEBNext Ultra RNA library Prep Kit for Illumina (NEB), with the library generated as per manufacturer’s instructions. During the final PCR amplification stage, 15 cycles of amplifications were performed to generate the adaptor ligated, fragmented cDNA for sequencing. Samples were assessed using the High Sensitivity D1000 ScreenTape assay (Agilent) to ensure the library did not contain primer-dimer contamination after last round of AMPure beads cleaning. The Qubit dsDNA HS assay kit (ThermoFisher Scientific) and the NEBNext Library Quant Kit for Illumina was used to accurately quantify the concentration of each library preparation. Samples were multiplexed with 12 indexes per lane and a total of 2 lanes of sequencing on Illumina HiSeq4000, single-end 50bp with an average depth of approximately 20 million reads per sample. Sample 37-42: ESC, EpiLC, or day 6 PGCLC (from the CRISPR screen) were dissociated into single cell solutions with TrypLE and sorted with a Sony SH800Z or a MoFlow high-speed cell sorter (Beckman Coulter) based on appropriate Stella-GFP and Esg1-tdTomato expression. Samples were sorted into 150ul of extraction buffer from the PicoPure RNA isolation kit (Life Technologies) and rapidly frozen on dry ice or liquid nitrogen. Total RNA was subsequently extracted using the PicoPure RNA isolation Kit, including a 15 minute on-column DNaseI digestion. RNA integrity number was assessed with RNA HS ScreenTape (Agilent), and all samples confirmed to have a RIN >8.5. For RNA-seq from CRISPR screen samples, 50 ng of total RNA was used as input for the Ovation RNA-seq System v2 (Nugen) as per manufacturer’s instructions. Amplified double-stranded (ds) cDNA was diluted into EDTA-low TE (Agilent) and sheared into ~230bp in length using S220 Focused-Ultrasonicator (Covaris) using settings: duty factor 10%, cycle burst 200, intensity 5, temp at 4°C and treatment time of 5 minutes per sample.  A high Sensitivity D1000 ScreenTape assay (Agilent) was used to assess the efficiency of library fragmentation. Fragmented ds-cDNA was concentrated with Qiagen Reaction Clean Up kit (MiniElute) and 1μg of the fragmented ds-cDNA used as input for the library preparation using Encore Rapid DR Multiplex Library System (Nugen). This kit ligated the adaptors to repaired-end ds-cDNA without amplification, which eliminated biases introduced during PCR amplification. The KAPA Library Quantification Kit (Kapa bioscience) was used to quantify the concentration of each adaptor-ligated libraries prior to multiplexing. The ESC, EpiLC and PGCLC RNA sequencing libraries were generated in parallel for each replicate, and the biological replicates were generated on independent occasions. Samples were multiplexed and sequenced with Illumina HiSeq1500, single-end 50bp read length with a minimum depth of approximately 15 million reads per sample.  Sample43-52: To quantify the relative frequencies of integrated gRNAs during the CRISPR screen in each population during cell fate transitions, genomic DNA was isolated from day 12 ESC post-lentiviral transduction, from SG–ET+ and SG+ET+ EpiLC populations at 42hr, and from SG+ETlow PGCLCs from day 6 embryoids, in biological duplicate using the DNeasy Blood & Tissue kit (Qiagen). Purified genomic DNA was used as template for custom primers that specifically amplify the gRNA region, and include overhanging Illumina adaptors and indexes to allow deep sequencing and multiplexing, respectively (synthesised as Ultramers from IDT) (see oligo tables). Prior to PCR, genomic DNA was sonicated with a Biorupter (Diagenode) for 15 seconds on ‘LOW’ power to improve efficiency of amplification. gRNA sequences were amplified in multiple PCR reactions to enable all isolated DNA to be utilised, each with NEBNext Q5 HotStart HiFi PCR Master Mix (NEB), 0.2 uM of universal forward primer (mix of staggers), 0.2 uM of indexed reverse primer and genomic DNA (~650 ng / 50 ul rxn). For amplification from the plasmid vector, 15 ng was used as template for replicate amplifications. The following cycling conditions were used: 95°C for 2 minutes, then between 21-26 cycles of (98°C for 20 seconds, 62°C for 20 seconds and 72°C for 20 seconds) followed by 72°C for 1 minute and hold at 4°C. The number of cycles was optimised for the point at which PCR products can be first visualised on an agarose gel. The PCR reaction was subsequently purified with AMPure XP beads (Beckman Coulter) using double size selection to remove primer dimers and genomic DNA. Briefly, 0.55x of AMPure beads were added to PCR reaction (1x) and incubated for 5 minutes at room temperature. The supernatant was collected; the beads contained the unwanted larger fragments and were discarded. An additional 0.3x of AMPure beads was subsequently added to the supernatant (1x) and incubated for 5 minutes at room temperature. The supernatant was removed and beads washed twice with 200 ul of 80% EtOH, air dried for 5 minutes and DNA was eluted from AMPure beads with EDTA-low TE buffer. The concentration of adaptor ligated gRNA amplicons was measured with the Qubit DNA Assay kit (ThermoFisher Scientific) and the fragment distribution determined with an Agilent D1000 ScreenTape System (Agilent Technologies). Libraries were subsequently multiplexed and sequenced with an Illumina HiSeq 1500 using single-end 50bp reads. As the sequences for all samples were identical up to the gRNA region, these types of low complexity libraries can produce low quality data. To counteract this, forward staggered primers were introduced at equal ratios during PCR amplification, generating offset reads. In addition, libraries were sequenced with 4 dark cycles and low density (70%) clustering.
Sample 1-42: RNA-seq; Sample 43-52: amplicon

tag: fluorescent reporter

value: unknown


title: Control_2

description: Dark grown/etilated


title: Raw264_Gpr137B-KO_IL4minus_rep1


title: C597 Tag#984


title: Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 2

description:
Blue Rep 2
Gene expression after 10 min blue light treatment.

source_name: Wild type 10 min under Blue light

value: Wild type

tag: culture type

value: Liquid

value: Blue light

tag: treatment duration

value: 10 min


title: Control_1

description: Dark grown/etilated


title: Vector gRNA 1

description: CRISPR screen reference library; replicate 1


title: mNET_unph_rep1

status: Public on Sep 30 2018

city: Guangzhou

first: Zhicheng

last: Dong

state: Guangdong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

country: China

institute: Guangzhou University

description: nascent RNA

data_processing:
Library strategy: mNET-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to TAIR10 whole genome using bowtie v1.1.2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include the position information of RNA Pol II for each sample
Supplementary_files_format_and_content: bedgraph

source_name: seedling

growth_protocol: The Arabidopsis (Col-0 ecotype) seeds were germinated and grown in 1/2 MS for 12 days at 20°C under 16 hour light/8 hour dark.

extract_protocol:
The tissue powder was solubilized in 30 ml lysis buffer (50 mM HEPES, pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% glycerol, 5 mM 2-mercaptoethanol, 2 μg/ml pepstatin A, 2 μg/ml aprotinin, 1 mM PMSF), mixed well and filtrated through 110 μm nylon mesh and a 40 μm cell strainer.  The nuclei were spanned down at 3,200 g for 20 min at 4°C, followed by two washes with HBB buffer (25 mM Tris–HCl, pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM 2-mercaptoethanol) and HBC buffer (20 mM Tris–HCl, pH 7.5, 352 mM sucrose, 8 mM MgCl2, 0.08% Triton-X, 8 mM 2-mercaptoethanol, 20% glycerol).
The obtained nuclei pellet were resuspended with 1 ml MNase buffer (20 mM Tris–HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2) and digested with 20 U MNase (TaKaRa, 20U/μl) for 5 minutes at 37°C rotating at 1,400 rpm. Stopped the digestion by adding 40 μl 500 mM EDTA. Pol II-nascent RNA complex was released by mild sonication. Supernatants were collected by centrifuging at 16,000 g for 5 min at 4°C and Pol II complex were immunoprecipitated according to Nojima et al. [14]. The Pol II bond nascent RNAs were treated by T4 PNK on beads and extracted with 500μl TRIzol Reagent (Invitogen). The IP RNA was resolved on an 8% TBE-urea polyacrylamide gel and RNA with size from 35-100 nt was recovered. The 35-100 nt IP RNA was used to construct the NET-SEQ cDNA library with NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific) according to the manual. The cDNA library was resolved in a non-denaturing 6% TBE polyacrylamide gel and size region 150-230 bp was recovered. cDNA library concentration was determined by Qubit QuantIT (Invitrogen) and kapa quantitative realtime PCR.

tag: cultivar

value: seedling

value: 12 days


title: mNET_unph_rep2

description: nascent RNA


title: Raw264_Gpr137B-KO_IL4plus_rep1

tag: cell type


title: mNET_total_rep1

description: nascent RNA


title: mNET_total_rep2

description: nascent RNA


title: GRO-seq_rep2

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to TAIR10 whole genome using bowtie v1.1.2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include the position information of RNA Pol II for each sample
Supplementary_files_format_and_content: bedgraph

extract_protocol:
The fine seedling powder was solubilized in 30 ml extraction buffer (2 M hexylene glycol, 20 mM PIPES pH 7.0, 10 mM MgCl2, 5 mM 2-mercaptoethanol) and filtrated through 110 μm and 60 μm nylon mesh. Add triton X-100 into the lysates to the final concentration of 1% and leave on ice for 10 minutes. Cell fractionation was performed using a 30%-80% percoll gradient solution and nuclei were collected at the 30%-80% interface.
Breifly, nascent RNA was treated with T4 PNK (NEB) and followed by acidic phenol/chloroform purification. Phosphorylated nascent RNA was polyA tailed using E. coli Poly(A) Polymerase (NEB) and reverse transcribed by superscript III reverse transcriptase (Invitrogen) with RT primer (GRO-oligo2, synthesized by IDT DNA, 5’-/5Phos/GA TCG TCG GAC TGT AGA ACT CTG AAC /idSp/CC TTG GCA CCC GAG AAT TCC ATT TTT TTT TTT TTT TTT TTT VN-3’). Free RT primer was removed by Exonuclease I (Fermentas) and RNA was eliminated by alkaline hydrolysis. The resulted 1st-strand cDNA was resolved from a 10% TBE-urea polyacrylamide gel. The cDNA with size above120 nt was recovered and self-ligated using CircLigase (Epicentre). The circularized single-stranded cDNA was relinearized by APE 1 (NEB). The linearized cDNA was recovered again by a 10% TBE-urea polyacrylamide gel. The cDNA was PCR amplified by Kapa HiFi polymerase with the illumina compatible primers (Universal primer F 5’GAT CGT CGG ACT GTA GAA CTC TGA ACG TGT AGA TCT CGG TGG TCG CCG TAT CAT T 3’, Reverse Index primer R 5’CAA GCA GAA GAC GGC ATA CGA GAT NNNNNN GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA 3’, NNNNNN: index). The PCR reaction starts with a 30s denaturation at 94˚C, followed by 12-14 cycles of 10s denaturation at 94˚C, 15s annealing at 60˚C and 15s extension at 72˚C. The PCR product was resolved in a non-denaturing 8% TBE polyacrylamide gel and size region 200-330 bp was recovered. cDNA library concentration was determined by Qubit QuantIT (Invitrogen) and kapa quantitative realtime PCR according to the manual.


title: RNA-seq_rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to TAIR10 whole genome using tophat.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include the position information of RNA Pol II for each sample
Supplementary_files_format_and_content: bedgraph

molecule: polyA RNA

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: mNET_Ser2P_rep1

description: nascent RNA


title: mNET_Ser5P_rep2

description: nascent RNA


title: mNET_Ser5P_rep1

description: nascent RNA


title: RNA-seq_rep2


title: GRO-seq_rep1

description: nascent RNA


title: Raw264_WT_IL4plus_rep2

source_name: Raw264 cells_wildtype_IL4plus


title: LNCaP_24hr_R1881, rep 1

city: Charlottesville

first: Aakrosh

last: Ratan

state: VA

address: 1335 Lee Street, West Complex

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
Aligned with STAR aligner (version 2.5.3a) using GRCh38.d1.vd1.fa.tar.gz
Generated raw counts using HTSeq (version 0.10.0) with parameters --mode=union --stranded=no --type=exon --idattr=gene_id --format=bam --order=pos. Using Homo_sapiens.GRCh38.89.chrchr.gtf as the annotation file.
Genome_build: hg38
Supplementary_files_format_and_content: text file of raw read counts

source_name: prostate

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to the manufacturer’s instructions.
Indexed libraries were made by Hudson Alpha using the standard polyA method.

treatment_protocol: Cells were plated in phenol-free medium supplemented with charcoal-stripped FBS serum for 48-72 hours prior to treatment. Cells were treated for the indicated timepoint with 2 nM R1881.

value: LNCaP


title: VCaP_24hr_R1881, rep 2

value: VCaP


title: LNCaP_unt, rep 2


title: LNCaP_24hr_R1881, rep 2


title: LNCaP_unt, rep 1


title: LNCaP_24hr_R1881, rep 3


title: VCaP_24hr_R1881, rep 3


title: LNCaP_unt, rep 3


title: mNET_Ser2P_rep2

description: nascent RNA


title: Raw264_WT_IL4minus_rep2

source_name: Raw264 cells_wildtype_IL4minus


title: VCaP_24hr_R1881, rep 1


title: VCaP_unt, rep 3


title: PC3-AR_12hr_R1881, rep 2


title: VCaP_unt, rep 2


title: VCaP_unt, rep 1


title: PC3-AR_12hr_R1881, rep 3


title: Raw264_WT_IL4minus_rep1


title: PC3-AR_6hr_R1881, rep 3


title: PC3-AR_6hr_R1881, rep 1


title: PC3-AR_12hr_R1881, rep 1


title: PC3-AR_unt, rep 3


title: PC3-AR_unt, rep 1


title: PC3-AR_unt, rep 2


title: Raw264_WT_IL4plus_rep1


title: WT MEF 2 days H3K4me3 A1

status: Public on Sep 29 2018

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

institute: European Institute of Oncology & University of Milano, Italy

data_processing:
Reads were trimmed for potential adapter contamination using scythe 0.981 (min 4 nucleotides).
Trimmed reads were aligned to the GRCm38 genome using bowtie 1.0 (Langmead et al., 2009) with –v 2 –m 1.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw bigWig tracks (not normalized) were generated with deepTools (bamCoverage 2.5.3-2-503c71b), extending reads to 200bp and using a bin size of 100bp.

source_name: MEFs undergoing transdifferentiation

growth_protocol: MEF were cultured in the medium published in Vierbuchen et al., 2010, at 37° C, 3% O2 and 5% CO2.

extract_protocol:
Cells were fixed with PBS 1% formaldehyde. Fixation was quenched with 0,125M glycine. Cells were collected in SDS Buffer (100mM NaCl, 50mM Tris-HCl pH 8.1, 5mM EDTA pH 8, 0.5% SDS), centrifuged, then resuspended in 3 ml of ice-cold IP buffer (2 volumes SDS Buffer: 1 volume Triton Dilution Buffer) (Triton Dilution Buffer: 100mM NaCl, 100mM Tris-HCl pH 8.6, 5mM EDTA pH 8, 5% Triton X-100) and sonicated through the Digital Sonifier 450 (Branson) (ChIP-seq for Menin: 700-bp DNA fragments; ChIP-seq for H3K4me3 and H3K27me3: 200-bp DNA fragments). The immunoprecipitated product was purified through Protein G dynabeads (ThermoFisher Scientific, 10003D), afterwards washed with low-salt (150mM NaCl, 20mM Tris-HCl pH 8, 2mM EDTA pH 8, SDS 0.1%, 1% Triton X-100) and high-salt wash (500mM NaCl, 20mM Tris-HCl pH 8, 2mM EDTA pH 8, SDS 0.1%, 1% Triton X-100) buffer 3 times with 1 ml of 150 mM Wash Buffer and once with 1 ml of 500 mM Wash Buffer with the use of a Dynamag magnet (ThermoFisher Scientific, catalog number 12321D). Decrossilinking occurred through the incubation of beads (and the 1% input) with Decrosslinking Buffer (1% SDS, 0.1M NaHCO3) at 65 °C overnight. DNA was purified with the QiaQuick PCR Purification kit (Qiagen) following manufacturer’s instructions.
Libraries were prepared as previously described in Adamo et al., Nature Genetics 2015.

treatment_protocol: Control and cKO MEFs at P1-P3 were treated for 5 days with 4-Hydroxytamoxifen (4-OHT), added to the MEF medium in a final concentration of 1000ng/ml, and then left either 2 or 7 days in medium not supplemented with 4-OHT.  Transdifferentiation was performed according to the protocol in Vierbuchen et al. (2010).

tag: chip target

tag: chip antibody

value: Active motif 39159 (rabbit)

tag: genotype

value: Wildtype

tag: Stage

value: MEF 2 days


title: WT MEF 7 days H3K27me3 A1

value: Cell signaling 9733F (rabbit)

value: MEF 7 days


title: WT MEF 7 days H3K4me3 A4


title: KO MEF 7 days H3K27me3 N1


title: WT MEF 7 days H3K27me3 A4


title: KO MEF 7 days H3K27me3 N5


title: KO MEF 2 days H3K4me3 N5


title: WT MEF 7 days H3K4me3 A1


title: WT MEF 2 days H3K4me3 A4


title: WT MEF 2 days H3K27me3 A4


title: KO MEF 2 days H3K27me3 N5


title: KO MEF 2 days H3K27me3 N1


title: KO MEF 7 days H3K4me3 N1


title: WT MEF 2 days H3K27me3 A1


title: KO MEF 7 days H3K4me3 N5


title: PC3-AR_6hr_R1881, rep 2

tag: cell line


title: KO MEF 7 days input

value: input


title: Double KO MEF 7 days H3K4me3

value: Kmt2b-/- Kmt2a-/-


title: KO MEF 2 days input


title: Double KO MEF 7 days input


title: Double KO MEF 7 days H3K27me3


title: WT MEF 2 days input


title: WT MEF 7 days input


title: Double KO MEF 2 days H3K4me3


title: KO BAM 5 days H3K4me3 M7

value: BAM 5 days


title: KO BAM 13 days H3K4me3 M7

value: BAM 13 days


title: KO MEF 2 days H3K4me3 N1


title: Kmt2a-/- BAM 5 days H3K27me3


title: WT BAM 5 days H3K4me3 L1


title: WT BAM 5 days H3K27me3 L7


title: WT BAM 13 days H3K4me3 L7


title: Kmt2a-/- BAM 5 days H3K4me3


title: WT BAM 5 days H3K27me3 L1


title: KO BAM 5 days H3K4me3 M6


title: WT BAM 5 days H3K4me3 L7


title: KO BAM 5 days input


title: KO BAM 13 days H3K4me3 M6


title: KO BAM 5 days H3K27me3 M6


title: KO BAM 5 days H3K27me3 M7


title: WT BAM 5 days input


title: WT BAM 5 days MENIN L6

value: MENIN

value: Abcam ab31902 (rabbit)


title: WT BAM 5 days input (for Menin)


title: KO BAM 5 days input (for Menin)


title: WT BAM 13 days H3K4me3 L1


title: Neg_control_2_1

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Library strategy: CUT&RUN
Alignment by bowtie2 version 2.3.3.1
Selection of paired-end insert size less than 120 by sambamba
Peak calling by macs2 version 20160309 with the parameters -f BAMPE -p 1e-2 --keep-dup auto
Genome_build: mm10
Supplementary_files_format_and_content: Quantification in each peak

source_name: murine MLL-AF9 leukemic cells overexpressing murine IKZF2

growth_protocol: RN2 cells were transduced with retrovirus expressing murine IKZF2 together with RFP. Cells were sorted and cultured for 2 weeks post transduction.

extract_protocol:
DNA was extracted using spin column.
barcoded library for Illumina sequencing was generated using with Tru-Seq adapters. 60 million reads using paired end Illumina sequencing was performed.

treatment_protocol: Cells were incubated with concavalin-beads and incubated with IKZF Ab. Cells were incubated with 0.1% digitonin wash buffer and pA-MNase was added. CaCl2 was added to initiate digestion and solution containing EDTA and EGTA was added to stop reaction. Reaction was incubated in 37° C for 10min for fragmented chromatin release.

value: murine MLL-AF9 leukemia cells with NRASG12D (RN2 cells)

tag: treatment

value: cells were incubated with control Rabbit Ab


title: Ikzf2_CUTRUN_3_1

value: cells were incubated with anti-IKZF2 Ab


title: KO BAM 13 days input


title: KO BAM 5 days MENIN M7


title: U937_Etoposide_3

city: cambridge

first: olivier

last: papapietro

state: Select

address: addenbrooke's hospital

department: medicine

institute: University cambridge

data_processing:
RNA-seq reads were aligned using HISAT
aligned reads were counted using HTSEQ-count
Deseq2 was used to determine differentially expressed features from count tables
Genome_build: Hg19
Supplementary_files_format_and_content: tab,csv

source_name: monocyte cell line

growth_protocol: cells were grown in RPMI+10% fetal calf serum+pen/strep at a concentration <1 million cells/ml

extract_protocol:
total RNA were extracted with Trizol using manufacturer's guidelines
RNA-seq libraries were preparded according to Illumina's instructions accompanying truseq RNA sample preparation kit

treatment_protocol: cells were treated with 10uM Etoposide for 4 hours

value: histiocytic leukemia

value: Etoposide


title: U937_Etoposide_1


title: U937_control_2

value: Control


title: U937_Etoposide_2


title: Ikzf2_CUTRUN_1_1


title: WT BAM 5 days MENIN L7


title: KO BAM 5 days MENIN M6


title: Ikzf2_CUTRUN_2_1


title: Neg_control_1_1


title: U937_control_1


title: THP1_Etoposide_2

value: acute monocytic leukemia


title: RAMOS_Etoposide_3

source_name: B lymphocyte cell line

value: RAMOS

value: Burkitt's lymphoma (American)


title: JURKAT_Etoposide_2

source_name: T lymphocyte cell line

value: JURKAT

value: acute T cell leukemia


title: THP1_control_2


title: JURKAT_Control_1


title: 697_Etoposide_2

source_name: pre-B cell line

value: acute lymphoblastic leukemia (ALL)


title: RAMOS_Control_3


title: JURKAT_Etoposide_3


title: THP1_Etoposide_3


title: THP1_control_3


title: JURKAT_Control_2


title: JURKAT_Control_3


title: THP1_Etoposide_1


title: RAMOS_Control_2


title: RAMOS_Etoposide_1


title: Neg_control_2_2


title: 697_Control_3


title: Neg_control_1_2


title: JURKAT_Etoposide_1


title: 697_Control_2


title: RAMOS_Control_1


title: Ikzf2_CUTRUN_3_2


title: 697_Control_1


title: NALM6_Etoposide_3


title: Ikzf2_CUTRUN_2_2


title: smpB3

city: Haikou

first: Hong

last: Li

address: NO. 58, Renmin Avenue

institute: Hainan Unversity

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequenced reads were mapped to NZ_CP012504.1 using Bowtie v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 -- no-mixed --no-discordant -p 1 -k 200
Gene abundances were quantified using RSEM v1.2.12 with parameter: --forward-prob=0.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Aeromonas veronii

growth_protocol: Strains were grown in 10mL M9 medium containing 50ug/mL ampicillin at 30℃ 150rpm for 20 hours.

extract_protocol:
Bacteria were collected by  refrigerated centrifuger and lysised by lysozyme. RNA samples were extracted by phenol-chloroform.The concentration and quanlity were  detected by Alilent 2100 Bioanalyzer
The samples were treated with Dnase I to degrade double-stranded and single-stranded DNA. And then the rRNA was depleted by Ribo-Zero Magnetic Kit. RNA moleculess were fragmented into small peces.First-strand cDNA was generated using random primers reverse transcription, followed by a second-strand cDNA synthesis.The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments.The cDNA fragments was inriched  by PCR amplification with PCR Primer Cocktail, and the product were purified and ready for sequencing.

tag: developmental stage

value: stationary phase

tag: genotype/variation

value: delta smpB


title: NALM6_Etoposide_2


title: RAMOS_Etoposide_2


title: 697_Etoposide_1


title: smpB2


title: NALM6_Control_3


title: NALM6_Etoposide_1


title: wt3

value: wild type


title: Ikzf2_CUTRUN_1_2

tag: strain


title: wt2


title: NALM6_Control_1


title: wt1


title: NALM6_Control_2


title: Control_late_tailbud

status: Public on Sep 28 2018

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: control embryo

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 2.0.1
Genome_build: Genome used was (Ciona intestinalis (KH2012, Ghost Database) plus mchsv40 and cfpsv40 inserts
Supplementary_files_format_and_content: 10x Cell Ranger HDF5 formatted matrix files and 10x loupe file (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

organism: Ciona intestinalis

source_name: Ciona late tailbud embryo

extract_protocol:
10x manual
single cell RNA seq

tag: tissue

value: whole embryo

value: Late tailbud 1 stage


title: Control_mid_tailbud

description: control embryo

source_name: Ciona mid tailbud embryo

value: Mid tailbud 1 stage


title: Ptf1a-Meis_mid_tailbud

description: β2tubulin drived Ptf1a and Meis expression embryo

value: PTF1a and Meis overexpression


title: Ptf1a_mid_tailbud

description: β2tubulin drived Ptf1a expression embryo

value: PTF1a overexpression


title: ChIP-seq from lung (ENCLB174YYR)

status: Public on Sep 21 2018

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR936FAH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR936FAH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB174YYR

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female embryo (120 days) lung tissue

extract_protocol: extraction method: see document

tag: antibody

value: lung

value: tissue

tag: description

value: Lung tissue from a healthy 120 day old female human fetus. Tissue provided by Ian Glass of University of Washington, Congenital Defects Lab.

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: embryonic

tag: age

value: 120 day

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS840NUY at ENCODE; https://www.encodeproject.org/ENCBS840NUY/

value: Derived from ENCODE donor ENCDO670CKN; https://www.encodeproject.org/ENCDO670CKN/


title: THP1_control_1

tag: cell type

value: acute monocytic leukemia

value: Control


title: ChIP-seq from lung (ENCLB669BZH)

description:
https://www.encodeproject.org/experiments/ENCSR413WJD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR413WJD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669BZH

source_name: Homo sapiens embryo (101 day) lung tissue

value: Lung tissue from a healthy day 101 fetus from Ian Glass of University of Washington, Congenital Defects Lab.

value: not collected

value: 101 day

value: ENCBS907UWS at ENCODE; https://www.encodeproject.org/ENCBS907UWS/

value: Derived from ENCODE donor ENCDO308YQF; https://www.encodeproject.org/ENCDO308YQF/


title: ChIP-seq from lung (ENCLB613EYW)

description:
https://www.encodeproject.org/experiments/ENCSR813HFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR813HFV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB613EYW


title: ChIP-seq from lung (ENCLB755OFI)

description:
https://www.encodeproject.org/experiments/ENCSR240ZWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR240ZWZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB755OFI


title: ChIP-seq from lung (ENCLB356PVG)

description:
https://www.encodeproject.org/experiments/ENCSR454WZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR454WZX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB356PVG


title: ChIP-seq from lung (ENCLB949QTK)

description:
https://www.encodeproject.org/experiments/ENCSR617SRM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR617SRM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB949QTK


title: WT sRNA <100: Infected human red blood cells with Plasmodium falciparum

status: Public on Aug 22 2018

first: Christian

last: Schmitz-Linneweber

address: Granseer Str. 7

department: Faculty of Life Sciences

institute: Humboldt University Berlin

description: WT sRNA <100

data_processing:
MiSeq Control Software v 2.4
Sequence trimming was done with CutAdapt
Trimmed sequences were mapped to the Plasmodium falciparum organellar genomes (NCBI apicoplast: DQ642846.1 and mitochondria: DQ642845.1) using Bowtie (version 1.1.1)  with the following parameters –a –best –strata –v 2
Genome_build: NCBI apicoplast: DQ642846.1 and mitochondria: DQ642845.1; nuclear plasmodium genome

organism: Plasmodium falciparum

growth_protocol: Plasmodium falciparum NF54 cells were grown in unsynchronized cultures and split every 2-3 days.

extract_protocol:
Parasites were extracted from infected red blood cells using saponin lysis. After centrifugation and washing Parasites were resuspended in TriZol and RNA was extracted with the standard TriZol method.
Library was constructed as described in NEBNext Multiplex Small RNA Library Prep

tag: genotype

value: wild type

value: asexual stages


title: ChIP-seq from lung (ENCLB280PEG)

description:
https://www.encodeproject.org/experiments/ENCSR111KKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR111KKC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254NDP
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB280PEG

value: lung

value: tissue


title: sci-ATAC GM12878 and HL-60

status: Public on Aug 02 2018

city: Seattle

first: Cole

last: Trapnell

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Accessible genomic DNA

data_processing:
BCL files were converted to fastq format with bcl2fastq v2.16.
Barcode sequences were corrected to expected barcodes with custom python script.
Reads were trimmed (for adapter read-through) with Trimmomatic v0.32.
Reads were mapped to hg19 with bowtie v2.2.3.
Reads not mapping to the assembled nuclear chromsomes, as well as reads with invalid cell barcodes, were filtered using samtools v1.1 and grep.
Duplicate reads from each cell were filtered out with a custom python script.
Filtered out barcodes with few reads using custom R script.
Called peaks using MACS2 v2.1.1
Overlapped reads with summits of accessibility using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: "counts.txt.gz": Gzipped multiple column tab-separated vector in sparse matrix format - Column 1 = location information for each hypersensitivity summit; Column 2 = barcode representing single cell; Column 3 = count of reads from that barcode overlapping that hypersensitivity summit
Supplementary_files_format_and_content: ".indextable.txt": 2 column tab-separated vector - Column 1 = list of valid barcode combinations included in experiment; Column2 = time of collection
Supplementary_files_format_and_content: "54_1_bulk_multi_cov_counts.txt.gz":  Multiple column tab-separated vector - Columns 1-3 = bed format genomic coordinates, Remaining Columns = count of reads overlapping the genomic coordinates from the named bulk ATAC seq library
Supplementary_files_format_and_content: “.index_conversion.txt.gz”: Multiple column tab-separated table. Column 1 = read number, same order as corresponding fastq, Column 2 = cell barcode as sequenced, Column 3 = corrected cell barcode, see paper for details. Corrected barcodes containing the string “barcode_fail” could not be confidently and unambiguously assigned to an expected barcode and were excluded from downstream analysis.

extract_protocol:
Nuclei were isolated (please see publication for more details).
Please see publication for details on library construction.

value: B-Lymphocyte and Promyeloblast

tag: crispr perturbation target

tag: crispr guide

tag: time


title: sci-ATAC HSMM to HSMMtube Experiment 1

description: Accessible genomic DNA

source_name: HSMM to HSMMtube

value: Skeletal Muscle Myoblasts/Myotubes


title: sci-ATAC HSMM to HSMMtube Experiment 2

description: Accessible genomic DNA


title: smpB1

tag: developmental stage

value: stationary phase

value: delta smpB


title: Late tailbud control

status: Public on Jul 31 2018

description: control embryo

extract_protocol:
Cells of each embryo were dissociated with 300 ul 1% trypsin in Ca2+-Free ASW with 5 mM EGTA for 5 min. Embryos were pipetted 5 min on ice to complete dissociation of individual cells. 500 ul ice cold Ca2+-Free ASW + 0.5% BSA was added to terminate digestion. Cells were collected by centrifuging at 900g for 5 min at 4 C and then resuspended in 50 ul ice cold Ca2+-Free ASW + 0.5% BSA.
Single cell suspensions were loaded onto the 10x Genomics Chromium system using Chromium Single Cell 3 Library and Gel Bead Kit v2 (Lot. 120267) to generate and amplify cDNAs, as recommended by the manufacturer (10X Genomics, CA). Illumina sequencing libraries were generated from the cDNA samples using the Nextera DNA library prep kit (Lot. FC-121-1030) and sequenced using Illumina HiSeq 2500 Rapid flowcells (Illumina Inc., CA) with paired-end 26nt + 125nt reads following standard Illumina protocols.

tag: resource

value: whole embryo

value: Late tailbud 1 stage

tag: genetic manipulation


title: Late tailbud Foxc

description: Pax3/7 drived FoxC expression embryo

value: FoxC overexpression


title: blast_NanogKD_Nanog_rep4

status: Public on Jul 20 2018

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
library strategy: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

growth_protocol: FVB females on superovulation were mated with FVB males and zygotes were collected ~17-19 h post-hCG. Zygotes were washed in M2 medium with hyaluronidase to remove surrounding cumulus cells, followed by additional 3 washes in M2. Zygote microinjections were performed on Ziess AxioVert200 microscope using Ependorf Femtojet microinjector. Around 5 pl of esiRNAs against GFP, Brg1 and Nanog was injected per zygote, at the concentration of 0.5 mg/ml. Zygotes were subsequently placed in KSOM media in 5% CO2, 5% O2 incubator and cultured until the blastocyst stage. Blastocysts were washed twice in M2 and zona pellucida was removed by acid Tyrode solution, followed by 2 additional M2 washes.

extract_protocol:
The CUT&RUN protocol was modified from Skene and Henikoff (eLife 2017), who made their modified protocol available online (http://blocks.fhcrc.org/steveh/papers/CUT&RUN_protocol.htm). Mouse ES cells were counted using a TC-10 cell counter (Biorad) and diluted manually to respective cell amounts. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were washed with 1mL cold PBS. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were resuspended in 1mL cold nuclear extraction (NE) buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% TritonX-100, 20% glycerol, freshly added protease inhibitors). Cells were pelleted at 600g for 3min at 4°C, the supernatant was discard and cells were resuspended in 600uL NE buffer. During the cell washes, Concanavalin A beads (Polysciences) were prepared. For 500,000 cells 200uL bead slurry were used, for 50,000 cells 150uL bead slurry were used, for 5,000 cells, 100uL bead slurry were used, for 500 cells and 50 cells 50uL bead slurry were used, and for 10 cells 20uL bead slurry were used. Beads were withdrawn and transferred to a microfuge tube containing 3X volume cold Binding buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Beads were washed twice in 1mL cold Binding buffer and resuspended in 300uL binding buffer. Extracted nuclei were added to beads with gentle vortexing and incubated for 10 minutes at room temperature. After nuclei binding, cytosolic fraction was discarded and beads were blocked with 1mL cold Blocking buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA, freshly added protease inhibitors) which was added with repeated gentle pipetting and incubated for 5 minutes at room temperature. Supernatant was discarded and nuclei/beads were washed in 1mL cold Wash Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, freshly added protease inhibitors) and resuspended in 250uL cold Wash Buffer. Primary antibody was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:100. Samples were incubated with rotation at 4°C for 2 hours. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 250uL cold Wash Buffer. ProteinA-MNase (kindly provided by Steven Henikoff) was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:400. Samples were incubated with rotation at 4°C for 1 hour. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 150uL cold Wash Buffer. Samples were equilibrated to 0°C on ice water for 5-10 minutes. 3uL 100mM CalC2 was added during gentle vortexing, samples were flicked quickly to mix and returned to 0C on ice water. After 5 minutes of digestion, reactions were stopped with addition of 150uL 2XSTOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNaseA, 40ug/mL glycogen, 10pg/mL yeast spike-in DNA). Samples were incubated at 37°C for 20 minutes to activate RNase and release fragments. Samples were centrifuged at 16,000g for 5minutes and supernatants were transferred to a new microfuge tube while pellets and beads were discarded. Following addition of 3uL 10% SDS and 2.5uL 20m/gmL ProteinaseK, samples were mixed by inversion and incubated at 70°C for 10 minutes. DNA was cleaned using PCI followed by chloroform extraction, and precipitated with glycogen and ethanol. DNA was pelleted with a high speed spin at 4C, washed, air dried for ~5 minutes and resuspended in 36.5uL 0.1XTE.
Libraries were prepared using a modification of the Henikoff available protocol. DNA end-repair, phosphorylation, and A-tailing was performed in a single reaction, as follows. T4 DNA Polymerase (NEB) was diluted 1:20. 5uL 10X T4 DNA ligase buffer (NEB), 2.5uL 10mM dNTPs, 1.25uL 10mM ATP, 3.13uL 40% PEG4000, 0.63uL T4 PNK (NEB), 0.5uL diluted T4 DNA Polymerase, and 0.5uL Taq polymerase (homemade) was added to 36.5uL of CUT&RUN enriched DNA. Samples were incubated at 12°C for 15 minutes, 37°C for 15 minutes, followed by 72°C for 20 minutes in a thermocycler. Samples were put on ice immediately and the following adapter ligation reaction was performed. PE inline Illumina adapters were used for these experiments. 55uL of 1X Quick ligase buffer (NEB), 5uL Quick ligase (NEB), and 5uL of 1.5uM adapter mix was added to 50uL of A-tailed DNA and samples were incubated at 20°C for 15 minutes in a thermocycler. Immediately following adapter ligation, samples were cleaned using Ampure XP beads (Beckman Coulter). Beads were warmed to room temperature during adapter ligation and 38uL well-mixed beads were added to libraries. Samples were mixed thoroughly and incubated for 15 minutes at room temperature. Following solution clearing on a magnetic rack, supernatants were discarded and beads were washed two times with 200uL 80% EtOH. Samples were briefly spun, residual liquid was discarded, and beads were allowed to air dry for ~5 minutes. DNA was eluted from beads by resuspending beads in 30uL 10mM Tris-HCL pH 8.0 and incubation at room temperature for 2 minutes. Following solution clearing on a magnetic rack, 27.5uL DNA was transferred to a 0.2mL PCR tube and library enrichment was performed. Libraries were enriched for 14-19 cycles of PCR, with the following conditions. 10uL 5X KAPA buffer, 1.5uL 10mM dNTPs, 5uL 20uM PE PCR 1.0, 20uM PE PCR 2.0, 1uL KAPA hotstart HiFi polymerase (KAPA) was added to 27.5uL of library DNA. The following PCR program was used to enrich the samples: 98°C 45 seconds, 98°C 15 seconds, 60°C 10 seconds, steps two and three were repeated specified number of times, 72°C 1 minute. Following library enrichment, samples were loaded on an agarose gel and DNA corresponding to 150-700 bases was extracted using the Qiagen extraction buffer and Econospin columns. Size distribution of libraries was determined using a Fragment analyzer, and libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Unfixed nuclei were bound to Concanavalin A beads (Polysciences, Inc), washed, followed by successive addition of primary antibody followed by proteinA-MNase. Cleavage of MNase was initiated by calcium chloride addition and chelated by EDTA. Fragments were released and deep sequencing libraries were prepared.

tag: strain background

value: FVB

value: blastocysts

tag: primary antibody

value: anti-Nanog, Active Motif, Cat# 61419, Lot 04613001, used at 1:100 final

tag: secondary antibody

value: proteinA-MNase kindly provided by Steven Henikoff, used at 1:400


title: blast_NanogKD_Nanog_rep1


title: blast_NanogKD_NoAb_rep4


title: blast_NanogKD_Nanog_rep2


title: blast_NanogKD_Nanog_rep3


title: blast_NanogKD_NoAb_rep2


title: blast_NanogKD_NoAb_rep3


title: blast_Brg1KD_Nanog_rep4


title: blast_NanogKD_NoAb_rep1


title: cDC2_UN_dataset3_#1

status: Public on Aug 23 2018

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package. These samples were normalized together with other samples. The complete normalized data set with all other samples, both batch-corrected and not batch-corrected, is available on the series record.

label_protocol: 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol. The lineage cocktail used was a combination of antibodies against CD19 (B cells), T cell receptor beta chain (alpha/beta T cells and NK T cells), NK1.1 (NK and NK T cells) and Ly6G (neutrophiles).

treatment_protocol: Mice were untreated or infected for 1.5 days i.p. with 2.5x10E4 pfu of salivary-gland extracted MCMV Smith strain.

tag: phenotype

value: Lin-CD11b+Ly6C-CD11chigh, viable (aquadead V-BV510 negative)

tag: tissue

value: spleen

value: resting (total) spleen WT CD45.2 CD11b+ DC

tag: strain

value: WT CD45.2 CD57BL/6

tag: treatment

value: Uninfected


title: cDC2_UN_dataset3_#2


title: blast_Brg1KD_NoAb_rep4


title: blast_Brg1KD_NoAb_rep2


title: blast_Brg1KD_NoAb_rep3


title: blast_Brg1KD_Nanog_rep1


title: blast_Brg1KD_NoAb_rep1


title: blast_EGFPKD_Nanog_rep4


title: blast_Brg1KD_Nanog_rep2


title: blast_Brg1KD_Nanog_rep3


title: blast_EGFPKD_Nanog_rep1


title: blast_EGFPKD_NoAb_rep4


title: blast_CTCF_rep2

growth_protocol: FVB females on superovulation were mated with FVB males and zygotes were collected ~17-19 h post-hCG. Zygotes were washed in M2 medium with hyaluronidase to remove surrounding cumulus cells, followed by additional 3 washes in M2.  Zygotes were subsequently placed in KSOM media in 5% CO2, 5% O2 incubator and cultured until the blastocyst stage. Blastocysts were washed twice in M2 and zona pellucida was removed by acid Tyrode solution, followed by 2 additional M2 washes.

value: anti-CTCF, millipore, Cat# 07-729, lot 2475698, used at 1:100 final


title: blast_EGFPKD_NoAb_rep2


title: blast_EGFPKD_NoAb_rep1


title: blast_EGFPKD_Nanog_rep3


title: blast_EGFPKD_Nanog_rep2


title: Nanog_1cell_rep2

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

value: E14 mouse embryonic stem cells (ESCs)


title: Sox2_1cell_rep1

value: anti-Sox2, Active Motif, Cat# 39843, Lot 19710001, used at 1:100 final


title: blast_CTCF_rep1


title: blast_NoAb_rep1


title: Sox2_1cell_rep2


title: blast_NoAb_rep2


title: CTCF_1cell_rep11

value: anti-CTCF, millipore, Cat# 07-729, lot 2971000, used at 1:100 final


title: CTCF_1cell_rep8

value: anti-CTCF, millipore, Cat# 07-729, lot 2887267, used at 1:100 final


title: CTCF_1cell_rep9


title: CTCF_1cell_rep7


title: Nanog_1cell_rep1


title: CTCF_1cell_rep12


title: CTCF_1cell_rep10


title: CTCF_1cell_rep6


title: blast_EGFPKD_NoAb_rep3


title: CTCF_1cell_rep1


title: CTCF_1cell_rep2


title: CTCF_1cell_rep4


title: CTCF_1cell_rep5


title: NoAb_1cell_rep10


title: NoAb_1cell_rep9


title: NoAb_1cell_rep6


title: NoAb_1cell_rep11


title: NoAb_1cell_rep4


title: NoAb_1cell_rep3


title: NoAb_1cell_rep7


title: NoAb_1cell_rep2


title: NoAb_1cell_rep5


title: NoAb_1cell_rep1


title: H3K27ac_50000cells

value: anti-H3K27ac, abcam, Cat# ab4729, Lot GR104852-1, used at 1:100 final


title: CTCF_1cell_rep3


title: H3K27me3_50cells

value: anti-H3K27me3, Millipore, Cat# 07449, Lot JBC1873477, used at 1:100 final


title: Nanog_50cells


title: Brg1_50cells

value: anti-Brg1, Bethyl, Cat# A300-813A, Lot 3, used at 1:100 final


title: NoAb_1cell_rep8


title: Sox2_50cells


title: Oct4_50000cells

value: anti-Oct4, Invitrogen, Cat# A13998, lot RK2423646, used at 1:100 final


title: Sox2_50000cells


title: Brg1_50000cells


title: Oct4_50cells


title: H3K4me3_50cells

value: anti-H3K4me3, millipore, Cat# 05-745R, lot 2848536, used at 1:100 final


title: H3K4me3_500cells


title: CTCF_10cells


title: H3K4me3_10cells


title: H3K4me3_500000cells


title: H3K4me3_5000cells


title: H3K4me3_50000cells


title: NoAb_500cells


title: CTCF_500000cells


title: CTCF_50cells


title: CTCF_500cells


title: CTCF_5000cells


title: CTCF_50000cells


title: NoAb_10cells


title: H3K27ac_50cells


title: H3K27me3_50000cells


title: Nanog_50000cells

value: anti-Nanog, Active Motif, Cat# 61419, Lot 04613001, used at 1:100 final


title: NoAb_5000cells

value: proteinA-MNase kindly provided by Steven Henikoff, used at 1:400


title: NoAb_50000cells