title: M-ATO DN2 sample 1

description:
immature T cell population generated in ATOs from T cell differentiation of murine bone marrow hematopoietic stem cells
GCAMmmATO_DN2.1

growth_protocol:
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Flow cytometry cell sorting of ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). DN2 (Lin- CD4- CD8- c-Kithi CD44hi CD25+).
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Thymic fragments from the mouse thymus were finely dissected in FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) and disrupted by pipetting to release thymocytes into suspension, followed by passage through a 70 µm nylon strainer. Cells were then stained for flow cytometry.  Flow cytometry cell sorting of thymic and ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). Early Thymic Progenitor (ETP; Lin- CD4- CD8- c-Kithi CD44hi CD25-), DN2 (Lin- CD4- CD8- c-Kithi CD44hi CD25+); DN3 (Lin- CD4- CD8- CD44- CD25+); ISP8 (Lin- CD4- CD8+ CD3-); DP early (Lin- CD4+ CD8+ CD3- TCRb-); DP late (Lin- CD4+ CD8+ CD3+ TCRb+); CD8 single positive (CD8SP; Lin- CD4- CD8+ CD3+ TCRb+ CD62L+); CD4 single positive (CD4SP; Lin- CD4+ CD8- CD3+ TCRb+ CD62L+).

treatment_protocol: The freshly sorted Mouse-ATO derived DN2 population was pelleted for RNA extraction

value: immature T cell population


title: M-ATO ETP sample 2

status: Public on Dec 15 2020

type: SRA

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

country: USA

institute: University of California Los Angeles

description:
immature T cell population generated in ATOs from T cell differentiation of murine bone marrow hematopoietic stem cells
GCAMmmATO_ETP.2

library_source: transcriptomic

data_processing:
The STAR ultrafast universal RNA-seq aligner v2.7.0d (Dobin et al., 2013) was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M20 comprehensive genome annotation).
Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Independent filtering was applied as follows: genes with less than half-count per million in all samples, count outliers or low mappability (<50bp) were filtered out for downstream analysis. This masked set included a total of 13760 mouse protein coding genes.
Counts were normalized per-sample in units of FPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCh38 primary assembly
Supplementary_files_format_and_content: Tab delimited. Table of per-gene and per-cell type average expression estimates in units of FPKMs

molecule: total RNA

organism: Mus musculus

source_name: mouse bone marrow hematopoietic stem cells

growth_protocol:
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Flow cytometry cell sorting of ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). Early Thymic Progenitor (ETP; Lin- CD4- CD8- c-Kithi CD44hi CD25-).
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Thymic fragments from the mouse thymus were finely dissected in FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) and disrupted by pipetting to release thymocytes into suspension, followed by passage through a 70 µm nylon strainer. Cells were then stained for flow cytometry.  Flow cytometry cell sorting of thymic and ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). Early Thymic Progenitor (ETP; Lin- CD4- CD8- c-Kithi CD44hi CD25-), DN2 (Lin- CD4- CD8- c-Kithi CD44hi CD25+); DN3 (Lin- CD4- CD8- CD44- CD25+); ISP8 (Lin- CD4- CD8+ CD3-); DP early (Lin- CD4+ CD8+ CD3- TCRb-); DP late (Lin- CD4+ CD8+ CD3+ TCRb+); CD8 single positive (CD8SP; Lin- CD4- CD8+ CD3+ TCRb+ CD62L+); CD4 single positive (CD4SP; Lin- CD4+ CD8- CD3+ TCRb+ CD62L+).

extract_protocol:
All samples were extracted using miRNeasy Micro Kit (Qiagen).
1.5ng of total RNA was input to generate sequencing libraries with SMARTer Stranded Total RNA-Seq (Pico) Kit (Clonetech, Cat. 635005).
Paired-end 150 bp sequencing was performed on an Illumina HiSeq 3000.

treatment_protocol: The freshly sorted Mouse-ATO derived ETP population was pelleted for RNA extraction

tag: tissue

value: thymic organoid

tag: phenotype

value: Lin- CD4- CD8- c-Kithi CD44hi CD25-

tag: cell type


title: M-ATO CD4SP sample 1

description:
Mature T cell population generated in ATOs from T cell differentiation of murine bone marrow hematopoietic stem cells
GCAMmmATO_SP4.1

growth_protocol:
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Flow cytometry cell sorting of ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). CD4 single positive (CD4SP; Lin- CD4+ CD8- CD3+ TCRb+ CD62L+).
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Thymic fragments from the mouse thymus were finely dissected in FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) and disrupted by pipetting to release thymocytes into suspension, followed by passage through a 70 µm nylon strainer. Cells were then stained for flow cytometry.  Flow cytometry cell sorting of thymic and ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). Early Thymic Progenitor (ETP; Lin- CD4- CD8- c-Kithi CD44hi CD25-), DN2 (Lin- CD4- CD8- c-Kithi CD44hi CD25+); DN3 (Lin- CD4- CD8- CD44- CD25+); ISP8 (Lin- CD4- CD8+ CD3-); DP early (Lin- CD4+ CD8+ CD3- TCRb-); DP late (Lin- CD4+ CD8+ CD3+ TCRb+); CD8 single positive (CD8SP; Lin- CD4- CD8+ CD3+ TCRb+ CD62L+); CD4 single positive (CD4SP; Lin- CD4+ CD8- CD3+ TCRb+ CD62L+).

treatment_protocol: The freshly sorted Mouse-ATO derived SP4 late population was pelleted for RNA extraction

value: Lin- CD4+ CD8- CD3+ TCRb+ CD62L+

value: mature T cell population


title: 2423_400mkd_Liver

city: Indianapolis

first: Kamin

last: Johnson

state: IN

address: 9330 Zionsville Rd

institute: Corteva Agriscience

data_processing:
Basecalls performed using Illumina CASAVA software version 1.8
Raw sequencing reads were trimmed and filtered for low quality bases using the fastq-mcf tool from the ea-utils software package (v1.1.0) with the minimum remaining sequence length option set to 30bp and quality threshold set to 30
Trimmed reads were subsequently mapped to the rat reference genome (version 6.0.80) using the hisat2 mapping software (v2.0.3) run using default parameter settings and in stranded mode
Using HTSeq (v0.6.1), the reads mapped to the antisense strand of each gene were counted
Genome_build: Rattus norvegicus (version 6.0.80)
Supplementary_files_format_and_content: tab-delimited text files include raw gene count values for each Sample ...

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was extracted from organs stored in RNAlater using a Qiagen RNeasy kit.  Samples were digested with DNAase during the RNA isolation process to avoid DNA contamination.  RNA quantity was measured using a NanoDrop ND-1000 spectrophotometer.  Total RNA quality was examined using the HT RNA Std Sens assay on a LabChip GX instrument (PerkinElmer; Waltham, MA) according to the manufacturer’s instructions.
The Illumina Truseq Stranded mRNA library preparation kit was used to prepare mRNA library templates following the manufacturer’s recommended protocol.  In brief, poly-A containing mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  Purified mRNA was fragmented to approximately 200 bp average length using divalent cations under high temperature.  Following fragmentation, SuperScript II reverse transcriptase and random primers were used to copy the mRNA into first strand cDNA.  The cDNA was further converted into double stranded cDNA using DNA polymerase I and RNase H.  These double stranded cDNA fragments then underwent end repair, A-tailing, and ligation to indexed Illumina adapters.  Finally, adapter-ligated library products were enriched with 15 cycles of PCR and purified.

value: Liver

tag: developmental stage

value: Adult

tag: strain

value: Crl:CD (SD); Sprague-Dawley

tag: age at study start

value: 8-10 weeks

tag: Sex

value: Male

tag: molecule exposure

value: Myclobutanil

tag: exposure

value: Daily via oral gavage for 14 days

tag: corn oil dose level

value: 4 ml/kg body weight

tag: dose level (mg/kg)

tag: sample deemed an outlier

value: No


title: 2422_400mkd_Liver


title: M-ATO ETP sample 1

description:
immature T cell population generated in ATOs from T cell differentiation of murine bone marrow hematopoietic stem cells
GCAMmmATO_ETP.1


title: 2424_400mkd_Liver


title: 2420_150mkd_Liver


title: 2418_150mkd_Liver


title: 2415_150mkd_Liver


title: 2416_150mkd_Liver


title: 2419_150mkd_Liver


title: 2414_30mkd_Liver


title: 2417_150mkd_Liver


title: 2412_30mkd_Liver


title: M-ATO DN2 sample 2

description:
immature T cell population generated in ATOs from T cell differentiation of murine bone marrow hematopoietic stem cells
GCAMmmATO_DN2.2

value: Lin- CD4- CD8- c-Kithi CD44hi CD25+


title: 2408_Vehicle_Liver

value: Corn oil (vehicle)


title: 2411_30mkd_Liver


title: 2409_30mkd_Liver


title: 2405_Vehicle_Liver


title: 2410_30mkd_Liver


title: M-ATO DN3 sample 1

description:
immature T cell population generated in ATOs from T cell differentiation of murine bone marrow hematopoietic stem cells
GCAMmmATO_DN3.1

growth_protocol:
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Flow cytometry cell sorting of ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). DN3 (Lin- CD4- CD8- CD44- CD25+).
ATOs were generated as previously described (Seet et al., 2017). MS5-mDLL4 cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“D/F12-B27”) composed of DMEM-F12 (Gibco, Cat# 11320033) (in some experiments, RPMI 1640 (CellGro, Cat# 10-040-CV) was used as basal media as indicated), 2% B27 supplement (ThermoFisher Scientific, Grand Island, NY, Cat# 17504-044) (in some experiments, 4% B27 was used as indicated), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO, Cat# A8960-5G) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA, Cat# 400-109), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY, Cat# 35050-061), 5 ng/ml rmFLT3L (Peprotech, Rocky Hill, NJ, Cat# 250-31L), 5 ng/ml rmIL-7 (Peprotech, Cat# 217-17), 10 ng/ml rmSCF (Peprotech, Cat# 250-03) (SCF was added only for the first week of culture) and beta mercaptoethanol (bME) (0.05mM) (Sigma-Aldrich, Cat# M7522). D/F12-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified murine HSPC cells (1- 4000 cells / ATO) in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 µl D/F12-B27 per ATO and mixed by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml D/F12-B27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh D/F12-B27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer.  Thymic fragments from the mouse thymus were finely dissected in FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) and disrupted by pipetting to release thymocytes into suspension, followed by passage through a 70 µm nylon strainer. Cells were then stained for flow cytometry.  Flow cytometry cell sorting of thymic and ATO-derived T cell populations used the following surface phenotypes: (Lin- stands here for: Ter119-, TCRγδ-, B220-, CD19-, CD11c-, CD11b-, Gr1-, NK1.1-). Early Thymic Progenitor (ETP; Lin- CD4- CD8- c-Kithi CD44hi CD25-), DN2 (Lin- CD4- CD8- c-Kithi CD44hi CD25+); DN3 (Lin- CD4- CD8- CD44- CD25+); ISP8 (Lin- CD4- CD8+ CD3-); DP early (Lin- CD4+ CD8+ CD3- TCRb-); DP late (Lin- CD4+ CD8+ CD3+ TCRb+); CD8 single positive (CD8SP; Lin- CD4- CD8+ CD3+ TCRb+ CD62L+); CD4 single positive (CD4SP; Lin- CD4+ CD8- CD3+ TCRb+ CD62L+).

treatment_protocol: The freshly sorted Mouse-ATO derived DN3 population was pelleted for RNA extraction

value: Lin- CD4- CD8- CD44- CD25+


title: 2407_Vehicle_Liver


title: 2421_400mkd_Liver


title: 2425_400mkd_Testis

source_name: Testis

value: Testis


title: 2424_400mkd_Testis


title: 2421_400mkd_Testis


title: 2419_150mkd_Testis


title: 2423_400mkd_Testis


title: 2422_400mkd_Testis


title: 2413_30mkd_Liver


title: 2418_150mkd_Testis


title: 2417_150mkd_Testis


title: 2406_Vehicle_Liver


title: 2404_Vehicle_Liver


title: 2413_30mkd_Testis


title: 2414_30mkd_Testis


title: 2411_30mkd_Testis


title: 2416_150mkd_Testis


title: 2426_400mkd_Testis


title: 2408_Vehicle_Testis


title: 2405_Vehicle_Testis


title: 2403_Vehicle_Liver


title: 2403_Vehicle_Testis


title: 2407_Vehicle_Testis


title: 2409_30mkd_Testis


title: 2412_30mkd_Testis


title: 2404_Vehicle_Testis


title: 2406_Vehicle_Testis


title: Sample16 Propofol control

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

description: stranded

data_processing:
Read alignments and expression read counts were generated using STAR.
Genome_build: rn5 (reference genome of Rattus norvegicus) from UCSC was used for read assembly and mapping.
Supplementary_files_format_and_content: Raw read counts summarized per gene per sample

source_name: liver tissue

extract_protocol:
Total RNA pooled from rat liver samples was isolated using the RNeasy plus mini kit (Qiagen) and concentrations were estimated using NanoDrop (ThermoFisher Scientific). mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Sepsis/CLP Vs. Control for Propofol and Isoflurane

tag: anesthetic background

value: Propofol

value: Sprague-Dawley

tag: age

value: 10 weeks old

tag: sepsis/control

value: control

tag: gender

value: male


title: 2415_150mkd_Testis

value: Adult


title: Sample11 Propofol sepsis

description: stranded

value: sepsis


title: Sample13 Propofol control

description: stranded


title: Sample 15 Propofol control

description: stranded


title: Sample10 Propofol sepsis

description: stranded


title: Sample 8 Isoflurane control

description: stranded

value: Isoflurane


title: Sample14 Propofol control

description: stranded


title: Sample 7 Isoflurane control

description: stranded


title: 2420_150mkd_Testis

value: Crl:CD (SD); Sprague-Dawley

value: 8-10 weeks

value: Male


title: Sample 6 Isoflurane control

description: stranded


title: Sample 5 Isoflurane control

description: stranded


title: 2410_30mkd_Testis

value: Myclobutanil

value: Daily via oral gavage for 14 days

value: 4 ml/kg body weight


title: Sample 4 Isoflurane sepsis

description: stranded


title: Sample9 Propofol sepsis

description: stranded


title: Sample 2 Isoflurane sepsis

description: stranded


title: Sample 1 Isoflurane sepsis

description: stranded


title: Sample 3 Isoflurane sepsis

description: stranded


title: ELA_rep5

city: Bethesda

first: Anton

last: Schulmann

state: Maryland (MD)

address: 35 Convent Dr

institute: NIH/NIMH

data_processing:
RNA-seq read alignment (STAR, 2.5.0)
gene-level read counting (HTSeq, 0.6.1)
Genome_build: rn6
Supplementary_files_format_and_content: counts, tab-delimited

molecule: polyA RNA

source_name: dorsal hippocampus

extract_protocol:
RNA was isolated using the Qiagen RNeasy Kit, according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq v2 kit with minor modifications. Briefly, 1 µg of total RNA was used as input, and poly(A) selection was carried out according to the protocol. Modifications to the TruSeq v2 protocol included a fragmentation time of 3 minutes. Additionally, 8 cycles of PCR were run for the enrichment of DNA fragments. Adapters were chosen according to protocol recommendations. Quantification of the libraries was accomplished using the KAPA qPCR kit for Illumina libraries.

value: dorsal hippocampus

value: 8 weeks

tag: condition

value: Early-life adversity


title: ELA_rep3

tag: tissue


title: CTL_rep4

value: Control rearing


title: ELA_rep2

value: Sprague-Dawley


title: CTL_rep3


title: CTL_rep2


title: Sample12 Propofol sepsis

description: stranded

value: Propofol

value: 10 weeks old


title: 1hrDex_HighDigest_1 MNase-seq

city: Philadelphia

first: Doris

last: Wagner

state: PA

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania

library_source: genomic

data_processing:
Base-calling was performed automatically in Illumina BaseSpace
Trimmed sequencing reads were mapped to Release 10 of the Arabidopsis Genome (TAIR10) using Bowtie v1.2.2 with the `--best -m1 --seed 0` parameters
Paired-end mapped read with fragment size <130 or >170 were removed
Duplicated reads were marked and removed using the MarkDuplicates function in Picard tools 2.9.4
Nucleosome occupancy values of each base pair for each biological replicate wer generated by DANPOS3 using parameter: `--smooth_width 10 -H 1 -m 1 --mifrsz 40 -q 50 -u .1`
For all conditions except 1 hr Dex-LowDigest both biological were analyzed using DANPOS3 and the parameters stated above
For 1hr Dex_LowDigest a merged pooled read was analyzed using DANPOS3 using the parameters stated above
Genome_build: TAIR10
Supplementary_files_format_and_content: *bw: Protein occupancy values of each base pair
Supplementary_files_format_and_content: *bigwig: Protein occupancy values of each base pair averaging two biological replicates
Supplementary_files_format_and_content: *bed: BED file indicating nucleosome regions with DANPOS3 `smt_value` set to score

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: callus on CIM for 5 days with dex treatment

growth_protocol: Plants were grown on 1/2 MS plates for 3 weeks. Roots were harvested from 3-week-old seedlings and put on CIM for up to 5 days with either 1hr of mock or dex treatment followed by standard ( high) or low MNase digest.

extract_protocol:
MNase-seq was conducted using the protocol discribed in Gevry, N., Methods Mol Biol, 2009. Mononuclesoome fractions were isolated and purified.
MNase DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406) and quantified by the NEBNext Library Quant Kit (cat. E7630L). Equal amounts of DNA were pooled from each library with different dual indexing primers and paired-end sequenced on a Next seq 500

tag: cultivar

value: Landsberg erecta

value: callus

tag: transgenic

tag: digest

value: High digest

tag: treatment

value: 1hr Dex treatment


title: 1hrMock_HighDigest_2 MNase-seq

source_name: callus on CIM for 5 days with mock treatment

value: 1hr Mock treatment


title: 1hrMock_HighDigest_1 MNase-seq


title: 1hrDex_HighDigest_2 MNase-seq


title: 1hrDex_LowDigest_2 MNase-seq

value: WT


title: 1hrMock_LowDigest_2 MNase-seq


title: 1hrDex_LowDigest_1 MNase-seq


title: 24hrDexB RNA-Seq

data_processing:
Base-calling was performed automatically in Illumina BaseSpace
FASTQ reads were trimmed using TRIMMOMATIC v0.36 (SE -phred33 ILLUMINACLIP:adapters.fasta:2:30:10 HEADCROP:15 MINLEN:70 TOPHRED33)
Sequencing quality metrics were obtained for the raw and trimmed FASTQ files with FASTQC v0.11.5
Trimmed sequencing reads were mapped to Release 10 of the Arabidopsis Genome (TAIR10) using STAR v2.5.3a (--sjdbOverhang 100 --outSAMprimaryFlag AllBestScore --outSJfilterCountTotalMin 10 5 5 5 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignIntronMin 60 --alignIntronMax 6000 --outFilterMismatchNmax)
Read counts at each gene for each sample and replicates was calculated with HT-Seq v0.7.2 htseq-count parameters: --stranded='no' --minaqual=30
Genome_build: TAIR10
Supplementary_files_format_and_content: htseq_result: unormalized read counts of each gene feature in the Arabidopsis genome for each individual RNA-seq sample and replicate calculated via HTSeq.
*A/B.bigwig: Bigwig showing 10RPM-normalized coverage
*Bigwigs on series record: showing 10RPM-normalized coverage after averaging the read counts from two biological replicates

growth_protocol: Plants were grown on 1/2MS plates for 3 weeks. Roots were harvested from 3-week-old seedlings and put on CIM for up to 5 days with either 1hr of mock or dex treatment, 6hr of mock or dex treatment and 24hr of mock or dex treatment

extract_protocol:
total RNAs were extracted by trizol and chloroform and further purified by Qiagen RNA cleanup kit
Manual library preparation with multiple steps -- steps described in detail in paper

treatment_protocol: 24hr Dex treatment

tag: mutant

tag: deseq2 analyzed for differential expression

value: yes


title: Heat shock clk-2 rep1

city: Oslo

first: Rafal

last: Ciosk

state: Oslo

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

data_processing:
RNAseq data were mapped to C.elegans genome using STAR 2.5.4a
Gene counts were generated by the function of summarizeOverlaps in GenomicAlignments package from Bioconductor
DESeq2 were used to normalize data and calculate differentially expressed genes.
Genome_build: WBcel235
Supplementary_files_format_and_content: txt file with raw read count per gene from each sample

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: worms were grown at 20C

extract_protocol:
Animals were grown to young adulthood, frozen in liquid nitrogen and RNA was extracted by Trizol treatment.
TruSeq mRNA Library preparation kit
Total RNA-seq ScriptSeq

treatment_protocol: worms were placed at 25C for 3 hours for heat shock treatment

tag: genotype

value: Heat shock

value: Whole animal


title: Heat shock N2 rep1

value: N2 wild type


title: 6hrMockA RNA-Seq

treatment_protocol: 6hr Mock treatment


title: clk-2 rep2


title: ELA_rep4

value: dorsal hippocampus

tag: strain

tag: Sex

value: male


title: 24hrDexA RNA-Seq


title: clk-2 rep1


title: 1hrMockB RNA-Seq

treatment_protocol: 1hr Mock treatment


title: 6hrMockB RNA-Seq


title: 6hrDexA RNA-Seq

treatment_protocol: 6hr Dex treatment


title: smg-2 rep2


title: 24hrMockB RNA-Seq

treatment_protocol: 24hr Mock treatment


title: 1hrDexA RNA-Seq

treatment_protocol: 1hr Dex treatment


title: 24hrMockA RNA-Seq


title: 1hrDexB RNA-Seq


title: 1hrMockA RNA-Seq


title: 6hrDexB RNA-Seq


title: smg-2 rep1


title: ELA_rep1

value: 8 weeks

value: Early-life adversity


title: N2 rep1


title: smg-1 rep1


title: N2 rep2


title: smg-1 rep2


title: CTL_rep1

value: Sprague-Dawley

value: Control rearing


title: u6bsD haploid MATa mRNA seq YPDlog replicate 1

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: RNA seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 3 --alignIntronMax 5000” was used to perform the read mapping to the S. cerevisiae SK1 genome assembly from Keeney lab. Alignments with mapping quality of <10 or soft/hard-clipping were filtered.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10" to split the alignments.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the RNA-seq BedGraph tracks across the genome, for both forward and reverse strands. The BedGraph tracks were normalized by the number of usable reads in each library.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both forward and reverse strands. See data processing step for more details.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in regular YPD  (2.0% (wt/vol) glucose) and grown to saturation (OD600 ~ 10) at 30°C and 300 rpm. About 0.4 OD of saturated yeast culture were inoculated into new flasks containing pre-sporualtion media which contains no glucose. After 16-18 hours, cells were then pelleted, washed with sterile miliQ water, and re-suspended in sporulation (SPO) media at an OD600 of 1.8.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
At least 5 μg of total RNA was treated with DNAse and purified on column (Macherey-Nagel). At least 500 ng of purified total RNA was used as the inputs for the KAPA mRNA Hyper Prep kit (KK8580, Roche). Libraries were prepared according to manufacturer’s instructions. After bead based clean up, libraries were sequenced on an Illumina HiSeq 4000 to an equivalent of 75 bases single-end reads, at a depth of approximately 20 million reads per library.

tag: strain/background

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1, u6bsD

value: no treatment


title: u6bsD haploid MATa mRNA seq YPDlog replicate 2

description: RNA seq


title: Wild-type diploid MATa/alpha mRNA seq SPO 6h replicate 2

description: RNA seq

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: Wild-type diploid MATa/alpha mRNA seq SPO 6h replicate 1

description: RNA seq


title: 1hrMock_LowDigest_1 MNase-seq

value: Landsberg erecta

value: callus


title: SPT16-AID control MNase seq 6h replicate 2

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”.
‘bwa mem’ (version 0.7.15) was used to perform the read mapping to the SK1 genome assembly.
The resulting alignments were filtered by SAMtools  (version 1.3.1) (Li et al. 2009) with parameters “-q 10 -f 2 -F 2828”.
bedtools bamtobed' was used to convert the BAM alignment files to BED files containing paired reads, which are input files for DANPOS2 analysis.
DANPOS2 ‘dpos’ command  (version 2.2.2) (Chen et al. 2013) was used for generating the genome-wide occupancy tracks (merging two replicates of each condition) and identifying regions with significant changes, with parameters “-q 1000 -a 1 -m 1 --clonalcut 1e-10 --testcut 1e-10 --extend 74”.
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: BED files containing properly paired Mnase-seq reads. See data processing step for more details.

source_name: SPT16-AID control MNase seq 6h

growth_protocol: Cells were grown in regular YPD  (2.0% (wt/vol) glucose) and grown to exponential phase (OD600 < 2.0) at 30°C and 300 rpm. Approximately 0.05 OD of exponentially growing yeast were inoculated into new flasks containing reduced glucose YPD (1.0% (wt/vol) glucose). After 16-18 hours, cells were then pelleted, washed with sterile miliQ water, and re-suspended in supplemented sporulation (SPO) media at an OD600 of 2.5.

extract_protocol:
Approximately 90 OD600 units of cells were crosslinked for 20 min with formaldehyde (1% v/v) and the reaction was quenched with glycine (125 mM). Subsequently, cells were resuspended in 20 ml of buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) plus β-mercaptoethanol (10mM) and treated with 50ul of 5mg/ml T100 Zymolase (MP Biomedicals) for 60 min. Next, cells were resuspended in 2.5 ml NP buffer (0.5 mM spermidine, 1 mM β-mercaptoethanol (β -ME), 0.075% (w/v) Tergitol solution-type NP-40 detergent (NP-40), 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2 , 1 mM CaCl2). 100ul of chromatin (equivalent to 10% of a 90 ODunit prep) was treated with various concentrations of MNase (NEB), equivalent to 1/5, 1/12 or 1/25 µl of a 2 mg/ml stock, for 30 min at 37 °C. The reaction was quenched with EDTA (10 mM).  To check for the extent of MNase digestion, 100 μl of MNase treated extracts were reverse crosslinked overnight in SDS-TE (1% (w/v) SDS, 10 mM Tris pH 8, 1 mM EDTA) and treated with RNase A.  DNA fragments were purified using phenol-chloroform-isoamyl alcohol, were extracted using ethanol precipitation, were resuspended in TE buffer and were separated by gel electrophoresis. The extracts which showed a mostly mono-nucleosome pattern were chosen. The gel fragments containing the mono-nucleosome band (100-200 bp) was excised, and the DNA purified using a gel purification kit (Macherey-Nagel).
At least 1 ng of purified DNA fragments was used as the inputs for the KAPA Hyper Prep kit (KK8504, Roche). Libraries were prepared according to manufacturer’s instructions. Amplified libraries were cleaned and purified by gel extraction and sequenced on an Illumina HiSeq 2500 to an equivalent of 50 bases paired-end reads, at a depth of approximately 8 million reads per library.

treatment_protocol: For the regular WT time course, 50 μM CuSO4 was added after 2h in SPO and 1 μM β-estradiol was added after 6h in SPO for synchronous sporulation. For the mutant samples and their controls,  50 μM CuSO4 was added after 2h in SPO. Additionally after 2h in SPO, all cells with the SPT16-AID allele were treated with 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO.

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative

value: 50 μM CuSO4 (2h), 500 μM indole-3-acetic acid (2h)

tag: molecule subtype

value: Nucleosome protected gDNA fragments


title: SPT16-AID control MNase seq 6h replicate 1


title: SPT16-AID, OsTIR MNase seq 6h replicate 2

source_name: SPT16-AID, OsTIR MNase seq 6h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: SPT16-AID, OsTIR MNase seq 0h  replicate 2

source_name: SPT16-AID, OsTIR MNase seq 0h


title: SPT16-AID control MNase seq 0h replicate 1

source_name: SPT16-AID control MNase seq 0h


title: SPT16-AID, OsTIR MNase seq 0h  replicate 1


title: SPT16-AID control MNase seq 0h replicate 2


title: Wild-type MNase seq 7h replicate 1

source_name: Wild-type MNase seq 7h

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative

value: 50 μM CuSO4 (2h), 1 μM β-estradiol (6h)


title: Wild-type MNase seq 7h replicate 2


title: Wild-type MNase seq 9h replicate 1

source_name: Wild-type MNase seq 9h


title: set3 MNase seq 6h replicate 1

source_name: set3 MNase seq 6h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative

value: 50 μM CuSO4 (2h)


title: SPT16-AID, OsTIR MNase seq 6h replicate 1


title: set3 MNase seq 6h replicate 2


title: set2 set3 MNase seq 6h replicate 2

source_name: set2 set3 MNase seq 6h

value: FW2912 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3, set3::His3MX, set2::His3MX) SK1 derivative


title: set2 MNase seq 6h replicate 1

source_name: set2 MNase seq 6h

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative


title: Wild-type MNase seq 6h replicate 2

source_name: Wild-type MNase seq 6h


title: Wild-type MNase seq 60 min RTG replicate 2

source_name: Wild-type MNase seq 60 min RTG

value: 50 μM CuSO4 (2h), shift from SPO to YPD (6h)


title: Wild-type MNase seq 60 min RTG replicate 1


title: Wild-type MNase seq 2h replicate 2

source_name: Wild-type MNase seq 2h


title: Wild-type MNase seq 3h replicate 2

source_name: Wild-type MNase seq 3h


title: Wild-type MNase seq 3h replicate 1


title: Wild-type MNase seq 6h replicate 1


title: set3 MNase seq 0h replicate 2

source_name: set3 MNase seq 0h


title: Wild-type MNase seq 15 min RTG replicate 2

source_name: Wild-type MNase seq 15 min RTG


title: Wild-type MNase seq 15 min RTG replicate 1


title: set3 MNase seq 0h replicate 1


title: Wild-type MNase seq 9h replicate 2


title: set2 MNase seq 0h replicate 2

source_name: set2 MNase seq 0h


title: set2 MNase seq 6h replicate 2


title: set2 set3 MNase seq 6h replicate 1


title: set2 MNase seq 0h replicate 1


title: set2 set3 MNase seq 0h replicate 2

source_name: set2 set3 MNase seq 0h


title: set2 set3 MNase seq 0h replicate 1


title: Wild-type MNase seq 0h replicate 2

source_name: Wild-type MNase seq 0h


title: Wild-type MNase seq 0h replicate 1


title: Wild-type MNase seq 2h replicate 1


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet pool B

type: RNA

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description:
Ri_AC.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.

hyb_protocol: After fragmentation, cRNA were hybridized on Affymetrix Mouse Gene 1.0 ST Array. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scan protocol was performed according to the manufacturer's instruction.

data_processing: mRNA signal intensities were background corrected by RMA and quantile normalized using the Bioconductor library oligo. Batch effect was attenuated with COMBAT algorithm. Probesets were annotated with mogene10sttranscriptcluster.db library of Bioconductor, and unassigned probes were removed. Duplicated probes were filtered by selecting the probe with the highest interquartile range. Differential expression was computed by an adjusted moderate t-test implemented in the limma package.

label: biotin

label_protocol: 3 pools per condition were evaluated for a total N=15 per tissue. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: We used male 7-week-old C57BL/6 mice (26 g ± 0.5 g of weight) purchased from the animal facility of the INCMNSZ. Animals were housed (4/cage) in a 12-h light–dark cycle at a constant temperature (23 ± 2 °C) and relative humidity (45-55%).

extract_protocol: RNA was isolated with TRIzol reagent (Invitrogen, USA), according to the manufacturer’s protocol from brain, kidney and liver.

treatment_protocol: Mice were assigned to one of following experimental groups (N=40, n=8 per experimental group) in a complete randomization strategy: 1) Control: Control diet (AIN-93); 2) HCD: High-cholesterol diet (0.5% cholesterol) (Sigma-Aldrich, New Zealand); 3) HCD+Sim: High-cholesterol diet (0.5%) plus simvastatin (0.03 g/100 g); 4) HCD+Gl-1: High-cholesterol diet (0.5%) plus the Gl-1 extract (1.0%); 5) HCD+Gl-2: High-cholesterol diet (0.5%) plus the Gl-2 extract (1.0%).

value: Male

value: 7 weeks

value: Kidney

tag: diet

value: AIN-93 + 0.5% cholesterol


title: Liver of C57BL/6 mice fed with normal diet pool C

description:
Hi_Control.3
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.

tag: age

value: Liver


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool B

description:
Ri_AC.Siv.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.

value: Simvastatin


title: Kidney of C57BL/6 mice fed with normal diet pool C

description:
Ri_Control.3
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with normal diet pool A

description:
Hi_Control.1
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with normal diet pool B

description:
Hi_Control.2
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool A

description:
Ri_AC.Siv.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet pool A

description:
Ri_AC.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool C

description:
Hi_AC.Siv.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool C

description:
Ri_AC.Siv.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.


title: Kidney of C57BL/6 mice fed with normal diet pool A

description:
Ri_Control.1
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool A

description:
Hi_AC.Siv.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool A

description:
Ri_AC.Gl2.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).

value: Ganoderma lucidum 2


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool B

description:
Ri_AC.Gl1.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.

value: Ganoderma lucidum 1


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool C

description:
Ri_AC.Gl2.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool A

description:
Ri_AC.Gl1.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet pool C

description:
Ri_AC.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool C

description:
Hi_AC.Gl2.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool C

description:
Ri_AC.Gl1.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.


title: Kidney of C57BL/6 mice fed with normal diet pool B

description:
Ri_Control.2
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: Kidney of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool B

description:
Ri_AC.Gl2.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool B

description:
Hi_AC.Siv.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet pool B

description:
Hi_AC.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool A

description:
Hi_AC.Gl2.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool C

description:
Hi_AC.Gl1.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool B

description:
Hi_AC.Gl2.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Liver of C57BL/6 mice fed with a high-cholesterol diet pool A

description:
Hi_AC.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool A

description:
Hi_AC.Gl1.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet pool C

description:
Hi_AC.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.


title: Liver of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool B

description:
Hi_AC.Gl1.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.


title: A/128PTX-37d - rep 1

city: Poznan

first: Aleksandra

middle: Maria

last: Swiercz

address: Piotrowo 2

department: Institute of Computing Science

country: Poland

institute: Poznan University of Technology

data_processing:
Sequencing by synthesis (SBS) was performed with Genome Analyzer IIx (Illumina). Technical replicates of the libraries were clustered and sequenced with the use of different flow cell, but with the same 75-cycle multiplexed single-read sequencing recipe. Finally, we obtained approximately 25 million 75 nt-long reads per library.
Raw reads were next filtered according to the quality with the use of FASTX-Toolkit.  Reads consisted of less than 80% nucleotides with at least 28 quality were discarded. On average 15% reads were filtered out per library.
The remaining reads were mapped to the human reference genome version hg19 with TopHat2. On average, 96% of reads remained after filtering were mapped to the genome.
After aligning reads, the number of reads (counts) mapped to known genes were obtained with usage of featureCounts function implemented in R package “Rsubread”. All the genes with very low expression values across the examined samples were discarded – only genes with more than 5 normalized reads mapped to the gene for at least 2 samples were included in further analysis.
The differential expression analysis was performed using linear models implemented in ‘limma’ package for R. The counts for every gene were normalized with voom function which calculates the log2 value of counts, estimates their mean and variance, and generates a precision weight for each observation. Next, the linear model was fitted to the data set including expression values for each gene (using lmfit function) and empirical Bayes statistics (eBayes function) was used to improve power of a test used for differential expression detection in sets with a high number of genes and a small number of replicates.
Genome_build: human reference genome version hg19
Supplementary_files_format_and_content: Matrix table coma delimited with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: ovarian cancer cell subline

growth_protocol: Cells were grown in monolayer and conventionally were maintained in RPMI 1640 medium with phenol red , supplemented with 5% heat-inactivated fetal bovine serum (FBS) (Life Technologies – Thermo Fisher Scientific), without antibiotics and antimycotics, at 37ºC and 5% CO2.

extract_protocol:
Total RNA was isolated from 5x106 cells using RNeasy Mini Kit (Qiagen) according to manufacturer instructions. Method is based on lysing cells in RLT buffer containing guanidine isothiocyanate, purification the product on spin column with silica-gel membrane and treatment by DNaseI to remove genomic DNA contamination. Isolated RNA was stored in -80ºC.
RNA integrity number (RIN) was analyzed using Bioanalyzer 2100 and RNA 6000 Nano Kit (Agilent Technologies), according to manufacturer instructions. RNA concentration was measured using fluorometer Qubit and Qubit RNA BR Assay Kit (Life Technologies), according to manufacturer instructions. Fourteen NGS libraries were prepared following the protocol  of the TrueSeq RNA Sample Preparation Kit v2 (Illumina). From 4 μg of total RNA input of each sample the poly-A containing mRNA molecules were purified using oligo-dT attached magnetic beads. Then the mRNA was fragmented into about 150 nucleotide (nt) pieces using divalent cations under 65ºC. The cleaved mRNA fragments were primed with random hexamers and reverse transcribed by SuperScript III reverse transcriptase into first strand cDNA. Subsequent stage involved second strand cDNA synthesis using DNA Polymerase I and removing the RNA template using RNaseH. Double stranded cDNA (ds cDNA) was purified using AMPure XP beads. Then the overhangs resulting from fragmentation were converted into blunt ends, phosphorylated on 5’ ends and a single A nucleotide was added to 3’ ends. Multiple indexing adapters with single T nucleotide 3’ ends were ligated to the ends of the ds cDNA. Finally, the 12 cycle PCR was performed to selectively enrich those DNA fragments that had adapter molecules on both ends and to amplify the amount of DNA to sequence. Libraries were qualified using Bioanalyzer 2100 and DNA 1000 Kit (Agilent),  according to manufacturer instructions. In all libraries the final product was an anticipated band at approximately 270 bp. The total concentration of the libraries was measured using fluorometer Qubit and Qubit dsDNA BR Assay Kit (Life Technologies), according to manufacturer instructions. Libraries were additionally quantified with qPCR according to Illumina recommended protocol, using Rotor-Gene Q (Qiagen) and KAPA SYBR FAST qPCR Master Mix Universal (Kapa Biosystems). Validated libraries were diluted to 10 nM concentration, then pooled in batches of two differentially indexed samples in equal amounts, denatured and diluted to 10 pM concentration. Cluster generation was performed in cBot (Illumina), where the libraries were bound with a flow cell (two libraries per lane). Sequencing by synthesis (SBS) was performed with Genome Analyzer IIx (Illumina). Technical replicates of the libraries were clustered and sequenced with the use of different flow cell, but with the same 75-cycle multiplexed single-read sequencing recipe. Finally, we obtained approximately 25 million 75 nt-long reads per library.

treatment_protocol:
A/64PTX-19d cells treated with 128 nM PTX for 37 days (15d of treatment, 10d of recovery, 22d of retreatment)
The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.

tag: growth phase

value: Log phase cells

tag: cell line

value: subline of  ECACC 93112519


title: A/64PTX-30d - rep 2

treatment_protocol:
A/32PTX-48d cells treated with 64 nM PTX for 30 days (30d of treatment and 7d of recovery)
The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.


title: Brain of C57BL/6 mice fed with a high-cholesterol diet pool C

description:
Ce_AC.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.

value: Brain


title: A/32PTX-48d - rep 2

treatment_protocol:
A/16PTX-26d cells treated with 32 nM PTX for 48 days (17d of treatment, 13 d of recovery, 31d of retreatment)
The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.


title: A/32PTX-48d - rep 1

value: 32 nM PTX for 48 days (17d of treatment, 13 d of recovery, 31d of retreatment)


title: A/128PTX-37d - rep 2

value: 128 nM PTX for 37 days (15d of treatment, 10d of recovery, 22d of retreatment)


title: A/16PTX-56d - rep 2

treatment_protocol:
A/8PTX-26d cells treated with 16 nM PTX for 56 days (26d of treatment, 11d of recovery, 30d of retreatment)
The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.


title: A/4PTX-63d - rep1

treatment_protocol:
A/2PTX-31days(d) cells treated with 4 nM PTX for 63 days (5d of treatment, 14d of recovery, 58d of retreatment)
The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.


title: A/64PTX-30d - rep 1

value: 64 nM PTX for 30 days (30d of treatment and 7d of recovery)


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool B

description:
Ce_AC.Siv.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool B

description:
Ce_AC.Gl2.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: A/8PTX-33d - rep 1

treatment_protocol:
A/4PTX-63d cells treated with 8 nM PTX for 33 days
The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.

value: 8 nM PTX for 33 days


title: Brain of C57BL/6 mice fed with normal diet pool C

description:
Ce_Control.3
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool C

description:
Ce_AC.Gl2.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Brain of C57BL/6 mice fed with normal diet pool A

description:
Ce_Control.1
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: A/8PTX-33d - rep 2


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 2 pool A

description:
Ce_AC.Gl2.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 2 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 2 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate enriched with acetylsalicylic acid (10 mM).


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool A

description:
Ce_AC.Gl1.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.


title: A2780 cells untreated - rep 2

source_name: ovarian cancer cell line

treatment_protocol: The process of resistance development was commenced from treatment A2780 parental cell line with 0.25 nM PTX for 7 days. After this time cells reached the stable growth in this drug concentration  and the first subline was generated - A/0.25PTX-7d. In the next steps PTX dose was dobled until the A/2PTX-31d cell subline was generated, which was the parental cell line for the first NGS- analyzed  cell line - A/4PTX-63d. A2780 cells and  6 sublines were cultured in duplicate in 25 cm2 flasks  without PTX for 3-4 days before total RNA isolation.  Then medium was removed, cells were rinsed two times with phosphate buffered saline (PBS) and  the cultures were terminated by adding RLT buffer and collecting cell lysate with a cell scraper. Cell extracts were frozen at -80°C or used immediately.

value: untreated


title: Brain of C57BL/6 mice fed with normal diet pool B

description:
Ce_Control.2
Gene expression data from brain tissue of C57BL/6 mice fed with normal diet sacrificed at day 43.


title: A/16PTX-56d - rep 1

value: 16 nM PTX for 56 days (26d of treatment, 11d of recovery, 30d of retreatment)


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool C

description:
Ce_AC.Gl1.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.

value: Male


title: A2780 cells untreated - rep 1


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool C

description:
Ce_AC.Siv.3
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.

value: 7 weeks


title: Brain of C57BL/6 mice fed with a high-cholesterol diet pool B

description:
Ce_AC.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.


title: 9372535016_H: Immune non-Responder (INR)

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

description: CD4 T cells <350/µL

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: Immune non-Responder (INR)

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Whole blood was collected from Immune Responder and Non-Responder HIV-infected ART-treated individuals and gene array analysis was performed

extract_protocol: Whole blood was collected from Immune Responder and Non-Responder HIV-infected ART-treated individuals. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software. Analysis of the genome array output data was conducted using the R statistical language and the Limma statistical package from Bioconductor.

treatment_protocol: Individuals were treated for at least 2-3 years with plasma HIV RNA levels below detectable levels using routine clinical assays; typically, less than 50 copies per milliliter. Transient blips in HIV RNA levels did not exclude participation if flanked by levels below limits of detection.

tag: subject

tag: group

value: INR

value: Whole Blood

tag: cell type

value: CD4 T cells


title: A/4PTX-63d - rep2

value: 4 nM PTX for 63 days (5d of treatment, 14d of recovery, 58d of retreatment)


title: 6330959014_K: Immune non-Responder (INR)

description: CD4 T cells <350/µL

tag: tissue


title: 9372535016_J: Immune Responder (IR)

description: CD4 T cells >500/µL

source_name: Immune Responder (IR)

value: IR


title: 9372535016_I: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6330959014_I: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 9372535016_A: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 9372535016_E: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6330959014_H: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6330959014_G: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299045_I: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6303299045_J: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 9372535016_K: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6330959014_E: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6330959014_J: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6330959014_B: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 9372535016_B: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin pool A

description:
Ce_AC.Siv.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Simvastatin sacrificed at day 43.
Simvastatin (0.03 g/100 g) added to food pellet daily.

value: AIN-93 + 0.5% cholesterol

value: Simvastatin


title: 6303299045_H: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 9372535016_C: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6330959014_L: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6303299045_K: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6330959014_F: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 9372535016_G: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299045_E: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: Brain of C57BL/6 mice fed with a high-cholesterol diet and extract of Ganoderma lucidum 1 pool B

description:
Ce_AC.Gl1.2
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet and Ganoderma lucidum 1 extract sacrificed at day 43.
Lyophilized Ganoderma lucidim 1 extract (1.0%) added to food pellet daily. Hydroalcoholic extracts (32% by volume) of cultivated basidiocarps in oak (Quercus acutifolia Née) sawdust substrate.

value: Ganoderma lucidum 1


title: 9372535016_F: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299045_L: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6303299045_B: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299009_L: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299009_J: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299045_G: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299009_E: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299009_C: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299009_D: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_K: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_L: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_H: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299045_D: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6303281014_G: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_E: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_F: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_C: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_A: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6260971076_G: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_B: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6260971076_J: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6260971076_K: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6260971076_L: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303281014_I: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6303299045_A: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6303299009_F: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6260971076_I: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6260971076_C: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: C57BL/6_TMEV BeAn_14 dpi_brain [TCI_81]

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization. Cook distance cutoff filter disabled
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: raw read counts per gene; des2rlog*.tab files:  DESeq2 rlog transformed read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

source_name: C57BL/6_TMEV BeAn_14 dpi_brain

extract_protocol:
Animals were euthanized, perfused with PBS and brain tissue was removed immediately, snap frozen on liquid nitrogen and stored at -80°C until further use.
RNA was isolated from transversal sections of the brain at the level of the hippocampus using QIAzol Lysis Reagent and RNeasy® Mini Kit (Qiagen).

tag: mouse strain

value: TMEV BeAn

tag: days post infection

value: brain


title: C57BL/6_TMEV BeAn_14 dpi_brain [TCI_83]


title: 6260971076_D: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6235783009_J: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6260971076_A: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6260971076_E: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6260971076_F: Immune Responder (IR)

description: CD4 T cells >500/µL


title: 6303281014_J: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: 6260971076_B: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: C57BL/6_TMEV BeAn_14 dpi_brain [TCI_82]


title: C57BL/6_TMEV BeAn_7 dpi_brain [TCI_77]

source_name: C57BL/6_TMEV BeAn_7 dpi_brain


title: C57BL/6_TMEV BeAn_14 dpi_brain [TCI_79]


title: C57BL/6_TMEV BeAn_7 dpi_brain [TCI_73]


title: C57BL/6_TMEV BeAn_7 dpi_brain [TCI_76]


title: C57BL/6_TMEV BeAn_7 dpi_brain [TCI_78]


title: C57BL/6_TMEV BeAn_4 dpi_brain [TCI_67]

source_name: C57BL/6_TMEV BeAn_4 dpi_brain


title: C57BL/6_TMEV BeAn_4 dpi_brain [TCI_69]


title: C57BL/6_TMEV BeAn_4 dpi_brain [TCI_70]


title: C57BL/6_mock_7 dpi_brain [TCP_24]

source_name: C57BL/6_mock_7 dpi_brain

value: mock


title: C57BL/6_mock_7 dpi_brain [TCP_23]


title: C57BL/6_mock_7 dpi_brain [TCP_22]


title: SJL/J_TMEV BeAn_14 dpi_brain [TAI_161]

source_name: SJL/J_TMEV BeAn_14 dpi_brain

value: SJL/J


title: SJL/J_TMEV BeAn_14 dpi_brain [TAI_160]


title: SJL/J_TMEV BeAn_14 dpi_brain [TAI_159]


title: SJL/J_TMEV BeAn_14 dpi_brain [TAI_157]


title: SJL/J_TMEV BeAn_7 dpi_brain [TAI_152]

source_name: SJL/J_TMEV BeAn_7 dpi_brain


title: SJL/J_TMEV BeAn_7 dpi_brain [TAI_151]


title: SJL/J_TMEV BeAn_7 dpi_brain [TAI_153]


title: SJL/J_mock_7 dpi_brain [TAP_75]

source_name: SJL/J_mock_7 dpi_brain


title: SJL/J_TMEV BeAn_4 dpi_brain [TAI_149]

source_name: SJL/J_TMEV BeAn_4 dpi_brain


title: SJL/J_TMEV BeAn_7 dpi_brain [TAI_155]


title: SJL/J_TMEV BeAn_14 dpi_brain [TAI_158]


title: SJL/J_TMEV BeAn_4 dpi_brain [TAI_145]


title: SJL/J_TMEV BeAn_4 dpi_brain [TAI_148]


title: SJL/J_TMEV BeAn_7 dpi_brain [TAI_154]


title: Brain of C57BL/6 mice fed with a high-cholesterol diet pool A

description:
Ce_AC.1
Gene expression data from brain tissue of C57BL/6 mice fed with a high-cholesterol diet sacrificed at day 43.

value: Brain

tag: treatment


title: H3K79me2 Th2 3

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with Bowtie2 (parameters: --no-mixed --no-discordant -X 1000)
Aligned bam files were then filtered to remove reads in black-listed regions, duplicate reads were marked using Picard MarkDuplicates
Bam files were filtered again to remove low quality reads (samtools view -q 10 -F 1800)
macs2 was used to call peaks on each sample individually using both sample and input bam under default settings (-f BAMPE)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: broadPeak

source_name: CD4+ T cell

growth_protocol: Enriched CD4+ T cells were cultured for 4 days under either Th1 (IL-2, IL-12, anti-IL-4) or Th2 (IL-2, IL-4, anti-IFNg) polarising conditions (plate bound anti-CD3 and anti-CD28)

extract_protocol:
2 µg of anti-H3K79me2 (ab3594) was used to perform ChIP. DNA was purified using the NucleoSpin Gel and PCR Clean-up kit according to the manufacturer's specifications
MGITech MGIEasy DNA FS Library preparation kit V1 (according to the manufacturer's instructions: document revision A0)

treatment_protocol: Th1 cells were sorted by expression of YFP (IFNg-YFP reporter mouse). Th2 cells were sorted by expression of IL-4 or IL-13 (4C13R - IL-4 AmCyan / IL-13 dsRed reporter mouse); naïve cells were directly sorted from WT mice (CD44- CD62L+), 1.5x10^6 cells were fixed for 10 min in 10 ml complete media in the presence of 0.6% formaldehyde.

value: WT

tag: antibody

tag: cell subtype


title: H3K79me2 Th2 2

tag: genotype


title: H3K79me2 Th2 1


title: SJL/J_mock_7 dpi_brain [TAP_74]


title: C57BL/6_TMEV BeAn_14 dpi_brain [TCI_80]


title: H3K79me2 Th1 2


title: H3K79me2 naïve 3

value: naive


title: H3K79me2 Th1 1


title: H3K79me2 naïve 2


title: C57BL/6_TMEV BeAn_4 dpi_brain [TCI_68]


title: input Th2 3

value: input, none


title: SJL/J_mock_7 dpi_brain [TAP_76]


title: H3K79me2 naïve 1


title: SJL/J_TMEV BeAn_4 dpi_brain [TAI_147]


title: 9372535016_D: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: input Th2 2


title: input Th2 1


title: input Th1 2


title: input naïve 3


title: H3K79me2 Th1 3


title: input naïve 1


title: input naïve 2


title: QBC-939 Bmi-1 shRNA rep2

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

country: China

institute: Qilu Hospital, Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cholangiocarcinoma cells

growth_protocol: QBC-939 was maintained in DMEM medium supplemented with 10% fetal bovine serum in 5% CO2 resuscitation.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: QBC-939 was treated with Bmi1 shRNA or scrambled shRNA for 48h.

value: Cholangiocarcinoma


title: QBC-939 Bmi-1 shRNA rep1


title: QBC-939 control rep1


title: QBC-939 control rep2


title: QBC-939 control rep3


title: Sample_B11-01032_Colon

city: Pohang

first: Sang Ick

last: Park

address: 558, Handong-ro, Buk-gu

country: South Korea

institute: Handong University

data_processing:
reads shorter than 50 bp were removed by using Cutadapt v.2.8
Filtered reads were mapped to the reference genome of the same species using STAR v.2.7.1a
The estimation of gene expression was performed by RSEM v.1.3.1
fragments per kilobase million mapped reads (FPKM) and transcripts per kilobase million mapped reads (TPM) values were calculated.
Supplementary_files_format_and_content: FPKM

source_name: paraffin embedded tumor tissue

extract_protocol: A cDNA library, consisting of 151 bp long fragments, was constructed for paired-end sequencing using the TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA), according to the manufacturer's instructions. Briefly, mRNA was purified from 1 μg of total RNA, which was extracted from the tissue samples, and fragmented using oligo (dT) magnetic beads. Single-stranded cDNA was synthesized from the fragmented mRNA through random hexamer priming. The single-stranded cDNA is then used as a template for the synthesis of the second strand in order to construct double-stranded cDNA molecules. After end repair, A-tailing, and adapter ligation, cDNA libraries were amplified using Polymerase Chain Reaction (PCR). The quality of the cDNA libraries was evaluated with the 2100 BioAnalyzer

tag: disease state

value: mucinous cancer


title: Sample_B09-00410_Colon


title: Sample_CAM10


title: Sample_B17-02706_Uterine_cervix


title: Sample_11-01032_T

source_name: frozen fresh tumor tissue


title: Sample_17-02706_T


title: Sample_09-00410_T


title: Sample_CAM8


title: input Th1 3


title: Sample_CAM11


title: Sample_CAM6


title: QBC-939 Bmi-1 shRNA rep3


title: Sample_CAM1


title: input Th1 1


title: Treat 3- Pre

city: Newcastle

first: Behnaz

last: Khavari

state: NSW

address: 1 University Dr Callaghan

department: School of Biomedical Sciences and Pharmacy

institute: University of Newcastle

description: Pre_treatment-differential.expression.results.txt

data_processing:
Reads Quality Control; Fastqc (v0.11.8)
Reads Trimming; Cutadapt (v2.10)
Reads Alignment to the Reference Genome; HISAT2 (v2.1.0)
Reads Quantification (Counting); htseq-count (v0.7.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing read counts for individual samples, generated by htseq-count
Space-delimited (Co-treatment) and tab-delimited (Pre-treatment) text files containing differential expression and FDR data

source_name: Bone marrow-derived cell line SK-N-SH

extract_protocol:
Cells were lysed directly in the culture plates by the addition of 1ml Trizol reagent. Lysate was transferred to microcentrifuge tubes and 200ml of chloroform was added before centrifugation at 13000g at 4°C for 10 minutes in accordance with the manufacturer’s instructions (ThermoFisher). The resultant aqueous phase, containing total RNA, was separated from organic phase and mixed with 80μg glycogen and 500μL isopropanol, and incubated at -20°C overnight for RNA to precipitate. After centrifuge at 9000g at 4°C for 30 minutes, the supernatant was discarded, and the pellet was washed with 75% cold ethanol twice. Finally, the RNA pellet was re-suspended in nuclease-free water and stored at -80°C.
Briefly, 350 ng of total RNA (RNA integrity number (RIN) ≥ 8.5) was DNAse I treated (1U/μg RNA, Thermo Scientific, Waltham, MA, USA), before ribosomal RNA depletion using the Ribo-Zero kit (Illumina, San Diego, CA, USA). The Illumina TruSeq Stranded Total RNA Library Prep Kit was applied to construct sequencing libraries according to the manufacturer’s protocol. In order to determine the quality and concentrations of libraries, High Sensitivity DNA Bioanalyzer chip was used,
Total RNA-Seq

value: Neuroblastoma

value: Treated (H2O2 72 hours before commencement of the ATRA differentiation protocol)


title: Treat 2- Pre


title: Sample_CAM3


title: Treat 1- Pre


title: Control 3- Co

description: Co_treatment-differential.expression.results.txt

value: Untreated


title: Treat 1- Co

value: Treated (simultaneously exposed to H2O2 and ATRA)


title: Treat 3- Co


title: Sample_CAM4


title: Control 2- Pre


title: Control 2- Co


title: Control 3- Pre


title: Treat 2- Co


title: Control 1- Co


title: Sample_CAM9


title: Control 1- Pre