title: 2,4-D_2d_rep1

status: Public on Jul 23 2019

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

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

data_processing:
Sequencing reads were cleaned with Trim Galore v0.5.0,  including removing bases with low quality score (<20)  and cutting sequencing adaptors followed by filtering short reads.
For de novo transcriptome assembly,cleaned reads were input into Trinity v2.8.4 separately for de novo assembly. The resulting transcriptomes were filtered and combined using CD-HIT v4.8.1 with ?sequence identity threshold at 0.8 and sequence minimum length at 500bp' parameters to reduce sequence redundancy and throw away short contigs.
For 2,4-D treated RNA-seq data analysis, Cleaned reads were mapped to Trinity transcriptome using Bowtie2 v2.3.4.3 for C.richardii, and mapped to the Arabidopsis thaliana genome (TAIR10) using STAR v2.7.2b for Arabidopsis. RSEM v1.3.2 was used to quantify transcript abundance.
Genome_build: de novo assembly transcriptomes
Supplementary_files_format_and_content: tab-delimited text file includes normalized read counts for each Trinity transcript

organism: Ceratopteris richardii

source_name: Ceratopteris richardii seedlings

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

extract_protocol:
The whole seedlings were harvested and frozen in liquid nitrogen, RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 30-d culture, sporophyte seedings were transferred to 1/2 MS medium with 2 μM 2,4-D  for 24 or 48 h.

value: sporophytes

value: wild type RNWT1

tag: Stage

value: 30 days after Spores were cultured

tag: treatment

value: 48 hours of 2,4-D treatment

value: seedling


title: S. robusta MT- + Roseovarius ( R) rep1

status: Public on Jul 15 2019

type: SRA

city: Jena

first: Emilio

last: Cirri

address: Lessingstrasse 8

country: Germany

institute: Friedrich Schiller University Jena

library_source: transcriptomic

data_processing:
Paired-end reads were quality-trimmed using FastQ Quality Filter from the FastX Toolkit v. 0.0.13  using the following settings : -q 28, -p 30. Using the Salmon software tool in quasi-mapping mode, the  quality-trimmed reads were mapped to an annotated genes model assembly of S. robusta. To generate the annotated assembly, Illumina paired-end reads and PacBio long reads were combined in a hybrid assembly approach and gene models were annotated using expression data as training for the BRAKER1 pipeline.  The transcript-level abundances generated with Salmon were imported into R (v.3.4.4) and aggregated to gene level counts using the tximport package. Genes with low overall counts (counts-per-million (CPM) < 1 in at least three samples) were removed from the libraries because they have little power for detecting differential expression. Differences in sequencing depth and RNA population were corrected using a weighted trimmed mean of the log expression ratios (TMM) normalization. Preliminary differences between expression profiles of different samples were explored with multi-dimensional scaling (MDS) plots based on the top 500 genes, generated using the plotMDS function included in the EdgeR package.
Genome_build: Sro genome v1.0
Supplementary_files_format_and_content: tab delimited text files includes counts for each sample. Gene ids are located at https://bioinformatics.psb.ugent.be/gdb/seminavis/Version1.0/

molecule: total RNA

organism: Seminavis robusta

source_name: Whole cell

extract_protocol:
RNA was extracted from all samples using the RNeasy® Plant Mini Kit (Qiagen).The 18 sequencing libraries were prepared using Illumina® TruSeq Stranded mRNA kit. The libraries were sequenced (2x75 bp) in one Illumina® NextSeq 500 H150 run.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: treatments

value: Roseovarius sp.

tag: sexually induced

value: no


title: S. robusta MT- ( C) rep2


title: Sexaully Induced S. robusta MT- (SIP) rep2

value: yes


title: Sexaully Induced S. robusta MT- (SIP) rep3


title: CK_rep2

country: China

tag: tissue

tag: genotype

value: mock group


title: 2,4-D_1d_rep2

value: 24 hours of 2,4-D treatment


title: 2,4-D_1d_rep1


title: S. robusta MT- + Maribacter (M) rep3

value: Maribacter sp.


title: S. robusta MT- ( C) rep3


title: S. robusta MT- + Maribacter (M) rep2


title: Sexaully Induced S. robusta MT- + Roseovarius (SIPR) rep3


title: Sexaully Induced S. robusta MT- + Maribacter (SIPM) rep3


title: 2,4-D_2d_rep2


title: Sexaully Induced S. robusta MT- + Maribacter (SIPM) rep2


title: S. robusta MT- ( C) rep1


title: S. robusta MT- + Maribacter (M) rep1


title: Sexaully Induced S. robusta MT- (SIP) rep1


title: S. robusta MT- + Roseovarius ( R) rep3


title: S. robusta MT- + Roseovarius ( R) rep2


title: 72_B1

status: Public on Jun 25 2019

city: Madison

first: Randolph

middle: Scott

last: Ashton

state: WI

address: 330 N. Orchard Street

department: Biomedical Engineering

country: USA

institute: University of Wisconsin Madison

description:
72 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
72hr_Neuromesoderm_Neuroectoderm_B1

data_processing:
FASTQ ﬁles were generated by CASAVA (v1.8.2).
Reads were mapped to the human transcriptome (RefGene v1.2.3) using Bowtie (v0.12.8) (Langmead et al., 2009) allowing 2-mismatches and a maximum of 20 multiple hits. The gene expression values TPMs (Transcript per Million Reads) were calculated by RSEM (v1.2.3) (Li and Dewey, 2011).
One sample (48_B1) was removed due to overabundance of 0 count genes.
Genome_build: hg19
Supplementary_files_format_and_content: genes.tpm.tab (tab-delimited RSEM-generated gene expression estimates in Transcripts Per Million)

organism: Homo sapiens

source_name: hESC-derived neural stem cells (WA09)

growth_protocol: hESCs were maintained at 37°C in 5% CO2 in Essential 8 (E8) medium on 35 mm Matrigel (WiCell) coated tissue culture-treated plates and were passaged when 70-80% confluent. Briefly, cells were washed once with phosphate buffered saline (PBS, Invitrogen), then incubated at 37°C in Versene (Invitrogen) for 5 minutes. Versene was aspirated, the cells were gently dissociated from the well with fresh E8, and re-plated at a 1:6 or 1:12 seeding ratio. Media was replenished daily (Lippmann et. al. 2014).

extract_protocol:
Following 4 days of RA treatment, NSCs were lysed directly with RLT Lysis Buffer (Qiagen) and stored at -80°C until used for RNA isolation with the RNEasy 96 kit (Qiagen) according to the manufacturer’s instructions.
To prepare cDNA, the Ligation Mediated RNA sequencing library protocol was performed (Hou et. al. 2015).  Briefly, mRNA was isolated from purified 100 ng total RNA using oligo-dT beads (NEB). Isolated mRNA was fragmented in reverse transcription buffer and reverse transcribed with SmartScribe reverse transcriptase (Clontech).   RNase A and RNase H treatments were then performed to remove RNA. The 5’ adapter was ligated to the cDNA using RNA ligase 1 (NEB) and purified using Ampure XP Beads (Beckman).  The cDNA was then amplified with 18 cycles of PCR.  The indexed cDNA libraries were normalized and pooled at thirty samples per lane and sequenced on an Illumina HiSeq 2500 with a single 51bp read and a 10bp index read.

treatment_protocol: INITIATION: To initiate differentiation, hESCs were washed once with PBS, incubated at 37°C in Accutase (Invitrogen) for 5 minutes, singularized by gentle trituration, and quenched with media. Following centrifugation for 5 minutes at 1000 rpm, hESCs were replated onto 35 mm Matrigel-coated plates at a density of 1.0 x 105 cells/cm2 in E8 medium with 10 μM ROCK inhibitor (Y27632, Tocris) to improve cell survival (Day -1). The media was replaced with Essential 6 (E6) medium on the following day (Day 0), and then changed to E6 supplemented with 200 ng/mL FGF8b 24 hours later (Day 1). On Day 2, cells were washed once with PBS, incubated in Accutase for 1.5-2 minutes, and removed from the surface by gentle pipetting. After centrifugation, the cells were gently resuspended in neuromesodermal progenitors (NMPs) Medium containing 10 μM Y27632 and seeded on 6-well plates coated with Matrigel at a 2:3 surface area ratio to initiate HOX propagation in differentiating NMPs. HOX PROPAGATION: Following subculture on Day 2, the cells were transferred to a custom built Tecan (Mannedorf, Switzerland), BigNeat (Hampshire, United Kingdom) and LiConiC (Woburn, MA) automated platform. The automated tissue culture system replenished NMP media on Day 4. To generate the spectrum of neural stem cells (NSCs) for time course RNA-seq data, the automated system switched media from NMP to NSC media at two-hour time points (from 2 to 24 hours) or six-hour time points (from 24 to 72 hours) following the initiation of HOX propagation by CHIR99021. NSC media was systematically replenished daily for 4 days.

tag: cell line

tag: developmental stage

value: neural stem cell

tag: time point [hours of of hox propagation]

tag: replicate


title: Sexaully Induced S. robusta MT- + Maribacter (SIPM) rep1


title: 72_A2

description:
72 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
72hr_Neuromesoderm_Neuroectoderm_A2


title: 72_A1

description:
72 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
72hr_Neuromesoderm_Neuroectoderm_A1


title: 66_A1

description:
66 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
66hr_Neuromesoderm_Neuroectoderm_A1


title: 66_B1

description:
66 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
66hr_Neuromesoderm_Neuroectoderm_B1


title: 66_A2

description:
66 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
66hr_Neuromesoderm_Neuroectoderm_A2


title: 60_B1

description:
60 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
60hr_Neuromesoderm_Neuroectoderm_B1


title: CK_rep1


title: Sexaully Induced S. robusta MT- + Roseovarius (SIPR) rep1


title: 60_A2

description:
60 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
60hr_Neuromesoderm_Neuroectoderm_A2


title: 54_A2

description:
54 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
54hr_Neuromesoderm_Neuroectoderm_A2


title: 54_A1

description:
54 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
54hr_Neuromesoderm_Neuroectoderm_A1


title: 42_B1

description:
42 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
42hr_Neuromesoderm_Neuroectoderm_B1


title: 42_A1

description:
42 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
42hr_Neuromesoderm_Neuroectoderm_A1


title: 42_A2

description:
42 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
42hr_Neuromesoderm_Neuroectoderm_A2


title: 48_A2

description:
48 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
48hr_Neuromesoderm_Neuroectoderm_A2


title: 54_B1

description:
54 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
54hr_Neuromesoderm_Neuroectoderm_B1


title: 36_A2

description:
36 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
36hr_Neuromesoderm_Neuroectoderm_A2


title: 36_B1

description:
36 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
36hr_Neuromesoderm_Neuroectoderm_B1


title: 30_A2

description:
30 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
30hr_Neuromesoderm_Neuroectoderm_A2


title: 30_A1

description:
30 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
30hr_Neuromesoderm_Neuroectoderm_A1


title: 36_A1

description:
36 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
36hr_Neuromesoderm_Neuroectoderm_A1


title: 30_B1

description:
30 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
30hr_Neuromesoderm_Neuroectoderm_B1


title: 24_A1

description:
24 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
24hr_Neuromesoderm_Neuroectoderm_A1


title: 22_A2

description:
22 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
22hr_Neuromesoderm_Neuroectoderm_A2


title: 24_A2

description:
24 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
24hr_Neuromesoderm_Neuroectoderm_A2


title: 24_B1

description:
24 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
24hr_Neuromesoderm_Neuroectoderm_B1


title: 22_B1

description:
22 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
22hr_Neuromesoderm_Neuroectoderm_B1


title: 22_A1

description:
22 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
22hr_Neuromesoderm_Neuroectoderm_A1


title: 20_B1

description:
20 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
20hr_Neuromesoderm_Neuroectoderm_B1


title: 20_A2

description:
20 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
20hr_Neuromesoderm_Neuroectoderm_A2


title: 18_A2

description:
18 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
18hr_Neuromesoderm_Neuroectoderm_A2


title: 18_B1

description:
18 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
18hr_Neuromesoderm_Neuroectoderm_B1


title: 20_A1

description:
20 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
20hr_Neuromesoderm_Neuroectoderm_A1


title: 16_A2

description:
16 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
16hr_Neuromesoderm_Neuroectoderm_A2


title: 60_A1

description:
60 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
60hr_Neuromesoderm_Neuroectoderm_A1


title: 18_A1

description:
18 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
18hr_Neuromesoderm_Neuroectoderm_A1


title: 16_B1

description:
16 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
16hr_Neuromesoderm_Neuroectoderm_B1


title: 48_A1

description:
48 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
48hr_Neuromesoderm_Neuroectoderm_A1


title: 16_A1

description:
16 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
16hr_Neuromesoderm_Neuroectoderm_A1


title: 14_B1

description:
14 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
14hr_Neuromesoderm_Neuroectoderm_B1


title: 14_A2

description:
14 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
14hr_Neuromesoderm_Neuroectoderm_A2


title: 10_B1

description:
10 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
10hr_Neuromesoderm_Neuroectoderm_B1


title: 12_B1

description:
12 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
12hr_Neuromesoderm_Neuroectoderm_B1


title: 12_A1

description:
12 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
12hr_Neuromesoderm_Neuroectoderm_A1


title: 12_A2

description:
12 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
12hr_Neuromesoderm_Neuroectoderm_A2


title: 10_A1

description:
10 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
10hr_Neuromesoderm_Neuroectoderm_A1


title: 10_A2

description:
10 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
10hr_Neuromesoderm_Neuroectoderm_A2


title: 6_A1

description:
6 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
6hr_Neuromesoderm_Neuroectoderm_A1


title: 6_A2

description:
6 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
6hr_Neuromesoderm_Neuroectoderm_A2


title: 4_A2

description:
4 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
4hr_Neuromesoderm_Neuroectoderm_A2


title: 4_A1

description:
4 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
4hr_Neuromesoderm_Neuroectoderm_A1


title: 2_A2

description:
2 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
2hr_Neuromesoderm_Neuroectoderm_A2


title: 4_B1

description:
4 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
4hr_Neuromesoderm_Neuroectoderm_B1


title: 6_B1

description:
6 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
6hr_Neuromesoderm_Neuroectoderm_B1


title: 2_A1

description:
2 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
2hr_Neuromesoderm_Neuroectoderm_A1


title: 8_A1

description:
8 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
8hr_Neuromesoderm_Neuroectoderm_A1


title: 8_A2

description:
8 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A2
8hr_Neuromesoderm_Neuroectoderm_A2


title: dme-2_DMEFL-2_BS-seq_endo

status: Public on Jun 01 2019

city: kannapolis

first: Tzung-Fu

last: Hsieh

state: NORTH CAROLINA

address: 600 Laureate way

department: Plant and Microbial Biology

institute: North Carolina State University

library_source: genomic

data_processing:
We used Perl scripts to convert all the Cs in the ‘forward’ reads to Ts, and all the Gs in the ‘reverse’ reads to As. The converted reads were then aligned to the equivalently converted TAIR10 reference genome, allowing up to two mismatches per read.
Single_C: We use Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR10
Supplementary_files_format_and_content: All processed files are in GFF format. Files contain fractional methylation data for individual cytosines (single-c) or in 50 bp windows.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: dme DMEFL endosperm

growth_protocol: Long day condition (16 hours light, 8 hours dark) at 23 °C

extract_protocol:
Genomic DNA were isolated from hand dissected, 5-6 DAP (torpedo to early-bend stage seed stage) dme-2 endosperm that has been complemented by nDMECTD (dme-2/dme-2; nDMECTD/nDMECTD).
Approximately 20-50 ng of purified genomic DNA was sheared to about 300bp using Covaris M220 (Covaris Inc., Woburn, Massachusetts). The sheared DNA was cleaned up and recovered by 1.2x AMPure XP beads then followed by end repaired and A-tailing (NEBNext Ultra II DNA Library Prep Kit for Illumina, NEB) before ligated to the NEBNext methylated multiplex adaptors (NEBNext Multiplex Oligos for Illumina, NEB) according to the manufacturer’s instructions. Adaptor-ligated DNA was cleaned up with 1x AMPure XP beads. The purified adaptor-ligated DNA was subjected to one round of sodium bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research Corporation, Irvine, CA) as outlined in the manufacturer’s instruction with 80 min of conversion time. Half of the bisulfite-converted DNA molecules was PCR amplified with the following condition: 2.5 U of ExTaq DNA polymerase (Takara), 5 ul of 10 x Extaq reaction buffer, 25 µM dNTPs, 1 ul of universal and index primers (10 uM) in 50 uL reaction. The thermocyling condition was as follows: 95 °C for 2 min and then 10 cycles each of 95 °C for 30 s, 65 °C for 30 s, and 72 °C for 60 s. The enriched libraries were purified twice with 0.8x (v/v) AMPure XP beads to remove adaptor dimers. High throughput sequencing was performed by Novogene Corporation (USA).

tag: ecotype

value: Col-gl

value: dme-2/dme-2; DMEFL/DMEFL

value: endosperm


title: dme-2_DMEFL-3_BS-seq_endo


title: dme-2_DMEFL-1_BS-seq_endo


title: 14_A1

description:
14 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate A1
14hr_Neuromesoderm_Neuroectoderm_A1


title: 8_B1

description:
8 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
8hr_Neuromesoderm_Neuroectoderm_B1


title: 2_B1

description:
2 hours of of HOX propagation by CHIR99021, followed by 4 days of retinoic acid (RA) treatment to generate Neural Stem Cells, replicate B1
2hr_Neuromesoderm_Neuroectoderm_B1


title: Naive t3 Treated Stimulated Donor 3

status: Public on May 29 2019

type: RNA

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

description:
200627770030_B
200627770030_B_Grn.idat
72h IL6 treated and 144h TCR stimulated cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background correction, transformation and normalization were performed using bgAdjust, VST and RSN Lumi R package methods, respectively.

label: biotin

source_name: Naïve CD4+ T-cells

label_protocol: Biotinylation of cRNA

growth_protocol: Naïve and memory CD4+ T-cells were isolated using a RosetteSep Human CD4+ T-cell Enrichment Cocktail (Stemcell Technologies) followed by CD45RO MicroBeads (MiltenyiBiotech) and cultured in serum-free medium (TexMACS, Miltenyi Biotech).

extract_protocol: RNA was extracted from naïve and memory CD4+ T-cells at indicated experimental timepoints using RNeasy Mini kit (Qiagen), as per manufacturer’s instructions.

treatment_protocol: CD4+ T-cells were treated with indicated final concentrations of IL-6 and equimolar sIL-6R (both PeproTech EC) in a 1ml total volume (24 well plate) or 0.5ml volume (48 well plate) for 72 hours at 37°C with 5% CO2. Cells were harvested and washed twice, to remove IL-6/sIL-6R, before stimulation for 3-6 days with plate bound anti-CD3 (0.2μg/ml or 0.5μg/ml; eBioscience) and 1μg/ml soluble anti-CD28 (Biolegend).

tag: cell type

value: Naïve CD4+ T-cells

tag: donor

value: Treated

value: Stimulated

tag: time point


title: Memory t1 Treated Unstimulated Donor 3

description:
200627770031_C
200627770031_C_Grn.idat
72h IL6 treated and 16h TCR stimulated cells

source_name: Memory CD4+ T-cells

value: Memory CD4+ T-cells

value: Unstimulated


title: Memory t2 Treated Unstimulated Donor 3

description:
200627770031_G
200627770031_G_Grn.idat
72h IL6 treated and 4h TCR stimulated cells


title: Memory t3 Treated Stimulated Donor 3

description:
200627770031_K
200627770031_K_Grn.idat
72h IL6 treated and 144h TCR stimulated cells


title: Naive t1 Treated Unstimulated Donor 3

description:
200627770030_E
200627770030_E_Grn.idat
72h IL6 treated and 16h TCR stimulated cells


title: Memory t0 Untreated Unstimulated Donor 2

description:
200627770018_H
200627770018_H_Grn.idat
0h IL6 untreated and TCR unstimulated cells

value: Untreated


title: Memory t2 Untreated Unstimulated Donor 3

description:
200627770031_E
200627770031_E_Grn.idat
72h IL6 untreated and 4h TCR stimulated cells


title: Memory t0 Untreated Unstimulated Donor 3

description:
200627770030_L
200627770030_L_Grn.idat
0h IL6 untreated and TCR unstimulated cells


title: Memory t1 Untreated Unstimulated Donor 2

description:
200627770018_J
200627770018_J_Grn.idat
72h IL6 untreated and 16h TCR stimulated cells


title: Naive t2 Treated Unstimulated Donor 2

description:
200627770018_E
200627770018_E_Grn.idat
72h IL6 treated and 4h TCR stimulated cells


title: Memory t3 Untreated Stimulated Donor 3

description:
200627770031_I
200627770031_I_Grn.idat
72h IL6 untreated and 144h TCR stimulated cells


title: Naive t1 Untreated Unstimulated Donor 3

description:
200627770030_C
200627770030_C_Grn.idat
72h IL6 untreated and 16h TCR stimulated cells


title: Naive t2 Treated Unstimulated Donor 1

description:
200627770010_I
200627770010_I_Grn.idat
72h IL6 treated and 4h TCR stimulated cells


title: Memory t0 Untreated Unstimulated Donor 1

description:
200627770010_L
200627770010_L_Grn.idat
0h IL6 untreated and TCR unstimulated cells


title: Naive t1 Treated Unstimulated Donor 1

description:
200627770010_E
200627770010_E_Grn.idat
72h IL6 treated and 16h TCR stimulated cells


title: Naive t3 Untreated Stimulated Donor 2

description:
200627770018_G
200627770018_G_Grn.idat
72h IL6 untreated and 144h TCR stimulated cells


title: Memory t1 Untreated Unstimulated Donor 3

description:
200627770031_A
200627770031_A_Grn.idat
72h IL6 untreated and 16h TCR stimulated cells


title: Naive t1 Untreated Unstimulated Donor 1

description:
200627770010_C
200627770010_C_Grn.idat
72h IL6 untreated and 16h TCR stimulated cells


title: Naive t1 Treated Unstimulated Donor 2

description:
200627770018_A
200627770018_A_Grn.idat
72h IL6 treated and 16h TCR stimulated cells


title: Naive t2 Treated Unstimulated Donor 3

description:
200627770030_I
200627770030_I_Grn.idat
72h IL6 treated and 4h TCR stimulated cells


title: Naive t2 Untreated Unstimulated Donor 2

description:
200627770018_C
200627770018_C_Grn.idat
72h IL6 untreated and 4h TCR stimulated cells


title: Naive t2 Untreated Unstimulated Donor 3

description:
200627770030_G
200627770030_G_Grn.idat
72h IL6 untreated and 4h TCR stimulated cells


title: Naive t3 Untreated Stimulated Donor 3

description:
200627770030_K
200627770030_K_Grn.idat
72h IL6 untreated and 144h TCR stimulated cells


title: Naive t3 Treated Stimulated Donor 1

description:
200627770010_B
200627770010_B_Grn.idat
72h IL6 treated and 144h TCR stimulated cells


title: Naive t0 Untreated Unstimulated Donor 3

description:
200627770030_A
200627770030_A_Grn.idat
0h IL6 untreated and TCR unstimulated cells


title: Naive t3 Untreated Stimulated Donor 1

description:
200627770010_K
200627770010_K_Grn.idat
72h IL6 untreated and 144h TCR stimulated cells


title: Naive t3 Treated Stimulated Donor 2

description:
200627770018_I
200627770018_I_Grn.idat
72h IL6 treated and 144h TCR stimulated cells


title: Naive t2 Untreated Unstimulated Donor 1

description:
200627770010_G
200627770010_G_Grn.idat
72h IL6 untreated and 4h TCR stimulated cells


title: Memory t1 Treated Unstimulated Donor 2

description:
200627770018_L
200627770018_L_Grn.idat
72h IL6 treated and 16h TCR stimulated cells


title: Naive t0 Untreated Unstimulated Donor 1

description:
200627770010_A
200627770010_A_Grn.idat
0h IL6 untreated and TCR unstimulated cells


title: EC_035_HUAEC_RNA-seq

status: Public on May 24 2019

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
BAM-formatted map files were generated using STAR version 2.6.1d with default parameters.
Genome_build: hg19 (GRCh37) and hg38 (GRCh38) for BAM, BigWig and expression values. hg19 (GRCh37) for expression matrix file (kallisto.GRCh37.xlsx).
Supplementary_files_format_and_content: The transcript-level expression values were estimated by kallisto version 0.43.1 with default paramters. These transcript-level expression values were then assembled to the gene-level by tximport.
Supplementary_files_format_and_content: BigWig files were generated both with and without the total read normaization (RPM) by DROMPA+ verision 1.1.2.

molecule: polyA RNA

source_name: Umbilical Artery Endothelial cells

growth_protocol: Purified ECs were cultured in VascuLife VEGF Endothelial Cell Culture Medium (Lifeline Cell Technology, Frederick, MD) with 250 pg/mL VEGF. Cells were maintained at 37°C in a humidified 5% CO2 incubator and the medium was changed every 3 days.

extract_protocol:
Poly(A)-containing mRNA molecules were isolated from total RNA
mRNA were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: newborn

value: Caucasian

value: female

value: Cessation of life

tag: disease

value: Disease type AND/OR category unknown

value: umbilical artery endothelial cell

value: RNA-Seq

tag: molecule

value: polyA RNA

value: Poly(A)-containing mRNA molecules were isolated from total RNA and were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).

value: cDNA

tag: amplified

value: True


title: EC_040_HUVEC_RNA-seq

source_name: Umbilical Vein Endothelial cells

value: male

value: endothelial cell of umbilical vein


title: EC_039_HUVEC_RNA-seq

value: Primary Cell

value: Arabic


title: EC_029_HUVEC_RNA-seq

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo


title: EC_028_HUAEC_RNA-seq

value: year

value: newborn


title: EC_154_HRAEC_RNA-seq

source_name: Renal Artery Endothelial cells

value: adult

value: Asian

value: kidney blood vessel cell


title: EC_160_HRAEC_RNA-seq

value: female

value: Cessation of life

value: Disease type AND/OR category unknown


title: EC_162_HRAEC_RNA-seq

value: RNA-Seq

value: polyA RNA

value: Poly(A)-containing mRNA molecules were isolated from total RNA and were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).


title: EC_158_HRAEC_RNA-seq

value: male

value: cDNA

value: True


title: EC_156_HRAEC_RNA-seq

value: Primary Cell


title: EC_146_HRAEC_RNA-seq

value: Epigenome and transcriptome database for human vascular endothelial cells


title: EC_150_HRAEC_RNA-seq

value: The University of Tokyo


title: Naive t0 Untreated Unstimulated Donor 2

description:
200627770004_J
200627770004_J_Grn.idat
0h IL6 untreated and TCR unstimulated cells

value: Naïve CD4+ T-cells

value: Untreated

value: Unstimulated


title: Memory t3 Treated Stimulated Donor 1

description:
200627770004_K
200627770004_K_Grn.idat
72h IL6 treated and 144h TCR stimulated cells

value: Memory CD4+ T-cells

value: Treated

value: Stimulated


title: EC_059_HENDC_RNA-seq

source_name: Endocardial cells

value: year

value: adult

value: Native American

value: female

value: Cessation of life

value: endocardial cell


title: EC_089_HGSVEC_RNA-seq

source_name: Great Saphenous Vein Endothelial cells

value: Asian

value: male

value: Disease type AND/OR category unknown

value: vein endothelial cell

value: RNA-Seq

value: polyA RNA

value: Poly(A)-containing mRNA molecules were isolated from total RNA and were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).

value: cDNA


title: Memory t3 Untreated Stimulated Donor 1

description:
200627770004_I
200627770004_I_Grn.idat
72h IL6 untreated and 144h TCR stimulated cells

value: Memory CD4+ T-cells

value: Untreated


title: Memory t2 Untreated Unstimulated Donor 1

description:
200627770004_E
200627770004_E_Grn.idat
72h IL6 untreated and 4h TCR stimulated cells

value: Unstimulated


title: Memory t1 Untreated Unstimulated Donor 1

description:
200627770004_A
200627770004_A_Grn.idat
72h IL6 untreated and 16h TCR stimulated cells


title: EC_112_HGSVEC_RNA-seq

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: True


title: EC_116_HGSVEC_RNA-seq

value: adult

value: Cessation of life


title: Memory t3 Treated Stimulated Donor 2

description:
200627770001_G
200627770001_G_Grn.idat
72h IL6 treated and 144h TCR stimulated cells

value: Treated

value: Stimulated


title: Memory t1 Treated Unstimulated Donor 1

description:
200627770004_C
200627770004_C_Grn.idat
72h IL6 treated and 16h TCR stimulated cells


title: Memory t2 Treated Unstimulated Donor 1

description:
200627770004_G
200627770004_G_Grn.idat
72h IL6 treated and 4h TCR stimulated cells


title: Memory t2 Treated Unstimulated Donor 2

description:
200627770001_C
200627770001_C_Grn.idat
72h IL6 treated and 4h TCR stimulated cells


title: EC_042_HENDC_RNA-seq

value: Caucasian

value: male

value: Disease type AND/OR category unknown

value: endocardial cell


title: EC_014_HPAEC_RNA-seq

source_name: Pulmonary Artery Endothelial cells

value: female

value: pulmonary artery endothelial cell

value: RNA-Seq

value: polyA RNA

value: Poly(A)-containing mRNA molecules were isolated from total RNA and were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).

value: cDNA


title: EC_025_HPAEC_RNA-seq

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo


title: EC_023_HENDC_RNA-seq

value: year

value: child

value: African American

value: True


title: EC_045_HCCaEC_RNA-seq

source_name: Common Carotid Artery Endothelial cells

value: adult

value: Asian

value: Cessation of life

value: endothelial cell of artery


title: EC_046_HCCaEC_RNA-seq

value: male

value: Disease type AND/OR category unknown


title: EC_055_HCCaEC_RNA-seq

value: Caucasian

value: female

value: RNA-Seq


title: EC_026_HCoAEC_RNA-seq

source_name: Coronary Artery Endothelial cells

value: endothelial cell of coronary artery

value: polyA RNA

value: Poly(A)-containing mRNA molecules were isolated from total RNA and were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).

value: cDNA


title: EC_015_HCoAEC_RNA-seq

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year


title: EC_047_HCCaEC_RNA-seq

value: adult

value: True


title: EC_052_HCCaEC_RNA-seq

value: Asian

value: Cessation of life


title: EC_034_HCoAEC_RNA-seq

value: child

value: male


title: EC_061_HCoAEC_RNA-seq

value: Native American

value: Disease type AND/OR category unknown


title: EC_060_HAoEC_RNA-seq

source_name: Aortic Endothelial cells

value: female

value: aortic endothelial cell

value: RNA-Seq


title: EC_031_HAoEC_RNA-seq

value: African/American

value: polyA RNA

value: Poly(A)-containing mRNA molecules were isolated from total RNA and were converted to cDNA with oligo dT primers using a TruSeq RNA Sample Preparation kit v2 (Illumina).


title: EC_038_HCCaEC_RNA-seq

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: endothelial cell of artery

value: cDNA


title: Memory t2 Untreated Unstimulated Donor 2

description:
200627770001_A
200627770001_A_Grn.idat
72h IL6 untreated and 4h TCR stimulated cells

value: Memory CD4+ T-cells

value: Untreated

value: Unstimulated


title: EC_013_HAoEC_RNA-seq

value: The University of Tokyo

value: year

value: adult

value: Caucasian

value: Cessation of life

value: True


title: Naive t1 Untreated Unstimulated Donor 2

description:
200627770004_L
200627770004_L_Grn.idat
72h IL6 untreated and 16h TCR stimulated cells

value: Naïve CD4+ T-cells


title: Subject N4 at Week 0,Normal

status: Public on May 02 2019

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: gene expression data from lesional and non-lesional skin phenotypes of patients with moderate-to-severe atopic dermatitis

hyb_protocol: RNA was hybridized to Affymetrix Human U133Plus 2.0 gene arrays

data_processing: Expression measures were obtained by using the GC Robust Multi-array Average algorithm.

source_name: homo sapiens skin biopsy, Week 0, Normal

extract_protocol: RNA was extracted according to manufacturer's instructions.

treatment_protocol: Atopic dermatitis patients randomized 1:1 to dupilumab 200mg or placebo weekly for 16 weeks, with lesional and non-lesional biopsies taken at baseline, week 4 (only lesional) and week 16 both lesional and non lesional

tag: Sex

tag: time

value: Normal

tag: treatment

tag: subject id

tag: race

tag: ethnicity

tag: easi

tag: scorad


title: Subject N12 at Week 0,Normal

tag: tissue


title: Subject N5 at Week 0,Normal


title: Subject N8 at Week 0,Normal


title: Subject N3 at Week 0,Normal


title: Subject N21 at Week 0,Normal


title: Subject N14 at Week 0,Normal


title: Subject 101008 at Week 16,non-lesional

source_name: homo sapiens skin biopsy, Week 16, non-lesional

value: M

value: NL

value: Dupilumab

value: WHITE

value: NOT HISPANIC OR LATINO


title: Subject N1 at Week 0,Normal


title: Subject N11 at Week 0,Normal


title: Subject N15 at Week 0,Normal


title: Subject N17 at Week 0,Normal


title: Subject N18 at Week 0,Normal


title: Subject N2 at Week 0,Normal


title: Subject N20 at Week 0,Normal


title: Subject 101007 at Week 16,lesional

source_name: homo sapiens skin biopsy, Week 16, lesional

value: LS

value: Placebo

value: ASIAN


title: Subject N7 at Week 0,Normal


title: Subject 101008 at Week 4,lesional

source_name: homo sapiens skin biopsy, Week 4, lesional


title: Subject 101007 at Week 4,lesional


title: Subject 101008 at Week 0,lesional

source_name: homo sapiens skin biopsy, Week 0, lesional


title: Subject N16 at Week 0,Normal


title: Subject N9 at Week 0,Normal


title: Subject 101008 at Week 16,lesional


title: Subject N13 at Week 0,Normal


title: Subject 101007 at Week 0,lesional


title: Subject 101008 at Week 0,non-lesional

source_name: homo sapiens skin biopsy, Week 0, non-lesional


title: Subject 201023 at Week 0,non-lesional


title: Subject N10 at Week 0,Normal


title: Subject 201023 at Week 0,lesional


title: Subject 201022 at Week 0,lesional


title: Subject 201021 at Week 0,lesional

value: F

value: BLACK OR AFRICAN AMERICAN


title: Subject 201020 at Week 4,lesional


title: Subject 201022 at Week 0,non-lesional


title: Subject 201021 at Week 4,lesional


title: Subject 201021 at Week 0,non-lesional


title: Subject 201021 at Week 16,non-lesional


title: Subject 201020 at Week 16,lesional


title: Subject 201020 at Week 16,non-lesional


title: Subject 201019 at Week 0,lesional


title: Subject 201019 at Week 4,lesional


title: Subject 201019 at Week 16,non-lesional


title: Subject 201018 at Week 0,non-lesional


title: Subject 201019 at Week 0,non-lesional


title: Subject 201020 at Week 0,non-lesional


title: Subject 201018 at Week 0,lesional


title: Subject N19 at Week 0,Normal


title: Subject 201013 at Week 4,lesional


title: Subject 201013 at Week 0,lesional


title: Subject 201019 at Week 16,lesional


title: Subject 201018 at Week 4,lesional


title: Subject 201013 at Week 0,non-lesional


title: Subject 201020 at Week 0,lesional


title: Subject 201012 at Week 0,non-lesional


title: Subject 201012 at Week 0,lesional


title: Memory t3 Untreated Stimulated Donor 2

description:
200627770001_E
200627770001_E_Grn.idat
72h IL6 untreated and 144h TCR stimulated cells

value: Memory CD4+ T-cells

value: Untreated

value: Stimulated


title: Subject 201011 at Week 16,non-lesional


title: Subject 201011 at Week 0,lesional


title: Subject 201011 at Week 0,non-lesional


title: Subject 101005 at Week 4,lesional


title: Subject 201011 at Week 4,lesional


title: Subject 201021 at Week 16,lesional


title: Subject 201008 at Week 4,lesional


title: Subject 201009 at Week 0,non-lesional


title: Subject 201008 at Week 16,lesional


title: Subject 201009 at Week 4,lesional


title: Subject 201008 at Week 0,non-lesional


title: Subject 201011 at Week 16,lesional


title: Subject 101005 at Week 0,lesional


title: Subject 201008 at Week 16,non-lesional


title: Subject 201008 at Week 0,lesional


title: Subject 201007 at Week 16,non-lesional


title: Subject 201007 at Week 4,lesional


title: Subject 201007 at Week 0,non-lesional


title: Subject 201005 at Week 4,lesional


title: Subject 201007 at Week 16,lesional


title: Subject 201007 at Week 0,lesional


title: Subject 201006 at Week 4,lesional


title: Subject 201004 at Week 4,lesional


title: Subject 201005 at Week 0,non-lesional


title: Subject 201004 at Week 0,non-lesional


title: Subject 201009 at Week 0,lesional


title: Subject 201006 at Week 0,lesional


title: Subject 201003 at Week 4,lesional


title: Subject 201006 at Week 0,non-lesional


title: Subject 201003 at Week 16,non-lesional


title: Subject 201005 at Week 0,lesional


title: Subject 201002 at Week 0,lesional


title: Subject 201004 at Week 0,lesional


title: Subject 201003 at Week 16,lesional


title: Subject 104007 at Week 4,lesional


title: Subject 201002 at Week 0,non-lesional


title: Subject 101004 at Week 16,lesional


title: Subject 101004 at Week 0,non-lesional


title: Subject 201001 at Week 4,lesional


title: Subject 201003 at Week 0,non-lesional


title: Subject 104007 at Week 0,non-lesional


title: Subject 104007 at Week 16,lesional


title: Subject 104006 at Week 0,lesional


title: Subject 104005 at Week 4,lesional


title: Subject 201002 at Week 4,lesional


title: Subject 104005 at Week 0,lesional


title: Subject 104007 at Week 0,lesional


title: Subject 201001 at Week 0,non-lesional


title: Subject 104007 at Week 16,non-lesional


title: Subject 104006 at Week 0,non-lesional


title: Subject 104006 at Week 4,lesional


title: Subject 201003 at Week 0,lesional


title: Subject 201001 at Week 0,lesional


title: Subject 101004 at Week 0,lesional


title: Subject 104005 at Week 0,non-lesional


title: Subject 104004 at Week 4,lesional


title: Subject 104004 at Week 16,lesional


title: Subject 101004 at Week 4,lesional


title: Subject 104004 at Week 0,lesional


title: Subject 104004 at Week 0,non-lesional


title: Subject 104003 at Week 0,lesional


title: Subject 103004 at Week 4,lesional


title: Subject 103004 at Week 0,lesional


title: Subject 104004 at Week 16,non-lesional


title: Subject 104002 at Week 0,lesional


title: Subject 104003 at Week 0,non-lesional


title: Subject 103002 at Week 0,lesional


title: Subject 103004 at Week 0,non-lesional


title: Subject 103001 at Week 0,non-lesional


title: Subject 101003 at Week 0,lesional


title: Subject 104002 at Week 4,lesional


title: Subject 103002 at Week 4,lesional


title: Subject 102015 at Week 16,lesional


title: Subject 103001 at Week 4,lesional


title: Subject 102012 at Week 16,lesional

value: OTHER


title: Subject 102013 at Week 16,non-lesional

value: HISPANIC OR LATINO


title: Subject 102015 at Week 0,lesional


title: Subject 102012 at Week 16,non-lesional


title: Subject 102015 at Week 16,non-lesional


title: Subject 103001 at Week 0,lesional


title: Subject 102013 at Week 16,lesional


title: Subject 102015 at Week 0,non-lesional


title: Subject 101003 at Week 4,lesional


title: Subject 102013 at Week 4,lesional


title: Subject 102012 at Week 0,non-lesional


title: Subject 102012 at Week 0,lesional


title: Subject 102011 at Week 16,lesional

value: NOT REPORTED


title: Subject 102011 at Week 0,lesional


title: Subject 102010 at Week 16,non-lesional


title: Subject 102011 at Week 16,non-lesional


title: Subject 102009 at Week 4,lesional


title: Subject 102010 at Week 0,lesional


title: Subject 104002 at Week 0,non-lesional


title: Subject 102011 at Week 4,lesional


title: Subject 102006 at Week 4,lesional


title: Subject 102009 at Week 16,lesional


title: Subject 102010 at Week 16,lesional


title: Subject 102010 at Week 0,non-lesional


title: Subject 102009 at Week 16,non-lesional


title: Subject 102010 at Week 4,lesional


title: Subject 102008 at Week 16,lesional


title: Subject 102006 at Week 16,non-lesional


title: Subject 102008 at Week 0,lesional


title: Subject 102006 at Week 16,lesional


title: Subject 102006 at Week 0,non-lesional


title: Subject 102005 at Week 16,non-lesional


title: Subject 102008 at Week 4,lesional


title: Subject 102006 at Week 0,lesional


title: Subject 102011 at Week 0,non-lesional


title: Subject 102005 at Week 4,lesional


title: Subject 102005 at Week 0,lesional


title: Subject 102009 at Week 0,non-lesional


title: Subject 102005 at Week 0,non-lesional


title: Subject 102005 at Week 16,lesional


title: Subject 101002 at Week 16,lesional


title: Subject 101002 at Week 0,lesional


title: Subject 102004 at Week 16,non-lesional


title: Subject 101002 at Week 4,lesional


title: Subject 102001 at Week 4,lesional


title: Subject 102002 at Week 16,lesional


title: Subject 102002 at Week 0,lesional


title: Subject 102004 at Week 0,lesional


title: Subject 102004 at Week 0,non-lesional


title: Subject 101014 at Week 16,lesional


title: Subject 102001 at Week 16,non-lesional


title: Subject 102002 at Week 4,lesional


title: Subject 101015 at Week 0,lesional


title: Subject 102002 at Week 0,non-lesional


title: Subject 102001 at Week 16,lesional


title: Subject 102001 at Week 0,lesional


title: Subject 101014 at Week 4,lesional


title: Subject 101012 at Week 0,lesional


title: Subject 102009 at Week 0,lesional


title: Subject 101013 at Week 0,non-lesional


title: Subject 101013 at Week 0,lesional


title: Subject 102001 at Week 0,non-lesional


title: Subject 101012 at Week 16,lesional


title: Subject 101013 at Week 4,lesional


title: 8016q3

status: Public on Apr 17 2019

data_processing:
RNA-seq count data at 3 timepoints was generated for Zika-exposed and Zika-naïve individuals, extracted from PAXgene RNA blood solution with the PAXgene Blood RNA Kit using DNase digestion and an additional clean-up using RNEasy MinElute kit.
Purified RNA samples were quantified by Qubit 3.0 fluorometer with RNA High Sensitivity Assay kit.
Quality of the RNA samples was confirmed with the RNA High Sensitivity ScreenTape using the TapeStation 2200 (Agilent Technologies).
Supplementary_files_format_and_content: csv files for count data, phenotype data

source_name: serum

extract_protocol:
Total RNA was extracted from PAXgene RNA blood solution with the PAXgene Blood RNA Kit  by following manufacturers’ instructions including DNase digestion and an additional clean-up using RNEasy MinElute kit. Purified RNA samples were quantified by Qubit 3.0 fluorometer with RNA High Sensitivity Assay kit. Quality of the RNA samples was confirmed with the RNA High Sensitivity ScreenTape using the TapeStation 2200.
Sample libraries were then prepared from the 267 samples’ libraries (from three time points of 89 paired patient samples). First, ribosomal RNA (rRNA) and globin mRNA were removed from 200 ng total RNA, and the remaining RNA was fragmented and primed for cDNA synthesis using TruSeq Total Stranded RNA HT kit with Ribo-Zero Globin on a Microlab STAR automated liquid handling system. The libraries were barcoded with TruSeq HT indices to allow for multiplexing, and ligation-mediated PCR was performed to enrich barcoded libraries for 15 cycles, then purified with the Agencourt AMPure XP beads system. The libraries were assessed for quality with the high-sensitivity DNA chip in a TapeStation 2200 and quantified with KAPA Library Quantification Kits for Illumina platforms. The libraries were diluted to 2nM and combined equimolarly in pools of 12. These pools were then clustered using a cBot with a HiSeq 3000/4000 paired-end cluster kit on a patterned flow cell, one pool per lane. The flow cell was sequenced on a HiSeq4000 using a HiSeq 3000/4000 SBS kit. Two technical replicates were sequenced per biological sample, for a total of 2 sequencing runs.

tag: patient

tag: sample

tag: visit

value: Convalescent

tag: age

value: nonnaive

value: DENV

value: 0 infcs

value: serum+

tag: exposure

value: serum+/?

value: NoFever

value: Fever

tag: priorinfectionbin


title: 8016q1

value: Late Acute

value: M


title: 7933q3

value: F

value: 1 infcs


title: Subject 102004 at Week 16,lesional

value: LS

value: Dupilumab

value: WHITE

value: NOT HISPANIC OR LATINO


title: Subject 102004 at Week 4,lesional


title: Subject 102002 at Week 16,non-lesional

value: NL


title: 7883q5

value: Early Acute

value: naive

value: urine-

value: serum+/urine-

value: Naive


title: 7886q3

value: Convalescent

value: 0 infcs

value: serum+

value: urine+

value: serum+/urine+


title: 7886q1

value: Late Acute

value: F

value: NoFever

value: Fever


title: 7886q5


title: 7871q3

value: M

value: serum-

value: serum-/urine+


title: 7871q2


title: Subject 101011 at Week 16,lesional

value: LS

value: Dupilumab

value: WHITE

value: NOT HISPANIC OR LATINO


title: Subject 101011 at Week 4,lesional


title: Subject 101011 at Week 0,lesional


title: Subject 101001 at Week 4,lesional


title: Subject 103002 at Week 0,non-lesional

value: NL

value: Placebo


title: 7883q3

value: Convalescent

value: naive

value: 0 infcs

value: urine-

value: serum+/urine-

value: Naive


title: Subject 101010 at Week 0,lesional

value: BLACK OR AFRICAN AMERICAN


title: 7706q3

value: serum+

value: urine+

value: serum+/urine+

value: NoFever

value: Fever


title: 7883q1

value: Late Acute

value: M


title: 7706q5

value: Early Acute


title: 7871q5

value: serum-

value: serum-/urine+


title: 7658q1

value: F


title: Subject 101014 at Week 0,lesional

value: LS

value: Dupilumab

value: WHITE

value: NOT HISPANIC OR LATINO


title: 7658q5

value: naive

value: 0 infcs

value: urine-

value: serum+/urine-

value: Naive


title: 7658q3

value: Convalescent

value: serum+

value: NoFever


title: Subject 101010 at Week 0,non-lesional

value: M

value: NL

value: Placebo

value: BLACK OR AFRICAN AMERICAN


title: 7612q5

value: Early Acute

value: F

value: urine+

value: serum+/urine+

value: Fever


title: Subject 101001 at Week 16,lesional

value: LS

value: Dupilumab

value: WHITE

value: NOT HISPANIC OR LATINO


title: Subject 101001 at Week 0,non-lesional


title: 7612q1

value: Late Acute

value: naive

value: 0 infcs

value: Naive


title: Subject 101001 at Week 0,lesional


title: 7543q5

value: serum+

value: urine-

value: serum+/urine-

value: NoFever


title: 7543q3

value: Convalescent


title: 7612q3

value: F


title: 7543q1


title: Subject 101001 at Week 16,non-lesional

value: NL


title: 7504q5

value: Early Acute

value: M

value: DENV

value: urine+

value: serum+/urine+


title: 7706q1

value: Fever


title: 7504q3


title: 7504q1

value: Late Acute


title: 7487q5

value: nonnaive


title: 7444q5

value: naive

value: 0 infcs


title: 7487q1

value: serum+


title: 7487q3


title: 7444q1

value: Naive


title: 7444q3


title: 7434q3

value: urine-

value: serum+/urine-


title: 7434q5

value: NoFever


title: 7434q1

value: F


title: 7418q1


title: 7418q3

value: Convalescent


title: 726q5

value: Early Acute

value: 1 infcs


title: 726q1

value: DENV


title: 7253q5

value: M


title: 7320q1


title: 7208q5


title: 7320q3


title: 7208q3


title: 726q3


title: 7208q1


title: Subject 101012 at Week 4,lesional

value: LS

value: Placebo

value: ASIAN

value: NOT HISPANIC OR LATINO


title: 7180q5

value: naive

value: Fever


title: 7418q5

value: nonnaive

value: 0 infcs

value: serum+


title: 7253q1

value: Late Acute

value: urine-

value: serum+/urine-

value: Naive


title: 7180q3

value: Convalescent

value: F

value: NoFever


title: 7253q3

value: M


title: 7180q1


title: 7134q5

value: Early Acute

value: urine+

value: serum+/urine+


title: 7134q3


title: 7127q5

value: DENV

value: serum-

value: serum-/urine+


title: 7134q1

value: naive


title: 7127q3

value: nonnaive

value: 0 infcs


title: 7127q1

value: Late Acute


title: 7119q3

value: naïve

value: serum+

value: Fever


title: 7119q5

value: Naive


title: 7100q3

value: Convalescent

value: F

value: urine-

value: serum+/urine-


title: 7100q5

value: Early Acute

value: NoFever


title: 7100q1


title: 7096q5

value: urine+

value: serum+/urine+


title: 7096q3


title: 7066q3

value: M


title: 7066q1

value: naive


title: 7066q5


title: 7096q1


title: 6819q1

value: nonnaive

value: DENV

value: serum-

value: serum-/urine+


title: 6819q5

value: 0 infcs


title: 6790q3

value: serum+


title: 6918q3

value: Naive


title: 6790q5


title: 6790q1

value: Late Acute


title: 6777q1


title: 6775q5

value: Fever


title: 6777q5

value: urine-


title: 6763q5

value: F

value: serum+/urine-


title: 7119q1

value: naïve

value: NoFever


title: 6763q3

value: Convalescent


title: 6775q3

value: M

value: urine+

value: serum+/urine+


title: 6777q3

value: nonnaive

value: DENV


title: 6775q1


title: 6763q1

value: naive


title: 6918q5

value: Early Acute

value: 0 infcs


title: 6739q3

value: serum+

value: Naive


title: 6739q1

value: Late Acute

value: Fever


title: 6697q3

value: urine-


title: 6918q1

value: F

value: serum+/urine-


title: 6739q5

value: NoFever


title: 6669q5


title: 6697q1


title: 6669q3

value: Convalescent


title: 6661q3

value: M


title: 6669q1


title: 6697q5


title: 6643q5


title: 6643q1


title: 6661q5

value: urine+


title: 6625q3

value: serum+/?


title: 6643q3


title: 6605q5

value: serum+/urine+


title: 6605q3


title: 6563q3


title: 6563q1


title: 6558q5


title: 6563q5


title: 6558q3


title: 6558q1


title: 6364q5

value: DENV

value: 1 infcs


title: 6364q3

value: naive


title: 6661q1

value: 0 infcs


title: 6364q1

value: serum+


title: 6547q1


title: 6253q5

value: Early Acute

value: Naive


title: 6547q5

value: Fever


title: 6547q3

value: urine-


title: 6253q1

value: Late Acute

value: F


title: 6248q5

value: NoFever


title: 6215q5

value: nonnaive

value: serum+/urine-


title: 6248q1

value: M

value: urine+


title: 6253q3

value: Convalescent

value: serum+/urine+


title: 6215q1

value: DENV


title: 5966q5

value: naive


title: 6625q1

value: 0 infcs

value: serum+/?


title: 5966q3

value: serum+


title: 6605q1

value: Naive


title: 5966q1

value: Fever


title: 5962q3

value: 1 infcs


title: 5953q5

value: Early Acute

value: urine-


title: 5953q3

value: F

value: NoFever


title: 5962q1

value: Late Acute


title: 5953q1

value: serum+/urine-


title: 5893q5

value: M


title: 5893q3

value: Convalescent


title: 5893q1


title: 5695q1

value: urine+

value: serum+/urine+


title: 5695q3

value: naive

value: DENV


title: 6248q3

value: 0 infcs


title: 5660q3

value: nonnaive

value: serum+


title: 5695q5


title: 5660q5


title: 5660q1


title: 6215q3


title: 5575q3

value: Fever


title: 5540q5


title: 5575q5

value: 1 infcs


title: 5540q3


title: 5540q1


title: 5575q1


title: 5506q5

value: Early Acute

value: 2 infcs


title: 5506q1

value: F

value: urine-


title: 5506q3

value: NoFever


title: 7933q5

value: serum+/?


title: 5406q3

value: M

value: Naive


title: 5406q1

value: Late Acute

value: urine+


title: 5376q5

value: naive

value: serum+/urine-


title: 5376q1

value: DENV


title: 5376q3

value: Convalescent


title: 5355q5

value: 0 infcs

value: serum+

value: serum+/urine+


title: 7933q1

value: nonnaive

value: 1 infcs

value: Fever


title: 5338q5

value: Early Acute

value: F

value: urine-


title: 5338q3

value: NoFever


title: 5329q5

value: M


title: 5338q1

value: Late Acute


title: 5256q1

value: 2 infcs


title: 5550q5

value: naive


title: 5406q5

value: urine+

value: Naive


title: 5256q3

value: Convalescent

value: DENV

value: serum+/urine-


title: 5256q5

value: serum+


title: 5248q5

value: 0 infcs


title: 5550q1

value: 1 infcs


title: 5066q1

value: nonnaive

value: serum+/urine+


title: 5149q1

value: F


title: 5138q3

value: naïve


title: 5149q3

value: NoFever


title: 5550q3

value: M

value: urine-

value: Fever


title: 5138q1

value: Late Acute

value: naive


title: 5013q5

value: Early Acute

value: serum-

value: urine+

value: serum-/urine+


title: 5248q3

value: Convalescent

value: serum+

value: serum+/urine-

value: Naive


title: 5138q5

value: 0 infcs

value: serum+/urine+


title: 5013q3

value: DENV

value: 1 infcs


title: 5329q3

value: M

value: nonnaive

value: NoFever


title: 5355q3


title: 5066q5

value: F


title: 4948q3

value: naive

value: urine-

value: Fever


title: 5066q3

value: urine+


title: 4948q5

value: Early Acute


title: 5355q1

value: Late Acute


title: 5149q5

value: serum+


title: 4948q1

value: serum+/urine-


title: 4858q3

value: Convalescent

value: 2 infcs


title: 4817q5


title: 4797q3

value: 0 infcs

value: serum+/urine+

value: Naive


title: 4817q1

value: M

value: DENV

value: 1 infcs


title: 4797q5

value: F


title: 4858q1

value: naive

value: NoFever


title: 4772q3

value: urine-


title: 4772q5


title: 4749q5

value: nonnaive

value: serum-

value: urine+

value: serum-/urine+


title: 4749q3


title: 4723q3

value: serum+

value: serum+/?

value: Fever


title: 4723q1

value: Late Acute

value: 0 infcs


title: 4606q5

value: Early Acute

value: Naive


title: 4723q5

value: M

value: DENV


title: 4606q3

value: Convalescent


title: 4749q1


title: 5329q1

value: serum+/urine-


title: 5013q1

value: naive

value: 1 infcs

value: NoFever


title: 4606q1

value: serum-


title: 4515q5

value: nonnaive

value: 2 infcs

value: urine-


title: 4515q3

value: serum+


title: 4515q1

value: Fever


title: 4445q5


title: 4858q5


title: 4445q3


title: 4817q3


title: 4445q2

value: Late Acute


title: 4797q1

value: F

value: 0 infcs

value: urine+

value: serum+/urine+


title: 4359q5

value: Early Acute

value: M

value: Naive


title: 5248q1

value: naive

value: serum+/urine-


title: 4772q1

value: DENV

value: 1 infcs

value: NoFever


title: 4359q3

value: Convalescent


title: 4243q5


title: 4359q1


title: 4243q1


title: 4203q5

value: serum+/?


title: 4069q3

value: serum+


title: 4069q1


title: 4041q1

value: urine-

value: Fever


title: 3758q3

value: F


title: 4203q1

value: Late Acute


title: 3758q5

value: 0 infcs

value: urine+


title: 4203q3


title: 4041q5

value: Early Acute


title: 3132q1

value: nonnaive


title: 3132q5


title: 3758q1

value: serum+/urine+

value: Naive


title: 3132q3

value: serum+/urine-


title: 2226q5

value: M

value: naive


title: 2226q3

value: NoFever


title: 2226q1


title: 201q3

value: Convalescent

value: DENV

value: 1 infcs

value: serum-

value: serum-/urine+


title: 201q5


title: 201q1


title: 4243q3

value: F

value: serum+


title: 4041q3

value: 0 infcs

value: urine-

value: Fever


title: 2007q3

value: 2 infcs


title: 2007q1

value: Late Acute


title: 2007q5

value: Early Acute


title: 1659q3

value: nonnaive

value: serum+/urine-


title: 1659q5


title: 1369q5

value: M

value: naive

value: urine+

value: serum+/urine+


title: 1369q1

value: DENV

value: 1 infcs

value: NoFever


title: 1369q3

value: Convalescent


title: 1304q3

value: serum+

value: Naive


title: NCOR2_RNA_Strd.Cre.5

status: Public on Apr 11 2019

city: Boston

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

description: processed data file: 180216_NCoR2_counts_invivo.txt

data_processing:
All samples were aligned to the mm10 genome using default parameters for the Subread (subread-1.4.6-p3, (Liao et al., 2013)) alignment software after quality trimming with Trimmomatic v0.33 (Bolger et al., 2014) with the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45. Truseq adapters were trimmed out in ChIP- and RNA-seq experiments; Nextera adapters were specified for ATAC-seq data.
To generate UCSC genome browser tracks for ChIP- and ATAC-seq data, the aligned bam files produced by Subread were converted to BED format with the bedtools bamtobed command. The 75 base pair reads were extended in the 3’ direction to 200 basepairs (bp) (average fragment length for ChIP- and ATAC-seq experiments as measured by bioAnalyzer) with the bedtools slop command using the following parameters: -l 0 -r 125 -g [CHR_SIZES_FILE]. Published mm10 ChIP-seq blacklisted regions (Consortium, 2012) were filtered out using the following command: bedops –not-element-of 1 [BLACKLIST_BED]. The filtered BED files were converted to coverageBED format using the bedtools genomecov command with the following options: -scale [NORM_FACTOR to scale each library to 20M reads] –bg –g [CHR_SIZES_FILE] | LC_COLLATE=C sort -k1,1 -k2,2n. Finally, bedGraphToBigWig (UCSC-tools) was used to generate the bigWIG files shown throughout the manuscript.
To quantify gene expression, we applied the featureCounts package (Liao et al., 2013) after aligning RNA-seq libraries to the genome as described above, using a custom filtered annotation file: gencode.v17.annotation.gtf filtered for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN") to obtain gene counts for each sample. These counts tables were TMM-normalized using the edgeR software analysis package (Robinson et al., 2010). Any genes that were not expressed in at least 3 samples with TMM-normalized CPM>1 were dropped from further analysis. Differential expression (DE) analyses were conducted using the voom/limma analysis software packages (requiring FDR-corrected q<0.05).
Regions of ATAC-seq enrichment were determined using MACS2 (v 2.1.0) parameters -p 1e-5 --nolambda --keep-dup all --slocal 10000, as previously described (Buenrostro et al., 2013). Peaks from individual sample replicates were intersected to find only reproducible regions of enrichment.  Blacklist regions were removed as previously described (Consortium, 2012).
To identify sites with enriched ChIP-seq signal (peaks), we applied the IDR pipeline (Li, 2011) using the MACS2 peak calling algorithm (Zhang et al., 2008) with the following additional parameters: --nomodel --extsize 200 --keep-dup all. An IDR threshold of .01 was used for self-consistency, true replicate, and pooled-consistency analyses. The ‘optThresh’ cutoff was then used to obtain a final set of high-confidence, reproducible ChIP-seq peaks for each factor or chromatin modification at each stimulus condition tested. After calling peaks using both ATAC-seq data and H3K27ac ChIP-Seq data, we constructed a set of all putative functional regulatory elements in the embryonic cultured neuronal system by taking the union of all sites that showed significant (IDR<0.01) ATAC or H3K27Ac ChIP-seq signal in any of the unstimulated, 2 hour KCl depolarized, or 6-hour KCl depolarized conditions ± any viral treatment, resulting in a total of 31,138 sites genome-wide (referred to hereafter as annotations). We then used the HOMER software package to quantify the number of reads present across each of these annotations from each ChIP-seq experiment by first constructing tag directories (makeTagDirectory –fragLength 200), and then using the annotatePeaks.pl script with the following parameters to obtain raw counts tables: -len 200 -size given -noadj -noann -nogene. Any annotations within 1 kb of an annotated TSS were considered ‘promoter’ regulatory elements; all other annotations were termed enhancers. Fixed line plots were generated with Homer’s annotatePeaks.pl script (Heinz et al., 2010), using the following parameters: annotatePeaks.pl [PEAK_BED] mm10 -d [INPUT_TAG_DIRS] -len 200 -size 4000 –ghist -hist 25 -noann -nogene. Bioreplicates were averaged at each 25 base pair bin by peak and the average log2(x + 1) signal intensity is displayed. To generate aggregate plots, the outputs of the commands above were summed across all relevant peaks within each sample, and then these aggregated sums were averaged by bin across all replicates. The standard error of the mean is shaded around each plot’s mean signal intensity.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 170815_MEAN_TF_around_OPTIMAL_ATAC.txt.gz: Matrix of mean transcription factor ChIP-seq count data across replicates normalized by sequencing depth in 4kb window flanking each IDR .01 thresholded ATAC summit; 170913_invitro_ctx_counts.txt: UMIFM counts for inDrops dataset by cell; 170815_MEAN_ATAC_around_OPTIMAL_ATAC.txt.gz: Matrix of mean ATAC-seq count data across replicates normalized by sequencing depth in 4kb window flanking each IDR .01 thresholded ATAC summit; 180413_MEAN_UPDATED_H3K27AC_around_OPTIMAL_ATAC.txt.gz: Matrix of mean H3K27Ac count data across replicates normalized by sequencing depth in 4kb window flanking each IDR .01 thresholded ATAC summit; 150805_n4oe_TMMnorm_agg_cpm.csv: TMM normalized RNA-seq expression values for Npas4-overexpression experiment; 181031_Arnt2_counts_invivo.txt: raw RNA-seq counts for Arnt2 shRNA experiments; 180216_NCoR2_counts_invivo.txt: raw RNA-seq gene counts for NCoR2 fl experiments

organism: Mus musculus

source_name: adult hippocampus

growth_protocol: Embryonic cortices from C57Bl/6 or transgenic (Npas4fl/fl) mice were dissected at ages E16.5-E17 and then dissociated with papain (Sigma Aldrich; 10108014001).  Papain digestion was terminated with the addition of ovomucoid (trypsin inhibitor; Worthington).  Cells were gently triturated through a P1000 pipette and passed through a 40 micron filter.  Neurons were plated onto cell cultures dishes pre-coated overnight with poly-D-lysine (20 μg/mL) and laminin (4 μg/mL).  Neurons were grown in Neurobasal medium (Gibco) containing B27 supplement (2%), penicillin-streptomycin (50 U/mL penicillin and 50 U/mL streptomycin) and glutaMAX (1 mM).  Neurons were grown in incubators maintained at 37C and a CO2 concentration of 5%.  Neurons were harvested in all experiments at 7DIV, and fresh media was added at 3-4DIV (25% total volume), unless otherwise indicated.  For IP-MS or ChIP, cortical neurons were plated at a density of 20-30 x 106 / dish on a 15-cm dish.  To prevent spurious activity, for IP-MS experiments, NCoR2 complex ChIPs, 7DIV neurons were silenced on 6DIV overnight by the addition of 1 mM TTX (Abcam ab120055) and 100 μM AP5 (Thermo Fisher 01-061-0 ).

extract_protocol:
For ChIP of transcription factors and histone modifications, primary neurons (E16.5) were crosslinked via addition of 1% formaldehyde for 10 min at room temperature and quenched by the addition of 0.125 M glycine for 5 min at room temperature.  To ChIP the NCoR2 complex, we found it necessary to perform dual crosslinking by incubating neurons for 30 min with 1.5 mM EGS (ethylene glycol bis(succinimidyl succinate) (Fisher, 21565)), followed by 10 min incubation in 1% formaldehyde and standard quenching with 0.125 M glycine.  Nuclei were isolated from cell pellets by incubation in lysis buffer 1 (in mM: 100 HEPES-NaOH pH 7.5, 280 NaCl, 2 EDTA, 2 EGTA, 0.5% Triton X-100, 1% NP-40, 20% Glycerol) followed by washing in buffer containing 10 mM Tris-HCl pH 8.0, 200 mM NaCl.  Chromatin was sheared using a Bioruptor (Diagenode) on high power mode for 50 cycles with 30 sec pulses in sonication buffer (in mM: 10 Tris-HCl pH 8.0, 100 NaCl, 1 EDTA, 0.5 EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine).  For H2K27ac ChIP, 10 mM sodium butyrate (Fisher NC9851678) was added to all buffers. Following sonication, chromatin was supplemented with 1% Triton and was incubated overnight with the following antibodies: H3K27ac (Abcam 4729, 0.2 μg for 2.5 million cells ), 5-8 μg Arnt2 (in house protein A purified anti-serum; see below), 8 μg Npas4 (custom made protein A purified anti-serum), NCoR2 (Millipore, 06891; 5 μg for 60-70 μg chromatin; Thermo PA1-843; 5 μg for 60-70 μg chromatin (40-50 million cells)); Tbl1 (Abcam 24528; 5 μg for 60-70 ug chromatin (40-50 million cells)); Hdac3 (Santa Cruz sc11416X; 5 μg for 60-70 μg chromatin (40-50 million cells).
Libraries were generated using the Ovation Ultralow V2 kit according to the manufacturer’s instructions and PCR amplified for 13-16 cycles depending on antibody. Library quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Seventy-five bp reads were generated on the Illumina Nextseq and subsequently analyzed with our standardized ChIP-seq data analysis pipeline (below).
Tissue was collected in Trizol reagent and RNA was extracted using the RNAeasy Kit (Qiagen) according to the manufacturer’s instructions.
Total RNA (1000 ng) was used to generate libraries following rRNA depletion according to the manufacturer’s instructions (NEBNext). Seventy-five bp reads were generated on the Illumina Nextseq and subsequently analyzed with our standardized RNA-seq data analysis pipeline (below).
To assess regions of open chromatin, neurons were washed with cold PBS and lysed with 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal-630.
50,000 nuclei per condition were transposed using the Nextera DNA Library Prep Kit (Illumina).  Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp.

tag: strain

value: Ncor2 f/f

tag: stimulus

tag: viral treatment

value: Cre


title: NCOR2_RNA_Strd.delta.2

value: dCre


title: NCOR2_RNA_Strd.delta.3


title: NCOR2_RNA_Strd.delta.5


title: NCOR2_RNA_Strd.delta.1


title: NCOR2_RNA_Strd.Cre.4


title: 1304q1

tag: time

value: Late Acute

tag: Sex

value: 0 infcs

value: urine-

value: Fever


title: 1659q1

value: F

value: nonnaive

value: 2 infcs

value: serum+/urine-


title: NCOR2_RNA_Strd.Cre.1


title: NCOR2_RNA_KA.delta.5


title: NCOR2_RNA_KA.delta.6


title: NCOR2_RNA_Strd.Cre.2


title: NCOR2_RNA_Strd.Cre.3


title: NCOR2_RNA_KA.delta.2


title: NCOR2_RNA_KA.delta.4


title: NCOR2_RNA_KA.delta.1


title: NCOR2_RNA_KA.delta.3


title: 1304q5

value: Early Acute

value: M

value: naive


title: NCOR2_RNA_KA.Cre.5


title: NCOR2_RNA_KA.Cre.6


title: NCOR2_RNA_KA.Cre.1


title: NCOR2_RNA_KA.Cre.3


title: NCOR2_RNA_KA.Cre.2


title: NCOR2_RNA_KA.Cre.4


title: Omni-ATAC-seq, ToMC, replicate-2

status: Public on Mar 17 2019

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

data_processing:
Basecalls performed using CASAVA
Reads were trimmed cutadapt v1.8.1, setting minimum-length option to 18, error-rate 0.2 and overlap 5
Reads were aligned to the hg19 genome assembly using BWA version 0.7.9a-r786 with default parameters
Peak calling was done by MACS version 2.1.1.20160309 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generated using MACS2

source_name: Tonsilitis patient

extract_protocol:
Omni-ATAC-seq libraries were prepared as previously described (Corces 2017, Nature Methods).
Paired-end - Illumina; Omni-ATAC-seq

tag: cell type

value: Tonsillar mast cells

tag: passages

value: fresh


title: Omni-ATAC-seq, IgE+2h anti-IgE-treated for IL-33 comparison, replicate-2

source_name: Healthy donor

growth_protocol: CD34+ cells were isolated from buffy coats and cultured for 10 weeks in the presence of 100 ng/ml hSCF, 50 ng/ml hIL-6 and 5 ng/ml hIL-3 (first 3 weeks only). Tonsillar MCs (ToMC) were isolated from tonsilitis patients.

treatment_protocol: Cells were left untreated or sensitized overnight with myeloma-IgE (0.5 μg/ml) and treated with anti-IgE (1 μg/ml) for 2h

value: Peripheral blood-derived mast cells

value: 10 weeks


title: Omni-ATAC-seq, ToMC, replicate-1


title: Omni-ATAC-seq, untreated for IL-33 comparison, replicate-1


title: Omni-ATAC-seq, 2h IL-33-treated, replicate-2


title: Omni-ATAC-seq, IgE+BAPTA-AM+2h anti-IgE-treated, replicate-2

treatment_protocol: Cells were left untreated or sensitized overnight with myeloma-IgE (0.5 μg/ml) and treated with DMSO control or BAPTA-AM (20 μM) for 30 min, before treatment with anti-IgE (1 μg/ml) for 2h.


title: Omni-ATAC-seq, 2h IL-33-treated, replicate-1


title: Omni-ATAC-seq, IgE+2h anti-IgE-treated, replicate-2


title: Omni-ATAC-seq, untreated, replicate-2


title: Omni-ATAC-seq, IgE+BAPTA-AM+2h anti-IgE-treated, replicate-1


title: Omni-ATAC-seq, IgE+2h anti-IgE-treated, replicate-1


title: RNA-seq, IgE+anti-IgE-treated, replicate-4

data_processing:
Reads were mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file of gene expression

growth_protocol: CD34+ cells were isolated from buffy coats and cultured for 10 weeks in the presence of 100 ng/ml hSCF, 50 ng/ml hIL-6 and 5 ng/ml hIL-3 (first 3 weeks only).

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols


title: NCOR2_RNA_Strd.delta.4

value: Ncor2 f/f


title: RNA-seq, untreated, replicate-4


title: RNA-seq, IgE-treated, replicate-3


title: RNA-seq, IgE+anti-IgE-treated, replicate-3


title: RNA-seq, IgE-treated, replicate-4


title: RNA-seq, untreated, replicate-3


title: RNA-seq, IgE+anti-IgE-treated, replicate-2


title: RNA-seq, IgE-treated, replicate-2


title: RNA-seq, untreated, replicate-2


title: Omni-ATAC-seq, untreated for IL-33 comparison, replicate-2


title: RNA-seq, IgE+anti-IgE-treated, replicate-1


title: RNA-seq, untreated, replicate-1


title: Input for H3K27ac ChIP-seq, replicate-2

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.6 with the following configurations : -v 2 -m 1 -k 1  --best
Peak calling was done by MACS version 2.1.1.20160309
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generated using MACS2

extract_protocol:
CHIP-seq libraries were prepared with NEB NEXT Ultra kit using 10 ng genomic DNA
Single read - Illumina

tag: chip antibody


title: H3K4me3 ChIP-seq, untreated, replicate-2

value: H3K4me3 (Millipore 07-473)


title: Omni-ATAC-seq, IgE+2h anti-IgE-treated for IL-33 comparison, replicate-1


title: Omni-ATAC-seq, IgE+24h anti-IgE-treated, replicate-2


title: Input for H3K27ac CHIP-seq, replicate-1


title: H3K4me3 ChIP-seq, untreated, replicate-1


title: H3K27ac ChIP-seq, IgE+anti-IgE-treated, replicate-1


title: Omni-ATAC-seq, IgE+24h anti-IgE-treated, replicate-1


title: H3K27ac ChIP-seq, untreated, replicate-2


title: H3K27ac ChIP-seq, untreated, replicate-1


title: ChIP-seq: Top2-1-Top1-TopAplasmid-nucleosome-IP

status: Public on Mar 11 2019

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: Log cells from 28 degree moved to 37 degree for 2hr15mins

data_processing:
The raw reads were filtered based on the quality value (-q 20 and –p 30) using FASTX Toolkit. The filtered reads were aligned to the reference genome (SacCer 2011) using TMAP aligner. The PCR duplicates were removed from the aligned BAM files using PICARD tools. The BAM files were sorted and indexed for the peak calling using SAMTOOLS. The bedgraph files were generated by comparing bam files of IP and Input (IP read coverage/Input read coverage) result in the ratio for every base across the whole genome using DEEPTOOLS (bamCompare) (Ramirez et al., 2014). Finally, peak calling was performed using DANPOS (dpos) toolkit (Chen et al., 2013) with the IP/Input threshold 1.4 (-q 1.4) where the output peaks corresponds to the individual nucleosome.
Genome_build: SacCer2011 fasta and Saccharomyces_cerevisiae.R64-1-1.89 GTF file
Supplementary_files_format_and_content: bedGraph file and bed file

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 28 C till 8X10e6 cells per ml, then shifted to 37 C for 2hr 15mins.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in culture medium for 15 min at room temperature followed by quenching with 0.125 M glycine for 5 min. Cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. Crosslinked chromatin was sheared to an average size of 200 bp in Covaris S220 Focused-ultrasonicators. The lysate was then centrifuged to remove cell debris. Chromatin fraction was incubated with Protein-G magnetic beads (Invitrogen, cat no 10003D) coated with Anti-Histone H3 antibody (Abcam, cat no ab1791) overnight at 40C. The immune complexes were washed with the following buffers 2X; Chip-lysis buffer, high-salt lysis buffer (Chip-lysis buffer + 360mM NaCl), Chip-wash buffer (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 50 mM Tris pH8.0, 10mM EDTA) at 650C for 20 min followed by the addition of proteinase K to 500 µg/ml and overnight incubation at 650C. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP).
IP and Input ChIP-seq libraries were prepared according to the manufacturer protocols for the Ion Proton sequencer (Thermo Fisher Scientific/Life Technologies). Briefly 10ng for ChIP DNA was end repaired and adapter ligated using the KAPA Library Preparation Kit for Ion Torrent™ (KAPABIOSYSTEMS, inc) and adapter barcode Kapa Barcode Adaptors 9-24 . After adapter ligation, each sample was size selected using AMPure XP Bead (Beckman Coulter, inc). An amplification reaction was set up in a final volume of 50ul . A SPRI cleanup with a 1.5X Bead:DNA ratio was performed post amplification and final libraries were eluted in 35ul. Libraries were quantified on Qubit fluorometer with HS DNA (Thermo Fisher Scientific/Life Technologies) and checked for size on an Agilent Bioanalyzer with HS DNA kit (Agilent, Santa Clara, CA). Each size selected library was diluted according to the final concentration of 11 pM and clonally amplified using the Ion Proton™ Hi‑Q™Template Kit (Thermo Fisher Scientific/Life Technologies) with IonOneTouch 2 instrument (Thermo Fisher Scientific/Life Technologies). After emulsion PCR, DNA positive ISPs were recovered and enriched according to standard protocols with the IonOneTouch ES Instrument (Thermo Fisher Scientific/Life Technologies). A sequencing primer was annealed to DNA positive ISPs and the sequencing polymerase bound, prior to loading of ISPs into Ion P1 sequencing chips. Sequencing of the samples was conducted according to the Ion Proton™ Hi-Q  Sequencing Kit Protocol. One P1 sequencing chips with 6 libraries were loaded and run on an Ion Proton sequencer.

tag: temperature

tag: genotype

value: top2-1;top1<delta>, Ecoli TopA expression using plasmid

tag: cell cycle

value: Log Cells


title: Input for H3K4me3 ChIP-seq


title: H3K27ac ChIP-seq, IgE-treated, replicate-1


title: H3K27ac ChIP-seq, IgE+anti-IgE-treated, replicate-2


title: ChIP-seq: Top2-1-Top1-TopAplasmid-nucleosome-Input


title: RNA-seq, IgE-treated, replicate-1


title: ChIP-seq: WT-TopAplasmid-nucleosome-IP

value: Wildtype, Ecoli TopA expression using plasmid


title: RET_BWK

status: Public on Mar 04 2019

city: Chicago

first: Alexander

last: Mankin

state: Illinois (IL)

address: 900 S. Ashland Avenue Room 3056

department: Pharmacognosy

institute: University of Illinois at Chicago

data_processing:
library strategy: Ribo-seq
Reads were trimmed with Cutadapt 1.1.a
Reads were first aligned to a ncRNA fasta file and the unmapped reads were subsequently mapped to the respective genomes with Bowtie 1.1.2
P-sites of the ribosomes were mapped as 15 nts away from the 3prime end of the read and used to calculate nucleotide rpm
Genome_build: U00096, CP001509_3
Supplementary_files_format_and_content: wig, rpm values of the calculated ribosmal P-site

organism: Escherichia coli

source_name: Bacterial culture

extract_protocol:
Ribosome protected fragments were isolated as described in Oh et al. 2011
Libraries were generated as described in Oh et al. 2011

value: BWK

tag: treatment

value: Retapamulin


title: ChIP-seq: WT-Controlplasmid-nucleosome-Input

value: Wildtype, Control plasmid expressed


title: ChIP-seq: Top2-1-Top1-Controlplasmid-nucleosome-Input

value: top2-1;top1<delta>, Control plasmid expressed


title: No_Drug_BWK

value: none (untreated)


title: ChIP-seq: Top2-1-Top1-Controlplasmid-nucleosome-IP


title: Patient derived xenograft 110

status: Public on Feb 26 2019

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Read alignment and count summarization were performed using CellRanger v2.0.0 using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: The matrix.mtx file contains genewise read counts for all cells in Matrix Market format. In this format, only cell-gene combinations with with one or more reads are included in the file. genes.tsv contains the corresponding Ensembl IDs and gene symbols as tab-delimited text and barcode.tsv contains the 10X barcodes used to identify cells.
A location-sorted BAM file is available from SRA.

source_name: mammary gland

extract_protocol:
Epithelial cells were isolated by FACS from each PDX. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture.
cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on Illumina NextSeq 500 platform using sequencing parameters recommended for Single Cell 3' V2.0 libraries.

tag: tissue

value: total epithelium

tag: number of cells


title: 501R_high

status: Public on Jan 01 2019

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

country: Switzerland

institute: University of Geneva

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
For ChIP-seq the reads were shifted by 150 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

source_name: whole organism

extract_protocol: Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700)

treatment_protocol: 60 minutes rapamycin 30 minutes auxin

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ISW2-FRB-HIS3MX; INO80-aid*-9myc-HphNT CHD1-FRB-KanMX; ISW1-aid*-9myc-HphNT Padh1-Os.TIR1

tag: antibody


title: ChIP-seq: WT-TopAplasmid-nucleosome-Input


title: ChIP-seq: WT-Controlplasmid-nucleosome-IP


title: 501R_low


title: H3K27ac ChIP-seq, IgE-treated, replicate-2


title: Nkx2-1+ lung endoderm (e15.5)

status: Public on Feb 08 2019

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

source_name: Lung endoderm

extract_protocol:
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two biological replicates were generated per sample.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

tag: genotype/variation

tag: age

value: Lung endoderm


title: Nkx2-1+ lung endoderm (e17.5)


title: Patient derived xenograft 322


title: 42126

status: Public on Dec 07 2018

city: Tampere

first: Arttu

last: Autio

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Life Sciences

country: Finland

institute: University of Tampere

data_processing:
Aligned using TopHat v2.0.13.
Non-unique mappings filtered out with SAMtools.
Raw expression estimates of genes and proviruses were calculated and normalized by geometric normalization using Cufflinks2 v.2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: normalized_read_counts.txt, TXT, normalized read counts of HERV-K (HML-2) and HERV-W proviruses

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA used for RNA sequencing was purified using a miRNeasy mini kit (Qiagen, CA, USA) and the RNA used for PCR analysis using RNeasy mini kit (Qiagen, CA, USA) according to manufacturer’s protocol with on-column DNA digestion (Qiagen). The concentration and quality of the RNA was assessed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Agilent Bioanalyzer RNA nano chips (Agilent) were used to evaluate the integrity of total RNA and Qubit RNA –kit (Life Technologies) to quantitate RNA in samples. 1 µg of total RNA was used for ScriptSeq™ Complete Gold System (Epicentre) to ribodeplete rRNA and further for RNA-seq library preparation. SPRI beads (Agencourt AMPure XP, Beckman Coulter) were used for purification of RNAseq libraries. The library QC was evaluated on High Sensitivity chips by Agilent Bioanalyzer (Agilent).

value: peripheral blood mononuclear cells

tag: age group

value: young control

tag: gender

value: female


title: 501V_low

treatment_protocol: no rapamycin/auxin

tag: strain


title: PRO-Seq of uninfected DMSO-treated HFF (Towne)

status: Public on Jan 16 2019

city: Iowa City

first: David

middle: H

last: Price

state: Iowa

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.4.4
Alignment of trimmed reads to hg38 using bowtie 1.2 (retain unmapped reads; Towne samples: --trim5 4 and --trim3 4)
Alignment of unmapped reads to Genbank FJ616285.1 using bowtie 1.2
Towne samples: filter duplicate mapped reads with dedup (https://github.com/P-TEFb/dedup)
Generate bedgraphs using bedtools genomecov 2.26
Convert bedgraphs to bigwigs using kentUtils
Upload hg38-mapped tracks to UCSC genome browser
Upload HCMV-mapped tracks to a custom track hub (https://github.com/P-TEFb/trackHub_HCMV)
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, PRO-Cap pileups, or PRO-Cap 5' read positions
Supplementary_files_format_and_content: bigbed files were generated from bed files using kentUtils bedToBigBed program

molecule: nuclear RNA

source_name: human foreskin fibroblast

growth_protocol: HFF were kept at 100% confluence at least one week before infection.

extract_protocol:
All PRO-Seq and PRO-Cap protocols are detailed in the manuscript. Nuclei were rapidly isolated as described in Nilson, et al. 2017 (10.1093/nar/gkx724).
Please consult the manuscript, Nilson, et al. 2017 (10.1093/nar/gkx724), and Mahat, et al. 2016 (10.1038/nprot.2016.086).

treatment_protocol: Infection details are in the manuscript. As indicated, 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest.

tag: hcmv strain

value: Towne varS

tag: infection duration

value: uninfected

tag: method

value: PRO-Seq


title: Omni-ATAC-seq, untreated, replicate-1

tag: cell type

value: Peripheral blood-derived mast cells

tag: passages

value: 10 weeks


title: 42109


title: 42004


title: 42028


title: 42016


title: 42113


title: 42003


title: 28647

value: nonagenarian


title: 28706


title: 28501


title: 28591


title: 28303


title: 28438


title: 28175


title: DKT_hepatoblastoma tumor 4  [DKT1366]

status: Public on Aug 09 2018

city: Pittsburgh

first: Edward

middle: V

last: Prochownik

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

data_processing:
Raw sequencing reads were quality checked for potential sequencing issues and contaminants using FastQC (Babraham Bioinformatics, Inc, Cambridge, UK.). Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and PRINSEQ (http://prinseq.sourceforge. net/manual.html). Reads with a remaining length of less than 20 bp after trimming were discarded. Paired end reads were mapped to the mouse genome (m10) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) in a strand specific manner. Read coverage on forward and reverse strands for genome browser visualization was computed using SAMtools, BEDtools, and UCSC Genome Browser utilities. Pairwise differential expression was quantified using Cuffdiff and DESeq [4, 5]. Cufflinks was used to determine FPKM levels for each gene from the TopHat alignment and was used as input for Cuffdiff. Significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05. DESeq was utilized
for raw read counts, which were calculated by HTSeq based on the STAR alignment (http://www-huber.embl.de/users /anders/HTSeq/doc/count.html). Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: cufflinks output including genes.fpkm_tracking and isoforms.fpkm_tracking values

source_name: DKT_hepatoblastoma tumor

extract_protocol:
Total RNAs were extracted using Qiagen RNeasy columns (Valencia, CA). Each RNA sample was assessed for quality and quantity using a Qubit 2.0 fluorometer and Agilent Bioanalyzer TapeStation 2200. The Sample preparation was replicated using Illumina TruSeq Stranded mRNA kit (San Diego, CA). mRNA was used to generate poly-A+ libraries using oligo-dT beads following 2 rounds of poly-A selection.
mRNA was fragmented to an average length of 260 nt by magnesium-catalyzed hydrolysis at 940C and then converted into cDNA by random priming. cDNA 3’ ends were adenylated, followed by adaptor ligation and a 9-cycle PCR to enrich DNA fragments. cDNA libraries were then validated using KAPA Biosystems (Wilmington, MA) primer premix kit with Illumina-compatible DNA primers on the Qubit 2.0 fluorometer and Tapestation 2200 systems described above. Libraries were diluted in 0.1% Tween 20 to concentrations of 2 nM for stabilization. The cDNA libraries were then pooled to final concentrations of 2.5 pM.

tag: strain background

value: Myc KO plus ChREBP KO

value: Hepatoblastoma Tumor


title: ery_input_1

status: Public on Oct 15 2018

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

data_processing:
Alignments were performed by hisat2, v2.0.3 or v2.0.5, with the --no-spliced-alignment option
Reads were filtered by alignment to nine vertebrate genomes, including human, and assigned to the best-matching genome.
Peak calling was by MACS2, and analysis of colocalisation was by the R package ChIPpeakAnno
Normalisation and subtraction was done using the deepTools 2.5.4 bamCompare function with option string  --outFileFormat bigwig --scaleFactorsMethod readCount --ratio subtract --binSize 50 --normalizeTo1x 3100000000 --minMappingQuality 30
Genome_build: hg38
Supplementary_files_format_and_content: A bigWig graph representing difference between ChIP and input, with the difference calculated after ChIP and input had each been normalised to 1x coverage genome-wide

source_name: erythroblast

extract_protocol:
as described by Pope SH et al, Eur J Haematol 64:292-303, 2000
library construction was provided by Oxford Genomics Centre, or by Edinburgh Genomics

value: Adult erythroblasts

tag: chip antibody

value: no antibody

tag: number of sonications


title: DKT_hepatoblastoma tumor 5  [DKT1369]


title: DKT_hepatoblastoma tumor 2  [DKT1310]


title: CKT_hepatoblastoma tumor 5  [CKT879]

source_name: CKT_hepatoblastoma tumor

value: ChREBP KO


title: CKT_hepatoblastoma tumor 4  [CKT877]


title: CKT_hepatoblastoma tumor 1  [CKT1115]


title: DKT_hepatoblastoma tumor 3  [DKT1316]


title: CKT_hepatoblastoma tumor 2  [CKT1145]


title: MKT_hepatoblastoma tumor 5  [KO-179]

source_name: MKT_hepatoblastoma tumor

value: Myc KO


title: MKT_hepatoblastoma tumor 4  [KO-173]


title: DKT_hepatoblastoma tumor 1  [DKT1306]


title: MKT_hepatoblastoma tumor 3  [KO-170]


title: MKT_hepatoblastoma tumor 1  [KO-167]


title: CKT_hepatoblastoma tumor 3  [CKT872]


title: WT_hepatoblastoma tumor 5  [WT-221]

source_name: WT_hepatoblastoma tumor

value: WT


title: MKT_hepatoblastoma tumor 2  [KO-168]


title: WT_hepatoblastoma tumor 4  [WT-169]


title: WT_hepatoblastoma tumor 3  [WT-165]


title: WT_hepatoblastoma tumor 1  [WT-160]


title: Myc KO plus ChREBP KO Liver_rep4  [DKL1351]

source_name: Myc KO plus ChREBP KO_liver

value: liver


title: Myc KO plus ChREBP KO Liver_rep5  [DKL1391]


title: WT_hepatoblastoma tumor 2  [WT-162]


title: Myc KO plus ChREBP KO Liver_rep1  [DKL1340]


title: ChREBP KO Liver_rep10  [CKL890]

source_name: ChREBP KO_liver


title: Myc KO plus ChREBP KO Liver_rep2  [DKL1346]


title: Myc KO plus ChREBP KO Liver_rep3  [DKL1350]


title: ChREBP KO Liver_rep8  [CKL1181]


title: ChREBP KO Liver_rep9  [CKL866]


title: ChREBP KO Liver_rep7  [CKL1177]


title: Myc KO Liver_rep4  [MKL527]

source_name: Myc KO_liver


title: Myc KO Liver_rep5  [MKL528]


title: Myc KO Liver_rep3  [MKL523]


title: Myc KO Liver_rep2  [MKL410]


title: Myc KO Liver_rep1  [MKL401]


title: ChREBP KO Liver_rep6  [CKL1142]


title: Wild type Liver_rep4 [WL1151]

source_name: Wild type_liver


title: Wild type Liver_rep1 [WL1103]