title: Opossum ESF PGE2 treated rep3

status: Public on Jun 21 2018

city: West Haven

first: Cong

last: Liang

address: 300 Heffernan Dr.

institute: Yale University

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the opossum (monDom5) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: opossum (monDom5)
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each sample.

organism: Monodelphis domestica

source_name: Endometrial stromal fibroblasts

extract_protocol:
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: Endometrial stromal fibroblasts


title: Opossum ESF PGE2 treated rep2

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: cell type

tag: treatment


title: Opossum ESF MPA and PGE2 treated rep1

value: MPA and PGE2


title: S. cerevisiae BY4741 wild type 15 min cold shock vs before cold shock replicate 3

status: Public on Jun 22 2018

type: RNA

city: Los Angeles

first: Kam

middle: D.

last: Dahlquist

state: CA

address: 1 LMU Drive, MS8220

department: Biology

institute: Loyola Marymount University

description: Ontario chip; post-washing slide coating of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene

hyb_protocol: 85 μL of hybridization master mix was added to each labeled, paired, and dried aRNA sample. The hybridization master mix contained 100 μL DIG Easy Hyb solution (Roche Applied Science, catalog #11796895001), 0.38 μL of 1 μg/μL oligo dA (10-20mer) solution (Invitrogen, catalog #POLYA.GF) , and 5 μL of 10 mg/mL DNA, MB-grade from fish sperm (Roche Applied Science, catalog #11467140001) and was heated to 65-70°C for two minutes and cooled to room temperature before adding 85 μL of it to the labeled aRNA. After the hybridization master mix was added to the aRNA, it was heated to 65-70°C for two minutes and cooled to room temperature for two minutes before being applied to the microarray chip. Hybri-slips (Sigma-Aldrich, catalog #H0784) cover slips were used and the chip hybridized in a Corning Hybridization Chamber (catalog #2551) with 2 X 11 μL nuclease-free water inside the wells of the chamber. Microarrays were incubated in a 37°C water bath for 15-16 hours. Cover slips were removed from the microarray by dunking in 1X SSC buffer at room temperature. Slides were immediately transferred to a 50 mL conical tube containing 1X SSC/1% SDS buffer and incubated in a 50°C water bath for 15 minutes; slides were transferred and incubated twice more in 1X SSC/1% SDS at 50°C for 15 minutes each time. Slides were then washed by plunging up and down 4-6 times in 1X SSC at room temperature and plunging up and down 4-6 times in 0.1X SSC at room temperature. Slides were pulled out slowly from this final wash and any remaining water droplets were chased off with a compressed air duster. Slides were optionally dipped in a slide coating solution of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene (see description column of SAMPLES table) before scanning. A complete protocol is found here: http://www.openwetware.org/wiki/Dahlquist:DNA_Microarray_Protocol

scan_protocol: Slides were scanned with an Axon GenePix 4000B Scanner (Molecular Devices). Preview scans were performed to manually or automatically set the PMT gain for the 635 wavelength channel and for the 532 wavelength channel; power was at 100% for both channels. For auto-PMT scans, the saturation tolerance was set to the default value of 0.05%. For the data scan, pixel size was set to 10 μm, lines to average was set to 2, and focus position was set to 0 μm. The GenePix Pro 6.1 software (v6.1.0.2) was used with the AxGenePixDemo.dll (v2.1.1.39) driver. When detecting features, the following settings were used: Find irregular features, Resize features during alignment to minimum diameter of 33% and maximum diameter of 200%, Flag features that fail background threshold criteria as Not Found, Estimate warping and rotation when finding blocks, and Automatic Image Registration: Max translation of 10 pixels. Note that two chip types were used in this study: GCAT and Ontario (see SAMPLES table). The GCAT chips had two sets of blocks representing the full genome of S. cerevisiae at the top and bottom of the chip. The .gal file provided for this chip only had information for one set of blocks, so each of the GCAT chips had its features found twice, once for the top and once for the bottom, generating two .gpr results files (see SAMPLES table). The GCAT .gal file can be found here: https://github.com/kdahlquist/DahlquistLab/raw/master/GEO_submission/yeast_GCAT_gal.gal. The Ontario chip had a single .gal file for the entire chip; duplicate spots for genes were placed side-by-side. The Ontario .gal file can be found here: https://github.com/kdahlquist/DahlquistLab/raw/master/GEO_submission/Ontario_Y6.4Kv7.GAL. Complete details are found here: http://www.openwetware.org/wiki/Dahlquist:GenePix_Pro_Software_Protocol.

data_processing: A full description of the data processing is found here: http://www.openwetware.org/wiki/Dahlquist:Microarray_Data_Analysis_Workflow. Briefly, an R script was written to perform the data processing steps. Follow the links to download the script (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/GCAT-and-Ontario_normalization_script.R) and required GCAT (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/GCAT_Targets_20160616.csv) and Ontario (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/Ontario_Targets_wt-dCIN5-dGLN3-dHAP4-dHMO1-dSWI4-dZAP1_20160616.csv) Targets files to run it. Put the script, Targets files, and all .gpr files in the same folder to run. A script to automatically generate MA and box plots showing the results of the normalization can be downloaded from here (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/generate_MA_and_box_plots.R) . The results reported here were produced with Version x64 3.1.0 of R. Version 3.20.1 of the limma package (Smyth, G. K., 2005, Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor, pp. 397-420, Springer New York.) was used to perform within-chip normalization. Briefly the script extracts the Log Ratio (635/532) values (column AS in Excel) of the .gpr file for each spot and removes bad spots (flagged as -50 in the .gpr file), and the control spots labeled Arabidopsis and 3XSSC. It performs the loess normalization using the normexp method. It performs between-chip normalization using the median absolute deviation (MAD). Ratios of the dye-swapped samples were corrected so that the ratio reported is experimental timepoint/t0 control. Then duplicate spots corresponding to the same gene are averaged and the data from the two chips are merged. The log2 ratios (experimental/control) are rounded to four decimal places. The processed data file only reports genes that were present on the Ontario chip type. Genes that were only found on the GCAT chip type and not the Ontario chip type were discarded because there was not enough replicate data for those genes to make downstream analysis meaningful.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: t15 15 min cold shock replicate 3

label_protocol: 1 μg aliquots of total RNA were converted to aRNA using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion/LifeTechnologies catalog #AM1753), according to the manufacturer's instructions. Five aliquots of each t0 sample were amplified and then mixed together and one aliquot of each of the other timepoints was amplified. 20 μg aliquots of aRNA (5 aliquots of the mixed t0, one aliquot each for the other timepoints) were then labeled with either Cy3 or Cy5 (CyDye Post-Labeling Reactive Dye Packs, GE Healthcare Life Sciences catalog #RPN5661), using the Amino Allyl MessageAmp II aRNA Amplification Kit, according to the dye orientation chosen for the particular replicate experiment (see SAMPLES table). Labeling efficiency was checked by spectroscopy using Bio-Rad trUView Cuvettes and SmartSpec 3000 or on an Implen Nanophotometer. The t0 labeled samples were mixed together and 5 μg aliquots of the labeled, mixed t0 sample were then combined with 5 μg aliquots of labeled aRNA from each of the other timepoints for that replicate flask. The combined aRNA samples were then fragmented using Ambion (now LifeTechnologies) RNA Fragmentation Reagents (catalog #AM8740) according to the manufacturer's instructions and dried in a speedvac to <= 5 μL. A complete protocol is found here: http://www.openwetware.org/wiki/Dahlquist:DNA_Microarray_Protocol.

growth_protocol: 5 mL liquid overnight cultures of the appropriate strain of S. cerevisiae were inoculated with a single colony into YEPD (wild type strain) or YEPD + 200 μg/mL G418 (gene deletion strains) medium and incubated overnight at 30°C, shaking at 250 rpm. The next morning, these cultures were used to inoculate larger 750 mL cultures by adding a 1/500th volume of the overnight culture to a 2800 mL Fernbach flask containing YEPD (wild type strain) or YEPD 200 μg/mL G418 (gene deletion strains) medium. Two independent biological replicate experiments (flasks) of the same strain were carried out on the same day. Growth was monitored by reading the OD600 of the cultures at appropriate time intervals.

extract_protocol: Total RNA was extracted from a single cell pellet from each timepoint using the Ambion (now LifeTechnologies) RiboPure Yeast Kit, catalog #AM1926, according to the manufacturer's instructions. The DNase treatment from the kit was substituted with the Turbo DNA-free Kit (Ambion/LifeTechnologies catalog #AM1907), using the rigorous DNAase treatment option of the manufacturer's protocol. Quality of the total RNA was checked by UV spectroscopy using Bio-Rad trUView Cuvettes and SmartSpec 3000 or on an Implen Nanophotometer and by non-denaturing agarose gel electrophoresis (Lonza Reliant Precast RNA Gel, catalog #54948). Total RNA was stored at -80°C.

treatment_protocol: Once the culture reached an OD600 of >= 0.2 at 30°C, the cold shock and recovery experiment was begun. Three 40 mL samples were collected at time zero (t0) before cold shock, and the flask was shifted to a 13°C water bath incubator/shaker, shaking at 250 rpm. Three 40 mL samples each were collected after 15 minutes (t15), 30 minutes (t30), and 60 minutes (t60) of cold shock at 13°C. The flask was then shifted to a 30°C water bath and manually swirled for 5 minutes, before being dried off and returned to the 30°C incubator/shaker at 250 rpm. Three 40 mL samples were collected after a total of 30 minutes at 30°C (t90) and 60 minutes at 30°C (t120). Immediately after collection, the samples were spun at 4000 rpm in a table-top centrifuge for 3 minutes at room temperature. The supernatant was discarded and the pellets were immediately frozen in a dry ice/ethanol bath and stored at -80°C.

tag: strain

tag: gene deleted

value: none (wild type parental strain)

value: t15 15 min cold shock 13 degrees

source_name: t0 before cold shock control replicate 3

value: t0 before cold shock control 30 degrees


title: S. cerevisiae BY4741 wild type 15 min cold shock vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

source_name: t15 15 min cold shock replicate 2


title: Opossum ESF MPA and PGE2 treated rep2


title: Opossum ESF MPA and PGE2 treated rep3


title: Opossum ESF PGE2 treated rep1


title: Opossum ESF MPA treated rep3

value: MPA


title: Opossum ESF MPA treated rep2


title: Opossum ESF rep3


title: Opossum ESF MPA treated rep1


title: Opossum ESF differentiation media treated rep1

value: Eutherian differentiation media


title: Opossum ESF rep2


title: Opossum ESF rep1


title: Opossum ESF differentiation media treated rep2


title: S. cerevisiae BY4741 wild type 15 min cold shock vs before cold shock replicate 1

description: GCAT chip; post-washing slide coating of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene

source_name: t0 before cold shock control replicate 1

source_name: t15 15 min cold shock replicate 1


title: Opossum ESF differentiation media treated rep3


title: Liver_Niacin 39

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

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

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

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

label: Biotin

organism: Bos taurus

source_name: Liver Niacin

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

growth_protocol: A total of 22 multiparous Holstein dairy cows were used which were part of a study carried out at the Educational and Research Centre for Animal Husbandry, Hofgut Neumühle (Münchweiler an der Alsenz, Germany) and approved by the Provincial Government of Coblenz, Germany (23 177-07/G 14-20-050). The experimental period lasted from 3 wk before expected calving until 1 wk p.p. Details on feeding and husbandry conditions are given in Zeitz et al. (2018).

extract_protocol: Total RNA was isolated from liver samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol and stored at -80 °C. Concentration and purity of the RNA were estimated from the optical density at 260 and 280 nm, respectively, using a NanoQuant plate (Infinite 200, Tecan, Mainz, Germany). Prior to sample processing at the Centre of Excellence for Fluorescent Bioanalytics at the University of Regensburg, the concentration and integrity of RNA was analyzed using an Agilent 2100 Bioanalyzer (Agilent technologies, Böblingen, Germany). The total RNA concentrations, optical density A260/A280 ratios and RNA integrity number (RIN) values of all samples were 0.22 ± 0.08 µg/µL, 2.00 ± 0.03 and 7.2 ± 0.5 (mean ± SD, n = 18), respectively. From the 11 available RNA samples per group, the two samples with the lowest RIN values were excluded.

treatment_protocol: the cows received either corn and grass silage-based antepartum (a.p.) or p.p. total mixed rations (control group, n = 11) or the same diets supplemented with rumen-protected NA (NiaShure; Balchem, New Hampton, NY, USA) (NA group, n = 11) at a dosage of 79 mg/kg BW. The diets were calculated to meet energy and protein requirements of dairy cows following the recommendations of the German Society of Nutrition Physiology (GfE, 2001). Considering the rumen degradability of NiaShure (Zeitz et al., 2018), the applied NA dosage was equivalent to 47 mg NA at the duodenum and estimated to be equivalent to 31 mg of absorbable NA per kg BW based on information given by the supplier. This NA dosage was close to that required for pharmacological use as an antilipidaemic drug in humans (approximately 10-30 mg NA/kg BW) (Offermanns et al., 2006). Biopsies of the liver were taken 1 wk after calving, and the liver tissue was snap-frozen in liquid N2 and stored at −80°C. More details about sample collection are given by Zeitz et al. (2018).

tag: gender

value: female (cow)

tag: condition

value: Niacin

tag: tissue

value: liver

tag: breed

value: Holstein


title: Liver_Niacin 40


title: Liver_Niacin 15


title: Liver_Niacin 33


title: Liver_Niacin 14


title: Liver_Niacin 19


title: Liver_Niacin 8


title: Liver_Control 42

source_name: Liver control

value: control


title: Liver_Control 23


title: Liver_Niacin 3


title: Liver_Control 37


title: Liver_Control 1


title: Liver_Control 36


title: Liver_Niacin 7


title: Liver_Control 16


title: Liver_Control 11


title: Liver_Control 20


title: Liver_Control 12


title: MP-HX treated HCT116

city: Kuala Lumpur

first: Johari

last: Mohd Ali

state: WP

address: Lembah Pantai

department: Department of Molecular Medicine

country: Malaysia

institute: University of Malaya

hyb_protocol: Following fragmentation and labeling, 3.5 µg of ss-CDNA was hybridized for 17 hours in GeneChip™ Hybridization Oven 645 at 45 °C and 60 rpm

scan_protocol: Gene chips were scanned using GeneChip™ Scanner 3000 7G

data_processing: Raw data (CEL files) was generated using GeneChip Operating Software (GCOS).  The CEL files were analyzed by Expression Console software (Applied Biosystem), to ensure the quality control parameters of the arrays were acceptable.  Gene expression data was analyzed using Transcriptome Analysis Console (TAC) software (Applied Biosystem). A cut off fold change value of ±2.0 was used for the analysis

organism: Homo sapiens

source_name: ATCC HCT116 24hr treatment with MP-HX extract at  60 microgram/mL

label_protocol: single stranded cDNA (ss-cDNA) was fragmented and biotin labelled by GeneChipTM WT PLUS Reagent Kit (Part No. 902280, Applied Biosystem), according to manufacturer's protocol

growth_protocol: 300K cells (HCT116, HepG2) were seeded in 6 wells plate containig DMEM growth medium supplemented with 10% FBS (fetal bovine serum) and 1% pen-strept (penicillin-streptomycin); and incubated at 37 °C in a humidified incubator containing 5% CO2

extract_protocol: RNA was extracted and purified using PureLink RNA mini kit (Catalogue No. 12183018A, Invitrogen), following manufacturer's instructions

treatment_protocol: HCT116 and HepG2 cells were treated with MP-HX for 24 hours at 60 µg/mL and 78 µg/mL respectively

tag: cell line

value: ATCC HCT116

value: Colorectal carcinoma


title: Vehicle control HepG2

source_name: ATCC HepG2 vehicle control (0.39%)

value: ATCC HepG2

value: vehicle control (0.39%)

value: Hepatocellular carcinoma


title: CS_SKBR3_GFPX2_minusDFO_Batch 3_06242014

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix HuGene 2.0 ST arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using Affymetrix Expression Console software and were also imported into GeneSpring GX11.5 (Agilent Technologies) where the data was quantile normalized using PLIER and baseline transformed to the median of the control samples. The probe sets were further filtered to exclude the bottom 20th percentile across all samples as well as probe sets with expression levels with CV > 20% across all replicates in a condition.

label: biotin

growth_protocol: DMEM 10% FBS

extract_protocol: SKBR3 cells expressing NDRG1 shRNA1 or vector control were harvested by trypsinization and total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA). The quality and the concentrations of total RNA were assessed using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA (100 ng) deemed to be of good quality (RNA integrity number (RIN) greater than 8) was processed according to the standard Affymetrix Whole Transcript Sense Target labeling protocol (Affymetrix, Santa Clara, CA).

tag: shRNA


title: CS_SKBR3_G8X3_minusDFO_Batch 2_06242014

source_name: CS_SKBR3_G8X3_minusDFO_Batch 2_06242014

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol


title: CS_SKBR3_G8X3_minusDFO_Batch 3_06242014

source_name: CS_SKBR3_G8X3_minusDFO_Batch 3_06242014


title: CS_SKBR3_G8x3-DFO_Batch1_02122014


title: CS_SKBR3_GFPX2_minusDFO_Batch 2_06242014


title: Vehicle control HCT116

source_name: ATCC HCT116  vehicle control (0.3% DMSO)

value: vehicle control (0.3% DMSO)


title: reactive skin lesions (inflammatory dermatosis) sample 27

city: Madrid

first: Rebeca

last: Manso

state: Madrid

address: Av. Reyes Católicos, 2

department: Pathology

country: Spain

institute: Fundación Jiménez Díaz

hyb_protocol: Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to agilent recomandation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Data are normalized to the median of the series (between arrays) by R program version 2.4, (available at http://www.r-project.org/). For normalization was used the Processed Signal of the feature extraction files (already includes background subtraction) was used. Average of miRs replicates was then applied using the following web page: http://prep.bioinfo.cnio.es/. Significance Analysis of Microarray excel macro (SAM) was used.

label_protocol: 100ng of total RNA were dephosphorilated, desnaturalizated, treated with ligase  T4 and labelled with Cy3 for 2 hours at 16ºC.

growth_protocol: Samples were frozen to preserve the RNA properties.

extract_protocol: Total RNA was extracted by Trizol reagent (Invitrogen, Carlsbad, CA, USA)

tag: disease status

value: cutaneous T-cell lymphoma (CTCL)


title: reactive skin lesions (inflammatory dermatosis) sample 26


title: MP-HX treated HepG2

source_name: ATCC HepG2 24hr treatment with MP-HX extract at  78 microgram/mL


title: reactive skin lesions (inflammatory dermatosis) sample 28


title: Mycosis Fungoides (patches-plaques)  sample 22

source_name: Mycosis Fungoides (patches-plaques)


title: Mycosis Fungoides (patches-plaques)  sample 24


title: reactive skin lesions (inflammatory dermatosis) sample 23


title: reactive skin lesions (inflammatory dermatosis) sample 25


title: H9 embryonic stem cells, EHT, CD34 positive CD43 positive sorted population, biological rep2

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

description: hESC-HPC_EHT_non-adherent_CD34+CD43+_rep2

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

growth_protocol: Endothelial-to-hematopoietic transition differentiation protocol, as previously described (Lee et al. The Journal of Clinical Investigation 2017), non-adherent day 12 cells were sorted for CD34+CD43+

extract_protocol: Extraction of total RNA using RNeasy Micro Kit (Qiagen) was performed according to the manufacturer's instructions.

tag: tissue/cell source

value: H9 embryonic stem cells


title: H9 embryonic stem cells, EHT, CD34 positive CD43 positive sorted population, biological rep1

description: hESC-HPC_EHT_non-adherent_CD34+CD43+_rep1

label_protocol: In accordance with manufacturer's protocols


title: Mycosis Fungoides (patches-plaques)  sample 19


title: reactive skin lesions (inflammatory dermatosis) sample 17


title: Mycosis Fungoides (patches-plaques)  sample 18


title: CA2 ESCs, CD34 positive CD45 positive GFP positive sorted population, pHIV-ires-eGFP, termed CXCR4-, biological rep2

description: hESC-HPC_(pHIV-ires-eGFP)_CD45+CD34+GFP+

growth_protocol: Cytokines & BMP4 differentiation protocol, as previously described (Chadwick et al. Blood 2013), sorted on EB day 16

treatment_protocol: Dissociated on EB day 14 and transduced with pHIV-ires-eGFP, in Cytokines & BMP4 media for 48 h

value: CA2 embryonic stem cells


title: Mycosis Fungoides (patches-plaques)  sample 20


title: CA2 ESCs, CD34+ CD45+ GFP- sorted population, pHIV-CXCR4-ires-eGFP, termed CXCR4-, biological rep1

description: hESC-HPC_(pHIV-CXCR4-ires-eGFP)_CD45+CD34+GFP-

treatment_protocol: Dissociated on EB day 14 and transduced with pHIV-CXCR4-ires-eGFP, in Cytokines & BMP4 media for 48 h

value: CD34 positive CD45 positive GFP negative sorted population, pHIV-CXCR4-ires-eGFP, termed CXCR4-


title: CA2 ESCs, CD34 positive CD45 positive GFP negative sorted population, pHIV-ires-eGFP, termed CXCR4-, biological rep3

description: hESC-HPC_(pHIV-ires-eGFP)_CD45+CD34+GFP-


title: Human umbilical cord blood, CD34 positive CD45 positive CD38 negative sorted population, biological rep2

growth_protocol: Non-cultured, human cord blood mononuclear cells

value: Cord blood


title: Human umbilical cord blood, CD34 positive CD45 positive CD38 negative sorted population, biological rep1


title: Human bone marrow, CD34 positive CD45 positive sorted population, biological rep1

growth_protocol: Non-cultured, human bone marrow mononuclear cells

value: Bone marrow


title: Mycosis Fungoides (patches-plaques)  sample 21


title: CA2 ESCs, CD34+ CD45+ GFP+ sorted population, pHIV-CXCR4-ires-eGFP, termed CXCR4+, biological rep2

description: hESC-HPC_(pHIV-CXCR4-ires-eGFP)_CD45+CD34+GFP+_rep2

value: CD34 positive CD45 positive GFP positive sorted population, pHIV-CXCR4-ires-eGFP, termed CXCR4+


title: reactive skin lesions (inflammatory dermatosis) sample 29


title: reactive skin lesions (inflammatory dermatosis) sample 15


title: Mycosis Fungoides (patches-plaques)  sample 13


title: Mycosis Fungoides (patches-plaques)  sample 16


title: Mycosis Fungoides (patches-plaques)  sample 14


title: Mycosis Fungoides (patches-plaques)  sample 11


title: reactive skin lesions (inflammatory dermatosis) sample 12


title: reactive skin lesions (inflammatory dermatosis) sample 5


title: reactive skin lesions (inflammatory dermatosis) sample 7


title: CS_SKBR3_GFPx2-DFO_Batch1_02122014


title: reactive skin lesions (inflammatory dermatosis) sample 10


title: CA2 ESCs, CD34+ CD45+ GFP+ sorted population, pHIV-CXCR4-ires-eGFP, termed CXCR4+, biological rep1

description: hESC-HPC_(pHIV-CXCR4-ires-eGFP)_CD45+CD34+GFP+_rep1


title: reactive skin lesions (inflammatory dermatosis) sample 9


title: Mycosis Fungoides (patches-plaques)  sample 3


title: Mycosis Fungoides (patches-plaques)  sample 8


title: SH-Sy5y CTRL-Rep3

city: Singapore

first: Meng How

last: Tan

address: 60 Biopolis Street, Genome Building #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Mapped the reads against the human genome assembly hg19 with STAR
Uniquely mapped reads with mapping quality ≥ 20 were reordered, sorted, and assigned group information
Duplicates were removed using Picard
Local realignment and recalibration were then performed with GATK toolkit
Variants were next called by samtools mpileup against the position list from RADAR editing database
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files

source_name: SH-Sy5y CTRL

growth_protocol: Cells were grown in DMEM suppl with 10% FBS and 2mM L-Glu; 1X Pen/Strep

extract_protocol:
Cells were harvested and RNA was purified using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

tag: genotype/variation

value: wild type


title: SH-Sy5y_A2OE-Rep1

value: ADAR2 overexpression


title: SH-Sy5y_SF9KD-Rep2

value: SRSF9 knockdown


title: reactive skin lesions (inflammatory dermatosis) sample 1


title: Mycosis Fungoides (patches-plaques)  sample 6


title: SH-Sy5y_A2OE-Rep2


title: SH-Sy5y_SF9KD-Rep1


title: reactive skin lesions (inflammatory dermatosis) sample 4


title: Mycosis Fungoides (patches-plaques)  sample 2


title: SH-Sy5y_A2OE-Rep3


title: SH-Sy5y_A2OE+SF9KD-Rep3

value: ADAR2 overexpression and SRSF9 knockdown


title: SH-Sy5y_SF9KD-Rep3


title: SH-Sy5y_A2OE+SF9KD-Rep1


title: Human_DSC_Foxo1KD_ rep1

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the reference genome using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
Genome_build: human (hg19)
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each sample.

source_name: Endometrial stromal fibroblasts

value: decidualizing endometrial stromal cells

value: siRNA targeting FOXO1


title: SH-Sy5y CTRL-Rep1


title: SH-Sy5y_A2OE+SF9KD-Rep2


title: Human_DSC_Foxo1KD_ rep2


title: DNase-seq from kidney tubule cell (ENCLB888MCL)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR175IWT/
***************
biological replicate number: 1
technical replicate number: 3
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR175IWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB888MCL
instrument models: Illumina HiSeq 2000,Illumina NextSeq 500

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens female adult (80 years) kidney tubule primary cell

extract_protocol: not provided

value: kidney tubule cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 80 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS546UCS at ENCODE; https://www.encodeproject.org/ENCBS546UCS/

value: Derived from ENCODE donor ENCDO421EJG; https://www.encodeproject.org/ENCDO421EJG/


title: DNase-seq from kidney tubule cell (ENCLB108PBP)

description:
https://www.encodeproject.org/experiments/ENCSR175IWT/
***************
biological replicate number: 1
technical replicate number: 2
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR175IWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB108PBP


title: DNase-seq from kidney tubule cell (ENCLB883POS)

description:
https://www.encodeproject.org/experiments/ENCSR175IWT/
***************
biological replicate number: 1
technical replicate number: 1
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR175IWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB883POS
instrument models: Illumina HiSeq 2000,Illumina NextSeq 500


title: Human_DSC_Foxo1KD_ rep3

tag: cell type

tag: treatment


title: SH-Sy5y CTRL-Rep2


title: WT HEK293

data_processing:
The raw reads were mapped against the human genome assembly hg19 with STAR
Uniquely mapped reads with mapping quality ¡Ý 20 were reordered, sorted, and assigned group information using Picard
Mark duplicates with Picard
Local realignment around indels and base quality score recalibration were performed with GATK toolkit
VCF files were generated by samtools mpileup only considering the position list from RADAR editing database
Genome_build: hg19
Supplementary_files_format_and_content: count

source_name: HEK 293T cells

value: WT ( no overexpression)

value: HEK 293T


title: HEK293+ADAR2+SRSF9

value: with SRSF9 and ADAR2 overexpression


title: HEK293+ADAR2

value: with only ADAR2 overexpression


title: SRSF9-ADAR2_eCLIP seq_2

data_processing:
Mapped the reads against the human genome assembly hg19
Call the peaks
Genome_build: hg19
Supplementary_files_format_and_content: peak list

growth_protocol: DMEM+10%FBS; 1X L-Glu; 1X Pen/strep

extract_protocol:
Cells were lysed in iCLIP lysis buffer with short pulses of sonication using the bioruptor. DNA was removed from the cell lysate by Turbo DNase treatment and RNA was fragmented by 5 minute-treatment with RNase I at 37⁰C.
Lysates were incubated with MYC-coupled Protein G Dynabeads (Invitrogen) for 4 hours at 4⁰C, and then eluted and transferred overnight onto nitrocellulose membrane. RNA-protein complex were cut and the bound complex was treated with Proteinase K (New England Biolabs) to remove the proteins. The RNA was then extracted by phenol:chloroform method and concentrated using RNA Clean & Concentrator-5 (Zymo research). The eluted RNA was reverse transcribed, ligated with adaptors, and PCR amplified to make the library.

value: with only SRSF9 overexpression

tag: antibody

value: anti-SRp30c(SRSF9) (sc-134036, Santa Cruz)


title: SRSF9-ADAR2_eCLIP seq_1


title: LPS_IC_DAPT_REP2_003

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
bcl2fastq2 Conversion Software v2.20 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using STAR version 2.5.0a with parameters --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outStd Log --outSAMunmapped within --outSAMtype BM SortedByCordinate limitGenomeGenerateRAM 40,000,000 --limitIObufferSize 40,000,000 --outWigType wiggle --chimSegmentMin 21
bam files were merge using picard and remove duplicate or PCR product contamination
Raw count from each samples were generated using HT-Seq program with parameters --HTSeq.GenomicArrayOfSets("auto", stranded = True)
Genome_build: mm10
Supplementary_files_format_and_content: tab-limited files with raw counts value

organism: Mus musculus

source_name: Bone marrow

growth_protocol: To generate bone marrow derived macrophages (BMDMs),bone marrow cells were plated in non-tissue culture treated plates (Hycon, Thailand) and cultured at 37°C, 5% CO2 in 8 mL of media containing DMEM supplemented with 10% Fetal Bovine Serum, HEPES, sodium pyruvate , streptomycin/penicillin G (all from LONZA, USA or Hyclone, UK), 5% (v/v) horse serum (Thermo Scientific, USA) and 20% (v/v) L929-conditioned media. Three mL of fresh DMEM media supplemented with 20% L929-conditioned media and 5% horse serum was added to the culture at day 4. Cells were harvested at the day 7 and used for all the experiments.

extract_protocol:
Total RNA samples were extracted from LPS/IC-activated BMDMs in the presence of DMSO or GSI for 1 hr using an RNeasy Mini Kit (Qiagen, USA). RNA samples were assessed for quality using an Agilent 2100 Bioanalyzer (Agilent, USA) and quantified using a Qubit 3.0 fluorometer (Life Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were primed overnight with recombinant murine IFNg (10 ng/mL) (BioLegend, USA) and washed twice by media and warm PBS, respectively. Salmonella LPS (100 ng/mL) (Sigma-Aldrich, USA), rabbit IgG against ovalbumin (OVA) (GeneTex, USA) and IgG-opsonized OVA (immune complex) were added to activate macrophages as indicated. Gamma secretase inhibitor (GSI), DAPT (25 µM) (Calbiochem, USA) and vehicle control DMSO (0.01%) (Sigma-Aldrich, USA) were added to macrophages.

tag: strain

value: Bone marrow

value: 8-10 weeks


title: LPS_IC_DAPT_REP2_002

tag: tissue


title: input RNA


title: LPS_IC_DAPT_REP2_001


title: LPS_IC_DAPT_REP1_004


title: LPS_IC_DAPT_REP1_003


title: SRSF9+ADAR2_eCLIP seq_2


title: LPS_IC_DMSO_REP2_004


title: LPS_IC_DMSO_REP2_003


title: LPS_IC_DMSO_REP2_002


title: LPS_IC_DAPT_REP1_002


title: SRSF9+ADAR2_eCLIP seq_1


title: LPS_IC_DMSO_REP1_003


title: LPS_IC_DAPT_REP1_001


title: Pogz-KO fetal liver. Biological replicate 3

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

state: MD

address: 1050 Boyles St.

department: MCGP

institute: NCI

description: Gene expression data from E14.5 Pogz-KO fetal liver.

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays in Affymetrix hybridization oven at 45C, 60 rpm for 16 hrs. Washing steps and staining were performed on Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 with AutoLoader. Data were collected using Affymetrix GeneChip Command Consol (AGCC) software.

data_processing:
Data was analyzed using the GeneSpring software workflow (Agilent Technologies Inc). The cutoff value was set at ±1.5 fold and the false discovery rate at P=0.05.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.28061

source_name: Fetal liver at E14.5

label_protocol: RNA (100 ng) was reverse transcribed and biotin labeled using the Affymetrix 3' IVTexpress Labeling Kit according to the manufacturer's instructions.

extract_protocol: standard extraction method

treatment_protocol: Fetal livers were extracted from E14.5 Pogz+/+ and Pogz-/- embryos, single cell solution generated by mincing the livers in ice cold DPBS and filtering through a cell strainer.

tag: strain background

value: congenic (backcrossed more than 10 generations) C57BL/6

value: Pogz-KO

tag: developmental stage

value: Fetal liver


title: Pogz-WT fetal liver. Biological replicate 2

description: Gene expression data from E14.5 Pogz-WT fetal liver.

value: Pogz-WT


title: LPS_IC_DMSO_REP2_001


title: Pogz-WT fetal liver. Biological replicate 1


title: Pogz-KO fetal liver. Biological replicate 2


title: LPS_IC_DMSO_REP1_002


title: C57BL6.JARID2_KO.SUZ12.iWTr_8days

city: New York

first: Danny

last: Reinberg

address: 522 First Avenue

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
Bowtie2 v2.2.6 was used to align reads to reference genome with default parameters.
Aligned reads were normalized based on the mapped reads in spike-in Drosophila control.
BedGraph files were generated from the aligned reads using 'genomecov' function in bedtools v2.17.0
BigWig files were generated from BedGraph files using 'bedGraphToBigWig' function in USCS.
Genome_build: mm10

growth_protocol: E14Tga2 and C57BL/6 ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent).

extract_protocol:
Cells were fixed with 1% Formaldehyde. Nuclei was isolated and  chromatin was fragmented. Chromatin immunoprecipitation (ChIP) was performed and the libraries was prepared using the eluted DNA from ChIP.
Eluted DNA from ChIP was repaired to generate blunt 5' P ends using 'EndIT DNA End Repair kit' (Epicentre), 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB).  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Next libraries were size selected using 'Ampure beads' (Beckman Coulter) .  After around 13 cycles of amplification, libraries were cleaned, quantified and pooled.

tag: genotype

value: inducible WT EED rescue  8days JARID2 KO

tag: chip antibody

value: SUZ12, Cell Signaling, #3737


title: LPS_IC_DAPT_REP2_004


title: ko_7: LSD1 KO rep3

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

country: China

institute: Zhejiang University School of Medicine

description:
LSD1 KO rep3: ko_7: LIB031892_TRA00114820
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv

data_processing:
For RNA-seq analysis, raw reads were aligned to hg19 or mm9 using STAR (v2.4.2a) with the parameter “quantMode” set as “GeneCounts” to produce count table for each gene. Differential gene analysis was performed on gene raw counts in R with edgeR package (v3.18.1) (PMID: 22287627) from bioconductor. Read count table was filtered so that genes with at least one count across conditions were kept. The negative binomial generalized log-linear model was used in differential analysis. A FDR cut-off of 0.05 was used to determine significantly differentially expressed genes.
The function analyzeRepeats.pl from Homer (PMID: 20513432) software was used to get raw counts for repeats from RNA-seq data. Differential expression for repeats was performed with edgeR the same way as for genes.
For RNA-seq analysis, raw reads were aligned to hg19 or mm9 using STAR (v2.4.2a) with the parameter “quantMode” set as “GeneCounts” to produce count table for each gene. Differential gene analysis was performed on gene raw counts in R with edgeR package (v3.18.1) (PMID: 22287627) from bioconductor. Read count table was filtered so that genes with at least one count across conditions were kept. The negative binomial generalized log-linear model was used in differential analysis. A FDR cut-off of 0.05 was used to determine significantly differentially expressed genes.
The function analyzeRepeats.pl from Homer (PMID: 20513432) software was used to get raw counts for repeats from RNA-seq data. Differential expression for repeats was performed with edgeR the same way as for genes.
Genome_build: hg19 and mm9

source_name: ex vivo B16 RNA-seq

growth_protocol: MCF-7 cells were cultured in normal DMEM supplemented with 10% FBS and 1% penicillin/streptomycin in 5% CO2 incubator at 37 °C. GFP-labeled B16 cells were transplanted into WT C56BL/6 mice subcutaneously and tumor grew for 14 days.

extract_protocol:
For MCF-7 cells, cell nuclei were obtained by lysing whole cells in hypotonic buffer (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% v/v glycerol, 1 mM DTT, and 0.1% v/v Triton X-100) supplemented with protease inhibitor. For GFP-labeled B16 cells isolated from tumor-bearing immunocompetent mice, intact cells were used for the following steps. After washing with PBS, nuclei/cells were fixed in 1% formaldehyde for 10 min at room temperature, followed by quenching in 125 mM glycine. Nuclei/cells were then washed twice with ice-cold PBS, lysed in ChIP sonication buffer (50 mM HEPES pH7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS) supplemented with protease inhibitor, and were subjected to sonication to obtain DNA fragments of 300-800 bp. Subsequent procedures were carried out by following the Epigenesys protocol (https://www.epigenesys.eu/en/). The following antibodies were used to ChIP: anti-LSD1 (Abcam, cat# ab17721), anti-H3K4me1 (Abcam, cat#ab8895), anti-H3K4me2 (EMDMillipore, cat#07-030), and mouse IgG (Santa Cruz Biotechnology, cat# sc-2025). || For RNA extraction, cells weredirectly lyzed in TRIzol and total RNA was extracted according to manufacture's instructions.
ChIP-seq libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, cat#E7370L) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, cat# E7335L) according to the manufacture’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at HiSeq 2500 (Illumina) to generate 50 bp reads from single-end. || Purified total RNA from MCF-7 cells or GFP-labeled B16 cells isolated from tumor-bearing immunocompetent mice was quantified by Qubit (Invitrogen) and analyzed by Agilent Bioanalyzer to assess RNA integrity. 1 μg RNA (RIN>9) was used to generate rRNA-depleted RNA with NEBNext® rRNA Depletion Kit (New England Biolabs, cat# E6310S) or poly(A)+ RNA with Magnetic mRNA Isolation Kit (New England Biolabs, cat# S1550S) according to the manufacturer’s instructions. The rRNA-depleted or poly(A)+ RNA was subjected to Agilent Bioanalyzer to ensure the complete removal of rRNA, and then used to generate directional RNA library with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, cat# E7760L) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, cat# E7335L) according to the manufacturer’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at HiSeq 2500 or Nextseq 500 (Illumina) to generate 50 bp reads (MCF-7) or 75 bp (B16) from paired-ends.

treatment_protocol: MCF-7 cells were infected with lentiviral shRNA targeting scramble or LSD1, and selected for 6-8 days before sample collections. B16 tumors grew in mice for 14 days before being excised and digested with collagenase for single cell suspension. GFP+ B16 cells were sorted.

value: B16 tumor transplanted in C56BL/6 mice

tag: molecule

value: Poly-A enriched RNA


title: dko_10: LSD1/MDA5 DKO rep3

description:
LSD1/MDA5 DKO rep3: dko_10: LIB031892_TRA00114823
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: dko_8: LSD1/MDA5 DKO rep1

description:
LSD1/MDA5 DKO rep1: dko_8: LIB031892_TRA00114821
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv

value: Ribosome depleted RNA


title: ko_5: LSD1 KO rep1

description:
LSD1 KO rep1: ko_5: LIB031892_TRA00114818
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: ko_6: LSD1 KO rep2

description:
LSD1 KO rep2: ko_6: LIB031892_TRA00114819
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: LPS_IC_DMSO_REP1_004


title: Pogz-WT fetal liver. Biological replicate 3

tag: genotype/variation


title: ctl_1: Scramble rep1

description:
Scramble rep1: ctl_1: LIB031892_TRA00114815
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: ctl_4: Scramble rep3

description:
Scramble rep3: ctl_4: LIB031892_TRA00114817
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: Pogz KO fetal liver. Biological replicate 1


title: LPS_IC_DMSO_REP1_001


title: C57BL6.MTF2_KO.SUZ12.iWTr_8days

value: inducible WT EED rescue  8days, MTF2 KO


title: C57BL6.JARID2_MTF2_WT.SUZ12.iWTr_8days

value: inducible WT EED rescue 8days, JARID2/MTF2 WT


title: C57BL6.JARID2_MTF2_dKO.SUZ12.iWTr_24hr

value: inducible WT EED rescue  24hr, JARID2/MTF2 dKO


title: C57BL6.MTF2_KO.SUZ12.iWTr_24hr

value: inducible WT EED rescue  24hr, MTF2 KO


title: C57BL6.JARID2_MTF2_dKO.SUZ12.iWTr_8days

value: inducible WT EED rescue  8days, JARID2/MTF2 dKO


title: ctl_2: Scramble rep2

description:
Scramble rep2: ctl_2: LIB031892_TRA00114816
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: C57BL6.JARID2_MTF2_WT.SUZ12.iWTr_24hr

value: inducible WT EED rescue  24hr, JARID2/MTF2 WT


title: C57BL6.JARID2_KO.SUZ12.iWTr_24hr

value: inducible WT EED rescue  24hr, JARID2 KO


title: C57BL6.JARID2_KO.SUZ12.iWTr_12hr

value: inducible WT EED rescue  12hr, JARID2 KO


title: C57BL6.JARID2_MTF2_dKO.SUZ12.iWTr_12hr

value: inducible WT EED rescue  12hr, JARID2/MTF2 dKO


title: C57BL6.SUZ12.iMTr_36hr

value: inducible MT EED rescue  36hr


title: dko_9: LSD1/MDA5 DKO rep2

description:
LSD1/MDA5 DKO rep2: dko_9: LIB031892_TRA00114822
2018-03-01_rnaseq_mm_counts.csv
2018-03-22_repeat_count_mm.csv


title: C57BL6.SUZ12.iMTr_12hr

value: inducible MT EED rescue  12hr


title: C57BL6.JARID2_MTF2_WT.SUZ12.iWTr_12hr

value: inducible WT EED rescue  12hr, JARID2/MTF2 WT


title: C57BL6.HA_EED.iMTr_36hr


title: C57BL6.SUZ12.iWTr_12hr

value: inducible WT EED rescue  12hr


title: C57BL6.SUZ12.iWTr_36hr

value: inducible WT EED rescue  36hr

value: SUZ12, Cell Signaling, #3737


title: C57BL6.HA_EED.iMTr_12hr


title: C57BL6.HA_EED.iWTr_36hr


title: C57BL6.HA_EED.iWTr_12hr


title: C57BL6.MTF2_KO.SUZ12.iWTr_12hr

value: inducible WT EED rescue  12hr, MTF2 KO


title: single cell RNA-seq batch 6

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

description:
facs_indexing.txt
HSCi_umitab.txt.gz

data_processing:
Bulk RNA seq data: Sequencing reads were processed using the blue collar bioinformatics (BcBio, https://github.com/chapmanb/bcbio-nextgen) RNA-seq pipeline. Briefly, after removal of Illumina adapter sequences with cutadapt, RNA-seq reads were mapped to the mouse genome (UCSC mm10) assembly using STAR with default parameters. Post alignment quantification was performed with featureCount. Read count data were then transformed with the variance stabilizing method from DESeq2.
WGBS data: (1) Quality control: quality trimming and adapter trimming of bisulfite sequencing data were done using Bismark v.0.19.0 with default parameters. Alignment and methylation calling of reads were also done using Bismark v.0.19.0. (2) Mapping: Methylation data were analysed using BiSeq v.1.18.0, CpG clusters were defined by 20 CpG sites covered in the majority of samples (3 out of 4), with a max. distance of 100 base pairs to nearest CpG cluster. (3) Differentially methylated regions: If methylation differences exceeded over 30% between the samples, differentially methylated regions were identified. (4) SuperDMRs: were defined by merging DMR together with at maximum distance of 100 base pairs to their nearest DMR neighbour. SuperDMRs were annotated to genes and enhancers by means of Granges object. In case of any overlaps the superDMRs were identified in genes/enhancers
sc RNA seq data: bcl2fastq/2.15.0.4  Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.  Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.  Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.  Genome_build: mm9  Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Genome_build: mm10

source_name: batch AB382

extract_protocol: Single HSCs were index sorted into cold 384-well capture plates containing 2 ul of cell lysis solution and barcoded poly(T) RT primers for scRNA-seq. cDNA from barcoded single cells was pooled using an automated pipeline  (Jaitin, D.A., et al. Science 2014). The pooled sample was amplified in-vitro and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during subsequent steps (ligation, RT, and PCR) (Jaitin, D.A., et al. Science 2014)

value: HSC

tag: selection markers

tag: cfp status

value: mixed

tag: mouse #

value: batch 6


title: single cell RNA-seq batch 1

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB377

value: batch 1


title: single cell RNA-seq batch 8

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB384

value: batch 8


title: Whole genome bisulphite sequencing HSC CFP Dim Pool 1

source_name: HSC CFP Dim Pool 1

extract_protocol:
 HSCs were lysed in 10 ul M-digestion buffer and 1 ul proteinase K both from the EZ DNA Methylation-Direct Kit (Zymo Research), and incubated for 20 min at 50 degrees. Bisulfite conversion of DNA and library preparation were performed using the Pico Methyl-Seq Library Prep Kit (Zymo Research) and sequenced on a NextSeq500 (Illumina)
 Libraries from two pooled replicates of RA-CFP-dim and –bright HSCs were sequenced on a NextSeq500

value: dim

value: Pool C

tag: extract protocol

value: Primary RA-CFP-dim and –bright HSCs (L-S+K+, CD150+, CD48-, CFP+, ~20% top and bottom) were isolated from the bone marrow of the -60/DR5-TA-RA-CFP  mouse  and pooled in order to obtain 1000 HSCs per replicates. .


title: single cell RNA-seq batch 2

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB378

value: batch 2


title: Whole genome bisulphite sequencing HSC CFP Dim Pool 2

source_name: HSC CFP Dim Pool 2

value: Pool D


title: single cell RNA-seq batch 4

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB380

value: batch 4


title: single cell RNA-seq batch 5

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB381

value: batch 5


title: Whole genome bisulphite sequencing HSC CFP Bright Pool 2

source_name: HSC CFP Bright Pool 2

value: bright


title: Bulk RNA-seq HSC CFP Dim samples 1

source_name: HSC CFP Dim samples 1

extract_protocol:
HSCs were separated into three groups depending on their CFP levels (~20% brightest, dimmest and an intermediate group) and 400-1000 cells were sorted into 50 ul of LiDS lysis/binding buffer (Life Technologies). mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life Technologies), washed and eluted with 10 ul of 10 mM Tris-HCl buffer (pH 7.5)
To produce gene expression libraries, a derivation of the protocol used for generating the single cell expression libraries was used (Jaitin, D.A., et al. Science 2014).


title: Bulk RNA-seq HSC CFP Dim samples 4

source_name: HSC CFP Dim samples 4


title: Bulk RNA-seq HSC CFP Intermediate sample 3

source_name: HSC CFP Intermediate sample 3

value: intermediate


title: Bulk RNA-seq HSC CFP Dim samples 2

source_name: HSC CFP Dim samples 2


title: Whole genome bisulphite sequencing HSC CFP Bright Pool 1

source_name: HSC CFP Bright Pool 1


title: Bulk RNA-seq HSC CFP Intermediate sample 2

source_name: HSC CFP Intermediate sample 2


title: Bulk RNA-seq HSC CFP Bright sample 3

source_name: HSC CFP Bright sample 3


title: Bulk RNA-seq HSC CFP Bright sample 4

source_name: HSC CFP Bright sample 4


title: Bulk RNA-seq HSC CFP Bright sample 1

source_name: HSC CFP Bright sample 1


title: Bulk RNA-seq HSC CFP Bright sample 2

source_name: HSC CFP Bright sample 2


title: single cell RNA-seq batch 7

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB383

value: batch 7


title: single cell RNA-seq batch 3

description:
facs_indexing.txt
HSCi_umitab.txt.gz

source_name: batch AB379

value: batch 3


title: nrpd1 rep2  [smallRNA-Seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were  mapped to TAIR10  genome using bowtie v0.12.2 with parameters - -a -p 4 -f -S -v 0
The TAIR10 genome was split into 500bp windows and the read counts of 24-nt reads in every window were normalized to reads per 10 million (RPTM) by the total number of clean reads that mapped to the nuclear genome .
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPTM values for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Total RNA was extracted from 1 g samples of 10-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for small RNA-seq

value: seedlings


title: hda6 rep2  [smallRNA-Seq]


title: nrpe1 rep2  [smallRNA-Seq]


title: arid2/3/4 rep2  [smallRNA-Seq]


title: Bulk RNA-seq HSC CFP Dim samples 3

source_name: HSC CFP Dim samples 3

value: HSC


title: WT rep2  [smallRNA-Seq]

value: wild type


title: Bulk RNA-seq HSC CFP Intermediate sample 4

source_name: HSC CFP Intermediate sample 4


title: Bulk RNA-seq HSC CFP Intermediate sample 1

source_name: HSC CFP Intermediate sample 1


title: hda6 rep1  [smallRNA-Seq]

value: had-/-


title: arid2/3/4 rep1  [smallRNA-Seq]


title: nrpe1 rep1  [smallRNA-Seq]


title: WT [ChIP-Seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.3.4 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f BAM -p 1e-3 -g 1.2e8  --bdg --nolambda --nomodel
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: histone H4K5 acetylation (abcam, ab51997)


title: arid2/3/4 [ChIP-Seq]


title: epcr1/2 rep1  [smallRNA-Seq]


title: nrpd1 rep1  [smallRNA-Seq]


title: epcr1/2 [ChIP-Seq]


title: WT rep1  [smallRNA-Seq]


title: epcr1/2 rep2  [smallRNA-Seq]


title: FA_CLIP_mock_2

first: Lianhuan

last: Wei

address: Chengfu road 202

department: College of chemistry and Molecular Engineering

institute: Peking university

description: Non-specific IP RNA

data_processing:
Adapter removing (used Cutadapt).
Reads were mapped to TAIR10 by bowtie.
PARAlyzer was used to identify mutation based peaks. At least two mutations sites are needed in each peak.
To call peaks based on enrichment, a previously reported method (Lijia Ma et al. 2017) was used (FA-CLIP/input).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_processed.txt: Tab-delimited text files.
Supplementary_files_format_and_content: FA_CLIP_input_1_processed.txt: RPKM abundance measurements.
Supplementary_files_format_and_content: FA_CLIP_input_2_processed.txt: RPKM abundance measurements.
Supplementary_files_format_and_content: FA_CLIP_mock_1_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.
Supplementary_files_format_and_content: FA_CLIP_mock_2_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.
Supplementary_files_format_and_content: FA_CLIP_1_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.
Supplementary_files_format_and_content: FA_CLIP_2_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.

source_name: 14-day-old seedlings

growth_protocol: All the Arabidopsis thaliana plants were grown on 1/2 Murashige and Skoog (MS) medium or soil under long day conditions (16 hr light/8 hr dark) at 22°C. The T-DNA insertion mutant line ect2 (SALK_002225) was obtained from the Arabidopsis Biological Resource Center.

extract_protocol:
Grind in Liquid N2.
NEBNext Ultra RNA Library Prep Kit for Illumina kit (NEB) for FA-CLIP input sample, NEB Next Multiplex Small RNA Library Prep Set for Illumina (NEB) for FA-CLIP and mock samples.

treatment_protocol: Formaldehyde fixation and crosslinking.

tag: ecotype/background

tag: age

value: 14 days

tag: ip antibody

value: ANTI-FLAG M2 Magnetic Beads (Sigma, M8823, Lot# SLBS8760)


title: ect2_2

description: mRNA

data_processing:
Adapter removing used Cutadapt.
Mapping to TAIR10 by Tophat.
RPKM were calculated by Cufflink.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_processed.txt: Tab-delimited text files include RPKM values for each Sample.

growth_protocol: All the Arabidopsis thaliana plants were grown on 1/2 Murashige and Skoog (Geula et al.) medium or soil under long day conditions (16 hr light/8 hr dark) at 22°C.

extract_protocol:
Total RNA was extracted by adding TRIzol into the ground samples. mRNA was then isolated using Dynabead oligos (dT)25 (Thermo).
100 ng of the extracted mRNA was used as the template for the library construction using an NEBNext Ultra RNA Library Prep Kit for Illumina kit (NEB).

treatment_protocol: Normal growth condition.

value: ECT2 T-DNA insertion mutant


title: ect2_1

description: mRNA


title: Col_0_2

description: mRNA


title: FA_CLIP_mock_1

description: Non-specific IP RNA


title: Col_0_1

description: mRNA


title: DNase-seq from kidney tubule cell (ENCLB997AWQ)

description:
https://www.encodeproject.org/experiments/ENCSR175IWT/
***************
biological replicate number: 2
technical replicate number: 1
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR175IWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB997AWQ
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens male adult (62 years) kidney tubule primary cell

value: kidney tubule cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 62 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS947UTL at ENCODE; https://www.encodeproject.org/ENCBS947UTL/

value: Derived from ENCODE donor ENCDO335XPZ; https://www.encodeproject.org/ENCDO335XPZ/


title: HCT116_invivo_DBDD_SC6

city: Rehovot

first: Eran

last: Kotler

address: 234 Herzl st.

country: Israel

institute: Weizmann Institute of Science

description:
processed data file: HCT116_invivo_DBDD.csv
in vivo enrichment in formed tumors

data_processing:
Paired-end reads were merged using Usearch (http://www.drive5.com/usearch/) setting a minimal overlap of 80 and merge length of 180-220. In runs containing multiple barcoded samples, these were un-pooled by sample barcodes (barcoded primers used for each sample are specified in Table S1). Variant sequences were extracted by matching the read-ends (primer sequences) to the wild-type p53 sequence and variants were mapped to the designed synthetic library. A minimal coverage of >200 reads for each sequence variant at the first experimental time point was required. In vitro relative fitness scores (RFS) were calculated by taking the median of the log (base 2) enrichment/depletion of each variant along the 3 latter time points. In vivo and 3D enrichment scores were defined as the median log (base 2) enrichment/depletion of each variant at the experiment end points (formed tumors/spheroids) compared to its abundance in the injected/seeded population. See STAR methods in the associated publication for details.
Genome_build: Not applicable
Lowly-processed data files:
The following files contain sequences of variants with their corresponding relative fraction of reads at different time-points or experimental conditions. Sequences were not mapped to the reference library, normalized to other sub-libraries, or filtered (other than the requirement for a minimal number of reads at first time point).
H1299_TC_DBDA.csv - Sub-library A tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDB.csv - Sub-library B tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDC.csv - Sub-library C tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDD.csv - Sub-library D tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDA_rep2.csv - Biological replication of time course experiment with sub-library A in H1299.
H1299_TC_DBDB_rep2.csv - Biological replication of time course experiment with sub-library B in H1299.
HCT116_TC_DBDD.csv - Sub-library D tissue-culture time course experiment in HCT116 cells.
HCT116_invivo_DBDD.csv - Sub-library D in vivo enrichment assay (fraction of reads of sequence variants in the injected pool (T0) and in formed subcutaneous tumors).
HCT116_3dCulture_DBDD.csv - Small-scale library measurements comparing relative growth in 2D and 3D culture settings (fraction of reads of sequence variants in the seeded pool (T0) and in 2D and 3D cultures at end-point).
Processed data files:
The following files contain further-processed data (following mapping of variants to library design, normalization, and calculation of RFS and enrichment scores). See manuscript for further details (STAR methods and additional supplementary information tables).
H1299_RFS_sequence variants.xlsx - In vitro RFS of all sequence variants. Column description: Var_seq - sequence of the variant sub-fragment; Identifier - unique identifier of each library sequence variant; SubLib - sub-library (DBD-A, B, C or D, see Methods); Backbone - background on which the mutation is presented (wt or SNP); Mut_type - mutation type; Position - nucleotide position within the CDS; Seq_change - sequence alteration in the given position; Codon_num - number of first affected codon/residue; AA_change - amino acid change, starting in Codon_num; Sec_mut_position - secondary mutation position, in variants containing multiple alterations; Sec_seq_change - sequence change in Sec_mut_position; Sec_codon_num - number of affected codon/residue by the secondary mutation; Sec_AA_change - amino acid change due to secondary mutation; MutID - Mutation ID from the IARC p53 database (Bouaoun et al., 2016); IARC_Desc - description of mutation in the IARC database; Silent - True for synonymous mutations, otherwise False; RFS_H1299 - Variant relative fitness score measured in H1299 cells. Note: IARC MutID and description are presented for mutations which are present in the database but were not covered by scanning mutagenesis of the DBD (i.e. not created by a single nucleotide substitution, insertion, deletion, amino acid deletion or substitution, dinucleotide substitutions, etc.).
HCT116_RFS_sequence variants.xlsx - in vitro RFS of sequence variants in sub-library “D”, as measured in HCT116 cells. See column descriptions for Table S2.
HCT116_invivo_enrichment_sequence_variants.xlsx - In vivo enrichment scores of single-mutation sequence variants in sub-library “D”. See column descriptions for Table S2.
HCT116_3D_enrichment.xlsx - 3D and 2D enrichment scores of sequence variants in the mini-library “D”. Corresponding in vivo enrichment scores are also shown. See column descriptions for Table S2.

source_name: Colorecteal cancer

growth_protocol: Pooled competition

extract_protocol:
From tissue-culture experiments: To maintain the complexity of the input libraries, PCR reactions were carried out on a genomic DNA (gDNA) amount calculated to contain an average of at least 200 copies of each variant included in the assayed library. Thus, at each time point along the time course experiments, gDNA was purified from a minimum of 1x10^7, 1.3x10^7, 2.5x10^7, and 2.5x10^7 H1299 cells infected with libraries A, B, C and D, respectively. gDNA was purified using DNeasy blood and tissue kit (Qiagen). For each measurement, a two-step nested PCR was performed: First, the entire DBD region was amplified (performed identically for all 4 sub-libraries). Then, in each experiment the relevant sub-library DBD fragment was amplified using primers specific to the modified region in that sub-library. In the first step (performed in multiple tubes to include the required amount of gDNA), each reaction contained a total volume of 100ul with 10ug gDNA, 50ul of Kapa Hifi ready mix X2 (KAPA Biosystems) and 5ul of each (10mM) primer. The parameters for PCR were 950C for 5min, 18 cycles of 94°C for 30s, 65°C for 30s, and 72°C for 30s, followed by one cycle of 72°C for 5 min. The primers used for this reaction were CTGAAGACCCAGGTCCAGATGAAG (Fw) and GGAGAGGAGCTGGTGTTGTTGG (Rv). In the second PCR step each reaction contained a total volume of 50ul with 2.5ul of the first PCR product (uncleaned), 25ul of Kapa Hifi ready mix X2 (KAPA Biosystems) and 2.5ul of each (10mM) primer. The parameters for PCR were as in the first step, performing 24 cycles. Primers used for this reaction included 5 random nucleotides at their 5’-end to increase sequence complexity and facilitate cluster calling during sequencing, and were specific for each of the 4 sub-libraries: sub-library A: Fw- NNNNNTGTCATCTTCTGTCCCTTCCCAGAAA, Rv- NNNNNATGGCGCGGACGCGGGT; sub-library B: Fw-NNNNNCTGTGCAGCTGTGGGTTGATTC, Rv-NNNNNCCAAATACTCCACACGCAAATTTC; sub-library C: Fw-NNNNNCCCTCCTCAGCATCTTATCCGAGT, Rv-NNNNNAGGATGGGCCTCCGGTT; sub-library D: Fw-NNNNNTGTGTAACAGTTCCTGCATGGG, Rv-NNNNNGCAGCTCGTGGTGAGGCT. Alternatively, for sequencing runs which included samples from various experiments or time points, this reaction was performed using alternatively barcoded Fw primers, used to barcode the different experimental samples. These primers included 3 random nucleotides at their 5' to increase sequence complexity followed by a unique 4-nucleotide barcode (see Table S1 for sequences). Amplicons were separated from nonspecific fragments by electrophoresis on a 1% agarose gel stained with EtBr, extracted from the gel and purified using a gel purification kit (Nucleospin). Products were further cleaned using a MinElute PCR Purification kit (Qiagen) and eluted in 12ul DDW. Concentration was measured using a monochromator (Tecan i-control), and sample size and purity were assessed by Tape-station using a high-sensitivity D1K screen tape (Agilent Technologies).   From mouse tumors: Primary tumors were dissected manually and flash-frozen in liquid nitrogen. Although each mouse was injected in a single location, in cases where more than a single clearly separated tumor was visible during dissection, each tumor was collected separately (labeled ‘T2a’, ‘T2b’, etc.). For DNA extraction, samples were thawed and divided to 2ml tubes each containing 25mg tissue. Genomic DNA was extracted using DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. For lysis, each sample was suspended in 180ul ATL buffer and homogenized for 10 minutes in a Qiagen TissueLyser LT with a single 5mm stainless steel bead (Qiagen). Following removal of the bead, 20ul proteinase K were added and samples were incubated for 1 hour at 56°C. Then, after samples cooled down to room temperature, they were supplemented with 4ul RNAse and incubated for 2 minutes at RT. To avoid bias due to tumor heterogeneity, DNA from the entire tumor was purified. Thus, all lysates originating from the same tumor were pooled together and purified using the kit’s columns and the manufacturer’s protocol. Amplicons of the DBD-D region and Illumina library preparations were then prepared as described above.
50ng DNA were used for library preparation for next-generation sequencing, specific Illumina adaptors were added, and DNA was enriched by 14 amplification cycles by a protocol adopted from Blecher-Gonen et al. (Blecher-Gonen et al., 2013). Samples were reanalyzed by Tape-station prior to sequencing.

treatment_protocol: At defined timepoints, genomic DNA was extracted and subjected to PCR amplification of the relevant part of the DNA binding domain of p53

tag: growth media

value: McCoy

tag: time points / samples

value: Tumor SC6

tag: sublibrary

value: D


title: HCT116_invivo_DBDD_SC5

value: Tumor SC5


title: HCT116_invivo_DBDD_SC4

value: Tumor SC4


title: HCT116_invivo_DBDD_SC2B

value: Tumor SC2B


title: HCT116_invivo_DBDD_SC3A

value: Tumor SC3A


title: HCT116_invivo_DBDD_SC2A

value: Tumor SC2A


title: FA_CLIP_2

description: IP RNA

value: transgenic ECT2:ETC2-Flag/ect2

value: 14 days

tag: tissue

value: seedlings

value: ANTI-FLAG M2 Magnetic Beads (Sigma, M8823, Lot# SLBS8760)


title: HCT116_invivo_DBDD_SC3B

value: Tumor SC3B


title: HCT116_invivo_DBDD_SC7

value: Tumor SC7


title: HCT116_TC_DBDD_14d

description:
processed data file: HCT116_TC_DBDD.csv
Tissue culture dynamics in HCT116 cells - sublib D

value: 14 days post infection


title: HCT116_invivo_DBDD_SC1

value: Tumor SC1


title: HCT116_TC_DBDD_2d

value: 2 days post infection


title: HCT116_TC_DBDD_9d

value: McCoy

value: 9 days post infection


title: FA_CLIP_1

description: IP RNA

tag: genotype/variation


title: H1299_TC_DBDA_rep2_14d

description:
processed data file: H1299_TC_DBDA_rep2.csv
Tissue culture dynamics in H1299 cells - sublib A

source_name: Non-small cell lung cancer

value: RPMI

value: A


title: HCT116_invivo_DBDD_T0

value: Time 0 (injected pool)

value: D


title: H1299_TC_DBDB_rep2_2d

description:
processed data file: H1299_TC_DBDB_rep2.csv
Tissue culture dynamics in H1299 cells - sublib B

value: B


title: H1299_TC_DBDB_rep2_14d


title: H1299_TC_DBDA_rep2_9d


title: H1299_TC_DBDB_rep2_6d

value: 6 days post infection


title: H1299_TC_DBDB_rep2_9d


title: H1299_TC_DBDA_rep2_6d


title: T CD8 DN from cHL 3 [gene-level]

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

country: France

institute: INSERM UMR1236

description:
Gene expression of CXCR5- ICOS- CD8+ T cells from cHD lymph node
CD8 DN3.CEL

hyb_protocol: Following fragmentation and end-labeling, 4.7 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Transcriptome Array 2.0 (Affymetrix)

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

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels

source_name: Ex-vivo Tfh

label_protocol: Biotinylated double strand cDNA targets were prepared with the NuGEN Ovation PicoSL WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kitaccording to manufacturer recommendations

extract_protocol: RNA was extracted using AllPrep ARN/ADN kit (Qiagen, Valencia, CA)

tag: pathology

value: Classical Hodgkin Lymphoma

tag: treatment

value: Untreated

tag: cell type

value: CXCR5- ICOS- CD8+ T cells


title: T CD8 DN from cHL 1 [gene-level]

description:
Gene expression of CXCR5- ICOS- CD8+ T cells from cHD lymph node
CD8 DN1.CEL


title: T CD8 DP from cHL 2 [gene-level]

description:
Gene expression of CXCR5+ ICOS+ CD8+ T cells from cHD lymph node
CD8 DP2.CEL

value: CXCR5+ ICOS+ CD8+ T cells


title: H1299_TC_DBDA_rep2_2d


title: T CD8 DP from cHL 3 [gene-level]

description:
Gene expression of CXCR5+ ICOS+ CD8+ T cells from cHD lymph node
CD8 DP3.CEL


title: T CD8 DN from cHL 2 [gene-level]

description:
Gene expression of CXCR5- ICOS- CD8+ T cells from cHD lymph node
CD8 DN2.CEL


title: HCT116_TC_DBDD_6d


title: H1299_TC_DBDD_9d

description:
processed data file: H1299_TC_DBDD.csv
Tissue culture dynamics in H1299 cells - sublib D


title: H1299_TC_DBDD_6d


title: LP3

city: WUHAN

first: Gan

last: Zhao

state: HUBEI

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using illumina Casava 1.8
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie v0.12.9
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 2.0.0.8 and srna-tools-cli v4.3 were used to obtain the potential miRNA and draw the secondary structures.
The available software miREvo and  mirdeep2 2.0.0.8  were integrated to predict novel miRNA through exploring the secondary structure
Genome_build: The cattle reference genome (UMD3.1.66) and gene model annotation files were downloaded directly from the cow genome website (ftp://ftp.ensembl.org/pub/release-69/fasta/bos_taurus/dna/).
Supplementary_files_format_and_content: tab-delimited text files include TPM (transcript per million)  values for each Sample.

source_name: exosomes

extract_protocol:
Blood samples sampled by coccygeal venipuncture and then collected in evacuated blood tubes containing K2EDTA as anticoagulant. Samples were placed immediately into iced water and centrifuged within 30 min at 1,500 × g for 12 min at 4°C. The plasma exosomes were isolated and characterized as described previously 70. In brief, plasma (2 mL) was diluted with an equal volume of 1x PBS (pH 7.4) and centrifuged at 2,000 × g for 30 min at 4°C. The supernatant was then centrifuged at 12,000 × g for 45 min at 4°C. The resultant supernatant fluid (4 mL) filtered through a 0.22-μm filter (Millipore, USA) and transferred to an ultracentrifuge tube and centrifuged at 100,000 × g for 75 min at 4°C (Beckman Optima XE- 90, SW32 Ti rotor). The pellet was suspended in PBS and filtered through a 0.22-μm filter (Millipore, USA) and centrifuged at 100,000 × g for 2 h at 4°C. Finally, the pellet containing the enriched exosome population was resuspended in 50 μL PBS (Hyclone, USA) and stored at -80 °C. Exosomal RNA  were isolated by exoRNeasy Serum/Plasma Midi Kit(#77044, Qiagen, Germany) according to the manufacturer’s instructions. its integrity, purity and concentration were determined using an RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), NanoPhotometer® spectrophotometer (IMPLEN, USA), and Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Chinese Holstein

tag: group

value: LATE  PREGNANCY

value: plasma

tag: Stage


title: H1299_TC_DBDC_14d

description:
processed data file: H1299_TC_DBDC.csv
Tissue culture dynamics in H1299 cells - sublib C

value: 14 days post infection

value: C


title: H1299_TC_DBDB_9d

description:
processed data file: H1299_TC_DBDB.csv
Tissue culture dynamics in H1299 cells - sublib B


title: H1299_TC_DBDB_2d

value: 2 days post infection


title: H1299_TC_DBDA_14d

description:
processed data file: H1299_TC_DBDA.csv
Tissue culture dynamics in H1299 cells - sublib A


title: H1299_TC_DBDC_2d


title: H1299_TC_DBDC_9d

value: 9 days post infection


title: H1299_TC_DBDC_6d

value: RPMI


title: LP1


title: MP2

value: MIDDLE  PREGNANCY


title: H1299_TC_DBDA_2d

value: A


title: LP2


title: H1299_TC_DBDB_14d


title: EP3

value: EARLY  PREGNANCY


title: UP2

value: UNPREGNANCY


title: H1299_TC_DBDA_9d


title: H1299_TC_DBDA_6d

value: 6 days post infection


title: UP3


title: T CD8 DP from cHL 1 [gene-level]

description:
Gene expression of CXCR5+ ICOS+ CD8+ T cells from cHD lymph node
CD8 DP1.CEL

value: Classical Hodgkin Lymphoma


title: H1299_TC_DBDD_14d

value: D


title: EP1


title: epcr1/2 rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR-2.5.2b with parameters  --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20  --alignSoftClipAtReferenceEnds No --readFilesCommand zcat-m 10 --best --strata
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuflink2.0.0 cuffdiff with parameters -p 16 -N
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from 1 g samples of 10-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

value: seedlings

tag: genotype


title: H1299_TC_DBDD_2d


title: arid2/3/4 rep1


title: UP1


title: MP1


title: epcr1/2 [BS-Seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
Bisulfite treated sequenced reads were map to TAIR10 genome assembly using Bismark v 0.19.0  bismark with parameters -N 1 -q --bowtie2 --sam -p 20
Context-dependent (CpG/CHG/CHH/CX) methylation were extracted using bismark_methylation_extractor with parameters --paired-end --no_overlap --report --bedGraph --buffer_size 20G --cytosine_report --CX --comprehensive
Genome_build: TAIR10
Supplementary_files_format_and_content: Bw format files for each chromosome for each cytosine context (CG, CHG, CHH or CX) with following tab-separated information: Chromosome, start coordinate, stop coordinate,and methylation level (methylated cytosines sequenced/total cytosines sequenced).

extract_protocol:
Genomic DNA was extracted from 10-day-old Arabidopsis seedlings with a DNeasy Plant Mini Kit (QIAGEN, 69104)
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bisulfite treatment


title: WT rep1

value: wild type


title: MP3

value: Chinese Holstein


title: WT [BS-Seq]


title: arid2/3/4 [BS-Seq]


title: 19556.DN2_sgPU1.rep2

city: Pasadena

first: Ellen

last: Rothenberg

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

description:
Sorted as LiveLin-CD45+CFP+CD44+CD25+cKit+
DN2_ATAC_sgPU1_ATAC_peaks.txt
DN2_ATAC_sgCtrl_sgPU1.edgeR_diff_expression.txt

data_processing:
ChIP-Sequencing and data analysis: ChIP sequences were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory {Heinz, 2010 #67} for further downstream analysis. In addition, read alignments from the Scid.adh.2c2-PU.1ert2 experiment were filtered against PCR duplicates using Samtools as well as genomic repeats and Broad blacklisted regions using Bedtools (full script provided upon request) prior to tag directory generation. Transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score >= 15, were considered for further analysis.  Regions enriched for histone modifications were identified with findPeaks.pl with the option –style histone against a matched input control. Only regions consistently called in two independent experiments were used for downstream analyses.  Motif enrichment analysis was performed with the findMotifsGenome.pl command in the HOMER package using a 200bp window or a window size defined by the width of each identified peak. Overlapping peaks between samples were derived using mergePeaks.pl (default parameters). Annotation of peaks to nearest genes and genomic regions (e.g. promoters, CG-rich regions, repeat regions) were performed with annotatePeaks.pl (default settings). Tag density plots and heat maps were created with annotatePeaks.pl ( –hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment.
RNA-Sequencing and data analysis:  RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) {Li, 2011 #81} according to the settings in the ENCODE long-rna-seq-pipeline with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. The resulting bam-files were used to create HOMER tag directories (makeTagDirectory with –keepAll setting). For analysis of statistically significance among differently expressed genes the data was raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) or the gene count tables were imported into R and analyzed for differential expression using the DESeq2 package (v1.4.5; https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html)  For data visualization rpkm normalized reads were derived analyzeRepeats.pl command with the options –count exons –¬condenseGenes –rpkm followed by log transformation, and separately performed replicate set normalizations to prevent nondevelopmental differences in gene expression. Processed data for all the, in the study, included RNA-seq samples were derived from HOMER tagdirectories as either raw counts (analyzeRepeats.pl rna mm9 -count exons -condenseGenes -noadj) or rpkm normalized values (analyzeRepeats.pl rna mm9 -count exons -condenseGenes -rpkm). Data is derived as one value per gene and the accession number associated with the highest expressing isoform is displayed (-condenseGenes option).
ATAC-Sequencing and data analysis: ATAC-sequences were mapped to mm9 as described in the Data processing-ChIP section. Additionally, Tag directories with reads mapped to the mitochondrial chromosome filtered were created using the HOMER platform (makeTagDirectory).  ATAC-seq peaks were identified using findPeaks.pl in HOMER (scipt available upon request). Only regions consistently called in two independent experiments were used for downstream analyses. Abundance of ATAC-tags on ATAC or transcription factor ChIP-seq peaks was analyzed in HOMER using the annotatePeaks.pl command.   For differential peak analysis, raw tag counts were derived from the tagdirectories using annotatePeaks.pl with the ”-noadj” setting  was carried out with the EdgeR  and limma (v3.20.9; http://bioconductor.org/packages/release/bioc/html/limma.html)  Bioconductor packages via  HOMER getDifferentialExpression.pl. Differential peaks with adjusted p-value <= 0.05 and log2 fold change >= |1| were considered significantly different.
Genome_build: mm9
Supplementary_files_format_and_content: All genomic coordinates are relative to mm9 mouse assembly.

source_name: Lin- BM derived DN2 cells

extract_protocol: Cell isolation: Fetal livers (FL) were disected from E13.5 (day of plug, E0.5) C57BL/6 animals. Suspensions of FL cells were then prepared, stained for lineage markers using biotin-conjugated lineage antibodies (CD11c, Gr1, TER-119, NK1.1, CD19, F4/80), incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec). Lineage-depleted (Lin−) cells were eluted and stored in liquid nitrogen in freezing media (50% FBS, 40% αMEM, 10% DMSO) for future use. Cell culture:  Frozen lineage depleted FL cells from E13.5 were thawed and used to initiate OP9-DL1 cultures in OP9 medium (α-MEM, 20% FBS, 50 μM β-ME, Pen-Step-Glutamine) supplemented with IL-7 and Flt3L (5 ng/ml each).  Cells were incubated at 7% CO2 and 37°C.  Scid.adh.2C2 cells were cultured in RPMI1640 with 10% fetal bovine serum (Sigma-Aldrich), sodium pyruvate, non-essential amino acids, Pen-Strep-Glutamine and 50 μM β-mercaptoethanol. Cells were incubated at 5% CO2 and 37°C.       FACS staining. For sorting of transduced CD25 enriched FLP derived cells, surface antibodies against c-Kit, CD25, CD44, CD45, Mac1/CD11b were used for staining of Lin- FLP derived CD25+ cells (7AAD-CD45+GFP+CD25+) (EVGFP, PU1WTHA, PU1ENGHA and PU1ETSHA) or CD44+CD25 cells (7AAD-CD45+GFP+CD44+CD25-) (PU1WTHA). Transduced Scid.adh.2c2 cells for Lzr-PU.1 ChIP and RNA-sequencing were sorted as LiveGFP+.  For sorting for primary cell ATAC experiment, thymocytes were pre-depleted with biotin-conjuagated a-CD8a, a-TCRrd, a-TCRb, a-Ter119 followed by MACS magnetic column purifcation as described above.  Depleted thymocytes were stained with CD45, CD44, c-Kit, CD25, and a biotin-conjugated lineage cocktail (CD8a,CD11b,CD11c,CD19,Ly-6G(Gr-1),NK1.1,TER119,TCRrd,TCRb) and were sorted for ETP progenitors (Lin−CD45+c-KithiCD44hiCD25−) or DN3 progenitors (Lin−CD45+c-KitlowCD44lowCD25+).

value: Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J (Cas9) x C57BL/6-Tg(Bcl2)25Wehi/J (Bcl2Tg)

value: Transduced with sgPU.1-CFP

tag: chip (antibody)


title: 19681.DN2_sgPU1.rep3


title: 19680.DN2_sgCtrl_ATAC.rep3

description:
Sorted as LiveLin-CD45+CFP+CD44+CD25+cKit+
DN2_ATAC_sgCtrl_ATAC_peaks.txt
DN2_ATAC_sgCtrl_sgPU1.edgeR_diff_expression.txt

value: Transduced with sgCIntrol-CFP


title: 19553.DN2_sgCtrl_ATAC.rep1


title: 19554.DN2_sgPU1.rep1


title: 19555.DN2_sgCtrl_ATAC.rep2


title: ICAM-1_KO_rep1

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through cutadapt. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data.
Index  of  the  reference  genome  was  download from Tophat official website  and clean reads were aligned to the reference genome using TopHat v2.0.11.
FPKM of each gene was calculated by Cufflinks 2.1.1

source_name: Bone marrow cell

extract_protocol:
LSK cells were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow


title: ICAM-1_KO_rep2


title: WT_rep3


title: ICAM-1_KO_rep3


title: 20166.Scid.adh.2c2.input_for_PU1_ChIP.sgRunx1.rep2

description: 20186_20162_sgRunx1_PU1_IDR_peaks-top-set_15_mm9.annotated.txt

source_name: Scid.adh.2c2 cells

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Transduced with pMxs-PU.1-hNGFR, MSCV-Cas9 and sgRunx1-CFP


title: 20165.Scid.adh.2c2.input_for_PU1_ChIP.sgRunx1.rep1


title: WT_rep1


title: 20164.Scid.adh.2c2.input_for_PU1_ChIP.sgCtrl.rep2

description: 20159_20160_sgCtrl_PU1_IDR_peaks-top-set_15_mm9.annotated.txt

value: Transduced with pMxs-PU.1-hNGFR, MSCV-Cas9 and sgCtrl-CFP


title: WT_rep2


title: 20163.Scid.adh.2c2.input_for_PU1_ChIP.sgCtrl.rep1

value: Transduced with pMxs-PU.1-hNGFR, MSCV-Cas9 and sgCtrl1-CFP


title: 20186.Scid.adh.2c2.PU1_ChIP.sgRunx1.rep1


title: Plasma Gel 5' mod Adapter AD  MD  2

city: Huntsville

first: Richard

middle: M

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Plasma Gel Extracted Modified 5' Adapter Adapter Dimer MAD-DASH
PlasmaGel_Samples_GSLv2-7_23_SL321701

data_processing:
Fastqs from multiple lanes of the same flowcell were merged with cat.
Reads were adaptor trimmed for both 5' adaptors (4 separate) and 3' adaptors. Raw files provided are not trimmed, in accordance with GEO guidelines).
Trimmed reads less than 15 bp were considered "short fails", and within short fails reads of 0 bp length were considered "adapter dimer" (corresponding to no sequence after adapter trimming) while reads with greater than 0 bp were considered "Non AD (adapter dimer) short fails".
Trimmed reads were aligned to pre-miRNA sequences mirBase v19 using bowtie2-2.1.0 with two mismatches allowd and keeping only unique best alignments.  Reads aligning to mutliple locii were assigned to each locii proportionally to the total number of reads. Total non-miRNA aligned reads were counted and considered "non-miRNA usable reads"
Reads as processed above were read into R and library replicates for each condition were summed.  Reads were normalized by downsampling within each group of replicates to a common count value, this table is provided as processed data and named MAD-DASH_count.table.txt
Treatment group comparisons were made by taking respective intra-group downsampled replicates, summing them, downsampling to a common inter-group count, and then performing regression analysis with the R package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text

source_name: human blood plasma

extract_protocol:
RNA was isolated from 1 mL of plasma using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) from Norgen Biotek using manufacturer's protocols.
Libraries were constructed exactly as detailed in "Blocking of targeted microRNAs from next-generation sequencing libraries", Roberts et al, PMID:26209131, with modification to incorporate MAD-DASH treatment. Modification to Roberts et al. 2015 protocol involves a short 4-cycle PCR amplifcation followed by Ampure bead cleanup, MAD-DASH CRISPR RNP in vitro digestion of specific sequences such as adapter dimer for 2 hrs followed by treatment with RNAse A and Proteinase K to inactivate the reaction, then a second 11-cycle PCR to complete library construction before futher cleanup with Ampure Beads or denaturing gel extraction.

treatment_protocol: Brain total RNA was purchased from Invitrogen. For human plasma RNA samples, blood was drawn from patients prior to undergoing colonoscopy. Plasma was isolated within 30 min using standard centrifugation protocol.

tag: library replicate

value: blood plasma


title: 20162.Scid.adh.2c2.PU1_ChIP.sgRunx1.rep2


title: Plasma Gel 5' mod Adapter AD  MD  1

description:
Plasma Gel Extracted Modified 5' Adapter Adapter Dimer MAD-DASH
PlasmaGel_Samples_GSLv2-7_22_SL321700


title: Plasma Gel 5' mod Adapter No MD Control 3

description:
Plasma Gel Extracted Modified 5' Adapter No MAD-DASH Control
PlasmaGel_Samples_GSLv2-7_18_SL321695


title: Plasma Gel 5' mod Adapter AD MD  3

description:
Plasma Gel Extracted Modified 5' Adapter Adapter Dimer MAD-DASH
PlasmaGel_Samples_GSLv2-7_24_SL321702


title: 20160.Scid.adh.2c2.PU1_ChIP.sgCtrl.rep2


title: Rop7-III biological replicate 3 [AR7III_R3]

city: London

first: Eva

last: Frickel

address: 1 Midland Road

department: Host-Toxoplasma Interaction Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.2.11) (Li and Dewey, 2011) was used for the alignment and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 27th May 2015.
Differential expression analysis between the triplicate groups was performed with DESeq2 (version 1.8.1) (Love et al., 2014) after removal of genes with a maximum transcript per million (TPM) value of 1 across all samples in the experiment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: CD8 T-cells_Rop7-III

growth_protocol: Cell were grown in RPMI medium 1640 supplemented with 10% fetal bovine serum, L-glutamine, penicillin/streptomycin, β-mercaptoethanol and recombinant mouse IL-2 (10 ng/ml).

extract_protocol:
RNA was isolated using Trizol and the RNeasy Micro-Kit (Qiagen).
A total of 200 ng of RNA was used to prepare the RNA library using TruSeq mRNA Library Prep Kit v2 (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: Cells were incubated overnight at 37°C and 5% CO2 with ROP7 peptide (10 μM). CD3+ CD8+ H-2Ld-Rop7+ cells were sorted, maintained at 4°C and purity determined to be 90-95%.

value: CD8 T-cells

tag: clone id

tag: incubated with

value: ROP7 peptide (10 μM)

tag: sorted cell type

value: CD3+ CD8+ H-2Ld-Rop7+


title: Rop7-III biological replicate 2 [AR7III_R2]


title: 20159.Scid.adh.2c2.PU1_ChIP.sgCtrl.rep1


title: Plasma Gel 5' mod Adapter No MD Control 1

description:
Plasma Gel Extracted Modified 5' Adapter No MAD-DASH Control
PlasmaGel_Samples_GSLv2-7_16_SL321693


title: Rop7-III biological replicate 1 [AR7III_R1]


title: Plasma Gel 5' Multiplex Adapter AD/mir16  MD  3

description:
Plasma Gel Extracted Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
PlasmaGel_Samples_GSLv2-7_15_SL321692


title: Rop7-II biological replicate 3 [AR7II_R3]

source_name: CD8 T-cells_Rop7-II


title: Plasma Gel 5' Multiplex Adapter mir16 MD  3

description:
Plasma Gel Extracted Multiplex 5' Adapter mir-16-5p MAD-DASH
PlasmaGel_Samples_GSLv2-7_12_SL321689


title: Plasma Gel 5' Multiplex Adapter mir16  MD  1

description:
Plasma Gel Extracted Multiplex 5' Adapter mir-16-5p MAD-DASH
PlasmaGel_Samples_GSLv2-7_10_SL321687


title: Plasma Gel 5' Multiplex Adapter mir16  MD  2

description:
Plasma Gel Extracted Multiplex 5' Adapter mir-16-5p MAD-DASH
PlasmaGel_Samples_GSLv2-7_11_SL321688


title: Plasma Gel 5' Multiplex Adapter AD /mir16 MD  2

description:
Plasma Gel Extracted Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
PlasmaGel_Samples_GSLv2-7_14_SL321691


title: Rop7-I biological replicate 3 [AR7I_R3]

source_name: CD8 T-cells_Rop7-I


title: Rop7-I biological replicate 2 [AR7I_R2]


title: Rop7-I biological replicate 1 [AR7I_R1]


title: Plasma Gel 5' Multiplex Adapter AD MD  3

description:
Plasma Gel Extracted Multiplex 5' Adapter Adapter Dimer MAD-DASH
PlasmaGel_Samples_GSLv2-7_06_SL321730


title: Plasma Gel 5' Multiplex Adapter AD  MD  1

description:
Plasma Gel Extracted Multiplex 5' Adapter Adapter Dimer MAD-DASH
PlasmaGel_Samples_GSLv2-7_04_SL321719