title: Patient L03 Sample 2

description: 352 Spots used for computation


title: Patient RF 22 Sample 1

status: Public on Nov 21 2013

type: other

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

description: 352 Spots used for computation

data_processing:
The arrays were scanned to obtain signal location, intensity quantification and identification information using GenePix Pro 6.1. For each array inter-array normalization was performed via the ProCAT algorithm (sliding window of length 15). The arrays were then quantile normalized and a comparison of intensities of probes was carried out using ANOVA in Mathematica 9.0.  The Negative Control was used to eliminate signals not related to plasma response.
Samples:  GenePix Pro intensities, normalized by ProCat Algorithm, and Quantile Normalized in Mathematica 9.  Control: GenePix Pro intensities, normalized by ProCAT Algorithmin Mathematica 9

label: Alexa Fluor 555

molecule: other

organism: Homo sapiens

source_name: Plasma

growth_protocol: Not Applicable

treatment_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array for the autoantibodyome profiling. The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software. All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

tag: mds class

value: t

tag: Sex

value: F

tag: age

tag: % blast

tag: iPSs

value: High

tag: disease state

value: tMDS


title: Patient RM 59 Sample 2

description: 352 Spots used for computation

hyb_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

scan_protocol: The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software.

extract_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array

value: M


title: Patient L15 Sample 1

description: 352 Spots used for computation

label_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

value: missing


title: Patient L03 Sample 1

description: 352 Spots used for computation


title: Patient L02 Sample 1

description: 352 Spots used for computation


title: Patient L02 Sample 2

description: 352 Spots used for computation


title: Patient T24 Sample 2

description: 352 Spots used for computation

value: s

value: sMDS


title: Patient L01 Sample 1

description: 352 Spots used for computation


title: Patient L01 Sample 2

description: 352 Spots used for computation


title: Patient T16 Sample 2

description: 352 Spots used for computation


title: Patient T16 Sample 1

description: 352 Spots used for computation


title: Patient RM 84 Sample 2

description: 352 Spots used for computation


title: Patient SF 9 Sample 2

description: 352 Spots used for computation

value: Low


title: Patient SF 8 Sample 2

description: 352 Spots used for computation


title: Patient SF 8 Sample 1

description: 352 Spots used for computation


title: Patient LF 3 Sample 1

description: 352 Spots used for computation


title: Patient SF 7 Sample 2

description: 352 Spots used for computation


title: Patient SF 7 Sample 1

description: 352 Spots used for computation


title: Patient SF 6 Sample 1

description: 352 Spots used for computation


title: Patient SF 52-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 6 Sample 2

description: 352 Spots used for computation


title: Patient SF 51-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 51-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 9 Sample 1

description: 352 Spots used for computation


title: Patient T24 Sample 1

description: 352 Spots used for computation


title: Patient SF 50-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 5 Sample 2

description: 352 Spots used for computation


title: Patient SF 49-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 5 Sample 1

description: 352 Spots used for computation


title: Patient SF 46-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 46-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 50-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 49-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 48-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 47-1 Sample 1

description: 352 Spots used for computation


title: Patient SF 47-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 45 Sample 1

description: 352 Spots used for computation


title: Patient SF 43 Sample 2

description: 352 Spots used for computation


title: Patient SF 48-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 42 Sample 2

description: 352 Spots used for computation


title: Patient SF 52-1 Sample 2

description: 352 Spots used for computation


title: Patient SF 41 Sample 2

description: 352 Spots used for computation


title: Patient SF 42 Sample 1

description: 352 Spots used for computation


title: Patient SF 43 Sample 1

description: 352 Spots used for computation


title: Patient SF 45 Sample 2

description: 352 Spots used for computation


title: Patient SF 4 Sample 2

description: 352 Spots used for computation


title: Patient SF 39 Sample 2

description: 352 Spots used for computation


title: Patient SF 4 Sample 1

description: 352 Spots used for computation


title: Patient SF 39 Sample 1

description: 352 Spots used for computation


title: Patient SF 41 Sample 1

description: 352 Spots used for computation


title: Patient SF 38 Sample 1

description: 352 Spots used for computation


title: Patient SF 38 Sample 2

description: 352 Spots used for computation


title: Patient SF 37 Sample 2

description: 352 Spots used for computation


title: Patient SF 36 Sample 2

description: 352 Spots used for computation


title: Patient SF 37 Sample 1

description: 352 Spots used for computation


title: Patient SF 35 Sample 1

description: 352 Spots used for computation


title: Patient SF 35 Sample 2

description: 352 Spots used for computation


title: Patient SF 34 Sample 2

description: 352 Spots used for computation


title: Patient SF 36 Sample 1

description: 352 Spots used for computation


title: Patient SF 33 Sample 2

description: 352 Spots used for computation


title: Patient SF 33 Sample 1

description: 352 Spots used for computation


title: Patient SF 32 Sample 2

description: 352 Spots used for computation


title: Patient SF 34 Sample 1

description: 352 Spots used for computation


title: Patient SF 31 Sample 2

description: 352 Spots used for computation


title: Patient SF 30 Sample 1

description: 352 Spots used for computation


title: Patient SF 31 Sample 1

description: 352 Spots used for computation


title: Patient SF 32 Sample 1

description: 352 Spots used for computation


title: Patient SF 30 Sample 2

description: 352 Spots used for computation


title: Patient SF 28 Sample 1

description: 352 Spots used for computation


title: Patient SF 27 Sample 2

description: 352 Spots used for computation


title: Patient SF 28 Sample 2

description: 352 Spots used for computation


title: Patient SF 3 Sample 2

description: 352 Spots used for computation


title: Patient SF 3 Sample 1

description: 352 Spots used for computation


title: Patient SF 26 Sample 2

description: 352 Spots used for computation


title: Patient SF 26 Sample 1

description: 352 Spots used for computation


title: Patient SF 25 Sample 1

description: 352 Spots used for computation


title: Patient SF 24 Sample 2

description: 352 Spots used for computation


title: Patient SF 23 Sample 2

description: 352 Spots used for computation


title: Patient SF 24 Sample 1

description: 352 Spots used for computation


title: Patient SF 23 Sample 1

description: 352 Spots used for computation


title: Patient SF 22 Sample 2

description: 352 Spots used for computation


title: Patient SF 20 Sample 2

description: 352 Spots used for computation


title: Patient SF 21 Sample 2

description: 352 Spots used for computation


title: Patient SF 22 Sample 1

description: 352 Spots used for computation


title: Patient SF 20 Sample 1

description: 352 Spots used for computation


title: Patient SF 21 Sample 1

description: 352 Spots used for computation


title: Patient SF 2 Sample 2

description: 352 Spots used for computation


title: Patient SF 2 Sample 1

description: 352 Spots used for computation


title: Patient SF 27 Sample 1

description: 352 Spots used for computation


title: Patient SF 17 Sample 1

description: 352 Spots used for computation


title: Patient SF 15 Sample 1

description: 352 Spots used for computation


title: Patient SF 19 Sample 2

description: 352 Spots used for computation


title: Patient SF 18 Sample 2

description: 352 Spots used for computation


title: Patient SF 15 Sample 2

description: 352 Spots used for computation


title: Patient SF 16 Sample 2

description: 352 Spots used for computation


title: Patient SF 18 Sample 1

description: 352 Spots used for computation


title: Patient SF 19 Sample 1

description: 352 Spots used for computation


title: Patient SF 16 Sample 1

description: 352 Spots used for computation


title: Patient SF 14 Sample 1

description: 352 Spots used for computation


title: Patient SF 14 Sample 2

description: 352 Spots used for computation


title: Patient SF 25 Sample 2

description: 352 Spots used for computation


title: Patient SF 13 Sample 1

description: 352 Spots used for computation


title: Patient SF 13 Sample 2

description: 352 Spots used for computation


title: Patient SF 12 Sample 2

description: 352 Spots used for computation


title: Patient SF 12 Sample 1

description: 352 Spots used for computation


title: Patient SF 17 Sample 2

description: 352 Spots used for computation


title: Patient SF 11 Sample 1

description: 352 Spots used for computation


title: Patient SF 1 Sample 1

description: 352 Spots used for computation


title: Patient SF 10 Sample 1

description: 352 Spots used for computation


title: Patient SF 10 Sample 2

description: 352 Spots used for computation


title: Patient S37 Sample 2

description: 352 Spots used for computation


title: Patient S37 Sample 1

description: 352 Spots used for computation


title: Patient S35 Sample 1

description: 352 Spots used for computation


title: Patient S35 Sample 2

description: 352 Spots used for computation


title: Patient S34 Sample 1

description: 352 Spots used for computation


title: Patient S34 Sample 2

description: 352 Spots used for computation


title: Patient S32 Sample 2

description: 352 Spots used for computation


title: Patient S33 Sample 1

description: 352 Spots used for computation


title: Patient S33 Sample 2

description: 352 Spots used for computation


title: Patient S31 Sample 2

description: 352 Spots used for computation


title: Patient S30 Sample 1

description: 352 Spots used for computation


title: Patient S29 Sample 1

description: 352 Spots used for computation


title: Patient S30 Sample 2

description: 352 Spots used for computation


title: Patient S31 Sample 1

description: 352 Spots used for computation


title: Patient S28 Sample 1

description: 352 Spots used for computation


title: Patient S29 Sample 2

description: 352 Spots used for computation


title: Patient S28 Sample 2

description: 352 Spots used for computation


title: Patient S27 Sample 1

description: 352 Spots used for computation


title: Patient SF 11 Sample 2

description: 352 Spots used for computation


title: Patient S27 Sample 2

description: 352 Spots used for computation


title: Patient S26 Sample 2

description: 352 Spots used for computation


title: Patient S26 Sample 1

description: 352 Spots used for computation


title: Patient SF 1 Sample 2

description: 352 Spots used for computation


title: Patient S25 Sample 2

description: 352 Spots used for computation


title: Patient S25 Sample 1

description: 352 Spots used for computation


title: Patient S24 Sample 1

description: 352 Spots used for computation


title: Patient S23 Sample 2

description: 352 Spots used for computation


title: Patient S24 Sample 2

description: 352 Spots used for computation


title: Patient S23 Sample 1

description: 352 Spots used for computation


title: Patient S32 Sample 1

description: 352 Spots used for computation


title: Patient S22 Sample 2

description: 352 Spots used for computation


title: Patient S21 Sample 2

description: 352 Spots used for computation


title: Patient S21 Sample 1

description: 352 Spots used for computation


title: Patient S20 Sample 2

description: 352 Spots used for computation


title: Patient S19 Sample 1

description: 352 Spots used for computation


title: Patient S18 Sample 2

description: 352 Spots used for computation


title: Patient S19 Sample 2

description: 352 Spots used for computation


title: Patient S17 Sample 2

description: 352 Spots used for computation


title: Patient S18 Sample 1

description: 352 Spots used for computation


title: Patient S15 Sample 2

description: 352 Spots used for computation


title: Patient S16 Sample 2

description: 352 Spots used for computation


title: Patient S14 Sample 2

description: 352 Spots used for computation


title: Patient S16 Sample 1

description: 352 Spots used for computation


title: Patient S15 Sample 1

description: 352 Spots used for computation


title: Patient S14 Sample 1

description: 352 Spots used for computation


title: Patient S13 Sample 2

description: 352 Spots used for computation


title: Patient S13 Sample 1

description: 352 Spots used for computation


title: Patient S12 Sample 2

description: 352 Spots used for computation


title: Patient S12 Sample 1

description: 352 Spots used for computation


title: Patient S11 Sample 2

description: 352 Spots used for computation


title: Patient S22 Sample 1

description: 352 Spots used for computation


title: Patient S10 Sample 2

description: 352 Spots used for computation


title: Patient S09 Sample 2

description: 352 Spots used for computation


title: Patient S10 Sample 1

description: 352 Spots used for computation


title: Patient S20 Sample 1

description: 352 Spots used for computation


title: Patient S17 Sample 1

description: 352 Spots used for computation


title: Patient S11 Sample 1

description: 352 Spots used for computation


title: Patient S08 Sample 2

description: 352 Spots used for computation


title: Patient S08 Sample 1

description: 352 Spots used for computation


title: Patient S09 Sample 1

description: 352 Spots used for computation


title: Patient S07 Sample 1

description: 352 Spots used for computation


title: Patient S07 Sample 2

description: 352 Spots used for computation


title: Patient S05 Sample 2

description: 352 Spots used for computation


title: Patient S05 Sample 1

description: 352 Spots used for computation


title: Patient S06 Sample 1

description: 352 Spots used for computation


title: Patient S06 Sample 2

description: 352 Spots used for computation


title: Patient S04 Sample 2

description: 352 Spots used for computation


title: Patient S04 Sample 1

description: 352 Spots used for computation


title: Patient S02 Sample 1

description: 352 Spots used for computation


title: Patient S01 Sample 2

description: 352 Spots used for computation


title: Patient S03 Sample 2

description: 352 Spots used for computation


title: Patient S03 Sample 1

description: 352 Spots used for computation


title: Patient S02 Sample 2

description: 352 Spots used for computation


title: Patient S01 Sample 1

description: 352 Spots used for computation


title: Patient RM 9 Sample 2

description: 352 Spots used for computation


title: Patient RM 9 Sample 1

description: 352 Spots used for computation


title: Patient RM 52 Sample 1

description: 352 Spots used for computation


title: Patient RM 52 Sample 2

description: 352 Spots used for computation


title: Patient RM 48 Sample 2

description: 352 Spots used for computation


title: Patient RM 48 Sample 1

description: 352 Spots used for computation


title: Patient RM 49 Sample 2

description: 352 Spots used for computation


title: Patient RM 49 Sample 1

description: 352 Spots used for computation


title: Patient RM 43 Sample 2

description: 352 Spots used for computation


title: Patient RM 46 Sample 2

description: 352 Spots used for computation


title: Patient RM 43 Sample 1

description: 352 Spots used for computation


title: Patient RM 46 Sample 1

description: 352 Spots used for computation


title: Patient RM 42 Sample 2

description: 352 Spots used for computation


title: Patient RM 41 Sample 2

description: 352 Spots used for computation


title: Patient RM 38 Sample 2

description: 352 Spots used for computation


title: Patient RM 41 Sample 1

description: 352 Spots used for computation


title: Patient RM 38 Sample 1

description: 352 Spots used for computation


title: Patient RM 37 Sample 1

description: 352 Spots used for computation


title: Patient RM 37 Sample 2

description: 352 Spots used for computation


title: Patient RM 32 Sample 1

description: 352 Spots used for computation

value: 16% by FLow Cytometry


title: Patient RM 28 Sample 2

description: 352 Spots used for computation

value: up to 10%


title: Patient RM 31 Sample 1

description: 352 Spots used for computation


title: Patient RM 28 Sample 1

description: 352 Spots used for computation


title: Patient RM 27 Sample 2

description: 352 Spots used for computation


title: Patient RM 31 Sample 2

description: 352 Spots used for computation


title: Patient RM 27 Sample 1

description: 352 Spots used for computation


title: Patient RM 26 Sample 2

description: 352 Spots used for computation


title: Patient RM 42 Sample 1

description: 352 Spots used for computation


title: Patient RM 26 Sample 1

description: 352 Spots used for computation


title: Patient RM 25 Sample 2

description: 352 Spots used for computation


title: Patient RM 25 Sample 1

description: 352 Spots used for computation


title: Patient RM 17 Sample 2

description: 352 Spots used for computation


title: Patient RM 17 Sample 1

description: 352 Spots used for computation


title: Patient RM 16 Sample 1

description: 352 Spots used for computation


title: Patient RM 15 Sample 2

description: 352 Spots used for computation


title: Patient RM 15 Sample 1

description: 352 Spots used for computation


title: Patient RM 11 Sample 2

description: 352 Spots used for computation


title: Patient RF 22 Sample 2

description: 352 Spots used for computation


title: Patient RM 11 Sample 1

description: 352 Spots used for computation


title: Patient RM 32 Sample 2

description: 352 Spots used for computation


title: Patient RM 13 Sample 2

description: 352 Spots used for computation


title: Patient RM 10 Sample 2

description: 352 Spots used for computation

value: 6% by FLow Cytometry


title: Patient RM 13 Sample 1

description: 352 Spots used for computation


title: Patient RM 10 Sample 1

description: 352 Spots used for computation


title: Patient RM 1 Sample 1

description: 352 Spots used for computation


title: Patient RM 1 Sample 2

description: 352 Spots used for computation


title: Patient RF 9 Sample 1

description: 352 Spots used for computation


title: Patient RF 8 Sample 1

description: 352 Spots used for computation


title: Patient RF 8 Sample 2

description: 352 Spots used for computation


title: Patient RM 16 Sample 2

description: 352 Spots used for computation


title: Patient RF 7 Sample 2

description: 352 Spots used for computation


title: Patient RF 6 Sample 2

description: 352 Spots used for computation


title: Patient RF 7 Sample 1

description: 352 Spots used for computation


title: Patient RF 23 Sample 2

description: 352 Spots used for computation


title: Patient RF 3 Sample 1

description: 352 Spots used for computation


title: Patient RF 23 Sample 1

description: 352 Spots used for computation


title: Patient RF 14 Sample 2

description: 352 Spots used for computation


title: Patient RF 2 Sample 1

description: 352 Spots used for computation


title: Patient RF 2 Sample 2

description: 352 Spots used for computation


title: Patient RF 10 Sample 2

description: 352 Spots used for computation


title: Patient RF 9 Sample 2

description: 352 Spots used for computation


title: Patient RMN 9 Sample 2

description: 352 Spots used for computation

value: N

value: healthy


title: Patient RMN 9 Sample 1

description: 352 Spots used for computation


title: Patient RF 10 Sample 1

description: 352 Spots used for computation


title: Patient RF 6 Sample 1

description: 352 Spots used for computation


title: Parkinson's Disease (PD) patient, post-DBS on electrical stimulation (ON-Stim), sample 11

type: SRA

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

library_source: transcriptomic

data_processing:
Prior to alignment, all of the reads were subjected to trimming of the 15 end-terminal base pairs using home-made software.
The adapter and primer sequences were further trimmed. These included trimming of the 5' small RNA adapter, discarding of the SOLiD miRNA reverse primer, trimming of the 3' small RNA adapter and removal of the 5' end-terminal nucleotide using CLC bio Genomics Workbench software version 4.0 beta. Of a total of 166,746,207 sequence reads, 71,939,833 were left post-filtering, average length: 21 bp.
The remaining sequence reads were subjected to alignment to miRBase (version 15) human sequences through CLC bio Genomics Workbench software version 4.0 beta.
The reads were further subjected to alignment to the human filter reference sequence database (Ambion, Inc.) of 764 small RNA sequences including snoRNA, tRNA, spliceosomal RNA, etc.
Genome_build: 1) miRBase version 15;  2) human filter reference sequences database (Ambion, Inc.)
Supplementary_files_format_and_content: 1) grouped_miRBase.txt: counts grouped by miRNA name and form (including * forms and sequence); 2) grouped_on_mature_miRBase.txt: counts grouped only by mature miRNA name; 3) unannotated.txt: unannotated sequences identified in the sample; 4) grouped_filter_seq_DB.txt: counts grouped by RNA molecule name (other than miRNA).

molecule: total RNA

source_name: Blood leukocytes, PD, post-DBS, on electrical stimulation

growth_protocol: Leukocytes were filtered from total blood samples (collected with EDTA vacutainer tubes) with Ambion Inc. LeukoLOCK™ filters within 10 minutes of blood extraction.

extract_protocol: RNA was harvested using the alternative protocol for extraction of RNA from cells captured on LeukoLOCK™ Filters Using TRI Reagent®. The amount of ethanol was adjusted to include the small RNA fraction. Libraries for deep sequencing were prepared from total leukocyte RNA with the manufacturer's SREK (Small RNA Expression Kit) protocol (Applied Biosystems, Foster City, CA, USA). The DNA libraries were tested using a DNA 1000 Lab Chip on Bioanalyzer 2100. Briefly, the total RNA samples were hybridized with Adaptor Mix A, which is a set of oligonucleotides with a single-stranded degenerate sequence at one end and a defined sequence required for SOLiD sequencing at the other end. The Adaptor Mix A constrains the orientation of the RNA in the ligation reaction such that hybridization with it yields template for SOLiD sequencing from the 5' end of the sense strand. After hybridization, the adaptors are ligated to the small RNA molecules using Ligation Enzyme Mix, which is a mixture of an RNA Ligase and other components. Ligation requires an RNA molecule with a 5'-monophosphate and a 3'-hydroxyl end; therefore, most small RNAs can participate in this reaction, and intact mRNA molecules with a 5' cap structure are excluded. Next, the small RNA population with ligated adaptors was reverse transcribed for each sample, to generate a cDNA library. This was followed by treatment with RNase H to digest the RNA from RNA/cDNA duplexes and to reduce the concentration of unligated adaptors and adaptor by-products. The cDNA libraries were amplified using bar-coded primer sets and 15-18 cycles of PCR. The amplified cDNA library was cleaned up and size selected from gel - PCR products ~105–150 bp are isolated, corresponding to inserts derived from the small RNA population. These contained 90 base pairs of primers and adapter sequences each. The amplified cDNA libraries generated with the SOLiD Small RNA Expression Kit were thereafter ready for attachment to beads at the emulsion PCR step of the SOLiD sample preparation workflow. The slides were analyzed on an Applied Biosystems SOLiD System 3.0 (V3.5). The Applied Biosystems SOLiD sequencer generated 50-base read sequences as .csfasta files and the corresponding quality control (.QUAL) files.

treatment_protocol: The captured leukocytes were treated with RNAlater immediately after filtration of the blood and were maintained frozen until RNA extraction.

tag: cell type

value: blood leukocytes

value: Parkinson's disease

tag: treatment state

value: post-deep brain stimulation on electrical stimulation

tag: gender

value: male


title: Parkinson's Disease (PD) patient, pre-DBS, sample 10

source_name: Blood leukocytes, PD, pre-DBS

value: pre-deep brain stimulation


title: Patient RF 3 Sample 2

description: 352 Spots used for computation

value: F


title: Patient RMN 6 Sample 2

description: 352 Spots used for computation


title: Patient RMN 8 Sample 2

description: 352 Spots used for computation


title: Patient RMN 8 Sample 1

description: 352 Spots used for computation


title: Patient RMN 5 Sample 2

description: 352 Spots used for computation


title: Patient RMN 7 Sample 1

description: 352 Spots used for computation


title: Patient RMN 7 Sample 2

description: 352 Spots used for computation


title: Patient RMN 4 Sample 2

description: 352 Spots used for computation


title: Patient RMN 5 Sample 1

description: 352 Spots used for computation


title: Patient RMN 4 Sample 1

description: 352 Spots used for computation


title: Patient RF 14 Sample 1

description: 352 Spots used for computation


title: Patient RMN 3 Sample 1

description: 352 Spots used for computation


title: Patient RMN 3 Sample 2

description: 352 Spots used for computation


title: Patient RMN 20 Sample 1

description: 352 Spots used for computation


title: Patient RMN 6 Sample 1

description: 352 Spots used for computation


title: Parkinson's Disease (PD) patient, pre-DBS, sample 4


title: Patient RMN 2 Sample 2

description: 352 Spots used for computation


title: Patient RMN 19 Sample 2

description: 352 Spots used for computation


title: Patient RMN 18 Sample 2

description: 352 Spots used for computation


title: Patient RMN 19 Sample 1

description: 352 Spots used for computation


title: Patient RMN 20 Sample 2

description: 352 Spots used for computation


title: Patient RMN 18 Sample 1

description: 352 Spots used for computation


title: Patient RMN 17 Sample 2

description: 352 Spots used for computation


title: Patient RMN 17 Sample 1

description: 352 Spots used for computation


title: Patient RMN 2 Sample 1

description: 352 Spots used for computation


title: Patient RMN 16 Sample 2

description: 352 Spots used for computation


title: Patient RMN 16 Sample 1

description: 352 Spots used for computation


title: Patient RMN 15 Sample 2

description: 352 Spots used for computation


title: Patient RMN 13 Sample 2

description: 352 Spots used for computation


title: Patient RMN 14 Sample 2

description: 352 Spots used for computation


title: Patient RMN 14 Sample 1

description: 352 Spots used for computation


title: Patient RMN 15 Sample 1

description: 352 Spots used for computation


title: Patient RMN 11 Sample 1

description: 352 Spots used for computation


title: Patient RMN 11 Sample 2

description: 352 Spots used for computation


title: 80 days old wild-type mice replicate 1

type: RNA

city: São Paulo

first: Gabriela

middle: Pintar

last: Oliveira

state: Outside the US or Canada

address: Dr Arnaldo Av, 455, 2nd floor

department: Neurology

country: Brazil

institute: University of Sao Paulo Medical School

description: Biological Replicate

hyb_protocol: Hybridation following manufacturer's instructions (Agilent)

scan_protocol: Scanned on an Agilent scanner.

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for extract data and Agi4x44PreProcess and limma Bioconductor packages were used for background correction and normalization in R.

organism: Mus musculus

source_name: Lumbar spinal cord

label_protocol: RNA amplification and labeling following manufacturer's instructions (Agilent)

extract_protocol: Total RNA extracted using MiniSpin Kit GE following manufacturer's instructions

value: 80 days

tag: genotype

value: NonTg

tag: tissue

value: Lumbar spinal cord

tag: genetic background

source_name: Pool of neonatal organs

value: Neonatal

value: pooled NonTg and SOD1G93A

value: Pool of neonatal organs


title: 80 days old wild-type mice replicate 3

description: Biological Replicate


title: 80 days old SOD1G93A transgenic mice replicate 2

description: Biological Replicate


title: MBD1 KO #1

city: San Francisco

first: Mark

middle: Stuart

last: Anderson

state: CA

address: 513 Parnassus Avenue, HSW Room  1102, Box 0540

department: Diabetes Center

institute: UCSF

hyb_protocol: Labeled Cy3-cDNA was assesed using the Nanodrop ND-8000 (nanodrop Technologies, INC, Wilmington DE), and equal amounts of Cy3 labeled target were hybridized for 17hrs to Agilent whole mouse genome 4x44K ink-jet arrays.

scan_protocol: Arrays were scanned using the Agilent microarray scanner.

data_processing: Raw Signal intensities were extracted with Feature Extraction v10.6 software.

source_name: Thymus

label_protocol: Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI)

extract_protocol: mTECs were sorted based on the following markers: DAPI-, CD11c-, CD45-, Ly51-, EPCAM+, Class II+.  RNA was isolated using Qiagen’s RNeasy Micro Plus Kit and amplified using Sigma Whole transcriptome amplification kits.

tag: genotype/variation

value: MBD1 KO

tag: tissue type

value: thymus

value: medullary thymic epithelial cell (mTECs)


title: 80 days old SOD1G93A transgenic mice replicate 4

description: Biological Replicate


title: 80 days old wild-type mice replicate 2

description: Biological Replicate


title: MBD1 KO #2


title: 80 days old SOD1G93A transgenic mice replicate 1

description: Biological Replicate


title: 80 days old wild-type mice replicate 4

description: Biological Replicate


title: Patient RMN 12 Sample 2

description: 352 Spots used for computation

value: N

value: M


title: MBD1 WT #2

value: MBD1 WT


title: MBD1 WT #1


title: Patient RMN 13 Sample 1

description: 352 Spots used for computation

value: healthy


title: MBD1 KO #3


title: 80 days old SOD1G93A transgenic mice replicate 3

description: Biological Replicate


title: MBD1 WT #3


title: Patient RMN 12 Sample 1

description: 352 Spots used for computation


title: Patient RMN 1 Sample 2

description: 352 Spots used for computation


title: Patient RMN 10 Sample 2

description: 352 Spots used for computation


title: Patient RMN 1 Sample 1

description: 352 Spots used for computation


title: Patient RMN 10 Sample 1

description: 352 Spots used for computation


title: 40 days old SOD1G93A transgenic micereplicate  2

description: Biological Replicate

value: 40 days


title: 40 days old SOD1G93A transgenic mice replicate 4

description: Biological Replicate


title: Patient RFN 9 Sample 1

description: 352 Spots used for computation


title: 40 days old SOD1G93A transgenic micereplicate  3

description: Biological Replicate


title: Patient RFN 9 Sample 2

description: 352 Spots used for computation


title: 40 days old SOD1G93A transgenic mice replicate 1

description: Biological Replicate


title: 40 days old wild-type mice replicate 4

description: Biological Replicate


title: 40 days old wild-type mice replicate 3

description: Biological Replicate


title: Patient RFN 8 Sample 2

description: 352 Spots used for computation


title: 40 days old wild-type mice replicate 2

description: Biological Replicate


title: Patient RFN 8 Sample 1

description: 352 Spots used for computation


title: Patient RFN 6 Sample 2

description: 352 Spots used for computation


title: Patient RFN 7 Sample 1

description: 352 Spots used for computation


title: Patient RFN 6 Sample 1

description: 352 Spots used for computation


title: 40 days old wild-type mice replicate 1

description: Biological Replicate


title: Patient RFN 5 Sample 2

description: 352 Spots used for computation


title: Patient RFN 4 Sample 2

description: 352 Spots used for computation


title: Patient RFN 7 Sample 2

description: 352 Spots used for computation


title: Patient RFN 4 Sample 1

description: 352 Spots used for computation


title: Patient RFN 3 Sample 2

description: 352 Spots used for computation


title: Patient RFN 3 Sample 1

description: 352 Spots used for computation


title: Patient RFN 2 Sample 2

description: 352 Spots used for computation


title: Patient RFN 2 Sample 1

description: 352 Spots used for computation


title: Patient RFN 10 Sample 2

description: 352 Spots used for computation


title: Patient RFN 5 Sample 1

description: 352 Spots used for computation


title: CTR24

city: Milan

first: Martina

last: Cesani

address: via Olgettina 58

country: Italy

institute: TIGET-HSR

hyb_protocol: 1.5 μg of cRNA were hybridized on 6-sample Illumina WG_v3 Beadchips for 20 hours at 55°C

scan_protocol: Beadchips were incubated with streptavidine-Cy3, dried and scanned on BeadArray Reader

data_processing: Data were normalized based on average values in BeadStudio. Significance Analysis of Microarray (SAM) algorithm (Stanford University Labs) was performed only on probes with a detection p value < 0.0001 on at least one array (corresponding to 11,883 probes out of more than 48,000).

label: biotin

source_name: healthy control

label_protocol: 350 ng of total RNA were transcribed into biotinilated cRNA (TotalPrep RNA amplification kit – Ambion).

growth_protocol: A T lymphocyte culture was established by stimulating peripheral blood cells at day 0 with PHA (1 μg/ml) and from day 2 with IL-2 (300 U/ml) in IMDM 5% Human Serum for 10 days. At the end of the culture, cells were collected and stored in liquid nitrogen. Prior to RNA extraction, frozen T lymphocytes were thawed, cultured for 18 hours in X-VIVO 10 5% HS + IL-2 100 U/ml, then collected, stratified over an equal volume of FBS and centrifuged for 15 minutes at 800 rpm.

extract_protocol: RNA was extracted from pelleted cells with RNeasy Mini Kit (Qiagen) and RNA quality was assessed calculating the RNA integrity number (RIN) (2100 Bioanalyzer – Agilent). Samples with a RIN higher than 9 were further processed.

value: T lymphocytes

tag: clinical form (onset)

value: N/A (healthy)

tag: age at sampling

tag: sex


title: Patient RFN 10 Sample 1

description: 352 Spots used for computation

tag: mds class

value: F


title: CTR22


title: CTR17


title: CTR23


title: CTR21


title: CTR19


title: CTR20


title: Patient RFN 1 Sample 2

description: 352 Spots used for computation

tag: Sex


title: CTR18


title: Patient RFN 1 Sample 1

description: 352 Spots used for computation

tag: age


title: 355107

city: Houston

first: Philip

last: Jonsson

state: TX

address: Department of Biology and Biochemistry – NSM Center for Nuclear Receptors and Cell Signaling 3605 Cullen Blvd, Science & Engineering Research Center Bldg 545

institute: University of Houston

hyb_protocol: Hybridization was performed at 42 °C for at least 40 hours after pooling of samples for each array. Subsequent to hybridization the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.

scan_protocol: Slides were scanned using an Axon GenePix 4400A (MDS Analytical Technologies) to obtain TIFF files.

data_processing: Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis. Cut-offs set as described in article.

label_protocol: Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester dured 30 min.

extract_protocol: RNA extraction was performed with TRIzol reagent (Invitrogen Carlsbad, CA) and chloroform extraction according to the manufacturer’s protocol.

tag: treatment


title: 355106

value: Vehicle


title: Patient N04 Sample 2

description: 352 Spots used for computation

tag: % blast

tag: iPSs


title: CTR14

tag: cell type


title: 355108


title: CTR13


title: 355110


title: CTR16


title: Patient N04 Sample 1

description: 352 Spots used for computation

tag: disease state


title: CTR15


title: CTR12


title: Patient N03 Sample 2

description: 352 Spots used for computation


title: CTR11


title: Patient N03 Sample 1

description: 352 Spots used for computation


title: Patient N02 Sample 2

description: 352 Spots used for computation


title: Patient N02 Sample 1

description: 352 Spots used for computation


title: Patient NM 3 Sample 2

description: 352 Spots used for computation


title: Patient NM 3 Sample 1

description: 352 Spots used for computation


title: 355117


title: Patient N01 Sample 2

description: 352 Spots used for computation


title: mouse brain tissue_contralateral and ipsilateral_rep 3

city: Leicester

first: Dalbir

middle: Kaur

last: Dhiraj

state: Leicestershire

address: Lancaster Road

department: MRC Toxicology Unit

institute: Medical Research Council

description:
in vivo 3
Biological replicate 3 of 3. mouse exposed to 3 vessel occlusion surgery. Contralateral side of brain is control and ipsilateral side (contains infarct) is treated.

hyb_protocol: Arrays were loaded with labelled RNA and hybridised overnight at 52oC in a Genetix hybridisation chamber. Following hybridisation slides were washed sequentially: wash 1: 1X SSC, 0.03% SDS for 5 minutes, wash 2: 0.2X SSC for 3 minutes, wash 3: 0.05X SSC for 3 minutes.

scan_protocol: lides scanned on a 4200 Axon scanner and data acquired using GenePix Pro v.6.0.

data_processing: Data was processed using R statistical computing and graphic package (Lucent Technologies). The data was normalised within arrays (included in the sample data table) and also further normalized between arrays to obtain LOWESS normalized average log fold changes, which was tested for significance using a two-labelled Ttest.

source_name: brain tissue_control

label_protocol: 1ug of total RNA was labelled using FlashTag 3DNA array detection kits, following manufacturer's instructuons.

growth_protocol: C57Bl/6 wild type mice were anaesthetised and three-vessel occlusion surgery was performed, as described by Yanamoto et al., 2003.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. All samples were bioanalysed and RIN of >8.0 were accepted

treatment_protocol: primary cortical neurons, dissected from Rat Wistar E17 embryos, were exposed to OGD by being removed from their maintanance medium and being placed in oxygen and glucose deprived Earl’s balanced salt solution (EBSS) for 4h. OGD was terminated by placing cells back into their maintenance medium. Control cultures were exposed to EbSS which was normoxic and contained glucose. RNA was extracted at 8h post-OGD termination. Mice were exposed to the 3-vessel occlusion model of stroke where complete ischemia was induced for 30 mins. After termination of ischemia total RNA was extracted from contralateral (control) or ipsilateral sides of the brain following 24h of reperfusion.

tag: strain

value: contralateral brain

tag: sample group

value: Control

source_name: brain tissueI_Ischemia

value: ipsilateral sides of the brain

tag: exposed to

value: 3- vessel occlusion model of stroke

value: Ischemia


title: 355118


title: 355119


title: 355116


title: Patient N01 Sample 1

description: 352 Spots used for computation


title: CTR10


title: Patient N09 Sample 2

description: 352 Spots used for computation


title: CTR7


title: CTR9


title: Patient N09 Sample 1

description: 352 Spots used for computation


title: Patient N08 Sample 2

description: 352 Spots used for computation


title: Patient N08 Sample 1

description: 352 Spots used for computation


title: Patient N10 Sample 1

description: 352 Spots used for computation


title: Patient N06 Sample 2

description: 352 Spots used for computation


title: mouse brain tissue_contralateral and ipsilateral_rep 2

description:
in vivo 2
Biological replicate 2 of 3. mouse exposed to 3 vessel occlusion surgery. Contralateral side of brain is control and ipsilateral side (contains infarct) is treated.

tag: tissue


title: cortical neuron_control and OGD_rep3

description:
in vitro 3
Biological replicate 3 of 3. primary neurons exposed o control or OGD treatments

organism: Rattus norvegicus

source_name: primary cortical neurons_control

growth_protocol: primary cortical neurons were dissected and maintaned in Neurobasal medium + 10% Heat inactivated FCS +1% Glutamax, 2% B27 and pen/strep for 10-11 DIV.

value: Wistar

tag: developmental stage

value: E17 embryo

value: primary neurons

value: control EBSS (normoxic, w/ glucose)

source_name: primary cortical neurons_Ischemia

value: oxygen and glucose deprived EBSS for 4h


title: Patient N06 Sample 1

description: 352 Spots used for computation

value: N

value: M


title: mouse brain tissue_contralateral and ipsilateral_rep 1

description:
in vivo 1
Biological replicate 1 of 3. mouse exposed to 3 vessel occlusion surgery. Contralateral side of brain is control and ipsilateral side (contains infarct) is treated.


title: Patient N07 Sample 1

description: 352 Spots used for computation

value: healthy


title: CTR8

value: T lymphocytes


title: cortical neuron_control and OGD_rep2

description:
In vitro 2
Biological replicate 2 of 3. primary neurons exposed o control or OGD treatments


title: cortical neuron_control and OGD_rep1

description:
In vitro 1
Biological replicate 1 of 3. primary neurons exposed o control or OGD treatments


title: Patient N05 Sample 2

description: 352 Spots used for computation


title: Patient N07 Sample 2

description: 352 Spots used for computation


title: Patient N05 Sample 1

description: 352 Spots used for computation


title: Patient NF 9 Sample 1

description: 352 Spots used for computation


title: Patient NF 9 Sample 2

description: 352 Spots used for computation


title: Patient NF 8 Sample 2

description: 352 Spots used for computation


title: CTR1

value: N/A (healthy)


title: Patient NF 7 Sample 2

description: 352 Spots used for computation

value: F


title: CTR5


title: CTR4


title: CTR2


title: Patient NF 7 Sample 1

description: 352 Spots used for computation


title: CTR3


title: Patient NF 6 Sample 2

description: 352 Spots used for computation


title: CTR6


title: Patient NF 6 Sample 1

description: 352 Spots used for computation


title: Patient NF 56 Sample 2

description: 352 Spots used for computation


title: Patient NF 56 Sample 1

description: 352 Spots used for computation


title: Patient N10 Sample 2

description: 352 Spots used for computation


title: Patient NF 55 Sample 2

description: 352 Spots used for computation


title: Patient NF 8 Sample 1

description: 352 Spots used for computation


title: Patient NF 55 Sample 1

description: 352 Spots used for computation


title: Patient NF 54 Sample 2

description: 352 Spots used for computation


title: Patient NF 54 Sample 1

description: 352 Spots used for computation


title: Patient NF 53 Sample 2

description: 352 Spots used for computation


title: Patient NF 53 Sample 1

description: 352 Spots used for computation


title: SMMC-7721 cells,  Eupolyphaga sinensis Walker extract, 0.1mg/mL, 48 h

city: Xi’an

first: yanmin

last: zhang

state: Shaanxi

address: No. 76, Yanta Weststreet, #54

country: China

institute: School of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province

description: Gene expression after Eupolyphaga sinensis Walker extract treated 0.1mg/mL for 48hr

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human hepatic cancer cell line SMMC-7721 was cultured in RPMI-1640 supplemented with 10 % FBS and  incubated at 37 °C in a 5 % CO2 atmosphere.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: Exponentially growing SMMC-7721 cell was plated to the 6-well plate and cultivated for 24 h. Then 0.1mg/mL Eupolyphaga sinensis Walker extract (ESWE) and  Taspine derivate of 2.5x10-5mol/L  were added to the 6-well plate. After 48 h, total RNA was extracted using TRIZOL Reagent.

tag: cell line

value: human hepatic cancer


title: MLD24

source_name: MLD patient

tag: clinical form (onset)

value: Adult


title: SMMC-7721 cells, Taspine derivate, 2.5x10-5 mol/L, 48 h

description: Gene expression after Taspine derivate treated at 2.5x10-5 mol/L for 48hr


title: MLD23

value: Late Juvenile

tag: age at sampling


title: MLD22b

tag: sex


title: MLD25


title: Patient NF 52 Sample 1

description: 352 Spots used for computation

tag: mds class


title: MLD22a

value: Early Juvenile


title: Patient NF 51 Sample 2

description: 352 Spots used for computation

tag: Sex


title: Patient NF 52 Sample 2

description: 352 Spots used for computation

tag: age


title: SMMC-7721 cells, 48 h

description: Gene expression in the absence of Eupolyphaga sinensis Walker extract (ESWE) and  Taspine derivate

source_name: SMMC-7721 cells, 48 h


title: Patient NF 51 Sample 1

description: 352 Spots used for computation


title: MLD21


title: Patient NF 50 Sample 2

description: 352 Spots used for computation


title: MLD20


title: MLD19b


title: MLD19a


title: NCT0030_pre_TX

first: Min

last: Zhang

state: Texas

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 26

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.

label_protocol: 100 ng or less of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: Needle biopsies obtained from lymph nodes involved with follicular lymphoma were collected in RNAlater fixative and stored at -80deg Celsius until RNA isolation.

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: Pidilizumab was administered at 3 mg/kg every 4 weeks for 4 infusions, plus 8 optional infusions every 4 weeks for patients with stable disease or better. Starting 2 weeks after the first infusion of pidilizumab, rituximab was given at 375 mg/m2 weekly for 4 weeks.

tag: gender

tag: treatment

value: pre-pidilizumab

value: tumor biopsy


title: NCT0027_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 24


title: NCT0019_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 22


title: NCT0015_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 21


title: NCT0012_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 20


title: NCT0020_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 23


title: Patient NF 50 Sample 1

description: 352 Spots used for computation

tag: % blast

tag: iPSs


title: MLD17

tag: cell type


title: NCT0028_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 25


title: Patient NF 5 Sample 2

description: 352 Spots used for computation

tag: disease state


title: Patient NF 5 Sample 1

description: 352 Spots used for computation


title: Patient NF 48 Sample 2

description: 352 Spots used for computation


title: MLD18


title: NCT0011_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 19


title: Patient NF 46 Sample 2

description: 352 Spots used for computation


title: Patient NF 47 Sample 2

description: 352 Spots used for computation


title: Patient NF 46 Sample 1

description: 352 Spots used for computation


title: Patient NF 47 Sample 1

description: 352 Spots used for computation


title: Patient NF 48 Sample 1

description: 352 Spots used for computation


title: Patient NF 45 Sample 2

description: 352 Spots used for computation


title: MLD16

value: Late Infantile


title: NCT005_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 18


title: MLD15


title: MLD14


title: NCT031_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 16

value: post-pidilizumab


title: NCT002_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 17


title: Patient NF 45 Sample 1

description: 352 Spots used for computation


title: Patient NF 44 Sample 1

description: 352 Spots used for computation


title: Patient NF 43 Sample 2

description: 352 Spots used for computation


title: Patient NF 44 Sample 2

description: 352 Spots used for computation


title: MLD13


title: Patient NF 43 Sample 1

description: 352 Spots used for computation


title: NCT031_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 15


title: MLD11


title: Patient NF 41 Sample 2

description: 352 Spots used for computation


title: Patient NF 42 Sample 1

description: 352 Spots used for computation


title: MLD6


title: Patient NF 41 Sample 1

description: 352 Spots used for computation


title: Patient NF 40 Sample 2

description: 352 Spots used for computation


title: Patient NF 42 Sample 2

description: 352 Spots used for computation


title: NCT009_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 14


title: MLD7


title: NCT009_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 13


title: MLD8


title: NCT010_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 12


title: MLD5


title: NCT010_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 11


title: NCT008_post_day14

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 10


title: Patient NF 40 Sample 1

description: 352 Spots used for computation


title: Patient NF 4 Sample 1

description: 352 Spots used for computation


title: Patient NF 4 Sample 2

description: 352 Spots used for computation


title: Patient NF 39 Sample 2

description: 352 Spots used for computation


title: MLD3


title: Patient NF 38 Sample 2

description: 352 Spots used for computation


title: Patient NF 39 Sample 1

description: 352 Spots used for computation


title: Patient NF 37 Sample 2

description: 352 Spots used for computation


title: Patient NF 37 Sample 1

description: 352 Spots used for computation


title: Patient NF 38 Sample 1

description: 352 Spots used for computation


title: NCT008_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 9


title: Patient NF 36 Sample 2

description: 352 Spots used for computation


title: Patient NF 36 Sample 1

description: 352 Spots used for computation


title: MLD2


title: Patient NF 35 Sample 2

description: 352 Spots used for computation


title: Negative Control 2

description: used to eliminate false signals

data_processing:
The arrays were scanned to obtain signal location, intensity quantification and identification information using GenePix Pro 6.1. For each array inter-array normalization was performed via the ProCAT algorithm (sliding window of length 15). The arrays were then quantile normalized and a comparison of intensities of probes was carried out using ANOVA in Mathematica 9.0.  The Negative Control was used to eliminate signals not related to plasma response.
Samples:  GenePix Pro intensities, normalized by ProCat Algorithm, and Quantile Normalized in Mathematica 9.  Control: GenePix Pro intensities, normalized by ProCAT Algorithm Mathematica 9

organism: unidentified


title: NCT007_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 8


title: NCT006_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 6


title: Negative Control 1

description: used to eliminate false signals


title: MLD4


title: NCT007_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 7


title: Patient L20 Sample

description: controls included for normalization

value: L

value: AML


title: Patient NF 35 Sample 1

description: 352 Spots used for computation


title: NCT006_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 5


title: Patient L19 Sample

description: controls included for normalization


title: Patient L18 Sample

description: controls included for normalization


title: Patient NF 34 Sample 1

description: 352 Spots used for computation


title: MLD1


title: Patient NF 33 Sample 2

description: 352 Spots used for computation


title: Patient NF 33 Sample 1

description: 352 Spots used for computation


title: Patient NF 32 Sample 1

description: 352 Spots used for computation


title: NCT001_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 2


title: Patient L17 Sample

description: controls included for normalization


title: NCT003_post_day15

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 4


title: NCT003_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 3


title: Patient NF 34 Sample 2

description: 352 Spots used for computation


title: Patient L16 Sample

description: controls included for normalization


title: Patient NF 31 Sample 2

description: 352 Spots used for computation


title: Patient NF 31 Sample 1

description: 352 Spots used for computation


title: Patient NF 30 Sample 2

description: 352 Spots used for computation


title: Patient L13 Sample

description: controls included for normalization


title: Patient NF 32 Sample 2

description: 352 Spots used for computation


title: NCT001_pre_TX

description:
Core needle biopsies from involved lymph nodes, obtained before and 14 days after the first infusion of pidilizumab, were collected in RNAlater fixative and stored at -80degC until RNA isolation. For samples with adequate RNA quantity and quality, determined with an Agilent 2100 Bioanalyzer, 300 ng of total RNA was amplified and biotin-labeled by the Eberwine method for hybridization to HT-12 version 4 BeadArrays from Illumina. Data processing was performed as previously described (PMID: 20805315).  In brief, bead-level values were  adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, quantile-normalized, and then averaged to give a single probe-level value.
SAMPLE 1


title: Patient L14 Sample

description: controls included for normalization


title: Patient NF 30 Sample 1

description: 352 Spots used for computation


title: Patient NF 3 Sample 2

description: 352 Spots used for computation


title: Patient NF 3 Sample 1

description: 352 Spots used for computation


title: Patient NF 29 Sample 2

description: 352 Spots used for computation


title: FL3_low

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 8

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina,  quantile-normalized, and then averaged to give a single probe-level value.

source_name: Tumor 3 biopsy

label_protocol: 300 ng total RNA was amplified and biotin-labeled through an Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: Excisional lymph node biopsies from advanced stage previously untreated follicular lymphoma patients were processed into single cell suspension by mechanical disruption and cryopreserved in aliquots. Cells were thawed, washed, stained with CD3, CD4, PD-1, and CXCR5 antibodies, and sorted by flow cytometry. Dead cells were excluded by 7-AAD staining.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit according to the manufactory's guideline.

treatment_protocol: Not applicable.

value: PD-1loCXCR5loCD4+ T cells

tag: histology

value: Follicular lymphoma grade 1

tag: Stage

value: IV


title: FL3_int

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 7

value: PD-1intCXCR5intCD4+ T cells

value: M


title: Patient NF 29 Sample 1

description: 352 Spots used for computation

value: N

value: healthy


title: Patient NF 28 Sample 1

description: 352 Spots used for computation

value: F


title: Patient NF 28 Sample 2

description: 352 Spots used for computation


title: Patient NF 27 Sample 1

description: 352 Spots used for computation


title: Patient NF 26 Sample 2

description: 352 Spots used for computation


title: FL2_low

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 5

source_name: Tumor 2 biopsy


title: Patient NF 27 Sample 2

description: 352 Spots used for computation


title: FL2_hi

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 4

value: PD-1hiCXCR5hiCD4+ T cells


title: Patient L11 Sample

description: controls included for normalization


title: Patient L12 Sample

description: controls included for normalization


title: Patient L10 Sample

description: controls included for normalization


title: Patient NF 26 Sample 1

description: 352 Spots used for computation


title: Patient L09 Sample

description: controls included for normalization


title: Patient L08 Sample

description: controls included for normalization


title: FL1_low

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 3

source_name: Tumor 1 biopsy


title: FL3_hi

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 6


title: FL1_int

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 2


title: FL1_hi

description:
RNA was extracted from sorted cells, and taken through two-round amplification and labeling, using Ambion’s MessageAmp II aRNA and Illumina® TotalPrep™ RNA amplification kits, for hybridization to Illumina HT12 version 4 human whole-genome BeadArrays.
SAMPLE 1


title: Patient NF 25 Sample 2

description: 352 Spots used for computation


title: Patient NF 24 Sample 1

description: 352 Spots used for computation


title: Patient NF 24 Sample 2

description: 352 Spots used for computation


title: Patient NF 25 Sample 1

description: 352 Spots used for computation


title: Patient NF 23 Sample 2

description: 352 Spots used for computation


title: Patient NF 23 Sample 1

description: 352 Spots used for computation


title: Patient NF 22 Sample 1

description: 352 Spots used for computation


title: Patient L05 Sample

description: controls included for normalization


title: Patient L07 Sample

description: controls included for normalization


title: 293 transfected with MBDVP16 replicate #3

description: 293 cells transfected with MBDVP16 only biologic replicate #3

hyb_protocol: See manufacturer protocol

data_processing: AGCC 3.2.2 Microarrays were normalized for array-specific effects using Affymetrix's Robust Multi-Array (RMA) normalization

source_name: 293 transfected with MBDVP16

label_protocol: NuGEN Ovation Pico WTA V2 and NuGEN Encore Biotin Module

growth_protocol: Transfected HEK 293 cells were grown for 72hrs in complete DMEM prior to RNA extraction.

extract_protocol: Total RNA was extracted with Qiagen RNAeasy mini kit according to manufacturers instructions.

treatment_protocol: HEK 293 cells were transfected using Mirus 293 transfection reagent following manufacturers protocol.

value: HEK 293

value: human embryonic kidney


title: 293 transfected with MBDVP16 replicate #1

description: 293 cells transfected with MBDVP16 only biologic replicate #1


title: 293 transfected with MBDVP16 replicate #2

description: 293 cells transfected with MBDVP16 only biologic replicate #2


title: Patient L04 Sample

description: controls included for normalization

source_name: Plasma


title: Patient L06 Sample

description: controls included for normalization


title: Patient N15 Sample 2

description: 352 Spots used for computation


title: Patient N15 Sample 1

description: 352 Spots used for computation


title: Patient N12 Sample 2

description: 352 Spots used for computation


title: Patient N12 Sample 1

description: 352 Spots used for computation


title: Patient N14 Sample 2

description: 352 Spots used for computation


title: Patient T21 Sample

description: controls included for normalization

value: t

value: tMDS


title: Patient NF 22 Sample 2

description: 352 Spots used for computation


title: Patient T19 Sample

description: controls included for normalization


title: Patient N14 Sample 1

description: 352 Spots used for computation


title: Patient N13 Sample 2

description: 352 Spots used for computation


title: 293 transfected with PCMV replicate #2

description: 293 cells transfected with vector only biologic replicate #2

source_name: 293 transfected with PCMV


title: 293 transfected with PCMV replicate #3

description: 293 cells transfected with vector only biologic replicate #3


title: Patient T17 Sample

description: controls included for normalization


title: 293 transfected with Aire replicate #1

description: 293 cells transfected with Aire only biologic replicate #1

source_name: 293 transfected with Aire


title: 293 transfected with Aire replicate #3

description: 293 cells transfected with Aire only biologic replicate #3


title: Patient T15 Sample

description: controls included for normalization


title: Patient NF 2 Sample 2

description: 352 Spots used for computation


title: Patient NF 2 Sample 1

description: 352 Spots used for computation


title: 293 transfected with PCMV replicate #1

description: 293 cells transfected with vector only biologic replicate #1


title: 293 transfected with Aire replicate #2

description: 293 cells transfected with Aire only biologic replicate #2


title: Patient N11 Sample 2

description: 352 Spots used for computation


title: Patient N16 Sample 1

description: 352 Spots used for computation


title: Patient N11 Sample 1

description: 352 Spots used for computation


title: Patient NF 13 Sample 2

description: 352 Spots used for computation


title: Patient NF 13 Sample 1

description: 352 Spots used for computation


title: Patient NF 12 Sample 2

description: 352 Spots used for computation


title: Patient T13 Sample

description: controls included for normalization


title: Patient T14 Sample

description: controls included for normalization


title: Patient N13 Sample 1

description: 352 Spots used for computation


title: Patient NF 11 Sample 2

description: 352 Spots used for computation


title: Patient NF 11 Sample 1

description: 352 Spots used for computation


title: Patient NF 10 Sample 2

description: 352 Spots used for computation


title: Patient N16 Sample 2

description: 352 Spots used for computation


title: Patient NF 1 Sample 2

description: 352 Spots used for computation


title: Patient T12 Sample

description: controls included for normalization


title: Patient NF 1 Sample 1

description: 352 Spots used for computation


title: Patient N34 Sample 2

description: 352 Spots used for computation


title: Epithelial cells MDAMB231 monocultured replicate-4

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

description: human cells cell cultured- tumors cell lines, human fibroblast strains

hyb_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.

data_processing: We used R package aroma.affymetrix to analyze raw data. Chip type is HuGene-1_0-st-v1, and we used HuGene-1_0-st-v1.r3 as annotation CDF. After RMA background correction and quantile normalization we got probe-level intensity values as shown in the data matrix. We ran quality assessment to check data (not shown). In the further analysis we averaged intensity values for genes with multiple probes, then took log2 tranformed values for each gene.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).

tag: cell

value: Epithelial cells MDAMB231 monocultured


title: Patient T11 Sample

description: controls included for normalization


title: Patient N34 Sample 1

description: 352 Spots used for computation


title: Patient T09 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 monocultured replicate-1

scan_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.


title: Patient NF 12 Sample 1

description: 352 Spots used for computation


title: Epithelial cells MDAMB231 monocultured replicate-2

label_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.


title: Epithelial cells MDAMB231 monocultured replicate-3


title: Patient T08 Sample

description: controls included for normalization


title: Epithelial cells Cal51 monocultured replicate-4

value: Epithelial cells Cal51 monocultured


title: Patient N33 Sample 2

description: 352 Spots used for computation


title: Patient T07 Sample

description: controls included for normalization


title: Epithelial cells Cal51 monocultured replicate-3


title: Patient NF 10 Sample 1

description: 352 Spots used for computation


title: Epithelial cells Cal51 monocultured replicate-2


title: Patient T10 Sample

description: controls included for normalization


title: Patient T05 Sample

description: controls included for normalization

value: High


title: Patient N32 Sample 2

description: 352 Spots used for computation


title: Epithelial cells Cal51 monocultured replicate-1


title: Patient N32 Sample 1

description: 352 Spots used for computation


title: Patient N31 Sample 2

description: 352 Spots used for computation


title: Patient N20 Sample 2

description: 352 Spots used for computation


title: Patient N31 Sample 1

description: 352 Spots used for computation


title: Patient T04 Sample

description: controls included for normalization


title: Patient T06 Sample

description: controls included for normalization


title: Patient N27 Sample 2

description: 352 Spots used for computation


title: Patient N30 Sample 2

description: 352 Spots used for computation


title: Patient N30 Sample 1

description: 352 Spots used for computation


title: Patient T03 Sample

description: controls included for normalization


title: Patient N23 Sample 2

description: 352 Spots used for computation


title: Patient N20 Sample 1

description: 352 Spots used for computation


title: Patient N27 Sample 1

description: 352 Spots used for computation


title: Patient N33 Sample 1

description: 352 Spots used for computation


title: Patient N24 Sample 2

description: 352 Spots used for computation


title: Patient N19 Sample 2

description: 352 Spots used for computation


title: Epithelial cells MDAMB231 cocultured with fibroblast HFFF2 replicate-3


title: Patient T01 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast HFFF2 replicate-2


title: Patient T02 Sample

description: controls included for normalization


title: Patient L03 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast HFFF2 replicate-1


title: Patient L01 Sample

description: controls included for normalization


title: Patient L15 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast HFFF2 replicate-4


title: Patient L02 Sample

description: controls included for normalization


title: Patient T24 Sample

description: controls included for normalization

value: s

value: sMDS


title: Epithelial cells Cal51 cocultured with fibroblast HFFF2 replicate-4


title: Patient N29 Sample 2

description: 352 Spots used for computation


title: Patient N26 Sample 2

description: 352 Spots used for computation


title: Patient N23 Sample 1

description: 352 Spots used for computation


title: Patient N29 Sample 1

description: 352 Spots used for computation


title: Patient N26 Sample 1

description: 352 Spots used for computation


title: Patient N22 Sample 2

description: 352 Spots used for computation


title: Patient N18 Sample 2

description: 352 Spots used for computation


title: Patient N28 Sample 2

description: 352 Spots used for computation


title: Patient N25 Sample 2

description: 352 Spots used for computation


title: Patient N18 Sample 1

description: 352 Spots used for computation


title: Patient N22 Sample 1

description: 352 Spots used for computation


title: Patient N28 Sample 1

description: 352 Spots used for computation


title: Patient N21 Sample 2

description: 352 Spots used for computation


title: Patient N17 Sample 2

description: 352 Spots used for computation


title: Epithelial cells Cal51 cocultured with fibroblast HFFF2 replicate-2


title: Patient S31 Sample

description: controls included for normalization


title: Patient S34 Sample

description: controls included for normalization


title: Patient S35 Sample

description: controls included for normalization


title: Patient S37 Sample

description: controls included for normalization


title: Patient S32 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast HFFF2 replicate-3


title: Patient T16 Sample

description: controls included for normalization


title: Patient S33 Sample

description: controls included for normalization

value: Low


title: Epithelial cells Cal51 cocultured with fibroblast HFFF2 replicate-1


title: Patient S30 Sample

description: controls included for normalization


title: Patient N25 Sample 1

description: 352 Spots used for computation


title: Patient S29 Sample

description: controls included for normalization


title: Patient N21 Sample 1

description: 352 Spots used for computation


title: Patient N17 Sample 1

description: 352 Spots used for computation


title: Patient S28 Sample

description: controls included for normalization


title: Patient S27 Sample

description: controls included for normalization


title: Patient S24 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast HFF1 replicate-3


title: Patient S21 Sample

description: controls included for normalization


title: Patient S22 Sample

description: controls included for normalization


title: Patient S23 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast HFF1 replicate-3


title: Patient S12 Sample

description: controls included for normalization


title: Patient S15 Sample

description: controls included for normalization


title: Patient S26 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast HFF1 replicate-1


title: Patient S14 Sample

description: controls included for normalization


title: Patient S17 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast HFF1 replicate-4


title: Patient S10 Sample

description: controls included for normalization


title: Patient S09 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast HFF1 replicate-1


title: Patient S20 Sample

description: controls included for normalization


title: Patient S25 Sample

description: controls included for normalization


title: Patient S11 Sample

description: controls included for normalization


title: Epithelial cells Cal51 cocultured with fibroblast HFF1 replicate-2


title: Epithelial cells MDAMB231 cocultured with fibroblast HFF1 replicate-2


title: Patient S16 Sample

description: controls included for normalization


title: Patient S08 Sample

description: controls included for normalization


title: Patient S18 Sample

description: controls included for normalization


title: Patient S13 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast Wi38 replicate-4


title: Patient S06 Sample

description: controls included for normalization


title: Patient S07 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast Wi38 replicate-3


title: Patient S05 Sample

description: controls included for normalization


title: Patient N34 Sample

description: controls included for normalization


title: Epithelial cells MDAMB231 cocultured with fibroblast Wi38 replicate-2


title: Patient S03 Sample

description: controls included for normalization


title: Patient S04 Sample

description: controls included for normalization


title: Circadian_44h

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

institute: Universidade de São Paulo - USP

description: Identification of circadian-regulated genes

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: standard Agilent Feature Extraction software protocol

organism: Saccharum hybrid cultivar (mixed)

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

extract_protocol: Trizol followed by DNase treatment and RNA cleanup using QIAGEN kit

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 44: collected at 44 h; experiment in: 14/07/2008

tag: tissue

value: leaves

tag: variety

tag: collect

tag: time

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; pool; experiment in: 14/07/2008

value: control pool


title: Circadian_60hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 60: collected at 60 h; experiment in: 14/07/2008


title: Circadian_24h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 24: collected at 24 h; experiment in: 14/07/2008


title: Circadian_48hsw

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 48: collected at 48 h; experiment in: 14/07/2008


title: Circadian_36hsw

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 36: collected at 36 h; experiment in: 14/07/2008


title: Patient N24 Sample 1

description: 352 Spots used for computation

value: M


title: Circadian_64h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 64: collected at 64 h; experiment in: 14/07/2008


title: Epithelial cells MDAMB231 cocultured with fibroblast Wi38 replicate-1


title: Patient S01 Sample

description: controls included for normalization


title: Circadian_56h

treatment_protocol: 5453: RB855453; C1: circadian; L1: leaf +1; Tr: transcriptome; 56: collected at 56 h; experiment in: 14/07/2008


title: Patient N33 Sample

description: controls included for normalization

value: N


title: Patient N19 Sample 1

description: 352 Spots used for computation

value: healthy


title: Circadian_28hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 28: collected at 28 h; experiment in: 14/07/2008


title: Patient N32 Sample

description: controls included for normalization


title: Circadian_32h

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 32: collected at 32 h; experiment in: 14/07/2008


title: Circadian_24hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 24: collected at 24 h; experiment in: 14/07/2008


title: Patient S02 Sample

description: controls included for normalization

treatment_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array for the autoantibodyome profiling. The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software. All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)


title: Epithelial cells Cal51 cocultured with fibroblast Wi38 replicate-3


title: Epithelial cells Cal51 cocultured with fibroblast Wi38 replicate-4


title: Circadian_56hsw

treatment_protocol: 5453: RB855453; C2: circadian; L1: leaf +1; Tr: transcriptome; 56: collected at 56 h; experiment in: 14/07/2008