title: Sample_132_Severe_Epithelial

source_name: Epithelial brushings gene expression data from severe asthmatic


title: Sample_137_Severe_Spm

status: Public on Oct 02 2017

type: RNA

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: hybridized to Affymetrix HG U133+ PM GeneChips following standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw microarray gene expression data was normalized using RMA in R and subjected to several quality control procedures. Differentially expressed genes were identified using a linear modelling approach in the limma package in R and only genes with FDR corrected p-values < 0.05 for multiple testing (using the Benjamini-Hochberg method) were considered significant.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Induced sputum gene expression data from severe asthmatic

label_protocol: standard Affymetrix protocol; RNA was isolated and reverse transcribed into cDNA using a High Capacity cDNA Reverse Transcription Kit with random hexamers. RT-qPCR was performed for each gene target in duplicate using Taqman Universal PCR Master Mix, No AmpErase UNG on 7900HT Fast Real-Time PCR System. GAPDH was used as a normalizer to obtain fold changes and t-tests were performed to determine significance. Thermal cycling conditions were 95˚C for 10 minutes followed by 40 cycles of 95˚C for 15 seconds and 60˚C for 1 minute.

growth_protocol: sample collection: Lung samples were obtained by hypertonic-saline sputum induction, bronchoscopy, bronchoalveolar lavage and endobronchial epithelial brushing as previously described (Hinks et al., 2015).

extract_protocol: RNA was isolated from the samples using the Absolutely RNA Nanoprep Kit. RNA quality was assessed using a Bioanalyzer 2100 and samples were hybridized to Affymetrix HG U133+ PM GeneChips

tag: Sex

value: F

tag: age (yrs)

tag: acq

tag: smoking

value: Never

tag: allergic rhinitis

value: Yes

tag: nasal polyps

value: No

tag: ics dose

tag: ocs dose

tag: fvc

tag: reversibility

tag: gina control


title: Sample_136_Severe_Epithelial


title: Sample_139_Severe_Spm

value: Former


title: Sample_134_Severe_Epithelial

value: Current


title: Sample_124_Severe_BAL

source_name: Bronchoalveolar lavage gene expression data from severe asthmatic


title: Sample_143_Severe_Spm


title: Sample_130_Severe_Epithelial


title: Sample_127_Severe_Epithelial


title: Sample_131_Severe_Epithelial


title: Sample_133_Severe_Epithelial

value: M


title: Sample_125_Severe_BAL


title: Sample_135_Severe_Epithelial


title: Sample_119_Severe_BAL


title: Sample_117_Severe_BAL


title: Sample_120_Severe_BAL


title: Sample_128_Severe_Epithelial


title: Sample_121_Severe_BAL


title: Sample_126_Severe_Epithelial


title: Sample_116_Severe_BAL


title: Sample_118_Severe_BAL


title: Sample_129_Severe_Epithelial


title: Sample_123_Severe_BAL


title: Sample_114_Moderate_Spm

source_name: Induced sputum gene expression data from moderate asthmatic


title: Sample_122_Severe_BAL


title: Sample_113_Moderate_Spm


title: Sample_110_Moderate_Spm


title: Sample_105_Moderate_Epithelial

source_name: Epithelial brushings gene expression data from moderate asthmatic


title: Sample_98_Moderate_Epithelial


title: Sample_99_Moderate_Epithelial


title: Sample_111_Moderate_Spm


title: Sample_104_Moderate_Epithelial


title: Sample_112_Moderate_Spm


title: Sample_107_Moderate_Epithelial


title: Sample_108_Moderate_Epithelial


title: Sample_103_Moderate_Epithelial


title: Sample_101_Moderate_Epithelial


title: Sample_89_Moderate_BAL

source_name: Bronchoalveolar lavage gene expression data from moderate asthmatic


title: Sample_88_Moderate_BAL


title: Sample_115_Severe_BAL


title: Sample_87_Moderate_BAL


title: Sample_93_Moderate_BAL


title: Sample_109_Moderate_Spm


title: Sample_92_Moderate_BAL


title: Sample_100_Moderate_Epithelial


title: Sample_97_Moderate_Epithelial


title: Sample_96_Moderate_Epithelial


title: Sample_94_Moderate_BAL


title: Sample_90_Moderate_BAL


title: Sample_106_Moderate_Epithelial


title: Sample_86_Moderate_BAL


title: Sample_102_Moderate_Epithelial


title: Sample_95_Moderate_BAL


title: Sample_91_Moderate_BAL


title: Sample_85_Moderate_BAL


title: Sample_82_Moderate_BAL


title: Sample_84_Moderate_BAL


title: Sample_80_Mild_Spm

source_name: Induced sputum gene expression data from mild asthmatic


title: Sample_83_Moderate_BAL


title: Sample_74_Mild_Spm


title: Sample_75_Mild_Spm


title: Sample_70_Mild_Epithelial

source_name: Epithelial brushings gene expression data from mild asthmatic


title: Sample_76_Mild_Spm


title: Sample_81_Mild_Spm


title: Sample_71_Mild_Epithelial


title: Sample_78_Mild_Spm


title: Sample_73_Mild_Spm


title: Sample_63_Mild_Epithelial


title: Sample_62_Mild_Epithelial


title: Sample_68_Mild_Epithelial


title: Sample_57_Mild_BAL

source_name: Bronchoalveolar lavage gene expression data from mild asthmatic


title: Sample_60_Mild_Epithelial


title: Sample_67_Mild_Epithelial


title: Sample_61_Mild_Epithelial


title: Sample_77_Mild_Spm


title: Sample_79_Mild_Spm


title: Sample_72_Mild_Spm


title: Sample_69_Mild_Epithelial


title: Sample_58_Mild_Epithelial


title: Sample_66_Mild_Epithelial


title: Sample_65_Mild_Epithelial


title: Sample_64_Mild_Epithelial


title: Sample_56_Mild_BAL


title: Sample_59_Mild_Epithelial


title: Sample_53_Mild_BAL


title: Sample_43_Healthy_Spm

source_name: Induced sputum gene expression data from healthy control


title: Sample_42_Healthy_Spm


title: Sample_44_Mild_BAL


title: Sample_49_Mild_BAL


title: Sample_48_Mild_BAL


title: Sample_55_Mild_BAL


title: Sample_45_Mild_BAL


title: Sample_47_Mild_BAL


title: Sample_52_Mild_BAL


title: Sample_54_Mild_BAL


title: Sample_37_Healthy_Spm


title: Sample_51_Mild_BAL


title: Sample_39_Healthy_Spm


title: Sample_46_Mild_BAL


title: Sample_34_Healthy_Spm


title: Sample_36_Healthy_Spm


title: Sample_50_Mild_BAL


title: Sample_33_Healthy_Epithelial

source_name: Epithelial brushings gene expression data from healthy control


title: Sample_32_Healthy_Epithelial


title: Sample_29_Healthy_Epithelial


title: Sample_35_Healthy_Spm


title: Sample_38_Healthy_Spm


title: Sample_40_Healthy_Spm


title: Sample_30_Healthy_Epithelial


title: Sample_28_Healthy_Epithelial


title: Sample_26_Healthy_Epithelial


title: Sample_27_Healthy_Epithelial


title: Sample_41_Healthy_Spm


title: Sample_25_Healthy_Epithelial


title: Sample_14_Healthy_BAL

source_name: Bronchoalveolar lavage gene expression data from heatlhy control


title: Sample_16_Healthy_Epithelial


title: Sample_15_Healthy_BAL


title: Sample_31_Healthy_Epithelial


title: Sample_17_Healthy_Epithelial


title: Sample_19_Healthy_Epithelial


title: Sample_24_Healthy_Epithelial


title: Sample_12_Healthy_BAL


title: Sample_23_Healthy_Epithelial


title: Sample_10_Healthy_BAL


title: Sample_20_Healthy_Epithelial


title: Sample_8_Healthy_BAL


title: Sample_4_Healthy_BAL


title: Sample_3_Healthy_BAL


title: Sample_11_Healthy_BAL


title: Sample_21_Healthy_Epithelial


title: Sample_5_Healthy_BAL


title: Sample_18_Healthy_Epithelial


title: Sample_13_Healthy_BAL


title: Sample_1_Healthy_BAL


title: Sample_22_Healthy_Epithelial


title: Sample_6_Healthy_BAL


title: Sample_7_Healthy_BAL


title: Sample_2_Healthy_BAL


title: bCat 2139

status: Public on Aug 23 2017

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

description: β-catΔEx3 mouse liver tissue

hyb_protocol: Labeled RNA was hybridized to arrays using the standard Agilent 1-color gene expression hybridization and wash protocol

scan_protocol: Arrays were scanned on an Agilent G2505C Microarray Scanner at 3 micron resolution

data_processing: Images were processed using the Agilent Feature Extraction software version 10.7.1.1. Control features were removed first and then remaining features for each probe  log2 transformed, and quantile normalized.

organism: Mus musculus

source_name: liver tissue

label_protocol: Total RNA was labeled with Cy3 using the Agilent One-Color Quick Amp Labeling Protocol

extract_protocol: RNA was isolated by us using RNA STAT-60 (AMSBIO),  followed by chloroform extraction and ethanol precipitation.

treatment_protocol: No treatment

tag: strain

value: A hybrid strain consisting of predominantly B6SJL and a minor contribution of 129S6

tag: gemder

value: male

tag: mut status

tag: age

tag: tissue

value: liver


title: bCat 2189

description: β-catΔEx3 mouse liver tissue

value: 30 days


title: bCat 2138

description: β-catΔEx3 mouse liver tissue


title: Diploid_34_35

status: Public on Jul 06 2017

type: SRA

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

library_source: genomic

data_processing:
Standard Illumina base-calling pipeline.
Sequence processing pipeline  Paired-end reads of sequencing batches were de-multiplexed to single cell datasets based on the two 8 bp unique identification tags attached to each cell during the Tn5-transposase tagmentation. Reads lacking a perfect match were discarded. Reads were broken down to segments on their matches to the MboI recognition site (GATC), concatenating segments shorter than 16 bp with their adjacent segment. Each segment was independently mapped to the Mus Musculus genome (assembly mm9) using Bowtie2 in end-to-end alignment mode. The uniquely mapped (MAPQ > 36) segments from each paired-end read were consolidated into a chain of segments by merging segments mapped to overlapping genomic regions. Next, the segments chain was translated to a chain of fragment-ends (fends) by associating each segment with its downstream fend. Finally, adjacent fend pairs from all chains were used to comprise the contact map of the cell. All the analysis following used the distinct contacts, ignoring the number of times each contact appeared in the map.
Genome_build: mm9
Supplementary_files_format_and_content: 2i_diploids_features_table.txt: Text summary table for the 2i diploid samples (the column names are self-explanatory, given one reads the methods)
Supplementary_files_format_and_content: haploids_features_table.txt: Text summary table for the haploid samples (the column names are self-explanatory, given one reads the methods)
Supplementary_files_format_and_content: serum_diploids_features_table.txt: Text summary table for the serum diploids samples (the column names are self-explanatory, given one reads the methods)

molecule: genomic DNA

source_name: Diploid F1 Mus musculus hybrid ESC cell line from an intercross of 129/SV-Jae and castaneus

growth_protocol: Two mouse ESC lines were used. One diploid F1 hybrid ESC from an intercross of Mus musculus 129/SV-Jae and Mus musculus castaneus (129 x Castaneus, a gift from Joost Gribnau) and one haploid ESC20 (H129-1; ECACC 14040203, gift from Martin Leeb and Anton Wutz) were grown either in 2i medium without feeder cells or ES-DMEM with fetal bovine serum (FBS) on feeder cells21. Both cells lines were tested for mycoplasma contamination.

extract_protocol:
For harvesting ESCs from cultures on feeder cells, the feeder cells were depleted using Feeder Removal MicroBeads (Miltenyi Biotec), followed by fixation and permeabilisation of the enriched ESCs and staining for Oct-3/4-immunoreactivity as described below, and Oct-3/4-positive cells were collected by Fluorescence-activated cell sorting (FACS), were ready for subsequent Hi-C processing.    To fix the cells, 50 to 200 million ESCs were suspended in relevant medium and fixed for 10 min by adding formaldehyde at a final concentration of 2% at room temperature before quenching with 127 mM glycine for 5 min on ice. The cells were washed with PBS and permeabilised in 10 mM Tris-HCl (pH 8), 10 mM NaCl, 0.2% IGEPAL CA-630 with cOmplete EDTA-free protease inhibitor cocktail (Roche) for 30 min on ice with intermittent agitation, and spun to collect the nuclei pellet, which was ready for Hi-C processing.    To enrich for specific cell types before the Hi-C process, cells were blocked with PBS-FT (5% FBS, 0.1% Tween-20 in PBS) at room temperature for 1 hr, incubated with a primary antibody in PBS-FT as required (anti-Oct3/4, Santa-Cruz sc-5279, at 1:100 dilution; or anti-Geminin, Abcam 175799 at 1:400 dilution) for 1 hr on ice. Samples were then washed with PBS-FT, and incubated with the secondary antibodies (Alexa Fluor 647-anti-mouse IgG, Thermo Fisher A-31571, or Alexa Fluor 555-anti-rabbit IgG, Thermo Fisher A-21428) for 30 min on ice, washed with 2% FBS in PBS, stained with Hoechst 33342 at the final concentration of 15 µg/ml and subjected to FACS by Influx (BD Biosciences) to collect nuclei cells of interest.
Hi-C processing  The cells (approximately half million to several million) were washed with 1.24 x NEBuffer 3 (New England Biolabs; 62 mM Tris-HCl [pH 7.9], 124 mM NaCl, 12.4 mM MgCl2, 1.24 mM DTT) and suspended in 400 µl of 1.24 x NEBuffer 3. Six µl of 20% SDS was added and incubated at 37˚C for 60 min with constant agitation, then 40 µl of 20% Triton X-100 was added and incubated at 37˚C for 60 min with constant agitation. Next, 50 µl of 25 U/µl Mbo I (New England Biolabs) was added and incubated at 37˚C overnight with constant agitation. To label the digested DNA ends, 1.56 µl of 10 mM dCTP, 1.56 µl of 10 mM dGTP, 1.56 µl of 10 mM dTTP, 39 µl of 0.4 mM biotin-14-dATP (Thermo Fisher) and 10.4 µl of 5 U/µl DNA polymerase I, large (Klenow) fragment (New England Biolabs) were added and incubated at 37˚C for 45 min with occasional mixing. The sample was then spun and supernatant partially removed leaving 50 µl with cells, followed by addition of 100 µl of 10x T4 DNA ligase reaction buffer (New England Biolabs), 10 µl of 100x BSA (New England Biolabs), water and 10 µl of 1 U/µl T4 DNA ligase (Thermo Fisher) were added to make the total volume 1 ml, and incubated at 16˚C overnight. Then the nuclei were passed through a 30 µm cell strainer and single nuclei were sorted into individual empty wells in 96 well plates using an Influx cell sorter. The plates were sealed and stored at -80˚C until further processing.    Single-cell Hi-C library preparation  To prepare single-cell Hi-C libraries from single nuclei in 96 well plate, 5 µl of PBS was added to each well, the plate was sealed and crosslinks reversed by incubating at 65˚C overnight. Hi-C concatemer DNA was fragmented and linked with sequencing adapters using the Nextera XT DNA Library Preparation Kit (Illumina), by adding 10 µl of Tagment DNA Buffer and 5 µl of Amplicon Tagment Mix, incubating at 55˚C for 5 min, then cooling down to 10˚C, followed by addition 5 µl of Neutralize Tagment Buffer and incubation for 5 min at room temperature. Hi-C ligation junctions were then captured by Dynabeads M-280 streptavidin beads (Thermo Fisher; 20 µl of original suspension per single-cell sample). Beads were prepared by washing with 1 x BW buffer (5 mM Tris-Cl pH 7.5, 0.5 mM EDTA, 1 M NaCl), resuspended in 4 x BW buffer (20 mM Tris-Cl pH 7.5, 2 mM EDTA, 4 M NaCl; 8 µl per sample), and then mixed with the 25 µl sample and incubated at room temperature overnight with gentle agitation. Using a Bravo automated liquid handling system (Agilent Technologies), the beads were then washed four times with 200 µl of 1 x BW buffer, twice with 200 µl of 10 mM Tris-Cl pH 7.5 at room temperature, and resuspended in 25 µl of 10 mM Tris-Cl pH 7.5. Single-cell Hi-C libraries were amplified from the beads by adding 15 µl of Nextera PCR Master Mix, 5 µl of Index 1 primer of choice and 5 µl of Index 2 primer of choice. Samples were then incubated at 72˚C for 3 min, 95˚C for 30 sec followed by the thermal cycling at 95˚C for 10 sec, 55˚C for 30 sec and 72˚C for 30 sec for 12 or 18 cycles, then incubated at 72˚C for 5 min. The supernatant was separated from the beads, and the 96 supernatants from a 96 well plate that had 12 cycles of amplification were combined together whereas the supernatants from 18 cycles of amplification were processed uncombined. The combined or uncombined supernatant was purified with AMPure XP beads (Beckman Coulter; 0.6 times volume of the supernatant) according to manufacturer's instructions and eluted with 10 mM Tris-Cl pH 8.5 (100 µl when 96 samples were combined; 30 µl when sample was uncombined). The eluate was purified once more with AMPure XP beads (equal volume to the previous eluate) and eluted with 11 µl of 10 mM Tris-Cl pH 8.5.

tag: sample type


title: Diploid_32_33

value: Diploid F1 Mus musculus hybrid ESC cell line from an intercross of 129/SV-Jae and castaneus


title: Diploid_28_29


title: Diploid_30_31


title: Diploid_27


title: bCatMyc 2185

description: β-catΔEx3:Myc mouse liver tissue

value: 29 days


title: WT 2130

description: WT mouse liver tissue

value: WT


title: Sample_9_Healthy_BAL

tag: Sex


title: Haploid_6

data_processing:
Library strategy: HiC-seq
Standard Illumina base-calling pipeline.
Sequence processing pipeline  Paired-end reads of sequencing batches were de-multiplexed to single cell datasets based on the two 8 bp unique identification tags attached to each cell during the Tn5-transposase tagmentation. Reads lacking a perfect match were discarded. Reads were broken down to segments on their matches to the MboI recognition site (GATC), concatenating segments shorter than 16 bp with their adjacent segment. Each segment was independently mapped to the Mus Musculus genome (assembly mm9) using Bowtie2 in end-to-end alignment mode. The uniquely mapped (MAPQ > 36) segments from each paired-end read were consolidated into a chain of segments by merging segments mapped to overlapping genomic regions. Next, the segments chain was translated to a chain of fragment-ends (fends) by associating each segment with its downstream fend. Finally, adjacent fend pairs from all chains were used to comprise the contact map of the cell. All the analysis following used the distinct contacts, ignoring the number of times each contact appeared in the map.
Genome_build: mm9

source_name: Haploid ESC20 (H129-1; ECACC 14040203) Mus musculus hybrid ESC cell line

value: ESC20 (H129-1; ECACC 14040203) hybrid ESC cell line


title: Haploid_18


title: Haploid_14


title: Haploid_7


title: Diploid_8

value: ESC cell line from an intercross of 129/SV-Jae and castaneus


title: Haploid_13


title: Haploid_3


title: Haploid_12


title: Diploid_9


title: Diploid_5_10


title: Haploid_19


title: Haploid_11


title: WT 2188

description: WT mouse liver tissue

value: 31 days


title: Haploid_17


title: bCatMyc 2133

description: β-catΔEx3:Myc mouse liver tissue


title: Haploid_20


title: bCatMyc 2134

description: β-catΔEx3:Myc mouse liver tissue


title: bCatMyc 2142

description: β-catΔEx3:Myc mouse liver tissue


title: Haploid_8


title: Diploid_4


title: Diploid_3


title: WT 2132

description: WT mouse liver tissue


title: Diploid_26


title: WT 2131

description: WT mouse liver tissue


title: Diploid_24


title: Diploid_25


title: Diploid_7


title: Diploid_23


title: Diploid_22


title: Diploid_19


title: Haploid_16


title: Diploid_2_14


title: Diploid_13


title: Diploid_1_6


title: Diploid_21


title: Diploid_15_16_17_18


title: Haploid_10


title: Haploid_15


title: Haploid_2


title: Haploid_9


title: Haploid_5


title: Haploid_4


title: Diploid_11


title: Diploid_12


title: Haploid_1


title: ctrl_24hr_2

status: Public on Feb 14 2017

description: Control 24hr-2

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC300 scanner 7G.

data_processing: Data was generated by using the robust multi-array average (RMA) expression measure implemented in R, directly processed from CEL files

source_name: primary MEFs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary MEFs were harvested from day 15.5 embryos of pregnant C57BL6/J female mice, plated (passage 0), expanded for 2 passages, growing cells in DMEM supplemented with 10% inactivated FBS plus antibiotics in a 37°C humidified incubator at 5% O2 and 95% CO2 atmosphere. Cells were kept and treated in the exponential phase of growing (60-70% confluence).

extract_protocol: RNA was harvested using the RNeasy protocol (Qiagen) and the purity of prepared RNA was determined using Agilent 2100 BioAnalyzer.

treatment_protocol: MMS exposure was 40 µg/mL final concentration in fresh medium.

value: mouse embryonic fibroblasts

tag: treatment

value: control

tag: time period

tag: replicate


title: ctrl_72hr_2

description: Control 72hr-2


title: mms_24hr_3

description: MMS 24hr-3

value: mms


title: ctrl_24hr_4

description: Control 24hr-4


title: mms_24hr_1

description: MMS 24hr-1


title: ctrl_8hr_1

description: Control 8hr-1


title: mms_1hr_2

description: MMS 1hr-2


title: ctrl_72hr_1

description: Control 72hr-1


title: mms_8hr_3

description: MMS 8hr-3


title: ctrl_72hr_4

description: Control 72hr-4


title: ctrl_24hr_1

description: Control 24hr-1


title: mms_1hr_4

description: MMS 1hr-4


title: ctrl_8hr_2

description: Control 8hr-2


title: mms_72hr_2

description: MMS 72hr-2


title: mms_72hr_1

description: MMS 72hr-1


title: mms_24hr_4

description: MMS 24hr-4


title: ctrl_72hr_3

description: Control 72hr-3


title: ctrl_24hr_3

description: Control 24hr-3


title: mms_24hr_2

description: MMS 24hr-2


title: mms_8hr_2

description: MMS 8hr-2


title: ctrl_8hr_3

description: Control 8hr-3


title: ctrl_1hr_4

description: Control 1hr-4


title: ctrl_1hr_2

description: Control 1hr-2


title: mms_8hr_1

description: MMS 8hr-1


title: ctrl_8hr_4

description: Control 8hr-4


title: mms_1hr_1

description: MMS 1hr-1


title: mms_72hr_3

description: MMS 72hr-3


title: ctrl_1hr_3

description: Control 1hr-3


title: mms_1hr_3

description: MMS 1hr-3


title: mms_8hr_4

description: MMS 8hr-4


title: ctrl_1hr_1

description: Control 1hr-1


title: ctrl_72hr_4

description: Control 72hr-4

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix fluidics station 450.

organism: Drosophila melanogaster

source_name: KC167 cells

growth_protocol: Kc167 cells were grown cells in Schneider's media supplemented with 10% inactivated FBS plus antibiotics in a 22°C humidified incubator. Cells were kept and treated in the exponential phase of growing (60-70% confluence).


title: droso_72hr_1

description: MMS 72hr-1


title: ctrl_0hr_3

description: Control 0hr-3


title: ctrl_0hr_4

description: Control 0hr-4


title: droso_24hr_2

description: MMS 24hr-2


title: droso_8hr_4

description: MMS 8hr-4


title: ctrl_0hr_2

description: Control 0hr-2


title: ctrl_0hr_1

description: Control 0hr-1


title: droso_8hr_3

description: MMS 8hr-3


title: droso_24hr_3

description: MMS 24hr-3


title: ctrl_24hr_4

description: Control 24hr-4


title: droso_24hr_1

description: MMS 24hr-1


title: droso_72hr_2

description: MMS 72hr-2


title: droso_72hr_4

description: MMS 72hr-4


title: ctrl_8hr_2

description: Control 8hr-2


title: droso_24hr_4

description: MMS 24hr-4


title: droso_8hr_1

description: MMS 8hr-1


title: ctrl_8hr_3

description: Control 8hr-3


title: ctrl_24hr_3

description: Control 24hr-3


title: ctrl_8hr_4

description: Control 8hr-4


title: droso_1hr_4

description: MMS 1hr-4


title: ctrl_72hr_3

description: Control 72hr-3


title: ctrl_24hr_1

description: Control 24hr-1


title: ctrl_24hr_2

description: Control 24hr-2


title: ctrl_72hr_2

description: Control 72hr-2


title: droso_8hr_2

description: MMS 8hr-2


title: ctrl_8hr_1

description: Control 8hr-1


title: ctrl_72hr_1

description: Control 72hr-1


title: droso_72hr_3

description: MMS 72hr-3


title: droso_1hr_3

description: MMS 1hr-3


title: droso_1hr_2

description: MMS 1hr-2


title: droso_1hr_1

description: MMS 1hr-1


title: ctrl_0hr_4

description: Control 0hr-4


title: ctrl_1hr_4

description: Control 1hr-4


title: ctrl_1hr_2

description: Control 1hr-2


title: ctrl_0hr_2

description: Control 0hr-2


title: ctrl_0hr_3

description: Control 0hr-3


title: ctrl_1hr_3

description: Control 1hr-3


title: ctrl_1hr_1

description: Control 1hr-1


title: ctrl_0hr_1

description: Control 0hr-1


title: KUL_patient_81

status: Public on Dec 31 2016

city: Brussels

first: Sylvain

last: Brohée

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

description: HER2 breast tumor patient treated with adjuvant trastuzumab

hyb_protocol: After purification of the aRNA, 12.5 μg were fragmented and labeled prior to hybridization to the HG-U133_Plus_2 chips.

scan_protocol: GeneChips were scanned using the GeneChip Scanner by Affymetrix.

data_processing: The data were analyzed with R-Bioconductor statistical suite. Data were normalized using the fRMA function (affy and fRMA packages)

molecule: polyA RNA

source_name: HER2 breast tumor sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using TRIzol (Life Technologies, Carlsbad, California) following the manufacturer’s instructions. RNA concentration was measured using the NanoDrop 1000 (Thermo Scientific, Waltham, Massachusetts), and RNA integrity (RIN: RNA Integrity Number) was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California).

value: HER2 breast cancer tumor

value: trastuzumab

tag: tumor size

tag: nodes positive

tag: er status

tag: pgr status

tag: distant metastasis

tag: time to ddfs

tag: intratumoral lymphocytic infiltration

tag: stromal lymphocytic infiltration


title: KUL_patient_79


title: IJB_patient_11


title: KUL_patient_77


title: IJB_patient_2


title: KUL_patient_80


title: KUL_patient_78


title: IJB_patient_8


title: IJB_patient_9


title: IJB_patient_4


title: IJB_patient_5


title: IJB_patient_1


title: IJB_patient_6


title: IJB_patient_7


title: IJB_patient_3


title: IJB_patient_10


title: KUL_patient_76


title: KUL_patient_75


title: KUL_patient_83


title: KUL_patient_82


title: KUL_patient_69


title: KUL_patient_73


title: KUL_patient_65


title: KUL_patient_68


title: KUL_patient_72


title: KUL_patient_74


title: KUL_patient_66


title: KUL_patient_70


title: KUL_patient_61


title: KUL_patient_62


title: KUL_patient_71


title: KUL_patient_52


title: KUL_patient_67


title: KUL_patient_56


title: KUL_patient_63


title: KUL_patient_45


title: KUL_patient_46


title: KUL_patient_58


title: KUL_patient_57


title: KUL_patient_53


title: KUL_patient_44


title: KUL_patient_49


title: KUL_patient_47


title: KUL_patient_51


title: KUL_patient_43


title: KUL_patient_50


title: KUL_patient_54


title: KUL_patient_60


title: KUL_patient_55


title: KUL_patient_48


title: KUL_patient_59


title: KUL_patient_64


title: KUL_patient_41


title: KUL_patient_40


title: KUL_patient_42


title: KUL_patient_39


title: KUL_patient_37


title: KUL_patient_36


title: KUL_patient_35


title: KUL_patient_28


title: KUL_patient_25


title: KUL_patient_19


title: KUL_patient_32


title: KUL_patient_20


title: KUL_patient_27


title: KUL_patient_31


title: KUL_patient_34


title: KUL_patient_30


title: KUL_patient_38


title: KUL_patient_24


title: KUL_patient_23


title: KUL_patient_33


title: KUL_patient_29


title: KUL_patient_21


title: KUL_patient_14


title: KUL_patient_15


title: KUL_patient_12


title: KUL_patient_18


title: KUL_patient_17


title: KUL_patient_26


title: KUL_patient_11


title: KUL_patient_22


title: KUL_patient_9


title: KUL_patient_8


title: KUL_patient_16


title: KUL_patient_13


title: KUL_patient_10


title: KUL_patient_6


title: KUL_patient_7


title: KUL_patient_5


title: KUL_patient_2


title: KUL_patient_1


title: conditional knockout replicate 3 (E9.5)

status: Public on Aug 23 2016

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

description:
8324341082_F_Grn
fldelcre
1371

hyb_protocol: Hybriidization carried out at Australian Genome Research Facility using standard Illumina protocols

scan_protocol: standard illumina scanning protocol

data_processing: log2 transformed and quantile normalized using tools in GenePattern

source_name: conditional knockout

label_protocol: labelling carried out at Australian Genome Research Facility using standard Illumina protocols

growth_protocol: mouse embryos collected at E9.5

extract_protocol: RNA extracted using QIAGEN RNA micro columns

treatment_protocol: Embryos of four genotypes were collected: Twist1flox/+; Mesp1+/+, Twist1flox/+; Mesp1Cre/+, Twist1flox/del; Mesp1+/+; Twist1flox/del; Mesp1Cre/+

tag: developmental stage

value: embryo

tag: genotype/variation

value: Twist1flox/del; Mesp1Cre/+

value: head

tag: strain

value: C57Bl/6 x 129 x BALB/c


title: conditional knockout replicate 2 (E9.5)

description:
8324341082_E_Grn
fldelcre
1358

tag: age

tag: tissue


title: KUL_patient_3


title: KUL_patient_4


title: control replicate 2 (E9.5)

description:
8324341101_A_Grn
flwt
1503

source_name: control

value: Twist1flox/+; Mesp1+/+


title: control replicate 3 (E9.5)

description:
8324341101_F_Grn
flwt
1519


title: mesoderm het replicate 2 (E9.5)

description:
8324341085_C_Grn
flwtcre
1432

source_name: mesoderm het

value: Twist1flox/+; Mesp1Cre/+


title: mesoderm het replicate 1 (E9.5)

description:
8324341085_B_Grn
flwtcre
1431


title: het replicate 3 (E9.5)

description:
8324341085_F_Grn
fldel
1501

source_name: het

value: Twist1flox/del; Mesp1+/+


title: conditional knockout replicate 1 (E9.5)

description:
8324341082_D_Grn
fldelcre
1342


title: mesoderm het replicate 3 (E9.5)

description:
8324341101_D_Grn
flwtcre
1513


title: het replicate 1 (E9.5)

description:
8324341082_C_Grn
fldel
1340


title: het replicate 4 (E9.5)

description:
8324341101_C_Grn
fldel
1506


title: het replicate 2 (E9.5)

description:
8324341085_A_Grn
fldel
1372


title: mesoderm het replicate 4 (E9.5)

description:
8324341101_E_Grn
flwtcre
1515


title: conditional knockout replicate 4 (E9.5)

description:
8324341101_B_Grn
fldelcre
1505


title: control replicate 1 (E9.5)

description:
8324341085_E_Grn
flwt
1437


title: isolated cranial mesoderm replicate 2

description:
9249051083_E_Grn
replicate 2
MESP1-4A

source_name: isolated cranial mesoderm

label_protocol: RNA extracted from GFP-positive cell populations was amplified using the Illumina TotalPrep RNA Amplification Kit (Ambion) and labelled using the MessageAmp II aRNA Kit (RNA Amplification for Array Analysis, Ambion). Subsequently the cDNA was purified with columns for the MessageAmp II aRNA Kit. In vitro transcription and labelling was performed with Illumina TotalPrep. The biotin labelled cRNA was purified using Illumina TotalPrep columns according to manufacturer’s instructions.

treatment_protocol: Cranial neural crest cells isolated from Wnt1-Cre x Z/EG embryos by flow sorting for GFP positive cells. Cranial mesoderm isolated from Mesp1-Cre x Z/EG embryos by flow sorting for GFP positive cells

tag: cross

value: Mesp1-Cre x Z/EG

value: isolated cranial mesoderm

value: C57Bl/6 x 129 x ARC/s


title: conditional knockout replicate 4 (E8.5)

description:
8324341082_B_Grn
fldelcre
fldelcre 4

growth_protocol: mouse embryos collected at E8.5


title: conditional knockout replicate 3 (E8.5)

description:
8324341082_A_Grn
fldelcre
fldelcre 3


title: conditional knockout replicate 2 (E8.5)

description:
8324341069_F_Grn
fldelcre
fldelcre 2


title: isolated cranial mesoderm replicate 1

description:
9249051083_D_Grn
replicate 1
MESP1-2_4


title: isolated cranial mesoderm replicate 3

description:
9249051083_F_Grn
replicate 3
MESP1-5


title: isolated cranial neural crest replicate3

description:
9249051083_C_Grn
replicate 3
WNT1-6

source_name: isolated cranial neural crest

value: Wnt1-Cre x Z/EG

value: isolated cranial neural crest


title: isolated cranial neural crest replicate 2

description:
9249051083_B_Grn
replicate 2
WNT1-5


title: isolated cranial neural crest replicate 1

description:
9249051083_A_Grn
replicate 1
WNT1_4


title: conditional knockout replicate 1 (E8.5)

description:
8324341069_E_Grn
fldelcre
fldelcre 1


title: dhawY17P5_m_rg_R1

status: Public on Jun 01 2016

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: single-species RNA preparation;

library_source: transcriptomic

data_processing:
We performed single-end 76 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer.  De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2.  For each mixed sample, the RNA-seq reads were first mapped to a merged genome and annotation including D. grimshawi (dgri_caf1 assembly; Drosophila_grimshawi.GCA_000005155.1.29.dna_sm.genome.fa), D. melanogaster (FlyBase release 6 version 04 ; FlyBase file: dmel-all-chromosome-r6.04.fasta), and A. stephensi (Anopheles-stephensi-Indian_SCAFFOLDS_AsteI2.fa), appended with ERCC sequences (Jiang et al., Genome Research, 2011, PMID 21816910) using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886). Errors in the original beta-ERCC annotation were corrected.  Specifically, the ERCC-00009, ERCC-00014, ERCC-00057, ERCC-00059, ERCC-00099, ERCC-00108, ERCC-00116 were strand-corrected from ERCC_reference.fa, and ERCC-00085 was re-identified as Subpool C.  The unmapped reads and reads mapping to D. melanogaster or A. stephensi are not reported here or in the associated SRA entry.  For each chromosome or scaffold in the merged annotation, we add a four letter prefix to identify the species (e.g., scaffold_15110 => dgri_ scaffold_15110) for bam file parsing using SAMtools (v0.1.19) (Li et al., 2009, PMID 19505943).  We used an in-house python script to fetch the uniquely mapped reads and species-specific multihit reads (2-10 hits) in bam format. We reconverted bam files for each species to raw read fastq files using BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID 20110278).
After this step, reads of each multi-species sample were split into three categories based on the mapped genome- D. grimshawi, ERCC, and leftover, which includes unmapped reads, reads mapped to multiple species (or multiple species plus ERCC), and reads mapped to either D. melanogaster or A. stephensi. For multi-species samples, the original fastq file can be restored by merging the reads of D. grimshawi as well as the ERCC and leftover reads. We provide both STAR (SRR3355*) and HiSAT2 (SRR724* & SRR725*) fastq files in this GEO entry. We provided associated gene-level read count files based on HiSAT2 alignments, and the read count files have both FlyBase version (*htseq_reverse.HiSAT2.FB.txt) and YO version (*htseq_reverse.HiSAT2.YO.txt) in Supplementary files of this GEO. For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level overlap (Jaccard index) between YO gene ID and FlyBase gene ID. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.

organism: Drosophila hawaiiensis

source_name: Other reproductive tract plus genitalia

growth_protocol: All lines were originated from a single wild-caught female (iso-female line) and were reared at the Hawaiian Drosophila Research Stock Center.  For D. grimishawi, the G1 strain was isolated from the Auwahi dry forest of East Maui in July 1965, the ZA27Z2 and ZA27Z3 strains were isolated from the Makawao Forest Reserve of East Maui in March 2010, and Mo010 strain was isolated from the southeast of Kawela Gulch of Molokai Island in December 2010, and Wm1041 strain was isolated from the Iao Valley of West Maui in July 2014. For D. silvestris, Y11R6 strain was isolated from the Olaa Forest Reserve of Hawaii in December 1986, and U26B9 strain was isolated from the Kahuku Ranch of Hawaii in January 1997.  The D. hemipeza strain W40B14 was isolated from the Palikea Ridge of Oahu in July 1983.  The D. heteroneura W48B6 strain was isolated from the base of Hinakapoula of Hawaii in August 1983.  The D. hawaiiensis Y17P5 strain was isolated from Kipuka Ki, Hawaii Volcano National Park in March 1987. 70-100 Flies were grown in gallon glass jars with a 5 cm bed of dry sterile sand.  Flies were fed once a week with five vials containing ~3ml of Yeastless Wheeler Clayton medium (placed horizontally in each jar).  A single batch of this media was prepared with: 16g each of agar, rice cereal, Kellogg’s Special K, and wheat germ powder, plus 400g Gerber’s banana baby food and 1400ml water.  These ingredients were mixed, cooked to boil and cooled.  After cooling (but still liquid), 6ml each of 95% ethanol and propionic acid was added and mixed and then used to fill glass dram vials, which were stored 4oC until needed.  1/5 sheet of folded non-bleached facial tissue paper saturated with a water extract of fermenting Clermontia sp. leaves was added to each vial.  Females of each strain laid eggs onto the tissue.  Vials with eggs were collected weekly.  Eggs hatched in about one week.  Larvae were fed weekly for 2 weeks (as needed based on density of larvae).  The recipe for cornmeal paste larval food was: 800g cornmeal, 100g brewers yeast, 90g soybean meal, 90g agar, 133ml karo syrup, 45g molasses and 4L water.  This mixture was boiled, cooled, and 45ml each of 95% ethanol and propionic acid was added.  The cornmeal paste is mixed with the water extract of fermenting Clermontia sp. leaves.  After 3 weeks the larval tubes were transferred to moist sterile sand jars.  Larvae burrow into the sand for pupation.  Adults eclosed after 6 weeks and were aged for dissection.  Females of all sequenced species began laying eggs around 4 weeks.  Males of some species tend to die much earlier than females, making it problematic to collect sexually mature flies of both sexes at the same age for dissection. All flies were grown at 18oC with a 12h/12h Day/Night cycle.

extract_protocol:
Flies were anesthetized by briefly chilling on a 0oC glass plate.  All samples were dissected in Phosphate Buffered Saline solution pH7.4 and transferred to 112ul of RNA later (Life Technologies, Carlsbad, CA) in 96-well plates at room temperature after being macerated with forceps.  After transport, plates were stored at -80oC.  For D. grimshawi samples, we added 20-30 1.0mm glass beads (BioSpec Products, Bartlesville, OK) to each sample and added 600ul RLT buffer from the RNeasy 96 kit (Qiagen, Valencia, CA) to each well.  We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville, OK). Extraction of total RNA was performed using the RNeasy 96 kit according to manufacturer's guide (spin version), except that we used 712μl of 70% ethanol in each well to dilute the RNAlater and RLT buffer. D. grimshawi RNA was added to D. melanogaster RNA and A. stephensi embryos for homogenization and a second round of RNA extraction using the RNeasy  kit. D. melanogaster and A. stephensi RNAseq will be reported elsewhere. Four head and gonad samples of Wm1041 were split into mixed-species and single-species RNA preparations. All other samples were prepared without mixing with other species using the same RNeasy protocol. RNA was quantified using the Quant-iT RiboGreen quantification kit Life Technologies, Carlsbad, CA).
We used the Truseq PolyA+ and stranded mRNA kit with half volumes (Illumina, San Diego, CA).  100ng total RNA was input for all samples.  We also added 20pg Pool 78A or 78B ERCC spike-ins (Jiang et al., Genome Research, 2011, PMID 21816910) added to the Fragment-Prime-Finish Mix during mRNA fragmentation step.  Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing.

value: Other reproductive tract plus genitalia

tag: Sex

value: Male


title: dhawY17P5_m_rg_R2

description: single-species RNA preparation;


title: dhawY17P5_m_hd_R1

description: single-species RNA preparation;

source_name: Head

value: Head


title: dhawY17P5_m_hd_R2

description: single-species RNA preparation;


title: dhawY17P5_m_go_R2

description: single-species RNA preparation;

source_name: Gonad

value: Gonad


title: dhawY17P5_m_go_R1

description: single-species RNA preparation;


title: dhawY17P5_f_hd_R1

description: single-species RNA preparation;

value: Female


title: dhawY17P5_f_go_R2

description: single-species RNA preparation;


title: dhawY17P5_m_ca_R1

description: single-species RNA preparation;

source_name: Carcass

value: Carcass


title: dhawY17P5_f_hd_R2

description: single-species RNA preparation;


title: dhawY17P5_m_ca_R2

description: single-species RNA preparation;


title: dhawY17P5_f_rg_R1

description: single-species RNA preparation;


title: dhawY17P5_f_go_R1

description: single-species RNA preparation;


title: control replicate 3 (E8.5)

description:
8324341069_C_Grn
flwt
flwt 3

value: embryo


title: het replicate 3 (E8.5)

description:
8324341046_E_Grn
fldel
fldel 3

value: head


title: control replicate 1 (E8.5)

description:
8324341069_A_Grn
flwt
flwt 1

value: C57Bl/6 x 129 x BALB/c


title: control replicate 4 (E8.5)

description:
8324341069_D_Grn
flwt
flwt 4

value: Twist1flox/+; Mesp1+/+


title: dhawY17P5_f_ca_R2

description: single-species RNA preparation;


title: het replicate 1 (E8.5)

description:
8324341046_D_Grn
fldel
fldel 1


title: het replicate 2 (E8.5)

description:
8324341046_F_Grn
fldel
fldel 2


title: dhawY17P5_f_ca_R1

description: single-species RNA preparation;


title: dgriZA27Z3_m_wb_R4

description: mixed-species RNA preparation;

organism: Drosophila grimshawi

source_name: Whole body

value: Whole body


title: dgriZA27Z3_m_wb_R2

description: mixed-species RNA preparation;


title: dgriZA27Z3_m_wb_R3

description: mixed-species RNA preparation;


title: dgriZA27Z3_m_wb_R1

description: mixed-species RNA preparation;


title: dgriZA27Z3_f_wb_R4

description: mixed-species RNA preparation;


title: mesoderm het replicate 2 (E8.5)

description:
8324341046_B_Grn
flwtcre
flwtcre 2

value: Twist1flox/+; Mesp1Cre/+


title: dgriZA27Z2_m_wb_R3

description: mixed-species RNA preparation;


title: dgriZA27Z3_f_wb_R3

description: mixed-species RNA preparation;


title: dgriZA27Z2_m_wb_R4

description: mixed-species RNA preparation;


title: dgriZA27Z2_m_wb_R2

description: mixed-species RNA preparation;


title: dgriZA27Z3_f_wb_R2

description: mixed-species RNA preparation;


title: mtlr_MCMV_S_XCR1+_LT_SetD_2

status: Public on Aug 22 2016

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: infection-matured (total) spleen XCR1+ DC

label_protocol: 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol.

treatment_protocol: Mice were untreated or infected for 1.5 days i.p. with 2.5x10E4 pfu of salivary-gland extracted MCMV Smith strain.

value: spleen

tag: phenotype

tag: cell type

tag: treatment

value: MCMV


title: 231-Control-24hr-1

status: Public on Aug 10 2016

description: Replicate 1, Vehicle

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Illumina GenomeStudio version 1.9.0

source_name: breast cancer cell-line, MDA-MB-231

label_protocol: Standard Ilumina BeadChip labeling protocol

extract_protocol: RNeasy Mini kit (Qiagen), following manufacturer's protocol

treatment_protocol: Cells were treated either with DMSO (0.02%, vehicle control) or Imipramine Blue (IB) at concentration of 5µM in DMSO for additional 24 in CO2 incubator at 37°C.

tag: cell line

value: Vehicle

tag: dosage

tag: time

value: 24 hrs


title: dgriZA27Z2_f_wb_R4

description: mixed-species RNA preparation;

tag: replicate


title: dgriZA27Z2_m_wb_R1

description: mixed-species RNA preparation;


title: dgriZA27Z2_f_wb_R2

description: mixed-species RNA preparation;


title: mesoderm het replicate 3 (E8.5)

description:
8324341046_C_Grn
flwtcre
flwtcre 3


title: dgriWm1041_m_rg_R2

description: mixed-species RNA preparation;


title: dgriZA27Z2_f_wb_R3

description: mixed-species RNA preparation;


title: dgriZA27Z2_f_wb_R1

description: mixed-species RNA preparation;


title: dgriWm1041_m_hd_R1

description: mixed-species RNA preparation;


title: dgriWm1041_m_hd_R2

description: mixed-species RNA preparation;


title: 231-IB-5uM-24hr-2

description: Replicate 2, IB treatment

value: IB

value: 5 uM


title: dgriZA27Z3_f_wb_R1

description: mixed-species RNA preparation;


title: dgriWm1041_f_rg_R2

description: mixed-species RNA preparation;

value: Other reproductive tract plus genitalia


title: 231-IB-5uM-24hr-1

description: Replicate 1, IB treatment


title: dgriWm1041_m_go_R1

description: mixed-species RNA preparation;

value: Male


title: mtlr_MCMV_S_XCR1+_LT_SetD_1

value: infection-matured (total) spleen XCR1+ DC


title: dgriWm1041_f_hd_R2b

description:
single-species RNA preparation;
Processed data file includes data from both GSM2113204 and GSM2113205 (technical replicates).

value: Head

value: Female


title: dgriWm1041_f_rg_R1

description: mixed-species RNA preparation;


title: dgriWm1041_f_hd_R2a

description:
mixed-species RNA preparation;
Technical replicate of sample GSM2113205. Processed data for merged technical replicates available on GSM2113205.


title: dgriWm1041_f_hd_R1b

description:
single-species RNA preparation;
Processed data file includes data from both GSM2113202 and GSM2113203 (technical replicates).


title: 231-Control-24hr-2

description: Replicate 2, Vehicle


title: dgriWm1041_f_hd_R1a

description:
mixed-species RNA preparation;
Technical replicate of sample GSM2113203. Processed data for merged technical replicates available on GSM2113203.


title: dgriWm1041_f_go_R2a

description:
mixed-species RNA preparation;
Technical replicate of sample GSM2113201. Processed data for merged technical replicates available on GSM2113201.

value: Gonad


title: dgriWm1041_f_go_R2b

description:
single-species RNA preparation;
Processed data file includes data from both GSM2113200 and GSM2113201 (technical replicates).


title: dgriWm1041_f_go_R1a

description:
mixed-species RNA preparation
Technical replicate of sample GSM2113199. Processed data for merged technical replicates available on GSM2113199.


title: dgriWm1041_f_go_R1b

description:
single-species RNA preparation;
Processed data file includes data from both GSM2113198 and GSM2113199 (technical replicates).


title: control replicate 2 (E8.5)

description:
8324341069_B_Grn
flwt
flwt 2

value: embryo

value: head


title: dgriWm1041_f_ca_R2

description: mixed-species RNA preparation;

value: Carcass


title: dgriMo010_m_wb_R4

description: mixed-species RNA preparation;

value: Whole body


title: dgriWm1041_f_ca_R1

description: mixed-species RNA preparation;


title: dgriMo010_m_wb_R1

description: mixed-species RNA preparation;


title: mesoderm het replicate 1 (E8.5)

description:
8324341046_A_Grn
flwtcre
flwtcre 1

value: Twist1flox/+; Mesp1Cre/+

value: C57Bl/6 x 129 x BALB/c


title: dgriMo010_f_wb_R1

description: mixed-species RNA preparation;


title: dgriMo010_f_wb_R4

description: mixed-species RNA preparation;


title: dgriMo010_f_wb_R2

description: mixed-species RNA preparation;


title: dgriMo010_f_wb_R3

description: mixed-species RNA preparation;


title: dgriMo010_m_wb_R3

description: mixed-species RNA preparation;


title: dgriG1_m_wb_R3

description: mixed-species RNA preparation;


title: dgriG1_m_wb_R2

description: mixed-species RNA preparation;


title: dgriG1_m_tx_R4

description: mixed-species RNA preparation;

source_name: Thorax

value: Thorax


title: dgriG1_m_tx_R3

description: mixed-species RNA preparation;


title: dgriG1_m_tx_R1

description: mixed-species RNA preparation;


title: dgriG1_m_tx_R2

description: mixed-species RNA preparation;


title: dgriG1_m_re_R4

description: mixed-species RNA preparation;

source_name: Other reproductive tract

value: Other reproductive tract


title: dgriG1_m_re_R3

description: mixed-species RNA preparation;


title: dgriG1_m_re_R2b

description: single-species RNA preparation; Redo sample to replace R2a (GSM2113177; Sample54)


title: dgriG1_m_re_R1

description: mixed-species RNA preparation;


title: dgriG1_m_hd_R4

description: mixed-species RNA preparation;


title: dgriG1_m_wb_R4

description: mixed-species RNA preparation;


title: dgriG1_m_hd_R3

description: mixed-species RNA preparation;


title: dgriG1_m_ge_R4

description: mixed-species RNA preparation;

source_name: Genitalia

value: Genitalia


title: dgriG1_m_hd_R1

description: mixed-species RNA preparation;


title: dgriG1_m_ge_R3

description: mixed-species RNA preparation;


title: dgriG1_m_ge_R2

description: mixed-species RNA preparation;


title: dgriG1_m_ge_R1

description: mixed-species RNA preparation;


title: dgriG1_m_go_R1

description: mixed-species RNA preparation;


title: dgriG1_m_dg_R4

description: mixed-species RNA preparation;

source_name: Digestive system

value: Digestive system


title: dgriG1_m_go_R3

description: mixed-species RNA preparation;


title: dgriG1_m_go_R2

description: mixed-species RNA preparation;


title: dgriG1_m_wb_R1

description: mixed-species RNA preparation;


title: dgriG1_m_go_R4

description: mixed-species RNA preparation;


title: dgriG1_m_dg_R1

description: mixed-species RNA preparation;


title: dgriG1_m_dg_R2

description: mixed-species RNA preparation;


title: dgriG1_m_ac_R4

description: mixed-species RNA preparation;

source_name: Abdomen carcass

value: Abdomen carcass


title: dgriG1_m_ac_R3

description: mixed-species RNA preparation;


title: dgriG1_m_ac_R2

description: mixed-species RNA preparation;


title: dgriG1_m_re_R2a

description:
mixed-species RNA preparation; Spearman correlation with other replicates < 0.9.
Sample not used in analysis. Replaced by GSM2113178.


title: dgriG1_m_ac_R1

description: mixed-species RNA preparation;


title: dgriG1_f_wb_R4

description: mixed-species RNA preparation;


title: dsilY11R6_m_hd_R2

description: single-species RNA preparation;

organism: Drosophila silvestris


title: dsilY11R6_m_hd_R1

description: single-species RNA preparation;


title: dgriG1_f_wb_R3

description: mixed-species RNA preparation;


title: dgriG1_m_hd_R2

description: mixed-species RNA preparation;


title: dgriG1_f_wb_R2

description: mixed-species RNA preparation;


title: dsilY11R6_m_go_R1

description: single-species RNA preparation;


title: dsilY11R6_f_hd_R2

description: single-species RNA preparation;


title: dgriG1_m_dg_R3

description: mixed-species RNA preparation;


title: dsilY11R6_f_hd_R1

description: single-species RNA preparation;


title: dgriG1_f_tx_R4

description: mixed-species RNA preparation;


title: dgriG1_f_wb_R1

description: mixed-species RNA preparation;


title: dsilY11R6_f_go_R2

description: single-species RNA preparation;


title: dgriG1_f_tx_R3

description: mixed-species RNA preparation;


title: dsilU26B9_m_hd_R2

description: single-species RNA preparation;


title: dsilY11R6_f_go_R1

description: single-species RNA preparation;


title: dgriG1_f_re_R3

description: mixed-species RNA preparation;


title: dgriG1_f_tx_R1

description: mixed-species RNA preparation;


title: dgriG1_f_tx_R2

description: mixed-species RNA preparation;


title: dsilU26B9_m_hd_R1

description: single-species RNA preparation;


title: dsilU26B9_m_go_R1

description: single-species RNA preparation;


title: dsilU26B9_m_go_R2

description: single-species RNA preparation;


title: dsilU26B9_f_hd_R2

description: single-species RNA preparation;


title: dgriG1_f_hd_R4

description: mixed-species RNA preparation;


title: dsilU26B9_f_go_R2

description: single-species RNA preparation;


title: dgriG1_f_re_R4

description: mixed-species RNA preparation;


title: dsilU26B9_f_hd_R1

description: single-species RNA preparation;


title: dgriG1_f_hd_R3

description: mixed-species RNA preparation;


title: dgriG1_f_hd_R2

description: mixed-species RNA preparation;


title: dhetW48B6_m_go_R1

description: single-species RNA preparation;

organism: Drosophila heteroneura


title: dgriG1_f_re_R1

description: mixed-species RNA preparation;


title: dsilU26B9_f_go_R1

description: single-species RNA preparation;


title: dgriG1_f_hd_R1

description: mixed-species RNA preparation;


title: dhetW48B6_m_hd_R2

description: single-species RNA preparation;


title: dhetW48B6_f_hd_R2

description: single-species RNA preparation;


title: dhemW40B14_m_hd_R1

description: single-species RNA preparation;

organism: Drosophila hemipeza


title: dgriG1_f_go_R4

description: mixed-species RNA preparation;


title: dhetW48B6_f_hd_R1

description: single-species RNA preparation;


title: dhemW40B14_m_go_R2

description: single-species RNA preparation;


title: dgriG1_f_go_R3

description: mixed-species RNA preparation;


title: dgriG1_f_re_R2

description: mixed-species RNA preparation;


title: dhetW48B6_f_go_R2

description: single-species RNA preparation;


title: dhemW40B14_m_go_R1

description: single-species RNA preparation;


title: dhetW48B6_f_go_R1

description: single-species RNA preparation;


title: dhemW40B14_f_hd_R1

description: single-species RNA preparation;


title: dhemW40B14_f_hd_R2

description: single-species RNA preparation;


title: dhemW40B14_f_go_R2

description: single-species RNA preparation;


title: dgriG1_f_ge_R4

description: mixed-species RNA preparation;


title: dgriG1_f_go_R2

description: mixed-species RNA preparation;


title: dgriG1_f_go_R1

description: mixed-species RNA preparation;


title: dhetW48B6_m_hd_R1

description: single-species RNA preparation;


title: dhemW40B14_m_hd_R2

description: single-species RNA preparation;


title: dgriG1_f_dg_R4

description: mixed-species RNA preparation;


title: dgriG1_f_dg_R2

description: mixed-species RNA preparation;


title: dgriG1_f_ge_R1

description: mixed-species RNA preparation;


title: dgriG1_f_ge_R2

description: mixed-species RNA preparation;


title: dgriG1_f_ac_R2

description: mixed-species RNA preparation;


title: dgriG1_f_ac_R1

description: mixed-species RNA preparation;


title: dgriG1_f_ac_R4

description: mixed-species RNA preparation;


title: dgriG1_f_dg_R1

description: mixed-species RNA preparation;


title: dgriG1_f_ac_R3

description: mixed-species RNA preparation;


title: dhemW40B14_f_go_R1

description: single-species RNA preparation;


title: dgriG1_f_ge_R3

description: mixed-species RNA preparation;


title: Osteosarcoma P24

status: Public on Mar 22 2016

data_processing: For each miR, the expression level was determined by the threshold cycle method (2^(-ΔCt)) of relative quantification (ΔCt  = Ct of sample – average Ct of endogenous controls of sample).  Quantile normalization was applied to compensate for the technical differences present among all the samples.

label: FAM

source_name: Right Proximal Tibia

label_protocol: miR expression was performed using the TaqMan Array Human MicroRNA Cards (Applied Biosystems), according to manufacturer's protocol

extract_protocol: Total RNA was extracted using the mirVana miR Isolation Kit (Ambion) according to manufacturer’s instructions

treatment_protocol: In a -20oC cryostat, 10 slices, each 10 μm thick frozen tissue were cut (total thickness 100 μm) and placed in 50 mL centrifuge tube containing pre-chill RNAlater-ICE solution (Ambion).

tag: ageatdiagnosis

tag: gender

value: M

tag: relapse

value: No

tag: dead

tag: survival-days


title: Osteosarcoma P26

source_name: Left Proximal Tibia

value: F

value: Yes (2nd primary)

value: Yes


title: Osteosarcoma P27

source_name: Right Distal Femur


title: Osteosarcoma P25


title: Osteosarcoma P18

value: Unknown


title: Osteosarcoma P21

source_name: Right Pelvis


title: dgriG1_f_dg_R3

description: mixed-species RNA preparation;

tag: strain

value: Female


title: Osteosarcoma P22

source_name: Right Distal Radius


title: Osteosarcoma P19


title: Osteosarcoma P14

source_name: Left Proximal Humerus


title: Osteosarcoma P15

source_name: Left Calf


title: Osteosarcoma P16

source_name: Right Humerus


title: Osteosarcoma P17

source_name: Left Distal Femur


title: Osteosarcoma P11


title: Osteosarcoma P10


title: Osteosarcoma P08

source_name: Right Proximal Humerus


title: Osteosarcoma P09


title: Osteosarcoma P23


title: Osteosarcoma P06

source_name: Left Femur


title: Osteosarcoma P07


title: Osteosarcoma P05

source_name: Right Tibia


title: Osteosarcoma P20

source_name: Sacrum


title: Osteosarcoma P03


title: Osteosarcoma P01


title: Osteosarcoma P02


title: Osteosarcoma P12


title: Kb102 flutamide rep 1

status: Public on Dec 21 2012

hyb_protocol: Hybridization, washing and scanning were performed according to the manufacturer's directions (Agilient Inc.)

data_processing: Expression values were normalized by Quantile Normalization (MATLAB Bioinformatics Toolbox, R2011a).

source_name: Kb102 flutamide

label_protocol: Lableing was performed according to the manufacturer's directions (Agilient Inc.).

growth_protocol: Sertoli Cells isolated from adult mouse

extract_protocol: We euthanized mice by asphyxiation with CO2, harvested their testes, and isolated Sertoli cells as previously described [Chang et al., 2011; Anway et al., 2003]. We extracted RNA from purified Sertoli cells (pooled from five to seven mice) by using a Qiazol miRNeasy kit (Qiagen, Valencia, CA). We converted 1 μg of total RNA into cDNA by using a MiScript cDNA synthesis kit (Qiagen) and analyzed with quantitative real-time RT-PCR using miRNA-specific primers. We normalized miRNA expression levels to RNU19/5S and gene expression to 18S.

value: sertoli cells


title: Kb102 Testosterone

scan_protocol: Hybridization, washing and scanning were performed according to the manufacturer's directions (Agilient Inc.)

source_name: Kb102 Testosterone


title: Kb102 flutamide rep 2


title: Kb102 control

source_name: Kb102 control


title: Control rat 1

status: Public on Mar 01 2015

scan_protocol: Standard Illumina microarray protocol (BeadStudio)

data_processing: Expression values were normalized by quantile normalization method (MATLAB Bioinformatics Toolbox, R2011a)

organism: Rattus norvegicus

source_name: Control rat

label_protocol: Total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

growth_protocol: Male Sprague-Dawley rats (2-3 months old) were purchased from Harlan Laboratories (Indianapolis, IN) and fed Teklad (Harlan Laboratories) mouse/rat diet ad libitum in an accredited facility using a 12h day/night cycle

extract_protocol: Total RNA was isolated from tissues using TRI Reagent (Molecular Research Center, Cincinnati, OH) and then treated with RNase-free DNase I (Applied Biosystems, Foster City, CA).  cDNA synthesis was performed by reverse transcription (Invitrogen, Carlsbad, CA).  For synthesis of cRNA, an Illumina TotalPrep RNA Amplification Kit (Life Technologies, Foster City, CA) was used to amplify 500ng of total RNA.

treatment_protocol: rats were injected intra-peritoneally with isoproterenol (20 mg/g body weight) or normal saline (control)

value: Sprague-Dawley

value: male

tag: age

value: 2-3 months old

tag: injected with

value: normal saline (control)

value: parotid glands


title: Isoproterenol rat 10 min

source_name: Isoproterenol rat 10 min

value: isoproterenol (20 mg/g body weight)

tag: tissue


title: Isoproterenol rat 30 min

source_name: Isoproterenol rat 30 min


title: Isoproterenol rat 60 min

source_name: Isoproterenol rat 60 min


title: 4.12T_024

status: Public on Mar 31 2012

type: genomic

description: Tumor vs. normal genomic DNA.

hyb_protocol: The Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis-ULS hybridization protocol.

scan_protocol: Raw intensity signals for each microarray were captured using an Agilent Microarray Scanner (at 5-micron res), and measured using Agilent Feature Extraction and Analysis software (ver 9.5 ).

data_processing: Quantile normalization (MATLAB Bioinformatics Toolbox, R2009a). Probes' chromosomal positions lifted over (LiftOver tool: http://genome.ucsc.edu) to human genome build hg18 (raw data is hg19).

source_name: Wilms' tumor DNA

label_protocol: The Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis-ULS labeling protocol.

growth_protocol: De-identified archival tumor and normal control tissues were used.

extract_protocol: See publication.

treatment_protocol: No treatments.

value: Wilms' tumor

tag: identifier

source_name: Normal genomic DNA

tag: sample type

value: control


title: 4.7T_020

description: Tumor vs. normal genomic DNA.


title: 4.4T_023

description: Tumor vs. normal genomic DNA.


title: Control rat 2


title: 2.6T_010

description: Tumor vs. normal genomic DNA.


title: 3.1T_015

description: Tumor vs. normal genomic DNA.


title: 3.4T_022

description: Tumor vs. normal genomic DNA.


title: 4.10T_026

description: Tumor vs. normal genomic DNA.


title: 3.7T_011

description: Tumor vs. normal genomic DNA.


title: miRHuman_36.4.2

description: Sample 36 4.2 tumor vs. normal

hyb_protocol: Per LC Sciences protocol

scan_protocol: Axon GenePix 4000B Microarray Scanner. Pixel size 10 µm

data_processing: ArrayPro. Lowess Global Normalization

source_name: kidney, 36T4.2

label_protocol: Per LC Sciences protocol

extract_protocol: Total RNA was extracted from samples with the mirVana miRNA isolation kit (Ambion) according to manufacturers protocol. The samples were then processed by LC Sciences

tag: disease state

value: tumor

source_name: kidney, 36N4.2

value: normal


title: 2.3T_009

description: Tumor vs. normal genomic DNA.


title: 1.1T_021

description: Tumor vs. normal genomic DNA.


title: 4.9T_025

description: Tumor vs. normal genomic DNA.


title: 3.6T_014

description: Tumor vs. normal genomic DNA.


title: 2.5T_018

description: Tumor vs. normal genomic DNA.


title: 4.3T_019

description: Tumor vs. normal genomic DNA.


title: miRHuman_36.1.2

description: Sample 36 1.2 tumor vs. normal

source_name: kidney, 36T1.2

source_name: kidney, 36N1.2


title: 1.3T_013

description: Tumor vs. normal genomic DNA.


title: 2.4T_017

description: Tumor vs. normal genomic DNA.


title: miRHuman_36.4.1

description: Sample 36 4.1 normal vs. tumor

source_name: kidney, 36N4.1

source_name: kidney, 36T4.1


title: 3.2T_016

description: Tumor vs. normal genomic DNA.


title: 3.8T_012

description: Tumor vs. normal genomic DNA.


title: miRHuman_36.1.1

description: Sample 36 1.1 normal vs. tumor

source_name: kidney, 36N1.1

source_name: kidney, 36T1.1


title: 293-ctrl and 293-miR-204

description: Analysis of HEK-293 cells overexpressing miR-204 compared to control cells.

hyb_protocol: Hybridization and washing were performed according to the manufacturer's directions (Agilient Inc.)

scan_protocol: Scanning was performed according to the manufacturer's directions (Agilient Inc.)

data_processing: The dye-swap sample was swapped, and then the expression log ratios were normalized by Quantile Normalization (MATLAB Bioinformatics Toolbox, R2009a).

source_name: HEK-293 control

label_protocol: Labeling was performed according to the manufacturer's directions (Agilient Inc.)

growth_protocol: HEK-293 cells were grown in 10% serum containing media at 37°C in a CO2 incubator.

extract_protocol: RNA was isolated using QIAzol (Qiagen, Inc.) as per the manufacturer's protocol.

treatment_protocol: HEK-293 cells were transfected with either 75 nM of scramble oligos (HEK-293 control) or miR-204-mimic (HEK-293 miR-204) (ABI Inc.) for 48 hrs. before being harvested for RNA isolation.

tag: transfection


title: 293-ctrl and 293-miR-204, dye-swap

description: Analysis of HEK-293 cells overexpressing miR-204 compared to control cells. Dye-swap.

tag: cell line


title: U227

status: Public on Jul 01 2011

description:
Pleomorphic spindle cell sarcoma versus pleomorphic LMS
4235982011_E

hyb_protocol: According to Illumina Protocol

scan_protocol: Illumina BeadScan

data_processing: Rank invariant set normalization on raw log2 transformed intensities. After normalization, the log2 values larger than 16 were set to 16; the inf values were replaced using knn impute.

label_protocol: According to Illumina Protocol

extract_protocol: For gene expression studies in mice, total RNA was extracted from tumor samples using TRIZOL according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). RNA was then purified using Qiagen RNeasy miniprep cleanup kit per manufacturer instructions (Qiagen, Valencia, CA). cDNA was generated using oligo-dT primers as previously described (Nishijo et al., 2009). Nishijo K, Chen QR, Zhang L, McCleish AT, Rodriguez A, Cho MJ et al (2009). Credentialing a preclinical mouse model of alveolar rhabdomyosarcoma. Cancer Res 69: 2902-11.

value: Mixed strain C57Bl/6 and SV/J129

tag: animal id

tag: genotype

value: Pax7(CREERp/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10), ROSA26(LUSAPm/WT) ZRED-Tg(Bgeo/WT)

tag: diagnosis

tag: morphology

value: spindle cell

value: WT

tag: dxage

tag: site

value: back


title: U240

description:
Pleomorphic spindle cell sarcoma, NOS (MFH)
4235982011_D

value: abdomen


title: U239

description:
Pleomorphic RMS
4235982011_B

source_name: Pleomorphic RMS

value: Pleomorphic RMS


title: CTRL and Ctnnb1 CKO testis_dye-swapped

status: Public on Mar 20 2012

description: Ctnnb1 CKO testis/CTRL testis dye-swapped

data_processing: Swapped the dye-swapped sample, then the expression log ratio were normalized by Quantile Normalization (MATLAB Bioinformatics Toolbox, R2011a)

source_name: Ctnnb1 CKO mice testis

label_protocol: Lableing was performed according to the manufacturer's directions (Agilient Inc.)

extract_protocol: Testis from 6-8 week old CTRL and Ctnnb1 CKO mice were homogenized in Qiazol and extracted according to manufacturer directions (Qiagen)

tag: genotyep/variation

value: Ctnnb1 CKO

value: 6-8 weeks

value: testis

source_name: CTRL mice testis

value: Control WT


title: U173

description:
poorly differentiated RMS (NOS)
4235982025_E

source_name: poorly differentiated RMS (NOS)

value: poorly differentiated RMS (NOS)

value: MUT

value: leg


title: U203

description:
Spindle cell sarcoma, NOS
4235982010_B

source_name: Spindle cell sarcoma, NOS

value: Spindle cell sarcoma, NOS

value: lt arm


title: U27

description:
mixed ERMS/ARMS
4235982007_E

source_name: mixed ERMS/ARMS

value: Myf6(ICNm/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10), ROSA26(LUSAPm/WT)

value: mixed ERMS/ARMS

value: round cell and spindle cell

value: lt-paw


title: U43

description:
ARMS
4235982007_F

source_name: ARMS

value: Mixed strain C57Bl/6 and SV/J129

value: ARMS

value: solid variant, epitheliod

value: WT

value: rt-leg


title: U206

description:
Pleomorphic RMS
4235982010_F

value: Pax7(CREERp/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10), ROSA26(LUSAPm/WT)

value: Pleomorphic RMS

value: spindle cell

value: abdomen


title: U214

description:
Pleomorphic RMS
4235982011_A

value: Pax7(CREERp/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10), ROSA26(LUSAPm/WT) ZRED-Tg(Bgeo/WT)


title: U251

description:
pleomorphic RMS
4235982031_E

source_name: pleomorphic RMS

value: Myf6(ICNm/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: pleomorphic RMS

value: epithelioid

value: MUT

value: arm


title: CTRL and Ctnnb1 CKO testis

description: Ctnnb1 CKO testis/CTRL testis

value: Control WT

value: 6-8 weeks

value: testis

value: Ctnnb1 CKO


title: U234

description:
malignant epithelioid neoplasm, NOS
4235982011_G

source_name: malignant epithelioid neoplasm, NOS

value: Mixed strain C57Bl/6 and SV/J129

value: malignant epithelioid neoplasm, NOS


title: U193

description:
poorly differentiated malignant epithelioid neoplasm
4235982025_G


title: U46

description:
ARMS
4235982008_A

value: ARMS

value: solid variant, epitheliod

value: WT

value: lt-leg


title: U2

description:
malignant epithelioid neoplasm, NOS
4235982007_A

value: Myf6(ICNm/WT), Pax3(P3Fm/P3Fm) CDKN2a (F2-3/DEL2-3)

value: tongue


title: U220

description:
spindle cell sarcoma, NOS
4235982025_D

source_name: spindle cell sarcoma, NOS

value: Myf6(ICNm/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: spindle cell sarcoma, NOS

value: epithelioid and spindle cell

value: back


title: U170

description:
Spindle cell sarcoma, NOS
4235982010_C

value: Pax7(CREERp/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10), ROSA26(LUSAPm/WT) ZRED-Tg(Bgeo/WT)

value: Spindle cell sarcoma, NOS

value: spindle cell

value: arm


title: U205

description:
Pleomorphic spindle cell sarcoma, NOS versus pleomorphic LMS
4235982010_D

value: abdomen


title: U11

description:
ARMS
4235982007_C

value: Mixed strain C57Bl/6 and SV/J129

value: round cell neoplasm


title: U242

description:
epithlioid to spindle cell neoplasm (hard to classify)
4235982011_F

value: Myf6 (ICNm/WT), Pax3 (P3Fm/P3Fm), CDKN2a (F2-3/F2-3)

value: epithelioid to spindle cell

value: neck


title: U89

description:
ARMS
4235982009_C

value: ARMS

value: solid variant, epitheliod

value: WT

value: leg


title: U224

description:
RMS, NOS
4235982029_A

source_name: RMS, NOS

value: Myf6(ICNm/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: RMS, NOS

value: MUT


title: U254

description:
malignant epithelioid neoplasm
4235982031_G

source_name: malignant epithelioid neoplasm

value: malignant epithelioid neoplasm

value: epithelioid

value: paw


title: U269

description:
malignant epithelioid neoplasm
4235982031_F

value: Pax7(CREERp/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)


title: U93

description:
ARMS or RMS (NOS)
4235982009_E

source_name: ARMS or RMS (NOS)

value: ARMS or RMS (NOS)


title: U150

description:
RMS, NOS
4235982010_A

value: Mixed strain C57Bl/6 and SV/J129

value: chest


title: U87

description:
ARMS
4235982009_A

value: arm


title: U238

description:
malignant epithelioid neoplasm
4235982029_F


title: U211

status: Public on Feb 17 2011

description:
ERMS
4235982010_H

source_name: ERMS

value: Pax7(CREERp/WT), PTC1(F1-2m) Trp53(F2-10/F2-10) ROSA26(LUSAPm/WT)

value: ERMS

value: spindle cell

value: left leg


title: U95

description:
ARMS
4235982009_G

value: ARMS

value: WT

value: foot


title: U216

description:
ERMS
4235982011_C

value: back


title: U114

description:
ERMS
4235982009_B

value: abdomen


title: U44

description:
ARMS
4235982007_H


title: U126

description:
ARMS
4235982009_F

value: MCre(Cre/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10), ROSA26(LUSAPm), Zred(Bgeo/WT)

value: solid variant, epitheliod

value: leg


title: U58

description:
normal muscle
4235982008_G

source_name: normal muscle

value: wildtype

value: normal muscle


title: U64

description:
normal muscle
4235982008_D

value: Mixed strain C57Bl/6 and SV/J129


title: U59

description:
normal muscle
4235982008_B


title: U190

description:
spindle cell sarcoma
4235982010_G

source_name: spindle cell sarcoma

value: spindle cell sarcoma

value: pleomorphic spindle cell


title: U244

description:
spindle cell sarcoma, NOS
4235982029_H

value: Pax7(CREERp/WT), PTC1(F1-2m/WT) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: spindle cell sarcoma, NOS

value: MUT

value: genital area


title: U125

description:
ERMS
4235982009_D

value: ERMS

value: spindle cell

value: neck


title: U47

description:
ARMS
4235982008_C

value: Myf6 (ICNm/WT), Pax3 (P3Fm/P3Fm), CDKN2a (F2-3/F2-3), ROSA26(LUSAPm/WT)

value: ARMS

value: epithelioid

value: WT


title: U57

description:
normal muscle
4235982008_E


title: U30

description:
ARMS
4235982007_G


title: U229

description:
malignant epithelioid and spindle cell neoplasm, NOS
4235982029_E

value: Pax7(CREERp/WT),  Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: epithelioid and spindle cell

value: arm


title: U222

description:
ARMS
4235982025_F

value: Mixed strain C57Bl/6 and SV/J129

value: Myf6(ICNm/WT), Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)


title: U230

description:
malignant epithelioid neoplasm, NOS
4235982029_G

value: Myf6(ICNm/WT), PTC1(F1-2m/WT) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: malignant epithelioid neoplasm, NOS

value: tongue


title: U245

description:
spindle cell sarcoma, NOS
4235982011_H

value: Pax7(CREERp/WT), PTC1(F1-2m) Trp53(F2-10/F2-10) ROSA26(LUSAPm/WT)

value: spindle cell sarcoma, NOS

value: epithelioid to spindle cell

value: abdomen


title: U228

description:
malignant epithelioid neoplasm
4235982029_C

value: malignant epithelioid neoplasm

value: MUT


title: U232

description:
spindle cell sarcoma, NOS, or reactive fibroblastic proliferation
4235982029_B

value: spindle cell


title: U250

description:
RMS, NOS
4235982031_C

value: Pax7(CREERp/WT), PTC1(F1-2m/WT) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: RMS, NOS

value: genital area


title: U177

description:
spindle cell sarcoma
4235982010_E

value: spindle cell sarcoma

value: pleomorphic spindle cell

value: WT

value: back


title: U259

description:
spindle cell sarcoma, NOS
4235982031_B

value: Mixed strain C57Bl/6 and SV/J129

value: face


title: U202

description:
pleomorphic RMS
4235982025_B

value: pleomorphic RMS

value: leg


title: U271

description:
RMS, NOS
4235982031_H

value: arm


title: U68

description:
ERMS
4235982008_F

value: ERMS

value: neck


title: U247

description:
pleomorphic malignant spindle cell neoplasm or pleomorphic RMS
4235982031_A

value: Pax7(CREERp/WT),  Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: mouth


title: U86

description:
ERMS
4235982008_H

value: spindle cell

value: buttock


title: U237

description:
pleomorphic malignant spindle cell neoplasm
4235982029_D

value: MUT


title: U41

description:
ARMS
4235982007_D

value: ARMS

value: epithelioid

value: lt-arm


title: Mo.6C+II+.Bl#3

status: Public on Oct 08 2010

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Mo.6C+II+.Bl#3, population 2 Ly6ChiMHCIIint

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: blood

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Disruption using syringe

value: 6 weeks

tag: exclusion markers

tag: genetic background

tag: phenotype markers

value: CD115+ B220- CD43+ Ly6C+ MHCIIint

tag: separation method

value: dissection/trimming

tag: Sex

value: male


title: U149

description:
mixed ERMS/ARMS
4235982009_H

tag: strain

value: Mixed strain C57Bl/6 and SV/J129

value: mixed ERMS/ARMS

value: WT

value: lt-leg


title: DC.pDC.8+.Sp#1

description: DC.pDC.8+.Sp#1, spleen CD8+ plasmacytoid dentritic cells

source_name: spleen

extract_protocol: gentle teasing with tweezers, Blendzyme Liberase III and DNAse I digestion, depletion of CD3e, CD19, NK1.1 and TER119 positive cells using MACS system

tag: age

value: streptavidin-PECy7, propidium iodide

value: GR1-PE CD11c-eFluor750 CD8-eFluor480 CD45-APC B220-FITC


title: DC.pDC.8-.Sp#3

description: DC.pDC.8-.Sp#3, spleen CD8- plasmacytoid dentritic cells


title: Mo.6C-II-.Bl#3

description: Mo.6C-II-.Bl#3, population 4 Ly6Clo MHCII-


title: Mo.6C-II+.Bl#4

description: Mo.6C-II+.Bl#4, Nonclassical monocytes MHC II high

value: CD115+ B220- CD43+ Ly6C- MHCIIhi


title: U35

description:
ERMS
4235982007_B

value: ERMS

value: spindle cell

value: rt-arm


title: Mo.6C+II-.Bl#2

description: Mo.6C+II-.Bl#2, population 1 Ly6ChiMHCII-


title: Mo.6C-II+.Bl#1

description: Mo.6C-II+.Bl#1, population 3 Ly6Clo MHCIIhi


title: Mo.6C+II+.Bl#1

description: Mo.6C+II+.Bl#1, population 2 Ly6ChiMHCIIint


title: Mo.6C-II-.Bl#4

description: Mo.6C-II-.Bl#4, Nonclassical monocytes MHC II-


title: DC.pDC.8+.Sp#2

description: DC.pDC.8+.Sp#2, spleen CD8+ plasmacytoid dentritic cells


title: Mo.6C+II-.Bl#1

description: Mo.6C+II-.Bl#1, population 1 Ly6ChiMHCII-


title: DC.pDC.8+.Sp#3

description: DC.pDC.8+.Sp#3, spleen CD8+ plasmacytoid dentritic cells


title: DC.pDC.8-.Sp#2

description: DC.pDC.8-.Sp#2, spleen CD8- plasmacytoid dentritic cells


title: Mo.6C+II-.Bl#3

description: Mo.6C+II-.Bl#3, population 1 Ly6ChiMHCII-


title: NK.MCMV1.Sp#3

status: Public on Apr 29 2010

description: NK.MCMV1.Sp#3, Splenic NK cells MCMV d1.5 PI

extract_protocol: Glass slide teasing,  FACS sorting

value: CD3 CD4 CD8 CD19 Ter119 Gr-1


title: NK.Sp#8

description: NK.Sp#8, Splenic NK cells


title: NK.Sp#7

description: NK.Sp#7, Splenic NK cells


title: NK.Sp#9

description: NK.Sp#9, Splenic NK cells


title: DC.pDC.8-.Sp#1

description: DC.pDC.8-.Sp#1, spleen CD8- plasmacytoid dentritic cells


title: NK.MCMV1.Sp#2

description: NK.MCMV1.Sp#2, Splenic NK cells MCMV d1.5 PI


title: Tgd.Sp#2

status: Public on Dec 02 2009

description: Tgd.Sp#2, Spleen TCRgamma-delta, all DN

extract_protocol: Glass Tissue Grinder  CD4 & CD8 Dynal Magnetic Bead Depletion  Flow Sorting

value: TCRd+ CD3e+


title: NK.MCMV1.Sp#1

description: NK.MCMV1.Sp#1, Splenic NK cells MCMV d1.5 PI


title: Tgd.Sp#3

description: Tgd.Sp#3, Spleen TCRgamma-delta, all DN


title: Tgd.Sp#1

description: Tgd.Sp#1, Spleen TCRgamma-delta, all DN


title: Affected biceps 1

status: Public on Sep 04 2008

city: Jerusalem

first: Noa

last: Novershtern

address: Admond Safra Campus

department: School of Computer Science and Engineering

country: Israel

institute: The Hebrew University

description: Gene expression data from HIBM affected muscle

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133A GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix Microarray Software Suite 5.0 and RMA normalization (using RMAExpress software)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Tissues were disrupted in dry ice and homogeneized and total RNA was isolated using TriReagent (Molecular Research Center,  Cincinnati, OH) according to the manufacturer’s recommended protocol. Integrity of the isolated RNA was analyzed using a standard 1% agarose gel electrophoresis and purified total RNA was quantified using Nanodrop ND1000.

treatment_protocol: All muscle biopsies were collected and immediately frozen in liquid nitrogen untill used for RNA extraction.

tag: Affected, tissue

value: biceps, age:29, gender:male