title: SNU16 Input

description: Input (background) for SNU16 CapStarr-seq

data_processing:
CapSTARR-seq consists of two parts of data with different types of readouts. The input library represents the insert fragments in original plasmid pool, while the output library measures the abundance of self-transcribed mRNA from insert fragments of the transfected plasmid pool.  Paired-end sequencing reads (2 × 100 bp) from Illumina Hiseq2000/2500 were aligned to human genome hg19 by BWA using default parameters. Only reads that mapped in proper pairs were used for downstream analysis. To exclude potential PCR amplification bias, fragments (inferred from paired-end reads) that have the same start and end positions were collapsed into distinct fragments by Picard (http://broadinstitute.github.io/picard/). Uniquely mapped distinct fragments from the 160 different indexing libraries were pooled and all included for downstream analysis, since duplicated fragments coming from different indexing libraries are considered as biological duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: Please refer to the website: https://github.com/taoliu/MACS for details

source_name: gastric cancer cell line

extract_protocol:
Generation of plasmid libraries was based on the method described by Vanhille et al (39). Briefly, SNU16 genomic DNA was extracted using the PerfectPure DNA Cultured Cell kit (5 Prime). The DNA was sheared by sonication (Covaris S2) and size-selected on 1% agarose gels (350–650 bp). Size-selected DNA fragments were ligated to adaptors (Adaptor 1: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; adaptor 2: 5’-GATCGGAAGAGCACACGTCT-3’) after end repair and A-tailing (NEBNext Ultra End Repair/dA- Tailing and Ultra Ligation Module, New England Biolabs) and subjected to capture (NimbleGen SeqCap EZ, Roche). Post-capture DNA was PCR amplified using Q5 High-Fidelity DNA polymerase (NEB) to add homology arms for subsequent cloning (forward primer: 5’-GTAATAATTCTAGAGTCGGGGCGGGAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse primer: 5’- TATCATGTCTGCTCGAAGCGGCATAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; PCR program: 98 °C for 30 s; 17 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s). The vector backbone was modified from pGL4.23[luc2/minP] (Promega). Briefly, the minP promoter was replaced with the SCP1 promoter and a CmR-ccdB cassette was cloned between luc2 ORF and SV40 poly (A). The PCR product was cloned into the vector backbone (linearized by SphI and NdeI restriction enzymes) through Gibson Assembly (Gibson Assembly Master Mix, New England Biolabs) and transformed into MegaX DH10B™ T1R electrocompetent cells (ThermoFisher Scientific). A total of 8 Gibson Assembly and transformations were performed. All transformed E. coli cells were pooled and cultured in 4 L LB medium and harvested at OD600 1.0. The input plasmid library was extracted using Plasmid Mega Kit (Qiagen) and drop dialyzed before transfection. Sequencing libraries were prepared from the input plasmid libraries by amplifying inserts from the plasmid DNA. 10 PCR reactions were set up, using Q5 High-Fidelity DNA polymerase (New England Biolabs), each with 1 ng plasmid as template (PCR program: 98 °C for 30 s; 12 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s). Reactions were pooled, cleaned up and submitted for sequencing.
Total RNA was extracted from transfected cells using PerfectPure RNA Cultured Cell Kit (5 Prime), followed by mRNA isolation using Dynabeads® Oligo (dT) kit (ThermoFisher Scientific) and treatment with TURBO DNase (ThermoFisher Scientific). Then target-specific first strand cDNA synthesis was performed with SuperScript III (ThermoFisher Scientific) to specifically reverse transcribe mRNA from the transfected plasmid library (RT primers: 5’-CAGTGACTGGAGTTCAGACG-3’, 5’-GCAGCTTATAATGGTTACAAATAAAGC-3’, 5’-ACATTTGTAGAGGTTTTACTTGCT-3’, 5’-TCAATGTATCTTATCATGTCTGCTCGAAG-3’). After reverse transcription, reactions were treated with RNase A + H. Finally, the cDNA was PCR amplified using 5 μL cDNA reaction as template in every 50 μL PCR reaction. Q5 High-Fidelity DNA polymerase (New England Biolabs) was used, and the following PCR program: 98 °C for 30s; 20 cycles of 98 °C for 10 secs, 65 °C for 30 secs and 72 °C for 30 secs. Illumina HiSeq platform compatible primers were used (forward: 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse: 5’-CAAGCAGAAGACGGCATACGAGAT-index-GTGACTGGAGTTCAGACGTG-3’). For each replicate, we set up separate final PCR reactions using 160 different indexing primers. PCR products for every 10 indexes were pooled and cleaned up by AmPure XP beads (Beckman Coulter; beads/reaction ratio = 0.8) and submitted for Illumina sequencing.
CapStarr-seq

tag: cell line


title: N2000877 H3K27ac

status: Public on Oct 02 2019

type: SRA

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

description: H3K27ac paired-end ChIP-seq in N2000877

library_source: genomic

data_processing:
DNA sequencing reads were aligned to the human reference genome, hg19. Processing was performed as described in Ooi et. al., 2016 (PMID: 27677335). Mapped reads were de-duplicated using Samtools. Genomic regions associated with histone modifications (H3K27ac) were predicted by MACS2 using default parameters (18798982).
Genome_build: hg19
Supplementary_files_format_and_content: Please refer to the website: https://github.com/taoliu/MACS for details

molecule: genomic DNA

organism: Homo sapiens

source_name: primary gastric normal

extract_protocol:
For primary tissues, fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized piece for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode).
ChIP was performed using antibodies: to H3K27ac (ab4729, Abcam). After recovery of ChIP and input DNA, whole-genome-amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers. Amplified DNAs were purified using PCR purification columns (QIAGEN) and digested with BpmI (New England Biolabs) to remove WGA adapters. 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs).

tag: sample id

tag: cell type

value: primary gastric normal

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: N990275 H3K27ac

description:
CHG537_HS004-PE-R00166_L001
H3K27ac paired-end ChIP-seq in N990275


title: SNU16 CapStarr-seq

description: CapStarr-seq in SNU16

library_source: transcriptomic

molecule: total RNA


title: T2001206 Input

description: Input (background) for T2001206 H3K27ac

source_name: primary gastric tumor

value: primary gastric tumor


title: T990275 Input

description:
CHG536_HS004-PE-R00166_L001
Input (background) for T990275 H3K27ac


title: T990275 H3K27ac

description:
CHG535_HS004-PE-R00166_L001
H3K27ac paired-end ChIP-seq in T990275


title: T2000085 H3K27ac

description: H3K27ac paired-end ChIP-seq in T2000085


title: N980447 H3K27ac

description: H3K27ac paired-end ChIP-seq in N980447


title: T980447 Input

description: Input (background) for T980447 H3K27ac


title: T980447 H3K27ac

description: H3K27ac paired-end ChIP-seq in T980447


title: G2Mpp_S1_L002

city: Grand Rapids

first: Eric

last: Kort

state: MI

address: 333 Bostwick NE

country: USA

institute: Van Andel Research Institute

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline with default settings
Genome_build: GRCH38
Supplementary_files_format_and_content: 10X Genomics mtx (market exchange) format

source_name: Human Episomal iPSC Line

growth_protocol: Episomal human iPSCs 1, 2 (Thermo Fisher Scientific) were maintained as a monolayer on Matrigel (Corning Life Sciences) coated plates and supplemented with Essential 8 Medium (Thermo Fisher Scientific). Identity and quality of the line was maintained/ensured by passage at three-day intervals and cryopreservation. Immunocytochemical characterization was carried out using antibodies against TRA-1-60, SOX2, OCT 3/4, and SSEA-4 to confirm pluripotency in vitro (Invitrogen Pluripotent Stem Cell 4-Marker Immunocytochemistry Kit, A24881, Life Technologies). Differentiations were conducted using hiPSCs within 15 passages from the last time the cells were thawed. For small molecule-based differentiations, hiPSCs were supplemented with RPMI 1640 (Gibco) medium containing B27 minus insulin (RPMI/B27 -insulin) with 6 µM of the GSK3 inhibitor CHIR990216 at D0-1 to induce mesoderm, followed with cardiac differentiation at D4-5 by changing media to RPMI 1640/B27 (-insulin) with 5 µM Wnt inhibitor IWR1 2. Typically, spontaneous contraction in cultures was observed at D7-8 of differentiation.

extract_protocol:
10X Genomics encapsulation, lysis, cDNA synthesis
10X Genomics library synthesis protocol

tag: cell cycle stage

value: CDC20 positive

value: SPG20 positive


title: G2Mpn_S2_L004

value: SPG20 negative


title: G2Mpp_S1_L001


title: T980417 Input

description: Input (background) for T980417 H3K27ac


title: N980417 H3K27ac

description: H3K27ac paired-end ChIP-seq in N980417


title: T980417 H3K27ac

description: H3K27ac paired-end ChIP-seq in T980417


title: G2Mpn_S2_L003


title: N2000877 Input

description: Input (background) for N2000877 H3K27ac


title: G2Mpn_S2_L002


title: T20020720 H3K27ac

description: H3K27ac paired-end ChIP-seq in T20020720


title: T20021007 Input

description: Input (background) for T20021007 H3K27ac


title: G2Mnn_S4_L003

value: CDC20 negative


title: G2Mnn_S4_L001


title: N990275 Input

description:
CHG538_HS004-PE-R00166_L001
Input (background) for N990275 H3K27ac


title: N20020720 Input

description: Input (background) for N20020720 H3K27ac


title: G2Mpn_S2_L001


title: G2Mnn_S4_L002


title: G2Mpp_S1_L004


title: G1nn_S3_L003


title: G1nn_S3_L002


title: G1nn_S3_L001


title: G2Mpp_S1_L003


title: d13_p2_5_mix_94_S94

city: Palo Alto

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive Room 3035

institute: Stanford University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg19 reference genome using bowtie version 0.12.7: bowtie -q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 --best -S -p 6
Cells expressing fewer than 200 genes and genes expressed by fewer than 3 cells were excluded from downstream analyses.
Reads for each cell were quantified and expressed as transcripts per million (TPM) using rsem version 1.2.19: rsem-calculate-expression --estimate-rspd --paired-end -sam -p 6
Genome_build: hg19
Supplementary_files_format_and_content: Processed TPM (non-log transformed) values for each cell  are compiled in a single matrix containing genes as rows and cells as columns. The column names of the TPM matrix reflect the cell line of sorted xenograft, the 96-well plate number and the well position within that plate. For instance D6_P1_S10 reflects a cell from the DIPG 6 xenograft, the first sorted plate and the 10th well in that plate

molecule: polyA RNA

source_name: patient-derived DIPG cell line developed in the Monje Lab

growth_protocol: Patient-derived DIPGVI and DIPGXIII-FL cells were cultured as neurospheres in defined-medium before being dissociated to single cell suspension for xenografting into the mouse hippocampus.

extract_protocol:
Cells were extracted from the mouse brain using mechanical and enzymatic dissociation (Brain Tumor Dissociation Kit, Miltenyi)
Libraries were constructed following Illumina Nextera XT protocol and a dual-unique indexing strategy.
Nextera XT single cell RNA-seq

treatment_protocol: Cells were lentivirally transduced to constitutively express GFP protein and firefly luciferase.

value: DIPG13FL (XIII-FL) cell line

tag: passages

tag: disease state

value: DIPG (diffuse intrinsic pontine glioma)


title: d13_p2_5_mix_9_S9


title: d13_p2_5_mix_95_S95


title: d13_p2_5_mix_88_S88


title: d13_p2_5_mix_96_S96


title: d13_p2_5_mix_91_S91


title: T2001206 H3K27ac

description: H3K27ac paired-end ChIP-seq in T2001206


title: G2Mnn_S4_L004


title: d13_p2_5_mix_8_S8


title: d13_p2_5_mix_93_S93


title: d13_p2_5_mix_90_S90


title: d13_p2_5_mix_92_S92


title: d13_p2_5_mix_85_S85


title: G1nn_S3_L004


title: d13_p2_5_mix_84_S84


title: d13_p2_5_mix_83_S83


title: d13_p2_5_mix_82_S82


title: d13_p2_5_mix_81_S81


title: d13_p2_5_mix_7_S7


title: d13_p2_5_mix_80_S80


title: d13_p2_5_mix_78_S78


title: d13_p2_5_mix_79_S79


title: d13_p2_5_mix_77_S77


title: d13_p2_5_mix_76_S76


title: d13_p2_5_mix_86_S86


title: d13_p2_5_mix_87_S87


title: d13_p2_5_mix_89_S89


title: d13_p2_5_mix_75_S75


title: d13_p2_5_mix_73_S73


title: d13_p2_5_mix_71_S71


title: d13_p2_5_mix_72_S72


title: d13_p2_5_mix_68_S68


title: d13_p2_5_mix_6_S6


title: d13_p2_5_mix_69_S69


title: d13_p2_5_mix_67_S67


title: d13_p2_5_mix_74_S74


title: ATL2_OR-S1

type: RNA

city: Minato-ku

first: Makoto

last: Yamagishi

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: The University of Tokyo

description: Gene expression after 7 days culture with OR-S1 in ATL pateint PBMC

hyb_protocol: 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent) for 1min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green, and No extended dynamic range was selected).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ATL patient #2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations. The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: ATL patient PBMC

tag: treatment

value: 7 days culture with OR-S1


title: d13_p2_5_mix_66_S66


title: d13_p2_5_mix_65_S65


title: d13_p2_5_mix_70_S70


title: d13_p2_5_mix_63_S63


title: d13_p2_5_mix_64_S64


title: TL-Om1_DMSO_1

description: Gene expression after 7 days culture with DMSO in TL-Om1

value: ATL cell line

value: 7 days culture with DMSO


title: TL-Om1_GSK126_2

description: Gene expression after 7 days culture with GSK126 in TL-Om1

value: 7 days culture with GSK126


title: TL-Om1_OR-S2_2

description: Gene expression after 7 days culture with OR-S2 in TL-Om1

value: 7 days culture with OR-S2


title: ATL2_DMSO

description: Gene expression after 7 days culture with DMSO in ATL pateint PBMC


title: d13_p2_5_mix_62_S62


title: TL-Om1_OR-S1_2

description: Gene expression after 7 days culture with OR-S1 in TL-Om1


title: Sample235 [388]

city: Köln

first: Martin

last: Lukačišin

state: Deutschland

address: Zülpicher Straße 47a

department: Institute for Biological Physics

country: Germany

institute: Universität zu Köln

data_processing:
The reads resulting from sequencing were demultiplexed, aligned to annotated reference S. cerevisiae genome R64-2 using TopHat (Kim et al., 2013), deduplicated using UMI-tools (Smith et al., 2017) and quantified using featureCounts (Liao et al., 2014). Gene expression changes were further analyzed using custom written Matlab scripts. Briefly, to account for sample-to-sample variation and low molecule noise, quantile normalisation was applied using the quantilenorm function over the entire dataset
Genome_build: https://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz

organism: Saccharomyces cerevisiae BY4741

source_name: CR_Cell lysate

growth_protocol: Saccharomyces cerevisiae strain BY4741 was grown in 20 ml of YPD broth - yeast extract (Sigma Aldrich cat. no. Y1625), peptone (Sigma Aldrich cat. no. 91249), dextrose (Sigma Aldrich cat. no. D9434) in a 100 ml conical flask shaken 220 rpm at 30°C overnight and then distributed into a 96-well plate (non-treated transparent flat bottom, Nunc). A customized liquid handling robot (Tecan Freedom Evo 150) with 8 liquid handling channels and a robotic manipulator was used to produce a two-dimensional discretised two drug 24×24-well gradient in YPD spread over six 96-well plates and to inoculate the yeast overnight culture to final optical density at 600 nm (OD600) of 0.15 and final liquid volume in the well of 200 ul. The discretized drug gradient was set up as in Chevereau and Bollenbach (2015), that is the concentration of each drug was spaced according to where cmax was the highest concentration used, x was linearly spaced from 0 to 22 steps (with replicate for no drug condition) and a = 1/3. Working drug solutions were prepared either by adding respective amounts of concentrated DMSO drug stocks thawed from -20°C storage (no refreezing) previously prepared from stock chemicals (cycloheximide 37094, myriocin M1177, rapamycin 37094, all from Sigma Aldrich), or by dissolving directly in YPD and sterile-filtering (LiCl, L9650 Sigma Aldrich). The six plates were incubated for three iterations, each lasting ~8 hrs. Each iteration consisted of incubation and a re-inoculation. Plates were incubated in an automated incubator (Liconic Storex) kept at 30°C, > 95% humidity, vigorously shaken at >1,000 rpm. During the incubation, OD600 was measured every ~15 mins in a Tecan Infinite F500 plate reader. In addition to shaking during incubation, directly before each measurement, plates were shaken on a magnetic shaker (Teleshake; Thermo Scientific) at 1,100 rpm for 20 s. During re-inoculation, a volume Vi of yeast culture specifically calculated for each well so as to achieve OD600=0.15 after dilution (while 1.5 ul ≤ Vi ≤100 ul) was added to a fresh medium in a new 96-well plate containing a drug cocktail pipetted in such a way that the final concentration of both drugs, when accounted for the size of the inoculum, was the same as before the re-inoculation step, and the total volume of liquid in the well was 200 ul. During the re-inoculation the plate to be re-inoculated was not shaken for a max. of 15 mins. The entire setup was kept in a climate room at 30°C and ~50% humidity. The growth rate for each well for each iteration was quantified from the OD increase over time by a linear fit of log2(OD) for the last 10 measurements (~2.5 hrs) before re-inoculation. All growth rates were normalized to the growth rate of the parent strain in the absence of any drugs measured on the same day.

extract_protocol:
For RNA extraction, wells growing at a relative growth rate close to 50% at the end of the third iteration of the automated re-inoculation culture were selected. RNA extraction was performed using the RiboPure RNA Purification Kit for yeast (Thermo Scientific, AM1926). The purity of extracted RNA was confirmed for selected samples using the Agilent RNA 6000 Nano Bioanalyzer Kit.
For RNA extraction, wells growing at a relative growth rate close to 50% at the end of the third iteration of the automated re-inoculation culture were selected. RNA extraction was performed using the RiboPure RNA Purification Kit for yeast (Thermo Scientific, AM1926). The purity of extracted RNA was confirmed for selected samples using the Agilent RNA 6000 Nano Bioanalyzer Kit. The library was prepared as in (Bar-Ziv et al., 2016). In brief, the purified RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module (New England Biolabs E6150S), poly(A)-selected using Dynabeads oligo-dT kit (Invitrogen, cat. No. 61012) and reverse-transcribed to cDNA using custom poly(T) primers barcoded for multiplexing as well as containing 4-nt-long unique molecular identifier. The resulting complementary DNA strands were pooled and purified (RNase H NEB M0297S, Agencourt AMPure XP Beckman Coulter A63881), a custom double stranded adapter ligated to the 3’ end (Quick Ligation Kit, NEB M2200S), second cDNA strand synthesized (KAPAHiFi Hot-Start ReadyMix VWR 733-2430), amplified and 50 bp single-end sequenced on Illumina HiSeq 2500 using a primer complementary to the adaptor at the end opposite to the poly(A).

tag: drug combination

value: CR

tag: myriocin [μg/ml]

tag: cycloheximide [μg/ml]

tag: licl [μg/ml]

tag: rapamycin [μg/ml]

tag: growthrateabsolute [1/h]

tag: growthraterelative

tag: finalod


title: Sample237 [390]


title: Sample238 [391]


title: TL-Om1_DMSO_2


title: TL-Om1_GSK126_1


title: ATL1_OR-S1

source_name: ATL patient #1


title: TL-Om1_OR-S2_1


title: ATL1_DMSO


title: d13_p2_5_mix_61_S61


title: TL-Om1_OR-S1_1


title: d13_p2_5_mix_60_S60


title: Sample232 [385]


title: Sample231 [384]


title: Sample233 [386]


title: d13_p2_5_mix_5_S5


title: d13_p2_5_mix_59_S59


title: d13_p2_5_mix_58_S58


title: Sample236 [389]


title: Sample234 [387]


title: Sample230 [383]


title: Sample229 [382]


title: d13_p2_5_mix_57_S57


title: Sample227 [380]


title: Sample226 [379]


title: d13_p2_5_mix_56_S56


title: Sample228 [381]


title: d13_p2_5_mix_55_S55


title: d13_p2_5_mix_51_S51


title: Sample221 [374]


title: Sample222 [375]


title: d13_p2_5_mix_53_S53


title: d13_p2_5_mix_54_S54


title: Sample224 [377]


title: Sample225 [378]


title: d13_p2_5_mix_52_S52


title: d13_p2_5_mix_4_S4


title: Sample220 [373]


title: d13_p2_5_mix_49_S49


title: d13_p2_5_mix_48_S48


title: Sample216 [369]


title: d13_p2_5_mix_47_S47


title: Sample217 [370]


title: Sample215 [368]


title: d13_p2_5_mix_45_S45


title: d13_p2_5_mix_46_S46


title: d13_p2_5_mix_44_S44


title: Sample213 [366]


title: Sample223 [376]


title: Sample214 [367]


title: d13_p2_5_mix_43_S43


title: Sample211 [364]


title: Sample212 [365]


title: d13_p2_5_mix_50_S50


title: d13_p2_5_mix_41_S41


title: Sample219 [372]


title: d13_p2_5_mix_42_S42


title: Sample209 [362]


title: Sample207 [360]


title: d13_p2_5_mix_38_S38


title: Sample208 [361]


title: Sample218 [371]


title: d13_p2_5_mix_39_S39


title: d13_p2_5_mix_3_S3


title: Sample206 [359]


title: d13_p2_5_mix_37_S37


title: d13_p2_5_mix_36_S36


title: Sample205 [358]


title: d13_p2_5_mix_35_S35


title: d13_p2_5_mix_34_S34


title: Sample202 [355]


title: d13_p2_5_mix_33_S33


title: Sample204 [357]


title: Sample201 [354]


title: d13_p2_5_mix_32_S32


title: Sample200 [353]


title: d13_p2_5_mix_31_S31


title: Sample199 [352]


title: d13_p2_5_mix_40_S40


title: Sample210 [363]


title: d13_p2_5_mix_30_S30


title: Sample198 [351]


title: d13_p2_5_mix_2_S2


title: d13_p2_5_mix_29_S29


title: Sample196 [349]


title: Sample195 [348]

source_name: LR_Cell lysate

value: LR


title: Sample194 [347]


title: Sample193 [346]


title: Sample192 [345]


title: d13_p2_5_mix_27_S27


title: d13_p2_5_mix_26_S26


title: d13_p2_5_mix_24_S24


title: d13_p2_5_mix_28_S28


title: Sample191 [344]


title: Sample203 [356]


title: d13_p2_5_mix_25_S25


title: d13_p2_5_mix_20_S20


title: Sample190 [343]


title: d13_p2_5_mix_21_S21


title: d13_p2_5_mix_22_S22


title: d13_p2_5_mix_1_S1


title: Sample189 [342]


title: Sample188 [341]


title: Sample187 [340]


title: Sample186 [339]


title: Sample197 [350]


title: d13_p2_5_mix_18_S18


title: Sample185 [338]


title: d13_p2_5_mix_19_S19


title: d13_p2_5_mix_17_S17


title: d13_p2_5_mix_16_S16


title: Sample183 [336]


title: Sample184 [337]


title: Sample182 [335]


title: d13_p2_5_mix_23_S23


title: d13_p2_5_mix_14_S14


title: d13_p2_5_mix_15_S15


title: d13_p2_5_mix_13_S13


title: Sample181 [334]


title: d13_p2_5_mix_12_S12


title: Sample179 [332]


title: d13_p2_5_mix_10_S10


title: Sample178 [331]


title: Sample177 [330]


title: D13_P1_S9


title: Sample176 [329]


title: D13_P1_S95


title: Sample175 [328]


title: Sample174 [327]


title: D13_P1_S93


title: Sample173 [326]


title: D13_P1_S96


title: D13_P1_S94


title: D13_P1_S92


title: Sample172 [325]


title: Sample170 [323]


title: Sample171 [324]


title: Sample180 [333]


title: D13_P1_S90


title: Sample169 [322]


title: Sample168 [321]


title: d13_p2_5_mix_11_S11


title: Sample167 [320]


title: Sample166 [319]


title: D13_P1_S89


title: D13_P1_S88


title: D13_P1_S87


title: D13_P1_S86


title: Sample164 [317]


title: Sample163 [316]


title: D13_P1_S85


title: Sample162 [315]


title: Sample161 [314]


title: Sample160 [313]


title: D13_P1_S91


title: Sample157 [310]


title: Sample158 [311]


title: D13_P1_S8


title: Sample156 [309]


title: D13_P1_S7


title: D13_P1_S82


title: D13_P1_S80


title: Sample155 [308]


title: D13_P1_S81


title: D13_P1_S79


title: Sample153 [306]


title: Sample152 [305]


title: Sample154 [307]


title: Sample165 [318]


title: D13_P1_S76


title: D13_P1_S75


title: D13_P1_S78


title: D13_P1_S77


title: Sample151 [304]


title: D13_P1_S74


title: Sample150 [303]


title: D13_P1_S73


title: Sample149 [302]


title: D13_P1_S72


title: D13_P1_S83


title: Sample159 [312]


title: Sample148 [301]


title: D13_P1_S71


title: D13_P1_S84


title: Sample147 [274]

source_name: CL_Cell lysate

value: CL


title: Sample146 [273]


title: D13_P1_S70


title: Sample145 [272]


title: D13_P1_S6


title: D13_P1_S69


title: Sample144 [271]


title: Sample143 [270]


title: D13_P1_S68


title: Sample142 [269]


title: D13_P1_S67


title: D13_P1_S66


title: Sample141 [268]


title: Sample140 [267]


title: Sample139 [266]


title: Sample137 [264]


title: D13_P1_S65


title: Sample138 [265]


title: Sample136 [263]


title: D13_P1_S61


title: Sample135 [262]


title: D13_P1_S5


title: D13_P1_S59


title: D13_P1_S62


title: D13_P1_S64


title: D13_P1_S60


title: D13_P1_S63


title: D13_P1_S58


title: Sample134 [261]


title: Sample133 [260]


title: Sample132 [259]


title: Sample131 [258]


title: D13_P1_S57


title: Sample130 [257]


title: D13_P1_S56


title: D13_P1_S54


title: Sample129 [256]


title: Sample127 [254]


title: Sample128 [255]


title: D13_P1_S51


title: D13_P1_S52


title: D13_P1_S50


title: D13_P1_S49


title: Sample126 [253]


title: Sample124 [251]


title: Sample123 [250]


title: D13_P1_S55


title: D13_P1_S48


title: D13_P1_S46


title: D13_P1_S53


title: Sample121 [248]


title: D13_P1_S4


title: Sample120 [247]


title: D13_P1_S45


title: Sample119 [246]

source_name: MR_Cell lysate

value: MR


title: Sample118 [245]


title: D13_P1_S43


title: Sample125 [252]


title: Sample117 [243]


title: D13_P1_S44


title: D13_P1_S42


title: D13_P1_S41


title: Sample115 [241]


title: Sample116 [242]


title: Sample113 [239]


title: Sample114 [240]


title: D13_P1_S3


title: D13_P1_S39


title: Sample122 [249]


title: D13_P1_S40


title: Sample112 [238]


title: D13_P1_S47


title: Sample111 [237]


title: D13_P1_S37


title: D13_P1_S38


title: D13_P1_S36


title: Sample110 [236]


title: Sample109 [235]


title: D13_P1_S34


title: D13_P1_S35


title: Sample107 [233]


title: Sample106 [232]


title: Sample105 [231]


title: Sample108 [234]


title: Sample103 [229]


title: Sample102 [228]


title: Sample104 [230]


title: D13_P1_S31


title: D13_P1_S30


title: D13_P1_S32


title: Sample100 [226]


title: D13_P1_S33


title: Sample101 [227]


title: D13_P1_S2


title: Sample99 [225]


title: D13_P1_S26


title: Sample98 [224]


title: Sample97 [223]


title: D13_P1_S28


title: Sample94 [220]


title: Sample92 [218]


title: D13_P1_S21


title: D13_P1_S23


title: Sample93 [219]


title: Sample91 [217]


title: D13_P1_S25


title: Sample90 [216]


title: D13_P1_S1


title: Sample96 [222]


title: D13_P1_S29


title: D13_P1_S27


title: D13_P1_S17


title: D13_P1_S16


title: D13_P1_S19


title: D13_P1_S18


title: D13_P1_S15


title: D13_P1_S24


title: Sample95 [221]


title: D13_P1_S14


title: D13_P1_S22


title: D13_P1_S13


title: Sample84 [210]


title: Sample83 [209]


title: Sample85 [211]


title: Sample87 [213]


title: Sample86 [212]


title: Sample88 [214]


title: D13_P1_S20


title: Sample81 [207]


title: D13_P1_S10


title: D13_P1_S11


title: Sample80 [206]


title: Sample89 [215]


title: D6_P2_96_S96

value: DIPG6 (VI) cell line


title: Sample79 [205]


title: D6_P2_9_S9


title: D6_P2_95_S95


title: Sample78 [204]


title: Sample77 [203]


title: Sample74 [174]

source_name: LM_Cell lysate

value: LM


title: D6_P2_94_S94


title: Sample76 [202]


title: Sample75 [201]


title: D13_P1_S12


title: D6_P2_93_S93


title: D6_P2_91_S91


title: D6_P2_90_S90


title: Sample82 [208]


title: Sample72 [172]


title: Sample70 [170]


title: D6_P2_8_S8


title: Sample71 [171]


title: D6_P2_89_S89


title: D6_P2_87_S87


title: Sample69 [169]


title: D6_P2_92_S92


title: D6_P2_85_S85


title: Sample66 [166]


title: Sample68 [168]


title: D6_P2_84_S84


title: Sample65 [165]


title: D6_P2_83_S83


title: Sample64 [164]


title: D6_P2_82_S82


title: Sample73 [173]


title: Sample63 [163]


title: D6_P2_88_S88


title: D6_P2_81_S81


title: Sample62 [162]


title: D6_P2_80_S80


title: D6_P2_86_S86


title: D6_P2_7_S7


title: Sample61 [161]


title: D6_P2_78_S78


title: D6_P2_79_S79


title: Sample59 [159]


title: D6_P2_77_S77


title: Sample58 [158]


title: D6_P2_76_S76


title: Sample60 [160]


title: Sample57 [157]


title: Sample56 [156]


title: D6_P2_75_S75


title: D6_P2_73_S73


title: Sample53 [153]


title: D6_P2_72_S72


title: Sample52 [152]


title: Sample51 [151]


title: D6_P2_71_S71


title: D6_P2_6_S6


title: Sample50 [150]


title: Sample48 [148]


title: Sample49 [149]


title: Sample47 [147]


title: D6_P2_68_S68


title: D6_P2_69_S69


title: D6_P2_67_S67


title: D6_P2_66_S66


title: D6_P2_65_S65


title: Sample46 [146]


title: Sample43 [143]


title: D6_P2_63_S63


title: D6_P2_64_S64


title: Sample54 [154]


title: Sample45 [145]


title: Sample55 [155]


title: Sample42 [142]


title: D6_P2_74_S74


title: Sample41 [141]


title: D6_P2_5_S5


title: D6_P2_61_S61


title: D6_P2_62_S62


title: Sample38 [138]


title: Sample39 [139]


title: Sample40 [140]


title: D6_P2_70_S70


title: Sample37 [137]


title: D6_P2_59_S59


title: Sample44 [144]


title: D6_P2_58_S58


title: Sample67 [167]


title: Sample35 [135]


title: Sample34 [134]


title: D6_P2_57_S57


title: Sample33 [133]


title: D6_P2_55_S55


title: D6_P2_52_S52


title: D6_P2_56_S56


title: D6_P2_51_S51


title: D6_P2_53_S53


title: Sample30 [130]


title: D6_P2_54_S54


title: D6_P2_50_S50


title: Sample29 [129]


title: Sample27 [127]


title: Sample28 [128]


title: D6_P2_49_S49


title: D6_P2_4_S4


title: D6_P2_48_S48


title: Sample26 [126]


title: Sample36 [136]


title: D6_P2_60_S60


title: Sample25 [125]


title: D6_P2_46_S46


title: D6_P2_47_S47


title: Sample31 [131]


title: Sample24 [124]

source_name: CM_Cell lysate

value: CM


title: D6_P2_45_S45


title: Sample32 [132]


title: D6_P2_44_S44


title: Sample20 [120]


title: Sample21 [121]


title: Sample23 [123]


title: D6_P2_43_S43


title: D6_P2_41_S41


title: D6_P2_40_S40


title: Sample18 [118]


title: Sample22 [122]


title: Sample17 [117]


title: Sample16 [116]


title: Sample19 [119]


title: D6_P2_39_S39


title: Muscle_Control 4

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

label: Biotin

organism: Sus scrofa

source_name: Muscle Control

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: The four-week feeding trial was approved by the local Animal Care and Use Committee (Regierungspräsidium Giessen; permission no: JLU 676_M). All experimental procedures described followed established guidelines for the care and handling of laboratory animals. The experiment included 30 five-week-old crossbreed pigs [Piétrain x (German Landrace x German Edelschwein)], which were randomly assigned to three groups of 10 pigs each [control (CON), 5 % insect meal (IM) (IM5), 10 % IM (IM10)], with similar initial body weights (BW) (CON: 8.66 ± 1.54 kg; IM5: 8.63 ± 1.49 kg; IM10: 8.79 ± 1.44 kg; mean ± SD; n = 10/group). The pigs were kept in groups of three or four animals in flat-deck pens under controlled conditions (23 ± 2°C room temperature, 50-60 % relative humidity, light from 07.00 a.m. to 07.00 p.m.).

extract_protocol: Total RNA from aliquots of gastrocnemius muscle (≈ 30 mg) was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. RNA quantity and quality were assessed spectrophotometrically using an Infinite 200M microplate reader equipped with a NanoQuant plate (both from Tecan, Mainz, Germany). The average RNA concentration and the A260/A280 ratio of all total RNA samples (n = 30, means ± SD) were 0.54 ± 0.10 µg/µL and 1.96 ± 0.02, respectively. Transcript profiling in gastrocnemius muscle was carried out for 6 randomly selected pigs per group. Following an RNA quality check using an Agilent 2100 Bioanalyzer (Agilent technologies, Böblingen, Germany), the total RNA samples were processed at the Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany) using an Affymetrix GeneChip Porcine Gene 1.0 Sense Target array, which represents 19,212 porcine genes, according to the manufacturer´s instructions. The average RNA integrity number (RIN) values of all samples (n = 18, means ± SD) were 7.72 ± 0.41 (gastrocnemius muscle).

treatment_protocol: Three different diets differing in their main protein source but with comparable levels of gross energy and crude nutrients were fed. Nutrient concentrations in the diets were sufficient to meet the requirements according to German Society for Nutrition Physiology. In the diet of group CON, which contained soybean extraction meal as the main protein source, the amount of insect meal (IM) was 0 %, while in the diets of groups IM5 and IM10 the amount of IM was 5 % and 10 %, respectively, through partial (50 %) or complete (100 %) isonitrogenous replacement of SEM (44 % crude protein) by IM. The IM was produced from industrialized mass-rearing of Tenebrio molitor L.. The diets were offered ad libitum and feed consumption was recorded daily. BWs were recorded once per week. Water was constantly available ad libitum from a nipple drinker system. At day 29, the pigs were killed by electronarcosis followed by exsanguination. Aliquots of gastrocnemius muscle were excised, washed in ice-cold NaCl solution (0.9 %) and snap-frozen in liquid nitrogen.

tag: gender

value: male

tag: condition

value: control

tag: tissue

value: gastrocnemius muscle


title: Muscle_Control 6


title: Muscle_Control 5


title: Muscle_Control 3


title: Muscle_Control 2


title: D6_P2_38_S38

tag: cell type

value: DIPG (diffuse intrinsic pontine glioma)


title: Muscle_Control 1


title: Sample15 [115]


title: Liver_IM10% 4

source_name: Liver IM10%

extract_protocol: Total RNA from aliquots of liver (≈ 20 mg) was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. RNA quantity and quality were assessed spectrophotometrically using an Infinite 200M microplate reader equipped with a NanoQuant plate (both from Tecan, Mainz, Germany). The average RNA concentration and the A260/A280 ratio of all total RNA samples (n = 30, means ± SD) were 2.06 ± 0.49 µg/µL and 1.97 ± 0.06, respectively. Transcript profiling in liver was carried out for 6 randomly selected pigs per group. Following an RNA quality check using an Agilent 2100 Bioanalyzer (Agilent technologies, Böblingen, Germany), the total RNA samples were processed at the Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany) using an Affymetrix GeneChip Porcine Gene 1.0 Sense Target array, which represents 19,212 porcine genes, according to the manufacturer´s instructions. The average RNA integrity number (RIN) values of all samples (n = 18, means ± SD) were 7.91 ± 0.28 (liver).

treatment_protocol: Three different diets differing in their main protein source but with comparable levels of gross energy and crude nutrients were fed. Nutrient concentrations in the diets were sufficient to meet the requirements according to German Society for Nutrition Physiology. In the diet of group CON, which contained soybean extraction meal as the main protein source, the amount of insect meal (IM) was 0 %, while in the diets of groups IM5 and IM10 the amount of IM was 5 % and 10 %, respectively, through partial (50 %) or complete (100 %) isonitrogenous replacement of SEM (44 % crude protein) by IM. The IM was produced from industrialized mass-rearing of Tenebrio molitor L.. The diets were offered ad libitum and feed consumption was recorded daily. BWs were recorded once per week. Water was constantly available ad libitum from a nipple drinker system. At day 29, the pigs were killed by electronarcosis followed by exsanguination. Aliquots of the liver were excised, washed in ice-cold NaCl solution (0.9 %) and snap-frozen in liquid nitrogen.

value: Liver


title: Sample14 [114]


title: Sample13 [113]


title: Liver_IM10% 1


title: D6_P2_37_S37


title: D6_P2_3_S3


title: Sample12 [112]


title: Liver_IM10% 5


title: D6_P2_36_S36


title: Liver_IM10% 6


title: Liver_IM5% 6

source_name: Liver IM5%


title: Liver_IM5% 5


title: Sample11 [111]


title: Liver_IM10% 3


title: D6_P2_42_S42


title: Liver_IM10% 2


title: Sample10 [110]


title: D6_P2_33_S33


title: Sample9 [109]


title: Liver_IM5% 2


title: Liver_IM5% 3


title: D6_P2_32_S32


title: Liver_IM5% 4


title: D6_P2_35_S35


title: Liver_Control 4

source_name: Liver Control


title: Sample7 [107]


title: Sample8 [108]


title: D6_P2_31_S31


title: Liver_Control 5


title: Liver_IM5% 1


title: Liver_Control 1


title: D6_P2_30_S30


title: Liver_Control 3


title: Sample5 [105]


title: D6_P2_2_S2


title: Liver_Control 2


title: Muscle_IM10% 1

source_name: Muscle IM10%


title: D6_P2_29_S29


title: D6_P2_34_S34


title: Muscle_IM10% 5


title: Muscle_IM10% 4


title: Muscle_IM5% 6

source_name: Muscle IM5%


title: D6_P2_28_S28


title: Muscle_IM10% 3


title: Muscle_IM5% 5


title: Muscle_IM5% 4


title: Sample3 [103]


title: Liver_Control 6


title: Muscle_IM10% 2


title: Sample4 [104]


title: Sample2 [102]


title: H3K27me3_NST7

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

description:
processed data file:
H3K27me3_rawcounts.txt

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
manual trimming of 5 bp at the 3’ end
mapping with bowtie2, allowing at most 3 substitutions per read and no indels
Genes significantly enriched for a ChIP-Seq with respect to the WC control or between two conditions were identified by multiple 2 x 2 χ2 tests
Genome_build: RefGen ZmB73 Assembly AGPv4 + Zea_mays.AGPv4.34.gtf Gramene annotation
Supplementary_files_format_and_content: tab-delimited matrix with raw read counts for each gene in each sample/antibody.  For H3K27me3 the gene boundaries are from TSS to TTS. For H3K4me3 and H3K9ac gene boundaries are from 0bp to +1000bp with respect to the TSS.

organism: Zea mays

source_name: immature wrapped leaf

growth_protocol: Maize plants were grown in greenhouse until V5-V6 leaf stage with normal watering

extract_protocol:
Chromatin was purified from frozen tisses, sonicated and immuno-precipitated with antibody.
Ovation Ultralow Library System kit (Nugen) for Illumina sequencing

treatment_protocol: Stresses were applied for 10 days: control plants (NS) were watered with 75% of disposable water at 0.1dS/m salt concentration; drought-stressed plants (WS) with 25% of disposable water at 0.1dS/m salt concentration.

tag: cultivar

value: immature wrapped leaf

tag: growth condition

value: control + recovery 7days

tag: antibody

value: H3K27me3 (Active Motif, Cat. 39155)


title: WholeChromatin

description:
processed data file:
wc_rawcounts.txt

value: control 10days


title: H3K27me3_WST7

value: drought stress + recovery 7days


title: Muscle_IM10% 6


title: D6_P2_25_S25

tag: passages

tag: disease state


title: Sample6 [106]

tag: drug combination


title: D6_P2_26_S26


title: Sample1 [101]

tag: myriocin [μg/ml]


title: CAOV2 primary ovarian cancer cells, TAZ silencing; biological replicate #3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive

institute: Duke University

data_processing:
FastQC was used for confirming quality of sequencing reads.
Sequenced reads were mapped to hg19 reference genome using Hisat2 with default parameters
Quntification of read counts of genes were performed using HTSeq
DESeq2 were applied for differential analysis to compare gene expressions between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: DEseq2 output

source_name: CAOV2 primary ovarian cancer cell

growth_protocol: CAOV2 ovarian cancer cells were grow in DMEM media (11995-DMEM, ThermoFisher Scientific) and supplement with 10% heat-inactivated fetal bovine serum (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, #74104) according to the manufacturer's instructions.
1μg of total RNA was used to generate cDNA library with Illumina TruSeq Stranded mRNA LT Sample Prep Kit – Set A (Illumina, RS-122-2101) according to manufacturer’s instructions.

treatment_protocol: Human ovarian cancer cells (1x10^5 CAOV2 cells) were seeded in a well on 6-well plate and transfected with 100 pmole of siRNAs (TAZ silencing (siTAZ): D-016083, Dharmacon; or non-targeting siRNA control (siNT): AllStars Negative Control siRNA, SI03650318) and 6μL of Lipofectamine RNAiMAX (ThermoFisher Scientific, #13778150) reagent for 2 days. Cells were collected at day 3 for RNAseq.

tag: cell line

value: CAOV2 ovarian cancer cell line

value: primary ovarian cancer cell

tag: genotype

value: TAZ silencing


title: Muscle_IM5% 2


title: H3K27me3_WST0

value: drought stress 10 days


title: Muscle_IM5% 3


title: D6_P2_24_S24

source_name: patient-derived DIPG cell line developed in the Monje Lab

value: DIPG6 (VI) cell line


title: Muscle_IM5% 1


title: H3K9ac_WST7

description:
processed data file:
H3K9ac_rawcounts.txt

value: H3K9ac (Millipore, Cat. 07-352)


title: H3K27me3_NST0


title: H3K9ac_NST7


title: CAOV2 primary ovarian cancer cells, TAZ silencing; biological replicate #2


title: H3K9ac_WST0


title: D6_P2_23_S23


title: H3K9ac_NST0


title: CAOV2 primary ovarian cancer cells, TAZ silencing; biological replicate #1


title: D6_P2_22_S22


title: CAOV2 primary ovarian cancer cells, control; biological replicate #3


title: D6_P2_21_S21


title: H3K4me3_WST0

description:
processed data file:
H3K4me3_rawcounts.txt

value: H3K4me3 (Active Motif, Cat. 39159)


title: CAOV2 primary ovarian cancer cells, control; biological replicate #2


title: H3K4me3_NST7


title: H3K4me3_NST0


title: CAOV2 primary ovarian cancer cells, control; biological replicate #1


title: set1 deletion input DNA

city: BOSTON

first: HYUN JIN

last: BAE

state: MA

address: 240 Longwood Ave, Building C1-207

department: BCMP

institute: Harvard Medical School

data_processing:
Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode
Demultiplexed reads were aligned to S.cerevisiae genome, with bowtie1.1.1, reads with multiple alignments removed.
S.pombe spiked-in samples were aligned first to S.pombe genome with bowtie1.1.1, S.pombe unaligned reads were aligned to S.cerevisiae genome, with reads with multiple alignments removed.
Genome_build: S.cerevisiae version R64-1-1, S.pombe version ASM294v2.31

organism: Saccharomyces cerevisiae

source_name: exponential growing culture

growth_protocol: Cells were grown in indicated media at 30 C to an OD of 0.500

extract_protocol:
Cells were lysed in FA buffer 0.5% SDS using glass beads. Cross-linked extracted were sonicated using a Misonix 300 with cup horns, with 10s on/off pulses for a total sonication time of 20 min. Soluble chromatin was recovered by centrifugation and protein concentration quantified by Bradford assay. A total of 700 ug of chromatin was used per immunoprecipitation. Where S.pombe “spike-in” was used, 10 % S.pombe chromatin prepared similarly was added to the immunoprecipitation. The indicated antibody and 10 ul of Protein-G sepharose beads were added, followed by overnight incubation at 4 C. Beads were washed once with FA buffer, 0.1% SDS, 275 mM NaCl, once with FA buffer, 0.1% SDS, 500 mM NaCl, once with 10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na Deoxycholate, and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). Immunoprecipitated material was eluted with 50 mM Tris-HCl 7.5, 10 mM EDTA, 1% SDS by incubating at 65 C for 20 min. Beads were washed once with TE, and the supernatant added to eluted material. Recovered immunoprecipitate was de-crosslinked with 40 ug of Pronase 1 hour at 42 C and overnight at 65 C. Samples were treated with 5 ug RNAse A and phenol-chloroform/chloroform extracted followed by precipitation with LiCl, 40 ug Glycogen, and 100 % EtOH. Precipitated DNA was resuspended in appropriate volume of water and quantified using Qubit assay.
1 ng of immunoprecipitated DNA was used for ChIP-Seq library production. Immunoprecipitated DNA was end repaired using T4 DNA polymerase, T4 PNK and DNA Polymerase I, Large (Klenow) fragment. A single adenosine “tail” was added to the 3’ end of fragments using Klenow (3’ to 5’ exo minus) and adapters containing inline multiplexing barcodes were added using T4 Quick DNA ligase. Adapter ligated DNA fragments between 200 and 500 bp were gel purified and PCR amplified with 16 cycles. Library quality was assessed using Agilent 2100 Bioanalyzer. Equal molarity of each library was mixed.

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1%. Cells were incubated for 20 min at room temperature and the reaction quenched for 5 minutes with 3M glycine. Cell pellets were recovered and washed with FA buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1mM EDTA,1% Triton X-100 and 0.1% Na Deoxycholate), 0.1% SDS.

tag: background

value: BY4741, set1 deletion

tag: s.pombe spike-in

value: YES


title: Input yeast DNA


title: D6_P2_1_S1


title: CAOV2 recurrent ovarian cancer cells; biological replicate #2

data_processing:
FastQC was used for confirming quality of sequencing reads.
Sequenced reads were mapped to hg19 reference genome using Hisat2 with default parameters
Quantification of read counts of genes were performed using HTSeq
DESeq2 were applied for differential analysis to compare gene expressions between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: DEseq2 output

source_name: CAOV2 recurrent ovarian cancer cell

growth_protocol: CAOV2 primary and recurrent ovarian cancer cells were grow in DMEM media (11995-DMEM, ThermoFisher Scientific) and supplement with 10% heat-inactivated fetal bovine serum (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

value: recurrent ovarian cancer cell


title: D6_P2_20_S20

value: DIPG (diffuse intrinsic pontine glioma)


title: D6_P2_19_S19


title: CAOV2 recurrent ovarian cancer cells; biological replicate #3


title: Set1 (1-200) deletion Input DNA rep2

tag: plasmid

value: Set1 N-term (1-200) deletion


title: se1 and swd2 deletion input DNA

value: BY4741, set1 and swd2 deletion


title: Full length (wt) Set1 Input DNA rep2

value: Full length Set1


title: Nrd1 fusion FLAG ChIP-Seq rep2

value: Nrd1CID fusion to Set1 N-terminal deletion


title: Nrd1 fusion Input DNA rep2


title: D6_P2_18_S18


title: CAOV2 recurrent ovarian cancer cells; biological replicate #1


title: Set1 (1-200) deletion FLAG  ChIP-Seq rep2


title: H3K4me3_WST7

value: immature wrapped leaf


title: Full length (wt) Set1 FLAG ChIP-Seq rep2


title: D6_P2_17_S17


title: CAOV2 primary ovarian cancer cells; biological replicate #3


title: D6_P2_16_S16


title: Nrd1 fusion H3K4me2 ChIP-Seq rep2


title: D6_P2_15_S15


title: Full length (wt) Set1 H3K4me2 ChIP-Seq rep2


title: CAOV2 primary ovarian cancer cells; biological replicate #2


title: Set1 (1-200) deletion H3K4me3 ChIP-Seq rep2


title: Nrd1 fusion H3K4me3 ChIP-Seq rep2


title: CAOV2 primary ovarian cancer cells; biological replicate #1


title: D6_P2_14_S14


title: D6_P2_13_S13


title: Full length (wt) Set1 H3K4me3 ChIP-Seq rep2


title: Set1 (1-200) deletion Input DNA rep1


title: Full length (wt) Set1 FLAG ChIP-Seq rep1


title: D6_P2_10_S10


title: D6_P2_11_S11


title: D6_P1__S9


title: Nrd1 fusion Input DNA rep1


title: Full length (wt) Set1 Input DNA rep1


title: D6_P1__S96


title: Set1 (1-200) deletion H3K4me2 ChIP-Seq rep1


title: D6_P2_12_S12


title: Nrd1 fusion FLAG ChIP-Seq rep1


title: Set1 (1-200) deletion H3K4me2 ChIP-Seq rep2


title: Nrd1 fusion H3K4me3 ChIP-Seq rep1


title: H4K16Ac ChIP-seq in nhp6ab_rep2

data_processing:
Quality control performed with FastQC
Reads trimmed manually by 5 bps at the 3' end
Reads mapped on the S.cerevisiae genome with Bowtie, whole read mapped with at most 2 substitutions
Mapped reads shifted by 100 bp in the 5'>3' direction
Read counts computed on nucleosome on shifted reads coordinates  (5' mapping position).
Genome_build: SacCer_Apr2011(S288C genome version=R64-2-1)  retrieved from the UCSC Genome Browser
Supplementary_files_format_and_content: Read counts for each nucleosome position on WT (merged replicates) and nhp6ab (merged replicates)

source_name: nhp6ab cells

growth_protocol: Yeast from WT or nhp6ab were grown in YPD medium untill 0,5O.D./ml is reached

extract_protocol:
Extract from glass beads brocken cells were sonicated and DNA-protein complexes were isolated with Antibody
For ChIP- seq:NuGEN's Ovation Ultralow DR Multiplex System kit was used for generating non-cohesive ends (end-repair) and for ligation of barcode adapters for multiplexing. Finally, DNA libraries were generated through PCR and subjected to quality control.Starting from these libraries, amplification of the clusters were generated using Bridge PCR technology inside the cBot Illumina. Sequencing was performed by means of a HiSeq 2000 Illumina and raw base files were processed through the HiSeq 2000 CASAVA pipeline for primary analysis.

treatment_protocol: 0,5 O.D./ml growing cells were treated with 1% formaldehyde for 20 min and then blocked with 330mM glycine for 5 min.

tag: growth phase

value: exponential

tag: growth medium

value: YPD

tag: chip antibody

value: anti H4K16Ac Santa Cruz

tag: genotype/variation

value: nhp6ab cells


title: H4K16Ac ChIP-seq in nhp6ab_rep1


title: Set1 (1-200) deletion FLAG  ChIP-Seq rep1


title: Nrd1 fusion H3K4me2 ChIP-Seq rep1


title: D6_P1__S94

tag: cell type


title: Full length (wt) Set1 H3K4me2 ChIP-Seq rep1


title: Set1 (1-200) deletion H3K4me3 ChIP-Seq rep1


title: D6_P1__S95


title: H4K16Ac ChIP-seq in WT_rep2

source_name: WT cells

value: WT cells


title: D6_P1__S93

value: DIPG6 (VI) cell line


title: RNA-seq in nhp6ab Rep2

data_processing:
Read mapped with Rsem (default parameters) on ORF sequences of the SGD annotation (sacCer3 retrieved from the UCSC genome browser)
Read counts for each ORF retrieved from the output of Rsem
Genome_build: sacCer3
Supplementary_files_format_and_content: Read counts

growth_protocol: exponential growth

extract_protocol:
RNA was extracted from yeast cells using phenol/chlorophorm standard procedure
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA-seq in nhp6ab Rep1


title: RNA-seq in WT Rep2

value: WT


title: D6_P1__S92


title: RNA-seq in WT Rep1


title: D6_P1__S91


title: D6_P1__S90


title: set2_bio1_lib1

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

description: Sample 15

data_processing:
Library strategy: TIF-Seq
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
5' and 3' sequences were extracted from paired-end sequences
5' and 3' sequences were aligned to the S288c reference R64 genome assembly using novoalign V2.07.10 with default parameters
Transcript isoforms (TIFs) were identified by exact identical 5' and 3' positions
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/)
Supplementary_files_format_and_content: tab-delimited text files include number of TIFs of each sample (abundance measurements)

growth_protocol: Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).

extract_protocol: Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment. The sample was subject to TIF-Seq protocol (Transcript IsoForm Sequencing) for the unambiguous identification of overlapping transcripts by sequencing both 5’ and 3’ ends of the each mRNA molecule. Briefly, full-length cDNA molecules for capped and polyadenylated mRNAs is produced. After that, they are subject to intramolecular ligation, fragmentation and capture of the 5’-3’ junctions. Finally paired end sequencing of those tags give information to reconstruct the transcriptome architecture.

tag: strain

value: set2 (delta set2::kanMX4, BY4741 background)

tag: media

value: YPAD media

value: mid-log phase cells, OD 1

value: delta set2 mutant


title: Full length (wt) Set1 H3K4me3 ChIP-Seq rep1

value: BY4741, set1 deletion

value: YES


title: cnt2

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

description:
PolyA RNA
processed data file: all_dmel6_exon_counts.txt

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignments were performed using Subread with subread-align command.
Counting were performed using featureCounts.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: all_dmel6_exon_counts.txt: Tab-delimited text file containing gene counts for every analyzed sample.

organism: Drosophila melanogaster

source_name: Drosophila adult ventral nerve cords containing or not tumors

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Total RNA-Seq libraries were generated from 130 ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: tissue

value: ventral nerve cords

value: prospero (pros) knockdown

tag: age

value: 6 days


title: wt1


title: D6_P1__S89

tag: passages

tag: disease state

value: DIPG (diffuse intrinsic pontine glioma)


title: D6_P1__S8


title: Syp2

value: prospero (pros) knockdown + Syncrip (syp) knockdown


title: cnt1


title: H4K16Ac ChIP-seq in WT_rep1

value: exponential

value: YPD


title: wt2


title: SNU16 4C-seq, rep1

description: 4C-seq in SNU16

data_processing:
Library strategy: 4C-seq
The package 4Cseqpipe was used to map, normalize and visualize 4C-seq data, as described in van de Werken et al., 2012. Custom restriction site tracks were built using the -build_re_db option of 4Cseqpipe for the hg19 human genome version (UCSC) and CATG and GTAC as first and second cutters, respectively. 4C primers (CACCTATTTTTCTTGTCATG) were removed from the reads and were then mapped to the custom hg19 tracks with the in-built 4Cseqpipe mapper. The 80th quantile of the distribution of normalized contact intensities for 2kb windows were put into wig files for visualization using the UCSC genome browser hg19 version
Genome_build: hg19
Supplementary_files_format_and_content: Refer the following URL for the wiggle format: https://genome.ucsc.edu/goldenpath/help/wiggle.html

source_name: gastric cancer cell line

extract_protocol: 10 million cells were cross-linked for 10 min with 1 % paraformaldehyde at RT, quenched with glycine, and lysed in 50 mL lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5 % NP-40, 1 % TX-100 and 1X protease inhibitors) for 30 min. Nuclei were then digested by NLAIII enzyme followed by inactivation of the restriction enzyme by incubating at 65 °C for 20 min. The digested chromatin was subsequently ligated (circularized) overnight at 16 °C with 3000 U T4 ligase (NEB). Ligated chromatin was then reverse cross-linked by incubating with proteinase K at 65 °C and the RNA was removed by additional incubation at 37 °C with RNase A. The purified DNA was further digested with CSP6I restriction enzyme followed by circularization of the DNA. 4C products were subsequently amplified with bait-specific inverse primers, pooled and purified. Amplified bait-containing DNA fragments were ligated to NEB adaptors. Adaptor-ligated DNA was purified by Agencourt AMPure XP purification system (Beckman Coulter, A63881), PCR amplified (eight cycles) using NEB index primers, and sequenced on the Illumina HiSeq3000 to obtain 150 bp long reads.


title: D6_P1__S87


title: D6_P2_27_S27


title: SNU16 Capture-C

description: Capture-C in SNU16

data_processing:
Library strategy: Capture-C
Pre-processing of raw reads was performed to remove adaptor sequences (trim_galore, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and overlapping reads were merged using FLASH. In order to achieve short read mapping to the hg19 reference genome, the resulting pre-processed reads were then in-silico digested with DpnII and aligned using Bowtie (using p1, m2, best and strata settings). Aligned reads were processed using Capture-C analyser to (i) remove PCR duplicates, and (ii) classify sub fragments as ‘capture’ if they were contained within the capture fragment; ‘proximity exclusion’ if they were within 1 Kb on either side of the capture fragment; or ‘reporter’ if they were outside of the ‘capture’ and ‘proximity exclusion’ regions. We additionally used the r3Cseq package on the capture and reporter fragments to identify significant interactions of the viewpoint against a scaled background (q-value <0.05, FDR).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SNU16_P25.txt: Tab-delimited text file includes RPMs.

extract_protocol: Capture-C probes at CCNE1 promoter regions were designed using CapSequm. Approximately 1 × 10e7 cells were crosslinked by 2% formaldehyde, followed by lysis, homogenization, DpnII digestion, ligation and de-crosslinking. DNA was sonicated using a Covaris to 150–200 bp to produce DNA suitable for oligo capture. Three micrograms of sheared DNA was used for sequencing library preparation (New England Biolabs). The promoter sequence of CCNE1 was double captured by sequential hybridization to customized biotinylated oligos (IDT, Supplementary Table 14) and enrichment with Dynabeads (LifeTech). Captured DNA was sequenced on the Illumina HiSeq 3000 instrument with the 2x150 bp configuration.

tag: tissue/cell type

value: gastric cancer cell line


title: T980319 Input

description: Input (background) for T980319 H3K27ac

source_name: primary gastric tumor

tag: sample id

value: primary gastric tumor


title: set2_bio2_lib1

description: Sample 16


title: N980319 H3K27ac

description: H3K27ac paired-end ChIP-seq in N980319

source_name: primary gastric normal

value: primary gastric normal

value: H3K27ac (ab4729, Abcam)


title: T980319 H3K27ac

description: H3K27ac paired-end ChIP-seq in T980319


title: Syp1


title: D6_P1__S85

value: DIPG6 (VI) cell line


title: N980319 Input

description: Input (background) for N980319 H3K27ac


title: D6_P1__S84


title: MKN7 4C-seq, rep1

description: 4C-seq in MKN7

data_processing:
The package 4Cseqpipe was used to map, normalize and visualize 4C-seq data, as described in van de Werken et al., 2012. Custom restriction site tracks were built using the -build_re_db option of 4Cseqpipe for the hg19 human genome version (UCSC) and CATG and GTAC as first and second cutters, respectively. 4C primers (CACCTATTTTTCTTGTCATG) were removed from the reads and were then mapped to the custom hg19 tracks with the in-built 4Cseqpipe mapper. The 80th quantile of the distribution of normalized contact intensities for 2kb windows were put into wig files for visualization using the UCSC genome browser hg19 version
Genome_build: hg19
Supplementary_files_format_and_content: Refer the following URL for the wiggle format: https://genome.ucsc.edu/goldenpath/help/wiggle.html

tag: cell line


title: Hi-C, T2000877

description: Hi-C (multiple enzyme) T2000877

data_processing:
Hi-C profiles were processed, analysed using Juicer version 1.5.6. Briefly, sequencing reads were mapped to the reference genome hg19 and a single restriction site file (for SNU16) or a multiple restriction site file (for T2000877, T990275)  was used.
Genome_build: hg19
Supplementary_files_format_and_content: see https://github.com/theaidenlab/juicer

source_name: gastric cancer primary sample

extract_protocol:
Hi-C experiments were performed by Arima Genomics (https://arimagenomics.com/) utilizing a single restriction enzyme and multiple restriction enzymes for chromatin digestion.
After the HiC protocol, Illumina-compatible sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting DNA fragments from ~200-600bp using SPRI beads. The size-selected fragments were then enriched for biotin, and converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. After adapter ligation, DNA was PCR amplified with Illumina primers and library fragments of ~525 bp (insert plus adaptor) were purified using SPRI beads. The purified DNA underwent standard QC (qPCR and Bioanalyzer) and sequenced on the Illumina HiSeq 3000 instrument following the manufacturer's protocols.

value: gastric cancer primary sample


title: Hi-C, T990275

description: Hi-C (multiple enzyme) T990275

data_processing:
Hi-C profiles were processed, analysed using Juicer version 1.5.6. Briefly, sequencing reads were mapped to the reference genome hg19 and a single restriction site file was used.
Genome_build: hg19
Supplementary_files_format_and_content: see https://github.com/theaidenlab/juicer


title: SNU16 4C-seq, rep2

description: 4C-seq in SNU16


title: D6_P1__S83

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg19 reference genome using bowtie version 0.12.7: bowtie -q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 --best -S -p 6
Cells expressing fewer than 200 genes and genes expressed by fewer than 3 cells were excluded from downstream analyses.
Reads for each cell were quantified and expressed as transcripts per million (TPM) using rsem version 1.2.19: rsem-calculate-expression --estimate-rspd --paired-end -sam -p 6
Genome_build: hg19
Supplementary_files_format_and_content: Processed TPM (non-log transformed) values for each cell  are compiled in a single matrix containing genes as rows and cells as columns. The column names of the TPM matrix reflect the cell line of sorted xenograft, the 96-well plate number and the well position within that plate. For instance D6_P1_S10 reflects a cell from the DIPG 6 xenograft, the first sorted plate and the 10th well in that plate


title: Hi-C, SNU16

description: Hi-C (single-enzyme) SNU16

data_processing:
Hi-C profiles were processed analysed using Juicer version 1.5.6. Briefly, sequencing reads were mapped to the reference genome hg19 and a single restriction site file was used.
Genome_build: hg19
Supplementary_files_format_and_content: see https://github.com/theaidenlab/juicer

extract_protocol: Hi-C experiments were performed by Arima Genomics (https://arimagenomics.com/) utilizing a single restriction enzyme and multiple restriction enzymes for chromatin digestion. After the HiC protocol, Illumina-compatible sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting DNA fragments from ~200-600bp using SPRI beads. The size-selected fragments were then enriched for biotin, and converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. After adapter ligation, DNA was PCR amplified with Illumina primers and library fragments of ~525 bp (insert plus adaptor) were purified using SPRI beads. The purified DNA underwent standard QC (qPCR and Bioanalyzer) and sequenced on the Illumina HiSeq 3000 instrument following the manufacturer's protocols.


title: D6_P1__S88


title: MKN7 4C-seq, rep2

description: 4C-seq in MKN7


title: D6_P1__S80


title: D6_P1__S82


title: D6_P1__S81


title: D6_P1__S7


title: D6_P1__S86


title: D6_P1__S78


title: D6_P1__S79


title: D6_P1__S77


title: D6_P1__S76


title: D6_P1__S75


title: D6_P1__S74


title: WT3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

organism: Mus musculus

source_name: Wild type fibroblasts derived from embryonic stem cells

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: cells were cultured in complete DMEM high glucose medium supplemented with 10% v/v FBS, 20 mM Hepes, pH 7.3, 100 μM non-essential amino acids,2 mM l-glutamine and 100 μM β-mercaptoethanol at 37 °C and 5% v/v CO2 in an humidified incubator

extract_protocol: RNAs were extracted from cultured ES-derived fbroblasts using Trizol reagent (GIBCO) and RNeasy kit (QUIAGEN)

tag: genotype

value: WT


title: KO3

source_name: CD98hc null fibroblasts derived from embryonic stem cells

value: CD98hc KO


title: KO1

value: fibroblasts derived from embryonic stem cells


title: KO5


title: D6_P1__S72

extract_protocol:
Cells were extracted from the mouse brain using mechanical and enzymatic dissociation (Brain Tumor Dissociation Kit, Miltenyi)
Libraries were constructed following Illumina Nextera XT protocol and a dual-unique indexing strategy.
Nextera XT single cell RNA-seq


title: WT1


title: WT5


title: KO+ TGFb  4

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

label: biotin

source_name: KO+ TGFb  4

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Murine MSCs were obtained as indicated in (Soleimani & Nadri, 2009) from p38-lox/lox Ub-Cre-ERT2 mice and cultured in Dulbecco-modified Eagle's medium (DMEM) plus 10% fetal bovine serum (FBS).

extract_protocol: RNA were obtained from MSCs, using PureLink RNA kit (Ambion #12183018A)

treatment_protocol: Cells were starved (0,5%FBS) and treated TGF-B 5ng/mL during 20h

value: MSC

tag: background strain

value: FVB/NJ

value: ko

tag: treatment

value: tgfb


title: D6_P1__S71

value: DIPG (diffuse intrinsic pontine glioma)


title: D6_P1__S70


title: CTRO 4

source_name: CTRO 4

value: wildtype

value: ctrl


title: KO 3

source_name: KO 3


title: KO+ TGFb  2

source_name: KO+ TGFb2


title: CTRO+TGFb 1


title: KO+ TGFb  1

source_name: KO+ TGFb  1


title: D6_P1__S73

source_name: patient-derived DIPG cell line developed in the Monje Lab


title: D6_P1__S6


title: CTRO 4b

source_name: CTRO 4b


title: D6_P1__S69


title: KO 1

source_name: KO 1


title: D6_P1__S68


title: CTRO 3

source_name: CTRO 3


title: D6_P1__S67


title: CTRO+TGFb  3


title: CTRO+TGFb  4


title: D6_P1__S64


title: CTRO 1

source_name: CTRO 1


title: D6_P1__S66


title: D6_P1__S63


title: Ab_rep1

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description: Single-end RNA-Seq libraries constructed using standard Illumina protocols (Illumina)

data_processing:
GSANP was used to map reads
Trimmed reads were aligned to the B73 RefGen_V2 using GSNAP, and uniquely mapped reads allowing ≤2 mismatches every 36 bp and less than 5 bases for every 75 bp as tails were used for subsequent analyses
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

growth_protocol: maize B73 seedlings were grown in growth-chambers at 16 hour 25 oC/light and 8 hour 21 oC/dark cycles

extract_protocol:
RNA was extracted with the PicoPure RNA isolation kit (Arcturus), treated with DNaseI (Qiagen) and linearly amplified with the TargetAmp 2-Round aRNA Amplification kit 2.0 (Epicentre Biotechnologies).
RNA-Seq Libraries were constructed from linearly amplified RNA using the TruSeq RNA Library Kit from Illumina following the recommended protocols.

treatment_protocol: B73 apices were dissected and embedded as described (Ohutsu et al., 2007). Sections of 8um were spread on MembraneSlides 1.0 PEN (Zeiss). Cells of interest were captured into AdhesiveCap 500 tubes (Zeiss) using PALM Micro-Beam system with following parameters: cut at 36 to 50 UV-Energy/65 UV-Focus and laser pressured catapulting at 61 to 75 UV-Energy/63 UV-Focus.

value: Abaxial sides of leaf primordia 2 and 3

value: 14-day-old seedlings

value: wild type


title: Ad_rep2

value: Adaxial sides of leaf primordia 2 and 3


title: Ab_rep2


title: D6_P1__S65


title: Ad_rep1


title: D6_P1__S61


title: D6_P1__S62


title: CZ_rep2

value: Center Zone of shoot apex


title: D6_P1__S59

value: DIPG6 (VI) cell line


title: D6_P1__S5


title: polydom  siRNAs_rep3_raised-Case8-mock

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: polydom knocked-down primary cultured cells

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM

source_name: knocked-down polydom in primary cultured cells from the matrix of neurofibromas using small interfering RNA

extract_protocol:
Total RNA was extracted from primary cultured cells treated for 6 h with mock, 5 ng/ml β-estradiol (SIGMA-ALDRICH, St. Louis, Missouri, USA), 10 ng/ml TGF-β1 (R&D SYSTEMS, Minneapolis, Minnesota, USA), 5 μM ITD1 (TOCRIS, Avonmouth, Bristol, BS11 9QD United Kingdom), or siRNA (QIAGEN) using the Maxwell 16 LEV simply RNA Tissue kit (Promega, Madison, WI).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Primary cultured cells from the matrix of neurofibromas (8×104/1.5 ml) were seeded on 6-well dishes 1 day prior to transfection. Cells were transfected with 30 nM polydom or control siRNAs (QIAGEN, Hilden, Germany) using RNAi MAX (Invitrogen, Carlsbad, California, USA). The culture medium was replaced 6 h later. One day after transfection, total RNA was purified.

value: fibroblasts surrounding neurofibromas

tag: gender

value: male

tag: type

value: trunk


title: CZ_rep1


title: 7959804122_R04C01: DNA methylation from saliva

type: genomic

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

institute: Max-Planck-Institute Psychiatry

hyb_protocol: as recommended by Illumina

scan_protocol: as recommended by Illumina

data_processing: as recommended by Illumina

label: Cy3, Cy5

source_name: saliva

label_protocol: as recommended by Illumina

extract_protocol: DNAdvance kit, Beckman Coulter Genomics

value: saliva


title: 7959804122_R02C01: DNA methylation from saliva


title: control siRNAs_rep3_raised-Case8-mock

description: control knocked-down primary cultured cells

source_name: knocked-down control siRNA in primary cultured cells from the matrix of neurofibromas using small interfering RNA


title: PTX, Replicate 2

city: La Jolla

first: Nathaniel

last: Delos Santos

address: 9500 Gilman Drive MC 0640

institute: University of California San Diego

description:
rat_neuron_rna_ptx-rep2_gb
After 24 hours, media replaced with 50 µM PTX (stimulated, + Stim).
processed data file: counts.raw.tsv

data_processing:
Binary base calls retrieved from NextSeq 500.
Conversion to fastq performed with bcl2fastq 2.17.
Reads preprocessed for quality and adapter removal with fastp 0.19.3.
Preprocessed reads aligned using STAR 2.5.3a.
Alignment files converted to tag directories using HOMER 4.9 makeTagDirectory.
Tag directories converted to raw counts using HOMER 4.9 analyzeRepeats.pl, counting on exons.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: counts.raw.tsv: HOMER analyzeRepeats.pl raw counts matrix, tab-separated values.

organism: Rattus norvegicus

source_name: Hippocampal neurons

growth_protocol: Neurons were grown 28 days in-vitro in maintenance media consisting of Neurobasal media (ThermoFisher Scientific Cat#21103049) supplemented with Glutamax (ThermoFisher Scientific Cat#35050061), Pen/Strep (ThermoFisher Scientific Cat#10378016), and B27 supplement (ThermoFisher Scientific Cat#17504044).

extract_protocol:
Cells were lysed in TRI-reagent and RNA was extracted using a Direct-zol kit (Zymo Research Cat#R2051) with on-column DNase treatment, following the manufacturer’s instructions.
Library construction was performed by the IGM Genomics Center, University of California, San Diego, La Jolla, CA. Libraries were sequenced 76 bp single-end on an Illumina NextSeq 500 instrument.

treatment_protocol: To augment neuronal activity, cells were incubated in the indicated drugs reconstituted in dimethyl sulfoxide (DMSO) or water, and diluted in maintenance media for 2 h (ChIP-seq and RNA-seq experiments). To silence neuronal activity for ChIP-seq and RNA-seq experiments, twenty seven DIV rat hippocampal neurons were incubated in (µM): 1 tetrodotoxin citrate (TTX), 10 3-((R)-2-Carboxypiperazin-4-yl)-propyl-1-phosphonic acid (CPP) , and 10 2,3-Dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide disodium salt (NBQX) reconstituted in water and diluted in maintenance media for 24 h prior to harvesting on day of experiment. The next day, media was then replaced according to treatment group (see characteristics: treatment), and incubated for 2 h at 37°C. Neurons were continuously maintained at 37°C and 5% CO2 until harvesting or fixation.

tag: strain/background

value: Sprague Dawley

value: Brain

value: Hippocampal neurons

value: PTX


title: TTX, Replicate 1

description:
rat_neuron_rna_ttx-rep1_gb
After 24 hours, media replaced with same media (silenced, - Stim).
processed data file: counts.raw.tsv

value: TTX


title: D6_P1__S57

value: DIPG (diffuse intrinsic pontine glioma)


title: 7959804152_R05C02: DNA methylation from saliva


title: D6_P1__S58


title: polydom  siRNAs_rep2_raised-Case24-mock

value: female

value: upper limb


title: 7959804111_R06C02: DNA methylation from saliva


title: control siRNAs_rep2_raised-Case24-mock


title: TTX, Replicate 2

description:
rat_neuron_rna_ttx-rep2_gb
After 24 hours, media replaced with same media (silenced, - Stim).
processed data file: counts.raw.tsv


title: 7959804152_R01C01: DNA methylation from saliva


title: 7959804099_R02C01: DNA methylation from saliva


title: 7959804111_R02C02: DNA methylation from saliva


title: 7959804152_R03C02: DNA methylation from saliva


title: 7927554047_R03C02: DNA methylation from saliva


title: D6_P1__S60


title: 7927554038_R03C01: DNA methylation from saliva


title: PTX with NIM, Replicate 2

description:
rat_neuron_rna_ptx-nim-rep2_gb
After 24 hours, media replaced with PTX plus Nimodipine (Nim; 20 µM reconstituted in DMSO).
processed data file: counts.raw.tsv

value: PTX with NIM


title: 7927554034_R06C02: DNA methylation from saliva


title: 7927554005_R03C02: DNA methylation from saliva


title: 7927554034_R03C02: DNA methylation from saliva


title: 7927554005_R06C02: DNA methylation from saliva


title: 7959804111_R02C01: DNA methylation from saliva


title: D6_P1__S55


title: 7927554047_R01C02: DNA methylation from saliva


title: D6_P1__S56


title: control siRNAs_rep1_raised-Case16-mock


title: 7959804152_R05C01: DNA methylation from saliva


title: polydom  siRNAs_rep1_raised-Case16-mock


title: 7927554006_R03C01: DNA methylation from saliva


title: 7927554006_R06C01: DNA methylation from saliva


title: D6_P1__S54


title: 7959804099_R04C01: DNA methylation from saliva


title: PTX with NIM, Replicate 1

description:
rat_neuron_rna_ptx-nim-rep1_gb
After 24 hours, media replaced with PTX plus Nimodipine (Nim; 20 µM reconstituted in DMSO).
processed data file: counts.raw.tsv


title: 7927554047_R06C02: DNA methylation from saliva


title: PTX with CPP, Replicate 2

description:
rat_neuron_rna_ptx-cpp-rep2_gb
After 24 hours, media replaced with PTX plus CPP (10 µM, reconstituted in water).
processed data file: counts.raw.tsv

value: PTX with CPP


title: D6_P1__S53


title: D6_P1__S52


title: PTX with CPP, Replicate 1

description:
rat_neuron_rna_ptx-cpp-rep1_gb
After 24 hours, media replaced with PTX plus CPP (10 µM, reconstituted in water).
processed data file: counts.raw.tsv


title: D6_P1__S51


title: silenced_RNAPII_ChIP-seq_rep2

first: Michael

last: Hayes

address: UCSD Campus Direct, Room 105H/GPL, 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

description:
RNAPII_gene_expression_rpkm.txt
rat_neuron_chip_TTX_RNAPII_comb.bw

data_processing:
Reads were first filtered for quality (QC>20) and length (>15bp) and adapter sequences were removed with FASTP (Chen et al., 2018) using default settings.
Reads were then mapped with Bowtie2 (Langmead and Salzberg, 2012) to the rat genome (RGSC 6.0/rn6) using –very-sensitive-local -N 1 and otherwise default settings.
Alignment files were converted to BAM files, sorted, indexed, and marked for read duplicates with samTools (Li et al., 2009).
Individual replicate alignment files for each ChIP and condition were concatenated. BAM files were further processed into tag directories for analysis with HOMER (Heinz et al., 2010) using the makeTagDirectory command with the -fragLength 150 option
ChIP-seq peaks were called with HOMER’s findPeaks program in “factor” (NPAS4, ARNT1, ARNT2) mode or "histone" mode (H3K27ac) with a peak size of 350 base-pairs (factors) or 500 base-pairs (histone), condition-matched inputs, local filtering set to 0 (-L 0) for histone peak-calling, and otherwise default settings.
Expression tables for RNAPII data was made by using HOMER's analyzeRepeats.pl tool in "rna" mode with the rn6 genome using -count genes -condenseGenes -rpkm options and using combined RNAPII tag directories as input
Bigwigs were made from all ChIP BAM files using the bamCoverage command from deepTools with -bs 1, --normalizeUsing BPM, and --extendReads 150 options
Genome_build: rn6
Supplementary_files_format_and_content: bed: provides chr, start, end, peakID, normalized tag counts (to 10 millions total reads), strand. Tsv: provides Transcript ID, chr, start, end, strand, length, copy number, annotation, stimuated RNAPII FPKM, silenced RNAPII FPKM. Bigwigs contain ChIP genome coverage data

source_name: hippocampal neurons

growth_protocol: Hippocampi from P0 Sprague–Dawley rats, obtained from timed-pregnant Sprague-Dawley adult females, of either sex were prepared as previously described (Djakovic et al., 2012), and plated at a density of 130 cells per mm2. Sex was not determined and neurons from male and female pups were pooled for sufficient material. Neurons were grown in maintenance media consisting of Neurobasal media (ThermoFisher Scientific Cat#21103049) supplemented with Glutamax (ThermoFisher Scientific Cat#35050061), Pen/Strep (ThermoFisher Scientific Cat#10378016), and B27 supplement (ThermoFisher Scientific Cat#17504044). Cells were grown at 37˚C, 5% CO2 for 28 days before harvesting.

extract_protocol:
ChIP-seq was essentially performed as described (Heinz et al., 2018), with modifications. Briefly, neuronal maintenance media was aspirated, 2 mM Disuccinimidyl glutarate (DSG; ThermoFisher Scientific Cat#20593) / PBS for 30 minutes at room temp with gentle agitation, followed by an additional 15 minutes with 16% PFA added to 1% final. The reactions were quenched by adding 2.625 M glycine to 125 mM final, incubated for 5 min, then 20% bovine serum albumin (BSA; Fisher Bioreagents Cat#BP9706-100) added to 1% final, the mixture of fixatives aspirated and replaced with ice-cold 0.5% BSA / PBS,  cells collected using a cell scraper into a chilled 15 mL conical tube, and centrifuged at 5000g for 5 min at 4°C. Cells were resuspended in ice-cold LB3 lysis buffer containg the following (in mM) (10 Tris / HCl pH 7.5, 100 NaCl, 0.5 EGTA, 0.1% deoxcycholate, 0.5% sarkosyl, 1× protease inhibitor cocktail (Sigma Aldrich Cat# P8340) and chromatin was sheared to an average DNA size of 300–500 bp by administering 7 pulses of 10 sec duration at 13 W power output with 30 sec pause on wet ice using a Misonix 3000 sonicator. The lysate was diluted in 1.1-fold (LB3) with ice-cold 10% Triton X-100. One percent of the lysate was removed for whole cells inputs. For each immunoprecipitation, aliquots of lysate equivalent to 3ₓ106 cells for transcription factor  and RNAPII antibodies, or 7.5ₓ105 cells for histone modification antibodies, 20 μl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein G (for murine monoclonal antibodies) and 2 μg of the indicated antibody were combined, and rotated overnight at 8 RPM and 4°C. The next day, beads were collected on a magnet and washed 3x each with wash buffer I (WB1; in mM: 10 Tris / HCl pH 7.5, 150 NaCl, 1% Triton X-100, 0.1% SDS, 2 EDTA), wash buffer III (WB3; in mM: 10 Tris / HCl pH 7.5, 250 LiCl, 1 EDTA, 1% Triton X-100, 0.7% Deoxycholate) and 2x with ice-cold TET (in mM: 10 Tris / HCl pH 7.5, 1 EDTA, 0.025% Tween-20). Beads were then resuspended in 20µL cold TT (in mM: 10 Tris / HCl pH 7.5, 0.025% Tween-20).
Libraries were prepared with NEBNext Ultra II DNA library prep kit reagents according to the manufacturer’s protocol on the beads suspended in TT, with reagent volumes reduced by half. ChIP samples were indexed by ligation to NEXTflex DNA Barcodes. DNA was eluted and crosslinks reversed by adding 4 μl 10% SDS, 4.5 μl 5 M NaCl, 3 μl EDTA, 1 μl proteinase K (20 mg / ml), 20 μl water, incubating for 1 h at 55°C, then 30 min to overnight at 65°C. DNA was cleaned up by adding 2 μl SpeedBeads 3 EDAC (Sigma Aldrich Cat#GE65152105050250) in 61 μl of 20% PEG 8000 / 1.5 M NaCl, mixing and incubating for 10 minutes at RT. SpeedBeads were collected on a magnet, washed twice by adding 150 μl 80 % EtOH for 30 seconds each, collecting beads and aspirating the supernatant. After air-drying the SpeedBeads, DNA was eluted in 25 μl TT and the DNA contained in the eluate was amplified for 12 cycles in 50 μl PCR reactions using NEBNext Ultra II Q5 PCR master mix (New England BioLabs Cat#M0544S) and 0.5 μM each of primers Solexa 1GA and Solexa 1GB (See Key Resources table). Libraries were cleaned up as above by adding 36.5 μl 20% PEG 8000 / 2.5 M NaCl and 2 μl Speedbeads, two washes with 150 μl 80% EtOH for 30 sec each, air-drying beads and eluting the DNA into 20 μl TT.

treatment_protocol: To silence neuronal activity for ChIP-seq experiments, cells were incubated in (µM): 1 tetrodotoxin citrate (TTX), 10 (R)-CPP (CPP), and 10 NBQX disodium salt (NBQX) reconstituted in water and diluted in maintenance media for 24 h prior to harvesting on day of experiment.

tag: day havested

value: postnatal day 1

tag: stimulation

tag: chip-seq antibody

value: anti-RPB2, Genetex, Cat#GTX102535


title: 7927554023_R03C02: DNA methylation from saliva


title: D6_P1__S50

tag: cell type

value: DIPG6 (VI) cell line


title: silenced_RNAPII_ChIP-seq_rep1

tag: strain


title: D6_P1__S4


title: MCF7_shBAP1

description: Gene expression in MCF7_shBAP1

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations. The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Breast cancer cell line

tag: shRNA


title: MCF7_shKDM6A

description: Gene expression in MCF7_shKDM6A


title: 7959804152_R03C01: DNA methylation from saliva

tag: tissue

tag: age


title: PTX, Replicate 1

description:
rat_neuron_rna_ptx-rep1_gb
After 24 hours, media replaced with 50 µM PTX (stimulated, + Stim).
processed data file: counts.raw.tsv


title: LCL2_OR-S2

description: Gene expression after 7 days culture with OR-S2 in LCL

value: EBV infected LCL

value: 7 days culture with OR-S2


title: silenced_Npas4_ChIP-seq_rep1

description:
ttx_npas4_peaks.bed
rat_neuron_chip_TTX_Npas4_comb.bw

value: anti-NPAS4, clone 92-3, DART Neuroscience


title: MCF7_shARID1A

description: Gene expression in MCF7_shARID1A


title: LCL2_OR-S1

description: Gene expression after 7 days culture with OR-S1 in LCL

value: 7 days culture with OR-S1


title: silenced_input_rep2

description:
none
rat_neuron_chip_TTX_Input_comb.bw

value: Sprague Dawley


title: D6_P1__S48

tag: passages

tag: disease state


title: silenced_Npas4_ChIP-seq_rep2


title: 7927554034_R06C01: DNA methylation from saliva

value: male

value: saliva


title: D6_P1__S49


title: D6_P1__S47


title: silenced_input_rep1

description:
none
rat_neuron_chip_TTX_Input_comb.bw


title: D6_P1__S46


title: silenced_H3K27ac_ChIP-seq_rep1

description:
ttx_h3k27ac_regions.bed
rat_neuron_chip_TTX_H3K27ac_comb.bw

value: anti-H3K27ac, Active Motif, Cat#39133


title: LCL2_GSK126

description: Gene expression after 7 days culture with GSK126 in LCL

value: 7 days culture with GSK126


title: D6_P1__S45

value: DIPG (diffuse intrinsic pontine glioma)


title: 7927554034_R03C01: DNA methylation from saliva

value: female


title: D6_P1__S44


title: 7927554005_R06C01: DNA methylation from saliva


title: 7959804152_R01C02: DNA methylation from saliva


title: silenced_Arnt2_ChIP-seq_rep2

description:
ttx_arnt2_peaks.bed
rat_neuron_chip_TTX_Arnt2_comb.bw

value: anti-ARNT2, clone B11, Santa Cruz Biotechnology, Cat#sc-3936


title: D6_P1__S43


title: LCL1_OR-S1


title: silenced_Arnt2_ChIP-seq_rep1


title: LCL2_DMSO

description: Gene expression after 7 days culture with DMSO in LCL

value: 7 days culture with DMSO


title: silenced_H3K27ac_ChIP-seq_rep2

value: postnatal day 1


title: LCL1_GSK126


title: LCL1_OR-S2


title: 7927554047_R03C01: DNA methylation from saliva


title: MCF7_shCtrl

description: Gene expression in MCF7_shCtrl

value: shCtrl


title: silenced_Arnt_ChIP-seq_rep2

description:
ttx_arnt1_peaks.bed
rat_neuron_chip_TTX_Arnt_comb.bw

value: anti-ARNT1, clone D28F3, Cell Signaling Technology, Cat#5537


title: D6_P1__S42

value: DIPG6 (VI) cell line


title: LCL1_DMSO

value: EBV infected LCL


title: D6_P1__S41


title: silenced_Arnt_ChIP-seq_rep1


title: D6_P1__S40


title: SUDHL8_GSK126

description: Gene expression after 7 days culture with GSK126 in SUDHL8

value: DLBCL cell line


title: stimulated_RNAPII_ChIP-seq_rep2

description:
RNAPII_gene_expression_rpkm.txt
rat_neuron_chip_PTX_RNAPII_comb.bw

value: 2 hours, 50 uM Picrotoxin

value: anti-RPB2, Genetex, Cat#GTX102535


title: D6_P1__S39


title: 7959804111_R06C01: DNA methylation from saliva


title: D6_P1__S3


title: 7927554023_R05C02: DNA methylation from saliva


title: SUDHL8_OR-S2

description: Gene expression after 7 days culture with OR-S2 in SUDHL8

value: 7 days culture with OR-S2


title: 7959804111_R04C02: DNA methylation from saliva


title: SUDHL8_DMSO

description: Gene expression after 7 days culture with DMSO in SUDHL8


title: DLCL2_OR-S2

description: Gene expression after 7 days culture with OR-S2 in WSU-DLCL2


title: SUDHL8_OR-S1

description: Gene expression after 7 days culture with OR-S1 in SUDHL8

value: 7 days culture with OR-S1


title: D6_P1__S38


title: 7927554023_R01C02: DNA methylation from saliva

value: male

value: saliva


title: stimulated_RNAPII_ChIP-seq_rep1

value: Sprague Dawley


title: stimulated_Npas4_ChIP-seq_rep1

description:
ptx_npas4_peaks.bed
rat_neuron_chip_PTX_Npas4_comb.bw

value: anti-NPAS4, clone 92-3, DART Neuroscience


title: stimulated_input_rep2

description:
none
rat_neuron_chip_PTX_Input_comb.bw


title: 7959804099_R01C02: DNA methylation from saliva


title: DLCL2_GSK126

description: Gene expression after 7 days culture with GSK126 in WSU-DLCL2

value: 7 days culture with GSK126


title: 7927554023_R03C01: DNA methylation from saliva

value: female


title: 7927554005_R03C01: DNA methylation from saliva


title: D6_P1__S36

value: DIPG (diffuse intrinsic pontine glioma)


title: stimulated_H3K27ac_ChIP-seq_rep2

description:
ptx_h3k27ac_regions.bed
rat_neuron_chip_PTX_H3K27ac_comb.bw

value: postnatal day 1

value: anti-H3K27ac, Active Motif, Cat#39133


title: D6_P1__S35


title: TL-Om1_DHMEQ

description: Gene expression after 24 hours culture with DHMEQ in TL-Om1

value: ATL cell line

value: 24 hours culture with DHMEQ


title: 7927554005_R01C01: DNA methylation from saliva


title: 7927554047_R05C01: DNA methylation from saliva


title: D6_P1__S34

value: DIPG6 (VI) cell line


title: DLCL2_DMSO

description: Gene expression after 7 days culture with DMSO in WSU-DLCL2

value: DLBCL cell line

value: 7 days culture with DMSO


title: stimulated_Arnt2_ChIP-seq_rep2

description:
ptx_arnt2_peaks.bed
rat_neuron_chip_PTX_Arnt2_comb.bw

value: 2 hours, 50 uM Picrotoxin

value: anti-ARNT2, clone B11, Santa Cruz Biotechnology, Cat#sc-3936


title: DLCL2_OR-S1

description: Gene expression after 7 days culture with OR-S1 in WSU-DLCL2

value: 7 days culture with OR-S1


title: TL-Om1_DMSO(DHMEQ)

description: Gene expression after 24 hours culture with DMSO in TL-Om1

value: 24 hours culture with DMSO


title: stimulated_Npas4_ChIP-seq_rep2


title: TL-Om1_shYY1

description: Gene expression_shYY1


title: 7927554047_R01C01: DNA methylation from saliva

value: male

value: saliva


title: 7927554029_R03C02: DNA methylation from saliva


title: D6_P1__S32


title: D6_P1__S33


title: 7959804122_R06C01: DNA methylation from saliva


title: stimulated_Arnt_ChIP-seq_rep2

description:
ptx_arnt1_peaks.bed
rat_neuron_chip_PTX_Arnt_comb.bw

value: Sprague Dawley

value: anti-ARNT1, clone D28F3, Cell Signaling Technology, Cat#5537


title: TL-Om1_shSUZ12_2

description: Gene expression_shSUZ12


title: stimulated_Arnt2_ChIP-seq_rep1


title: D6_P1__S31


title: D6_P1__S37


title: stimulated_Arnt_ChIP-seq_rep1


title: D6_P1__S30


title: TL-Om1_shSUZ12_1

description: Gene expression_shSUZ12


title: 7959804111_R04C01: DNA methylation from saliva


title: 7927554029_R05C02: DNA methylation from saliva

value: female


title: TL-Om1_shEZH2_2

description: Gene expression_shEZH2


title: stimulated_H3K27ac_ChIP-seq_rep1


title: D6_P1__S2

value: DIPG (diffuse intrinsic pontine glioma)


title: 7927554029_R01C02: DNA methylation from saliva


title: LPS/IL4/IL13_2

city: Calgary

first: Manoj

middle: Kumar

last: Mishra

state: AB

address: 3330 Hospital Dr NW

department: Clinical Neuroscience

country: Canada

institute: Hotchkiss Brain Institute

description:
Gene expression data from 6h of LPS/IL4/IL13 treatment
LPS IL4 IL13_2  (MoGene-1_0-st-v1).mas5-Signal

hyb_protocol: Following fragmantation, hybridized to an Affymetrix GeneChip™ Mouse Gene 1.0 ST Array  at 45 °C for 16 h.

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 7G System.

data_processing: Array data files were generated with GeneChip Command Console Software (AGCC) and statistical significant analysis was carried out on software of GeneSpring (Agilent Technologies). The fold change between treatment and control was based on the P < 0.05 from unpaired t test (Asymptotic and Benjamini Hochberg FDR).

source_name: BMDM exposed to LPS/IL4/IL13

label_protocol: 100 μg of RNA of each sample with a RIN higher than 9 was labeled with the 3′ _IVT Express Kit (Ambion)

extract_protocol: RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Total RNA was purified with the RNeasy Plus Micro Kit (Qiagen) to remove genomic DNA. The RNA quality of integrity number (RIN) was measured with an Agilent RNA 6000 NanoChip on 2100 Bioanalyzer (Agilent Technologies).

value: bone marrow derived cells (BMDM)

value: exposed to LPS/IL4/IL13


title: stimulated_input_rep1

description:
none
rat_neuron_chip_PTX_Input_comb.bw

value: postnatal day 1


title: TL-Om1_shEZH2_1

description: Gene expression_shEZH2

value: ATL cell line


title: D6_P1__S28

value: DIPG6 (VI) cell line


title: 7927554004_R03C02: DNA methylation from saliva


title: 7927554038_R05C02: DNA methylation from saliva


title: 7927554023_R01C01: DNA methylation from saliva


title: D6_P1__S27


title: TL-Om1_shCtrl

description: Gene expression_shCtrl

value: shCtrl


title: D6_P1__S25


title: D6_P1__S26


title: IL4/IL13_1

description:
Gene expression data from 6h of IL4/IL13 treatment
IL4 IL13_1  (MoGene-1_0-st-v1).mas5-Signal

source_name: BMDM exposed to IL4/IL13

value: exposed to IL4/IL13


title: 7959804122_R02C02: DNA methylation from saliva


title: 7927554004_R01C02: DNA methylation from saliva


title: TL-Om1_shEZH1_2

description: Gene expression_shEZH1


title: D6_P1__S24


title: 7927554029_R05C01: DNA methylation from saliva


title: IFN/LPS1

description:
Gene expression data from 6h of IFN gamma/LPS treatment
IFN LPS_1  (MoGene-1_0-st-v1).mas5-Signal

source_name: BMDM exposed to IFN gamma/LPS

value: exposed to IFN gamma/LPS


title: Control 2

description:
Gene expression data from 6h of untreated sample
Control_2  (MoGene-1_0-st-v1).mas5-Signal

source_name: BMDM untreated

value: untreated


title: IFN/LPS2

description:
Gene expression data from 6h of IFN gamma/LPS treatment
IFN LPS_2  (MoGene-1_0-st-v1).mas5-Signal


title: D6_P1__S23


title: 7927554004_R05C02: DNA methylation from saliva


title: 7959804099_R05C02: DNA methylation from saliva


title: D6_P1__S22


title: Control 1

description:
Gene expression data from 6h of untreated sample
Control_1  (MoGene-1_0-st-v1).mas5-Signal


title: 7927554038_R03C02: DNA methylation from saliva