title: IDH-MUT_MGH107_scRNAseq

status: Public on May 31 2021

first: Federico

last: Gaiti

state: NY

address: 413 East 69th St.

institute: Weill Cornell Medicine

description:
scRNA_cell_statistics.xlsx
MscRRBS_to_scRNA_barcodes_matching_key.xlsx
scRNA_conversion_key_filename_to_MscRRBS_barcode.csv

data_processing:
Each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. Read pairs with a read shorter than 36bp after trimming were discarded. We aligned trimmed reads to the hg38 human genome assembly using Bismark117 (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner118. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For downstream analyses, a site was considered methylated or unmethylated only if there was 90% agreement of the methylation state for all reads mapped to the site. Cells with coverage of at least 50,000 unique CpGs and bisulfite conversion rates of at least 99% were retained for downstream analyses.
The sequenced read fragments were mapped against the GRCh38 (hg38 Ensembl version 94) genome assembly using the 2pass default mode of STAR (version 2.5.2a). The number of read counts overlapping with annotated genes were quantified using RSEM120 (rsem-calculate-expression). Cells with mitochondrial and ribosomal reads of less than 20% and a minimum of 2000 detected genes were retained for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include Transcpit per Million (TPM) counts overlapping with annotated genes for all cells. Excel and comma-separated values files contain the filename conversion key to match scRNA with MscRRBS cells, and the sequencing summary statistics for each cell.

source_name: glioma cells from patient sample

extract_protocol:
Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA/HBSS). Tumors were first stained first with CD45-Vioblue direct antibody conjugate (clone REA747, Miltenyi Biotec) for 30 min at 4°C. Cells were washed with cold PBS, and then resuspended in 1 ml of BSA/HBSS containing 1 μM calcein AM (Life Technologies) and 0.33 μM TO-PRO-3 iodide (Life Technologies) to co-stain for 30 min before sorting. CD45 negative cells were stained with calcein AM (Life Technologies) for viability and CD24-APC (human antibody, clone REA832, Miltenyi Biotec) and CD44-VioBlue (human antibody, clone REA690, Miltenyi Biotec) to sort subpopulations of viable non-immune cells. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488nm (calcein AM, 530/30 filter), 640nm (TO-PRO-3 or CD24-APC, 670/14 filter), and 405nm (CD45-VioBlue or CD44-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein AM positive and TO-PRO-3 negative. We sorted individual, viable, immune and non-immune single cells into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol.
MscRRBS and whole-transcriptome library preparation and sequencing were performed as previously described. Briefly, genomic DNA (gDNA) and mRNA have been separated manually as previously described. A modified oligo-dT primer (5′-biotin-triethyleneglycol-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, where V is either A, C or G, and N is any base; IDT) was conjugated to streptavidin-coupled magnetic beads (Dynabeads, Life Technologies) according to the manufacturer's instructions. To capture polyadenylated mRNA, we added the conjugated beads (10 μl) directly to the cell lysate and incubated them for 20 min at room temperature with mixing to prevent the beads from settling. The mRNA was then collected to the side of the well using a magnet, and the supernatant, containing the gDNA, was transferred to a fresh plate. Single-cell complementary DNA was amplified from the tubes containing the captured mRNA according to a variation of the Smart-Seq2 protocol using molecular crowding to increase sensitivity. After amplification and purification using 0.8X SPRI beads, 0.5ng cDNA was used for Nextera Tagmentation and library construction. Library quality and quantity were assessed using Agilent Bioanalyzer 2100 and Qubit, respectively.
Genomic DNA present in the pooled supernatant and wash buffer from the mRNA isolation step was concentrated on 0.8X SPRI beads and eluted directly into the reaction mixtures for Msp1 (Fermentas) enzymatic reaction (10mL final reaction) for 90 min at 37°C. Heat-inactivation was performed for 10 min at 70°C. Digested DNA was filled-in and A-tailed at the 3’ sticky ends in 8.5 mL final volume of 1X CutSmart with 2.5 units of Klenow fragment (Exo-, Fermentas). Reaction was supplemented with 1 mM dATP and 0.1 mM dCTP and 0.1 mM dGTP (NEB) and performed as follows in a thermocycler: 30°C for 25 min, 37°C for 25 min and heat-inactivation at 70°C for 10 min. Custom barcoded methylated adaptors (0.1 mM) were then ligated overnight at 16°C with the dA-tailed DNA fragments in the presence of 800 units of T4 DNA ligase (NEB) and 1 mM ATP (Roche) in a final volume of 11.5 mL of 1X CutSmart buffer. T4 DNA ligase heat-inactivation was performed at 70°C for 15 min the next day. Genomic DNA from 24 individual cells were pooled together according to their barcodes, giving, for a 96-well plate, 4 pools of 24 cells. Pooled genomic DNA was cleaned-up and concentrated using 1.8X SPRI beads (Agencourt AMPure XP - Beckman Coulter). Each pool was then sodium bisulfite converted (Fast Epitect Bisulfite, Qiagen) following manufacture recommendations. To ensure full bisulfite conversion, two cycles of conversion were performed. The double-stranded DNA was first denatured 10 min at 98°C and then incubated for 20 min at 60°C. 100 ng of dephosphorylated and sheared bacterial DNA was added as carrier to every pool prior to conversion. Converted DNA was then amplified using primers containing Illumina i7 and i5 index. Following Illumina pooling guidelines, a different i7 index was used for every 24-cell pool, allowing multiplexing of 96 cells for sequencing on one Illumina HiSeq lane. Library enrichment was done using KAPA HiFi Uracil+ master mix (Kapa Biosystems) and the following PCR condition was used: 98°C for 45 secs; 6 cycles of: 98°C for 20 secs, 58°C for 30 secs, 72°C for 1 min; followed by 12 cycles of: 98°C for 20 secs, 65°C for 30 secs, 72°C for 1 min. PCR was terminated by an incubation at 72°C for 5 min. Enriched libraries were cleaned-up and concentrated using 1.3X SPRI beads. DNA fragments between 200 bp and 1 Kb were size-selected and recovered after resolving on a 3% NuSieve 3:1 agarose gel. Libraries molarity concentration calculation was obtained by measuring concentration of double stranded DNA (Qubit) and quantifying the average library size (bp) using an Agilent Bioanalyzer. Every 24-cells pool was mixed with the others pool in an equimolar ratio. All cells from a 96-well plate were sequenced as paired-end on HiSeq 2500 with 10% PhiX spike-in. Negative controls (empty wells with no cells) were used to control for non-specific amplification of the libraries.
Single cell bisulfite-seq (reduced representation) and single-cell RNA-seq (full-length transcriptome profiling)

value: glioma cells

tag: cell surface marker


title: 2049_Day2

status: Public on Jun 25 2021

type: SRA

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 729 Lagunita Dr

country: USA

institute: Stanford

description: RNA

library_source: transcriptomic

data_processing:
Cellranger 3.1.0
Seurat 3.6.3 used for all downstream processing
Genome_build: Hg38
Supplementary_files_format_and_content: gene expression matrices (mtx)

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
PBMC isolation directly after blood sample collection
10x Single Cell 3' v3

tag: cell type

value: PBMCs

tag: patient

tag: time (days)

tag: age

tag: Sex

value: Male

tag: race

value: Asian

tag: ethnicity

value: Chinese American


title: 2049_Day0

description: RNA


title: GBM_MGH124_scRNAseq

city: New York

description:
scRNA_cell_statistics.xlsx
MscRRBS_to_scRNA_barcodes_matching_key.xlsx

molecule: polyA RNA


title: GBM_MGH121_Plate4_scRNAseq


title: 2047_Day42

description: RNA

value: White

value: Non-Hispanic


title: 2047_Day21

description: RNA


title: IDH-MUT_MGH64_scRNAseq


title: GBM_MGH121_Plate1_scRNAseq


title: IDH-MUT_MGH45_scRNAseq


title: IDH-MUT_MGH135_scRNAseq


title: GBM_MGH105D_scRNAseq


title: 2047_Day2

description: RNA


title: GBM_MGH211_scRNAseq


title: GBM_MGH105C_scRNAseq


title: GBM_MGH129_scRNAseq


title: GBM_MGH122_scRNAseq


title: IDH-MUT_MGH135_MscRRBS

description:
Bisulfite-treated genomic DNA
MscRRBS_cell_statistics.xlsx
MscRRBS_to_scRNA_barcodes_matching_key.xlsx

library_source: genomic

molecule: genomic DNA


title: IDH-MUT_MGH107_MscRRBS


title: IDH-MUT_MGH64_MscRRBS


title: IDH-MUT_MGH45_MscRRBS


title: GBM_MGH121_Plate2_scRNAseq


title: GBM_MGH121_Plate3_scRNAseq


title: GBM_MGH124_MscRRBS


title: GBM_MGH121_Plate1_MscRRBS


title: GBM_MGH121_Plate4_MscRRBS


title: GBM_MGH121_Plate3_MscRRBS


title: GBM_MGH105C_CD45pos_scRNAseq


title: GBM_MGH115_scRNAseq


title: GBM_MGH105B_scRNAseq


title: GBM_MGH115_MscRRBS


title: GBM_MGH211_MscRRBS


title: GBM_MGH105C_CD45pos_MscRRBS


title: GBM_MGH122_MscRRBS


title: GBM_MGH129_MscRRBS


title: GBM_MGH105D_MscRRBS


title: GBM_MGH105B_MscRRBS


title: GBM_MGH105A_MscRRBS


title: IDH-MUT MGH208_Plate2_scRNAseq

description:
GSE151506_scRNA_cell_statistics.xlsx
MGH208_P2.tpm.txt
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx

data_processing:
Each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. Read pairs with a read shorter than 36bp after trimming were discarded. We aligned trimmed reads to the hg38 human genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For downstream analyses, a site was considered methylated or unmethylated only if there was 90% agreement of the methylation state for all reads mapped to the site. Cells with coverage of at least 50,000 unique CpGs and bisulfite conversion rates of at least 99% were retained for downstream analyses.
The sequenced read fragments were mapped against the GRCh38 (hg38 Ensembl version 94) genome assembly using the 2pass default mode of STAR (version 2.5.2a). The number of read counts overlapping with annotated genes were quantified using RSEM (rsem-calculate-expression). Cells with mitochondrial and ribosomal reads of less than 20% and a minimum of 2000 detected genes were retained for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include Transcpit per Million (TPM) counts overlapping with annotated genes for all cells. Excel and comma-separated values files contain the filename conversion key to match scRNA with MscRRBS cells, and the sequencing summary statistics for each cell.

extract_protocol:
Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA/HBSS). Tumors were first stained first with CD45-Vioblue direct antibody conjugate (clone REA747, Miltenyi Biotec) for 30 min at 4°C. Cells were washed with cold PBS, and then resuspended in 1 ml of BSA/HBSS containing 1 μM calcein AM (Life Technologies) and 0.33 μM TO-PRO-3 iodide (Life Technologies) to co-stain for 30 min before sorting. CD45 negative cells were stained with calcein AM (Life Technologies) for viability and CD24-APC (human antibody, clone REA832, Miltenyi Biotec) and CD44-VioBlue (human antibody, clone REA690, Miltenyi Biotec) to sort subpopulations of viable non-immune cells. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488nm (calcein AM, 530/30 filter), 640nm (TO-PRO-3 or CD24-APC, 670/14 filter), and 405nm (CD45-VioBlue or CD44-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein AM positive and TO-PRO-3 negative. We sorted individual, viable, immune and non-immune single cells into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80°C prior to joint multiplexed single-cell reduced representation bisulfite sequencing (MscRRBS) and whole transcriptome library preparation and sequencing.
MscRRBS and whole-transcriptome library preparation and sequencing were performed as previously described. Briefly, genomic DNA (gDNA) and mRNA have been separated manually as previously described. A modified oligo-dT primer (5′-biotin-triethyleneglycol-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, where V is either A, C or G, and N is any base; IDT) was conjugated to streptavidin-coupled magnetic beads (Dynabeads, Life Technologies) according to the manufacturer's instructions. To capture polyadenylated mRNA, we added the conjugated beads (10 μl) directly to the cell lysate and incubated them for 20 min at room temperature with mixing to prevent the beads from settling. The mRNA was then collected to the side of the well using a magnet, and the supernatant, containing the gDNA, was transferred to a fresh plate. Single-cell complementary DNA was amplified from the tubes containing the captured mRNA according to a variation of the Smart-Seq2 protocol using molecular crowding to increase sensitivity. After amplification and purification using 0.8X SPRI beads, 0.5ng cDNA was used for Nextera Tagmentation and library construction. Library quality and quantity were assessed using Agilent Bioanalyzer 2100 and Qubit, respectively.
Genomic DNA present in the pooled supernatant and wash buffer from the mRNA isolation step was concentrated on 0.8X SPRI beads and eluted directly into the reaction mixtures for Msp1 (±HaeIII) (Fermentas) enzymatic reaction (10mL final reaction) for 90 min at 37°C. Heat-inactivation was performed for 10 min at 70°C. Digested DNA was filled-in and A-tailed at the 3’ sticky ends in 8.5 mL final volume of 1X CutSmart with 2.5 units of Klenow fragment (Exo-, Fermentas). Reaction was supplemented with 1 mM dATP and 0.1 mM dCTP and 0.1 mM dGTP (NEB) and performed as follows in a thermocycler: 30°C for 25 min, 37°C for 25 min and heat-inactivation at 70°C for 10 min. Custom barcoded methylated adaptors (0.1 mM) were then ligated overnight at 16°C with the dA-tailed DNA fragments in the presence of 800 units of T4 DNA ligase (NEB) and 1 mM ATP (Roche) in a final volume of 11.5 mL of 1X CutSmart buffer. T4 DNA ligase heat-inactivation was performed at 70°C for 15 min the next day. Genomic DNA from 24 individual cells were pooled together according to their barcodes, giving, for a 96-well plate, 4 pools of 24 cells. Pooled genomic DNA was cleaned-up and concentrated using 1.8X SPRI beads (Agencourt AMPure XP - Beckman Coulter). Each pool was then sodium bisulfite converted (Fast Epitect Bisulfite, Qiagen) following manufacture recommendations. To ensure full bisulfite conversion, two cycles of conversion were performed. The double-stranded DNA was first denatured 10 min at 98°C and then incubated for 20 min at 60°C. 100 ng of dephosphorylated and sheared bacterial DNA was added as carrier to every pool prior to conversion. Converted DNA was then amplified using primers containing Illumina i7 and i5 index. Following Illumina pooling guidelines, a different i7 index was used for every 24-cell pool, allowing multiplexing of 96 cells for sequencing on one Illumina HiSeq lane. Library enrichment was done using KAPA HiFi Uracil+ master mix (Kapa Biosystems) and the following PCR condition was used: 98°C for 45 secs; 6 cycles of: 98°C for 20 secs, 58°C for 30 secs, 72°C for 1 min; followed by 12 cycles of: 98°C for 20 secs, 65°C for 30 secs, 72°C for 1 min. PCR was terminated by an incubation at 72°C for 5 min. Enriched libraries were cleaned-up and concentrated using 1.3X SPRI beads. DNA fragments between 200 bp and 1 Kb were size-selected and recovered after resolving on a 3% NuSieve 3:1 agarose gel. Libraries molarity concentration calculation was obtained by measuring concentration of double stranded DNA (Qubit) and quantifying the average library size (bp) using an Agilent Bioanalyzer. Every 24-cells pool was mixed with the others pool in an equimolar ratio. All cells from a 96-well plate were sequenced as paired-end on HiSeq 2500 with 10% PhiX spike-in. Negative controls (empty wells with no cells) were used to control for non-specific amplification of the libraries.
Single cell bisulfite-seq (reduced representation) and single-cell RNA-seq (full-length transcriptome profiling)


title: IDH-MUT MGH201_Plate1_scRNAseq

description:
GSE151506_scRNA_cell_statistics.xlsx
MGH201_P1.tpm.txt
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx


title: IDH-MUT MGH208_Plate1_scRNAseq

description:
GSE151506_scRNA_cell_statistics.xlsx
MGH208_P1.tpm.txt
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx


title: GBM_MGH105C_MscRRBS


title: IDH-MUT MGH201_Plate2_scRNAseq

description:
GSE151506_scRNA_cell_statistics.xlsx
MGH201_P2.tpm.txt
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx


title: IDH-MUT MGH142_Plate1_scRNAseq

description:
GSE151506_scRNA_cell_statistics.xlsx
MGH142_P1.tpm.txt
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx


title: IDH-MUT MGH142_Plate2_scRNAseq

description:
GSE151506_scRNA_cell_statistics.xlsx
MGH142_P2.tpm.txt
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx


title: IDH-MUT MGH208_Plate2_MscRRBS

description:
GSE151506_MscRRBS_cell_statistics.xlsx
GSE151506_MscRRBS_to_scRNA_barcodes_matching_key.xlsx


title: IDH-MUT MGH201_Plate1_MscRRBS


title: GBM_MGH105A_scRNAseq


title: GBM_MGH121_Plate2_MscRRBS


title: IDH-MUT MGH208_Plate1_MscRRBS


title: IDH-MUT MGH142_Plate2_MscRRBS


title: IDH-MUT MGH142_Plate1_MscRRBS


title: EAE1

status: Public on May 21 2021

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description: unbiased total nuclei isolation

data_processing:
Chromiun Single Cell ATAC v1 Chemistry was used to create the scATAC-seq libraries. Samples were sequenced in Illumina NovaSeq and demultiplexed. Demultiplexed samples were converted to fastq files and aligned to mm10 reference assembly and process using Cellranger-ATAC count (version 1.2.0) and cellranger-atac aggr. Normalizing the sequencing depth.
Cellranger-atac aggr output bam files, peaks file and fragment file were used as input for Seurat/Signac v0.25 R packages for downstream analysis.
Final cells were selected following the QC parameters below, min peak region 1000 fragments and maximun 20000 resulting in 4895 cells.
Cells were clustered based on peaks and annotated using reference annotations from Falcao, van Bruggen et al. 2018 Nature Medicine.
Genome_build: mm10
Supplementary_files_format_and_content: The bam files belong to individual samples as bam files from Cellranger ATAC v1.2.0 preprocessing.
Supplementary_files_format_and_content: fragments.tsv, fragments coordenates including cell barcode ID and number of duplicate reads pairs per fragment. peaks.bed refers to scATAC peaks that were called individually for each sample and then merged, samples were normalized to depth with cellranger ATAC v1.2.0 aggr.
Supplementary_files_format_and_content: Meijer_Agirre_scATAC_metadata_umap.csv.gz file includes scATAC-seq metadata, including QC metrics, cluster/celltype annotations and UMAP coordenates in csv file format. Where columns are cell Ids and rows peak coordenates.
Supplementary_files_format_and_content: Meijer_Agirre_EAEscATAC_signac025.Robj belongs to the R object from Seurat/Signac.0.25 R packages including gene activity matrices and peak matrices used in the study.

organism: Mus musculus

source_name: spinal cord tissue

extract_protocol:
Mice were sacrificed with a ketaminol/xylazine intraperitoneal injection followed by intracardiac perfusion with PBS where after brain and spinal cords were collected and dissociated using the adult brain dissociation kit (130-107-677, Miltenyi) following manufacturer’s instructions including myelin debris removal, but excluding the red blood cell removal step.
Immediately after dissociation, cells were stained with DAPI and sorted on a FACS Aria III cell sorter (BD Biosciences). Sox10GFP+/DAPI- cells were collected in PBS + 0.5% BSA and pooled with Sox10GFP-/DAPI- cells with a 4:1 ratio. The pool of cells was then lysed and washed according to the Demonstrated Protocol: Nuclei Isolation for Single cell ATAC Sequencing (10x Genomics) as follows: the cells were centrifuged for 10 minutes at 300xg and 4°C, resuspended in ATAC lysis buffer (containing 0.1% IGEPAL (CA-630), 0.1% Tween-20, 0.01% Digitonin, 1% BSA, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and incubated on ice for 3 minutes. After the incubation, wash buffer (containing 0.1% Tween-20, 1% BSA, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) was added on top without mixing and the nuclei were centrifuged for 5 min at 500xg and 4°C. Nuclei were washed once in Diluted Nuclei buffer (10x Genomics) containing 1% BSA, before adding to the tagmentation mix (10x Genomics). The Chromium Single Cell ATAC v1 Chemistry was used to create single-cell ATAC libraries. Two EAE and four CFA-control animals were used for independent replicates. Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-16-49 read set-up and a minimum of 25 000 read pairs per cell.
Chromium Single Cell ATAC v1 Chemistry

treatment_protocol: For the induction of EAE, the mouse model of MS, animals were injected subcutaneously with an emulsion of MOG35-55 peptide in complete Freud’s adjuvant (CFA; EK-2110 kit from Hooke Laboratories) followed by intraperitoneal injection with pertussis toxin in PBS (200 ng per animal) on the day of immunization and with 24 hours delay (according to manufacturer’s instructions). Control animals underwent the same treatment, but CFA without MOG35-55 peptide (CK-2110 kit from Hooke Laboratories) was used instead. Spinal cord and brains were collected at the peak of the disease when clinical score 3 has been reached, which corresponds to limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analyzed in this study.

tag: tissue

value: spinal cord tissue

tag: disease state

value: EAE (MS mouse model)


title: EAE2

description: unbiased total nuclei isolation


title: Ctr4

description: unbiased total nuclei isolation

value: control


title: MCF7 cells_E4 10-7M+ R5020 10-8M_rep4

status: Public on May 17 2021

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: MCF7 cells_E4 10-7M+ R5020 10-8M_rep4

data_processing:
Basecalling performed using Illumina bcl2fastq v2.17
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Trimmed reads were mapped in to the human genome hg19 using STAR software v.2.5.2b (Dobin et al., 2013) and gene expression was measured from the mapped reads by using built-in STAR module (--quantMode GeneCounts).
Genome_build: Illumina iGenomes hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for annotations for each Sample

source_name: MCF7 cells

growth_protocol: Routinely cultured MCF7 cells were seeded (500,000 cells/well in 6-well plates)in DMEM with red phenol (Gibco Invitrogen Corporation, Paisley, UK), supplemented with 10% of heat-inactivated foetal bovine serum (FBS, Gibco Invitrogen Corporation, Paisley, UK), L-Glutamine (2mmol/L,Gibco Invitrogen Corporation, Paisley, UK), penicillin (100IU/mL, Gibco Invitrogen Corporation, Paisley, UK) and streptomycin (100µg/mL, Gibco Invitrogen Corporation, Paisley, UK) at 37°C and 5% CO2 humid atmosphere. When cells reached a confluency of 70%, medium was removed. The cells were washed with PBS and DMEM without phenol red (Gibco Invitrogen Corporation, Paisley, UK), supplemented with 2% heat-inactivated and dextran-coated charcoal- treated FBS (FBS-cs, Lonza, Basel, Switzerland), L-Glutamine (2mmol/L, Gibco Invitrogen Corporation, Paisley, UK), penicillin (100IU/mL, Gibco Invitrogen Corporation, Paisley, UK) and streptomycin (100µg/mL, Gibco Invitrogen Corporation, Paisley, UK) was added.

extract_protocol:
Total RNA was then extracted using High Pure RNA Isolation Kit (#11828665001, Roche Diagnostics GmbH, Mannheim, Germany) following manufacture’s protocol. The quantity and quality of RNA were measured with the 1000 nanoDrop Spectrophotometer .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 24 hours of deprivation, steroid treatment of E2 (10-9M) or E4 (10-7M or 10-10M) were initiated for 20 hours. Estrogens (E2 or E4), combined or not with progesterone (10-7M) or R5020 (10-8M) treatments, were added and lasted 4 hours. After 24hours of total treatment, the medium was removed andMCF7 cells were washed with PBS.

tag: cell line

value: Epithelial cell line

tag: disease

value: breast adenocarcinoma

tag: classification

value: hormone-dependent

tag: treatments


title: MCF7 cells_E4 10-7M+ R5020 10-8M_rep3

description: MCF7 cells_E4 10-7M+ R5020 10-8M_rep3


title: MCF7 cells_E4 10-7M+ R5020 10-8M_rep2

description: MCF7 cells_E4 10-7M+ R5020 10-8M_rep2


title: MCF7 cells_E4 10-10M+ R5020 10-8M_rep5

description: MCF7 cells_E4 10-10M+ R5020 10-8M_rep5


title: EAE3

description: unbiased total nuclei isolation


title: Ctr1

description: unbiased total nuclei isolation


title: MCF7 cells_E4 10-10M+ R5020 10-8M_rep2

description: MCF7 cells_E4 10-10M+ R5020 10-8M_rep2


title: MCF7 cells_E4 10-10M+ R5020 10-8M_rep1

description: MCF7 cells_E4 10-10M+ R5020 10-8M_rep1


title: MCF7 cells_E4 10-7M+ R5020 10-8M_rep1

description: MCF7 cells_E4 10-7M+ R5020 10-8M_rep1


title: MCF7 cells_E2 10-9M+ R5020 10-8M_rep5

description: MCF7 cells_E2 10-9M+ R5020 10-8M_rep5


title: MCF7 cells_E4 10-7M+ R5020 10-8M_rep5

description: MCF7 cells_E4 10-7M+ R5020 10-8M_rep5


title: MCF7 cells_E2 10-9M+ R5020 10-8M_rep4

description: MCF7 cells_E2 10-9M+ R5020 10-8M_rep4


title: MCF7 cells_E4 10-10M+ R5020 10-8M_rep4

description: MCF7 cells_E4 10-10M+ R5020 10-8M_rep4


title: MCF7 cells_E2 10-9M+ R5020 10-8M_rep1

description: MCF7 cells_E2 10-9M+ R5020 10-8M_rep1


title: MCF7 cells_E4 10-7M+ P4 10-7M_rep3

description: MCF7 cells_E4 10-7M+ P4 10-7M_rep3


title: MCF7 cells_E4 10-7M+ P4 10-7M_rep5

description: MCF7 cells_E4 10-7M+ P4 10-7M_rep5


title: MCF7 cells_E4 10-10M+ R5020 10-8M_rep3

description: MCF7 cells_E4 10-10M+ R5020 10-8M_rep3


title: MCF7 cells_E4 10-10M+ P4 10-7M_rep5

description: MCF7 cells_E4 10-10M+ P4 10-7M_rep5


title: MCF7 cells_E4 10-7M+ P4 10-7M_rep1

description: MCF7 cells_E4 10-7M+ P4 10-7M_rep1


title: MCF7 cells_E2 10-9M+ R5020 10-8M_rep3

description: MCF7 cells_E2 10-9M+ R5020 10-8M_rep3


title: MCF7 cells_E2 10-9M+ R5020 10-8M_rep2

description: MCF7 cells_E2 10-9M+ R5020 10-8M_rep2


title: MCF7 cells_E4 10-10M+ P4 10-7M_rep2

description: MCF7 cells_E4 10-10M+ P4 10-7M_rep2


title: Ctr2

description: unbiased total nuclei isolation


title: MCF7 cells_E2 10-9M+ P4 10-7M_rep3

description: MCF7 cells_E2 10-9M+ P4 10-7M_rep3


title: MCF7 cells_E2 10-9M+ P4 10-7M_rep1

description: MCF7 cells_E2 10-9M+ P4 10-7M_rep1


title: MCF7 cells_E4 10-7M+ P4 10-7M_rep4

description: MCF7 cells_E4 10-7M+ P4 10-7M_rep4


title: MCF7 cells_E4 10-7M_rep4

description: MCF7 cells_E4 10-7M_rep4


title: MCF7 cells_E4 10-7M+ P4 10-7M_rep2

description: MCF7 cells_E4 10-7M+ P4 10-7M_rep2


title: MCF7 cells_E4 10-10M_rep3

description: MCF7 cells_E4 10-10M_rep3


title: MCF7 cells_E4 10-10M+ P4 10-7M_rep4

description: MCF7 cells_E4 10-10M+ P4 10-7M_rep4


title: MCF7 cells_E4 10-10M_rep2

description: MCF7 cells_E4 10-10M_rep2


title: MCF7 cells_E4 10-7M_rep5

description: MCF7 cells_E4 10-7M_rep5


title: Ctr3

description: unbiased total nuclei isolation


title: MCF7 cells_E4 10-10M_rep1

description: MCF7 cells_E4 10-10M_rep1


title: MCF7 cells_E2 10-9M_rep4

description: MCF7 cells_E2 10-9M_rep4


title: MCF7 cells_E2 10-9M_rep1

description: MCF7 cells_E2 10-9M_rep1


title: MCF7 cells_E4 10-10M+ P4 10-7M_rep1

description: MCF7 cells_E4 10-10M+ P4 10-7M_rep1


title: MCF7 cells_E4 10-10M+ P4 10-7M_rep3

description: MCF7 cells_E4 10-10M+ P4 10-7M_rep3


title: MCF7 cells_E2 10-9M+ P4 10-7M_rep5

description: MCF7 cells_E2 10-9M+ P4 10-7M_rep5


title: MCF7 cells_E2 10-9M_rep2

description: MCF7 cells_E2 10-9M_rep2


title: MCF7 cells_E2 10-9M+ P4 10-7M_rep2

description: MCF7 cells_E2 10-9M+ P4 10-7M_rep2


title: MCF7 cells_E2 10-9M+ P4 10-7M_rep4

description: MCF7 cells_E2 10-9M+ P4 10-7M_rep4


title: MCF7 cells_DMSO 0.001%_rep4

description: MCF7 cells_DMSO 0.001%_rep4

value: Vehicle (DMSO 0.001%)


title: MCF7 cells_E4 10-7M_rep3

description: MCF7 cells_E4 10-7M_rep3


title: MCF7 cells_E4 10-7M_rep1

description: MCF7 cells_E4 10-7M_rep1


title: MCF7 cells_E4 10-10M_rep4

description: MCF7 cells_E4 10-10M_rep4


title: MCF7 cells_E4 10-7M_rep2

description: MCF7 cells_E4 10-7M_rep2


title: Wild-type H3K27me3 rep 1

status: Public on May 14 2021

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Raw reads were mapped to the SL3.0 build of the tomato genome using Bowtie2 with default parameters.
Raw mapped reads were then processed using Samtools to retain only those with a mapping quality score greater than or equal to 2.
Enriched regions (peaks) for H3K27me3 were then identified for each ChIP replicate (in comparison to the corresponding input) using the “Findpeaks” function of the HOMER package
Genome_build: SL3.0

organism: Solanum lycopersicum

source_name: shoot apex of 28 day old plants

growth_protocol: Plants were grown on soil under 16 hrs of light/8 hrs dark cycles for 28 days after germination. Shoot apices, (0.8 g for each replicate and two replicates per genotype) containing approximately three visible expanding leaves, were harvested and fixed in 1% formaldehyde + 0.2% Silwet L-77 for 17 minutes under vacuum. Glycine was then added to a final concentration of 0.125 M and tissue was placed under vacuum for an additional 5 minutes, followed by washing several times in water. ChIP was performed on the fixed tissue using the procedure of Gendrel et al (2005) Nature Methods . 2: 213-218

extract_protocol:
For each ChIP reaction, we used 2 ug of a rabbit polyclonal antibody against H3K27me3 (Millipore, catalog #07-449).
Input and ChIP DNAs were converted to Illumina sequencing libraries using the Accel-NGS 2S Plus DNA library kit according to the manufacturer’s instructions (Swift Biosciences)

tag: genotype/variation

value: Wild-type

value: Shoot apex with three expanding leaves

tag: chip antibody

value: H3K27me3(Millipore, catalog #07-449)


title: Wild-type H3K27me3 rep 2


title: MCF7 cells_E4 10-10M_rep5

description: MCF7 cells_E4 10-10M_rep5


title: crel input rep 2

value: crel mutant


title: MCF7 cells_E2 10-9M_rep5

description: MCF7 cells_E2 10-9M_rep5


title: MCF7 cells_DMSO 0.001%_rep5

description: MCF7 cells_DMSO 0.001%_rep5


title: MCF7 cells_DMSO 0.001%_rep2

description: MCF7 cells_DMSO 0.001%_rep2


title: MCF7 cells_DMSO 0.001%_rep3

description: MCF7 cells_DMSO 0.001%_rep3


title: crel H3K27me3 rep 2


title: MCF7 cells_DMSO 0.001%_rep1

description: MCF7 cells_DMSO 0.001%_rep1


title: crel input rep 1


title: crel H3K27me3 rep 1


title: Wild-type input rep 2


title: 160701_SND393_B_L002_3_GDU-33

status: Public on Apr 01 2021

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

data_processing:
3’ adapter removal by Trimmomatic
Mapping to the genome by Bowtie, Tophat and Samtools
Quantification, expression estimation, normalization and comparison via Cufflinks. Transcript abundances was measured in FPKM
Genome_build: Ensembl GRCh37

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in RPMI medium supplemented with 10% FBS and 1 % penicillin-streptomycin

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA samples were subjected to DNAse treatment and poly(A) enrichment

treatment_protocol: Hela cells were treated with 40 nM Negative GapmeR and DR5-AS GapmeR for 72h.

value: HeLa

value: cervix epithelial

tag: passages

tag: treatment

value: Negative GapmeR


title: Wild-type input rep 1


title: 160701_SND393_B_L002_3_GDU-31

tag: cell type


title: 160701_SND393_B_L002_3_GDU-32


title: 343

status: Public on Mar 17 2021

city: Dublin

first: William

middle: P.

last: Martin

state: - Select State/Province -

address: Diabetes Complications Research Centre, Conway Institute, University College Dublin

country: Ireland

institute: University College Dublin

data_processing:
Quality control of reads performed with fastqc.
Quality filtering of reads performed with trim_galore.
Alignment towards rn5 rat reference genome using STAR.
Quantification of aligned reads using featureCounts (Subread package).
Differential expression analysis using DESeq2.
Genome_build: rn5 (Rnor_5.0) rat reference genome
Supplementary_files_format_and_content: *_featureCounts.txt: Tab-delimited text files providing raw counts of aligned reads for each rat renal cortical sample.

organism: Rattus norvegicus

source_name: Renal cortex

extract_protocol:
RNA extraction from renal cortex was performed using an RNeasy Mini Kit (Qiagen). RNA was isolated according to manufacturer’s instructions. Renal cortical samples were preserved on dry ice prior to lysis steps. RNA samples were stored at -80 degrees Celsius until RNA-sequencing. RNA integrity was checked using a Bioanalyser system prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library preparation kit: TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold.

tag: strain

value: Zucker Diabetic Sprague Dawley

value: 37 weeks

value: Renal cortex

tag: experimental group

value: SHAM


title: 333

tag: age


title: 315


title: 357

value: Sprague Dawley


title: 348


title: 340


title: CochlearLateralWall_YoungAdult_rep1

status: Public on Apr 14 2021

type: RNA

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Targets (21.5 ul of labeled product) were hybridized to Affymetrix microRNA 3.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files imported into Affymetrix Expression Console software and data were summarized by the RMA+DABG-Mouse_only algorithm to obtain RMA normalized log2 expression values and detection calls for the mouse content on the microarray.

label: biotin

source_name: Cochlear lateral wall, young adult

label_protocol: Total RNA (130 ng) was converted into biotin-labeled product using the FlashTag™ Biotin HSR RNA Labeling Kit in accordance with manufacturer protocols.

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).  All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.  Prior to treatment, mice were examined for signs of external ear canal and middle ear obstruction, and mice exhibiting these signs were excluded from the study.

extract_protocol: Microdissected CLW underwent total RNA preparation using the miRNeasy Minikit (Qiagen). RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure that total RNA samples retained small molecular weight RNA and were of sufficient quality for transcripomic analysis.

treatment_protocol: CBA/CaJ young adult (1-3 months) and aged (1.5 years) mice were used in this study. Mice were euthanized and CLW tissues were micro-dissected from the inner ear. All sample types were prepared in experimental triplicate (n=3).

value: cochlear lateral wall

value: 1-3 month

tag: age type

value: young


title: CochlearLateralWall_YoungAdult_rep2


title: 334


title: CochlearLateralWall_YoungAdult_rep3


title: CochlearLateralWall_OldAdult_rep1

source_name: Cochlear lateral wall, old adult

value: 1.5 year

value: old


title: CochlearLateralWall_OldAdult_rep2

treatment_protocol: CBA/CaJ young adult (1-3 months) and aged (1-2.5 years) mice were used in this study. Mice were euthanized and CLW tissues were micro-dissected from the inner ear. All sample types were prepared in experimental triplicate (n=3).

value: 1-5 year


title: CochlearLateralWall_OldAdult_rep3


title: 355


title: 352


title: CochlearLateralWall_OldAdult_rep2

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Mouse 430 2.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

data_processing: CEL files imported into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls.

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.


title: CochlearLateralWall_YoungAdult_rep2


title: MCF7 cells_E2 10-9M_rep3

description: MCF7 cells_E2 10-9M_rep3

value: Epithelial cell line

value: breast adenocarcinoma

value: hormone-dependent


title: CochlearLateralWall_OldAdult_rep3


title: CochlearLateralWall_OldAdult_rep1


title: CochlearLateralWall_YoungAdult_rep3


title: CochlearLateralWall_YoungAdult_rep1


title: 317


title: 321


title: 311


title: 356


title: 353


title: IBC_HUG-12b

status: Public on Jan 22 2021

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the Homo sapiens NCBI GRCh38 genome using HISAT2.
Assemble the mapped reads into possible transcripts and generate a transcriptome assembly with Cufflinks.
Calculation of counts with HTSeq.
Variance stabilization performed using log2 scaling.
Batch effect correction after integration with RNA-seq data from the Sequence Read Archive (SRA) database for wild type motoneurons MN wtMN-1(BJ) (SRR2038215), wtMN-2(S+P) (SRR606336) and human ESC H9 (SRR3647179)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include log2 counts values for each sample

growth_protocol:
OI-MSCs from 10 OI pediatric patients were seeded in 96-well plates (1 000 cells/well) and the following day cultured in the presence of OIM.
Next, total RNA was isolated with the AllPrep  kit (QIAGEN, USA). cDNA library (TrueSeq stranded Total cDNA library, Illumina, USA) and sequencing at
HiSeq 4000 (PE100nt, 50 million reads/sample).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
OI-MSCs were cultured under standard growth medium (DMEM low glucose with glutamax (Gibco),
penicillin/streptomycin (Gibco) and fetal bovine serum at 10% (Sigma-Aldrich, USA).

tag: individual

value: OI pediatric patient 12

value: OI-MSCs

value: Basal

tag: gender

value: Male


title: 354

value: 37 weeks

tag: tissue


title: IBC_HUG-15b

description: replicate 1

value: OI pediatric patient 15


title: IBC_HUG-15v2

description: replicate 1

value: 2nd Visit


title: TAM_sorted

status: Public on Mar 16 2021

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

country: China

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

description: MMP9+ tumor-associated macrophages sorted from a primary HCC tumor

data_processing: The Bulk RNA-seq data were processed using the STAR-rsem pipeline. Read counts per gene were normalized to gene length and to the total read counts.

source_name: Tumor-associated macrophages sorted from a primary HCC tumor

extract_protocol:
Total RNAs were extracted from the co-cultured THP-1 cells, or FACS-sorted cells from the tumor and non-tumor liver tissues using the RNeasy Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions. The qualities of total RNAs were measured by spectrophotometer (NanoDrop, Thermo Fisher, USA).
Libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB, USA) and NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB, USA). Samples were sequenced on the Illumina Hiseq 4000 sequencer with 150 bp paired-end reads.

value: primary HCC tumor


title: IBC_HUG-12v2

description: replicate 1


title: IBC_HUG-19v2

description: replicate 1

value: OI pediatric patient 19


title: IBC_HUG-3b

description: replicate 1

value: OI pediatric patient 3


title: IBC_HUG-3v2

description: replicate 1


title: IBC_HUG-7v2

description: replicate 1

value: OI pediatric patient 7


title: IBC_HUG-2v2

description: replicate 1

value: OI pediatric patient 2

value: Female


title: SC3

status: Public on Jan 12 2021

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

data_processing:
Quality control of reads was assessed with FastQC
Trimming of the reads was performed with Skewer
Mapping to the reference genome was done using TopHat
Counts per gene were calculated with HTSeq
Differential gene expression analysis was calculated with DESeq2
Genome_build: Biocodex, S288C
Supplementary_files_format_and_content: Counts files containing the genome's ORFs and the number of read counts for each ORF
Supplementary_files_format_and_content: RNA-Seq-assisted annotation file (.gff3)

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Cells were grown in ILM for 6h until mid-exponential phase

extract_protocol:
Ambion Ribopure-Yeast RNA kit, according to manufacturer’s instructions.
Nugen Universal Plus mRNA-Seq

treatment_protocol: Cell pellets were collected and immediately stored at -80ºC


title: IBC_HUG-2b

description: replicate 1


title: IBC_HUG-16v2

description: replicate 1

value: OI pediatric patient 16


title: ET rep 2

status: Public on Jan 26 2021

description: replicate 2

hyb_protocol: Hybridization was performed following the standard Agilent Protocol for the miRNA Microarray System with a miRNA Complete hybridization, including Agilent miRNA Spike-ins.

scan_protocol: The hybridized arrays were washed, dried and finally scanned on using an Agilent Microarray Scanner G2565CA (Agilent Technologies, USA). The scanned TIFF image files were processed using Agilent Feature Extraction Software vs 10.7.3.1 to extract raw data and obtain QC reports.

data_processing:
The microarray raw data were normalized using the quantile method.
To find the statistically significant differentially expressed miRNAs (DEMs) between two groups of samples,
we calculated the mean of each probe across all the samples of the group.
Next, we filtered out all the probes whose absolute value of the difference of mean values between the two groups was less than a
selection threshold thetaDEM = 4 (that corresponds to a fold change of 2 in log2 scale),
and we applied a Student's t-test with a significance threshold alphaDEM = 0.05.
The PCA and the hierarchical clustering of genes and samples were performed with one minus the correlation metric and the
unweighted average distance (UPGMA) linkage method.
All the analysis algorithms and graphics were implemented functions in Matlab.

source_name: ET rep 2

label_protocol:
Labelling was performed following the standard Agilent Protocol for the miRNA Microarray System with a
miRNA Complete Labelling, including Agilent miRNA Spike-ins.

extract_protocol: 100 ng of total RNA was extracted

tag: tumor

value: Yes

value: Balb/c


title: IBC_HUG-19b

description: replicate 1


title: EC rep 1

description: replicate 1

source_name: EC rep 1

value: No


title: EC rep 2

description: replicate 2

source_name: EC rep 2


title: ET rep 1

description: replicate 1

source_name: ET rep 1


title: SC2


title: IBC_HUG-16b

description: replicate 1


title: SC1


title: SB3

value: Biocodex


title: IBC_HUG-14b

description: replicate 1

value: OI pediatric patient 14

value: OI-MSCs


title: IBC_HUG-11b

description: replicate 1

value: OI pediatric patient 11

value: Basal


title: SB1


title: IBC_HUG-8b

description: replicate 1

value: OI pediatric patient 8


title: IBC_HUG-14v2

description: replicate 1

value: 2nd Visit


title: IBC_HUG-8v2

description: replicate 1


title: IBC_HUG-7b

description: replicate 1

value: Male


title: ET rep 3

description: replicate 3

source_name: ET rep 3


title: IBC_HUG-11v2

description: replicate 1


title: TP rep 2

status: Public on Nov 02 2020

description: replicate 2

hyb_protocol: Agilent mouse whole genome 8x60K oligo microarrays (design 028005) were used for hybridizations. The Agilent Gene Expression Hybridization Kit was used for hybridization as detailed in the Agilent processing protocol (Agilent technologies). In brief, 600 ng Cy3- abd Cy5 labelled fragmented cRNA in hybridization buffer was hybridized overnight at 65C to the microarrays using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed with the Agilent Gene Expression Wash Buffer 1 (1 min at 23C) and then with preheated Agilent Gene Expression Wash Buffer 2 (1 min at 37C).

scan_protocol: The Agilent’s Microarray Scanner Sytem (Agilent Technologies) was used for detecting fluorescence signals on the hybridized microarrays. The microarray image files were processed with the Agilent Feature Extraction Software (FES),

data_processing: The microarray raw data were normalized using the quantile method.

source_name: TP rep 2

label_protocol:
Each RNA sample was used to produce Cy3-labeled and Cy5 cRNA.
Eqivalents of 100 ng from the individual RNA samples were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies)
according to the manufacturer’s instructions.

extract_protocol:
Trizol standard RNA extraction. An additional cleaning up of  RNA followed using the miRNeasy Kit (Qiagen, Hilden, Germany).
Integrity and quality of RNA was checked with the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

tag: type of cell

value: Colorectal cancer (CRC) primary cells


title: TP rep 1

description: replicate 1

source_name: TP rep 1


title: SB2


title: TP rep 3

description: replicate 3

source_name: TP rep 3


title: TM rep 4

description: replicate 4

source_name: TM rep 4

value: Tumor liver metastasis cells


title: KT rep 4

description: replicate 4

source_name: KT rep 4

value: Kupffer tumour microenvironment (TME) cells


title: KT rep 3

description: replicate 3

source_name: KT rep 3


title: KC rep 3

description: replicate 3

source_name: KC rep 3

value: Kupffer control cells


title: TM rep 1

description: replicate 1

source_name: TM rep 1


title: TM rep 2

description: replicate 2

source_name: TM rep 2


title: IT rep 2

description: replicate 2

source_name: IT rep 2

value: Ito tumour microenvironment (TME) cells


title: KT rep 2

description: replicate 2

source_name: KT rep 2


title: TM rep 3

description: replicate 3

source_name: TM rep 3


title: KC rep 4

description: replicate 4

source_name: KC rep 4


title: KC rep 1

description: replicate 1

source_name: KC rep 1


title: IC rep 3

description: replicate 3

source_name: IC rep 3

value: Ito control cells


title: IC rep 1

description: replicate 1

source_name: IC rep 1


title: EC rep 4

description: replicate 4

source_name: EC rep 4

value: Enthothelial control cells


title: KC rep 2

description: replicate 2

source_name: KC rep 2


title: ET rep 1

description: replicate 1

source_name: ET rep 1

value: Enthothelial tumour microenvironment (TME) cells


title: IT rep 3

description: replicate 3

source_name: IT rep 3


title: IT rep 4

description: replicate 4

source_name: IT rep 4


title: IC rep 2

description: replicate 2

source_name: IC rep 2


title: IC rep 4

description: replicate 4

source_name: IC rep 4


title: KT rep 1

description: replicate 1

source_name: KT rep 1


title: ET rep 4

description: replicate 4

source_name: ET rep 4


title: IT rep 1

description: replicate 1

source_name: IT rep 1


title: ET rep 3

description: replicate 3

source_name: ET rep 3


title: TP rep 4

description: replicate 4

source_name: TP rep 4


title: ET rep 2

description: replicate 2

source_name: ET rep 2


title: EC rep 2

description: replicate 2

source_name: EC rep 2


title: EC rep 1

description: replicate 1

source_name: EC rep 1


title: EC rep 3

description: replicate 3

source_name: EC rep 3


title: TP rep 3

description: replicate 3

hyb_protocol: The hybridized arrays were washed, dried and finally scanned on using an Agilent Microarray Scanner G2565CA (Agilent Technologies, USA).

source_name: TP rep 3


title: KT rep 2

description: replicate 2

source_name: KT rep 2


title: TM rep 3

description: replicate 3

source_name: TM rep 3


title: TM rep 2

description: replicate 2

source_name: TM rep 2


title: KT rep 1

description: replicate 1


title: KC rep 1

description: replicate 1

source_name: KC rep 1


title: IT rep 2

description: replicate 2

source_name: IT rep 2


title: KC rep 3

description: replicate 3

source_name: KC rep 3


title: KC rep 2

description: replicate 2

source_name: KC rep 2


title: BT20_ERLOTINIB_24hr_Rep1

status: Public on Nov 01 2020

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description:
ML_all22_BTe24h_1
Replicate 1: BT20 (TNBC cell line) 24-hr Erlotinib (10uM) treatment

data_processing:
barcode and adapter removal FASTX toolkit (v0.0.14) NaN
quality filtering FastQC (v0.11.8) quality >20, leading/trailing 5, minlength 36
remove non-mRNAs Bowtie2 rRNA, miRNA, tRNA, piRNA, snRNA, rmsk removal
RSEM RSEM (v1.3.1) strand-specific, bowtie2, genome-bam
DESeq2 DESeq2(1.26.0) Controls (DMSO); Treatment (ERLOTINIB); parametric
Genome_build: hg19; GRCh38
Supplementary_files_format_and_content: RSEM expected counts, TPMs; DeSeq2 L2FC & FDR-adjusted pvalues for comparisons

growth_protocol: BT20 cells were cultured with MEM + FBS + glutamine + penicillin/streptomycin

extract_protocol:
Phenol-chloroform extraction of whole RNA
Illumina TruSeq HT Stranded (mRNA)

treatment_protocol: 24-hour treatment with either DMSO (v/v%) or ERLOTINIB (10uM)

tag: agent

value: ERLOTINIB

tag: cell line


title: IC rep 1

description: replicate 1

source_name: IC rep 1


title: TM rep 1

description: replicate 1

source_name: TM rep 1


title: ET rep 1

description: replicate 1

source_name: ET rep 1


title: BT20_DMSO_24hr_Rep2

description:
ML_all20_BTD24h_2
Replicate 2: BT20 (TNBC cell line) 24-hr DMSO (v/v%) treatment

value: DMSO


title: TP rep 1

description: replicate 1

source_name: TP rep 1


title: IT rep 3

description: replicate 3

source_name: IT rep 3


title: IT rep 1

description: replicate 1

source_name: IT rep 1


title: IC rep 3

description: replicate 3

source_name: IC rep 3


title: TP rep 2

description: replicate 2

source_name: TP rep 2


title: EC rep 1

description: replicate 1

source_name: EC rep 1


title: BT20_ERLOTINIB_24hr_Rep2

description:
ML_all23_BTe24h_2
Replicate 2: BT20 (TNBC cell line) 24-hr Erlotinib (10uM) treatment


title: EC rep 2

description: replicate 2

source_name: EC rep 2


title: IC rep 2

description: replicate 2

source_name: IC rep 2


title: ET rep 2

description: replicate 2

source_name: ET rep 2


title: BT20_DMSO_24hr_Rep3

description:
ML_all21_BTD24h_3
Replicate 3: BT20 (TNBC cell line) 24-hr DMSO (v/v%) treatment


title: BT20_DMSO_24hr_Rep1

description:
ML_all19_BTD24h_1
Replicate 1: BT20 (TNBC cell line) 24-hr DMSO (v/v%) treatment


title: lung30, 3BMB

status: Public on Oct 07 2020

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol:
All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: type (3bmb, highsft, lowsft)

value: lung biopsy


title: lung388, 3BMB


title: lung401, 3BMB


title: lung552, 3BMB


title: lung691, 3BMB


title: lung469, 3BMB


title: lung62, 3BMB


title: ET rep 3

description: replicate 3

source_name: ET rep 3


title: lung293, 3BMB


title: lung458, 3BMB


title: lung730, 3BMB


title: lung340, 3BMB


title: lung199, 3BMB


title: lung564, 3BMB


title: lung341, lowSFT

value: lowSFT


title: lung297, 3BMB


title: lung181, 3BMB


title: lung109, 3BMB


title: lung281, 3BMB


title: lung491, 3BMB


title: lung617, 3BMB


title: lung599, 3BMB


title: lung423, 3BMB


title: lung632, 3BMB


title: lung82, 3BMB


title: lung761, 3BMB


title: lung22, 3BMB


title: lung257, 3BMB


title: lung83, 3BMB


title: lung570, 3BMB


title: lung621, 3BMB


title: lung431, 3BMB


title: lung529, 3BMB


title: lung382, 3BMB


title: lung254, 3BMB


title: lung284, 3BMB


title: lung574, 3BMB


title: lung192, 3BMB


title: lung560, 3BMB


title: lung586, 3BMB


title: lung555, 3BMB


title: lung759, 3BMB


title: lung348, 3BMB


title: lung215, 3BMB


title: lung437, 3BMB


title: lung515, 3BMB


title: lung475, 3BMB


title: lung688, 3BMB


title: lung66, 3BMB


title: lung212, 3BMB


title: lung41, 3BMB


title: lung129, 3BMB


title: lung448, 3BMB


title: lung255, 3BMB


title: lung118, 3BMB


title: lung487, 3BMB


title: lung309, 3BMB


title: lung753, 3BMB


title: lung98, 3BMB


title: lung704, 3BMB


title: lung436, 3BMB


title: lung232, 3BMB


title: lung527, 3BMB


title: lung183, 3BMB


title: BT20_ERLOTINIB_24hr_Rep3

description:
ML_all24_BTe24h_3
Replicate 3: BT20 (TNBC cell line) 24-hr Erlotinib (10uM) treatment


title: lung372, 3BMB


title: lung676, 3BMB


title: lung260, 3BMB


title: lung418, 3BMB


title: lung235, 3BMB


title: lung720, 3BMB


title: lung23, 3BMB


title: lung369, 3BMB


title: lung345, 3BMB


title: lung6, 3BMB


title: lung121, 3BMB


title: lung668, 3BMB


title: lung14, 3BMB


title: lung579, 3BMB


title: lung122, 3BMB


title: lung679, 3BMB


title: lung316, 3BMB


title: lung762, 3BMB


title: lung750, 3BMB


title: lung86, 3BMB


title: lung561, 3BMB


title: lung356, 3BMB


title: lung154, 3BMB


title: lung58, 3BMB


title: lung170, 3BMB


title: lung198, 3BMB


title: lung421, 3BMB


title: lung655, 3BMB


title: lung331, 3BMB


title: lung577, 3BMB


title: lung330, 3BMB


title: lung536, 3BMB


title: lung666, 3BMB


title: lung52, 3BMB


title: lung165, 3BMB


title: lung494, 3BMB


title: lung107, 3BMB


title: lung1, 3BMB


title: lung134, 3BMB


title: lung424, 3BMB


title: lung214, 3BMB


title: lung703, 3BMB


title: lung131, 3BMB


title: lung658, 3BMB


title: lung476, 3BMB


title: lung503, 3BMB


title: lung365, 3BMB


title: lung47, 3BMB


title: lung3, 3BMB


title: lung451, 3BMB


title: lung446, 3BMB


title: lung722, 3BMB


title: lung329, 3BMB


title: lung484, 3BMB


title: lung450, 3BMB


title: lung236, 3BMB


title: lung551, 3BMB


title: lung179, 3BMB


title: lung517, 3BMB


title: lung610, 3BMB


title: lung409, 3BMB


title: lung729, 3BMB


title: lung732, 3BMB


title: lung237, 3BMB


title: lung245, 3BMB


title: lung630, 3BMB


title: lung242, 3BMB


title: lung749, 3BMB


title: lung614, 3BMB


title: lung381, 3BMB


title: lung193, 3BMB


title: lung279, 3BMB


title: lung344, 3BMB


title: lung40, 3BMB


title: lung327, 3BMB


title: lung754, 3BMB


title: lung266, 3BMB


title: lung500, 3BMB


title: lung65, 3BMB


title: lung768, 3BMB


title: lung385, 3BMB


title: lung223, 3BMB


title: lung508, 3BMB


title: lung104, 3BMB


title: lung188, 3BMB


title: lung746, 3BMB


title: lung769, 3BMB


title: lung326, 3BMB


title: lung178, 3BMB


title: lung594, 3BMB


title: lung612, 3BMB


title: lung36, 3BMB


title: lung611, 3BMB


title: lung707, 3BMB


title: lung97, 3BMB


title: lung228, 3BMB


title: lung433, 3BMB


title: lung250, 3BMB


title: lung760, 3BMB


title: lung631, 3BMB


title: lung81, 3BMB


title: lung640, 3BMB


title: lung282, 3BMB


title: lung271, 3BMB


title: lung656, 3BMB


title: lung19, 3BMB


title: lung144, 3BMB


title: lung724, 3BMB


title: lung176, 3BMB


title: lung447, 3BMB


title: lung120, 3BMB


title: lung687, 3BMB


title: lung706, 3BMB


title: lung439, 3BMB


title: lung650, 3BMB


title: lung639, 3BMB


title: lung662, 3BMB


title: lung619, 3BMB


title: lung721, 3BMB


title: lung25, 3BMB


title: lung63, 3BMB


title: lung27, 3BMB


title: lung514, 3BMB


title: lung175, 3BMB


title: lung580, 3BMB


title: lung234, 3BMB


title: lung190, 3BMB


title: lung534, 3BMB


title: lung454, 3BMB


title: lung379, 3BMB


title: lung690, 3BMB


title: lung740, 3BMB


title: lung92, 3BMB


title: lung468, 3BMB


title: lung681, 3BMB


title: lung227, 3BMB


title: lung262, 3BMB


title: lung522, 3BMB


title: lung767, 3BMB


title: lung126, 3BMB


title: lung276, 3BMB


title: lung241, 3BMB


title: lung718, 3BMB


title: lung59, 3BMB


title: lung114, 3BMB


title: lung735, 3BMB


title: lung651, 3BMB


title: lung697, 3BMB


title: lung302, 3BMB


title: lung133, 3BMB


title: lung752, 3BMB


title: lung156, 3BMB


title: lung693, 3BMB


title: lung602, 3BMB


title: lung416, 3BMB


title: lung376, 3BMB


title: lung689, 3BMB


title: lung590, 3BMB


title: lung180, 3BMB


title: lung368, 3BMB


title: lung461, 3BMB


title: lung321, 3BMB


title: lung445, 3BMB


title: lung513, 3BMB


title: lung667, 3BMB


title: lung95, 3BMB


title: lung427, 3BMB


title: lung290, 3BMB


title: lung528, 3BMB


title: lung172, 3BMB


title: lung766, 3BMB


title: lung189, 3BMB


title: lung717, 3BMB


title: lung582, 3BMB


title: lung347, 3BMB


title: lung357, 3BMB


title: lung18, 3BMB


title: lung364, 3BMB


title: lung136, 3BMB


title: lung48, 3BMB


title: lung213, 3BMB


title: lung205, 3BMB


title: lung17, 3BMB


title: lung117, 3BMB


title: lung417, 3BMB


title: lung141, 3BMB


title: lung84, 3BMB


title: lung287, 3BMB


title: lung108, 3BMB


title: lung725, 3BMB


title: lung627, 3BMB


title: lung584, 3BMB


title: lung426, 3BMB


title: lung533, 3BMB


title: lung415, 3BMB


title: lung35, 3BMB


title: lung597, 3BMB


title: lung478, 3BMB


title: lung224, 3BMB


title: lung197, 3BMB


title: lung268, 3BMB


title: lung716, 3BMB


title: lung273, 3BMB


title: lung137, 3BMB


title: lung354, 3BMB


title: lung361, 3BMB


title: lung233, 3BMB


title: lung429, 3BMB


title: lung443, 3BMB


title: lung270, 3BMB


title: lung140, 3BMB


title: lung506, 3BMB


title: lung569, 3BMB


title: lung11, 3BMB


title: lung609, 3BMB


title: lung231, 3BMB


title: lung99, 3BMB


title: lung135, 3BMB


title: lung670, 3BMB


title: lung296, 3BMB


title: lung395, 3BMB


title: lung103, 3BMB


title: lung613, 3BMB


title: lung391, 3BMB


title: lung678, 3BMB


title: lung75, 3BMB


title: lung206, 3BMB


title: lung53, 3BMB


title: lung771, 3BMB


title: lung31, 3BMB


title: lung253, 3BMB


title: lung516, 3BMB


title: lung460, 3BMB


title: lung444, 3BMB


title: lung171, 3BMB


title: lung496, 3BMB


title: lung664, 3BMB


title: lung323, 3BMB


title: lung459, 3BMB


title: lung295, 3BMB


title: lung79, 3BMB


title: lung71, 3BMB


title: lung91, 3BMB


title: lung634, 3BMB


title: lung116, 3BMB


title: lung267, 3BMB


title: lung169, 3BMB


title: lung222, 3BMB


title: lung490, 3BMB


title: lung68, lowSFT


title: lung159, highSFT

value: highSFT


title: lung403, 3BMB


title: lung625, highSFT


title: lung187, lowSFT


title: lung203, highSFT


title: lung61, highSFT


title: lung455, lowSFT


title: lung715, 3BMB


title: lung102, highSFT


title: lung745, highSFT


title: lung645, 3BMB


title: lung161, lowSFT


title: lung692, highSFT


title: lung677, highSFT


title: lung669, highSFT


title: lung633, lowSFT


title: lung425, highSFT


title: lung588, highSFT


title: lung432, highSFT


title: lung541, highSFT


title: lung338, highSFT


title: lung20, lowSFT


title: lung38, highSFT


title: lung558, highSFT


title: lung581, highSFT


title: lung57, highSFT


title: lung93, highSFT


title: lung218, highSFT


title: lung219, highSFT


title: lung510, highSFT


title: lung463, highSFT


title: lung288, highSFT


title: lung605, highSFT


title: lung143, highSFT


title: lung64, highSFT


title: lung550, highSFT


title: lung367, highSFT


title: lung644, highSFT


title: lung519, lowSFT


title: lung457, highSFT


title: lung392, highSFT


title: lung200, highSFT


title: lung322, lowSFT


title: lung393, highSFT


title: lung764, lowSFT


title: lung34, highSFT


title: lung339, highSFT


title: lung653, highSFT


title: lung111, highSFT


title: lung483, highSFT


title: lung39, lowSFT


title: lung452, highSFT


title: lung757, highSFT


title: lung147, highSFT


title: lung643, highSFT


title: lung464, highSFT


title: lung248, highSFT


title: lung719, lowSFT


title: lung67, highSFT


title: lung130, highSFT


title: lung485, lowSFT


title: lung758, highSFT


title: lung380, highSFT


title: lung435, highSFT


title: lung149, highSFT


title: lung414, highSFT


title: lung230, highSFT


title: lung701, highSFT


title: lung589, highSFT


title: lung350, lowSFT


title: lung489, highSFT


title: lung438, highSFT


title: lung332, highSFT


title: lung741, lowSFT


title: lung694, highSFT


title: lung56, highSFT


title: lung313, highSFT


title: lung537, lowSFT


title: lung441, highSFT


title: lung683, highSFT


title: lung636, highSFT


title: lung737, highSFT


title: lung646, lowSFT


title: lung616, highSFT


title: lung333, highSFT


title: lung371, highSFT


title: lung556, lowSFT


title: lung486, highSFT


title: lung474, highSFT


title: lung221, highSFT


title: lung105, lowSFT


title: lung412, highSFT


title: lung168, highSFT


title: lung360, highSFT


title: lung269, highSFT


title: lung320, highSFT


title: lung479, highSFT


title: lung60, highSFT


title: lung398, highSFT


title: lung319, highSFT


title: lung148, highSFT


title: lung127, lowSFT


title: lung261, highSFT


title: lung572, highSFT


title: lung46, highSFT


title: lung289, highSFT


title: lung49, highSFT


title: lung265, highSFT


title: lung578, lowSFT


title: lung709, highSFT


title: lung635, highSFT


title: lung726, highSFT


title: lung101, highSFT


title: lung70, highSFT


title: lung324, highSFT


title: lung160, lowSFT


title: lung132, highSFT


title: lung411, highSFT


title: lung428, highSFT


title: lung731, highSFT


title: lung263, lowSFT


title: lung355, highSFT


title: lung396, highSFT


title: lung509, highSFT


title: lung249, lowSFT


title: lung343, highSFT


title: lung73, highSFT


title: lung283, highSFT


title: lung337, highSFT


title: lung744, highSFT


title: lung80, lowSFT


title: lung264, highSFT


title: lung698, lowSFT


title: lung13, highSFT


title: lung521, highSFT


title: lung652, highSFT


title: lung374, highSFT


title: lung539, highSFT


title: lung157, highSFT


title: lung85, highSFT


title: lung119, highSFT


title: lung256, highSFT


title: lung654, highSFT


title: lung549, highSFT


title: lung89, highSFT


title: lung592, highSFT


title: lung713, highSFT


title: lung649, highSFT


title: lung373, lowSFT


title: lung504, lowSFT


title: lung294, highSFT


title: lung708, highSFT


title: lung466, lowSFT


title: lung624, lowSFT


title: lung69, highSFT


title: lung113, highSFT


title: lung736, highSFT


title: lung473, highSFT


title: lung587, highSFT


title: lung5, highSFT


title: lung453, highSFT


title: lung512, highSFT


title: lung739, highSFT


title: lung742, highSFT


title: lung377, highSFT


title: lung700, highSFT


title: lung112, highSFT


title: lung246, highSFT


title: lung648, highSFT


title: lung42, highSFT


title: lung4, highSFT


title: lung638, highSFT


title: lung647, highSFT


title: lung598, highSFT


title: lung45, highSFT


title: lung363, lowSFT


title: lung315, highSFT


title: lung728, highSFT


title: lung554, highSFT


title: lung477, highSFT


title: lung151, highSFT


title: lung50, highSFT


title: lung604, highSFT


title: lung680, highSFT


title: lung32, highSFT


title: lung208, highSFT


title: lung449, highSFT


title: lung618, highSFT


title: lung72, highSFT


title: lung472, highSFT


title: lung488, highSFT


title: lung226, highSFT


title: lung481, highSFT


title: lung568, highSFT


title: lung29, lowSFT


title: lung532, highSFT


title: lung77, highSFT


title: lung155, highSFT


title: lung684, highSFT


title: lung511, highSFT


title: lung705, highSFT


title: lung275, highSFT


title: lung349, highSFT


title: lung467, highSFT


title: lung278, highSFT


title: lung573, highSFT


title: lung299, highSFT


title: lung359, highSFT


title: lung620, highSFT


title: lung525, lowSFT


title: lung204, lowSFT


title: lung378, lowSFT


title: lung493, highSFT


title: lung142, highSFT


title: lung562, lowSFT


title: lung659, highSFT


title: lung462, highSFT


title: lung456, lowSFT


title: lung600, highSFT


title: lung177, highSFT


title: lung755, lowSFT


title: lung576, highSFT


title: lung259, highSFT


title: lung163, highSFT


title: lung78, highSFT


title: lung115, lowSFT


title: lung723, highSFT


title: lung765, highSFT


title: lung240, lowSFT


title: lung158, lowSFT


title: lung346, lowSFT


title: lung44, highSFT


title: lung607, highSFT


title: lung43, highSFT


title: lung128, highSFT


title: lung7, highSFT


title: lung399, highSFT


title: lung675, highSFT


title: lung747, highSFT


title: lung734, highSFT


title: lung220, highSFT


title: lung733, highSFT


title: lung272, highSFT


title: lung505, highSFT


title: lung542, highSFT


title: lung559, lowSFT


title: lung387, highSFT


title: lung518, highSFT


title: lung186, highSFT


title: lung763, lowSFT


title: lung756, highSFT


title: lung686, highSFT


title: lung16, lowSFT


title: lung738, highSFT


title: lung406, highSFT


title: lung252, highSFT


title: lung661, highSFT


title: lung629, highSFT


title: lung682, highSFT


title: lung196, highSFT


title: lung366, lowSFT


title: lung247, highSFT


title: lung162, highSFT


title: lung545, highSFT


title: lung125, highSFT


title: lung543, highSFT


title: lung370, highSFT


title: lung314, lowSFT


title: lung585, highSFT


title: lung501, highSFT


title: lung583, highSFT


title: lung277, highSFT


title: lung520, highSFT


title: lung150, highSFT


title: lung699, highSFT


title: lung185, lowSFT


title: lung229, highSFT


title: lung502, highSFT


title: lung603, highSFT


title: lung10, highSFT


title: lung465, lowSFT


title: lung87, lowSFT


title: lung751, highSFT


title: lung495, highSFT


title: lung665, highSFT


title: lung546, highSFT


title: lung714, highSFT


title: lung191, highSFT


title: lung312, highSFT


title: lung311, highSFT


title: lung21, highSFT


title: lung563, highSFT


title: lung413, highSFT


title: lung334, highSFT


title: lung548, highSFT


title: lung202, highSFT


title: lung394, highSFT


title: lung567, highSFT


title: lung615, highSFT


title: lung318, highSFT


title: lung601, highSFT


title: lung243, highSFT


title: lung225, highSFT


title: lung384, highSFT


title: lung110, highSFT


title: lung310, highSFT


title: lung167, highSFT


title: lung244, highSFT


title: lung497, highSFT


title: lung352, highSFT


title: lung608, highSFT


title: lung362, lowSFT


title: lung400, highSFT


title: lung375, lowSFT


title: lung353, highSFT


title: lung51, highSFT


title: lung430, highSFT


title: lung15, highSFT


title: lung402, highSFT


title: lung544, lowSFT


title: lung397, highSFT


title: lung291, highSFT


title: lung710, highSFT


title: lung166, lowSFT


title: lung593, highSFT


title: lung471, highSFT


title: lung553, highSFT


title: lung482, highSFT


title: lung54, highSFT


title: lung207, highSFT


title: lung672, highSFT


title: lung628, highSFT


title: lung90, lowSFT


title: lung139, highSFT


title: lung298, highSFT


title: lung300, highSFT


title: lung251, highSFT


title: lung557, highSFT


title: lung106, highSFT


title: lung526, highSFT


title: lung499, highSFT


title: lung201, highSFT


title: lung591, lowSFT


title: lung507, lowSFT


title: lung571, highSFT


title: lung88, highSFT


title: lung24, highSFT


title: lung410, highSFT


title: lung408, highSFT


title: lung303, lowSFT


title: lung258, highSFT


title: lung28, highSFT


title: lung405, highSFT


title: lung301, highSFT


title: lung727, highSFT


title: lung74, lowSFT


title: lung442, lowSFT


title: lung182, highSFT


title: lung8, lowSFT


title: lung743, highSFT


title: lung702, highSFT


title: lung328, highSFT


title: lung626, highSFT


title: lung492, highSFT


title: lung305, highSFT


title: lung209, lowSFT


title: lung210, highSFT


title: lung673, highSFT


title: lung623, highSFT


title: lung342, highSFT


title: lung696, highSFT


title: lung422, highSFT


title: lung153, lowSFT


title: lung657, highSFT


title: lung530, highSFT


title: lung138, lowSFT


title: lung174, highSFT


title: lung575, highSFT


title: lung100, lowSFT


title: lung152, lowSFT


title: lung96, highSFT


title: lung547, lowSFT


title: lung217, lowSFT


title: lung404, highSFT


title: lung336, highSFT


title: lung711, highSFT


title: lung194, highSFT


title: lung383, highSFT


title: lung239, highSFT


title: lung306, lowSFT


title: lung146, highSFT


title: lung94, highSFT


title: lung351, highSFT


title: lung595, highSFT


title: lung606, highSFT


title: lung770, highSFT


title: lung642, lowSFT


title: lung685, lowSFT


title: lung440, lowSFT


title: lung164, highSFT


title: lung195, lowSFT


title: lung524, highSFT


title: lung540, highSFT


title: lung420, lowSFT


title: lung76, highSFT


title: lung358, highSFT


title: lung292, lowSFT


title: lung2, highSFT


title: lung748, highSFT


title: lung286, lowSFT


title: lung55, highSFT


title: lung325, highSFT


title: lung173, highSFT


title: lung9, highSFT


title: lung637, lowSFT


title: lung308, highSFT


title: lung238, highSFT


title: lung566, lowSFT


title: lung335, lowSFT


title: lung565, highSFT


title: lung695, highSFT


title: lung145, highSFT


title: lung211, lowSFT


title: lung37, highSFT


title: lung674, lowSFT


title: lung434, highSFT


title: lung124, highSFT


title: lung280, lowSFT


title: lung26, lowSFT


title: lung538, highSFT


title: lung216, highSFT


title: lung12, highSFT


title: lung596, lowSFT


title: lung285, highSFT


title: lung407, lowSFT


title: lung523, highSFT


title: lung274, highSFT


title: lung390, lowSFT


title: lung498, highSFT


title: lung386, highSFT


title: lung184, highSFT


title: lung304, highSFT


title: lung317, highSFT


title: lung663, highSFT


title: lung307, highSFT


title: lung389, highSFT


title: lung33, highSFT


title: lung470, lowSFT


title: lung123, highSFT


title: lung660, lowSFT


title: lung535, highSFT


title: lung641, highSFT


title: lung480, highSFT


title: lung622, highSFT


title: lung671, highSFT


title: lung531, lowSFT


title: lung712, highSFT


title: lung419, lowSFT


title: ISPY2_pre-treatment breast cancer tumor_771813

status: Public on Sep 20 2020

city: San Francisco

first: Denise

middle: M

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
gnormalized signal (log2) data, as provided in the sample data table and raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-confirmity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 150 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 150 samples for batch correcting on raw files.  An updated probe annotation for platform GPL16233 was used and is provided as Series supplementary file.
The platform corrected, normalized expression values (from two different platforms) are provided in the 'ExpDat_ISPY2_MK2206_n150.txt'.  Data is collapsed on the gene level as was used in the analysis.

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: standard Agilent protocol

extract_protocol: not provided

tag: hr

tag: pcr

tag: arm

value: Control Arm


title: ISPY2_pre-treatment breast cancer tumor_573919

value: MK2206 Arm


title: ISPY2_pre-treatment breast cancer tumor_426106


title: ISPY2_pre-treatment breast cancer tumor_942017


title: ISPY2_pre-treatment breast cancer tumor_520258


title: ISPY2_pre-treatment breast cancer tumor_680881


title: ISPY2_pre-treatment breast cancer tumor_357017


title: ISPY2_pre-treatment breast cancer tumor_549172


title: ISPY2_pre-treatment breast cancer tumor_775346


title: ISPY2_pre-treatment breast cancer tumor_946927


title: ISPY2_pre-treatment breast cancer tumor_395076


title: ISPY2_pre-treatment breast cancer tumor_112606


title: ISPY2_pre-treatment breast cancer tumor_955953


title: ISPY2_pre-treatment breast cancer tumor_203254


title: ISPY2_pre-treatment breast cancer tumor_960963


title: ISPY2_pre-treatment breast cancer tumor_809037


title: ISPY2_pre-treatment breast cancer tumor_515565


title: ISPY2_pre-treatment breast cancer tumor_698094


title: ISPY2_pre-treatment breast cancer tumor_590220


title: ISPY2_pre-treatment breast cancer tumor_286984


title: ISPY2_pre-treatment breast cancer tumor_298101


title: ISPY2_pre-treatment breast cancer tumor_159352


title: ISPY2_pre-treatment breast cancer tumor_255388


title: ISPY2_pre-treatment breast cancer tumor_771443


title: ISPY2_pre-treatment breast cancer tumor_835137


title: ISPY2_pre-treatment breast cancer tumor_145513


title: ISPY2_pre-treatment breast cancer tumor_284593


title: ISPY2_pre-treatment breast cancer tumor_183831


title: ISPY2_pre-treatment breast cancer tumor_963303


title: ISPY2_pre-treatment breast cancer tumor_421917


title: ISPY2_pre-treatment breast cancer tumor_752469


title: ISPY2_pre-treatment breast cancer tumor_688955


title: ISPY2_pre-treatment breast cancer tumor_580541


title: ISPY2_pre-treatment breast cancer tumor_631337


title: ISPY2_pre-treatment breast cancer tumor_172168


title: ISPY2_pre-treatment breast cancer tumor_679787


title: ISPY2_pre-treatment breast cancer tumor_578975


title: ISPY2_pre-treatment breast cancer tumor_293142


title: ISPY2_pre-treatment breast cancer tumor_414286


title: ISPY2_pre-treatment breast cancer tumor_748611


title: ISPY2_pre-treatment breast cancer tumor_162562


title: ISPY2_pre-treatment breast cancer tumor_363669


title: ISPY2_pre-treatment breast cancer tumor_711476


title: ISPY2_pre-treatment breast cancer tumor_123660


title: ISPY2_pre-treatment breast cancer tumor_107700

data_processing:
gnormalized signal (log2) data, as provided in the sample data table and raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-confirmity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 150 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 150 samples for batch correcting on raw files. An updated probe annotation for platform GPL16233 was used and is provided as Series supplementary file.
The platform corrected, normalized expression values (from two different platforms) are provided in the 'ExpDat_ISPY2_MK2206_n150.txt'.  Data is collapsed on the gene level as was used in the analysis.


title: ISPY2_pre-treatment breast cancer tumor_706169


title: ISPY2_pre-treatment breast cancer tumor_517870


title: ISPY2_pre-treatment breast cancer tumor_970839


title: ISPY2_pre-treatment breast cancer tumor_808714


title: ISPY2_pre-treatment breast cancer tumor_938719


title: ISPY2_pre-treatment breast cancer tumor_116603


title: ISPY2_pre-treatment breast cancer tumor_752372


title: ISPY2_pre-treatment breast cancer tumor_252748


title: ISPY2_pre-treatment breast cancer tumor_885871


title: ISPY2_pre-treatment breast cancer tumor_136536


title: ISPY2_pre-treatment breast cancer tumor_532183


title: ISPY2_pre-treatment breast cancer tumor_796558


title: ISPY2_pre-treatment breast cancer tumor_259899


title: ISPY2_pre-treatment breast cancer tumor_501303


title: ISPY2_pre-treatment breast cancer tumor_493519


title: ISPY2_pre-treatment breast cancer tumor_906795


title: ISPY2_pre-treatment breast cancer tumor_384830


title: ISPY2_pre-treatment breast cancer tumor_219545


title: ISPY2_pre-treatment breast cancer tumor_539904


title: ISPY2_pre-treatment breast cancer tumor_591810


title: ISPY2_pre-treatment breast cancer tumor_266840


title: ISPY2_pre-treatment breast cancer tumor_689076


title: ISPY2_pre-treatment breast cancer tumor_294739


title: ISPY2_pre-treatment breast cancer tumor_783427


title: ISPY2_pre-treatment breast cancer tumor_233191


title: ISPY2_pre-treatment breast cancer tumor_609642


title: ISPY2_pre-treatment breast cancer tumor_706639


title: ISPY2_pre-treatment breast cancer tumor_220471


title: ISPY2_pre-treatment breast cancer tumor_879224


title: ISPY2_pre-treatment breast cancer tumor_104268


title: ISPY2_pre-treatment breast cancer tumor_179369


title: ISPY2_pre-treatment breast cancer tumor_929391


title: ISPY2_pre-treatment breast cancer tumor_629371


title: ISPY2_pre-treatment breast cancer tumor_824234


title: ISPY2_pre-treatment breast cancer tumor_375954


title: ISPY2_pre-treatment breast cancer tumor_727804


title: ISPY2_pre-treatment breast cancer tumor_856159


title: ISPY2_pre-treatment breast cancer tumor_637566


title: ISPY2_pre-treatment breast cancer tumor_263143


title: ISPY2_pre-treatment breast cancer tumor_132463


title: ISPY2_pre-treatment breast cancer tumor_361701


title: ISPY2_pre-treatment breast cancer tumor_490023


title: ISPY2_pre-treatment breast cancer tumor_287961


title: ISPY2_pre-treatment breast cancer tumor_834418


title: ISPY2_pre-treatment breast cancer tumor_413961


title: ISPY2_pre-treatment breast cancer tumor_712276


title: ISPY2_pre-treatment breast cancer tumor_755914


title: ISPY2_pre-treatment breast cancer tumor_520986


title: ISPY2_pre-treatment breast cancer tumor_343898


title: ISPY2_pre-treatment breast cancer tumor_803677


title: ISPY2_pre-treatment breast cancer tumor_416434


title: ISPY2_pre-treatment breast cancer tumor_309830


title: ISPY2_pre-treatment breast cancer tumor_905264


title: ISPY2_pre-treatment breast cancer tumor_414971


title: ISPY2_pre-treatment breast cancer tumor_317641


title: ISPY2_pre-treatment breast cancer tumor_929980


title: ISPY2_pre-treatment breast cancer tumor_801641


title: ISPY2_pre-treatment breast cancer tumor_402384


title: ISPY2_pre-treatment breast cancer tumor_573605


title: ISPY2_pre-treatment breast cancer tumor_700549


title: ISPY2_pre-treatment breast cancer tumor_639663


title: ISPY2_pre-treatment breast cancer tumor_839274


title: ISPY2_pre-treatment breast cancer tumor_887594


title: ISPY2_pre-treatment breast cancer tumor_102212


title: ISPY2_pre-treatment breast cancer tumor_664111


title: ISPY2_pre-treatment breast cancer tumor_323721


title: ISPY2_pre-treatment breast cancer tumor_635632


title: ISPY2_pre-treatment breast cancer tumor_180663


title: ISPY2_pre-treatment breast cancer tumor_748583


title: ISPY2_pre-treatment breast cancer tumor_535415


title: ISPY2_pre-treatment breast cancer tumor_601489


title: ISPY2_pre-treatment breast cancer tumor_729732


title: ISPY2_pre-treatment breast cancer tumor_200222


title: ISPY2_pre-treatment breast cancer tumor_317402


title: ISPY2_pre-treatment breast cancer tumor_332655


title: ISPY2_pre-treatment breast cancer tumor_732137


title: ISPY2_pre-treatment breast cancer tumor_422454


title: ISPY2_pre-treatment breast cancer tumor_477994


title: ISPY2_pre-treatment breast cancer tumor_342959


title: ISPY2_pre-treatment breast cancer tumor_609151


title: ISPY2_pre-treatment breast cancer tumor_319324


title: ISPY2_pre-treatment breast cancer tumor_894673


title: ISPY2_pre-treatment breast cancer tumor_130892


title: ISPY2_pre-treatment breast cancer tumor_791321


title: ISPY2_pre-treatment breast cancer tumor_845147


title: ISPY2_pre-treatment breast cancer tumor_786753


title: ISPY2_pre-treatment breast cancer tumor_793155


title: ISPY2_pre-treatment breast cancer tumor_651145


title: ISPY2_pre-treatment breast cancer tumor_294265


title: Minimal rep B

status: Public on Sep 01 2020

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description: 3' READS library

data_processing:
library strategy: 3' READS
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls): python3
Mapping to yeast genome build Sac cer3 (first 17 non-A bases; accepting perfect matches and unique reads only): Bowtie (Langmead et al., 2009)
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome: python3
Tally reads by UTR position if they map to the first 400nt after an ORF end: python3
Genome_build: Sac cer 3
Supplementary_files_format_and_content: tab-delimited text files with isoform expression percentages for every position in the first 400 nt after yeast genes

source_name: Minimal_yeast cells

growth_protocol: Growth in the specified culture medium to mid-log phase except for diauxic cells, which were cultured for approximately 72 hours

extract_protocol:
Hot acid phenol RNA extraction followed by Qiagen RNeasy purification
3' READS starting with 25µg total RNA (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

tag: genotype

value: Wild-type RPO21-FRB

tag: growth medium

value: Minimal

tag: culture stage

value: log phase


title: YPGal rep B

description: 3' READS library

source_name: YPGal_yeast cells

tag: strain

value: YP + 2% Galactose


title: YPD log phase rep B

description: 3' READS library

source_name: YPD log phase_yeast cells

value: YPD


title: Minimal rep A

description: 3' READS library


title: Sorbitol rep A

description: 3' READS library

source_name: Sorbitol_yeast cells

value: YPD + 1M Sorbitol


title: YPD log phase rep A

description: 3' READS library


title: ISPY2_pre-treatment breast cancer tumor_506623


title: ISPY2_pre-treatment breast cancer tumor_518000


title: ISPY2_pre-treatment breast cancer tumor_999733


title: ISPY2_pre-treatment breast cancer tumor_779739


title: ISPY2_pre-treatment breast cancer tumor_614434


title: ISPY2_pre-treatment breast cancer tumor_861745


title: ISPY2_pre-treatment breast cancer tumor_345907


title: ISPY2_pre-treatment breast cancer tumor_654064


title: ISPY2_pre-treatment breast cancer tumor_604199


title: ISPY2_pre-treatment breast cancer tumor_778527


title: ISPY2_pre-treatment breast cancer tumor_572793


title: ISPY2_pre-treatment breast cancer tumor_863161


title: K. lactis WT expression data [252035410019_2_4_Klac_T60_WT]

status: Public on Aug 26 2020

city: Cambridge

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_4.txt
K. lactis WT expression data

hyb_protocol: For each time point, either two or three biological replicates were hybridized. We used two-color Agilent 55- or 60-mer oligo-arrays in the 4 × 44 K or 8 × 15 K format for the S. cerevisiae strain (commercial array; four to five probes per target gene) or the custom 8 × 15 K format for all other species (two probes per target gene)

scan_protocol: After hybridization and washing per the manufacturer’s instructions, arrays were scanned using an Agilent scanner and analyzed with Agilent’s Feature Extraction software (release 10.5.1.).

data_processing:
From each set of data in the raw data the ProbeName, SystematicName, gMeanSignal, rMeanSignal, gBGMeanSignal, rBGMeanSignal features were selected for each DATA entry.
To define a value for each probe in the attached matrices, the values for gMeanSignal, rMeanSignal, gBGMeanSignal, rBGMeanSignal features were first averaged for the multiple entries for each individual probe. Then, for each probe in each data set the averaged values were background-subtracted, log-transformed. Each value in the species matrices corresponds to log(<gMeanSignal>-<gBGMeanSignal>+1) or log(<rMeanSignal>-<rBGMeanSignal>+1) for the Cy3 and Cy5 data, respectively. In cases where <gBGMeanSignal> < <gMeanSignal> or <rBGMeanSignal> < <rMeanSignal>, 0 was inserted. So it is these averaged and transformed values that appear in the attached matrices for each probe in each species dataset. For interpretability the systematic gene name mapped to each of the probes is given for each species data set.

organism: Kluyveromyces lactis

label_protocol: Samples were quality controlled with the RNA 6000 Nano ll kit of the Bioanalyzer 2100 (Agilent, Palo Alto, CA). cDNA samples were labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe DeRisi (University of California at San Francisco) and Rosetta Inpharmatics that can be obtained at http://www.microarrays.org (Wapinski et al., 2010).

growth_protocol: We used the following strains for each species: S. cerevisiae RM11-1a and BY4741, C. glabrata CBS 138, N. castellii 4310 (MATa ho::loxp), K. lactis Say 509  (MATa ade2 leu2 metA1 trp1 uraA1 nej1::LEU2, and S. pombe SPY73h+. All species were grown in the following rich medium (termed BMW): yeast extract (1.5%), peptone (1%), dextrose (2%), SC amino acid mix (Sunrise Science) 2 g/l, adenine 100 mg/l, tryptophan 100 mg/l, uracil 100 mg/l. The medium was chosen to minimize cross-species variation in growth. All strains were grown at 30°C except for N. castellii, which was grown at 25°C. Cultures were grown exactly as described above. SFP1 was deleted from haploid strains of each specie using homologous recombination. Parent and deletion strains are listed in Table S1, and the primers used in Table S2 of the associated paper for this dataset.  For S. cerevisiae (RM11-1a), SFP1 was deleted with URA3.  The plasmid, 106,pRS406 (URA3) was used to create the transformation fragment.  URA3 was amplified from the vector with primers containing ~60 base pairs of homology to the up- and downstream sequences to SFP1. Phusion enzyme (NEB) was used with standard protocol and a gradient PCR was done to find the optimal annealing temperature. PCR fragments were pooled and cleaned up with a phenol/chloroform extraction. Transformation was done using a standard S. cerevisiae electroporation protocol. Correct integration was checked by PCR of genomic DNA isolated from deletion candidates using sequences that were up- and downstream of the gene and internal to the drug cassette.  Negative PCR controls included the PCR for the ORF and PCR running from the ORF to the up and downstream locations. Positive PCR controls included the same PCR reactions on the genomic DNA of the parent strain. S. cerevisiae (BY4741) was obtained from Open Biosystems (5312).      For N. castellii, C. glabrata, K. lactis and S. pombe, the transformation fragment was created using a fusion PCR method as described by Szewczyk et al.(Szewczyk et al., 2007)  The Pringle primers were used to amplify the drug cassette of the NAT1MX4 (pAG25) and pFA6a-KANMX6 vectors (Wach et al., 1994).  The P1/P3 and P4/P6 primer combinations were used to amplify the up and downstream sequences of SFP1 and also contained homology to the drug cassette.  The P2/P5 primers were used to fuse the three fragments together in a single PCR reaction. The basic PCR cycling parameters used were as previously described (Wach et al., 1994), except that PCRs were done using Phusion enzyme (NEB) and temperatures were adjusted accordingly. Optimal PCR cycling conditions for each species was determined using a gradient PCR. PCR fragments were pooled and cleaned up with a phenol/chloroform extraction. Transformation was done using a protocol adapted from Kooistra et al., 2004 (Kooistra, Hooykaas and Steensma, 2004). Correct integration was checked by PCR of genomic DNA isolated from deletion candidates using sequences that were up and downstream of the gene (P1 and P6 primers) and internal to the drug cassette (Pringle internal check)., For S. paradoxus, the drug cassette was amplified out of pFA6a-3HA-KANMX6 vector with ultramer primers of 200 bp length, designed to amplify this region and also to add ~180 bp of homology to the upstream and downstream regions of the S. paradoxus SFP1 ORF. Additional PCRs were carried out to add ~1kb of homology up and downstream of the SFP1 ORF and then fusion PCR was carried out as described above. Negative PCR controls included the PCR for the ORF and also PCR running from the ORF to the up and downstream locations.  Positive PCR controls included doing all of the same PCR reactions on the genomic DNA of the parent strains.

extract_protocol: RNA extraction and microarray hybridization were completed as described by Thompson et al.(Thompson et al., 2013): RNA preparation and labeling Total RNA was isolated using the RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) according to the provided instructions for mechanical lysis.

treatment_protocol: On day 1, cells were grown in BMW with growth saturation times as follows: S. cerevisiae, N. castellii, C. glabrata: ~24 hours, K. lactis: ~48 hours, S. pombe: ~36 hours. On day 2, 50 ml cultures, inoculated at 1x106 cells/ml from the overnights were grown in BMW until glucose reached zero, in the New Brunswick shaker. Glucose levels were measured throughout growth, but more frequently as they were reaching zero, using the YSI 2700 Biochemistry Analyzer. When glucose levels reached zero, cells were counted using the Cellometer Auto M10, and enough cells were removed to inoculate 300 ml of BMW at 1x107 cells/ml. Samples were collected at 30 minutes, 60 minutes, 90 minutes as previously described (Thompson et al., 2013). Briefly,  50-ml conical tubes filled with the appropriate amount of 100% methanol to produce a 60/40 mixture once the sample is added. The methanol-filled tubes were stored at −80°C until ready for use. During sample collection tubes were placed in a rack in a dry-ice ethanol bath kept at approximately −40°C. Once the sample was added to the methanol, the methanol and media were separated from the cells by centrifugation and poured off. The conicals containing a cell pellet were then stored at −80°C until processed for permanent storage. For permanent storage, the cell pellets were then washed in 5 ml of nuclease-free water and spun for 5 min at 3700 rpm at 4°C. The supernatant was discarded and the pellet re-suspended in 2 ml of RNA later (Invitrogen) and transferred to 2 ml Sarstadt tubes for storage. The samples were left at 4°C for 24 hr before being moved to a −80°C freezer.

tag: genotype/varation

value: K. lactis WT


title: K. lactis WT expression data [252035410019_2_3_Klac_T30_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_3.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410019_2_4_Klac_T60_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_4.txt
K. lactis Sfp1 mutant expression data

value: K. lactis Sfp1 mutant


title: K. lactis Sfp1 mutant expression data [252035410019_2_2_Klac_T90_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_2.txt
K. lactis Sfp1 mutant expression data


title: ISPY2_pre-treatment breast cancer tumor_547405


title: K. lactis Sfp1 mutant expression data [252035410019_2_3_Klac_T30_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_3.txt
K. lactis Sfp1 mutant expression data


title: ISPY2_pre-treatment breast cancer tumor_797639


title: ISPY2_pre-treatment breast cancer tumor_753109


title: K. lactis WT expression data [252035410019_2_1_Klac_T60_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_1.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410019_1_4_Klac_T30_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_4.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410019_1_4_Klac_T30_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_4.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410019_1_3_Klac_T90_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_3.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410019_1_2_Klac_T60_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_2.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410019_1_3_Klac_T90_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_3.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410018_2_2_Klac_T90_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_2.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410018_2_3_Klac_T30_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_3.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410019_1_1_Klac_T30_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_1.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410019_1_2_Klac_T60_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_2.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410018_1_4_Klac_T30_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_4.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410018_1_2_Klac_T60_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_2.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410018_1_4_Klac_T30_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_4.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410018_1_1_Klac_T30_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_1.txt
K. lactis WT expression data