title: Rbpj KO input replicate 2

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description: ChIP-Seq

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1)  (Martin M, 2011) with parameters “-a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”.
BWA (version 0.6.2) (Li et al., 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the human mm10 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Duplicate marking was performed using the picard tool MarkDuplicates (version 2.1.1).
Read filtering was carried out with BamTools (version 2.4.0) (Barnett et al., 2011) with the parameters “-isMapped true -isMateMapped true -isPaired true -isProperPair true -isPrimaryAlignment true -mapQuality '>=1' -insertSize '<=2000'”.
Additional filtering was also performed to remove duplicates alignments, and those which were not represented by both reads of a pair in the alignment file.
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bedGraph files were generated from the filtered alignments using the genomeCoverageBed command from BEDTools (version 2.26.0) (Quinlan & Hall, 2010) with parameters "-bg -pc -scale <NORM_FACTOR>". Normalisation factors were generated by scaling the number of mapped pairs to 1 million. bedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (version 20161115) (Kent et al., 2010).

source_name: Intestinal crypt epithelial cells

growth_protocol: To isolate the mouse crypts, the intestinal tissues from VillinCreER, Rbpjfl/fl mice 4days after TM injection were incubated in cold PBS containing 2mM EDTA (Sato et al., 2009).

extract_protocol:
The samples were washed twice in PBS and resuspended in commercial lysis buffer containing protease inhibitors from the MAGnify Chromatin Immunoprecipitation System kit (Thermo Scientific; 492024). The chromatin was sheared using the Covaris S2 sonicator (Covaris) at 4°C for 10 minutes with the following settings; duty cycle 5%, intensity: 2, cycles per burst: 200, cycle time: 60 seconds.
The DNA library for sequencing was prepared using 20 ng of ChIP’ed DNA for the Kapa Hyper Prep kit with 16 cycles of PCR amplification. The quality of the final DNA library was confirmed on the Agilent Tapestation before the samples were submitted to sequencing on the HiSeq 4000 (Illumina).

treatment_protocol: Isolated mouse crypts were dual cross-linked first in 2 mM Di(N-succinimidyl) glutarate (DSG; Sigma) for 45 min at room temperature followed by incubation in 1% formaldehyde for 10 minutes as previously described (Tian B. et al 2012)). The fixation was terminated by quenching with glycine for 5 minutes at room temperature.

value: Intestinal crypt epithelial cells

tag: genotype/variation

value: Rbpj KO

value: Tamoxifen induced RBPJ knock-out


title: DpnII SisterC on G1 arrested cells released in BrdU - R1

status: Public on Jun 17 2020

type: SRA

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

library_source: genomic

data_processing:
Hi-C and SisterC FASTQ sequencing files were mapped to saccer3 yeast reference genome using
publicly available distiller-nf mapping pipeline (https://github.com/mirnylab/distiller-nf) and downstream
analysis tools pairtools (https://github.com/mirnylab/pairtools) and cooltools
(https://github.com/mirnylab/cooltools).
All DpnII replicates were combined.
Genome_build: Saccer3
Supplementary_files_format_and_content: multitire cooler files '.mcool' of all interactions, inter-sister interactions and intra-sister interactions (cis signal only)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: YLV11 (Vernis et al 2003, NAR)

growth_protocol: Cells were grown in YP-Galactose at 30C. Supplemented with 100uM Thymidine

extract_protocol:
For each sisterC and Hi-C library ~300 million cells were crosslinked.
Hi-C and SisterC were performed as described in detail in supplemental methods.
Hi-C and SisterC

treatment_protocol: Cells were arrested using alpha factor, followed by a release in media containing 1mM Thymidine or BrdU. Cells were arrested in mitosis using nocodazole or the subsequent G1 using alpha factor.

tag: protocol

value: SisterC

tag: enzyme

value: DpnII

tag: cell line

value: S cervisiae with mutated cdc1 and galactose induced nucleoside importer and kinase


title: prostate_tissue-C-replicate_RIB0034493

type: RNA

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

hyb_protocol: We used 1.65 µg of labeled cRNA for hybridization with the custom microarray following manufacturer's instructions.

scan_protocol: After hybridization the arrays were washed according to the manual and scanned using the Agilent G2565CA Microarray Scanner System with Agilent Scan Control Software (Version A851) and following settings for scanning: Profile: AgilentG3_GX_1Color; Channels: Green; Scan Region: Agilent HD (61x 21,6 mm); Resolution: 3 µm double pass; Tiff: 20 bit; Green PMT Gain: 100 %. We extracted the result tables after grid placement using Agilent Feature Extraction Software (Version 11.5.1.1).

data_processing: Three microarray were excluded from further processing due to scratches on array slides (data not included in GEO series). Quality control of remaining arrays (N=255) was performed by checking distribution of ``bright corner'', ``dark corner'' probes, and relative spike-in concentration versus normalized signal. Quality control confirmed high quality of the results and consequently all remaining microarray data were included in the downstream analysis. To retrieve a set of probes mapping to unique genomic positions in hg19 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites. All probes mapping to more than one distinct genomic region were discarded. Normalization between arrays was done by using quantile normalization. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least 20 arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model to detect expression variation between BPH and tumor specimens adjusted for array processing batches was fitted using limma v3.24.15 and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment.

molecule: total RNA

organism: Homo sapiens

source_name: prostate

label_protocol: We prepared all samples assembled for expression analysis with the custom microarray using the Agilent Quick Amp Labeling Kit for single color following the manufacturer's instructions. Instead of the Oligo-dT/T7-primer delivered with the Quick Amp Labeling Kit, we used 120 pmol of a random N6/T7 primer synthesized by Metabion (Planegg, Germany) and used 200 ng RNA as input for the labeling procedure. cRNA quantity was checked using a NanoDrop ND-1000 UV-VIS Spectrophotometer, as enlisted in the manufacturer's instructions.

extract_protocol: Stacks of consecutive cryosections were generated from frozen RP tissue samples and immediately transferred to 1ml Qiazol (Qiagen, Hilden, Germany). A pathologist evaluated HE-stained cryosections flanking the stacks concerning tumor and stroma cell content (Supplementary Figure S1). Only PCa tissue stacks, which were flanked on either side by sections containing at least 50% tumor cells underwent RNA isolation. In case of insufficient RNA quantity, we combined multiple tissue stacks with suitable tumor cell content. We isolated total RNA using the miRNeasy Mini Kit on the QIAcube (Qiagen) followed by manual DNase I digestion. After determining the RNA concentration with a NanoDrop 1000 (Peqlab, Erlangen, Germany), we verified the RNA integrity on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with an RNA-Integrity-Number (RIN) of at least six passed for further processing.

tag: risk group

value: C

tag: tissue

value: prostate

tag: gender

value: male

tag: gleason score

tag: diagnosis

value: benign prostate hyperplasia


title: prostate_tissue-H-sf-replicate_RIB0034482

description: Gene expression of prostate RP tissue specimen (prostate cancer)

value: H-sf

value: prostate cancer


title: DpnII SisterC on G1 arrested cells released in Thymidine - R1

description:
2019-MOsisC-G1-DpnII-Thy-UV-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-UV-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-UV-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: 202226400129_R04C01

type: genomic

city: San Francisco

first: Harish

last: Vasudevan

state: CA

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

country: USA

institute: University of California San Francisco

description:
Primary human meningioma methylation profile
M10-5
Run1

hyb_protocol: Methylation analysis was performed according to the manufacturer’s instructions on the Illumina Methylation EPIC Beadchip

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

data_processing:
BeadStudio software v3.2, raw data uploaded as IDAT; processed beta values obtained using the 'preprocessFunnorm()' function as part of the Minfi bioconductor package
Beta Values obtained using minfi package function "getBeta" from normalized data as noted above
BetaValues_MeningiomaMethylation_Run*.txt files represent raw beta values.

label: Cy5 and Cy3

source_name: Meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from primary tumor samples using Qiagen AllPrep Kit according to standard instructions

tag: individual

tag: disease state

value: Meningioma

tag: age

value: M

tag: site

value: Intracranial


title: DpnII Hi-C on G1 arrested cells released in BrdU - R1

description:
2019-MOsisC-G1-DpnII-BrdU-NO-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-NO-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-NO-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: Hi-C


title: DpnII Hi-C on G1 arrested cells released in Thymidine - R1

description:
2019-MOsisC-G1-DpnII-Thy-NO-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-NO-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-NO-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: prostate_tissue-C-replicate_RIB0034967


title: RNAseq_Syn_WH7803_HL_Ct_T0_C1

city: Roscoff

first: Laurence

last: Garczarek

address: Place Georges Teissier

department: UMR7144-Adaptation and Diversity in Marine Ecosystems

country: France

institute: Station Biologique (Sorbonne University and CNRS)

library_source: transcriptomic

data_processing:
Reads quality checks were performed with the FastQC tool.
Illumina adapters, found in 23.5 +/- 4.5 % of all reads, were removed using Cutadapt v1.8.3.
rRNA, constituting 5.0 +/- 5.9 % of all reads, were removed with Sortmerna v2.1.
Reads under 50 bp size and with a mean quality score lower than 25 were filtered out using Prinseq v0.20.4.
Remaining reads were then aligned on the reference genome of Synechococcus sp. WH7803 using Bowtie2 v2.2.9 software with ‘--non-deterministic --end-to-end –sensitive’ parameters and by selecting only the properly paired reads (i.e. SAM flagged as 99, 147, 163 or 83)
Read counts table were obtained using HTSeq Count v0.6.0 with following parameters: ‘--stranded=reverse -a 10 -m intersection-nonempty’.
Genes expression level between stress and control conditions as well as adjusted p-value based on the Benjamini-Hochberg procedure were determined using SARTools v1.4.0 with embedded DESeq2 v1.14.1.
Genome_build: NC_009481.1
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each sample, log2FC and  their associated pvalues and adjusted pvalues

organism: Synechococcus sp. WH 7803

source_name: culture of Synechococcus sp. WH7803 cells

growth_protocol: Synechococcus sp. WH7803, an axenic strain retrieved from the Roscoff culture collection (RCC752; http://roscoff-culture-collection.org/), was grown in modified PCR-S11 culture medium with 1 mM sodium nitrate and 1 μg/L vitamin B12. Cultures were acclimated for at least two weeks at 22°C (hereafter medium temperature: MT) and 20 μmol photon.m-2.s-1 (LL and μE.m-2.s-1) or 250 μE.m-2.s-1 (HL) provided by multicolor (cool white: 6500K, blue: 470 nm, green: 530 nm) LED systems (Alpheus, France). For each growth irradiance, 9 L of exponentially growing culture were split in 500 mL aliquots in 1 L flasks (Nalgene, St. Louis, MO, USA) and left under their initial growth irradiance overnight before being submitted to light, UV or temperature stress conditions and sampled at different times for various parameters.

extract_protocol:
RNA extractions were performed from 150 mL of culture harvested by centrifugation for 7 min at 10,414 × g and 4°C in an Eppendorf 5804R, followed by 2 min centrifugation at 20,817 × g in Eppendorf tubes and 4°C in an Eppendorff 5417R centrifuge. Cell pellet was then resuspended in 1 mL Qiazol (Qiagen, Valencia, CA, USA) and quickly frozen in liquid nitrogen. After thawing the tubes at 65 °C, followed by and additional incubation of 5 min at this temperature, RNA was extracted using the Direct-Zol kit (Zymo Research Corp, Proteigene) as recommended by the manufacturer. Three successive DNase treatments were performed on the Zymo-Spin™-IIC Column using the Qiagen RNase-free DNase Set (Qiagen), followed by elution from the column in 30 L DEPC-treated water. RNA quantification and quality check were performed using a Qubit (Invitrogen) and a BioAnalyzer 2100 with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA), respectively. RNA samples were then frozen in liquid nitrogen and stored at -80°C.
Ribodepletion was performed at the Genotoul platform (Toulouse, France) from 5 µg of RNA using the Ribo-Zero Bacteria Magnetic Kits (Illumina) in presence of RiboGuard RNase Inhibitor (Epicentre) and treated RNA samples were purified and concentrated using RNA Clean & Concentrator™-5 columns (Zymo research). 0.5 µL of ribo-depleted RNA was then used for quantification (Qubit RNA HS Assay Kit) and quality check (Bioanalyzer RNA Pico kit or Labchip GX). Libraries were then prepared using 100 to 400 ng of RNA with the Illumina TruSeq Stranded mRNA kit and sequenced as 150 bp paired-end reads on Illumina HiSeq 3000 System (Illumina, San Diego, CA, USA) at Genotoul (Toulouse, France). 18.5 +/- 4.7·10^6 paired-end reads were generated per sample.

treatment_protocol: For shift experiments, High light (HL) stress was induced by a shift from LL acclimated conditions (LL, 20 μE m-2 s-1) to HL ((250 μE m-2 s-1). Cultures were then sampled after 20 min (T0.3), 1h (T1), 3h (T3) and 6h (T6). UV stress was induced by a shift from LL-acclimated conditions or HL-acclimated conditions to 3 W.m −2  of UV-A and 0.3 W.m −2  of UV-B. Cultures were then sampled after 20 min (T0.3), 1h (T1), 3h (T3) and 6h (T6). Low temperature (LT) stress was performed on LL- or HL-acclimated culture by shifting them from 22 °C to 13 °C. Cultures were then sampled after 12h (J0-5), 24h (J1), 48h (J2), 72h (J3) or after 4h (J0-17), 8h (J0-33), 16h (J0-67), 24h (J1), for LL and HL-acclimated cultures, respectively. High temperature (HT) stress was performed on LL- or HL-acclimated culture by shifting them from 22°C to 30 °C. Cultures were then sampled after 12h (J0-5), 1 day (J1), 2 days (J2), 3 days (J3) and after 4h (J0-17), 8h (J0-33), 14.5h (J0-67), 24h (J1), for LL and HL-acclimated cultures, respectively. UVA and UVB radiations, generated from UVA-351 and UVB-313 fluorescent bulbs (Q-Panel Lab products, Cleveland, OH, USA), were measured between 280–320 and 320–400 nm, respectively using a USB2000 spectroradiometer (Ocean Optics, Ew Duiven, The Netherlands). Temperature stress were performed in temperature-controlled chambers (Liebherr-Hausgeräte, Lienz, Austria).  For diel cycle experiments, run at two temperatures (21 and 27°C), a bell-shaped 12/12 h L/D cycle, triggering a good synchronization of cell division, was generated using the multicolor LED systems and the Ether software (Alpheus, France). The maximal irradiance (at virtual noon) was set at 669 μE.m-2.s-1. Two replicate cultures per temperature were acclimated to L/D cycles for at least 2 weeks prior to start monitoring the different parameters. During the experiment, two replicate cultures were grown with a continuous input of fresh medium, in order to maintain cells in exponential growth throughout the whole sampling period. To study the kinetics of the response of cells to light fluctuations, cultures were sampled at 6:00, 9:00, 12:00, 15:00, 18:00, 20:00, 22:00, and 2:00 over 3 days.

tag: strain

tag: acclimation condition

value: High light

tag: stress condition

value: Control condition

tag: timepoint

value: 0 hour

tag: replicate


title: 202226400129_R03C01

description:
Primary human meningioma methylation profile
M10-3
Run1


title: TyM

city: Ribeirão Preto

first: Rubens

middle: Daniel Miserani

last: Magalhães

state: SP

address: Av. Bandeirantes 3900

department: Department of Cellular and Molecular Biology and Pathogenic Bioagents

country: Brazil

institute: Ribeirão Preto Medical School

data_processing:
First step was the avaluation of quality of the reads sequenced using FASTQC tool.
ChIP-seq reads were aligned to the T cruzi CL-Brener Esmeraldo-like genome (TriTrypDB, release 9) using BWA v 0.7.15-1140, "bwa aln" default parameters. Bwa SAMPE was used to group the files containing the pairs of reads and Samtools was used to obtain the final file properly filled in BAM format.
A Phred mapping quality filter (MAPQ) of 30 was implemented to select the uniquely mapped reads in the T. cruzi genome.
Peaks were called using MACS v2.2 with two distinct sets of parameters for identification of narrow and broad regions. The parameter "--keep-dup auto", using cutoff value of 1e-5 was used to remove part of duplicated reads. The GEM-Mappability Calculator was used to calculate the effective genome size used in MACS2.
The DiffBind v2.2.12 was used to determine the differential profiles of enrichment in each treatment, TY and MTY considering "False Discovery Rate" (FDR) lower than 5%. The statistical analysis is done using DESeq 2 model.
Genome_build: T. cruzi CL-Brener Esmeraldo-like (TritrypDB, release 9)
Supplementary_files_format_and_content: Bedgraph files was generate from MACS2 (Treat and lambda control).

organism: Trypanosoma cruzi

source_name: Parasite cell culture

growth_protocol: Cell culture of T. cruzi trypomastigotes (Y strain) were maintained by infection of LLC-MK2 cells in Minimum Essential Medium (MEM – GIBCO®) containing 2% of Fetal Bovine Serum (FBS), under 5% CO2 and 37oC. Five days after infection of the host cell, culture supernatants containing the trypomastigotes were centrifuged and purified.

extract_protocol:
After cell lysis in 3 steps, the samples were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
The libraries of the immunoprecipitated DNA fragments from each sample and the corresponding INPUTs were constructed using the TruSeq ChIP Sample Prep Kit (Illumina, IP-202-1012), following the manufacturer's recommendations.

treatment_protocol: The commercially available extracellular matrix (Geltrex ™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix, Gibco, 150 μl ECM per sample) was used to incubate part of the T cruzi trypomastigotes (5 x 10^8 cells). After incubation, the parasites were collected and used for chromatin extraction (Sample named MTy). As a control, 5 x 10^8 trypomastigotes from the same culture were subjected to the same conditions mentioned above in the absence of ECM (sample named Ty). The samples were frozen at -80°C for further use.

value: Y strain

tag: cell type

value: T.cruzi Trypomastigotes

tag: treatment

value: incubated with ECM

tag: chip antibody

value: Anti-Nitroturosine, clone 1A6 (Millipore 05-233,Lot2325108)


title: DpnII Hi-C on mitotic cells released in Thymidine - R1

description:
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

tag: protocol

tag: enzyme

value: DpnII

tag: cell line

value: S cervisiae with mutated cdc1 and galactose induced nucleoside importer and kinase


title: 202226400129_R02C01

description:
Primary human meningioma methylation profile
M10-2
Run1

tag: gender


title: Rbpj KO Mtg16 IP replicate 2

city: London

country: United Kingdom

description: ChIP-Seq

organism: Mus musculus

tag: tissue

value: Intestinal crypt epithelial cells

tag: genotype/variation

value: Rbpj KO

value: Mtg16 (Abcam, ab33072)

value: Tamoxifen induced RBPJ knock-out


title: 202226400129_R06C01

description:
Primary human meningioma methylation profile
M10-7
Run1

tag: individual

tag: disease state

value: Meningioma


title: Rbpj KO Mtg16 IP replicate 1

description: ChIP-Seq


title: DpnII Hi-C on mitotic cells released in BrdU - R1

description:
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: Rbpj KO input replicate 1

description: ChIP-Seq


title: 202226400129_R01C01

description:
Primary human meningioma methylation profile
M10-1
Run1

tag: age

value: M

tag: site


title: 202229250119_R08C01

description:
Primary human meningioma methylation profile
M1-7
Run1

value: F

value: Intracranial


title: 202229250119_R05C01

description:
Primary human meningioma methylation profile
M1-3
Run1


title: 202229250119_R06C01

description:
Primary human meningioma methylation profile
M1-4
Run1


title: DpnII SisterC on mitotic cells released in BrdU - R1

description:
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: SisterC


title: HindIII SisterC on mitotic cells released in Thymidine - R1

description:
20190901-MOsisC-M-HindIII-Thy-UV-R1T2S2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-Thy-UV-R1T2S2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-Thy-UV-R1T2S2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: HindIII


title: HindIII Hi-C on mitotic cells released in Thymidine - R1

description:
20190901-MOsisC-M-HindIII-Thy-NO-R1T2S2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-Thy-NO-R1T2S2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-Thy-NO-R1T2S2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: Hi-C


title: HindIII Hi-C on G1 arrested cells released in Thymidine - R1

description:
20190901-MOsisC-G1-HindIII-Thy-NO-R1T2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-Thy-NO-R1T2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-Thy-NO-R1T2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: 202229250119_R03C01

description:
Primary human meningioma methylation profile
M1-1
Run1


title: 202229250119_R04C01

description:
Primary human meningioma methylation profile
M1-2
Run1


title: GPCMV infected AECDs rep 3

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

description:
AECD_GPCMV_C
GPCMV infected primary AEC, 24 hpi
AECD_Mock_V_GPCMV.xlsx
AECD_GPCMV_C_S6

data_processing:
Base calling was completed using bcl2Fastq
FastQ reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC.
Read mapping was performed via Hisat2 (v2.1.0) using the “Cavpor3.0” genome (GCF_000151735.1) as reference
Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen) using raw read counts. The generated list was filtered based on a minimum 2X Absolute Fold Change and False Discovery Rate corrected p < 0.05.
Genome_build: Cavpor3.0 (GCF_000151735.1)
Supplementary_files_format_and_content: Excel files. Each dataset contains data from infected and uninfected cells of a single type. One sheet contains filtered gene expression changes with ≥2 fold differences in expression between the two conditions. The second sheet in each file contains all gene expression data.

organism: Cavia porcellus

source_name: AECD HPV16 E6/E7-transduced guinea pig amniotic epithelial cells

growth_protocol: Guinea pig lung fibroblasts (JH4 Clone 1; ATCC CCL-158) are propagated on F-12 Nutrient Mix (Gibco 11765) supplemented with 10% FBS, 0.075% sodium bicarbonate (Gibco 25080094) and 1X Pen Strep (Sigma 15-140-122). A confluent monolayer of JH4 cells contains approximately 1X10^5 cells/cm^2. Primary guinea pig AECs are isolated by enzymatic digests of amnion from near-term pregnancies. The primary cells used for this experiment were pooled from two amnions. AEC growth media is comprised of Ham's F-12 Nutrient Mix (Gibco 11765) supplemented with 10% FBS, 10 ng/ml epidermal growth factor (EGF, Recombinant Mouse Protein, Gibco PMG8041), and 1X Pen Strep (Sigma 15-140-122). Primary guinea pig AECs isolated from a single amnion were transduced with HPV16 E6/E7 and subjected to G418 selection and clonal isolation. Growth media for these “AECDs” is AEC growth media plus 250 ug/ml G418 (Genticin, Gibco 11811031); G418 is omitted for infection studies. Confluent monolayers of primary and transduced AECs contain approximately 3X10^4 cells/cm^2.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) with the on-column DNase digestion
Dual indexed TruSeq stranded mRNA libraries (Illumina) were prepared and sequenced by Illumina RNA-Seq. JH4 samples were subjected to Ribozero rRNA removal prior to library generation.

treatment_protocol: Confluent monolayers were infected with 1.91x10^7 PFU of GPCMV per well or mock infected. Virus was diluted in 1 ml of growth media per well and allowed to adsorb to the cells for 2 hours. The infected cells were washed with dPBS and fresh complete growth media was added.

tag: strain

value: Hartley

tag: passage

tag: infection

value: GPCMV SG13 J2


title: prostate_tissue-C-replicate_RIB0034755

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

tag: risk group

value: C

value: prostate

value: male

tag: gleason score

tag: diagnosis

value: benign prostate hyperplasia


title: HindIII SisterC on G1 arrested cells released in Thymidine - R1

description:
20190901-MOsisC-G1-HindIII-Thy-UV-R1T2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-Thy-UV-R1T2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-Thy-UV-R1T2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: S cervisiae with mutated cdc1 and galactose induced nucleoside importer and kinase


title: HindIII SisterC on mitotic cells released in BrdU - R1

description:
20190901-MOsisC-M-HindIII-BrdU-UV-R1T2S2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-BrdU-UV-R1T2S2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-BrdU-UV-R1T2S2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: GPCMV infected AECDs rep 2

description:
AECD_GPCMV_B
GPCMV infected primary AEC, 24 hpi
AECD_Mock_V_GPCMV.xlsx
AECD_GPCMV_B_S5

tag: cell type

value: AECD HPV16 E6/E7-transduced guinea pig amniotic epithelial cells


title: 201959750125_R08C01

description:
Primary human meningioma methylation profile
M7-7
Run1


title: HindIII Hi-C on G1 arrested cells released in BrdU - R1

description:
20190901-MOsisC-G1-HindIII-BrdU-NO-R1T2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-BrdU-NO-R1T2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-BrdU-NO-R1T2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

tag: protocol


title: Rb-deficient islet cells 2

city: Kyoto city

first: YUKI

last: YAMAUCHI

state: Kyoto

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto university

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: Processed signal intensities normalized by the global scaling method.A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500. Features flagged in Feature Extraction as not positive and significant or not above background in more than half of samples were excluded.

source_name: isolated islet cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ug Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was prepared from the isolated islets with an RNeasy Mini Kit according to the manufacturer’s instructions (#74104, Qiagen), and the RNA concentration was measured using a Qubit RNA HS Assay Kit (#Q32855, Thermo Fisher Scientific).

value: pancreatic islet cells

tag: genotype


title: GPCMV infected AECDs rep 1

description:
AECD_GPCMV_A
GPCMV infected primary AEC, 24 hpi
AECD_Mock_V_GPCMV.xlsx
AECD_GPCMV_A_S4


title: 202229250119_R07C01

description:
Primary human meningioma methylation profile
M1-5
Run1


title: Rb-deficient islet cells 1


title: wild type islet cells 2


title: HindIII Hi-C on mitotic cells released in BrdU - R1

description:
20190901-MOsisC-M-HindIII-BrdU-NO-R1T2S2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-BrdU-NO-R1T2S2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-M-HindIII-BrdU-NO-R1T2S2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

tag: enzyme

tag: cell line


title: prostate_tissue-C-replicate_RIB0034971

tag: tissue

tag: gender


title: HindIII SisterC on G1 arrested cells released in BrdU - R1

description:
20190901-MOsisC-G1-HindIII-BrdU-UV-R1T2__sacCer3.sacCer3.all_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-BrdU-UV-R1T2__sacCer3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
20190901-MOsisC-G1-HindIII-BrdU-UV-R1T2__sacCer3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: 201959750125_R05C01

description:
Primary human meningioma methylation profile
M7-4
Run1

tag: individual


title: prostate_tissue-C-replicate_RIB0034201


title: wild type islet cells 1


title: Mock infected AECDs rep 2

description:
AECD_Mock_B
Mock infected primary AEC, 24 hpi
AECD_Mock_V_GPCMV.xlsx
AECD_Mock_B_S2

value: Mock


title: Mock infected AECDs rep 3

description:
AECD_Mock_C
Mock infected primary AEC, 24 hpi
AECD_Mock_V_GPCMV.xlsx
AECD_Mock_C_S3


title: DpnII SisterC on mitotic cells released in BrdU - R2

description:
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: DpnII


title: 201959750125_R07C01

description:
Primary human meningioma methylation profile
M7-6
Run1

tag: disease state

value: Meningioma


title: 201959750125_R04C01

description:
Primary human meningioma methylation profile
M7-3
Run1

tag: age

value: F


title: prostate_tissue-C-replicate_RIB0034742


title: DpnII SisterC on mitotic cells released in Thymidine - R1

description:
2019-MOsisC-M-DpnII-Thy-UV-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-UV-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-UV-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: DpnII Hi-C on mitotic cells released in BrdU - R2

description:
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: DpnII Hi-C on mitotic cells released in Thymidine - R2

description:
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: GPCMV infected 1° AECs  rep 3

description:
008_GPCMV_C
GPCMV infected AECD, 24 hpi
AEC__Mock_V_GPCMV.xlsx
008_GPCMV_C_S6

source_name: Primary  guinea pig amniotic epithelial cells


title: 201959750125_R03C01

description:
Primary human meningioma methylation profile
M7-2
Run1

tag: site

value: Intracranial


title: GPCMV infected JH4 cells rep 3

description:
24hpiFib3
GPCMV infected JH4, 24 hpi
JH4_Mock_V_GPCMV.xlsx
24hpiFib3_S15

source_name: JH4 guinea pig lung fibroblasts

tag: strain

value: Strain 13

value: JH4 guinea pig lung fibroblasts


title: prostate_tissue-C-replicate_RIB0034238

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)


title: DpnII SisterC on mitotic cells released in Thymidine - R2

value: SisterC


title: GPCMV infected 1° AECs  rep 2

description:
008_GPCMV_B
GPCMV infected AECD, 24 hpi
AEC__Mock_V_GPCMV.xlsx
008_GPCMV_B_S5

value: Hartley

value: Primary  guinea pig amniotic epithelial cells

tag: passage


title: Mock infected AECDs rep 1

description:
AECD_Mock_A
Mock infected primary AEC, 24 hpi
AECD_Mock_V_GPCMV.xlsx
AECD_Mock_A_S1

tag: infection


title: GPCMV infected 1° AECs  rep 1

description:
008_GPCMV_A
GPCMV infected AECD, 24 hpi
AEC__Mock_V_GPCMV.xlsx
008_GPCMV_A_S4

value: GPCMV SG13 J2


title: 201959750125_R02C01

description:
Primary human meningioma methylation profile
M7-1
Run1


title: 201959750125_R01C01

description:
Primary human meningioma methylation profile
M6-7
Run1


title: DpnII SisterC on G1 arrested cells released in BrdU - R2

description:
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: GPCMV infected JH4 cells rep 2

description:
24hpiFib2
GPCMV infected JH4, 24 hpi
JH4_Mock_V_GPCMV.xlsx
24hpiFib2_S14


title: Mock infected 1° AECs  rep 3

description:
008_Mock_C
Mock infected AECD, 24 hpi
AEC__Mock_V_GPCMV.xlsx
008_Mock_C_S3


title: Mock infected 1° AECs  rep 2

description:
008_Mock_B
Mock infected AECD, 24 hpi
AEC__Mock_V_GPCMV.xlsx
008_Mock_B_S2


title: Mock infected JH4 cells rep 3

description:
NoVirusFib3
Mock infected JH4, 2 hpi
JH4_Mock_V_GPCMV.xlsx
NoVirusFib3_S3


title: DpnII Hi-C on G1 arrested cells released in Thymidine - R2

description:
2019-MOsisC-G1-DpnII-Thy-NO-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-NO-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-NO-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: Hi-C


title: 201959750116_R07C01

description:
Primary human meningioma methylation profile
M6-5
Run1


title: Mock infected JH4 cells rep 2

description:
NoVirusFib2
Mock infected JH4, 2 hpi
JH4_Mock_V_GPCMV.xlsx
NoVirusFib2_S2


title: 201959750116_R08C01

description:
Primary human meningioma methylation profile
M6-6
Run1


title: prostate_tissue-C-replicate_RIB0034351

tag: risk group

value: C

value: prostate

value: male


title: Mock infected 1° AECs  rep 1

description:
008_Mock_A
Mock infected AECD, 24 hpi
AEC__Mock_V_GPCMV.xlsx
008_Mock_A_S1


title: prostate_tissue-H+sf-replicate_RIB0034257

description: Gene expression of prostate RP tissue specimen (prostate cancer)

value: H+sf

tag: gleason score

value: prostate cancer


title: 201959750116_R06C01

description:
Primary human meningioma methylation profile
M6-4
Run1


title: Mock infected JH4 cells rep 1

description:
NoVirusFib1
Mock infected JH4, 2 hpi
JH4_Mock_V_GPCMV.xlsx
NoVirusFib1_S1

value: Mock


title: DpnII Hi-C on G1 arrested cells released in BrdU - R2

description:
2019-MOsisC-G1-DpnII-BrdU-NO-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-NO-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-NO-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: DpnII

value: S cervisiae with mutated cdc1 and galactose induced nucleoside importer and kinase


title: prostate_tissue-C-replicate_RIB0034345

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

tag: diagnosis

value: benign prostate hyperplasia


title: DpnII SisterC on G1 arrested cells released in Thymidine - R2

description:
2019-MOsisC-G1-DpnII-Thy-UV-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-UV-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-Thy-UV-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: 201959750125_R06C01

description:
Primary human meningioma methylation profile
M7-5
Run1

value: Meningioma

value: F

value: Intracranial


title: 201959750116_R05C01

description:
Primary human meningioma methylation profile
M6-3
Run1


title: 201959750116_R04C01

description:
Primary human meningioma methylation profile
M6-2
Run1


title: DpnII SisterC on G1 arrested cells released in Thymidine - R3

value: SisterC


title: fli1a:GFP- sox10:DsRed- cells from 36 hpf wt embryos

city: Cincinnati

first: Lindsey

last: Barske

state: OH

address: 3333 Burnet Ave MLC 7016

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

description: DN

data_processing:
Illumina NextSeq control software version 4.0 is used for Basecalling
FASTQ files are aligned by Bowtie2 and with ENCODE settings
BAM files are filtered to keep only properly paired reads by using samtools -f 2 -F 256 -b
Bigwig files are normalized against the library depth (X million reads in the BAM file)
Genome_build: GRCz10
Supplementary_files_format_and_content: bigwig files corresponding to regions of accessible chromatin

organism: Danio rerio

source_name: non-neural crest, non-vascular, non-otic cells

extract_protocol:
FACS-sorted cells were centrifuged at 700 x g, and the supernatant was carefully removed. Next, 20 μl lysis buffer (10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 10% DMF, 0.2% NP40) was added to the cell pellet and mixed by pipetting up and down 5-10 times. A 30-μl aliquot of reaction buffer (10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 10% DMF) containing homemade Tn5 transposase was then immediately added to the lysis, and the samples were incubated for 20 min at 37℃. DNA fragments were extracted with the Qiagen MinElute kit
DNA fragments are amplified by PCR for 5 cycles using NEBnext master mix, with primers containing various indexes. Additional cycles are determined by qPCR on 1/10 of the amplified libraries. After amplification, the libraries are cleaned using AMPURE beads, to only keep the fragments larger than 100bp. The libraries are pooled before sequencing.

tag: cell population

value: double negative


title: fli1a:GFP+ sox10:DsRed+ cells from 36 hpf wt embryos

description: DP

source_name: pharyngeal arch neural crest cells

value: double positive


title: DpnII Hi-C on G1 arrested cells released in Thymidine - R3

tag: protocol


title: 201959750116_R03C01

description:
Primary human meningioma methylation profile
M6-1
Run1


title: CRK5KO_15MIN_rep 2

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Quality trimmed read sequences were mapped to Plasmodium berghei ANKA genome reference genomes using TopHat2. Gene expression estimates were made as raw read counts using the Pyhton script ‘HTSeq- count’ (model type – union). Counts data were converted to counts per million (cpm) and genes were filtered if they failed to achieve a cpm value of 1 in at least 30% of libraries per conditions.
Normalization of raw read counts was done using voom tmm method and differential gene expression analysis was carried out using DeSeq2
Genome_build: P. berghei strain ANKA
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Plasmodium berghei

source_name: P. berghei strain ANKA

growth_protocol: Gametocytes (non-activated -0 min- and activated -15 min-) were collected from CRK5-KO and WT lines. Total RNA was isolated from purified parasites using an RNeasy purification kit (Qiagen). RNA was vacuum concentrated (SpeedVac) and transported using RNA stable tubes (Biomatrica).

extract_protocol:
Total RNA was isolated from TRIzol treated samples according to the manufacturer’s instructions (Life Technologies).
Strand-specific mRNA sequencing was performed from total RNA using TruSeq Stranded mRNA Sample Prep Kit LT (Illumina) according to the manufacturer's instructions. Briefly, polyA+ mRNA was purified from total RNA using oligo-dT dynabead selection. First strand cDNA was synthesised primed with random oligos followed by second strand synthesis where dUTPs were incorporated to achieve strand-specificity. The cDNA was adapter-ligated and the libraries amplified by PCR. Libraries were sequenced in an Illumina Hiseq machine with paired-end 100bp read chemistry.  RNA-seq read alignments were mapped onto the P. berghei ANKA genome (May 2015 release in GeneDB—http://www.genedb.org/) using Tophat2 (version 2.0.13) with parameters “-library-type fr-firststrand–no-novel-juncs–r 60”. Transcript abundances were extracted as raw read counts using the Python script ‘HTseq-count’ (model type – union, http://www-huber.embl.de/users/anders/HTSeq/). Counts per million (cpm) values were obtained from count data and gene were filtered if they failed to achieve a cpm value of 1 in at least 30% of samples per condition. Library sizes were normalized by the TMM method using EdgeR software and further subjected to linear model analysis using the voom function in the limma package43. Differential expression analysis was performed using DESeq2 in R version 3.2.1. Genes with fold change greater than 2 and p-value less than 0.05 were considered as significantly differentially expressed. P. berghei GO terms (Gene Ontology) were downloaded from GeneDB (http://www.genedb.org/; May 2015 release) and gene ontology enrichment analysis was performed for the DEG lists using GOstats R package. All analyses and visualizations were done with R packages- cummeRbund and ggplot2.

value: ANKA

tag: cell type

value: Gametocytes

tag: genotype

tag: activation

value: 15 min


title: CRK5KO_15MIN_rep 1


title: DpnII SisterC on G1 arrested cells released in BrdU - R3

description:
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-G1-DpnII-BrdU-UV-R1R2R3R4.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

tag: enzyme

tag: cell line


title: CRK5KO_0MIN_rep 1

value: 0 min


title: 201959750116_R02C01

description:
Primary human meningioma methylation profile
M5-7
Run1

tag: individual

tag: gender


title: DpnII Hi-C on G1 arrested cells released in BrdU - R3

value: Hi-C


title: dNET-seq Late S2P replicate 2

city: Lisbon

first: Maria

last: Carmo-Fonseca

address: Av. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: nascent RNA

data_processing:
Library strategy: dNET-seq
Adapter sequences were removed from all dNET-seq paired-end samples using Cutadapt (version 1.18) with the following parameters: -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10 -e 0.05 --match-read-wildcards -n 1.
Paired-end read merging was performed using bbmerge.sh from BBMap with the ‘xloose’ parameter.
Merged reads were then aligned to the Drosophila reference genome (dm6; Ensembl release 95) using STAR (version 2.6.0b) with –chimSegmentMin set to 20. Only uniquely mapped reads were considered, extracted using SAMtools (version 1.7) with -q set to 255.
PCR internal priming events generated during library preparation were removed using a custom Python script.
Single-nucleotide peaks for detecting splicing intermediate and intron lariat reads were called using a custom Python script (https://github.com/kennyrebelo).
Peaks of variable size for detecting putative pause sites were called using custom Python code (https://github.com/rosinaSav).
Custom Python code (https://github.com/rosinaSav) was used to randomise the coordinates of reads whilst preserving nucleotide compositon around the 5' end of the read. (The resulting peaks have been uploaded in the file NET_Dros_emb_4-6h_S5P_rep1_sorted_MNase_control_peaks_0.01_5_5_5_3_5_with_ups_intron.bed).
Genome_build: dm6.18
Supplementary_files_format_and_content: BED files for peaks and bigWig files for aligned reads.

organism: Drosophila melanogaster

source_name: Whole embryos

growth_protocol: Drosophila melanogaster flies (Oregon R (OrR) strain) were raised at 25°C. Embryos were collected into apple juice-agar plates supplemented with fresh yeast.

extract_protocol:
Embryos were harvested from the plates, dechorionated in 50% bleach solution and washed prior to flash freeazing in liquid nitrogen. Lysates from frozen embryos were obtained and chromatin was precipitated. Chromatin was digested with MNase and DNA-RNA-Pol II complexes were immunoprecipitated with antibodies. 5' ends were phosphorylated using T4 PNK 3′phosphatase minus and RNA fragments were isolated and using Quick-RNA MicroPrep (Zymo research)
Libraries were prepared following the standard protocol of the Truseq small RNA library prep kit (Illumina). Libraries were PCR amplified using 16 PCR cycles and cDNA libraries were fractionated in the gel between 130 to 300bp

tag: developmental stage

value: 4-6 hours post-fertilisation

tag: net-seq antibody

value: anti-Pol II CTD S2P (ab5095 Abcam)

tag: tissue

value: whole embryo


title: DpnII Hi-C on mitotic cells released in Thymidine - R3

description:
2019-MOsisC-M-DpnII-Thy-UV-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-UV-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-UV-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: DpnII


title: 201959750116_R01C01

description:
Primary human meningioma methylation profile
M5-2
Run1

tag: disease state

tag: age

tag: site


title: dNET-seq  Late S2P replicate 1

description: nascent RNA


title: DpnII SisterC on mitotic cells released in Thymidine - R3

description:
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-Thy-NO-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: S cervisiae with mutated cdc1 and galactose induced nucleoside importer and kinase


title: dNET-seq  Late S5P replicate 2

description: nascent RNA

value: anti-Pol II CTD S5P (ab5131 Abcam)


title: WTGFP_15MIN_rep 2

tag: strain

value: WT


title: WTGFP_15MIN_rep 1


title: CRK5KO_0MIN_rep 2


title: DpnII Hi-C on mitotic cells released in BrdU - R3

description:
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-NO-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool


title: dNET-seq Early S5P replicate 2

description: nascent RNA

value: 2-3 hours post-fertilisation


title: WTGFP_0MIN_rep 2


title: WTGFP_0MIN_rep 1


title: dNET-seq Early S5P replicate 1

description: nascent RNA


title: dNET-seq  Late S5P replicate 1

description: nascent RNA


title: Hydroxytyrosol  10 min replicate 3

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

description: Biological replicate 3 of 3

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60 ºC for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65ºC, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned.

scan_protocol: Images were captured with a Agilent Technologies Scanner G2505C / GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5. FC was calculated as the average of the fold change between significantly regulated probes.

organism: Lactiplantibacillus plantarum

source_name: Untreated cells: Control

label_protocol: Fluorescently labelled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen): 20 ug of total RNA was transformed to cDNA with SuperscriptTM III Reverse Transcriptase using anchored oligo(dT)20 primers, and including aminoallyl-modified nucleotides. After cDNA purification, the Cy3 and HyPer5 fluorescent dyes (Amersham Biosciences) were coupled to the aminoallyl-modified first-strand cDNA. Purification of Cy3- and HyPer5-labeled cDNA probes was carried out with the CyScribe GFX Purification Kit.

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS lacking hydroxytyrosol to an OD600 ≈ 0.8-0.9, then one pair of the culture were exposed  to hydroxytyrosol to bring their final concentration to 10 mM. Cell cultures were centrifuged after 10 minutes of exposure to hydroxytyrosol and RNA was extracted and purified.

extract_protocol: For RNA extraction the celular pellet was mixed with 2 mL of quenching buffer (60% methanol, 66.7 mM HEPES, pH 6.5, -40 ºC) . Following quenching, the cells were pelleted by centrifugation at 9,000 x g for 10 min at -10 ºC, transferred to a screw cap tube containing an extraction mixture (500 uL 1:4 chloroform-acid phenol, 30uL of 10% SDS, 30uL Na-acetate 3M pH 5.2, 400uL Tris-EDTA buffer [10 mM Tris(hydroxymethyl)amino methane, 1 mM EDTA] pH 7.4, 15 mg of polyvinylpoly-pyrrolidone, and 500 mg of 75-150um glass beads). The cells were broken under frozen conditions in the Mini-BeadBeather (BIOSPEC Products, INC.) using three treatments of 4600 rpm for 40 seconds cycles (and chilled on dry ice for 60 seconds between cycles). The suspension was then centrifuged at 4 ºC at 10,000 x g for 2 min. Two extractions with 500 uL of chloroform were performed, and the supernatant containing the RNA was separated by centrifugation.  The sample was immediately frozen in liquid nitrogen, and stored at -80 ºC. NanoDrop ND-1000 instrument was used for quantification of RNA. Continued with the QUIAGEN RNA isolation kit. Two treatments with DNase I (Ambion) were applied and the absence of genomic DNA was confirmed by PCR.

tag: compound

value: without Hydroxytyrosol

source_name: Treated cells: Experimental

value: Hydroxytyrosol


title: Hydroxytyrosol  10 min replicate 2

description: Biological replicate 2 of 3

treatment_protocol: Cell cultures were centrifuged after 10 minutes of exposure to hydroxytyrosol and RNA was extracted and purified.


title: Hydroxytyrosol  10 min replicate 1

description: Biological replicate 1 of 3


title: DpnII SisterC on mitotic cells released in BrdU - R3

description:
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.all_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.inter_sister_1500_cis_mapq.1000.mcool
2019-MOsisC-M-DpnII-BrdU-UV-R1R2R3.sacCer3.intra_sister_1500_cis_mapq.1000.mcool

value: SisterC


title: control_U251_48h_rep2

status: Public on Jun 16 2020

city: Xi'an

first: Peng-Cheng

last: Qiu

address: Changle West Road 169

country: China

institute: Fourth Military Medical University

description: Gene expression data from U251 MG cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: Human glioma cell lines U251 was cultured in DMEM (Hyclone) supplemented with 10 % FBS (Biowest) at 37 ℃ with 5 % CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells was treated with culcita novaeguineae saponin


title: control_U251_48h_rep1

description: Gene expression data from U251 MG cells


title: asterosaponin_U251_48h_rep3

description: Gene expression data from U251 MG cells treated with a new culcita novaeguineae saponin.

source_name: asterosaponin treated U251, 48h


title: Z3_Vein_day 28_rep1

city: Chengdu

first: JIAYU

last: SHEN

state: Sichuan

address: GuoXue Alley 37#

institute: West China Hospital, Sichuan University

description: Gene expression in day 28 rats after bypass grafting surgery

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (part number G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using homemade scripts.

organism: Rattus norvegicus

source_name: Vein sample, day 28, replicate 1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total of RNA was extracted from acquired vessels from four groups using Trizol reagent following the manufacturer’s instructions (Invitrogen, CA, USA). ND-1000 Nanodrop (Nano Drop Technologies, Inc., Wilmington, DE, USA) and Agilent 2200 TapeStation (Agilent Technologies, CA, USA) were used to determine the purity and integrity of the RNA, respectively.

treatment_protocol: All the obtained vein blood vessels were stored at -80℃ for further analysis

value: vein blood vessel

value: male

tag: day post surgery


title: Z1_Vein_day 28_rep1


title: 40197 post

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from PBMCs collected from subject 40197 post-CPAP treatment.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene10sthsentrezgcdf R package (version 16.0.0).

source_name: peripheral blood mononuclear cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted using Qiagen's miRNeasy Mini kit following the manufacturer's standard protocol.

value: peripheral blood mononuclear cells

tag: subject

tag: timepoint

value: post-CPAP


title: 3_Vein_day 14_rep1

description: Gene expression in day 14 rats after bypass grafting surgery

source_name: Vein sample, day 14, replicate 1


title: HJ17_Vein_day 7_rep1

description: Gene expression in day 7 rats after bypass grafting surgery

source_name: Vein sample, day 7, replicate 1


title: Z4_Vein_day 7_rep1


title: asterosaponin_U251_48h_rep1


title: asterosaponin_U251_48h_rep2


title: Z2_Vein_day 7_rep1


title: 40197 pre

description: Gene expression data from PBMCs collected from subject 40197 pre-CPAP treatment.

value: pre-CPAP


title: 14A_Vein_day 0_rep1

description: Gene expression in day 0 rats without bypass grafting surgery

source_name: Vein sample, day 0, replicate 1


title: asterosaponin_U251_48h_rep4


title: 30624 post

description: Gene expression data from PBMCs collected from subject 30624 post-CPAP treatment.


title: 15A_Vein_day 0_rep1


title: Z5_Vein_day 28_rep1


title: 40971 post

description: Gene expression data from PBMCs collected from subject 40971 post-CPAP treatment.


title: 30624 pre

description: Gene expression data from PBMCs collected from subject 30624 pre-CPAP treatment.


title: GPCMV infected JH4 cells rep 1

description:
24hpiFib1
GPCMV infected JH4, 24 hpi
JH4_Mock_V_GPCMV.xlsx
24hpiFib1_S13

value: Strain 13

tag: cell type

value: JH4 guinea pig lung fibroblasts

tag: passage

tag: infection

value: GPCMV SG13 J2


title: 2_Vein_day 14_rep1


title: 1_Vein_day 14_rep1


title: 40971 pre

description: Gene expression data from PBMCs collected from subject 40971 pre-CPAP treatment.


title: 40269 post

description: Gene expression data from PBMCs collected from subject 40269 post-CPAP treatment.


title: 40657 pre

description: Gene expression data from PBMCs collected from subject 40657 pre-CPAP treatment.


title: 11928 post

description: Gene expression data from PBMCs collected from subject 11928 post-CPAP treatment.


title: 40269 pre

description: Gene expression data from PBMCs collected from subject 40269 pre-CPAP treatment.


title: 11928 pre

description: Gene expression data from PBMCs collected from subject 11928 pre-CPAP treatment.


title: 40266 post

description: Gene expression data from PBMCs collected from subject 40266 post-CPAP treatment.


title: 40044 pre

description: Gene expression data from PBMCs collected from subject 40044 pre-CPAP treatment.


title: 30234 pre

description: Gene expression data from PBMCs collected from subject 30234 pre-CPAP treatment.


title: 40266 pre

description: Gene expression data from PBMCs collected from subject 40266 pre-CPAP treatment.


title: 11992 post

description: Gene expression data from PBMCs collected from subject 11992 post-CPAP treatment.


title: 30031 post

description: Gene expression data from PBMCs collected from subject 30031 post-CPAP treatment.


title: 30665 pre

description: Gene expression data from PBMCs collected from subject 30665 pre-CPAP treatment.


title: 30838 post

description: Gene expression data from PBMCs collected from subject 30838 post-CPAP treatment.


title: Fig4BK28175SWCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: 60 mins after release from G1 (alpha factor)

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC and trimming of reads was carried out using fastx_trimmer
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: bigwig files

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: antibody

value: none (input)


title: Fig4BK28175SIP

value: anti-PK antibody (Bio-Rad)


title: Fig4BK28175G1IP

description: Arrested G1 (alpha factor)


title: Fig4BK28175G1WCE

description: Arrested G1 (alpha factor)


title: Fig4BK28061SWCE


title: 40044 post

description: Gene expression data from PBMCs collected from subject 40044 post-CPAP treatment.


title: 30234 post

description: Gene expression data from PBMCs collected from subject 30234 post-CPAP treatment.


title: 30665 post

description: Gene expression data from PBMCs collected from subject 30665 post-CPAP treatment.


title: 40657 post

description: Gene expression data from PBMCs collected from subject 40657 post-CPAP treatment.


title: Fig4BK28061SIP


title: 11874 post

description: Gene expression data from PBMCs collected from subject 11874 post-CPAP treatment.


title: 30838 pre

description: Gene expression data from PBMCs collected from subject 30838 pre-CPAP treatment.


title: 11992 pre

description: Gene expression data from PBMCs collected from subject 11992 pre-CPAP treatment.


title: Fig4BK28061G1WCE

description: Arrested in late G1 (Gal-sic1)


title: Fig2FS1K24697G160WCE

description: Arrested G1 (alpha factor)


title: 11874 pre

description: Gene expression data from PBMCs collected from subject 11874 pre-CPAP treatment.


title: Fig4BK24697G1IP

description: Arrested G1 (alpha factor)


title: 10031 post

description: Gene expression data from PBMCs collected from subject 10031 post-CPAP treatment.


title: C2_Vein_day 0_rep1

description: Gene expression in day 0 rats without bypass grafting surgery


title: Fig2FS1K24697G160IP

description: Arrested G1 (alpha factor)


title: Fig2FS1K24697G10WCE

description: Arrested G1 (alpha factor)


title: NaCl WT 40min rep3 [NaCl.WT.40min.d169060]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
processed data file: terhorst_l2tpm.txt.gz
NaCl.WT.40min.d169060

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were aligned to a S. cerevisiae transcriptome with STAR version 2.5.3a and gene expression was quantified with RSEM version 1.3.0. Transcript per million (TPM) values were offset by +1 and transformed to log 2 space.
Genome_build: SacCer3 plus spike-ins with an ensembl annotation
Supplementary_files_format_and_content: text format file of log2 TPM with a +1 offset of protein coding genes

molecule: polyA RNA

source_name: NaCl WT 40min

growth_protocol: W303 wild-type cells (Supplementary Table 1, A2587) were inoculated in 25 mL YEPD and grown overnight at 30ºC. After approximately 12-14 hours of growth, cells were diluted to OD(600nm) = 0.1 with YEPD + 2% glucose and grown for an additional 4 hours at 30ºC. 500 mM NaCl was added to culture and grown for 40 minutes before samples for transcriptomics were taken.

extract_protocol:
3-5 mL samples of culture were taken, spun down at 3000rpm for 5 minutes, washed with 1 mL DEPC water, and transferred to a 2 mL RNase-free screw-cap tube. Samples were spun again at 8000rpm for 3 minutes, and supernatant was aspirated. Cells were snap frozen with liquid nitrogen and stored at -80C. RNA samples were prepared with RNeasy mini kit from Qiagen and treated with DNase on-column treatment (RNase-free) from Qiagen.
Illumina Truseq or KAPA

tag: strain background

value: Haploid Strain (A2587)

tag: growth phase/cell type

value: 500mM NaCl Treated Cells

value: Illumina Truseq


title: NaCl WT 40min rep2 [NaCl.WT.40min.d169059]

description:
processed data file: terhorst_l2tpm.txt.gz
NaCl.WT.40min.d169059


title: NaCl WT 40min rep1 [NaCl.WT.40min.d169058]

description:
processed data file: terhorst_l2tpm.txt.gz
NaCl.WT.40min.d169058


title: Timecourse WT 8h rep1 [time.WT.8h.d286060]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.8h.d286060

source_name: Timecourse WT 8h

growth_protocol: S288C wild-type cells (Supplementary Table 1, A2050) were inoculated in 25 mL YEPD and grown overnight at 25ºC. After approximately 12-14 hours of growth, cells were diluted to OD(600nm) = 0.1 with YEPD + 2% glucose and grown for an additional 4 hours. Once the (OD600nm) reached approximately OD(600nm) = 0.3, samples for transcriptomics were taken and OD(600nm) was measured every 2 hours at 25ºC over 28 hours.

value: Haploid Strain (A2050)

value: ESR Timecourse Cells

value: KAPA


title: Timecourse WT 8h rep2 [time.WT.8h.d286061]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.8h.d286061


title: Fig4BK24697SWCE


title: Fig4BK24738SWCE


title: Fig4BK24697G1WCE

description: Arrested G1 (alpha factor)


title: Fig4BK28061G1IP

description: Arrested in late G1 (Gal-sic1)


title: Fig4BK24738SIP


title: Fig4BK24738G1WCE

description: Arrested G1 (alpha factor)


title: Fig4BK24738G1IP

description: Arrested G1 (alpha factor)


title: 10031 pre

description: Gene expression data from PBMCs collected from subject 10031 pre-CPAP treatment.


title: Timecourse WT 6h rep1 [time.WT.6h.d286058]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.6h.d286058

source_name: Timecourse WT 6h


title: Timecourse WT 4h rep2 [time.WT.4h.d286057]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.4h.d286057

source_name: Timecourse WT 4h


title: Timecourse WT 4h rep1 [time.WT.4h.d286056]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.4h.d286056


title: Timecourse WT 2h rep2 [time.WT.2h.d286055]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.2h.d286055

source_name: Timecourse WT 2h


title: Timecourse WT 2h rep1 [time.WT.2h.d286054]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.2h.d286054


title: Fig4BK24697SIP

description: 60 mins after release from G1 (alpha factor)


title: Timecourse WT 26h rep2 [time.WT.28h.d286079]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.28h.d286079

source_name: Timecourse WT 26h


title: Fig2FS1K24697G10IP

description: Arrested G1 (alpha factor)


title: Timecourse WT 6h rep2 [time.WT.6h.d286059]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.6h.d286059


title: Timecourse WT 22h rep2 [time.WT.22h.d286075]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.22h.d286075

source_name: Timecourse WT 22h


title: Timecourse WT 24h rep1 [time.WT.24h.d286076]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.24h.d286076

source_name: Timecourse WT 24h


title: Timecourse WT 26h rep1 [time.WT.28h.d286078]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.28h.d286078


title: Timecourse WT 22h rep1 [time.WT.22h.d286074]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.22h.d286074


title: Timecourse WT 24h rep2 [time.WT.24h.d286077]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.24h.d286077


title: Timecourse WT 20h rep1 [time.WT.20h.d286072]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.20h.d286072

source_name: Timecourse WT 20h


title: Timecourse WT 20h rep2 [time.WT.20h.d286073]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.20h.d286073


title: Timecourse WT 10h rep1 [time.WT.10h.d286062]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.10h.d286062

source_name: Timecourse WT 10h


title: Timecourse WT 16h rep1 [time.WT.16h.d286068]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.16h.d286068

source_name: Timecourse WT 16h


title: Timecourse WT 10h rep2 [time.WT.10h.d286063]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.10h.d286063


title: Timecourse WT 0h rep2 [time.WT.0h.d286053]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.0h.d286053

source_name: Timecourse WT 0h


title: Timecourse WT 14h rep2 [time.WT.14h.d286067]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.14h.d286067

source_name: Timecourse WT 14h


title: Timecourse WT 14h rep1 [time.WT.14h.d286066]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.14h.d286066


title: Timecourse WT 16h rep2 [time.WT.16h.d286069]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.16h.d286069


title: Timecourse WT 18h rep1 [time.WT.18h.d286070]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.18h.d286070

source_name: Timecourse WT 18h


title: Tsai euploid population rep3 [heterogen.L2N.d105009]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.L2N.d105009

source_name: Tsai euploid population

growth_protocol: pRS315-STE2pr-spHIS5 S288C diploids (A40877) and triploids (A40878) (Supplementary Table 1) were grown overnight in SD - LEU and subsequently sporulated in the “Super Sporulation Media” mentioned above. Sporulated tetrads were then tetrad dissected. Individual colonies were grown for 14-16 hours in 200 μL of YEPD in a 96 deep-well plate. Cultures were then diluted 1:20 in YEPD + 2% glucose, grown for another 5 hours, then pooled, and diluted to approximately OD(600nm) = 0.3. The pooled aneuploid populations were grown for an additional 2 hours, and samples were collected.

value: Het. Euploid

value: Tsai Protocol Cells


title: Tsai aneuploid population rep2 [heterogen.L3N.d105011]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.L3N.d105011

source_name: Tsai aneuploid population

value: Het. Aneuploid


title: Tsai aneuploid population rep1 [heterogen.L3N.d105010]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.L3N.d105010


title: WT exponentially growing rep1 [heterogen.WT.d105019]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.WT.d105019

source_name: WT exponentially growing

value: Exponentially Growing Cells


title: Timecourse WT 12h rep2 [time.WT.12h.d286065]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.12h.d286065

source_name: Timecourse WT 12h


title: WT exponentially growing rep3 [heterogen.WT.d105021]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.WT.d105021


title: Timecourse WT 18h rep2 [time.WT.18h.d286071]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.18h.d286071


title: WT exponentially growing rep2 [heterogen.WT.d105020]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.WT.d105020


title: Timecourse WT 12h rep1 [time.WT.12h.d286064]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.12h.d286064


title: Tsai aneuploid population rep3 [heterogen.L3N.d105012]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.L3N.d105012


title: Tsai euploid population rep2 [heterogen.L2N.d105008]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.L2N.d105008


title: Timecourse WT 0h rep1 [time.WT.0h.d286052]

description:
processed data file: terhorst_l2tpm.txt.gz
time.WT.0h.d286052


title: Dilution aneuploid population rep1 [heterogen.A3N.d105016]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.A3N.d105016

source_name: Dilution aneuploid population

value: Dilution Protocol Cells


title: Dilution aneuploid population rep3 [heterogen.A3N.d105018]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.A3N.d105018


title: Dilution euploid population rep2 [heterogen.A2N.d105014]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.A2N.d105014

source_name: Dilution euploid population


title: Tsai euploid population rep1 [heterogen.L2N.d105007]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.L2N.d105007


title: Dilution euploid population rep3 [heterogen.A2N.d105015]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.A2N.d105015


title: Dilution aneuploid population rep2 [heterogen.A3N.d105017]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.A3N.d105017


title: Dilution euploid population rep1 [heterogen.A2N.d105013]

description:
processed data file: terhorst_l2tpm.txt.gz
heterogen.A2N.d105013


title: Chemostat A38 rep1 [chemo.A38.F11.d236023]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A38.F11.d236023

source_name: Chemostat A38

growth_protocol: Selected complex aneuploid strains were grown on YEPD + 2% glucose plate for 2 days at 25ºC. Strains were inoculated in phosphate-limited media (http://dunham.gs.washington.edu/chemostatv2.htm) and grown overnight. Once chemostat was set up and filled, phosphate-limited media in the chemostat was inoculated with 2 mL of overnight culture, and cells were allowed to grow for 30-36 hours although some strains required 48+ hours of growth. The dilution pumps were then turned on, and the dilution rate was 0.17 +/- 0.01 chemostat volumes per hour. The chemostat was sampled daily to measure effluent volume, hemocytometer counts, and OD(600nm) measurements. When the chemostat had reached a steady-state, defined by less than 5% change from the previous day’s measurements, samples were harvested

value: Chemostat Cultured Cells


title: Chemostat A38 rep2 [chemo.A38.F6.d236024]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A38.F6.d236024


title: Chemostat A37 rep1 [chemo.A37.F11.d236022]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A37.F11.d236022

source_name: Chemostat A37


title: Chemostat A37 rep2 [chemo.A37.F8.d236021]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A37.F8.d236021


title: Chemostat A18 rep2 [chemo.A18.F7.d236013]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A18.F7.d236013

source_name: Chemostat A18


title: Chemostat A24 rep2 [chemo.A24.F10_2.d236018]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A24.F10_2.d236018

source_name: Chemostat A24


title: Chemostat A34 rep1 [chemo.A34.F7.d236020]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A34.F7.d236020

source_name: Chemostat A34


title: Chemostat A34 rep2 [chemo.A34.F9.d236019]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A34.F9.d236019


title: Chemostat A24 rep1 [chemo.A24.F10_1.d236017]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A24.F10_1.d236017


title: Chemostat A21 rep2 [chemo.A21.d204036]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A21.d204036

source_name: Chemostat A21


title: Chemostat A21 rep1 [chemo.A21.d204035]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A21.d204035


title: Chemostat A22 rep2 [chemo.A22.F9.d236015]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A22.F9.d236015

source_name: Chemostat A22


title: Chemostat A20 rep2 [chemo.A20.d204034]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A20.d204034

source_name: Chemostat A20


title: Chemostat A23 rep2 [chemo.A23.d204038]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A23.d204038

source_name: Chemostat A23


title: Chemostat A23 rep1 [chemo.A23.d204037]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A23.d204037


title: Chemostat A22 rep1 [chemo.A22.F6.d236016]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A22.F6.d236016


title: Chemostat A18 rep1 [chemo.A18.F11.d236014]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A18.F11.d236014


title: A36 exp5 rep2 [AT_an.A36.d356034]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A36.d356034

source_name: A36 exp5

growth_protocol: Selected complex aneuploid strains were grown on YEPD + 2% glucose plate for 2 days at 25ºC. Colonies were inoculated overnight in 25 mL YEPD + 2% glucose and grown at 25ºC. After 12-14 hours of growth at 25ºC, cells were diluted to approximately OD(600nm) = 0.1 and grown for an additional 4 hours at 25ºC.


title: A38 exp5 rep2 [AT_an.A38.d356036]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A38.d356036

source_name: A38 exp5


title: A38 exp6 rep2 [AT_an.A38.d204029]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A38.d204029

source_name: A38 exp6


title: A38 exp6 rep3 [AT_an.A38.d204030]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A38.d204030


title: A38 exp6 rep1 [AT_an.A38.d204028]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A38.d204028


title: A35 exp5 rep1 [AT_an.A35.d356031]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A35.d356031

source_name: A35 exp5


title: A35 exp5 rep2 [AT_an.A35.d356032]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A35.d356032


title: Chemostat A20 rep1 [chemo.A20.d204033]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.A20.d204033


title: A36 exp5 rep1 [AT_an.A36.d356033]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A36.d356033


title: A34 exp5 rep2 [AT_an.A34.d356030]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A34.d356030

source_name: A34 exp5


title: Chemostat 2N rep1 [chemo.2N.d204031]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.2N.d204031

source_name: Chemostat 2N


title: A34 exp5 rep1 [AT_an.A34.d356029]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A34.d356029


title: Chemostat 2N rep2 [chemo.2N.d204032]

description:
processed data file: terhorst_l2tpm.txt.gz
chemo.2N.d204032


title: A34 exp6 rep2 [AT_an.A34.d204026]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A34.d204026

source_name: A34 exp6


title: A34 exp6 rep1 [AT_an.A34.d204025]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A34.d204025


title: A33 exp6 rep2 [AT_an.A33.d204023]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A33.d204023

source_name: A33 exp6


title: A32 exp5 rep2 [AT_an.A32.d356026]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A32.d356026

source_name: A32 exp5


title: A32 exp6 rep3 [AT_an.A32.d204021]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A32.d204021

source_name: A32 exp6


title: A33 exp5 rep2 [AT_an.A33.d356028]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A33.d356028

source_name: A33 exp5


title: A32 exp6 rep1 [AT_an.A32.d204019]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A32.d204019


title: A30 exp5 rep2 [AT_an.A30.d356024]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A30.d356024

source_name: A30 exp5


title: A33 exp6 rep3 [AT_an.A33.d204024]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A33.d204024


title: A33 exp6 rep1 [AT_an.A33.d204022]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A33.d204022


title: A32 exp5 rep1 [AT_an.A32.d356025]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A32.d356025


title: A30 exp5 rep1 [AT_an.A30.d356023]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A30.d356023


title: A38 exp5 rep1 [AT_an.A38.d356035]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A38.d356035


title: A30 exp6 rep2 [AT_an.A30.d204017]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A30.d204017

source_name: A30 exp6


title: A30 exp6 rep1 [AT_an.A30.d204016]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A30.d204016


title: A29 exp5 rep2 [AT_an.A29.d356022]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A29.d356022

source_name: A29 exp5


title: A30 exp6 rep3 [AT_an.A30.d204018]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A30.d204018


title: A28 exp6 rep2 [AT_an.A28.d204011]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A28.d204011

source_name: A28 exp6


title: A32 exp6 rep2 [AT_an.A32.d204020]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A32.d204020


title: A29 exp5 rep1 [AT_an.A29.d356021]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A29.d356021


title: A34 exp6 rep3 [AT_an.A34.d204027]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A34.d204027


title: A28 exp6 rep3 [AT_an.A28.d204012]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A28.d204012


title: A29 exp6 rep2 [AT_an.A29.d204014]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A29.d204014

source_name: A29 exp6


title: A29 exp6 rep1 [AT_an.A29.d204013]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A29.d204013


title: A26 exp5 rep1 [AT_an.A26.d356017]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A26.d356017

source_name: A26 exp5


title: A28 exp5 rep2 [AT_an.A28.d356020]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A28.d356020

source_name: A28 exp5


title: A26 exp6 rep3 [AT_an.A26.d204009]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A26.d204009

source_name: A26 exp6


title: A33 exp5 rep1 [AT_an.A33.d356027]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A33.d356027


title: A28 exp6 rep1 [AT_an.A28.d204010]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A28.d204010


title: A26 exp6 rep1 [AT_an.A26.d204007]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A26.d204007


title: A26 exp6 rep2 [AT_an.A26.d204008]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A26.d204008


title: A24 exp5 rep1 [AT_an.A24.d356015]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A24.d356015

source_name: A24 exp5


title: A24 exp5 rep2 [AT_an.A24.d356016]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A24.d356016


title: A1 exp5 rep2 [AT_an.A1.d356014]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A1.d356014

source_name: A1 exp5


title: A37 exp4 rep1 [AS_an.exp4.A37.d10181]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A37.d10181

source_name: A37 exp4


title: A37 exp4 rep2 [AS_an.exp4.A37.d10182]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A37.d10182


title: A1 exp5 rep1 [AT_an.A1.d356013]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A1.d356013


title: A36 exp4 rep1 [AS_an.exp4.A36.d10179]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A36.d10179

source_name: A36 exp4


title: A29 exp6 rep3 [AT_an.A29.d204015]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A29.d204015


title: A36 exp4 rep2 [AS_an.exp4.A36.d10180]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A36.d10180


title: A28 exp5 rep1 [AT_an.A28.d356019]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A28.d356019


title: A27 exp4 rep2 [AS_an.exp4.A27.d10178]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A27.d10178

source_name: A27 exp4


title: A27 exp4 rep1 [AS_an.exp4.A27.d10177]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A27.d10177


title: A25 exp4 rep1 [AS_an.exp4.A25.d10174]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A25.d10174

source_name: A25 exp4


title: A24 exp4 rep2 [AS_an.exp4.A24.d10171]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A24.d10171

source_name: A24 exp4


title: A24 exp4 rep1 [AS_an.exp4.A24.d10170]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A24.d10170


title: A23 exp4 rep1 [AS_an.exp4.A23.d10168]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A23.d10168

source_name: A23 exp4


title: A26 exp5 rep2 [AT_an.A26.d356018]

description:
processed data file: terhorst_l2tpm.txt.gz
AT_an.A26.d356018


title: A23 exp4 rep2 [AS_an.exp4.A23.d10169]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A23.d10169


title: A22 exp4 rep1 [AS_an.exp4.A22.d10164]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A22.d10164

source_name: A22 exp4


title: A22 exp4 rep2 [AS_an.exp4.A22.d10165]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A22.d10165


title: A21 exp4 rep1 [AS_an.exp4.A21.d10160]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A21.d10160

source_name: A21 exp4


title: A21 exp4 rep2 [AS_an.exp4.A21.d10161]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A21.d10161


title: A18 exp4 rep1 [AS_an.exp4.A18.d10153]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A18.d10153

source_name: A18 exp4


title: A27exp3 rep2 [AS_an.exp3.A27.d10176]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A27.d10176


title: A27 exp3 rep1 [AS_an.exp3.A27.d10175]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A27.d10175

source_name: A27 exp3


title: A25 exp3 rep2 [AS_an.exp3.A25.d10173]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A25.d10173

source_name: A25 exp3


title: A20 exp4 rep1 [AS_an.exp4.A20.d10157]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A20.d10157

source_name: A20 exp4


title: A25 exp3 rep1 [AS_an.exp3.A25.d10172]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A25.d10172


title: A23 exp3 rep2 [AS_an.exp3.A23.d10167]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A23.d10167

source_name: A23 exp3


title: A23 exp3 rep1 [AS_an.exp3.A23.d10166]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A23.d10166


title: A22 exp3 rep1 [AS_an.exp3.A22.d10162]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A22.d10162

source_name: A22 exp3


title: A21 exp3 rep1 [AS_an.exp3.A21.d10158]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A21.d10158

source_name: A21 exp3


title: A20 exp3 rep2 [AS_an.exp3.A20.d10156]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A20.d10156

source_name: A20 exp3


title: A21 exp3 rep2 [AS_an.exp3.A21.d10159]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A21.d10159


title: A18 exp3 rep2 [AS_an.exp3.A18.d10152]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A18.d10152

source_name: A18 exp3


title: A20 exp3 rep1 [AS_an.exp3.A20.d10155]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A20.d10155


title: A18 exp3 rep1 [AS_an.exp3.A18.d10151]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A18.d10151


title: 2N exp3 rep1 [AS_an.exp3.2N.d10133]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.2N.d10133

source_name: 2N exp3


title: A22 exp2 rep1 [AS_an.exp2.A22.d6051]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A22.d6051

source_name: A22 exp2


title: A23 exp2 rep1 [AS_an.exp2.A23.d6055]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A23.d6055

source_name: A23 exp2


title: A21 exp2 rep1 [AS_an.exp2.A21.d6049]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A21.d6049

source_name: A21 exp2


title: A18 exp4 rep2 [AS_an.exp4.A18.d10154]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp4.A18.d10154


title: A20 exp2 rep2 [AS_an.exp2.A20.d6046]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A20.d6046

source_name: A20 exp2


title: A20 exp2 rep1 [AS_an.exp2.A20.d6045]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A20.d6045


title: A21 exp2 rep2 [AS_an.exp2.A21.d6050]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A21.d6050


title: A1 exp2 rep2 [AS_an.exp2.A1.d6062]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A1.d6062

source_name: A1 exp2


title: A22 exp3 rep2 [AS_an.exp3.A22.d10163]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.A22.d10163


title: A19 exp2 rep1 [AS_an.exp2.A19.d6041]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A19.d6041

source_name: A19 exp2


title: A35 exp1 rep1 [AS_an.exp1.A35.d6057]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A35.d6057

source_name: A35 exp1


title: A35 exp1 rep2 [AS_an.exp1.A35.d6058]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A35.d6058


title: 2N exp2 rep2 [AS_an.exp2.2N.d6025]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.2N.d6025

source_name: 2N exp2


title: A1 exp2 rep1 [AS_an.exp2.A1.d6061]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A1.d6061


title: A23 exp1 rep2 [AS_an.exp1.A23.d6054]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A23.d6054

source_name: A23 exp1


title: 2N exp2 rep1 [AS_an.exp2.2N.d6024]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.2N.d6024


title: A21 exp1 rep1 [AS_an.exp1.A21.d6047]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A21.d6047

source_name: A21 exp1


title: A20 exp1 rep2 [AS_an.exp1.A20.d6044]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A20.d6044

source_name: A20 exp1


title: 2N exp3 rep2 [AS_an.exp3.2N.d10134]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp3.2N.d10134


title: A19 exp1 rep2 [AS_an.exp1.A19.d6040]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A19.d6040

source_name: A19 exp1


title: A23 exp2 rep2 [AS_an.exp2.A23.d6056]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A23.d6056


title: 2N exp1 rep4 [AS_an.exp1.2N.d6023]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.2N.d6023

source_name: 2N exp1


title: A19 exp1 rep1 [AS_an.exp1.A19.d6039]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A19.d6039


title: A23 exp1 rep1 [AS_an.exp1.A23.d6053]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A23.d6053


title: A20 exp1 rep1 [AS_an.exp1.A20.d6043]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A20.d6043


title: A21 exp1 rep2 [AS_an.exp1.A21.d6048]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A21.d6048


title: 2N exp1 rep3 [AS_an.exp1.2N.d6022]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.2N.d6022


title: A22 exp2 rep2 [AS_an.exp2.A22.d6052]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A22.d6052


title: 2N exp1 rep2 [AS_an.exp1.2N.d6017]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.2N.d6017


title: 2N exp1 rep1 [AS_an.exp1.2N.d6016]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.2N.d6016


title: A19 exp2 rep2 [AS_an.exp2.A19.d6042]

description:
processed data file: terhorst_l2tpm.txt.gz
AS_an.exp2.A19.d6042


title: 30031 pre

description: Gene expression data from PBMCs collected from subject 30031 pre-CPAP treatment.

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells

value: pre-CPAP