title: skin samples from subject o3

status: Public on Mar 31 2020

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

description: the cell barcode of this samples for the processed data files is -5

data_processing:
alignment of the raw fastq-data with the programm cellranger 2.1.0 to the reference genome
filtering of the data with cellranger 2.1.0
combination of samples with cellranger
filtering of data with seurat 2.3.4
clustering and t-SNE projection of data with seurat 2.3.4
Genome_build: hg19
seurat object containing clustered and analyzed data
Supplementary_files_format_and_content: counts

source_name: skin

extract_protocol:
For each experiment, 4-mm punch biopsies were obtained from healthy whole skin specimens, immediately after resection from the inguinoiliac region of five male subjects. Samples were kept in MACS Tissue Storage Solution (Miltenyi Biotec) for no longer than 1 h before their enzymatical and mechanical dissociation with the Whole Skin Dissociation kit for human material (Miltenyi Biotec) and the Gentle MACS dissociator (Miltenyi Biotec), following the manufacturer’s instructions. Cell suspensions were then filtered through 70-µm cell strainers (Falcon) and depleted of apoptotic and dead cells with the Dead Cell Removal Kit (Miltenyi Biotec).
Sequencing libraries were subsequently prepared following the Drop-seq methodology (Macosko et al., 2015), using a Chromium Single Cell Controller and the v2 chemistry from 10X Genomics. Thus, approximately 20,000 cells per sample were mixed with the retrotranscription reagents and pipetted into a Chip A Single Cell, also containing the Single Cell 3’ Gel Bead suspension and Partitioning Oil. The Chip was subsequently loaded into a Chromium Single Cell Controller (10X Genomics) where the cells were captured in nanoscale droplets containing both the reagents needed for reverse transcription and a gel bead. Resulting Gel Bead-In-EMulsions (GEMs) were then transferred to a thermocycler in order to perform the retrotranscription following the manufacturer’s protocol. Each gel bead contained a specific 10X Genomics barcode, an Illumina R1 sequence, a Unique Molecular Identifier (UMI) and a poly-dT primer sequence. Therefore, from poly-adenylated mRNA the reaction produced full-length cDNA with a unique barcode per cell and transcript, which allowed tracing back all cDNA coming from each individual cell. Following an amplification step, cDNA was further processed by fragmentation, end repair and A-tailing double-sided size selection using AMPure XP beads. Finally, Illumina adaptors and a sample index were added through PCR using a total number of cycles adjusted to the cDNA concentration. After sample indexing, libraries were again subjected to double-sided size selection. Quantification of the libraries was carried out using the Qubit dsDNA HS Assay Kit (Life Technologies), and cDNA integrity was assessed using D1000 ScreenTapes (Agilent Technologies). Paired-end (26+74bp) sequencing (100 cycles) was finally performed with a HiSeq 4000 device (Illumina).

tag: subject


title: NC24: Normal pediatric cerebellum

status: Public on Apr 10 2020

type: genomic

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

department: Biochemistry

country: USA

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

hyb_protocol: Bisulfite converted D was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC (850K) Beadchip using standard Illumina protocol

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

data_processing: Rnbeads Version 2.0.0

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal pediatric cerebellum

label_protocol: Standard Illumina Protocol

extract_protocol: Isolated genomic D using the RecoverAll kit

tag: tissue

value: Normal pediatric cerebellum

tag: age (years)

tag: Sex

value: M

tag: subgroup

value: NORMAL


title: NC17: Normal adult cerebellum

source_name: Normal adult cerebellum

value: Normal adult cerebellum

value: UNKNOWN


title: NC25: Normal pediatric cerebellum

value: F


title: skin samples from subject o2

type: SRA

description: the cell barcode of this samples for the processed data files is -4

library_source: transcriptomic

molecule: polyA RNA


title: NC4: Normal adult cerebellum


title: NC23: Normal pediatric cerebellum


title: Q12: UNKNOWN

source_name: UNKNOWN


title: skin samples from subject o1

description: the cell barcode of this samples for the processed data files is -3


title: NC6: Normal adult cerebellum


title: NC5: Normal adult cerebellum


title: NC19: Normal pediatric cerebellum


title: skin samples from subject y2

description: the cell barcode of this samples for the processed data files is -2


title: NPC: Normal progenitor cell line

source_name: Normal progenitor cell line

value: Normal progenitor cell line


title: D425: Grp3 MB cell line

source_name: Grp3 MB cell line

value: Grp3 Medulloblastoma cell line

value: Grp3 MB cell line


title: NHA: Normal human astrocyte cell line

source_name: Normal human astrocyte cell line

value: Normal human astrocyte cell line


title: NC22: Normal pediatric cerebellum


title: D283: Grp3 MB cell line


title: D341: Grp3 MB cell line


title: NC20: Normal pediatric cerebellum


title: SVG_P12: Normal Astroglia, SV40 transformed

source_name: Normal Astroglia, SV40 transformed

value: Normal Astroglia, SV40 transformed


title: UUD - uninfected cells from uninfected well

status: Public on Nov 19 2019

city: Seattle

first: Effie

middle: Efthimia

last: Bastounis

state: WA

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

department: Biology

institute: University of Washington

description: 2x10^5 cells grown on 12 mm collagen I coated glass coverslips for 48 h

data_processing:
Raw sequencing data generated from Illumina NovaSeq 6000 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤ 20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM (fragments per kilobase of transcript per million mapped reads) in group ≥ 0.5. FPKM is equal to the number of fragments that map a certain gene or transcipt times a million divided by the length of the gene in Kb and the fragmnets number that map to all genes/transcripts.
Differentially expressed gene and transcript analyses were performed with R package ballgown. Fold change (cutoff 1.5), p-value (≤ 0.05) and FPKM (≥ 0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Genome_build: CanFam3
Supplementary_files_format_and_content: Expression_Gene.xlsx file contains in column A the Track_id which is the database name in gene level, in column B the name of the gene, in column C its locus, in column D the strand of the gene, in column E the gene type and in colunms F through U the FPKM of each gene for each one of the samples. Likewise, Expression_Transcript.xlsx file contains in column A the Track_id which is the database name in transcript level, in column B the name of the transcript, in column C the ENSEMBL gene id of the transcript, in column D the name of the gene, in column E the locus, in column F the strand, in column F the biological type of the transcript and in colunms H through W the FPKM of trasncript in samples. Differentially_Expressed_Genes.xlsx and Differentially_Expressed_Transcripts.xlsx show differentially expressed genes or transcripts when comparisons between different groups os samples are performed. Different groups compared are shown in different sheets within the xlsx file.

organism: Canis lupus familiaris

source_name: uninfected cells from uninfected well

growth_protocol:
In DMEM media supplemented with fetal bovine serum to a final concentration of 10%
G-MDCK cells were cultured in high glucose DMEM medium (Thermofisher; 11965092) containing 4500 mg/L glucose and supplemented with 10% FBS (GemBio; 900-108) as previously suggested. To generate confluent cell monolayers, 24-well plates glass-bottom for microscopy were coated with 50 µg/ml rat-tail collagen-I (diluted in 0.2 N acetic acid) for 1 h at 37°C, air-dried for 15 min, and UV-sterilized for 30 min in a tissue culture hood. MDCK cells were seeded at a density of 2 × 10^5 cells/well for 24 h.

extract_protocol:
Cells were harvested and lyzed using the QIAshredder Kit (Qiagen; 79656). mRNA was harvested using the RNeasy Plus Micro Kit (Qiagen; 74004) and eluted in 30 μL RNAase free water. RNA concentrations were measured using the nanodrop machine and were comparable between conditions. RNA quality and quantity were confirmed via bioanalyzer analysis performed by Arraystar Inc.
The total RNA was depleted of rRNAs by Arraystar rRNA Removal Kit. We used Illumina kits for the RNA-seq library preparation, which included procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Finally, the prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method
The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, loaded onto channels of the flow cell at 8 pM concentration, and amplified in situ using TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina). Sequencing was carried out using the Illumina X- ten/NovaSeq according to the manufacturer’s instructions. Sequencing was carried out by running 150 cycles.

treatment_protocol: 24 h post-seeding MDCK cells were exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria three times with PBS, media containing 20 μg/mL gentamycin was added to cells to kill extracellular bacteria. 24 h post-infection cells were trypsinized and either left in tubes or sorted to infected and uninfected populations. All tubes containing cells in solution were treated in parallel so to lyze the cells and extract their RNA.

tag: cell line

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule

tag: nature

value: immortalized

tag: vendor/source

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: skin samples from subject y1

description: the cell barcode of this samples for the processed data files is -1


title: UUC - uninfected cells from uninfected well


title: UUA - uninfected cells from uninfected well


title: NC1: Normal pediatric cerebellum


title: UUB - uninfected cells from uninfected well


title: NC18: Normal pediatric cerebellum


title: DAOY: SHH MB cell line

source_name: SHH MB cell line

value: SHH Medulloblastoma cell line

value: SHH MB cell line


title: Shank3 mutant harvested following 5 hours of sleep deprivation, replicate 3

status: Public on Dec 31 2018

city: Spokane

first: Lucia

last: Peixoto

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

data_processing:
HiSeq Cobtrol Software (HC) version 2.2.68 was used for base calling. The raw bcl files were converted to fastq files using software program bcl2fastq2.17.1.14.  Adaptors were trimmed from the fastq files during the conversion.
Sequenced reads were mapped with GSNAP (parameters = -N 1 -m 7 -A sam --nofails) to mm10. The count matrix was obtained with featureCounts(parameters = isPairedEnd = TRUE, requireBothEndsMapped = TRUE, annot.inbuilt = "mm10") from the package Rubread(version 1.26.1) under bioconductor(version 3.6) with R(version3.4.1) using mm10 built-in annotations(Mus_musculus.GRCm38.90) with ENTREZ ID as row names.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files contain peak coordinates and counts for each sample.  Count matrix provided as supplementary file

organism: Mus musculus

source_name: PFC

growth_protocol: Heterozygous Shank3e21+/- mutant mice (Kouser, et al 2013) breeding pairs were established to obtain wild type (WT) and mutant Shank3e21-/- (S3) littermates. Mice were house in standard cages on a 12:12 h light:dark cycle with food and water ad libitum. At 4 weeks old, mice were weaned from their mothers and ear tissue was collected and sent to Transnetyx to be genotyped.

extract_protocol:
RNA was extracted from thawed tissue using the Qiagen RNAeasy Microarray Tissue kit with RWT buffer. Lyse and homogenize the tissue using a TissueLyzer: Add 1ml of Qiazol to the pre-sterilized 2ml round bottom tubes with one 5mm steel bead inside, then add the tissue. Operate the TissueLyzer for 3 min at 50Hz, let it come to a stop and repeat. Spin down before opening the tubes. Transfer lysate to a clean 2 ml tube. Isolate RNA through phase separation. Add 200 µl pf chloroform and shake vigorously. Incubate at RT of 3 min. Centrifuge at 12,000 g (max of centrifuge) for 15 min at 4 C. Transfer aqueous phase to a new tube. Purify Total RNA (Binding and washing with the RNAeasy column). Add 600 µl (1 volume) of 100% EtOH. Transfer 600 µl to and RNAeasy mini spin column placed inside a 2ml collection tube, centrifuge 15s at max speed at RT. Repeat with remaining 600 µl. Add 500 µl of buffer RWT (buy separately from Qiagen) centrifuge 15s at max speed at RT, discard the flow through, keep the collection tube. Add 500 µl of buffer RPE 15s at max speed at RT, discard the flow through, keep the collection tube. Add 500 µl of buffer RPE 2min at max speed at RT, discard the flow through, discard the collection tube. Place the spin column on a new collection tube and centrifuge at max speed for a minute (to prevent EtOH carryover). Elute the RNA from the column. Place the column into a 1.5 ml Eppendorf. Add 30 µl of RNAse free water, Centrifuge for 1 min at max speed at room temp. Pippette the volume in the Eppendorf back into the column and repeat previous step. Use 1 µl to quantify using Nanodrop Spectrophotometer. After quantification freeze RNA at -80 C.
The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit.  RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality.  “10” stands for a perfect RNA sample without any degradation, whereas “1” marks a completely degraded sample.  RNA samples with RQNs ranging from 8 to 10 were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).  Briefly, mRNA was isolated from 2.5 µg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation and PCR enrichment.  The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit.  The concentrations of RNA libraries were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA).  The libraries were diluted to 2 nM with RSB (10 mM Tris-HCl, pH8.5) and denatured with 0.1 N NaOH.  Eighteen pM libraries were clustered in a high-output flow cell using HiSeq Cluster Kit v4 on a cBot (Illumina).  After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina).  DNA was sequenced from both ends (paired-end) with a read length of 100 bp.

treatment_protocol: Begining at light onset, sleep deprived mice were kept awake for 5 hours via gentle handling. Prefrontal cortex tissue was collected at the conclusion of sleep deprivation (SD5) and immediately flash frozen in liquid nitrogen. Control animals that were left in their home cage to sleep were dissected at the same time of day (HC5).

tag: genotype

value: Shank3 Mutant

value: Pre-frontal cortex

tag: age

value: 8-12 weeks

value: male


title: Shank3 mutant harvested following 5 hours of sleep deprivation, replicate 5


title: NC14: Normal adult cerebellum

value: Normal adult cerebellum

value: UNKNOWN

value: NORMAL


title: Shank3 mutant harvested following 5 hours of sleep deprivation, replicate 4


title: Shank3 mutant harvested following 5 hours of sleep deprivation, replicate 2


title: D556: Grp3 MB cell line

value: Grp3 Medulloblastoma cell line


title: HDMBO3: Grp3 MB cell line

value: Grp3 MB cell line


title: Shank3 mutant homecage control at ZT hour 5, replicate 3


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 3

value: WT


title: D458: Grp3 MB cell line


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 1


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 2


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 5


title: NC15: Normal pediatric cerebellum

value: Normal pediatric cerebellum


title: Shank3 mutant homecage control at ZT hour 5, replicate 5


title: Shank3 mutant homecage control at ZT hour 5, replicate 2


title: Shank3 mutant homecage control at ZT hour 5, replicate 1


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 4


title: Wildtype homecage control harvested at ZT hour 5, replicate 2


title: Wildtype homecage control harvested at ZT hour 5, replicate 1


title: Wildtype homecage control harvested at ZT hour 5, replicate 5


title: NC13: Normal pediatric cerebellum


title: Shank3 mutant harvested following 5 hours of sleep deprivation, replicate 1


title: Shank3 mutant homecage control at ZT hour 5, replicate 4


title: RNA_35S_TET1_2

status: Public on Mar 02 2018

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: mRNA 35S:TET1-2

data_processing:
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
TAB-seq: TAB-seq analysis was performed as described in (Schmtiz et al. 2013)
ChIP-seq: MethylC-seq was performed using bowtie1.1.1
RNA-seq: MethylC-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
Genome_build: TAIR10 reference genome
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "ChIP_column_header_descriptions.txt" and "RNA_column_header_descriptions.txt" for column headers

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: The hTET1-CD sequence in the pMDC32 vector was transformed into Agrobacterium tumefaciens strain C58C1 and plated on LB-agar supplemented with kanamycin (50 µg/mL). A single kanamycin resistant colony was selected and used to start a 250-mL culture in LB Broth Miller liquid media supplemented with gentamicin (25 µg/mL), kanamycin (50 µg/mL), and rifampicin (15 µg/mL), which was incubated for two days at 30˚C. Bacterial cells were pelleted by centrifugation at 4,000 RPM for 30 minutes and the supernatant decanted. The remaining bacterial pellet was re-suspended in 200 mL of 5% sucrose with 0.05% Silwet L77. Plant transformation was performed using the floral dip method described by (Clough and Bent. 1998). Seeds were harvested upon senescence and transgenic plants were identified via selection on ½ LS plates supplemented with Hygromycin B (15 µg/mL).

extract_protocol: Genomic DNA libraries were prepared following the MethylC-seq protocol without use of the bisulfite conversion step. MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). TAB-seq libraries were prepared as previously described in (Yu et al. 2012). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. ChIP library preparation. Leaves were treated with formaldehyde to covalently link protein to DNA, washed several times with distilled water, patted dry and ground into fine powder in liquid nitrogen. Chromatin was extracted with a series of extraction buffers and sonicated. The final chromatin solution was incubated overnight with anti-H3K9me2 antibody (Cell Signaling Technology, 9753S) coated Dynabeads protein A (Life Technologies, 10002D) to precipitate the immune complex. After a few washes, the immune complex was eluted and incubated at 65 degrees in the presence of a high concentration of NaCl in a water-bath overnight. After degrading the proteins with proteinase K, DNA was recovered by phenol/chloroform/isoamyl alcohol extraction followed by ethanol precipitation. The DNA pellet was then dissolved in 30µl of nuclease-free water.

tag: ecotype

value: leaf


title: Wildtype homecage control harvested at ZT hour 5, replicate 3


title: RNA_Col_0_WT_rep2

description: mRNA Col-0 WT

source_name: Col-0 WT


title: AZA_100

status: Public on Jun 24 2016

description: Whole Genome Bisulfite Sequencing 100 µM AZA-treated

library_source: genomic

data_processing:
Data were mapped to the TAIR 10
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR 10
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_sampel.tsv”) column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0
Supplementary_files_format_and_content: RNA-seq data (marked as "gene_exp.diff") column 1 = Tested id = A unique identifier describing the transcipt, gene, primary transcript, or CDS being tested; column 2 = gene = The gene_name(s) or gene_id(s) being tested; column 3 = locus = Genomic coordinates for easy browsing to the genes or transcripts being tested.; column 4 = sample 1 = Label (or number if no labels provided) of the first sample being tested; column 5 = sample 2 = Label (or number if no labels provided) of the second sample being tested; column 6 = Test status = Can be one of OK (test successful), NOTEST (not enough alignments for testing), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing.; column 7 = FPKMx = FPKM of the gene in sample x; column 8 = FPKMy = FPKM of the gene in sample y; column 9 = log2(FPKMy/FPKMx) = The (base 2) log of the fold change y/x; column 10 = test stat = The value of the test statistic used to compute significance of the observed change in FPKM; column 11 = p = The uncorrected p-value of the test statistic; column 12 = q = The FDR-adjusted p-value of the test statistic; column 13 = significant = Can be either “yes” or “no”, depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing

source_name: AZA 100

growth_protocol: Agarose gel (Ameresco) with added half-strength Linsmaier and Skoog nutrients (Caisson Laboratories, Inc) was prepared and autoclaved. 5-azacytidine (Sigma) and zebularine (APExBIO) were dissolved in dimethyl-sulfoxide (DMSO) and water, respectively, before being added to the liquefied cooling agar at final concentrations of 25 µM, 50 µM and 100 µM. Columbia-0 (col-0) background Arabidopsis thaliana seeds were then subjected to a ethanol-based seed sterilization and approximately 30 seeds were plated on the solid agar. As a control, seeds were plated on agar containing DMSO with no chemical demethylating agent (AZA mock-treated control) and agar containing no DMSO or chemical demethylating agent (untreated control). Three replicates of each treatment type were simultaneously plated and grown in parallel. After a two-day stratification period at 4ºC, the seeds were removed to room temperature and allowed to grow for 8 days under constant light.

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions.
RNA-seq: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).

value: whole seedling

tag: treatment

value: 100 uM 5-azacytidine


title: RNA_Col_0_WT_rep1

description: mRNA Col-0 WT


title: RNA_Col_0_WT_rep3

description: mRNA Col-0 WT


title: Wildtype homecage control harvested at ZT hour 5, replicate 4


title: Q33: Grp4 MB

source_name: Grp4 MB

value: Grp4 Medulloblastoma

value: M

value: Grp4 MB


title: AZA_50

description: Whole Genome Bisulfite Sequencing 50 µM AZA-treated

source_name: AZA 50

value: 50 uM 5-azacytidine


title: Mock_control

description: Whole Genome Bisulfite Sequencing Mock-treated control

source_name: Mock control

value: 0 uM


title: S. cerevisiae and S. bayanus L7

status: Public on Feb 22 2010

city: Berkeley

first: Rachel

middle: B

last: Brem

state: CA

address: 321 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

description: process data counts are in L7 column of gene_level_statistics file

data_processing: We downloaded 4,853 ortholog pairs (http://www.broad.mit.edu/regev/orthogroups/orthologs.html) and, in each, converted the S. cerevisiae reference sequence to that of the W303 strain using the sequence of the latter from Liti et al., Nature 2009.  For each lane, 30-bp reads were mapped to either strand of the ortholog pair set using Bowtie, allowing no mismatches between the read and the reference sequence.  As the S. bayanus and S. cerevisiae species are close in sequence, we ensured specificity of the expression measures by requiring that a read assigned to a certain location was likely to have originated from that location and not as a result of sequencing errors.  Specifically, for each position in the combined orfeome, we determined whether the read starting at that location was uniquely-mappable (2), i.e., had an edit distance of 2 or greater to any other position in the combined (double-stranded) reference orfeome or genome. The combined orfeome consists of all 4,853 S. bayanus and S. cerevisiae ortholog pairs; the combined genome consists of the concatenation of the S. bayanus (http://downloads.yeastgenome.org/sequence/fungal_genomes/S_bayanus/WashU/contig/) and S. cerevisiae (ftp://ftp.yeastgenome.org/yeast/data_download/sequence/NCBI_genome_source/) reference genomes, converting the latter to that of the W303 strain as above.  The ensuing analysis considered only uniquely-mappable (2) reads and the 4,238 ortholog pairs with a minimum of 200 uniquely-mappable (2) bases in both species and a maximum difference in length of 100 bp.

organism: Saccharomyces bayanus x Saccharomyces cerevisiae

source_name: biological replicate 2, run at UCR

growth_protocol: Strain OZY27, a hybrid of S. cerevisiae (isogenic to W303; his3 leu2 lys2 trp1 ura3) and S. bayanus (derived from CBS 4001; ade2 his3 lys2), was kindly provided by O. Zill, UC Berkeley.  For each of two biological replicates, an OZY27 culture was grown to log phase at 25°C in YPD media.

extract_protocol: Total RNA was isolated by the hot acid phenol method and treated with Turbo DNase (Ambion) according to the manufacturer’s instructions.  A Solexa/Illumina 1G Genome Analyzer library was constructed for each biological replicate as described.

tag: strain


title: S. cerevisiae and S. bayanus L5

description: process data counts are in L5 column of gene_level_statistics file

source_name: biological replicate 1, run at UCB


title: S. cerevisiae and S. bayanus L6

description: process data counts are in L6 column of gene_level_statistics file

source_name: biological replicate 1, run at UCR


title: S. cerevisiae and S. bayanus L8

description: process data counts are in L8 column of gene_level_statistics file


title: S. cerevisiae and S. bayanus L3

description: process data counts are in L3 column of gene_level_statistics file

source_name: biological replicate 2, run at UCB


title: S. cerevisiae and S. bayanus L1

description: process data counts are in L1 column of gene_level_statistics file


title: S. cerevisiae and S. bayanus L4

description: process data counts are in L4 column of gene_level_statistics file


title: Untreated_control

description: Whole Genome Bisulfite Sequencing Untreated control

source_name: Untreated control


title: RNA_35S_TET1_1

description: mRNA 35S:TET1-1


title: S. cerevisiae and S. bayanus L2

description: process data counts are in L2 column of gene_level_statistics file


title: AZA_25

description: Whole Genome Bisulfite Sequencing 25µM AZA-treated

source_name: AZA 25

value: 25 uM 5-azacytidine


title: 26-2-dCy3

status: Public on Jun 23 2005

type: RNA

description: RNA from a haploid F1 segregant from a cross between the lab strain BY4716 (isogenic to S288c) and a wild isolate strain from a California vineyard collected by R. Mortimer.  The reference sample is RNA from haploid BY4716 and is the same as in Yvert et al. Nat. Genet. 2003.

data_processing: First compute l = log2(median 635 - median background 635) - log2(median 532 - median background 532).  Do this for every spot on chip c.  Next compute m, the mean of these l values over all spots on chip c.  Now subtract m from every l value on chip c to get the final the VALUE here; if the SAMPLE has Cy5 in the name, -n is the VALUE. NULL indicates missing data due to a misshapen spot (FLAG < 0) or saturated signal.

organism: Saccharomyces cerevisiae

source_name: reference pool of BY4716 strain

tag: reference pool of BY4716 strain

source_name: segregant from BY4716 x wild wine strain


title: 26-1-dCy5

tag: segregant from BY4716 x wild wine strain


title: 25-4-dCy3


title: 25-3-dCy3


title: 24-1-dCy3


title: 23-5-dCy5


title: 23-5-dCy3


title: 26-2-dCy5


title: 25-1-dCy3


title: 22-5-dCy3


title: 23-2-dCy5


title: 24-1-dCy5


title: 26-1-dCy3


title: 23-3-dCy3


title: 23-3-dCy5


title: 25-3-dCy5


title: 22-4-dCy3


title: 23-2-dCy3


title: 22-3-bCy5


title: 22-2-dCy5


title: 21-5-cCy3


title: 22-4-dCy5


title: 21-5-cCy5


title: 22-2-dCy3


title: 22-3-bCy3


title: 25-1-dCy5


title: 22-5-dCy5


title: 21-4-dCy3


title: 21-4-dCy5


title: 25-4-dCy5


title: 21-3-dCy3


title: 21-2-dCy5


title: 21-3-dCy5


title: 20-4-cCy3


title: 20-3-cCy3


title: 20-2-dCy5


title: 20-1-dCy3


title: 20-3-cCy5


title: 21-1-dCy3


title: 19-5-bCy3


title: 20-1-dCy5


title: 21-2-dCy3


title: 20-4-cCy5


title: 19-4-bCy5


title: 21-1-dCy5


title: 19-3-cCy5


title: 19-2-cCy3


title: 19-4-bCy3


title: 18-6-dCy5


title: 19-2-cCy5


title: 20-2-dCy3


title: 18-6-dCy3


title: 19-1-cCy5


title: 19-3-cCy3


title: 19-1-cCy3


title: 18-3-dCy3


title: 18-4-cCy3


title: 18-4-cCy5


title: 18-1-dCy3


title: 17-1-aCy3


title: 18-2-dCy3


title: 18-1-dCy5


title: 17-4-aCy3


title: 17-5-bCy3


title: 19-5-bCy5


title: 17-2-dCy5


title: 17-5-bCy5


title: 17-2-dCy3


title: 18-3-dCy5


title: 18-2-dCy5


title: 16-1-dCy5


title: 15-6-cCy5


title: 16-1-dCy3


title: 15-6-cCy3


title: 15-3-bCy5


title: 15-5-bCy3


title: 15-3-bCy3


title: 15-4-dCy3


title: 14-6-dCy3


title: 14-7-cCy5


title: 15-5-bCy5


title: 15-2-dCy3


title: 14-7-cCy3


title: 15-2-dCy5


title: 14-6-dCy5


title: 17-4-aCy5


title: 15-4-dCy5


title: 17-1-aCy5


title: 14-4-aCy3


title: 14-1-bCy5


title: 13-5-cCy3


title: 14-3-dCy3


title: 14-2-cCy5


title: 14-5-bCy3


title: 14-2-cCy3


title: 13-4-aCy3


title: 14-3-dCy5


title: 13-5-cCy5


title: 14-4-aCy5


title: 14-5-bCy5


title: 13-3-bCy5


title: 12-2-bCy3


title: 14-1-bCy3


title: 12-2-bCy5


title: 13-1-aCy5


title: 13-1-aCy3


title: 13-2-cCy3


title: 11-3-bCy5


title: 12-1-dCy3


title: 11-3-bCy3


title: 13-3-bCy3


title: 11-1-aCy3


title: 13-4-aCy5


title: 12-1-dCy5


title: 11-1-aCy5


title: 11-2-dCy3


title: 10-4-dCy5


title: 10-2-dCy3


title: 10-3-cCy5


title: 9-6-dCy3


title: 9-7-dCy5


title: 10-1-cCy3


title: 9-5-dCy3


title: 9-4-dCy5


title: 10-4-dCy3


title: 10-3-cCy3


title: 9-7-dCy3


title: 9-6-dCy5


title: 9-4-dCy3


title: 9-5-dCy5


title: 9-1-dCy5


title: 9-3-dCy5


title: 9-1-dCy3


title: 10-1-cCy5


title: 9-2-dCy5


title: 8-7-bCy5


title: 9-3-dCy3


title: 8-6-cCy5


title: 11-2-dCy5


title: 10-2-dCy5


title: 8-7-bCy3


title: 8-5-bCy3


title: 13-2-cCy5


title: 9-2-dCy3


title: 8-6-cCy3


title: 8-5-bCy5


title: 8-3-aCy3


title: 8-4-cCy5


title: 8-3-aCy5


title: 7-7-cCy5


title: 7-7-cCy3


title: 7-4-cCy5


title: 7-8-dCy5


title: 7-6-cCy3


title: 6-7-dCy5


title: 7-8-dCy3


title: 7-4-cCy3


title: 7-3-dCy3


title: 7-2-cCy3


title: 7-6-cCy5


title: 7-3-dCy5


title: 7-5-dCy3


title: 6-6-dCy3


title: 6-7-dCy3


title: 8-2-dCy3


title: 7-1-dCy5


title: 8-1-aCy3


title: 6-5-dCy5


title: 7-5-dCy5


title: 7-1-dCy3


title: 7-2-cCy5


title: 6-5-dCy3


title: 6-4-dCy5


title: 6-4-dCy3


title: 6-1-dCy3


title: 5-5-dCy3


title: 5-3-dCy3


title: 6-2-bCy5


title: 5-1-dCy3


title: 5-5-dCy5


title: 4-1-cCy3


title: 5-4-dCy5


title: 6-3-cCy5


title: 5-2-dCy3


title: 6-6-dCy5


title: 6-1-dCy5


title: 5-3-dCy5


title: 4-3-dCy3


title: 4-4-dCy5


title: 5-1-dCy5


title: 4-4-dCy3


title: 3-3-dCy3


title: 5-4-dCy3


title: 3-4-dCy3


title: 3-5-dCy3


title: 4-1-cCy5


title: 5-2-dCy5


title: 2-6-dCy3

status: Public on Jan 20 2005


title: 3-1-dCy5


title: 3-1-dCy3


title: 3-3-dCy5


title: 3-5-dCy5


title: 2-6-dCy5


title: 3-4-dCy5


title: 2-5-dCy3


title: 2-4-aCy3


title: 8-2-dCy5


title: 4-3-dCy5


title: 8-1-aCy5


title: 2-3-dCy3


title: 2-4-aCy5


title: 8-4-cCy3


title: 2-2-dCy5


title: 2-2-dCy3


title: 2-3-dCy5


title: 2-5-dCy5


title: 1-5-cCy3


title: 1-4-dCy3


title: RM2Cy5_2

source_name: parent wild isolate RM11-1a

tag: parent wild isolate RM11-1a


title: 1-1-dCy3


title: 1-3-dCy3


title: RM4Cy3_3


title: RM1Cy3_2


title: 6-3-cCy3


title: 1-3-dCy5


title: RM3Cy5_3


title: RM4Cy5_2


title: RM1Cy5_2


title: RM6Cy5


title: 6-2-bCy3


title: RM3Cy3_3


title: RM3Cy3_2


title: RM6Cy3


title: RM3Cy3_1


title: 1-1-dCy5


title: 1-5-cCy5


title: RM4Cy3_2


title: RM4Cy3_1


title: 1-4-dCy5


title: RM5Cy5


title: RM4Cy5_3


title: RM5Cy3


title: RM3Cy5_2


title: RM4Cy5_1


title: RM2Cy3_2


title: BY6Cy5

source_name: parent strain BY4716

tag: parent strain BY4716


title: RM2Cy3_1


title: BY6Cy3


title: RM1Cy5_1


title: RM2Cy5_1


title: RM1Cy3_1


title: BY5Cy5


title: BY4Cy3


title: By2Cy3


title: By1Cy3


title: BY5Cy3


title: RMA-BY

status: Public on May 01 2002

description:
RNA from the lab strain BY4716 (isogenic to S288c)
and a wild isolate strain from a California vineyard
collected by R. Mortimer.  See Brem et al., Science
296(5568):752-755.
Lot batch =

source_name: independent culture of wild strain


title: RMB-BY


title: RM2-BY


title: BY4Cy5


title: By1Cy5


title: RM3Cy5_1


title: BY-RMB


title: BYC-BY

description:
RNA from the lab strain BY4716 (isogenic to S288c).
See Brem et al., Science 296(5568):752-755.
Lot batch =

source_name: independent culture of BY4716


title: By2Cy5


title: RMC-BY


title: BY3Cy5


title: BY-RM2


title: BY3Cy3


title: BY-RMC


title: BY-RMA


title: BY-RM1


title: BY-BYC


title: BY-RM3


title: BYA-BY


title: BY3-BY


title: BY1-BY


title: BYB-BY


title: BY-BYB


title: BY-BY3


title: BY-BY2


title: RM3-BY


title: BY2-BY


title: BY-7.7.c

description:
RNA from a haploid F1 segregant from a cross between the
lab strain BY4716 (isogenic to S288c) and a wild isolate
strain from a California vineyard collected by R.
Mortimer.  The reference sample is RNA from haploid
BY4716.  See Brem et al., Science 296(5568):752-755.
Lot batch =


title: BY-BYA


title: BY-7.5.d


title: BY-7.3.d


title: BY-7.4.c


title: BY-7.6.c


title: BY-6.7.d


title: 7.5.d-BY


title: BY-7.2.c


title: 7.2.c-BY


title: 7.4.c-BY


title: 7.3.d-BY


title: BY-6.5.d


title: BY-BY1


title: 7.7.c-BY


title: 6.7.d-BY


title: 7.1.d-BY


title: 6.6.d-BY


title: BY-6.6.d


title: BY-6.4.d


title: 6.5.d-BY


title: 7.6.c-BY


title: BY-6.1.d


title: 6.3.c-BY


title: BY-6.3.c


title: BY-7.1.d


title: BY-5.5.d


title: 6.2.b-BY


title: 6.1.d-BY


title: BY-5.4.d


title: BY-6.2.b


title: 5.5.d-BY


title: 4.4.d-BY


title: 5.2.d-BY


title: BY-4.3.d


title: BY-4.4.d


title: BY-5.1.d


title: 5.3.d-BY


title: 5.1.d-BY


title: 4.3.d-BY


title: BY-5.2.d


title: 4.2.a-BY


title: BY-4.1.c


title: BY-4.2.a


title: 3.4.d-BY


title: 5.4.d-BY


title: BY-3.5.d


title: BY-3.1.d


title: 3.5.d-BY


title: BY-2.6.d


title: BY-3.2.d


title: 4.1.c-BY


title: BY-5.3.d


title: 3.3.d-BY


title: BY-2.5.d


title: BY-3.3.d


title: BY-3.4.d


title: 3.1.d-BY


title: 2.6.d-BY


title: 3.2.d-BY


title: 2.5.d-BY


title: BY-1.5.c


title: BY-2.3.d


title: BY-1.3.d


title: BY-1.1.d


title: 1.1.d-BY


title: BY-2.1.d


title: 2.2.d-BY


title: 2.3.d-BY


title: BY-1.4.d


title: BY-2.2.d


title: 1.2.d-BY


title: 1.3.d-BY


title: 1.4.d-BY


title: BY-2.4.a


title: 2.7.d-BY


title: BY-1.2.d


title: 1.5.c-BY


title: 2.4.a-BY


title: 2.1.d-BY


title: BY-2.7.d


title: 6.4.d-BY