title: Buffy coat from peripheral blood [C30] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_D01

status: Public on Aug 31 2018

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: total number of detected mRNA molecules from each gene in each cell

molecule: total RNA

organism: Mus musculus

extract_protocol:
After the recording, weak negative pressure was applied in order to aspirate the recorded cells into the glass capillary patch electrode. Using positive pressure the pipette content was quickly ejected into a 1 μL drop of RNase-free lysis buffer. placed on the side of a 0.2 mL RNase free tight-lock tube (TubeOne). The sample was rapidly spun down (5-10 s) and stored at −80 before reverse transcription (RT).
20 microL lysis buffer (0.15% Triton X-100, 1 U/microL TaKaRa RNase inhibitor, 4 microM reverse transcription primer C1-P1-T31, 5% C1 Loading Reagent and 1:50,000 Life Technologies ERCC  Spike-In Mix 1), reverse transcription mix (1x SuperScript II First-Strand Buffer supplemented with 3 mM MgCl2, 1.5 mM dNTP, 4 mM DTT, 3.3% C1 Loading Reagent, 1.8 microM template-switching oligo C1-P1-RNA-TSO, 1.5 U/microL TaKaRa RNase inhibitor and 18 U/microL Life Technologies Superscript II reverse transcriptase) and PCR mix (1.1x Clontech Advantage2 PCR buffer, 440 microM dNTP, 530 nM PCR primer C1-P1-PCR-2, 5% C1 Loading Reagent and 2x Advantage2 Polymerase Mix) were added to wells. The plate was put in the Fluidigm C1 and the mRNA Seq: RT + Amp (1772x/1773x) script was executed, which took about 8.5 hours and included lysis, reverse transcription and 21 cycles of PCR. When the run finished, the amplified cDNA was harvested in a total of 13 microL C1 Harvesting Reagent and quantified on an Agilent BioAnalyzer. The typical yield was 1 ng/microL. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation, i.e. using Tn5 DNA transposase to transfer adapters to the target DNA. 96 different 10x transposome stocks (6.25 microM barcoded adapter C1-TN5-x, 40% glycerol, 6.25 microM Tn5 transposase, where x denotes a well-specific barcode) were prepared, each with a different barcode sequence.  6 microL harvested cDNA was mixed with 5 microL tagmentation buffer (50 mM TAPS-NaOH pH 8.5, 25 mM MgCl2 and 50% DMF), 11.5 microL nuclease-free water and 2.5 microL 10x transposome stock. The mix was incubated for 5 minutes at 55 degeees C then cooled on ice. 100 microL Dynabeads MyOne Streptavidin C1 beads were washed in 2xBWT (10 mM Tris HCl pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) then resuspended in 2 mL 2xBWT. 20 microL beads was added to each well and incubated at room temperature for 5 minutes. All fractions were pooled, the beads were immobilized and the supernatant removed (thus removing all internal fragments, and retaining only the 5'- and 3'-most fragments). The beads were then resuspended in 100 microL TNT (20 mM Tris pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 microL Qiagen Qiaquick PB, then twice in 100 microL TNT. The beads were then resuspended in 100 microL restriction mix (1x NEB NEBuffer 4, 0.4 U/microL PvuI-HF enzyme), designed to cleave 3' fragments carrying the PvuI recognition site. The mix was incubated for one hour at 37 degrees C, then washed three times in TNT. Finally, the single-stranded library was eluted by resuspending the beads in 100 microL 100 mM NaOH, incubating for 5 minutes, removing the beads, then adding 100 microL 100 mM HCl and 50 microL Neutralization buffer (200 mM Tris pH 7.5, 0.05% Tween-20). At this point, the typical yield was 1-5 nM single-stranded library. Aliquots were rom these were run on  with 187ds_).

treatment_protocol: Whole-cell patch-clamp recordings were performed as previously described (Muñoz-Manchado et al., Cereb. Cortex 26 (2016), pp. 96-105) on 5HT3aEGFP, Pvalbcre::RCE and Pvalbcre::tdTomato animals. Prior to brain dissection, animals were transcardially perfused using ice-cold oxygenated cutting solution (in mM): 87 NaCl, 2.5 KCl, 1.25 NaH2PO4, 26 NaHCO3, 75 sucrose, 12.5 glucose. Electrophysiological parameters were acquired using depolarizing and hyperpolarizing current steps.

tag: strain

tag: age (days)

tag: tissue

value: dorso-lateral striatum

tag: cell id

tag: cell type

value: No


title: 1772100100_D02


title: Buffy coat from peripheral blood [C29] copy number

type: genomic

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

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

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: Hybridized to SNP6 Affymetrix

hyb_protocol: DNA was digested with NspI and StyI enzymes (New England Biolabs), ligated to the respective Affymetrix adapters using T4 DNA ligase (New England Biolabs) amplified (Clontech), purified using magnetic beads (Agencourt), labeled, fragmented, and hybridized to the arrays

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
Background correction and extraction of raw fluorescence intensity were performed with the Affymetrix Genotyping Console. To generate the copy number profiles we used the “Copy Number Inference” pipeline implemented in genepattern: (http://genepattern.broadinstitute.org/gp/pages/index.jsf). In brief, probe-level signal intensities from Affymetrix SNP6 (cel files) were normalized to a uniform brightness and merged to obtain values for each probe set using SNP File Creator. These intensities measurements were converted into a copy number call by the Copy Number Inference model. After reducing the noise by subtracting out the variation that is also seen within the normal samples (peripheral blood), the CBS segmentation algorithm identifies regions in the genome that have a uniform underlying copy number, creating a segmentation file. Finally, we identified the significantly somatic alterations with GISTIC using the cnv segmentation results.
Matched normalized SCNA and SNPs

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood from breast cancer patient

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA from peripheral blood lymphocytes was extracted with the QIAamp DNA Blood Maxi Kit (Qiagen, Valencia, CA), according to manufacturer’s instructions

value: Buffy coat from peripheral blood

value: Germinal cell fraction

tag: population

value: Mexican hispanic


title: Buffy coat from peripheral blood [C27] copy number

description: Hybridized to SNP6 Affymetrix


title: TN52

type: RNA

description: Gene expression Affymetrix Human Transcriptome Array 2.0

hyb_protocol: Hybridization according to manufacter (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) in the GeneChip Fluidics Station 450(Affymetrix)

data_processing: Computational analysis of the microarray data Cel files was processed with the Expression consule of Affymetrix. Microarray background correction and normalization was done using Robust Multichip Analysis (RMA) and quantile algorithm, respectively. To define Lehmann subtypes based in mRNA expression TBNCtool was computed on the data.

label: Biotin

source_name: FFPE breast cancer tumor

label_protocol: Samples were hybridized with  Gene Chip Human Transcriptome Array (HTA) 2.0 (Affymetrix) and scanned at the INMEGEN Microarray Core Facility.

extract_protocol: From FFPE breast cancer tissues, total RNA was extracted with miRNeasy mini kit (Qiagen)

value: Triple negative breast cancer

tag: lehmann subtype

value: M

value: Mexico Hispanic


title: 1772100100_C12

value: Pthlh


title: TN54


title: TN56


title: TN65


title: Luminal A breast cancer LAtp37

description: miRNA expression data from triple negative tumors.

hyb_protocol: Total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

scan_protocol: Washed and stain processes were performed in the GeneChip Fluidics Station 450. The probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Computational analysis of the microarray data Cel files was processed with the Oligo library in R Bioconductor. Microarray background correction and normalization was done using Robust Multichip Analysis (RMA) and quantile algorithm, respectively. To define subgroups a non-hierarchical analysis was performed by a non-negtaive matrix factorization (NMF). Differentially expression patterns between triple negative tumors, subtypes and other immunophenotypes were determined using the limma package to perform an adjusted Student’s t-test using a Bayesian estimation of the variance.

source_name: Macrodissection of FFPE breast cancer tumor

growth_protocol: 3×106 cells were cultured in medium DMEM supplemented at 37ºC on 5% CO2

extract_protocol: Total RNA including the small fraction was isolated using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE

treatment_protocol: Paraffin embedded tissue from breast cancer tumors in adjuvance

value: breast cancer tissue

tag: subtype

value: Luminal A

tag: miRNA subtype


title: TN61

value: MSL


title: Buffy coat from peripheral blood [C26] copy number

description: Hybridized to SNP6 Affymetrix


title: TN50

value: LAR


title: TN51

value: IM


title: TN55


title: Buffy coat from peripheral blood [C18] copy number

description: Hybridized to SNP6 Affymetrix


title: TN60


title: TN58


title: TN48


title: TN53


title: TN49


title: TN66

value: UNS


title: 1772100100_C10

value: Npy/Mia


title: TN47


title: 1772100100_C11


title: Buffy coat from peripheral blood [C16] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C17] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_C08


title: Buffy coat from peripheral blood [C15] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_C05


title: 1772100100_C03


title: Buffy coat from peripheral blood [C13] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C9] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_C01


title: Buffy coat from peripheral blood [C6] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C5] copy number

description: Hybridized to SNP6 Affymetrix


title: TN39


title: TN45


title: 1772100100_B11


title: TN40


title: TN36


title: 1772100100_B10


title: TN26


title: TN32


title: TN23


title: TN22


title: TN42


title: TN38


title: 1772100100_B12


title: TN20


title: TN30


title: TN29


title: Buffy coat from peripheral blood [C4] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_B09


title: TN19


title: Buffy coat from peripheral blood [C2] copy number

description: Hybridized to SNP6 Affymetrix


title: TN18


title: TN24


title: Buffy coat from peripheral blood [C1] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_B07


title: 1772100100_B04


title: 1772100100_B03


title: patient 95, normal colonic mucosa, single array  [P95_N_SNP6]

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

hyb_protocol: Biotin-labeled fragments were hybridized to a Genechip Affymetrix SNP 6.0 arrays at 50°C for 16-18 hours in a GeneChip® Hybridization Oven 640 (Affymetrix, Inc.). Washing and staining with streptavidin-phycoerthrin was performed in a GeneChip® Fluidics Station 450 (Affymetrix, Inc.).

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix, Inc.) and raw data processing was performed using the  “GeneChip Operating Software”.

data_processing:
Data processing was performed by the software "Genotyping Console v3.0.1 ". The following algorithms were used: 1) SNP 6.0 Birdseed v2 algorithm for genotyping, 2) BRLMM-P-Plus algorithm and Hidden Markov Model with regional GC correction for copy number analysis, 3) the LOH algorithm.
Intensity Data files (.cel) and Copy Number Data files (.cnchp)  are provided
affymetrix-algorithm-name = CN5
affymetrix-algorithm-version = 5.0.0
affymetrix-array-type = GenomeWideSNP_6
affymetrix-algorithm-param-ArraySet = GenomeWideSNP_6
program-name = apt-copynumber-workflow.exe
program-version = ${bamboo.custom.jiraversion.name}
program-company = Affymetrix

source_name: normal colonic mucosa

label_protocol: Amplification and labeling were performed according to the protocol supplied by the Affymetrix for  SNP 6.0 arrays. 500 ng of gDNA was digested with NspI and StyI restriction enzymes, ligated to respectively NspI and StyI adaptors, amplified by PCR using a single primer. PCR products were purified and the amplicons were quantified using a NanoDrop spectrophotometer. 40-70 µg of purified amplicons were fragmented and biotin end-labeled

extract_protocol: Genomic DNA (gDNA) was extracted from colorectal adenocarcinoma samples and matched normal colonic tissues  using the QIAamp DNA Mini Kit (Qiagen, Italy) according to the manufacturer’s instructions. The concentration and the quality of the DNA were determined using  NanoDrop spectrophotometer.

tag: patient id

value: patient 95

value: frozen sample

tag: anatomical site

value: sigmoid colon

tag: gender

value: male

tag: patient age

tag: tumor stage

value: normal colonic mucosa


title: patient 97, normal colonic mucosa, single array  [P97_N_SNP6]

value: patient 97


title: patient 93, normal colonic mucosa, single array  [P93_N_SNP6]

value: patient 93

value: rectum

value: female


title: patient 91, normal colonic mucosa, single array  [P91_N_SNP6]

value: patient 91

value: right colon


title: 1772100100_B02

value: dorso-lateral striatum

value: Pthlh


title: 1772100100_B01


title: TN14

value: Triple negative breast cancer

value: M

value: Mexico Hispanic


title: patient 89, normal colonic mucosa, single array  [P89_N_SNP6]

value: patient 89


title: TN11

value: UNS


title: TN7


title: TN04

value: LAR


title: TN17


title: 1772100100_A12

value: Th


title: TN13

value: IM


title: TN16


title: TN10


title: 1772100100_A11


title: TN8


title: patient 85, normal colonic mucosa, single array  [P85_N_SNP6]

value: patient 85

value: frozen sample

value: normal colonic mucosa


title: TN09


title: 1772100100_A10


title: 1772100100_A09


title: TN01


title: patient 83, normal colonic mucosa, single array  [P83_N_SNP6]

value: patient 83

value: left colon


title: patient 79, normal colonic mucosa, single array  [P79_N_SNP6]

value: patient 79

value: female


title: DTN6


title: BQ62

value: Italy Caucasian


title: patient 75, normal colonic mucosa, single array  [P75_N_SNP6]

value: patient 75

value: right colon


title: 1772100100_A05

value: dorso-lateral striatum

value: Pthlh


title: BQ66

value: Triple negative breast cancer


title: BQ63

value: UNS


title: patient 73, normal colonic mucosa, single array  [P73_N_SNP6]

value: patient 73

value: male


title: patient 87, normal colonic mucosa, single array  [P87_N_SNP6]

value: patient 87

value: rectum


title: TN63

value: Mexico Hispanic


title: BQ59

value: LAR


title: BQ60

value: M


title: patient 71, normal colonic mucosa, single array  [P71_N_SNP6]

value: patient 71

value: frozen sample

value: normal colonic mucosa


title: TN5


title: BQ58

value: Italy Caucasian


title: BQ56


title: patient 69, normal colonic mucosa, single array  [P69_N_SNP6]

value: patient 69

value: left colon

value: female


title: BQ55


title: BQ52


title: BQ49


title: BQ47B

value: MSL


title: BQ44

value: Triple negative breast cancer


title: patient 61, normal colonic mucosa, single array  [P61_N_SNP6]

value: patient 61

value: colon


title: E12.5 wildtype mouse skin

city: NEW YORK

first: Jianwen

last: Que

state: NJ

address: 650 W 168TH ST BLACK BLDG 8-810

department: Department of Medicine

country: USA

institute: Columbia University

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR (2.5.2b) and featureCounts (v1.5.0-p3).
Genome_build: Human: NCBI/build37.2; Mouse: UCSC/mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw count values for each sample

source_name: Mouse skin

growth_protocol: Mouse and human fetal esophageal epithelia were isolated and subjected to RNA extraction. For RUES2-derived esophageal progenitor cells, we purified EPCAM+ ITGB4+ cells through fluorescence activated cell sorting and extracted RNA from the purified cells.

extract_protocol:
RNA was extracted using PicoPure RNA Isolation Kit ((Thermo Fisher Scientific).
We used poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceeded on library preparation using Illumina TruSeq RNA prep kit.

value: Mouse skin

tag: developmental stage


title: patient 59, normal colonic mucosa, single array  [P59_N_SNP6]

value: patient 59

value: right colon

value: male


title: E12.5 wildtype mouse esophageal epithelium sample_2

source_name: Mouse embryonic esophagus

value: Mouse embryonic esophagus


title: patient 43, normal colonic mucosa, single array  [P43_N_SNP6]

value: patient 43


title: BQ43

value: IM


title: TN3

value: Mexico Hispanic


title: E12.5 wildtype mouse esophageal epithelium sample_3


title: BQ53


title: BQ42

value: LAR


title: BQ39

value: Italy Caucasian


title: patient 37, normal colonic mucosa, single array  [P37_N_SNP6]

value: patient 37

value: frozen sample

value: normal colonic mucosa


title: BQ51

value: MSL


title: BQ48

value: Triple negative breast cancer


title: patient 29, normal colonic mucosa, single array  [P29_N_SNP6]

value: patient 29

value: left colon


title: BQ36


title: patient 25, normal colonic mucosa, single array  [P25_N_SNP6]

value: patient 25

value: colon

value: female


title: patient 19, normal colonic mucosa, single array  [P19_N_SNP6]

value: patient 19

value: right colon

value: male


title: BQ34


title: BQ35

value: M


title: BQ38

value: IM


title: patient 15, normal colonic mucosa, single array  [P15_N_SNP6]

value: patient 15


title: E12.5 wildtype mouse esophageal epithelium sample_1

value: Mouse embryonic esophagus


title: BQ30

value: Italy Caucasian


title: patient 11, normal colonic mucosa, single array  [P11_N_SNP6]

value: patient 11

value: frozen sample


title: BQ28


title: BQ29

value: LAR


title: BQ33

value: Triple negative breast cancer


title: BQ24


title: BQ21

value: MSL


title: patient 7, normal colonic mucosa, single array  [P7_N_SNP6]

value: patient 7

value: sigmoid colon

value: normal colonic mucosa


title: BQ25


title: BQ27


title: BQ17

value: UNS


title: patient 1, normal colonic mucosa, single array  [P1_N_SNP6]

value: patient 1

value: rectum


title: patient 5, normal colonic mucosa, single array  [P5_N_SNP6]

value: patient 5

value: left colon

value: female


title: patient 3, normal colonic mucosa, single array  [P3_N_SNP6]

value: patient 3

value: male


title: BQ19

value: IM

value: Italy Caucasian


title: BQ15


title: BQ16


title: BQ14

value: M


title: BQ26


title: BQ08


title: BQ10


title: BQ22


title: patient AA1, normal colonic mucosa,  single array  [PAA1_N_SNP6]

value: patient AA1

value: frozen sample


title: BQ06

value: Triple negative breast cancer


title: patient 97, tumoral sample2, single array  [P97_T2_SNP6]

source_name: colon adenocarcinoma

value: patient 97

value: tumor stage 2


title: patient 97, tumoral sample1, single array  [P97_T1_SNP6]

value: sigmoid colon


title: BQ09

value: MSL


title: patient 95, tumoral sample2, single array  [P95_T2_SNP6]

source_name: rectal adenocarcinoma

value: patient 95

value: tumor stage 3


title: BQ03


title: BQ00


title: BP99


title: BQ01


title: BQ02


title: BQ07

value: UNS


title: BP98


title: patient 93, tumoral sample2, single array  [P93_T2_SNP6]

value: patient 93

value: rectum


title: patient 95, tumoral sample1, single array  [P95_T1_SNP6]


title: BP96


title: BP97


title: Normal adjacent tissue [C167]

description: Gene expression data from breast normal adjacent tissue.

hyb_protocol: Samples were hybridized with  Gene Chip Human Transcriptome Array (HTA) 2.0 (Affymetrix) and scanned at the INMEGEN Microarray Core Facility.

scan_protocol: Microarrays were read in a scanner and high-resolution model 7Gimage analysis and quality control was performed using the Affymetrix Expression Console software

data_processing: The mRNA expression values were normalized with RMA and quantile algorithms in R with the oligo library from Bioconductor. In order to obtain the intrinsic subtype classification the PAM50 algorithm was performed as described by Parker.

source_name: Fresh frozen normal tissue

label_protocol: cDNA synthesis, amplification, and gene expression profiling were done with the WT PLUS Reagent Kit for fresh samples (Affymetrix) and and labeled with the Genechip hybridization wash and stain kit (Affymetrix).

extract_protocol: RNA were extracted from the frozen tissue using the AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA)

tag: molecular subtype

tag: theraoy

value: Adjuvant

value: Mexico Hispanic


title: Normal adjacent tissue [C150]


title: Normal adjacent tissue [C168]


title: BQ05


title: Normal adjacent tissue [C190]


title: Normal adjacent tissue [C184]


title: Normal adjacent tissue [C198]


title: BP92

value: IM


title: Normal adjacent tissue [C171]


title: BP94

value: Italy Caucasian


title: BP95

value: LAR


title: patient 93, tumoral sample1, single array  [P93_T1_SNP6]

value: female


title: BP88


title: BP90

value: M


title: Normal adjacent tissue [C160]


title: patient 89, tumoral sample1, single array  [P89_T1_SNP6]

value: patient 89

value: frozen sample

value: right colon


title: BP86

value: Triple negative breast cancer


title: patient 89, tumoral sample2, single array  [P89_T2_SNP6]

value: tumor stage 2


title: Normal adjacent tissue [C124]


title: patient 91, tumoral sample1, single array  [P91_T1_SNP6]

value: patient 91

value: male


title: BP82


title: patient 87, tumoral sample1, single array  [P87_T1_SNP6]

value: patient 87


title: Normal adjacent tissue [C125]


title: patient 85, tumoral sample2, single array  [P85_T2_SNP6]

value: patient 85

value: tumor stage 3


title: BP83


title: Normal adjacent tissue [C110]

value: Adjuvant


title: BP80


title: Normal adjacent tissue [C85]

value: Mexico Hispanic


title: BP81

value: IM


title: Normal adjacent tissue [C105]


title: BP85

value: Italy Caucasian


title: BP79


title: BP72


title: Normal adjacent tissue [C106]


title: Normal adjacent tissue [C81]


title: BP71


title: BP75

value: UNS


title: BP78


title: BP77


title: BP73


title: BQ12


title: Normal adjacent tissue [C80]


title: patient AA3, normal colonic mucosa,  single array  [PAA3_N_SNP6]

value: patient AA3

value: rectum

value: normal colonic mucosa


title: patient 83, tumoral sample2, single array  [P83_T2_SNP6]

value: patient 83

value: frozen sample

value: female


title: patient 83, tumoral sample1, single array  [P83_T1_SNP6]

value: right colon


title: patient 81, tumoral sample1, single array  [P81_T1_SNP6]

value: patient 81

value: tumor stage 2


title: patient 79, tumoral sample2, single array  [P79_T2_SNP6]

value: patient 79


title: Normal adjacent tissue [C75]


title: BP65

value: Triple negative breast cancer

value: MSL


title: Normal adjacent tissue [C74]

value: Adjuvant


title: patient 77, tumoral sample2, single array  [P77_T2_SNP6]

value: patient 77

value: male

value: tumor stage 3


title: Normal adjacent tissue [C62]

value: Mexico Hispanic


title: BP63

value: Italy Caucasian


title: BP70


title: patient 81, tumoral sample2, single array  [P81_T2_SNP6]


title: BP66

value: LAR


title: BP69

value: IM


title: BP62


title: BP60


title: BP61

value: UNS


title: Normal adjacent tissue [C48]


title: BP55


title: BP58


title: patient 77, tumoral sample1, single array  [P77_T1_SNP6]

value: frozen sample


title: Normal adjacent tissue [C71]


title: patient 79, tumoral sample1, single array  [P79_T1_SNP6]

value: female


title: BP51


title: BP56

value: M


title: Normal adjacent tissue [C59]


title: BP52


title: BP54


title: patient 75, tumoral sample2, single array  [P75_T2_SNP6]

value: patient 75

value: right colon


title: BP50


title: BP53


title: Normal adjacent tissue [C41]


title: patient 73, tumoral sample2, single array  [P73_T2_SNP6]

value: patient 73


title: patient 73, tumoral sample1, single array  [P73_T1_SNP6]


title: BP48

value: Triple negative breast cancer


title: BP49


title: Normal adjacent tissue [C39]


title: patient 71, tumoral sample2, single array  [P71_T2_SNP6]

value: patient 71

value: tumor stage 2


title: patient 71, tumoral sample1, single array  [P71_T1_SNP6]


title: patient 75, tumoral sample1, single array  [P75_T1_SNP6]


title: patient 69, tumoral sample2, single array  [P69_T2_SNP6]

value: patient 69

value: left colon


title: BP46


title: Normal adjacent tissue [C38]

value: Adjuvant


title: Normal adjacent tissue [C28]

value: Mexico Hispanic


title: BP45

value: Italy Caucasian


title: Normal adjacent tissue [C36]


title: B63


title: B43


title: Normal adjacent tissue [C29]


title: B16


title: B89


title: BP44


title: patient 69, tumoral sample1, single array  [P69_T1_SNP6]


title: B22


title: B3


title: Normal adjacent tissue [C37]


title: B91


title: Normal adjacent tissue [C15]


title: BP87


title: patient 67, tumoral sample2, single array  [P67_T2_SNP6]

value: patient 67


title: patient 65, tumoral sample2, single array  [P65_T2_SNP6]

value: patient 65

value: rectum

value: male


title: HUVEC-mock infected

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: RNA-seq analysis

data_processing:
The libraries were run on Illumina Next-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the human genome database sequence to calculate the RPKM values of cellular gene using CLC Workbench
Relative expressions were calculated with reference of mock infected control cells
Genome_build: NCBI genome build of human genome, Homo sapiens (hg19) sequence

source_name: HUVECs

growth_protocol: HUVEC cells were grown in Medium 200 with 10% FBS

extract_protocol:
Total mRNA was extracted from the mock infected control and ZIKV infected cells
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: Cells were infected with ZIKV virus and allowed to grow for 12h

value: HUVEC cells

tag: treatment

value: Mock infected control cells


title: HUVEC-PRVABC59 infected

description: RNA-seq analysis

value: PRVABC59 ZIKV infected cells-12hpi


title: HUVEC-IBH30656 infected

description: RNA-seq analysis

value: IBH30656 ZIKV infected cells-12hpi


title: patient 63, tumoral sample1, single array  [P63_T1_SNP6]

value: patient 63

value: frozen sample

value: sigmoid colon

value: female


title: patient 61, tumoral sample1, single array  [P61_T1_SNP6]

value: patient 61

value: colon

value: tumor stage 3


title: RNASeq_DIPG-X_3_R1

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

data_processing:
Quality of sequencing was assessed with FastQC v0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.3
Reads were aligned to the human hg19 reference genome from Illumina igenomes UCSC collection using bowtie v1.0.0 allowing 3 mismatches and keeping uniquely aligned reads
Sam ouputs were converted to Bam with Samtools v1.0.6
Data were further processed with Pasha v0.99.21 with the following parameters: WIGvs = TRUE, incrArtefactThrEvery = 7000000, elongationSize = NA.
Fixed steps wiggle files were converted to bigwigs with the script wigToBigWig available on the UCSC Genome Browser website (http://hgdownload.soe.ucsc.edu/admin/exe/)
Spike-in normalization was achieved using Drosophila Melanogaster DNA aligned to Illumina igenomes dm3
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: Fastq files for raw data, bigwigs of the processed and spike-in normalized experiments are provided.

molecule: polyA RNA

growth_protocol: 293 TREX cells and their derivatives were cultured using standard DMEM media (Gibco/Thermo) supplemented with 10% fetal bovine serum (Gemini), 1x NEAA (Sigma), 1x Pen/Strep (sigma), 1xGlutaMAX (Gibco/Thermo Fisher), 1X sodium pyruvate (Sigma). Stable cell lines in which the expression of the integrated transgene, either H3.3K27WT or H3.3K27M, under the control of doxycycline were cultured using 200 mg/mL zeocin and 10 mg/mL blasticidin. Glioma and diffuse intrinsic pontine glioma (DIPG) cell lines were maintained in a 1:1 mixture of DMEM/F12 to Neurobasal (Gibco/Thermo Fisher) supplemented with 1x NEAA (Sigma), 1xGlutaMAX (Gibco/Thermo Fisher), 1X sodium pyruvate (Sigma), 1x antibiotic-antimycotic (Sigma), h-EGF (20ng/mL; Shenandoah Biotech), h-FGF basic 154 (20ng/mL; Shenandoah Biotech) and 1X B27 supplement without vitamin A (Gibco/Thermo Fisher).

extract_protocol:
For ChIP-seq, nuclei was isolated from cells fixed with 1% Formaldehyde. Next, chromatin was fragmented into ~250bp.  Chromatin immunoprecipitation was performed with the indicated antibodies. For RNA-seq, total RNA was isolated with RNAeasy (Qiagen) and reverse transcribed using Superscript III and random hexamers (Life Technologies) to synthesize the 1st strand. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I (NEB, M0209L) and the E. coli ligase (Enzymatics, L6090L).
For ChIP-seq and RNA-seq, libraries were prepared by standard protocol. First, fragments are repaired to generate  blunt 5' P ends  using 'EndIT DNA End Repair kit' (Epicentre). Second, 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB). Third,  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Lastly, libraries were size selected using 'Ampure beads' (Beckman Coulter), then amplified, quantified and pooled.

tag: genotype

value: Wild type

tag: chip antibody

value: NR


title: RNASeq_DIPG-XIII_2_R1


title: RNASeq_DIPG-X_1_R1


title: RNASeq_DIPG-XIII_3_R1


title: 293TRex_INPUT_K27M_72hr

library_source: genomic


title: 293TRex_HA_K27M_72hr

value: HA, ChIP-grade, Abcam, Cat# ab9110


title: 293TRex_HA_K27WT_72hr


title: Normal adjacent tissue [C14]

value: Adjuvant

value: Mexico Hispanic


title: patient 59, tumoral sample2, single array  [P59_T2_SNP6]

value: patient 59

tag: tissue

value: right colon

value: male


title: 293TRex_H3K36me2_K27WT_72hr

value: H3K36me2, C75H12, Cell Signaling Technology, Cat# 2901


title: Normal adjacent tissue [C5]


title: Normal adjacent tissue [C6]


title: patient 67, tumoral sample1, single array  [P67_T1_SNP6]

value: patient 67

value: tumor stage 2


title: Normal adjacent tissue [C13]


title: Breast cancer tissue [NT204]

description: Gene expression data from breast tumor.

source_name: Fresh frozen tumor tissue

value: Normal-like


title: patient 65, tumoral sample1, single array  [P65_T1_SNP6]

value: patient 65

value: frozen sample

value: rectum


title: Breast cancer tissue [NT198]

description: Gene expression data from breast tumor.


title: RNASeq_DIPG-XIII_1_R1


title: RNASeq_DIPG-X_2_R1


title: 293TRex_INPUT_K27WT_72hr


title: patient 59, tumoral sample1, single array  [P59_T1_SNP6]


title: patient 57, tumoral sample2, single array  [P57_T2_SNP6]

value: patient 57


title: 293TRex_H3K27me3_K27M_72hr

value: H3K27me3, Cell Signaling Technology, Cat# 9733 RRID:AB_2616019


title: Normal adjacent tissue [C45]


title: DIPG_X_INPUT

value: Wild type


title: DIPG_XIII_INPUT

value: NR


title: DIPG_XIII_H3K36me2


title: patient 55, tumoral sample1, single array  [P55_T1_SNP6]

value: patient 55

value: female


title: DIPG_X_H3K36me2


title: patient 53, tumoral sample1, single array  [P53_T1_SNP6]

value: patient 53

value: left colon


title: DIPG_XIII_H3K27me3


title: 293TRex_H3K36me2_K27M_72hr


title: Breast cancer tissue [T175]

description: Gene expression data from breast tumor.

value: Adjuvant

value: Mexico Hispanic


title: patient 49, tumoral sample1, single array  [P49_T1_SNP6]

value: patient 49

value: male


title: patient 51, tumoral sample1, single array  [P51_T1_SNP6]

value: patient 51

value: right colon

value: tumor stage 2


title: 293TRex_H3K27me3_K27WT_72hr


title: DIPG_N_H3K36me2

value: H3K36me2, C75H12, Cell Signaling Technology, Cat# 2901


title: DIPG_X_H3K27me3


title: DIPG_N_INPUT


title: pcGBM2_H3K27me3


title: pcGBM2_INPUT


title: pcGBM2_H3K36me2


title: Breast cancer tissue [NT143]

description: Gene expression data from breast tumor.

value: Normal-like


title: patient 47, tumoral sample1, single array  [P47_T1_SNP6]

value: patient 47

value: frozen sample


title: DIPG_N_H3K27me3

value: H3K27me3, Cell Signaling Technology, Cat# 9733 RRID:AB_2616019


title: INPUT_K27WT_6-12-24-EZH2-72H

value: Wild type

value: NR


title: patient 45, tumoral sample1, single array  [P45_T1_SNP6]

value: patient 45

value: cecum


title: Breast cancer tissue [NT142]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [NT168]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [NT58]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [NT138]

description: Gene expression data from breast tumor.


title: INPUT_K27WT_0H


title: Breast cancer tissue [NT80]

description: Gene expression data from breast tumor.


title: HA_K27WT_6hr

value: HA, ChIP-grade, Abcam, Cat# ab9110


title: patient 43, tumoral sample1, single array  [P43_T1_SNP6]

value: patient 43

value: tumor stage 4


title: INPUT_K27M_6-12-24-EZH2-72H


title: INPUT_K27M_0H


title: patient 41, tumoral sample1, single array  [P41_T1_SNP6]

value: patient 41

value: tumor stage 3


title: HA_K27WT_0Hr


title: HA_K27WT_24hr


title: Breast cancer tissue [NT48]

description: Gene expression data from breast tumor.

value: Adjuvant

value: Mexico Hispanic


title: Breast cancer tissue [NT44]

description: Gene expression data from breast tumor.


title: patient 37, tumoral sample2, single array  [P37_T2_SNP6]

value: patient 37

value: left colon

value: female


title: Breast cancer tissue [NT17]

description: Gene expression data from breast tumor.

value: Normal-like


title: BP57

value: Triple negative breast cancer

value: MSL

value: Italy Caucasian


title: Breast cancer tissue [NT43]

description: Gene expression data from breast tumor.


title: HA_K27WT_12hr

value: Wild type


title: HA_K27M_6hr


title: HA_K27M_12hr


title: HA_K27M_24hr


title: patient 37, tumoral sample3, single array  [P37_T3_SNP6]

value: frozen sample

value: transverse colon


title: Breast cancer tissue [NT1]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [NT31]

description: Gene expression data from breast tumor.


title: patient 37, tumoral sample1, single array  [P37_T1_SNP6]


title: patient 35, tumoral sample1, single array  [P35_T1_SNP6]

value: patient 35

value: right colon


title: HA_K27M_0Hr

value: HA, ChIP-grade, Abcam, Cat# ab9110


title: Breast cancer tissue [HT234]

description: Gene expression data from breast tumor.


title: patient 39, tumoral sample1, single array  [P39_T1_SNP6]

value: patient 39

value: male


title: Breast cancer tissue [HT230]

description: Gene expression data from breast tumor.

value: Adjuvant


title: H3K36me2_K27WT_24hr

value: H3K36me2, C75H12, Cell Signaling Technology, Cat# 2901


title: patient 85, tumoral sample1, single array  [P85_T1_SNP6]

value: patient 85

value: tumor stage 3


title: patient 31, tumoral sample1, single array  [P31_T1_SNP6]

value: patient 31

value: tumor stage 4


title: H3K36me2_K27WT_12hr


title: patient 29, tumoral sample1, single array  [P29_T1_SNP6]

value: patient 29

value: left colon


title: patient 27, tumoral sample1, single array  [P27_T1_SNP6]

value: patient 27


title: H3K36me2_K27WT_0Hr

value: Wild type


title: patient 33, tumoral sample1, single array  [P33_T1_SNP6]

value: patient 33

value: frozen sample

value: no available

value: female

value: tumor stage 2


title: H3K36me2_K27WT_6hr


title: H3K36me2_K27M_6hr


title: H3K36me2_K27M_24hr


title: Breast cancer tissue [HT226]

description: Gene expression data from breast tumor.

value: Mexico Hispanic


title: patient 25, tumoral sample1, single array  [P25_T1_SNP6]

value: patient 25

value: colon


title: H3K36me2_K27M_12hr

value: H3K36me2, C75H12, Cell Signaling Technology, Cat# 2901


title: Control Plasma with no FSGS

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Downstream bioinformatics analyses was performed by using a combination of programs including Bowtie2, Tophat2, HTseq and Cufflink .
Reference genome and gene model annotation files were acquired from NCBI/UCSC/Ensemble genome browser.
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Gene expression level quantification was done using HTSeq v0.6.1 and for each gene read numbers counts were mapped, whereas, Reads Per Kilobase of exon model (RPKM) of each gene was calculated based on the length of the gene and expression levels were analyzed
DESeq2 R package (2_1.6.3) database was used for the differential expression (DE) analyses. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach and adjusted P-value <0.05 found by DESeq2 were assigned as DE. Analyses of DE of two conditions was performed using the DEGSeq R package (1.12.0). The P-values were also adjusted using Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as threshold for significantly differential expression.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Kidney

extract_protocol:
RNA samples were isolated from independent experiments performed in triplicate using Qiagen RNAeasy Mini Kit.
RNA libraries were prepared for sequencing using standard HiSeq/MiSeq Illumina platform for the RNA sequencing

tag: cell type

value: podocytes cell line

tag: sample type

value: control patients plasma with no FSGS


title: patient 23, tumoral sample1, single array  [P23_T1_SNP6]

value: patient 23

value: rectum


title: patient 21, tumoral sample1, single array  [P21_T1_SNP6]

value: patient 21

value: tumor stage 3


title: Recurrent FSGS plasma, rep1

value: recurrent FSGS patients plasma


title: Breast cancer tissue [HT209]

description: Gene expression data from breast tumor.

value: Adjuvant

tag: population


title: sh-LINC01116-3

city: shanghai

first: chun

last: luo

address: 415# fengyang road

department: neurosurgery

country: China

institute: changzheng hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: U251 cell with linc01116 knockdown

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: U251 cells were cultured in 37℃,5%CO2 incubator and high glucose medium with 10%calf serum.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresi

treatment_protocol: For stable knockdown of LINC01116, U251 cells were transfected with lentiviral construct (LV3-pGLV-h1-GFP-puro) containing LINC01116 short hairpin RNA (shRNA) or non-targeting shRNA in the presence of polybrene (8 mg/ml) (GenePharma, China) after 48-h transfection.

tag: cell line

value: U251 cell line

tag: genotype/variation

value: linc01116 knockdown


title: Breast cancer tissue [HT215]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [HT191]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [HT193]

description: Gene expression data from breast tumor.


title: sh-LINC01116-1


title: sh-NC-1

source_name: U251 cell with shRNA negative control

value: control


title: Breast cancer tissue [HT166]

description: Gene expression data from breast tumor.


title: sh-LINC01116-2


title: 17-week human fetal esophageal epithelium_sample_2

source_name: human fetal esophageal epithelium

value: human fetal esophageal epithelium

value: 17 week fetal


title: sh-NC-3


title: sh-NC-2


title: Breast cancer tissue [HT108]

description: Gene expression data from breast tumor.

value: Mexico Hispanic


title: patient 19, tumoral sample1, single array  [P19_T1_SNP6]

tag: patient id

value: patient 19

value: frozen sample

value: right colon

value: male

value: tumor stage 2


title: H3K27me3_K27WT_6hr

value: Wild type

value: H3K27me3, C36B11, Cell Signaling Technology, Cat# 9733 RRID:AB_2616019


title: patient 17, tumoral sample1, single array  [P17_T1_SNP6]

value: patient 17

tag: anatomical site

value: sigmoid colon


title: 17-week human fetal esophageal epithelium_sample_1


title: H3K27me3_K27WT_24hr


title: patient 15, tumoral sample1, single array  [P15_T1_SNP6]

value: patient 15

tag: gender

value: tumor stage 3


title: H3K27me3_K27WT_12hr


title: 18-week human fetal esophageal epithelium

value: 18 week fetal


title: Breast cancer tissue [HT85]

description: Gene expression data from breast tumor.

value: Adjuvant


title: RUES2-derived esophageal progenitor cells sample_3


title: patient 11, tumoral sample1, single array  [P11_T1_SNP6]

value: patient 11

value: left colon

value: female

tag: patient age


title: Breast cancer tissue [HT146]

description: Gene expression data from breast tumor.

value: Mexico Hispanic


title: H3K27me3_K27WT_0Hr


title: H3K36me2_K27M_0Hr

value: H3K36me2, C75H12, Cell Signaling Technology, Cat# 2901


title: patient 9, tumoral sample1, single array  [P9_T1_SNP6]

value: patient 9

value: frozen sample

tag: tumor stage


title: H3K27me3_K27M_6hr


title: H3K27me3_K27M_24hr


title: RUES2-derived esophageal progenitor cells sample_1


title: RUES2-derived esophageal progenitor cells sample_2


title: Breast cancer tissue [HT76]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [HT75]

description: Gene expression data from breast tumor.


title: Donor 2 PBMC

city: Los Angeles

first: Samuel

middle: Jackson

last: Balin

state: CA

address: 10833 Le Conte Ave, Div of Dermatology, 52-121 CHS

institute: UCLA

description:
donor 2 total PBMC
Donor 2 normalized counts GEO.csv

data_processing:
Sequenced reads were aligned to the human reference genome (build hg19 UCSC) using TopHat and Bowtie2.
Raw counts were calculated with HTseq using the hg19 Ensembl annotation.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values file containing raw counts of mapped reads

source_name: PBMC

extract_protocol:
RNA was isolated according to the MARIS protocol (Hrvatin, S et al. MARIS: method for analyzing RNA following intracellular sorting. 2014 PLoS One Vol 9, e89459)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBMC were acquired from peripheral blood,cells were surfaced stained with CD3, then intracellularly stained with Granzyme B, perforin and granulysin.  Subsets of cytotoxic CD3 postiive cells were sorted.

value: Total PBMC

tag: exprssion pattern

value: Unsorted PBMC

tag: donor

value: donor 2


title: Breast cancer tissue [HT78]

description: Gene expression data from breast tumor.

tag: molecular subtype

tag: theraoy


title: Breast cancer tissue [HT95]

description: Gene expression data from breast tumor.


title: patient 5, tumoral sample1, single array  [P5_T1_SNP6]

value: patient 5

value: tumor stage 2


title: H3K27me3_K27M_12hr

tag: genotype

value: H3K27me3, C36B11, Cell Signaling Technology, Cat# 9733 RRID:AB_2616019


title: Donor 2 TCTL

description:
donor 2 Tricytotoxic cells
Donor 2 normalized counts GEO.csv

source_name: T cells

value: Tricytotoxic cells

value: CD3+ GZMB+, PRF+,GNLY+


title: patient 13, tumoral sample1, single array  [P13_T1_SNP6]

value: patient 13

value: transverse colon

value: male

value: tumor stage 3


title: H3K27me3_K27M_0Hr

tag: chip antibody


title: patient 3, tumoral sample1, single array  [P3_T1_SNP6]

value: patient 3

tag: tissue

value: rectum


title: Breast cancer tissue [HT47]

description: Gene expression data from breast tumor.

value: Adjuvant

value: Mexico Hispanic


title: EZH2_K27WT_72hr

value: Wild type

value: EZH2,  D2C9, Cell Signaling Technology, Cat# 5246, RRID:AB_10694683


title: Breast cancer tissue [HT15]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [HT5]

description: Gene expression data from breast tumor.


title: patient 1, tumoral sample1, single array  [P1_T1_SNP6]

value: patient 1

value: frozen sample


title: Donor 2 DCTL

description:
donor 2 Dicytotoxic cells
Donor 2 normalized counts GEO.csv

tag: cell type

value: Dicytotoxic cells

value: CD3+ GZMB+, PRF+,GNLY-

value: donor 2


title: patient 7, tumoral sample1, single array  [P7_T1_SNP6]

value: patient 7

value: sigmoid colon

value: tumor stage 2


title: 14-week human fetal esophageal epithelium

value: human fetal esophageal epithelium

tag: developmental stage

value: 14 week fetal


title: Donor 2 MCTL

description:
donor 2 monocytotoxic cells
Donor 2 normalized counts GEO.csv

value: Monocytotoxic cells

value: CD3+ GZMB+, PRF-,GNLY-


title: EZH2_K27WT_6hr


title: patient AA3, tumoral sample1, single array  [PAA3_T1_SNP6]

value: patient AA3

value: rectum

value: male


title: patient AA1, tumoral sample1, single array  [PAA1_T1_SNP6]

value: patient AA1

value: tumor stage 4


title: Breast cancer tissue [BT248]

description: Gene expression data from breast tumor.

value: Luminal B

value: Adjuvant

tag: population

value: Mexico Hispanic


title: Breast cancer tissue [BT239]

description: Gene expression data from breast tumor.


title: Donor 2 NCTL

description:
donor 2 Noncytotoxic cells
Donor 2 normalized counts GEO.csv

value: Non cytotoxic cells

value: CD3+ GZMB-, PRF-, GNLY-


title: Donor 1 TCTL

description:
donor 1 Tricytotoxic cells
Donor 1 normalized counts GEO.csv

value: Tricytotoxic cells

value: CD3+ GZMB+, PRF+,GNLY+

value: Donor 1


title: EZH2_K27WT_0Hr

value: Wild type

value: EZH2,  D2C9, Cell Signaling Technology, Cat# 5246, RRID:AB_10694683


title: EZH2_K27WT_24hr


title: EZH2_K27M_72hr


title: Donor 1 DCTL

description:
donor 1 Dicytotoxic cells
Donor 1 normalized counts GEO.csv

value: Dicytotoxic cells

value: CD3+ GZMB+, PRF+,GNLY-


title: Donor 1 PBMC

description:
donor 1 total PBMC
Donor 1 normalized counts GEO.csv

value: Total PBMC

value: Unsorted PBMC


title: EZH2_K27M_6hr


title: Donor 1 MCTL

description:
donor 1 monocytotoxic cells
Donor 1 normalized counts GEO.csv

value: Monocytotoxic cells

value: CD3+ GZMB+, PRF-,GNLY-


title: EZH2_K27M_24hr


title: Breast cancer tissue [BT232]

description: Gene expression data from breast tumor.


title: Donor 1 NCTL

description:
donor 1 non cytotoxic cells
Donor 1 normalized counts GEO.csv


title: EZH2_K27WT_12hr


title: Full depth skin from outer arm 89_C-15.1

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

description: miRNA expression data from sun-exposed skin of old age

hyb_protocol: cRNA were hybridized  to the standard Affymetrix protocol  (GeneTitan® Instrument User Guide for Affymetrix GeneTitan plate format miRNA 4.1).

scan_protocol: Array plate was scanned using Affymetrix GeneTitan Scanner.

data_processing: The data were analyzed with Expression Console using  global scaling as normalization method.

source_name: Sun-exposed skin old age

label_protocol: FlashTag labelling was performed according to the standard Affymetrix protocol from  total RNA (GeneTitan® Instrument User Guide for Affymetrix GeneTitan plate format miRNA 4.1).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

value: Skin

tag: age

value: >70 years


title: Full depth skin from inner arm 90_C-15.2

description: miRNA expression data from sun-protected skin of old age

source_name: Sun-protected skin old age


title: Breast cancer tissue [BT227]

description: Gene expression data from breast tumor.

value: Luminal B

value: Adjuvant


title: Full depth skin from inner arm 88_C-14.2


title: Full depth skin from outer arm 87_C-14.1


title: Donor 1 T cells

description:
donor 1 Unsorted T cells
Donor 1 normalized counts GEO.csv

value: Total T cells

value: Unsorted total T cells


title: Breast cancer tissue [BT218]

description: Gene expression data from breast tumor.

value: Mexico Hispanic


title: Breast cancer tissue [BT213]

description: Gene expression data from breast tumor.


title: cckA(L228P)

city: Thiruvananthapuram

first: Sharath

last: Narayanan

state: Kerala

address: CET campus

department: Biology

country: India

institute: IISER

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2
Pre-processing: Fasts-toolkit 0.0.14, Cutadapt 1.13  Raw fastq reads were trimmed at the 5' end for 10 bases using fastx_trimmer tool. The adapters were removed using Cutadapt. Along with adapter removal, bases which were called as N, were also trimmed.
Alignment: Bowtie 1.0.0, samtools-0.1.19, bedtools 2.25.0  Pre-processed reads were aligned to the genome with the following Bowtie parameters: -m 1, -S, -v 2. The SAM file with aligned reads were filtered using samtools. First,unmapped reads were filtered out using '-F 4' option and simultaneously, converted to BAM format using '-b' option under the 'view' tool. The BAM files were then sorted using default parameters of the 'sort' tool.  The BAM files were converted to BEDGRAPH format using bedtools.
Peak calling: SeqMonk software (Braham Bioinformatics Institute)  Peak refinement and annotation: SeqMonK output were processed by Perl programs (in house written, described in the paper) to refine the peaks annotation and eliminate background
ChIPseq comparisons: Peaks list after being processed were scanned for common target, then ratio of each peak abundance were computed and reported as the log2 fold variation
Genome_build: Caulobacter Cresentus NA 1000 (Accession: CP001340.1)
Supplementary_files_format_and_content: Bedgraph files – contains the genome coverage of the aligned reads  XLS files – contains the peak abundance and annotation

organism: Caulobacter vibrioides

source_name: Mutant Caulobacter crescentus strain, ∆nstA cckA(L228P)

growth_protocol: The bacterial cultures grown in PYE media harvested at mid-log phase

extract_protocol:
Cell lysates immunoprecipitated with polyclonal antibodies to CtrA and DNA extracted by phenol:chloroform:isoamyl alcohol
Next Generation Sequencing on Ilumina Platform at Fasteris, Switzerland.

treatment_protocol: Formaldehyde crosslinking and sonication of the lysates.

value: cckA (L228P)

value: polyclonal antibodies to CtrA


title: EZH2_K27M_0Hr


title: NA1000 (WT)

source_name: Wild type Caulobacter crescentus strain, NA1000

value: WT


title: Full depth skin from inner arm 84_C-12.2


title: Breast cancer tissue [BT196]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 86_C-13.2


title: Full depth skin from outer arm 85_C-13.1


title: EZH2_K27M_12hr

value: EZH2,  D2C9, Cell Signaling Technology, Cat# 5246, RRID:AB_10694683


title: SAM17865152 LCM BCC ki67-

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: laser capture micro-dissected (LCM) tumour nests from fresh frozen skin of K14Cre-ER; Ptch1fl/fl; p53fl/fl mice

extract_protocol: Tumour nests were collected in RLT lysis buffer and total RNA was extracted with the RNeasy Micro kit (Qiagen). The concentration and integrity of RNA samples was determined with the NanoDrop 8000 (Thermo Scientific) and the Bioanalyzer RNA 6000 Pico Kit (Agilent), respectively.

tag: treatment

value: LCM BCC ki67-

tag: strain/genotype

value: K14Cre-ER; Ptch1fl/fl; p53fl/fl; Lgr5GFP

tag: tissue diagnosis

value: Carcinoma Basal Cell Ki67-

value: control


title: SAM17865151 LCM BCC ki67-


title: SAM17865149 LCM BCC ki67-


title: Full depth skin from outer arm 83_C-12.1


title: Breast cancer tissue [BT176]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 82_C-11.2


title: Full depth skin from inner arm 80_C-10.2


title: Breast cancer tissue [BT159]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 79_C-10.1


title: Breast cancer tissue [BT158]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT150]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT186]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 78_C-9.2


title: Breast cancer tissue [BT137]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT126]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 77_C-9.1


title: Breast cancer tissue [BT149]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT116]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 81_C-11.1


title: Breast cancer tissue [BT123]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT94]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT105]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 75_C-8.1


title: SAM17865148 LCM BCC ki67-


title: SAM17865150 LCM BCC ki67-


title: Breast cancer tissue [BT79]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT82]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 74_C-7.2


title: Breast cancer tissue [BT55]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT73]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 76_C-8.2


title: Full depth skin from outer arm 71_C-6.1


title: Full depth skin from inner arm 72_C-6.2


title: Full depth skin from inner arm 70_C-5.2


title: Full depth skin from inner arm 68_C-4.2


title: Full depth skin from outer arm 67_C-4.1


title: Breast cancer tissue [BT38]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 66_C-3.2


title: Full depth skin from outer arm 65_C-3.1


title: Full depth skin from outer arm 69_C-5.1


title: Full depth skin from inner arm 30_A-15.2

description: miRNA expression data from sun-protected skin of young age

source_name: Sun-protected skin young age

value: 18-25 years


title: Full depth skin from inner arm 62_C-1.2


title: Full depth skin from outer arm 61_C-1.1


title: Full depth skin from outer arm 63_C-2.1


title: Breast cancer tissue [BT13]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT6]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 73_C-7.1


title: Breast cancer tissue [BaT195]

description: Gene expression data from breast tumor.

value: Basal-like


title: Breast cancer tissue [BaT250]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BT16]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BaT189]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 64_C-2.2

value: Skin


title: Breast cancer tissue [BaT201]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BaT162]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BaT144]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BaT249]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 29_A-15.1

description: miRNA expression data from sun-exposed skin of young age

source_name: Sun-exposed skin young age


title: Full depth skin from inner arm 28_A-14.2


title: Breast cancer tissue [BaT174]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 26_A-13.2


title: Breast cancer tissue [BaT122]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 25_A-13.1


title: Full depth skin from outer arm 21_A-11.1


title: Full depth skin from inner arm 18_A-9.2


title: Full depth skin from inner arm 22_A-11.2


title: Full depth skin from inner arm 20_A-10.2


title: Full depth skin from outer arm 19_A-10.1


title: Breast cancer tissue [AT206]

description: Gene expression data from breast tumor.

value: Luminal A


title: Full depth skin from inner arm 24_A-12.2


title: Breast cancer tissue [BaT97]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 27_A-14.1


title: Full depth skin from inner arm 16_A-8.2


title: Breast cancer tissue [BaT45]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 23_A-12.1


title: Breast cancer tissue [AT244]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT229]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BaT120]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT203]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT200]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [BaT3]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT212]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 14_A-7.2


title: Breast cancer tissue [AT194]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 15_A-8.1


title: Full depth skin from outer arm 13_A-7.1


title: Breast cancer tissue [AT192]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT190]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT187]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 17_A-9.1


title: Breast cancer tissue [AT184]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 11_A-6.1


title: Full depth skin from inner arm 10_A-5.2


title: Breast cancer tissue [BaT140]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT178]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 07_A-4.1


title: Full depth skin from inner arm 08_A-4.2


title: Full depth skin from inner arm 06_A-3.2


title: Breast cancer tissue [AT172]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT170]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 09_A-5.1


title: Breast cancer tissue [AT171]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT160]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT165]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT183]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT169]

description: Gene expression data from breast tumor.


title: Full depth skin from outer arm 05_A-3.1


title: Breast cancer tissue [AT154]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 02_A-1.2


title: Full depth skin from outer arm 03_A-2.1


title: Full depth skin from inner arm 12_A-6.2


title: Full depth skin from outer arm 01_A-1.1


title: Breast cancer tissue [AT141]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT125]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT129]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT167]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT124]

description: Gene expression data from breast tumor.


title: Full depth skin from inner arm 04_A-2.2


title: 1310_Chorion

city: North Mymms

first: Amanda

middle: M

last: de Mestre

state: Hertfordshire

address: Hawkshead Lane

department: Comparative Biomedical Sciences

country: United Kingdom

institute: Royal Veterinary College

description: mare/stallion (replicate) number: 4

hyb_protocol: cRNA was hybridized to the microarray chip (G2519F, AMADID Release GE 4 x 44 60 mer) using the gene expression hybridization kit (Agilent Technologies UK Ltd.), using the manufacturer’s instructions and then hybridized for 17 hours at 65°C and 10 g using the Tecan HS Pro hybridization station (Tecan group Ltd, Reading, UK).

scan_protocol: Microarray chips were washed with wash buffer and scanned by the Agilent DNA microarray scanner G2505C (Agilent Technologies UK Ltd).

data_processing:
Samples were subjected to Agilent quality control measures, which all entities passed.
Background correction (normexp, offset=1) and between array normalization (quantile) was performed.

label: Cyanine 3-CTP

organism: Equus caballus

source_name: Chorion- 34 days

label_protocol: Using RNA spike-in kits (Agilent Technologies UK Ltd) and via the manufacturer’s instructions, 50 ng of RNA sample was spiked with quality controls and run. Complimentary RNA (cRNA) was synthesised and amplified using the low input quick amp labelling kit via the manufacturer’s instructions (Agilent Technologies UK Ltd.). A specific T7 RNA polymerase blend was used to generate fluorescent cRNA via incorporation of Cyanine 3-CTP.

growth_protocol: Chorionic girdle of chorion tissue was dissected free of surrounding placental tissue following recovery from a mare (within 30 minutes of isolation of conceptus tissue) and immediately snap frozen.

extract_protocol: Total RNA was isolated from snap-frozen equine conceptus tissue, following homogenization by QIAshredder (Qiagen, Veno, The Netherlands), using a Qiagen RNeasy kit (Qiagen) as directed by the manufacturer. RNA was additionally treated with DNase on a column (Qiagen) as described by the manufacturer.

treatment_protocol: Not treated. Tissue immediately snap frozen

value: Chorion

tag: gestational age

value: 34 days


title: Breast cancer tissue [AT110]

description: Gene expression data from breast tumor.

value: Adjuvant


title: 1303_Chorion

description: mare/stallion (replicate) number: 2


title: Breast cancer tissue [AT98]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT135]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT71]

description: Gene expression data from breast tumor.


title: 1216_Chorion

description: mare/stallion (replicate) number: 3


title: Breast cancer tissue [AT83]

description: Gene expression data from breast tumor.


title: 1305_Chorion

description: mare/stallion (replicate) number: 1


title: Breast cancer tissue [AT50]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT106]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT81]

description: Gene expression data from breast tumor.


title: 1309_Chorion

description: mare/stallion (replicate) number: 5

source_name: Chorion- 30 days

value: 30 days


title: 1211_Chorion

description: mare/stallion (replicate) number: 5


title: 1212_Chorion

description: mare/stallion (replicate) number: 5

source_name: Chorion- 31 days

value: 31 days


title: 1304_Chorion

description: mare/stallion (replicate) number: 4


title: Breast cancer tissue [AT74]

description: Gene expression data from breast tumor.

source_name: Fresh frozen tumor tissue

value: Mexico Hispanic


title: Breast cancer tissue [AT69]

description: Gene expression data from breast tumor.


title: 1207_Chorion

description: mare/stallion (replicate) number: 3


title: Breast cancer tissue [AT59]

description: Gene expression data from breast tumor.


title: 1204_Chorion

description: mare/stallion (replicate) number: 1


title: 1210_Chorion

description: mare/stallion (replicate) number: 4


title: Breast cancer tissue [AT41]

description: Gene expression data from breast tumor.


title: 1205_Chorion

description: mare/stallion (replicate) number: 2


title: 1203_Chorion

description: mare/stallion (replicate) number: 3


title: Breast cancer tissue [AT40]

description: Gene expression data from breast tumor.


title: 1209_Chorion

description: mare/stallion (replicate) number: 1


title: Breast cancer tissue [AT62]

description: Gene expression data from breast tumor.


title: 1306_Chorion

description: mare/stallion (replicate) number: 5

source_name: Chorion- 27 days

value: 27 days


title: 1311_Chorion

description: mare/stallion (replicate) number: 2


title: Breast cancer tissue [AT37]

description: Gene expression data from breast tumor.


title: 1214_Chorion

description: mare/stallion (replicate) number: 2


title: Breast cancer tissue [AT36]

description: Gene expression data from breast tumor.


title: 1307_CG

description: mare/stallion (replicate) number: 3


title: 1213_Chorion

description: mare/stallion (replicate) number: 1


title: Breast cancer tissue [AT29]

description: Gene expression data from breast tumor.


title: 1304_Girdle

description: mare/stallion (replicate) number: 4

source_name: Chorionic Girdle-34 days

value: Chorionic Girdle


title: Breast cancer tissue [AT27]

description: Gene expression data from breast tumor.


title: 1211_Girdle

description: mare/stallion (replicate) number: 5


title: Breast cancer tissue [AT34]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT30]

description: Gene expression data from breast tumor.


title: 1303_Girdle

description: mare/stallion (replicate) number: 2


title: Dox_chr_2 (6)

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
Abundance measurements in cuffdiff output
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file reports RPKMs and log2fold change of average RPKM between noDox and Dox

source_name: embryonic stem cells

growth_protocol: ESC were grown on 0.1% gelatin in DMEM supplemented with 15% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1mM Sodium Pyruvate and 1000 U/ml recombinant leukemia inhibitory factor.

extract_protocol:
Cells were fractionated and the cytoplasmic and nucleoplamic fractions disgarded. The purified chromatin fraction was resuspended in TRIzol and the chromatin bound RNA isolated.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion

treatment_protocol: 15 h before cell harvesting, transgene expression was induced with 2.5 ug/ml doxycycline in ESC.

tag: cells

value: ESC doxycycline-inducible expressing HA-Flag-AGO2

tag: passages

tag: fraction

value: chromatin


title: No_dox_Chr_1 (6)


title: Breast cancer tissue [AT24]

description: Gene expression data from breast tumor.


title: Dox_chr_3 (6)


title: No_dox_Chr_2 (6)


title: 1212_Girdle

description: mare/stallion (replicate) number: 5

source_name: Chorionic Girdle-31 days


title: Dox_chr_1 (6)


title: Breast cancer tissue [AT4]

description: Gene expression data from breast tumor.


title: Breast cancer tissue [AT7]

description: Gene expression data from breast tumor.


title: 1305_Girdle

description: mare/stallion (replicate) number: 1


title: 1216_Girdle

description: mare/stallion (replicate) number: 3


title: Breast cancer tissue [AT26]

description: Gene expression data from breast tumor.


title: 1205_CG

description: mare/stallion (replicate) number: 2


title: Breast cancer tissue [AT28]

description: Gene expression data from breast tumor.


title: 1310_Girdle

description: mare/stallion (replicate) number: 3


title: 1207_Girdle

description: mare/stallion (replicate) number: 4


title: 1309_Girdle

description: mare/stallion (replicate) number: 5

source_name: Chorionic Girdle-30 days


title: 1210_Girdle

description: mare/stallion (replicate) number: 4


title: ESC_Total_nodox_2 (5)

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx reports Normalized counts

extract_protocol:
Cells were fractionated and AGO2 was immunoprecipitated from cytoplasmic and nuclear fraction.  The RNA was isolated using Trizol.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

value: Total

tag: rip antibody

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse (Sigma-Aldrich, catalog# M8823)


title: ESC_Total_nodox_1 (5)


title: ESC_Total_dox_3 (5)


title: 1204_Girdle

description: mare/stallion (replicate) number: 1


title: ESC_Total_dox_2 (5)


title: ESC_Nuc_nodox_3 (5)

value: Nuc


title: 1203_Girdle

description: mare/stallion (replicate) number: 3


title: ESC_Total_dox_1 (5)


title: ESC_Nuc_nodox_2 (5)


title: ESC_Total_nodox_3 (5)


title: ESC_Nuc_dox_1 (5)


title: ESC_Cnot7_shRNA rep1 (4)

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
log2 fold change of average RPKM of noTarget vs Cnot1 or Cnot7
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file reports RPKMs, the Log2Fold change between noTarget shRNA and Cnot1 shRNA as well as between noTarget shRNA and Cnot7 shRNA

extract_protocol:
Cells were fractionated and nuclear RNA was isolated using TRIzol.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion

treatment_protocol: ESC were  treated with 2.5 ug/ml doxycycline and infected with lenitvirus for 24hrs. 1ug/ml puromycine was used for selection of virus infected cells.

tag: shRNA

value: shRNA with Cnot7

value: nuclear


title: ESC_Nuc_dox_2 (5)


title: ESC_Cnot7_shRNA rep2 (4)


title: ESC_Cnot1_shRNA rep2 (4)

value: shRNA with Cnot1


title: ESC_Cnot1_shRNA rep1 (4)


title: 1311_Girdle

description: mare/stallion (replicate) number: 2


title: ESC_NoTarget_shRNA rep2 (4)

value: shRNA with NoTarget


title: ESC_Nuc_nodox_1 (5)


title: ESC_Nuc_dox_3 (5)


title: ESC_NoTarget_shRNA rep1 (4)


title: 1306_Girdle

description: mare/stallion (replicate) number: 5

source_name: Chorionic Girdle-27 days


title: 1307_CHR

description: mare/stallion (replicate) number: 3


title: wild-type TAZ-expressing HOMC-D4 cells #3

city: Aichi

first: Akihiro

last: Matsushita

address: 1-1 Kanokoden, Chikusa-ku, Nagoya

department: Division of Cancer Biology

country: Japan

institute: Aichi Cancer Center Research Institute

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent) following the manufacturers instructions and hybridized to a SurePrint G3 Human GE 8x60K V2 Microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, the microarray was washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting for 8x60K array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: wild-type TAZ-expressing HOMC-D4 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.15 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini kit (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using an RNeasy Plus RNA extraction kit (Qiagen, Tokyo, Japan) following the manufacturer's recommendations.

tag: cell line

value: HOMC-D4 immortalized mesothelial cell line

value: wild type TAZ


title: wild-type TAZ-expressing HOMC-D4 cells #2

tag: genotype


title: wild-type TAZ-expressing HOMC-D4 cells #4


title: ESC_Total_dox_3 (3)

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
The Bam files were further analysed using the Partek6.6 program
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file reports log2 (rpkm+0.001)

extract_protocol:
Cells were fractionated and nuclear RNA was isolated using TRIzol. Total RNA was extracted by lysing the whole cell in TRIzol
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion


title: activated TAZ-S89A-expressing HOMC-D4 cells #3

value: TAZ S89A mutant


title: ESC_Total_nodox_3 (3)


title: ESC_Total_nodox_1 (3)


title: UM139-2_24

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC (version 0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).  We trimmed reads based on quality scores using CutAdapt with default parameters.
Aligment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads to the reference transcriptome using TopHat (version 2.0.13) and Bowtie (version 2.2.1.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive”.
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.2.1) for expression quantitation, normalization, and differential expression analysis, using UCSC hg19.fa as the reference genome sequence and UCSC hg19.gtf for the reverence transcriptome. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: .txt table of mapped read counts for each gene for each sample

source_name: FXS (UM 139-2) hESCs_CGG guide RNA and dCas9-VP192

growth_protocol: hESC were grown on Matrigel coated plate in mTSER1 media

extract_protocol:
Total RNA was extracted using the Quick RNA miniprep kit
single-end sequencing

treatment_protocol: Transfection was done using Mirus TransIT-LT1 reagent

tag: cell line background

value: FXS embryonic stem cells

tag: transfected with

value: CGG guide RNA and dCas9-VP192


title: activated TAZ-S89A-expressing HOMC-D4 cells #1


title: 1209_Girdle

description: mare/stallion (replicate) number: 1

tag: tissue

value: 30 days


title: 1213_Girdle

description: mare/stallion (replicate) number: 1

value: 27 days


title: activated TAZ-S89A-expressing HOMC-D4 cells #2


title: wild-type TAZ-expressing HOMC-D4 cells #1


title: activated TAZ-S89A-expressing HOMC-D4 cells #4


title: ESC_Total_dox_2 (3)


title: 1214_CG

description: mare/stallion (replicate) number: 2

value: Chorionic Girdle


title: UM139-2_22

tag: cell type


title: UM139-2_17

source_name: FXS (UM 139-2) hESCs_scramble guide RNA control and dCas9-VP192


title: FattyAcid-NonReplicativePhase2

city: Bogota

first: Juan

middle: Manuel

last: Anzola

state: Bogota

country: Colombia

institute: CorpoGen

description:
NRP2_F_RPKM
Total RNA then removal or ribosomal

data_processing:
Trimming with Trimmomatic Q30 in a window of 4 nucleotides, minlength 50 nt.
Reads were mapped against the Mtb H37Rv reference genome (accession number NC 000962.2) using Bowtie v. 0.12.7
Resulting SAM files were used with the Tophat package (Langmead et al., 2009) to compute gene expression, differential gene expression and statistical significance. Gene expression was computed as RPKM (Reads Per Kilobase Million of mapped Reads). Statistical significance was determined on a binary basis between conditions by False Discovery Rate (FDR).
Supplementary_files_format_and_content: RPKM

organism: Mycobacterium tuberculosis

source_name: Bacterial culture

growth_protocol: M. tuberculosis H37Rv was cultured at 37 ºC in Dubos medium (Difco Dubos Broth Base, USA) and supplemented with either: 1) 0.2% dextrose (D) or 2) long chain fatty acids (F) (oleic acid, stearic acid and palmitic acid at a final concentration of 0.001% each). Cultures from exponential phase were subjected to hypoxia as described by Wayne and Hayes (Wayne and Hayes, 1996) and NRP1 and NRP2 phases were determined for each medium (fatty acids or dextrose). A parallel culture supplemented with methylene blue (1.5 μg/mL) was used as an indicator of oxygen depletion to establish NRP stages.

extract_protocol:
RNA from each culture condition (exponential, NRP1 and NRP2 phases) was isolated as follows: cells resuspended in guanidium chloride buffer (6 M guanidinium chloride, 0.1% Tween 80, 1 mM 2-mercaptoethanol, 10 mM EDTA) were lysed mechanically in a FastPrep (Thermo Scientific), nucleic acids were purified using phenol- chloroform- isoamyl alcohol and RNA were selectively precipitated with absolute ethanol and washed three times with Trizol reagent (Invitrogen). RNA integrity was estimated by bioanalyzer (Agilent Technologies) and quantified by Nano-drop ND 1000 (Thermo Scientific).
Total RNA was fragmented, poly A tailing and, end repairing (NEB reagents, USA). Strand-specific labeling was carried out by ligation of a 5´ hybrid DNA-RNA primer, the first strand cDNA synthesis reaction was carried out using Super Script II reverse transcriptase (Invitrogen, USA), Illumina’s poly T primer and dNTPs (20 mM). Illumina adaptors and barcodes were ligated by PCR following manufacturer instructions and pair end sequencing was performed on Illumina HiSeq sequencer.

treatment_protocol: Oxygen was gradually eliminated from an exponential Mtb culture, originally in Dubos medium, with dextrose added as the source of carbon. These conditions allow Mtb to adapt to non-replicating persistence (NRP) 1 and 2 (NRP1 with a remaining of 1% of oxygen and NRP2, with 0.06%). Depending on the conditions of aeration desired, solid caps with latex liners were either loosely or tightly screwed down; in some instances, tightly sealed caps with rubber septa were used to permit addition of reagents by needle without opening the container.

tag: strain

value: Exponential - Stress Hypoxia

tag: agent

value: long chain fatty acids


title: ESC_Nuc_nodox_3 (3)

value: ESC doxycycline-inducible expressing HA-Flag-AGO2


title: Dextrose-NonReplicativePhase2

description:
NRP2_D_RPKM
Total RNA then removal or ribosomal

value: dextrose


title: ESC_Total_nodox_2 (3)

value: Total


title: UM139-2_16

value: scramble guide RNA control and dCas9-VP192


title: ESC_Nuc_nodox_2 (3)

value: Nuc


title: UM139-2_sample2

source_name: untransfected FXS(UM 139-2) hESC cell line

value: none (untransfected)


title: ESC_Nuc_nodox_1 (3)


title: Dextrose-NonReplicativePhase1

description:
NRP1_D_RPKM
Total RNA then removal or ribosomal


title: UM139-2_sample1


title: UM4-6_sample2

source_name: untransfected WT FXS hESCs cell line (UM 4-6)


title: UM4-6_sample1


title: ESC_Nuc_dox_2 (3)


title: FattyAcid-NonReplicativePhase1

description:
NRP1_F_RPKM
Total RNA then removal or ribosomal


title: ESC_Nuc_dox_1 (3)


title: ESC_Total_dox_1 (3)


title: ESC_Nuc_dox_3 (3)


title: WT

city: Boston

first: Alaattin

last: Kaya

state: MA

address: 77 Avenue Louis Pasteur

institute: Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA

description:
Disomic yeast strain
WT.w

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Ensembl build R64-1-1 using Bowtie 2 v2.1.0 with default parameters
Read counts per gene were calculated using Feature Counts
To filter out genes with the low number of reads, only the genes with at least 1 count per million (cpm) in at least half of the strains were retained, resulting in an expression set of 6,059 genes across 32 evolved lines
Filtered data was then subjected to RLE normalization
Differential gene expression analysis was performed using the R package EdgeR, using a FDR of 10%.
Genome_build: Ensembl build R64-1-1
Supplementary_files_format_and_content: tab-delimited tsv file include normalized  count values per gene for each Sample ...

organism: Saccharomyces cerevisiae W303

source_name: transcriptome  of W303

growth_protocol: 5 mL cells were grown at 30 oC to mid log phase and frozen immediately after centrifugation

extract_protocol:
We used epicentre masterpure yeast RNA purification kit for total RNA isolation
Cell-Seq method was used to generate transcriptome libraries; poly-A selection

tag: ploidy

value: wildtype

tag: background genetic strain


title: D16-3

description:
Disomic yeast strain
D16.3

source_name: transcriptome  of chromosome XVI disomic yeast strain, evolved line 3

value: Disomes


title: MT_Cyto (2)

data_processing:
Illumina high-seq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using PARalyzer
normalized reads and clusters were combined in a .xls file
Genome_build: mm10
Supplementary_files_format_and_content: PARalyzer output

source_name: C2C12 2 Day Myotubes

growth_protocol: ESC were grown on 0.1% gelatin in DMEM supplemented with 15% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1mM Sodium Pyruvate and 1000 U/ml recombinant leukemia inhibitory factor. C2C12 2day MTs were grown in DMEM supplemnted with 2% horse serum 1% Insuline-Transferrin-Selenium.

extract_protocol:
ESC and MT cells were fractinated into cytoplasmic and nulcear fractions and lysates was clarified by centrifugation. First RNase T1 was followed by immunoprecipitation with FLAG-M2 antibody (ESC) or Pan-AGO Affinity Peptide (MT). After washing, second RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was radioactively 5´end-labeled using l T4 PNK and 32P-γ-ATP. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, small RNA cDNA library preparation was performed.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 15 h before cell harvesting, transgene expression was induced with 2.5 ug/ml doxycycline in ESC. Cells were crosslinked with 312 nm UV-light for 5 min

value: cells differentiate from Myoblast to Myotubes

value: Cyto

value: PAN-AGO affinity peptide


title: MT_Nucl (2)

value: Nucl


title: D16

description:
Disomic yeast strain
D16.a

source_name: transcriptome  of chromosome XVIdisomic yeast strain


title: ESC_Nucl (2)

value: ESCs doxycycline-inducible expressing HA-Flag-AGO2

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse (Sigma-Aldrich, catalog# M8823)


title: ESC_Cyto (2)


title: D15-2

description:
Disomic yeast strain
D15.2

source_name: transcriptome  of chromosome XV disomic yeast strain, evolved line 2


title: ESC_NLS_Day6_1 (1)

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
Log2fold change of "noDox_day6" vs "Dox_Day6" or "NLS_Day6" or "E14_Day6"  was extracted by Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs and Log2fold change of RPKMs

growth_protocol: ESC were grown on 0.1% gelatin in DMEM supplemented with 15% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1mM Sodium Pyruvate and no recombinant leukemia inhibitory factor.

extract_protocol:
RNA was extracted by lysing the whole cell in TRIzol
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion

treatment_protocol: transgene expression was induced with 2.5 ug/ml doxycycline in ESC daily and LIF withdrawal for 6 days

value: ESC AGO1-4-/- expressing only NLS-AGO2 (called NLS)


title: D15

description:
Disomic yeast strain
D15.a

source_name: transcriptome  of chromosome XV disomic yeast strain


title: cDNA  mog1 on filters V11-L1

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
p_RA_mog1
cDNA labelling for mog1Δ strain, representing 3 replicates
The raw data files  TRA_mog1_1.txt, RA_mog1_2.txt, and RA_mog1_3.txt conatins raw data for three replicates cDNA1  mog1 on filter V11-L1-13, cDNA1  mog1 on filter V11-L1-16, cDNA1  mog1 on filter V11-L1-14 samples, respectively.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Typhoon FLA7000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Deviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines present in each probe-coding strand as described in García-Martinez et al 2004.

organism: Saccharomyces cerevisiae

source_name: cDNA  mog1

label_protocol: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC to 0.5 OD600. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain background

tag: genotype/variation


title: ESC_NLS_Day6_2 (1)

tag: cells


title: D15-3

description:
Disomic yeast strain
D15.3

source_name: transcriptome  of chromosome XV disomic yeast strain, evolved line 3


title: GRO wt on filters V11-L1

description:
p_GRO_wt
GRO labelling for BY4741 strain, representing 3 replicates
The raw data files  TR_wt_1.txt, TR_wt_2.txt, and TR_wt_3.txt conatins raw data for three replicates GRO1  wt on filter V11-L1-12, GRO2  wt on filter V11-L1-15, GRO3  wt on filter V11-L1-13 samples, respectively.

data_processing: Raw data were pre-processed from image quantization and local background subtracted. Only data above 10% regard to local background was considered.  Processed data are the average that results from Median Absolute Deviation normalization of each replicate using ArrayStat software. The average processed value for each gene was corrected by percentage of uridines present in each probe-coding strand as described in García-Martinez et al 2004.

source_name: GRO  wt

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

value: wt


title: D14-3

description:
Disomic yeast strain
D14.3

source_name: transcriptome  of chromosome XIV disomic yeast strain, evolved line 3


title: cDNA  wt on filters V11-L1

description:
p_RA_wt
cDNA labelling for BY4741 strain, representing 3 replicates
The raw data files  RA_wt_1.txt, RA_wt_2.txt, and RA_wt_3.txt conatins raw data for three replicates cDNA1  wt on filter V11-L1-12, cDNA2  wt on filter V11-L1-15, cDNA3  wt on filter V11-L1-13 samples, respectively.

data_processing: Raw image quantization with background subtracted and Median Absolute Deviation normalization of each triplicate.The average processed value for each gene was corrected by percentage of guanines present in each probe-coding strand as described in García-Martinez et al. 2004.

source_name: cDNA  wt

label_protocol: cDNA was synthesized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labeling.


title: GRO  mog1 on filters V11-L1

description:
p_GRO_mog1
GRO labelling for mog1Δ strain, representing 3 replicates
The raw data files  TR_mog1_1.txt, TR_mog1_2.txt, and TR_mog1_3.txt conatins raw data for three replicates GRO1  mog1 on filter V11-L1-13, GRO2  mog1 on filter V11-L1-16, GRO3  mog1 on filter V11-L1-14 samples, respectively.

data_processing: Raw data were pre-processed from image quantification and local background subtracted. Only data above 10% regard to local background was considered. Processed data are the average that results from Median Absolute Deviation normalization of each replicate using ArrayStat software. For TR the average processed value for each gene was corrected by percentage of uridines present in each probe-coding strand as described in García-Martinez et al.  2004.

source_name: GRO  mog1


title: ESC_E14_Day6_2 (1)

tag: passages

value: WT E14 ESC


title: D13-3

description:
Disomic yeast strain
D13.3

source_name: transcriptome  of chromosome XIII disomic yeast strain, evolved line 3


title: D13-2

description:
Disomic yeast strain
D13.2

source_name: transcriptome  of chromosome XIII disomic yeast strain, evolved line 2


title: ESC_DOX_Day6_2 (1)

value: ESC doxycycline-inducible expressing HA-Flag-AGO2

value: ESC AGO1-4-/- expressing only AGO2 with doxycycline (called Dox)


title: D14

description:
Disomic yeast strain
D14.a

source_name: transcriptome  of chromosome XIV disomic yeast strain


title: ESC_noDox_Day6_2 (1)

value: ESC AGO1-4-/- (called NoDOX)