title: WT vs lntR Mutant Dye Swap

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: Biological replicate 2

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 wild type/mutant ratios from a single array experiment.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003-lntR grown on Ribose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Wild type and mutant Bifidobacterium breve UCC2003 cultures were grown separately in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of Ribose as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) until OD600 was 0.5. Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis were performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: strain/background

tag: genotype/variation

value: lntR

tag: carbon source

value: ribose

source_name: Bifidobacterium breve UCC2003 Wild Type grown on Ribose

value: wild type


title: AorticValve_200

status: Public on Mar 14 2018

type: RNA

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by log2-transformation and quantile normalized using the lumi package in R (Du et al 2008)

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: IlluminaTotalPrep™-96 RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted from valve leaflets using RNeasy Plus Universal Mini kit (Qiagen)

tag: tissue

value: aortic valve


title: AorticValve_199


title: AorticValve_205


title: WT vs nagR2 Mutant Dye Swap

description: Biological replicate 2

source_name: Bifidobacterium breve UCC2003-nagR2 grown on Ribose


title: AorticValve_194


title: AorticValve_196


title: WT vs nagR2 Mutant

description: Biological replicate 1


title: AorticValve_198


title: WT vs nagR1 Mutant Dye Swap

description: Biological replicate 2

source_name: Bifidobacterium breve UCC2003-nagR1 grown on Ribose


title: AorticValve_191


title: WT vs nahR Mutant

description: Biological replicate 1

source_name: Bifidobacterium breve UCC2003-nahR grown on Ribose

value: nahR


title: AorticValve_195


title: AorticValve_202


title: AorticValve_192


title: WT vs nahR Mutant Dye Swap

description: Biological replicate 2


title: WT vs lntR Mutant

description: Biological replicate 1


title: AorticValve_190


title: AorticValve_188


title: AorticValve_187


title: AorticValve_197


title: AorticValve_193


title: AorticValve_189


title: WT vs nagR1 Mutant

description: Biological replicate 1


title: AorticValve_182


title: AorticValve_183


title: AorticValve_181


title: AorticValve_184


title: AorticValve_185


title: AorticValve_176


title: AorticValve_180


title: AorticValve_175


title: AorticValve_177


title: AorticValve_178


title: AorticValve_171


title: AorticValve_174


title: AorticValve_164


title: DLD-1Δα-Cat_3D_96h_rep1

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Hybridization and washing was performed according to manufacturers instructions.

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

data_processing: The data were analyzed with the Affymetrix Expression console using standard values, quantile normalization and RMA procedure.

label: Biotin

source_name: DLD-1 subpopulations, cultivated for 96h in collagen type I

label_protocol: Biotinylated cRNA were prepared according to manufacturers instructions.

growth_protocol: DLD-1 subpopulations were cultivated for 96h in 3D collagen type I (1 mg/ml)

extract_protocol: mRNA was isolated according to the manufacturer's instructions using NucleoSpin RNA II Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: no treatment applied

tag: cell line

value: subclone derived from DLD-1 cell line


title: myc-R495X replicate 3

city: Baltimore

first: Jiou

last: Wang

state: MD

address: 615 N. Wolfe St.

country: USA

institute: Johns Hopkins University

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Exon array CEL files were processed with Partek Genomics Suite 6.4 software. RMA probe summarization and normalization was performed with options for GC context and probe sequence adjustment, RMA Background Correction, Quantile Normalization, and summarization with Median Polish. Library files used in this analysis included: HuEx-1_0-st-v2.r2.pgf (Probe Group File), HuEx-1_0-st-v2.r2.qcc (Quality Control Content File), and HuEx-1_0-st-v2.r2.dt1.hg18.core.mps (Meta Probeset File for gene level summarization).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HEK 293T

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: 6x106 HEK293T cells were plated onto 100mm2 plates prior to transfection with either myc-FUS or mutant myc-R495X and pMax-EGFP (Amaxa) marker with Lipofectamine 2000 (Life Technologies).

extract_protocol: Twenty-four hours after transfection, cells were trypsinized and resuspended in FACS Buffer (1X PBS, 100mM EDTA, 1% FBS) and sorted based upon GFP fluorescence. RNA was immediately isolated from sorted cells using phenol-chloroform extraction with TRIzol reagent (Invitrogen) according to manufacturer’s instructions. RNA was further purified using Qiagen’s RNeasy Kit, which included an on-column DNase treatment

treatment_protocol: Not applicable

value: HEK 293T

tag: genotype


title: AorticValve_165


title: DLD-1Δα-Cat_3D_96h_rep3


title: AorticValve_179


title: AorticValve_162


title: DLD-1α-Cat_3D_96h_rep1


title: AorticValve_186


title: AorticValve_166


title: AorticValve_167


title: AorticValve_172


title: AorticValve_170


title: DLD-1α-Cat_3D_96h_rep3


title: AorticValve_163


title: AorticValve_173


title: AorticValve_161


title: myc-R495X replicate 2


title: myc-R495X replicate 1


title: AorticValve_159


title: AorticValve_157


title: AorticValve_156


title: AorticValve_155


title: AorticValve_158


title: AorticValve_152


title: AorticValve_153


title: DLD-1Δα-Cat_3D_96h_rep2


title: AorticValve_148


title: myc-FUS replicate 1

value: myc-FUS


title: AorticValve_150


title: DLD-1α-Cat_3D_96h_rep2


title: AorticValve_147


title: myc-FUS replicate 2


title: AorticValve_143


title: AorticValve_154


title: myc-FUS replicate 3


title: AorticValve_145


title: AorticValve_141


title: AorticValve_140


title: AorticValve_149


title: AorticValve_144


title: AorticValve_139


title: AorticValve_142


title: AorticValve_138


title: AorticValve_151


title: AorticValve_146


title: AorticValve_136


title: AorticValve_137


title: AorticValve_134


title: AorticValve_135


title: AorticValve_132


title: AorticValve_133


title: AorticValve_128


title: AorticValve_131


title: AorticValve_124


title: AorticValve_130


title: AorticValve_127


title: AorticValve_122


title: Baldo untreated roots 2

type: SRA

city: PADOVA

first: Stefano

last: Toppo

address: viale G. Colombo, 3

department: Molecular Medicine

country: Italy

institute: University of Padova

library_source: transcriptomic

data_processing:
Illumina raw reads were preprocessed with FASTX Toolkit 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
Preprocessed reads were mapped with TopHat 2.0.6 (Kim et al., 2013) on the Oryza sativa v. Nipponbare genome, downloaded from the MSU Rice Genome Annotation Project (version 7.0) (Kawahara et al., 2013). Commandline used with -G option to map vs. annotation "gtf" file of MSU genome
Reads multimapped were removed from the final results, together with those reads sharing less than 96% identity with the reference. Finally, read counts were computed using bedtools (Quinlan & Hall 2010)
Functional annotation enrichment of rice genes was carried out using the Argot web server (Falda et al., 2012 and 2016, Lavezzo et al., 2016) which assigns Gene Ontology terms to each input sequence
Raw counts were analyzed with standard differential expression analysis workflow (Anders et al., 2013) and the edgeR bioconductor package (Robinson et al., 2010)
Complete analysis pipeline of differential gene expression was performed using PathwayInspector tool version 1.0 (Bianco et al., 2017). Web site: http://pathwayinspector.dmm.unipd.it/
Genome_build: MSU Rice Genome Annotation Project (version 7.0)
Supplementary_files_format_and_content: File contains raw counts: first column reports gene/locus names from MSU Rice Genome Annotation Project (version 7.0). Remaining colums refer samples as reported in SAMPLES section. Rows report raw counts of mapped reads in the different samples

organism: Oryza sativa Japonica Group

source_name: roots

growth_protocol: Dehulled seeds of Italian rice varieties (O. sativa L. spp. japonica “temperate”) were sterilized for 1 min in 70% ethanol and rinsed 5 times with deionized water. Seeds were sown on water-wetted filter paper in Petri dishes and left to germinate for 48 h at 24 °C in the dark. Uniformly germinated seedlings were transferred to agar-filled (0.55% w/v) seed-holders in an Araponics system (www.araponics.com) with a modified Hoagland solution (Hoagland & Arnon 1938; Table S1). Plants were grown until the vegetative stage V2 (collar formation on the second leaf; Counce et al., 2000) at approximately 6 days in a growth chamber at 26/21 °C, with a 16/8 h photoperiod, an approximate RH of 70%, and light of 120-150 µmol photons m-2 s-1.

extract_protocol:
Total RNA was extracted from both leaves and roots of 3-day treated and untreated plants (not exposed to salt) using an RNeasy Plant Mini Kit followed by in-column DNase treatment (Qiagen, Hilden, Germany). The RNA quality was measured using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).
IGA Technology Services (Udine, Italy) performed RNA sequencing using Illumina techniques on polyA+ RNA.

treatment_protocol: Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.

tag: agent

tag: cultivar

value: Baldo

value: root


title: AorticValve_123


title: AorticValve_119


title: AorticValve_120


title: Testis from wt mouse_rep3

city: shanghai

first: Xuan

last: Shang

state: shanghai

address: No.197, Ruijin 2nd Road, Huangpu District, Shanghai

department: Research Center for Experimental Medicine

country: China

institute: Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: wt3L testis

hyb_protocol: Each slide was hybridized with 1.65ug Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

organism: Mus musculus

source_name: Testis_WT mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using the RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer's recommendations and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: strain background

value: mixed 129Sv/C57BL/6

value: wt

tag: gender

value: male

tag: age

value: 6-8 weeks

value: testis


title: AorticValve_116


title: AorticValve_125


title: Testis from Prss54KO mouse_rep3

description: Prss54ko3L testis

source_name: Testis_Prss54KO mouse


title: AorticValve_126


title: AorticValve_121


title: Testis from Prss54KO mouse_rep2

description: Prss54ko2L testis


title: Baldo untreated roots 1


title: Baldo untreated roots 3


title: Testis from Prss54KO mouse_rep1

description: Prss54ko1L testis


title: AorticValve_117


title: Baldo treated roots 3

value: 100 mM NaCl


title: AorticValve_118


title: Baldo treated roots 2


title: Baldo untreated leaves 2

source_name: leaf blade and sheath

value: leaf


title: Baldo untreated leaves 3


title: Baldo untreated leaves 1


title: Baldo treated leaves 3


title: Testis from wt mouse_rep1

description: wt1L testis


title: Baldo treated leaves 2


title: Testis from wt mouse_rep2

description: wt2L testis


title: AorticValve_114


title: AorticValve_112


title: Baldo treated leaves 1


title: Vialone Nano untreated roots 2

value: Vialone Nano


title: Vialone Nano untreated roots 1


title: Vialone Nano untreated roots 3


title: Baldo treated roots 1


title: AorticValve_113


title: AorticValve_111


title: AorticValve_110


title: AorticValve_115


title: AorticValve_107


title: Vialone Nano treated roots 3


title: AorticValve_109


title: AorticValve_102


title: AorticValve_108


title: AorticValve_104


title: AorticValve_103


title: Vialone Nano treated roots 2


title: AorticValve_106


title: Vialone Nano treated roots 1


title: AorticValve_101


title: Vialone Nano untreated leaves 2


title: AorticValve_105


title: Vialone Nano untreated leaves 3


title: AorticValve_100


title: AorticValve_99


title: AorticValve_98


title: Vialone Nano treated leaves 3


title: Vialone Nano treated leaves 2


title: Vialone Nano treated leaves 1


title: AorticValve_96


title: AorticValve_97


title: AorticValve_91


title: AorticValve_94


title: AorticValve_90


title: Vialone Nano untreated leaves 1


title: AorticValve_88


title: AorticValve_93


title: AorticValve_92


title: AorticValve_85


title: AorticValve_83


title: AorticValve_87


title: AorticValve_95


title: AorticValve_89


title: AorticValve_81


title: AorticValve_78


title: AorticValve_86


title: AorticValve_82


title: AorticValve_84


title: AorticValve_79


title: AorticValve_80


title: AorticValve_77


title: AorticValve_75


title: AorticValve_74


title: AorticValve_72


title: AorticValve_73


title: heat_3

city: Copenhagen

first: Malte

last: Thodberg

address: Blegdamsvej 3B, Building 7 (Maersk Tower)

department: CBMR

country: Denmark

institute: University of Copenhagen

description:
gene_normalized_matrix.tab
gene_count_matrix.tab
TSS_normalized_matrix.tab
TSS_count_matrix.tab
TSSs.bed
YES_heat_plus.bw
YES_heat_minus.bw

data_processing:
Base-calling with Illumina CASAVA v1.6
Removing of 5' adapters and trimming of read ends (keeping from bp 12 to bp 36) and filtering for Q30 over 50% remaining length with Fastx Toolkit v0.0.13
Mapping with Bowtie v0.12.7
Counting 5'-ends per position and shift positions by 1
Tag clustering, quantification and annotation via CAGEfightR 0.3.
Genome_build: ASM294v2
Supplementary_files_format_and_content: sample-wise bigWig files are number of CAGE tags per basepair, group-wise bigWigs are pooled TPM per basepair; bed files are location of TSSs with score column being pooled TPM; matrix files are counts  or normalized TPM for TSSs or Genes.

organism: Schizosaccharomyces pombe

source_name: cells

growth_protocol: Triplicate liquid cultures were grown at 30°C to a density of 5 X 10^6 cells/ml

extract_protocol:
Total RNA was extracted from 108 cells.  In brief, cells were harvested by 5 minutes of centrifugation at 3000 rpm. Pellets were resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to 65˚C preheated acidic phenol-chloroform (Sigma P-1944). After 1 hour of incubation at 65˚C with mixing every 10 minutes, RNA was extracted with chloroform-isoamyl alcohol (Sigma C-0549), ethanol precipitated and resuspended in water.
CAGE libraries were prepared as in Takahashi, H., Lassmann, T., Murata, M. & Carninci, P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7, 542–561 (2012).

treatment_protocol: Media were YES or EMM. For nitrogen starvation, cells were transferred by vacuum filtration From EMM2 to EMM2 without ammonium chloride and incubated for 16 hours at 30°C. Heat shock was imposed by transferring YEL cultures to 39°C for 15 minutes. Oxidative stress was inflicted by treating YEL cultures with 0.5 mM H2O2 for 15 minutes at 30°C.

tag: strain

value: cells

tag: media

value: YES

tag: stress

value: heat


title: heat_1


title: heat_2


title: AorticValve_129

value: aortic valve


title: H2O2_3

description:
gene_normalized_matrix.tab
gene_count_matrix.tab
TSS_normalized_matrix.tab
TSS_count_matrix.tab
TSSs.bed
YES_H2O2_plus.bw
YES_H2O2_minus.bw


title: AorticValve_76


title: H2O2_1


title: H2O2_2


title: exp_2

description:
gene_normalized_matrix.tab
gene_count_matrix.tab
TSS_normalized_matrix.tab
TSS_count_matrix.tab
TSSs.bed
YES_exp_plus.bw
YES_exp_minus.bw


title: exp_3


title: exp_1


title: AorticValve_71


title: EMM_nitro_3

description:
gene_normalized_matrix.tab
gene_count_matrix.tab
TSS_normalized_matrix.tab
TSS_count_matrix.tab
TSSs.bed
EMM_nitro_plus.bw
EMM_nitro_minus.bw

value: EMM

value: nitrogen starvation


title: AorticValve_69


title: resistant CCRF-CEM, mock, total RNA, bio_rep_3

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

description:
Total RNA sample extracted from resistant CCRF-CEM cells, mock.
resistant_mock_3

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3).

data_processing: The scanned TIFF images were analyzed and background corrected using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: resistant CCRF-CEM cells, mock

growth_protocol: CCRF-CEM cells were grown in RPMI supplemented with 10% FBS, antibiotics (100 units/ml penicillin-streptomycin) and 2mM L-Glutamine at 37° C under 5% CO2. For isolation of the resistant population, cells were cultured with gradually increasing concentration of FK866 (for the experiment cells resistant to 100 nM FK866 were used)

extract_protocol: Total RNA was extracted using TRIZOL reagent according to the manufacturer's protocol.

treatment_protocol: resistant CCRF-CEM cells were treated with DMSO for 48 hr (5*10^5 cells/ ml)

value: resistant CCRF-CEM cells

value: mock

tag: biological replicate


title: resistant CCRF-CEM, mock, total RNA, bio_rep_2

description:
Total RNA sample extracted from resistant CCRF-CEM cells, mock.
resistant_mock_2


title: EMM_nitro_1


title: EMM_nitro_2


title: AorticValve_67


title: AorticValve_70


title: resistant CCRF-CEM, mock, total RNA, bio_rep_4

description:
Total RNA sample extracted from resistant CCRF-CEM cells, mock.
resistant_mock_4


title: AorticValve_68


title: resistant CCRF-CEM, FK866 treated, total RNA, bio_rep_3

description:
Total RNA sample extracted from resistant CCRF-CEM cells treated for 48h with FK866.
resistant_FK866_3

source_name: resistant CCRF-CEM cells, FK866 treated

treatment_protocol: resistant CCRF-CEM cells were treated with 5nM FK866 for 48 hr (5*10^5 cells/ ml)


title: resistant CCRF-CEM, mock, total RNA, bio_rep_1

description:
Total RNA sample extracted from resistant CCRF-CEM cells, mock.
resistant_mock_1


title: AorticValve_65


title: resistant CCRF-CEM, FK866 treated, total RNA, bio_rep_4

description:
Total RNA sample extracted from resistant CCRF-CEM cells treated for 48h with FK866.
resistant_FK866_4


title: EMM_exp_3

description:
gene_normalized_matrix.tab
gene_count_matrix.tab
TSS_normalized_matrix.tab
TSS_count_matrix.tab
TSSs.bed
EMM_exp_plus.bw
EMM_exp_minus.bw


title: AorticValve_66


title: AorticValve_64


title: parental CCRF-CEM, mock, total RNA, bio_rep_3

description:
Total RNA sample extracted from parental CCRF-CEM cells, mock.
parental_mock_3

source_name: parental CCRF-CEM cells, mock

treatment_protocol: parental CCRF-CEM cells were treated with DMSO for 48 hr (5*10^5 cells/ ml)

value: parental CCRF-CEM cells


title: parental CCRF-CEM, mock, total RNA, bio_rep_1

description:
Total RNA sample extracted from parental CCRF-CEM cells, mock.
parental_mock_1


title: AorticValve_61


title: resistant CCRF-CEM, FK866 treated, total RNA, bio_rep_2

description:
Total RNA sample extracted from resistant CCRF-CEM cells treated for 48h with FK866.
resistant_FK866_2


title: AorticValve_62


title: parental CCRF-CEM, mock, total RNA, bio_rep_2

description:
Total RNA sample extracted from parental CCRF-CEM cells, mock.
parental_mock_2


title: AorticValve_63


title: EMM_exp_2


title: resistant CCRF-CEM, FK866 treated, total RNA, bio_rep_1

description:
Total RNA sample extracted from resistant CCRF-CEM cells treated for 48h with FK866.
resistant_FK866_1


title: parental CCRF-CEM, FK866 treated, total RNA, bio_rep_2

description:
Total RNA sample extracted from parental CCRF-CEM cells treated for 48h with FK866.
parental_FK866_2

source_name: parental CCRF-CEM cells, FK866 treated

treatment_protocol: parental CCRF-CEM cells were treated with 5nM FK866 for 48 hr (5*10^5 cells/ ml)


title: AorticValve_60


title: EMM_exp_1


title: AorticValve_58


title: AorticValve_56


title: parental CCRF-CEM, FK866 treated, total RNA, bio_rep_1

description:
Total RNA sample extracted from parental CCRF-CEM cells treated for 48h with FK866.
parental_FK866_1


title: AorticValve_55


title: LPA_[25uM]_replicate1 (24h time point)

city: Vienna

first: Jan-Philip

last: Medelnik

state: Vienna

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: Gene expression after 24 h (LPA)

hyb_protocol: The target cRNAs were hybridized to SurePrint G3 Human GE 8×60K Microarrays (AMADID 039494, Agilent Technologies).

scan_protocol: Scanned images were analysed with the Feature Extraction software 10.7.1.1 (Agilent Technologies) using default parameters (protocol: GE1_107_Sep09, grid: 039494_D_F_20120628) to obtain background-corrected signal intensities.

data_processing: The data were further analysed with the GeneSpring GX Software (Version 13.0, Agilent Technologies), where quantile normalization of the data and removal of unreliable signal intensities (filtering of data by expression: in three out of six experiments the signal intensity of a probe had to be above the 20th percentile to be retained in the data set) were performed. For statistical analysis a one-way ANOVA analysis with a p-value cutoff of 0.05 was performed.

label_protocol: RNA was used to reverse transcribe double stranded cDNA and subsequently in-vitro transcribe Cy3-labeled target cRNA with the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: NPCs were cultured in N2B27 + human FGF2 and mouse EGF. HESCs were differentiated into NPCs using a three-dimensional Dual SMAD signaling inhibitino protocol. NPCs were kept in 24-well plates with a daily medium change (N2B27 =FGF2/EGF medium)

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini Kit. RNA was DNAse treated and re-purified using the Qiagen Rneasy Mini Kit. RNAse quality was confirmed using Agilent Bioanalyzer.

treatment_protocol: NPCs were cultured in 0.5 ml N2B27 + FGF2/EGF in 24-well plates without- or in the presence of LPA [25 uM] for 2h, 10h and 24h.

tag: Sex

value: female

tag: cell type

value: neural progenitor cells (NPCs)

tag: derived from

value: WA-09 (H9 HESC-line)

tag: passage

value: rosette passaging number 2 (RP2)

tag: time point


title: control_[noLPA]_replicate2 (24h time point)

description: Gene expression after 24 h (control)


title: LPA_[25uM]_replicate2 (24h time point)

description: Gene expression after 24 h (LPA)


title: control_[noLPA]_replicate1 (24h time point)

description: Gene expression after 24 h (control)


title: AorticValve_57

tag: tissue


title: AorticValve_54


title: control_[noLPA]_replicate3 (24h time point)

description: Gene expression after 24 h (control)


title: control[noLPA]_replicate3 (10h time point)

description: Gene expression after 10 h (control)


title: LPA_[25uM]_replicate3 (24h time point)

description: Gene expression after 24 h (LPA)


title: LPA_[25uM]_replicate2 (10h time point)

description: Gene expression after 10 h (LPA)


title: LPA_[25uM]_replicate3 (10h time point)

description: Gene expression after 10 h (LPA)


title: AorticValve_59


title: LPA_[25uM]_replicate1 (10h time point)

description: Gene expression after 10 h (LPA)


title: AorticValve_53


title: AorticValve_52


title: AorticValve_50


title: AorticValve_51


title: AorticValve_49


title: AorticValve_46


title: control_[noLPA]_replicate2 (10h time point)

description: Gene expression after 10 h (control)


title: AorticValve_48


title: control_[noLPA]_replicate3 (2h time point)

description: Gene expression after 2 h (control)


title: LPA_[25uM]_replicate3 (2h time point)

description: Gene expression after 2 h (LPA)


title: control_[noLPA]_replicate1 (10h time point)

description: Gene expression after 10 h (control)


title: AorticValve_47


title: LPA_[25uM]_replicate2 (2h time point)

description: Gene expression after 2 h (LPA)


title: LPA_[25uM]_replicate1 (2h time point)

description: Gene expression after 2 h (LPA)


title: control_[noLPA]_replicate1 (2h time point)

description: Gene expression after 2 h (control)


title: Sample_shZc3h13_m6A_Input_rep2

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
m6A-seq:
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
RNA-seq:
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Ensembl genes were calculated by cufflinks.
RIP-seq:
RIP-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Zc3h13 protein RIP signal was calculated as FPKM by FPKM_count.
FPKM value of Ensembl genes were calculated by FPKM_count.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks; bedGraph files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome;
tab-delimited text file include the genes with Zc3h13 binding on mRNA transcripts.

growth_protocol: E14 murine embryonic stem cell was cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 1% none essential amino acid, 0.1% beta-mercaptoethanol, 100u/ml penicillin/ Streptomycin and 1000u LIF.

extract_protocol:
Total RNAs from mESCs were isolated using Trizol reagent according to the manufacturer’s instruction (Life technology, 15596018). Polyadenylated RNAs were extracted by oligodT beads (NEB, S1419S), followed by removal of contaminated rRNA with RiboMinus transcriptome isolation kit (Life technologies, A15026).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
m6A-seq: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody.
RNA-seq: RNAs were isolated from Zc3h13 knockdown, scramble knockdown and Zc3h13 rescue mouse ESCs. Polyadenylated RNA was extracted for library generation and sequencing.
RIP-seq: RNA was fragmented and subject to immunoprecipitation with a anti-Zc3h13 specific antibody.

tag: genotype/variation

value: Zc3h13 knock-down

tag: developmental stage

value: murine embryonic stem cell

tag: molecule subtype

value: total RNA


title: Sample_scr_m6A_Input_rep2

value: scr


title: control_[noLPA]_replicate2 (2h time point)

description: Gene expression after 2 h (control)


title: Sample_shZc3h13-2_RNA-seq_rep2


title: Sample_scr_RNA-seq_rep2


title: AorticValve_43


title: Sample_shZc3h13_nucleus_m6A_Input_rep2

data_processing:
library strategy: m6A-seq
Basecalls performed using CASAVA version 1.4
m6A-seq:
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
RNA-seq:
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Ensembl genes were calculated by cufflinks.
RIP-seq:
RIP-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Zc3h13 protein RIP signal was calculated as FPKM by FPKM_count.
FPKM value of Ensembl genes were calculated by FPKM_count.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks; bedGraph files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome;
tab-delimited text file include the genes with Zc3h13 binding on mRNA transcripts.

value: nucleus RNA


title: AorticValve_40


title: AorticValve_45


title: AorticValve_42


title: AorticValve_44


title: DC day5 for 6h +Cholera Toxin, biological rep1

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

description: Gene expression data from MoDCs treated with Cholera Toxin

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on am Affymetrix Human Gene Expression Array. Arrays were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and RMA as normalization method

source_name: MoDC, CT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual, Affymetrix).

growth_protocol: Human monocyte derived DCs were generated from the plastic-adherent fraction of PBMCs and culture for 5 days in GM-CSF + IL-4.

extract_protocol: Cells were lysed in Trizol reagent and complete RNA was isolated according to manufacturer's instructions.

treatment_protocol: At day 5 the different stimuli were added to the cells. TNF 500 U/ml, LPS 0.1 µg/ml and CT 1 µg/ml.

value: Blood (Monocytes)

value: Monocyte-derived DCs

tag: agent

value: Cholera Toxin


title: Sample_shZc3h13-1_RNA-seq_rep2


title: DC day5 for 6h +TNF, biological rep1

description: Gene expression data from MoDCs treated with TNF

source_name: MoDC, TNF

value: TNF


title: AorticValve_34

value: aortic valve


title: AorticValve_41


title: AorticValve_35


title: AorticValve_36


title: DC day5 for 6h +LPS, biological rep1

description: Gene expression data from MoDCs treated with LPS

source_name: MoDC, LPS

value: LPS


title: AorticValve_37


title: Sample_shZc3h13_nucleus_m6A_rep2

tag: antibody

value: Rabbit anti-m6A (Synaptic, 202003)


title: Sample_shZc3h13_nucleus_m6A_rep1


title: Sample_shZc3h13_cyto_m6A_Input_rep2

value: cytoplasmic RNA


title: AorticValve_33


title: DC day5 for 6h +medium, biological rep1

description: Gene expression data from untreated MoDCs

source_name: MoDC, unstimulated


title: Sample_shZc3h13_nucleus_m6A_Input_rep1


title: AorticValve_39


title: AorticValve_31


title: AorticValve_32


title: Sample_shZc3h13_cyto_m6A_Input_rep1


title: Sample_shZc3h13_cyto_m6A_rep2


title: Sample_shZc3h13_cyto_m6A_rep1


title: Sample_scr_nucleus_m6A_Input_rep1


title: Serum_normal_rep2

city: Beijing

first: XiaoKui

last: Yang

address: 251, Yaojiayuan Road, Chaoyang DIstrct

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

description: The 6th generation of miRNA array contains more than 1891 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 16.0, as well as all viral microRNAs related to these species. In addition, this array contains capture probes for 66 new miRPlus™ human microRNAs.

hyb_protocol: The Hy3TM-labeling samples were hybridized on the miRCUYTM LNA Array (v,16.0) (Exiqon) according to array annual. The total 12.5 µl Hy3TM-labeled samples, 90 µl 2 × Hybridization buffer, 77.5 µl Nuclease-free Buffer were first denatured for 2 min at 95℃, incubated on ice for 2 min. Then hybridized to the microarray for 16-20 h at 56℃. Following hybridization, the slides were achieved, washed several times Wash buffer kit (Exiqon).

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing:
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged. Median Normalization Method was used to obtain “Normalized Data”, Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. So, if "Foreground-Background" is a negative number, the "Normalized Data" was determined to be "null". After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.
GenePix Pro 6.0 software (Axon) was used for grid alignment and data extraction.

source_name: Normal serum

label_protocol: The miRCURYTM Hy3TM/ Hy5TM Power labeling kit (Exiqon) was used according to the manufacturer’s guideline for miRNA labelling by following steps: 1 µl RNA in 3.0 µl of water was combined with 1.0 µl of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37℃. The Reaction was terminated by incubation for 5 min at 95℃. Then 3.0 µl of labeling buffer, 1.5 µl of fluorescent label (Hy3TM), 2.0 µl of DMSO, 2.0 µl  of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16℃. Terminated by incubation for 15 min at 65℃.

extract_protocol: Total RNA was isolated using TRIzol LS (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop 1000. RNA integrity was determined by gel electrophoresis.

tag: disease state

value: Normal

tag: sample type

value: serum

value: 26 years

tag: afc

tag: fsh

tag: lh


title: Serum_normal_rep3

tag: age

value: 28 years


title: AorticValve_27


title: AorticValve_28


title: Serum_normal_rep1

value: 30 years


title: AorticValve_29


title: AorticValve_26


title: Granulosa cell_normal_rep3

source_name: Normal granulosa cell

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop 1000. RNA integrity was determined by gel electrophoresis.

value: granulosa cell

value: 23 years

tag: fsh (miu/ml)

tag: lh (miu/ml)


title: Serum_DOR_rep1

source_name: DOR serum

value: DOR

value: 33 years


title: Serum_DOR_rep2

value: 34 years


title: Serum_DOR_rep3


title: Granulosa cell_normal_rep1

tag: cell type


title: AorticValve_23


title: Sample_scr_nucleus_m6A_Input_rep2

value: scr

value: murine embryonic stem cell

value: nucleus RNA


title: Sample_scr_cyto_m6A_Input_rep2


title: Sample_scr_nucleus_m6A_rep1


title: AorticValve_24

value: aortic valve


title: AorticValve_25


title: AorticValve_22


title: AorticValve_30


title: AorticValve_20


title: AorticValve_17


title: AorticValve_21


title: Sample_scr_cyto_m6A_Input_rep1


title: Granulosa cell_normal_rep2

value: 31 years


title: Sample_Zc3H13_rescue_RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.4
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
FPKM value of Ensembl genes were calculated by cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks;and bg files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Ensembl genes in Mus musculus genome;

source_name: murine embryonic stem cell

treatment_protocol: RNAs were isolated from Zc3h13 knockdown, scramble knockdown and Zc3h13 rescue mouse ESCs. Polyadenylated RNA was extracted for library generation and sequencing.

value: Zc3H13 knock-down plus Zc3H13


title: Sample_shZc3H13_rep2_RNA-seq

value: Zc3H13 knock-down


title: Sample_shZc3H13_rep1_RNA-seq


title: AorticValve_18


title: Granulosa cell_DOR_rep3

source_name: DOR granulosa cell

value: 25 years


title: 24hr Control

first: Norman

middle: J

last: Haughey

address: 600N Wolfe Street, Pathology 608

department: Department of Neurology

institute: Joohns Hopkins School of Medcine

description: miRNA

hyb_protocol: RNA was further prepped for hybridization by adding water (40μl), heating the samples to 85°C for 10min, then immediately placing them on ice. RNA (5μl) was hybridized to miRNA Reporter CodeSet master mix (20μl) at 65°C for 18h.

scan_protocol: Hybridized RNAs were bound to nCounter cartridges, and analyzed using an nCounter Digital Analyzer (NanoString).

data_processing: The data was normalised to internal standards and housekeeping genes and then fold change of each miRNA was calculated by dividing the IL-1beta normalised count with the control count. Any miRNA with insufficient reads was removed from the raw data.

label: not provided

source_name: Extracellular vesicles from cultured primary astrocytes, control

label_protocol: Small RNAs were tagged on their 3' end to normalize Tm's according to the manufacturer's instructions (NanoString Technologies). Briefly, small RNA's were bridged with tagged DNA in annealing buffer (94°C for 1min, 65°C for 2min, 45°C for 10min, hold at 48°C), PEG and ligation buffer were added at 48°C for 5min, then Ligase was added (48°C for 3min, 47°C for 3min, 46°C for 3min, 45°C for 5min, 65°C for 10min, hold at 4°C). To remove excess tags and bridges, samples were purified using a ligation clean-up enzyme (37°C for 120min, 70°C for 10min, hold at 4°C).

growth_protocol: Primary cortical astrocyte cell cultures were established and maintained using methods similar to those described previously. Briefly, primary astrocytes were isolated from the cerebral cortex of postnatal day 1 C57B6J mice and GFAP-EGFP mice. Cells were mechanically dissociated in HBSS, and plated in poly-D-lysine culture flasks containing DMEM/F12 MEDIA (Gibco BRL) AND 10% fetal bovine serum (Gibco BRL). Type 1 astrocytes were purified by the mechanical removal of less adherent cells. Cultures were 98% GFAP+ astrocytes with type I morphology and were used for experiments between 3-10 passages.

extract_protocol: RNA was isolated from EV using the miRNeasy Micro Kit (Qiagen).

treatment_protocol: Eight-ten T150 culture flasks of GFAP-EGFP primary astrocytes (~80% confluent) were gently washed 3X with warm PBS to remove endogenous EV. Astrocyte EV release was stimulated by the addition of fresh EV-free media containing IL-1β (200ng per ml, R&D systems). Media was collected 2h after stimulation, and EVs isolated by a multistep ultracentrifugation. Media was centrifuged at 10,000g for 15min (4°C). Supernatant was removed and ultracentrifuged at 100,000 g for 3h (4°C) to isolate EVs. This short stimulation procedure resulted in the release of EVs with a narrow size range and protein markers consistent with exosomes. EV size, distribution, and concentrations were determined using a NS500 NanosightTM nanoparticle tracking analysis system (Malvern Instruments). EV were visualized with scattered light from a 488nM laser beam onto an optical microscope containing a CCD video camera. Five exposures of 20sec each were randomly chosen by the software to measure EV size and concentration based on the Stokes-Einstein equation, and linear fitting using standard particles with a known diameter. Data was binned and plotted as a continuous histogram.

tag: strain/background

value: GFAP-EGFP

tag: treatment


title: Granulosa cell_DOR_rep1

value: 32 years


title: AorticValve_19

tag: tissue


title: IL-1beta

description: miRNA

source_name: Extracellular vesicles from cultured primary astrocytes, IL-1beta


title: AorticValve_16


title: Granulosa cell_DOR_rep2


title: Sample_scr_cyto_m6A_rep1

tag: genotype/variation

value: Rabbit anti-m6A (Synaptic, 202003)

value: cytoplasmic RNA


title: Sample_scr_RNA-seq

tag: developmental stage


title: AorticValve_15


title: AorticValve_10


title: AorticValve_13


title: AorticValve_11


title: AorticValve_12


title: AorticValve_3


title: AorticValve_4


title: AorticValve_6


title: AorticValve_7


title: AorticValve_14


title: AorticValve_2


title: AorticValve_5


title: AorticValve_1


title: AorticValve_8


title: AorticValve_9


title: RGS5 KO mouse with hypertension, biological rep. 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
RGS5_Hyp_16
Gene expression data of femoral arteries of DOCA/salt-treated RGS5 KO mice.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse MoGene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez Gene-based gene definitions was used to annotate the arrays. The raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Median polish Probeset Summary.

source_name: RGS5 KO mouse treated with DOCA/salt

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Animal studies were performed with permission of the Regional Council Karlsruhe and conformed to the Guide for the Care and Use of Laboratory Animals published by the US National Institutes of Health (NIH Publication No. 85-23, revised 1996). The rgs5GFP/GFP mouse strain (genetic background: F1H4 ((129S6/SvEvTac x C57BL/6NTac)F1) * C57BL/6) was backcrossed >15 generations onto the C57BL/6 background.

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

treatment_protocol: At least 12-week-old male wild type C57BL/6J or RGS-deficient mice were anesthetized with 1.75% isoflurane/0.8 L/min room air and hypertension was induced by subcutaneously implanting slow-release DOCA pellets (M-121, 21-day-release, 50 mg/kg, Innovative Research of America, Sarasota, FL) according to the manufacturer’s instructions and feeding the mice with 1% NaCl in the drinking water. The animals were euthanized after 10 days after in situ perfusion of the arterial system with ice-cold PBS. Femoral arteries were isolated and cleared from any surrounding tissue and denuded by cannulation. The arteries were then collected in RNAlater (Qiagen) and frozen in Trizol.

value: RGS5 KO

tag: gender

value: male

value: femoral arteries

value: DOCA/salt

tag: hypertension

value: Hyp


title: transgenic rat kidney, nondiabetic, replicate 3

description: kidney from transgen rat (AT2R overexpression)

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of rat Ragene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Rattus norvegicus

source_name: transgenic rat kidney, nondiabetic

growth_protocol: 3-months old transgenic rats and their wildtype littermates were injected with 35 mg/kg i.v. streptozotocin and kept for 28 days

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions,  then RNA was DNAse digested  and cleaned up with quiagen Rneasy Mini kit

treatment_protocol: 28 days after streptozotocin injection rats were sacrified in deep isoflurane anaestesia and kidneys were harvesten, corteces isolated and immediately deep frozen in liquid nitrogene, further stored in -80°C.

tag: strain

value: Sprague Dawley

tag: genotype

value: TGR

tag: diabetic

value: Control


title: wildtype rat kidney, nondiabetic, replicate 3

description: kidney from wildtype rat

source_name: wildtype rat kidney, nondiabetic

value: WT


title: RGS5 KO mouse with hypertension, biological rep. 2

description:
RGS5_Hyp_15
Gene expression data of femoral arteries of DOCA/salt-treated RGS5 KO mice.


title: transgenic rat kidney, diabetic, replicate 4

description: kidney from diabetic induced transgen rat (AT2R overexpression)

source_name: transgenic rat kidney, diabetic

value: Diabetic


title: AorticValve_38

value: aortic valve


title: RGS5 KO mouse, biological rep. 3

description:
RGS5_Ctrl_12
Gene expression data of femoral arteries of untreated RGS5 KO mice.

source_name: RGS5 KO mouse untreated

value: Ctrl


title: RGS5 KO mouse, biological rep. 1

description:
RGS5_Ctrl_9
Gene expression data of femoral arteries of untreated RGS5 KO mice.


title: wildtype rat kidney, nondiabetic, replicate 2

description: kidney from wildtype rat


title: WT mouse with hypertension, biological rep. 3

description:
WT_Hyp_8
Gene expression data of femoral arteries of DOCA/salt-treated WT mice.

source_name: WT mouse treated with DOCA/salt


title: transgenic rat kidney, nondiabetic, replicate 1


title: transgenic rat kidney, nondiabetic, replicate 2


title: wildtype rat kidney, diabetic, replicate 2

description: kidney from diabetic induced wildtype rat

source_name: wildtype rat kidney, diabetic


title: RGS5 KO mouse, biological rep. 2

description:
RGS5_Ctrl_11
Gene expression data of femoral arteries of untreated RGS5 KO mice.


title: transgenic rat kidney, diabetic, replicate 3


title: RGS5 KO mouse with hypertension, biological rep. 1

description:
RGS5_Hyp_14
Gene expression data of femoral arteries of DOCA/salt-treated RGS5 KO mice.


title: transgenic rat kidney, diabetic, replicate 2


title: WT mouse, biological rep. 1

description:
WT_Ctrl_1
Gene expression data of femoral arteries of untreated WT mice.

source_name: WT mouse untreated


title: WT mouse with hypertension, biological rep. 2

description:
WT_Hyp_7
Gene expression data of femoral arteries of DOCA/salt-treated WT mice.


title: transgenic rat kidney, diabetic, replicate 1


title: WT mouse, biological rep. 2

description:
WT_Ctrl_18
Gene expression data of femoral arteries of untreated WT mice.


title: wildtype rat kidney, nondiabetic, replicate 1

description: kidney from wildtype rat


title: wildtype rat kidney, diabetic, replicate 1


title: WT mouse with hypertension, biological rep. 1

description:
WT_Hyp_6
Gene expression data of femoral arteries of DOCA/salt-treated WT mice.


title: Adjacent non tumoral liver tissue from N°81

status: Public on Mar 13 2018

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

description: Gene expression data

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Mouse Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V18 was used for annotation. We ve used the custom CDF file from BrainArray :  mogene20st_Mm_ENTREZG V18.

source_name: Non tumoral adjacent liver

label_protocol: 50 ng of total RNA is reverse transcribed  following the Ovation PicoSL WTA System V2 (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 2.5 ug of single strand DNA is used for fragmentation and biotin labelling using Encore Biotin Module (Nugen).

treatment_protocol: Mutant mice were obtained by breeding Axin1 fl/fl mice with mice expressing Cre recombinase in embryonic hepatocytes (Alfp-Cre). Axin1-/- mice develop liver tumors after 9 months

value: Liver

value: 16 months


title: WT mouse, biological rep. 3

description:
WT_Ctrl_19
Gene expression data of femoral arteries of untreated WT mice.


title: Liver Tumor from Axin1 deleted mouse N°93

description: Gene expression data

source_name: Liver tumor


title: Liver Tumor from Axin1 deleted mouse N°81

description: Gene expression data


title: Adjacent non tumoral liver tissue from N°1931

description: Gene expression data


title: Liver Tumor3 from Axin1 deleted mouse N°121

description: Gene expression data


title: POLR1D overexpression group

city: guangzhou

first: wenbo

last: niu

address: shatai road 1023

institute: southern medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
The data is first filtered to remove the low quality and adaptor sequence to get HQ Clean Data. There may be differences in rRNA removal efficiency due to the kit. The rRNA-containing reads is compared with the rRNA, and the rRNA after filter reading is compared to the reference genomes, followed by gene reorganization, FPKM filtering, low coverage sequences that may be contaminated with background noise, and then comparing the assembled genes with known mRNA reference sequences to identify known RNAs, encoding potential The prediction of novel genes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Ensembl release 85
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values and reads counts for each Sample.

source_name: colorectal cancer cell line SW1116

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

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 30-40% confluence before infected with lentivirus overexpressing POLR1D and negative control lentivirus. After 72h, the GFP-positive cells were isolated by FACS. POLR1D overexpression was confirmed by RT-PCR and Western blotting.

tag: cell line

value: colorectal cancer cell line

value: POLR1D overexpression


title: Adjacent non tumoral liver tissue from N°123

description: Gene expression data


title: Liver Tumor from Axin1 deleted mouse N°123

description: Gene expression data


title: Liver Tumor from Axin1 deleted mouse N°124

description: Gene expression data


title: Adjacent non tumoral liver tissue from N°121

description: Gene expression data


title: Tumor Axin1 deleted mouse N°121

description: Gene expression data


title: Adjacent non tumoral liver tissue from N°124

description: Gene expression data


title: Tumor Axin1 deleted mouse N°90

description: Gene expression data


title: Liver from non deleted mouse (control)_11

description: Gene expression data

source_name: Non tumoral liver same age


title: Donor2_TCR_cell20

city: Basel

first: Monica

last: Golumbeanu

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

data_processing:
Software tools Cutadapt v1.7.1 and Prinseq-lite were used for adapter trimming and read filtering, respectively.
Alignment of the sequencing reads was performed against the Ensembl GRCh38 assembly of the human genome concatenated with the HIV viral sequence using the STAR v2.5 aligner. The following alignment parameters were different from default: --outFilterMismatchNoverLmax 0.1 -- seedSearchStartLmax 50.
Gene expression levels were quantified by counting the number of reads within each gene with HTSeq v0.5.3, using the Ensembl genome annotations for human and HIV.
For scRNA-Seq samples, the total number of reads associated to genes, the proportion of mitochondrial reads, and the proportion of ERCC spike-ins reads were used to filter low-quality cells.
For scRNA-Seq, for the data produced from the experimental latency model, single-cell read counts were normalized using linear size factors calculated from the ERCC spike-ins with the package scran. In absence of ERCC spike-ins, single-cell read counts for the scRNA-Seq data from HIV+ individuals were normalized using a normalization procedure, available with package scran, specifically designed for single-cell data without spike-ins measurements, based on computing cell-specific size factors by considering random pools of cells. Normalized read counts were log2-transformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: For scRNA-Seq data from the primary latency model and from the HIV+ donors, tables(tab delimited txt files) with raw numbers of counted reads for each gene, condition and cell, and corresponding normalized read counts. For the scRNA-Seq data from the primary latency model, table (tab delimited txt file) with raw numbers of counted reads for each ERCC spike-in per condition and cell. For bulk RNA-Seq, table (tab delimited txt files) with the raw numbers of counted reads for each gene and condition.

molecule: polyA RNA

source_name: CD4+ T cells

growth_protocol: For the latency model, CD4+ T cells were purified from the buffy coat of uninfected donors by Ficoll gradient separation followed by negative selection and magnetic separation using the human CD4+ T Cell enrichment kit (Stem Cell Technologies #17952). Then the cells were resuspended at 106 cells/ml in Activation Medium (Immunocult XF T cell expansion medium (Stem Cell Technologies #10981) supplemented with 100 U/ml IL-2 (RD #202-IL) and 25 μl/ml of ImmunoCult™ Human CD3/CD28 T Cell Activator (Stem Cell Technologies #10971)). Three days post-TCR activation, cells (2 mio) were transduced with 1.2x105 TU of HIVGFP/VSV-G in presence of 5 μg/ml polybrene by spinoculation (3h, 1500g, 25°C). Cells were then washed with RPMI-1640 supplemented with 10% heat inactivated fetal calf serum (R-10) and resuspended in 4 ml Expansion Medium (Immunocult XF T cell expansion medium supplemented with 100 U/ml IL-2). After three days, cells were washed, resuspended in RPMI without phenol red and sorted by FACS based on GFP expression. Infected GFP+ cells were resuspended in 0.5 ml Activation Medium and then maintained in Expansion Medium at 106 cells/ml for ~2.5 weeks. Cells were stimulated once again in Activation Medium and maintained in Expansion Medium for further 2.5 weeks. Cells were then allowed to revert to a resting phenotype by long-term culture in Latency Medium (50% R-10/50% H80 feeder cell supernatant supplemented with 40 U/ml IL-2) for 8 weeks. In parallel, blood was collected from two HIV-infected individuals participating in the Swiss HIV Cohort Study (http://www.shcs.ch), that were on antiretroviral therapy for more than 3 years, with undetectable viremia and a CD4 cell count above 300 for more than one year. Blood (~25 ml) was directly collected in 4 CPT tubes (BD Vacutainer CPT; BD Biosciences #362753) and processed for peripheral blood mononuclear cells (PBMC) isolation according to manufacturer’s instructions. Resting CD4+ T cells were purified by negative selection and magnetic separation using the human CD4+ T Cell enrichment kit supplemented with anti-HLA-DR, anti-CD25 and anti-CD69 (Stem Cell Technologies #19052/#17962), and resuspended in R-10 (0.45 μm filtered).

extract_protocol:
Cells were washed and collected for bulk or single-cell RNA-Seq. On one hand, cells (1 mio) were resuspended in 400 μl lysis buffer of the ZR-Duet DNA/RNA miniprep (Zymo Research #D7001) and processed for RNA extraction according to manufacturer’s instructions, and used for bulk RNA-Seq (Illumina HiSeq Ribo-Zero TruSeq str RNA-Seq). On the other hand, cells were resuspended at 0.5-1x106 cells/ml in R-10 (0.45 μm filtered) and processed for single cell isolation and cDNA synthesis on a small 5-10 μm fluidigm plate (fluidigm C1 Single Cell AutoPrep System, Clontech SMARTer Ultra Low RNA kit for Illumina sequencing), followed by single-cell RNA-Seq (Illumina Nextera XT DNA Sample Preparation).
High-throughput sequencing (100 cycles, single end) was performed on Illumina HiSeq2500 (University of Lausanne, Genomic Technology Facility).
Illumina HiSeq2500: 100 NT, single end (bulk and scRNA-Seq)

treatment_protocol: For the latency model, 2 million cells were, either left untreated, or incubated with 0.5 μM SAHA for 24h, or exposed to anti-CD3/CD28/IL-2 for TCR stimulation for 48h. Cells were then washed and collected for bulk and single-cell RNA-Seq. For the cells from donors, the cell samples were either left untreated (control cells) or were activated by T-Cell Receptor (TCR)-mediated stimulation for 48 hours in a 48-well plate.

value: TCR-treated

tag: rna-seq experiment type

value: single-cell

tag: experiment setup

value: HIV+ donor 2


title: Donor2_TCR_cell21


title: Donor2_TCR_cell24


title: Donor2_TCR_cell23


title: Donor2_TCR_cell18


title: Liver Tumor2 from Axin1 deleted mouse N°121

description: Gene expression data

tag: age

value: male


title: Liver from non deleted mouse (control)_12

description: Gene expression data


title: Control group

value: control


title: Donor2_TCR_cell22


title: Donor2_TCR_cell14


title: Donor2_TCR_cell17


title: Donor2_TCR_cell12


title: Donor2_TCR_cell16


title: Donor2_TCR_cell15


title: Donor2_TCR_cell19


title: Liver from non deleted mouse (control)_10

description: Gene expression data


title: Donor2_TCR_cell11


title: Donor2_TCR_cell10


title: Donor2_TCR_cell6


title: Donor2_TCR_cell9


title: Donor2_TCR_cell7


title: Donor2_TCR_cell8


title: Donor2_TCR_cell5


title: Donor2_TCR_cell3


title: Donor2_TCR_cell1


title: Donor2_untreated_cell24

value: untreated


title: Donor2_untreated_cell22


title: Donor2_untreated_cell23


title: Donor2_untreated_cell21


title: Donor2_untreated_cell20


title: Donor2_TCR_cell4


title: Donor2_TCR_cell13


title: Donor2_untreated_cell18


title: Donor2_untreated_cell17


title: Donor2_untreated_cell15


title: Donor2_untreated_cell13


title: Donor2_untreated_cell16


title: Donor2_untreated_cell14


title: Donor2_untreated_cell12


title: Sample_scr_cyto_m6A_rep2

value: scr

value: murine embryonic stem cell

tag: antibody

value: Rabbit anti-m6A (Synaptic, 202003)

tag: molecule subtype

value: cytoplasmic RNA


title: Donor2_untreated_cell10


title: Donor2_untreated_cell11


title: Donor2_untreated_cell9


title: Donor2_TCR_cell2


title: Donor2_untreated_cell8


title: Donor2_untreated_cell7


title: Donor2_untreated_cell19


title: Donor2_untreated_cell6


title: Donor2_untreated_cell3


title: Donor2_untreated_cell2


title: Donor2_untreated_cell5


title: Donor1_TCR_cell22

value: HIV+ donor 1


title: Donor1_TCR_cell20


title: Donor1_TCR_cell17


title: Donor1_TCR_cell24


title: Donor1_TCR_cell18


title: Donor1_TCR_cell23


title: Donor1_TCR_cell19


title: Donor1_TCR_cell16


title: Donor1_TCR_cell14


title: Donor1_TCR_cell12


title: Donor1_TCR_cell10


title: Donor1_TCR_cell13


title: Donor1_TCR_cell21


title: Donor2_untreated_cell4


title: Donor1_TCR_cell9


title: Donor1_TCR_cell11


title: Donor1_TCR_cell5


title: Donor1_TCR_cell8


title: Donor1_TCR_cell6


title: Donor2_untreated_cell1


title: Donor1_TCR_cell7


title: Donor1_TCR_cell4


title: Donor1_untreated_cell24


title: Donor1_untreated_cell22


title: Donor1_untreated_cell23


title: Donor1_TCR_cell15


title: Donor1_TCR_cell1


title: Donor1_TCR_cell2


title: Donor1_TCR_cell3


title: Donor1_untreated_cell18


title: Donor1_untreated_cell19


title: Donor1_untreated_cell17


title: Donor1_untreated_cell20


title: Donor1_untreated_cell15


title: Donor1_untreated_cell16


title: Donor1_untreated_cell10


title: Donor1_untreated_cell12


title: Donor1_untreated_cell14


title: Donor1_untreated_cell13


title: Donor1_untreated_cell11


title: Donor1_untreated_cell7


title: Donor1_untreated_cell9


title: Donor1_untreated_cell2


title: Donor1_untreated_cell6


title: Donor1_untreated_cell3


title: Donor1_untreated_cell5


title: Donor1_untreated_cell8


title: Donor1_untreated_cell4


title: Latency_model_TCR

value: bulk

value: Primary latency model


title: Donor1_untreated_cell1


title: Donor1_untreated_cell21


title: Latency_model_untreated


title: Latency_model_SAHA

value: SAHA-treated


title: Latency_model_TCR_cell_96


title: Latency_model_TCR_cell_95


title: Latency_model_TCR_cell_93


title: Latency_model_TCR_cell_94


title: Latency_model_TCR_cell_92


title: Latency_model_TCR_cell_91


title: Latency_model_TCR_cell_90


title: Latency_model_TCR_cell_89


title: Latency_model_TCR_cell_87


title: Latency_model_TCR_cell_88


title: Latency_model_TCR_cell_86


title: Latency_model_TCR_cell_85


title: Latency_model_TCR_cell_82


title: Latency_model_TCR_cell_81


title: Latency_model_TCR_cell_84


title: Latency_model_TCR_cell_79


title: Latency_model_TCR_cell_76


title: Latency_model_TCR_cell_73


title: Latency_model_TCR_cell_83


title: Latency_model_TCR_cell_75


title: Latency_model_TCR_cell_74


title: Latency_model_TCR_cell_77


title: Latency_model_TCR_cell_78


title: Latency_model_TCR_cell_80


title: Latency_model_TCR_cell_71


title: Latency_model_TCR_cell_69


title: Latency_model_TCR_cell_68


title: Latency_model_TCR_cell_67


title: Latency_model_TCR_cell_72


title: Latency_model_TCR_cell_65


title: Latency_model_TCR_cell_66


title: Latency_model_TCR_cell_70


title: Latency_model_TCR_cell_64


title: Latency_model_TCR_cell_62


title: Latency_model_TCR_cell_63


title: Latency_model_TCR_cell_61


title: Latency_model_TCR_cell_58


title: Latency_model_TCR_cell_59


title: Latency_model_TCR_cell_60


title: Latency_model_TCR_cell_48


title: Latency_model_TCR_cell_50


title: Latency_model_TCR_cell_43


title: Latency_model_TCR_cell_46


title: Latency_model_TCR_cell_44


title: Latency_model_TCR_cell_56


title: Latency_model_TCR_cell_45


title: Latency_model_TCR_cell_55


title: Latency_model_TCR_cell_51


title: Latency_model_TCR_cell_52


title: Latency_model_TCR_cell_57


title: Latency_model_TCR_cell_53


title: Latency_model_TCR_cell_42


title: Latency_model_TCR_cell_40


title: Latency_model_TCR_cell_39


title: Latency_model_TCR_cell_36


title: Latency_model_TCR_cell_47


title: Latency_model_TCR_cell_35


title: Latency_model_TCR_cell_54


title: Latency_model_TCR_cell_41


title: Latency_model_TCR_cell_32


title: Latency_model_TCR_cell_34


title: Latency_model_TCR_cell_31


title: Latency_model_TCR_cell_33


title: Latency_model_TCR_cell_30


title: Latency_model_TCR_cell_28


title: Latency_model_TCR_cell_38


title: Latency_model_TCR_cell_37


title: Latency_model_TCR_cell_27


title: Latency_model_TCR_cell_25


title: Latency_model_TCR_cell_26


title: Latency_model_TCR_cell_29


title: Latency_model_TCR_cell_24


title: Latency_model_TCR_cell_23


title: Latency_model_TCR_cell_18


title: Latency_model_TCR_cell_22


title: Latency_model_TCR_cell_21


title: Latency_model_TCR_cell_20


title: Latency_model_TCR_cell_19


title: Latency_model_TCR_cell_16


title: Latency_model_TCR_cell_14


title: Latency_model_TCR_cell_15


title: Latency_model_TCR_cell_17


title: Latency_model_TCR_cell_13


title: Latency_model_TCR_cell_11


title: Latency_model_TCR_cell_10


title: Latency_model_TCR_cell_9


title: Latency_model_TCR_cell_1


title: Latency_model_TCR_cell_3


title: Latency_model_TCR_cell_8


title: Latency_model_TCR_cell_5


title: Latency_model_TCR_cell_7


title: Latency_model_TCR_cell_6


title: Latency_model_SAHA_cell_95


title: Latency_model_SAHA_cell_96


title: Latency_model_TCR_cell_2


title: Latency_model_SAHA_cell_90


title: Latency_model_SAHA_cell_88


title: Latency_model_SAHA_cell_91


title: WGBS_Day2_rep2

first: Chenhuan

last: Xu

address: 1 Beichen West Road

institute: Beijing Institute of Genomics

description:
processed file: E14-CAID_D2_Wat.bed
processed file: E14-CAID_D2_Cri.bed

library_source: genomic

data_processing:
50 bp paired-end reads were first trimmed with Trimmomatic (0.36) (33) to remove any remnant adaptor sequence and bases with Phred quality score <20. Only pairs with both reads ≥20 bp were retained for subsequent analysis. Reads were aligned to the human genome (hg38, XX) using bismark (0.19.0) (34) with bowtie2 (2.2.9) (35). In rare cases of mapping rate <50%, two adjustments were made sequentially to improve the yield: 1) The 5’ end of the mate 2 reads were trimmed 5-10 bases off, which generally increased the mapping rate by 10-20%. 2) The mate 1 reads from the unmapped paired-end reads were retrieved for single-end mapping, given the fact that mate 1 reads alone could achieve >70% mapping rate under such circumstances. Alignment score was controlled by applying bowtie2 option --score-min L,0,-0.4. Mapping uniqueness was controlled by selecting alignments with mapping quality Q>10 using Samtools (1.6) (36). For each library, reads were specifically mapped to either the Watson or Crick strand, and duplicate reads were removed by bismark. Methylation of single cytosines was called from strand-specific alignments. For each strand, methylation calls from all biological replicates were pooled together unless otherwise noted. Methylation of CpGs was extracted from certain pairs of Watson/Crick strand methylation calls using bedtools (2.27.0) (37). The unmapped reads from bismark were re-aligned to the lambda genome to determine the bisulfite conversion rate of each library.
Genome_build: hg38

molecule: genomic DNA

growth_protocol: H9 human embryonic stem cells were obtained from WiCell. Cells were cultured in STEMPRO hESC SFM on cultureware coated with Geltrex Matrix at 37 °C under 5% CO2. Medium was changed every day. Cells were grown to 60-70% confluence before EdU labeling.

extract_protocol: Approximately 3-5x107 H9 hESCs were used to make a pair of parent and daughter strand nasChIP-BS-seq libraries under each condition. Anti-DNMT1 (Abcam), -DNMT3A (Abcam) or -DNMT3B (Abcam) antibodies were used. All steps were the same as described above for nasChIP-seq except that ligation with methylated adaptors, strand separation, and bisulfite conversion steps were done as described above for nasBS-seq to generate a pair of parental and daughter strand libraries for each condition.

tag: cell type

value: mouse embryonic stem cells


title: Latency_model_SAHA_cell_94


title: Latency_model_SAHA_cell_89


title: Latency_model_SAHA_cell_93


title: WGBS_Day0_rep2

description:
processed file: E14-CAID_D0_Wat.bed
processed file: E14-CAID_D0_Cri.bed


title: WGBS_Day0_rep1


title: Latency_model_TCR_cell_12


title: WGBS_Day2_rep1


title: Latency_model_SAHA_cell_86


title: Latency_model_SAHA_cell_85


title: Latency_model_TCR_cell_4


title: Latency_model_SAHA_cell_79


title: Latency_model_SAHA_cell_81


title: Latency_model_SAHA_cell_80


title: Latency_model_SAHA_cell_83


title: Latency_model_SAHA_cell_78


title: Latency_model_SAHA_cell_76


title: Latency_model_SAHA_cell_75


title: Latency_model_SAHA_cell_82


title: Latency_model_SAHA_cell_92


title: Latency_model_SAHA_cell_84


title: Latency_model_SAHA_cell_74


title: Latency_model_SAHA_cell_77


title: Latency_model_SAHA_cell_72


title: Latency_model_SAHA_cell_70


title: Latency_model_SAHA_cell_69


title: Latency_model_SAHA_cell_68


title: Latency_model_SAHA_cell_67


title: Latency_model_SAHA_cell_87


title: Latency_model_SAHA_cell_65


title: Latency_model_SAHA_cell_64


title: Latency_model_SAHA_cell_63


title: Latency_model_SAHA_cell_61


title: Latency_model_SAHA_cell_62


title: Latency_model_SAHA_cell_58


title: Latency_model_SAHA_cell_59


title: Latency_model_SAHA_cell_60


title: Latency_model_SAHA_cell_55


title: Latency_model_SAHA_cell_56


title: Latency_model_SAHA_cell_73


title: Latency_model_SAHA_cell_71


title: Latency_model_SAHA_cell_52


title: Latency_model_SAHA_cell_54


title: Latency_model_SAHA_cell_53


title: Latency_model_SAHA_cell_51


title: Latency_model_SAHA_cell_66


title: Latency_model_SAHA_cell_48


title: Latency_model_SAHA_cell_47


title: Latency_model_SAHA_cell_45


title: Latency_model_SAHA_cell_57


title: Latency_model_SAHA_cell_43


title: Latency_model_SAHA_cell_50


title: Latency_model_SAHA_cell_41


title: Latency_model_SAHA_cell_49


title: Latency_model_SAHA_cell_42


title: Latency_model_SAHA_cell_39


title: Latency_model_SAHA_cell_40


title: 17Tb: total blood RNA_posttraining_17

city: São Paulo

first: Michelle Sabrina

last: Moreira Silva

state: SP

address: Av. Dr. Enéas de Carvalho Aguiar

country: Brazil

institute: Heart Institute - InCor

description: Fasting blood samples were withdrawn at baseline and after the 18-weeks exercise training protocol, 48 hours after the last exercise session

hyb_protocol: Affymetrix standard procedure in Gene Chip Human Transcriptome Array 2.0

scan_protocol: Affymetrix standard procedure.

data_processing: The raw data were preprocessed in Expression Console (Affymetrix). RMA algorithm was used. Only transcripts that had detection above background with p≤0.05 and were expressed in ≥25% of arrays in both conditions (pre- and post-training) were selected for further analysis. Overall, 49372 to 62620 out of 67539 transcripts represented on the arrays met these criteria. Transcriptome Analysis Console (TAC, Affymetrix) was used for this step.  Differentially expressed transcripts in response to exercise training were identified in TAC using ANOVA, with FDR method. When no transcript reached a significance q value of 0.05 in the FDR test, only transcripts with P<0.05 (ANOVA) and fold change (FC) above ±1.5 were retained.

source_name: PAX gene blood, posttraining, resting state

label_protocol: Affymetrix standard procedure.

extract_protocol: Qiagen kit

treatment_protocol: total blood (leukocytes) isolated in PAXgene tubes for 24-48h. Storage of PAX gene tubes in -80°C until RNA extraction protocol.

tag: height

tag: body weight

value: total blood (leukocytes)

tag: vo2peak (l/min)

tag: vo2peak (ml/min/kg)


title: 13Tb: total blood RNA_posttraining_13

tag: tissue


title: 18Tb: total blood RNA_posttraining_18

tag: gender


title: 19Tb: total blood RNA_posttraining_19


title: 15Tb: total blood RNA_posttraining_15


title: 14Tb: total blood RNA_posttraining_14


title: 16Tb: total blood RNA_posttraining_16


title: Latency_model_SAHA_cell_44

tag: treatment


title: 20Tb: total blood RNA_posttraining_20


title: 8Tb: total blood RNA_posttraining_8


title: Latency_model_SAHA_cell_46


title: 7Tb: total blood RNA_posttraining_7


title: Latency_model_SAHA_cell_38


title: 6Tb: total blood RNA_posttraining_6


title: 11Tb: total blood RNA_posttraining_11


title: Latency_model_SAHA_cell_37


title: 10Tb: total blood RNA_posttraining_10


title: Latency_model_SAHA_cell_36


title: 9Tb: total blood RNA_posttraining_9


title: Latency_model_SAHA_cell_35


title: Latency_model_SAHA_cell_30


title: Latency_model_SAHA_cell_31


title: Latency_model_SAHA_cell_32


title: Latency_model_SAHA_cell_33


title: Latency_model_SAHA_cell_34


title: Latency_model_SAHA_cell_29


title: Latency_model_SAHA_cell_28


title: Latency_model_SAHA_cell_27


title: Latency_model_SAHA_cell_26


title: 12Tb: total blood RNA_posttraining_12


title: 1Tb: total blood RNA_posttraining_1


title: 4Tb: total blood RNA_posttraining_4


title: 2Tb: total blood RNA_posttraining_2


title: Latency_model_SAHA_cell_23


title: 5Tb: total blood RNA_posttraining_5


title: 16Ta: total blood RNA_baseline_16

source_name: PAX gene blood, pretraining, resting state


title: 18Ta: total blood RNA_baseline_18


title: 17Ta: total blood RNA_baseline_17


title: 20Ta: total blood RNA_baseline_20


title: 13Ta: total blood RNA_baseline_13


title: Latency_model_SAHA_cell_21


title: 14Ta: total blood RNA_baseline_14


title: 15Ta: total blood RNA_baseline_15


title: Latency_model_SAHA_cell_20


title: Latency_model_SAHA_cell_24


title: 9Ta: total blood RNA_baseline_9


title: 12Ta: total blood RNA_baseline_12


title: 10Ta: total blood RNA_baseline_10


title: 11Ta: total blood RNA_baseline_11


title: Latency_model_SAHA_cell_25


title: 7Ta: total blood RNA_baseline_7


title: Latency_model_SAHA_cell_19


title: Latency_model_SAHA_cell_22


title: Latency_model_SAHA_cell_18


title: 8Ta: total blood RNA_baseline_8


title: 19Ta: total blood RNA_baseline_19


title: Latency_model_SAHA_cell_16


title: Latency_model_SAHA_cell_14


title: 6Ta: total blood RNA_baseline_6


title: Latency_model_SAHA_cell_13


title: Latency_model_SAHA_cell_11


title: Latency_model_SAHA_cell_17


title: 5Ta: total blood RNA_baseline_5


title: Latency_model_TCR_cell_49


title: Latency_model_SAHA_cell_15


title: Latency_model_SAHA_cell_10


title: Latency_model_SAHA_cell_9


title: Latency_model_SAHA_cell_8


title: Latency_model_SAHA_cell_7


title: Latency_model_SAHA_cell_12


title: Latency_model_SAHA_cell_5


title: Latency_model_SAHA_cell_6


title: Latency_model_SAHA_cell_4


title: 3Ta: total blood RNA_baseline_3


title: 1Ta: total blood RNA_baseline_1


title: Latency_model_SAHA_cell_3


title: Latency_model_SAHA_cell_1


title: Latency_model_SAHA_cell_2


title: 39Tb: total blood RNA_posttraining_39


title: 41Tb: total blood RNA_posttraining_41


title: 4Ta: total blood RNA_baseline_4


title: 38Tb: total blood RNA_posttraining_38


title: 42Tb: total blood RNA_posttraining_42


title: 40Tb: total blood RNA_posttraining_40


title: 36Tb: total blood RNA_posttraining_36


title: 37Tb: total blood RNA_posttraining_37


title: 35Tb: total blood RNA_posttraining_35


title: 34Tb: total blood RNA_posttraining_34


title: Latency_model_untreated_cell_96


title: 33Tb: total blood RNA_posttraining_33


title: 2Ta: total blood RNA_baseline_2


title: Latency_model_untreated_cell_95


title: 31Tb: total blood RNA_posttraining_31


title: Latency_model_untreated_cell_93


title: Latency_model_untreated_cell_94


title: 30Tb: total blood RNA_posttraining_30


title: Latency_model_untreated_cell_91


title: Latency_model_untreated_cell_92


title: Latency_model_untreated_cell_90


title: Latency_model_untreated_cell_87


title: 26Tb: total blood RNA_posttraining_26


title: 27Tb: total blood RNA_posttraining_27


title: 3Tb: total blood RNA_posttraining_3


title: 25Tb: total blood RNA_posttraining_25


title: 28Tb: total blood RNA_posttraining_28


title: Latency_model_untreated_cell_89


title: 29Tb: total blood RNA_posttraining_29


title: 32Tb: total blood RNA_posttraining_32


title: Latency_model_untreated_cell_86


title: Latency_model_untreated_cell_85


title: 41Ta: total blood RNA_baseline_41


title: 42Ta: total blood RNA_baseline_42


title: 22Tb: total blood RNA_posttraining_22


title: 40Ta: total blood RNA_baseline_40


title: 23Tb: total blood RNA_posttraining_23


title: 24Tb: total blood RNA_posttraining_24


title: 21Tb: total blood RNA_posttraining_21


title: Latency_model_untreated_cell_88


title: Latency_model_untreated_cell_84


title: Latency_model_untreated_cell_83


title: Latency_model_untreated_cell_81


title: Latency_model_untreated_cell_79


title: Latency_model_untreated_cell_82


title: Latency_model_untreated_cell_77


title: 39Ta: total blood RNA_baseline_39


title: Latency_model_untreated_cell_80


title: Latency_model_untreated_cell_78


title: Latency_model_untreated_cell_76


title: Latency_model_untreated_cell_75


title: Latency_model_untreated_cell_73


title: Latency_model_untreated_cell_72


title: Latency_model_untreated_cell_71


title: 38Ta: total blood RNA_baseline_38


title: 35Ta: total blood RNA_baseline_35


title: 34Ta: total blood RNA_baseline_34


title: Latency_model_untreated_cell_69


title: Latency_model_untreated_cell_70


title: 37Ta: total blood RNA_baseline_37


title: 33Ta: total blood RNA_baseline_33


title: 31Ta: total blood RNA_baseline_31


title: Latency_model_untreated_cell_68


title: Latency_model_untreated_cell_67


title: Latency_model_untreated_cell_65


title: 36Ta: total blood RNA_baseline_36


title: 32Ta: total blood RNA_baseline_32


title: 30Ta: total blood RNA_baseline_30


title: 29Ta: total blood RNA_baseline_29


title: Latency_model_untreated_cell_74


title: 28Ta: total blood RNA_baseline_28


title: 27Ta: total blood RNA_baseline_27


title: Latency_model_untreated_cell_63


title: 26Ta: total blood RNA_baseline_26


title: Latency_model_untreated_cell_62


title: Latency_model_untreated_cell_66


title: 25Ta: total blood RNA_baseline_25


title: 24Ta: total blood RNA_baseline_24


title: Latency_model_untreated_cell_61


title: 23Ta: total blood RNA_baseline_23


title: 22Ta: total blood RNA_baseline_22


title: 21Ta: total blood RNA_baseline_21


title: Latency_model_untreated_cell_60


title: Latency_model_untreated_cell_59


title: Latency_model_untreated_cell_58


title: Latency_model_untreated_cell_57


title: Latency_model_untreated_cell_55


title: Latency_model_untreated_cell_56


title: 18Pb: PBMC RNA_posttraining_15

source_name: PBMCs, posttraining, resting state

extract_protocol: RNA extraction from EDTA tubes was performed within two hours after collection.Peripheral blood mononuclear cells (PBMCs) isolated with Ficoll-Paque™ (GE Healthcare, Fairfield, CT) using TRIzol reagent (Invitrogen, Waltham, MA). RNA was purified in RNeasy columns (Qiagen, Germantown, MD) and treated with RNase-Free DNase Set (Qiagen)

treatment_protocol: Blood was collected in EDTA tubes.

value: peripheral blood mononuclear cells (PBMCs)


title: Latency_model_untreated_cell_54


title: 19Pb: PBMC RNA_posttraining_16


title: Latency_model_untreated_cell_53


title: 16Pb: PBMC RNA_posttraining_13


title: Latency_model_untreated_cell_51


title: Latency_model_untreated_cell_50


title: Latency_model_untreated_cell_49


title: 17Pb: PBMC RNA_posttraining_14


title: 14Pb: PBMC RNA_posttraining_11


title: 15Pb: PBMC RNA_posttraining_12


title: Latency_model_untreated_cell_52


title: 13Pb: PBMC RNA_posttraining_10


title: Latency_model_untreated_cell_47


title: Latency_model_untreated_cell_48


title: Latency_model_untreated_cell_46


title: 10Pb: PBMC RNA_posttraining_8


title: 12Pb: PBMC RNA_posttraining_9


title: 9Pb: PBMC RNA_posttraining_7


title: 7Pb: PBMC RNA_posttraining_5

source_name: PBMCs, pretraining, resting state


title: Latency_model_untreated_cell_45


title: Latency_model_untreated_cell_44


title: 8Pb: PBMC RNA_posttraining_6


title: 3Pb: PBMC RNA_posttraining_3


title: Latency_model_untreated_cell_43


title: 1Pb: PBMC RNA_posttraining_1


title: 2Pb: PBMC RNA_posttraining_2


title: 16Pa: PBMC RNA_baseline_13


title: Latency_model_untreated_cell_42


title: 17Pa: PBMC RNA_baseline_14


title: Latency_model_untreated_cell_41


title: Latency_model_untreated_cell_40


title: 6Pb: PBMC RNA_posttraining_4


title: 15Pa: PBMC RNA_baseline_12


title: 19Pa: PBMC RNA_baseline_16


title: Latency_model_untreated_cell_37


title: Latency_model_untreated_cell_39


title: 18Pa: PBMC RNA_baseline_15


title: Latency_model_untreated_cell_38


title: Latency_model_untreated_cell_36


title: Latency_model_untreated_cell_35


title: Latency_model_untreated_cell_34


title: Latency_model_untreated_cell_33


title: Latency_model_untreated_cell_32


title: Latency_model_untreated_cell_31


title: Latency_model_untreated_cell_30


title: 10Pa: PBMC RNA_baseline_8


title: Latency_model_untreated_cell_29


title: 12Pa: PBMC RNA_baseline_9


title: 13Pa: PBMC RNA_baseline_10


title: 9Pa: PBMC RNA_baseline_7


title: 3Pa: PBMC RNA_baseline_3


title: 7Pa: PBMC RNA_baseline_5


title: Latency_model_untreated_cell_28


title: 6Pa: PBMC RNA_baseline_4


title: 8Pa: PBMC RNA_baseline_6


title: Latency_model_untreated_cell_27


title: 14Pa: PBMC RNA_baseline_11


title: Latency_model_untreated_cell_26


title: Latency_model_untreated_cell_25


title: 1Pa: PBMC RNA_baseline_1


title: 14Mb: muscle RNA_posttraining_14

description: Muscle biopsy was performed at baseline and after the 18-weeks exercise training protocol, 48 hours after the last exercise session

source_name: muscle, posttraining, resting state

extract_protocol: using TRIzol reagent (Invitrogen) and purified with RNeasy Mini Kit (Qiagen). Extracted RNA was was stored at -80 °C until microarray process.

treatment_protocol: The muscle fragment obtained in the procedure was embedded in optimal cutting temperature compound (Tissue-Tek, Sakura Finetek), precooled in isopentane, and immediately frozen in liquid nitrogen for further processing.

value: vastus lateralis (leg muscle)


title: 16Mb: muscle RNA_posttraining_16


title: Latency_model_untreated_cell_24

value: single-cell


title: 20Mb: muscle RNA_posttraining_20


title: 2Pa: PBMC RNA_baseline_2


title: 18Mb: muscle RNA_posttraining_18


title: Latency_model_untreated_cell_22


title: Latency_model_untreated_cell_21


title: Latency_model_untreated_cell_18


title: Latency_model_untreated_cell_64


title: Latency_model_untreated_cell_20


title: Latency_model_untreated_cell_19


title: Latency_model_untreated_cell_17


title: Latency_model_untreated_cell_16


title: Latency_model_untreated_cell_15


title: Latency_model_untreated_cell_23


title: 12Mb: muscle RNA_posttraining_12


title: 19Mb: muscle RNA_posttraining_19


title: 13Mb: muscle RNA_posttraining_13


title: Latency_model_untreated_cell_14


title: Latency_model_untreated_cell_13


title: 9Mb: muscle RNA_posttraining_9


title: 6Mb: muscle RNA_posttraining_6


title: 8Mb: muscle RNA_posttraining_8


title: 19Ma: muscle RNA_baseline_19

source_name: muscle, pretraining, resting state


title: 10Mb: muscle RNA_posttraining_10


title: 1Mb: muscle RNA_posttraining_1


title: 20Ma: muscle RNA_baseline_20


title: 18Ma: muscle RNA_baseline_18


title: 2Mb: muscle RNA_posttraining_2


title: 14Ma: muscle RNA_baseline_14


title: 16Ma: muscle RNA_baseline_16


title: 13Ma: muscle RNA_baseline_13


title: Latency_model_untreated_cell_11


title: Latency_model_untreated_cell_12


title: Latency_model_untreated_cell_10


title: Latency_model_untreated_cell_6


title: Latency_model_untreated_cell_9


title: Latency_model_untreated_cell_7


title: Latency_model_untreated_cell_4


title: Latency_model_untreated_cell_5


title: Latency_model_untreated_cell_2


title: Latency_model_untreated_cell_8


title: Latency_model_untreated_cell_3


title: Latency_model_untreated_cell_1


title: PTEN_VAMP-seq_Exp7

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description: Targeted barcode amplification from DNA

data_processing:
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
For TPMT, after converting from the bcl to fastq format using Illumina’s bcl2fastq version 2.18, a custom script was used to demultiplex the samples by index and call a consensus barcode from the read1 and read2 sequences. To collapse the barcode copies associated with unique UMIs, the UMI (bases 10-20 of the index read) were pasted onto the consensus barcode and unique combinations were identified (sort | uniq -c). The barcode from each unique barcode-UMI pair was used to populate a fastq file that could be used by the Enrich 2 software package to count variants. The barcode from each unique barcode-UMI pair was used to populate a fastq file that could be used by the Enrich 2 software package to count variants.
For PTEN, sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. Barcode paired sequencing reads for the plasmid library, as well as as PTEN VAMP-seq experiments 1 through 4, were joined using the fastq-join tool within the ea-utils package using the default parameters, whereas only one barcode read was collected for PTEN experiments 5 through 8. FASTQ files from these technical replicate amplification and sequencing runs were concatenated for analysis with Enrich2.
The supplied TPMT replicate bin-wise sorting data is the 15-base degenerate barcode followed by a space and the 10 base UMI.
The abundance scores for PTEN and TPMT were calculated as follows: The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average (w_ave) was calculated for each variant, with all weighted average values ranged from a value of 0.25 to 1. Finally, for each experiment, an abundance score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of WT, which was given a score of 1, and the median weighted average value for non-terminal nonsense variants at positions 51 through 349 for PTEN, or positions 51 through 219 for TPMT, which was given an abundance score of 0. The final abundance score for each variant was calculated by taking the mean of the min-max normalized abundance scores across the eight replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each abundance score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed. Lastly, the lower bound of the 95% confidence interval was calculated by multiplying the standard error with the 97.5 percentile value of a normal distribution and subtracting this product from the abundance score. The upper bound of the 95% confidence interval was calculated by instead adding the product with the abundance score.
genome build: NONE
processed data files format and content: The PTEN_barcodeInsertAssignments.tsv.gz and TPMT_barcodeInsertAssignments.tsv.gz processed data files are in gzip-compressed tab-separated text file format, containing the variant-barcode maps determined by subassembly. The TPMT_Barcode_UMI.tar file is a tar archive of gzipped text files containing the 15nt barcode attached to a 10nt unique molecular identifier (separated by a space), for each TPMT sorting bin for each experiment.

source_name: Human-derived cultured cell line

growth_protocol: HEK 293T TetBxb1BFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2 μg/mL doxycycline.

extract_protocol:
Cells were transferred into a microfuge tube, pelleted and stored at -20˚C. Genomic DNA was prepared using the GentraPrep kit (Qiagen) or Dneasy kit (Qiagen).
For TPMT: for each bin, all the purified DNA was spread over eight 25 uL PCR reactions containing Kapa Robust, primers GPS-landing-f (in the genome) and BC-GPS-P7-i#-UMI (3’ of the barcode) to tag the barcodes with a unique molecular index (UMI) and add a sample index.  UMI-tagging PCR were performed using the following conditions: initial denaturation 95 ˚C 2 minutes, followed by three cycles of (95 ˚C 15 seconds, 60 ˚C 20 seconds, 72 ˚C 3 minutes). The eight PCR reactions were pooled and the PCR amplicon was purified using 1x Ampure XP (Beckman Coulter). To shorten the amplicon and add the p5 and p7 Illumina cluster-generating sequences, the UMI-tagged barcodes were then amplified with primers BC-TPMT-P5-v2 and Illumina p7. This PCR was performed with Kapa Robust and SYBR green II on a Bio-Rad mini-opticon qPCR machine, reactions were monitored and removed before saturation of the SYBR green II signal, at around 25 cycles. The amplicons were pooled and gel purified. For PTEN: .  Eight 50 μL first-round PCR reactions were each prepared with a final concentration of ~50 ng/μL input genomic DNA, 1x Kapa HiFi ReadyMix, and 0.25 μM of the KAM499/JJS_501a primers. The reaction conditions were 95 °C for 5 minutes, 98 °C for 20 seconds, 60 °C for 15 seconds, 72 °C for 90 seconds, repeat 7 times, 72 °C for 2 minutes, 4 °C hold. Eight 50 μL reactions were combined, bound to AMPure XP (Beckman Coulter), cleaned, and eluted with 40 μL water. 40% of the eluted volume was mixed with 2x Kapa Robust ReadyMix; JJS_seq_F and one of the indexed reverse primers, JJS_seq_R1a through JJS_seq_R12a were added at 0.25 μM each. Reaction conditions for the second round PCR were 95 °C for 3 minutes, 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, repeat 14 times, 72 °C for 1 minutes, 4 °C hold.  Amplicons were extracted after separation on a 1.5% TBE/agarose gel using a Quantum Prep Freeze ‘N Squeeze DNA Gel Extraction Kit (Bio-Rad).

treatment_protocol: Cells harboring variant libraries, prepared as described above, were sorted using a FACSAria III into bins according to the abundance of their expressed, EGFP tagged variant. First, live, single, recombinant cells were selected using forward and side scatter, mCherry and mTagBFP2 signals. Then, a FITC:PE-Texas Red ratiometric parameter in the BD FACSDIVA software was created. A histogram of the FITC:PE-Texas Red ratio was created and gates dividing the library into four equally populated bins based on the ratio were established.

value: HEK 293T TetBxb1BFP


title: PTEN_VAMP-seq_Exp8

description: Targeted barcode amplification from DNA


title: PTEN_VAMP-seq_Exp6

description: Targeted barcode amplification from DNA


title: PTEN_VAMP-seq_Exp3

description: Targeted barcode amplification from DNA


title: PTEN_VAMP-seq_Exp4

description: Targeted barcode amplification from DNA


title: PTEN_VAMP-seq_Exp5

description: Targeted barcode amplification from DNA


title: 12Ma: muscle RNA_baseline_12

value: male


title: PTEN_VAMP-seq_Exp2

description: Targeted barcode amplification from DNA


title: 9Ma: muscle RNA_baseline_9


title: 10Ma: muscle RNA_baseline_10


title: 8Ma: muscle RNA_baseline_8


title: 6Ma: muscle RNA_baseline_6


title: PTEN_VAMP-seq_Exp1

description: Targeted barcode amplification from DNA


title: 2Ma: muscle RNA_baseline_2


title: 1Ma: muscle RNA_baseline_1


title: Ishi_E2_1_RNA_seq

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description:
processed data files:
Ishi_RNAseq_allsets_raw.counts
Ishi_RNAseq_allsets_normalized.counts

data_processing:
Reads were aligned to the hg19 build of the human genome using hisat2 V 2.0.4 with the following commands: hisat2 --dta  -t -q
counts were quantified with Subread FeatureCounts V. 1.5.1
Differential expression was determined using DESeq2 V 1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values.  These files contain raw and normalized counts for genes from the hg19 genome.

source_name: Ishikawa

growth_protocol: Ishikawa cells were grown in phenol red-free RPMI-1640 media supplemented with 10% charcoal/dextran treated fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin for at least 4 days before lysis.

extract_protocol:
Cells were lysed with RLT (Qiagen) plus 1% BME and total RNA was extracted from the lysis using Zymo's Quick RNA miniprep kit.
Libraries were constructed usinig the Kapa stranded mRNA-seq kit.

treatment_protocol: Cells were treated with 100 nM dexamethasone, 10 nM 17-beta-estradiol, or vehicle control (DMSO) for 1 hour prior to trypsinization.

value: Ishikawa

value: 10 nM Estradiol 8 hr

tag: replicate


title: IshI_Dex_E2_1_RNA_seq

value: 100 nM Dexamethasone and 10 nM Estradiol 8 hr


title: Ishi_Dex_E2_2_RNA_seq


title: Ishi_E2_2_RNA_seq


title: Ishi_DMSO_2_RNA_seq

value: DMSO 8hr