title: 150 minutes after rapamycin addition, biological replicate 2

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description:
Sample 16
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

library_source: transcriptomic

data_processing:
alignment to genome (Helicos Helisphere))
counting of sequence tags by coordinate on each strand (both reps combined)
classification of coordinates by gene on appropriate strand
comparison of read count at each coordinate over time to compute half-lives
Genome_build: SacCer2
Supplementary_files_format_and_content: Tab-delimited .txt file with half-life for each mRNA isoform (one file consolidating data from both reps across all timepoints)

source_name: 150 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

growth_protocol: Cells were cultured to mid-log phase in YPD medium

extract_protocol:
Total RNA was isolated by the hot acidic phenol method and purified with DNase treatment on Qiagen RNeasy columns.
RNA sequenced directly by Helicos (DRS method); purified RNA was not modified

treatment_protocol: Rapamycin was added to induce depletion of Rpb1 from the nucleus

tag: agent

value: rapamycin

tag: time

value: 150 minutes


title: Late EPC rep2

status: Public on Apr 02 2014

type: RNA

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang-Ming University

description: The outgrowth LEPC population after 2 week culture

hyb_protocol: cRNA were hybridized, washed and stained on U133 plus 2.0 chips according to standard Affymetrix protocol.

scan_protocol: Chips are stained on Affymetrix GCS3000 scanner (scanner type M10)

data_processing: The CEL file was loaded to R/Bioconductor software and normalized by GC-RMA with default settings.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Late EPC, Umblical cord blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cord blood mononuclear cells (MNCs) were Histopaque-1077 isolated and plated in endothelial growth medium-2 on fibronectin-coated six-well plates at 37°C. After 3 days of culturing, attached eEPCs appeared, and medium and nonadherent cells were removed. Thereafter, the medium were replaced every 2 days, and a certain number of eEPCs continued to grow into the LEPCs colonies, which emerge 2–4 weeks after the start of MNC culture.

extract_protocol: Total RNA was extracted by Qiagen miRNeasy kit according to the manufacturer's instructions.

treatment_protocol: No pre-treatment

tag: cell type

value: Late endothelial precursor cell

value: late (2-4 weeks)


title: UC Sample 5

city: Singapore

first: Dennis

last: Wang

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtraction was performed in GenomeStudio then data was exported.  Probes were filtered for detection p-value <0.05 and NBEADS>3 in R.  Data was then loaded into Arraystudio version 6 (Omicsoft). All technical replicates were combined after sample QC. Data were normalised amongst samples using quantile normalization and subjected to Combat to removed batch effect.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Umbilical cord

label_protocol: Standard Illumina Infinium HD assay protocol

extract_protocol: A weighed amount of pulverized umbilical cord tissue was lysed and homogenised via Hyaluronidase solution treatment, additionof TNES lysis buffer and Proteinase K.

tag: gender

value: Female

tag: ethnicity

value: Indian

tag: batch


title: UC Sample 4

value: Male

value: Chinese


title: UC Sample 26

type: genomic

hyb_protocol: Standard Illumina protocol; standard hybridization for Illumina is 48C for 16-24 hours

scan_protocol: Standard Illumina protocol on the Illumina iScan

data_processing: Standard Illumina protocol for Infinium Human Genotyping beadchips Beadchip quantificatin and processing in GenomeStudio v2011.1

label: C-Bio and A-DNP

label_protocol: Standard Illumina protocol using the Infinium OmniExpressExome DNA Analysis Kit v 1.2

extract_protocol: A weighed amount of pulverized umbilical cord tissue was lysed and homogenised via Hyaluronidase solution treatment,  addition of TNES lysis buffer and Proteinase K.


title: cortex_adult_treated AV4

city: Perugia

first: Stefano

last: Fiorucci

address: Via E dal Pozzo

department: Dipartimento di Medicina Clinica e Sperimentale

country: Italy

institute: Universita di Perugia

description: adult (22 months) animals, VSL#3 treated

hyb_protocol: The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 6.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Rat Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) 10.7.3.1 was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).

organism: Rattus norvegicus

source_name: cortex

label_protocol: Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 6.5, part number G4140-90040). Briefly, 100 ng of each total RNA samples was used for the amplification and labeling step using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Rats were housed 2 per cage and allowed to acclimatize for 1 week following delivery. Body weights and food and water intake were assessed during this time. On each day thereafter, 2 rats per day were assigned to a control or treatment group and received maple syrup either alone or with the probiotic every day over a course of 6 weeks. Stool samples were taken before treatment, mid-way through treatment, and at the end of the treatment period. Six weeks after the onset of treatment, rats were assessed for their ability to sustain LTP in the hippocampus. At the end of the period of electrophysiological recordings, blood samples were taken (for metabolomics analysis) and brain tissue was harvested for microarray analysis of the cortex.

extract_protocol: Rat total RNA was isolated  from rat cortex samples by using standard RNA extraction protocols (Trizol). RNA quality and integrity were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

tag: strain

value: Han Wistar

tag: tissue

value: brain cortex

tag: treatment

tag: age

value: adult


title: UC Sample 28


title: 120 minutes after rapamycin addition, biological replicate 2

type: SRA

state: MA

country: USA

description:
Sample 15
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

organism: Saccharomyces cerevisiae

source_name: 120 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: 120 minutes


title: cortex_adult_treated AV3

data_processing: FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).


title: EPC-FIR mRNA

source_name: PB-EPC, High glucose, FIR treated

growth_protocol: PB-EPC were maintained in Endothelial growth medium 2 (Lonza)

treatment_protocol: PB-EPC were seeded  in Endothelial growth medium 2 with 25mM glucose for 48 hours prior to 30 minute far infrared exposure.

value: Endothelial precursor cell

value: Far Infrared


title: UC Sample 1


title: UC Sample 25

value: Malay


title: UC Sample 2


title: Early EPC pooled

description: The adherent eEPC population after 3 days culture

source_name: Early EPC, Umblical cord blood

value: Early endothelial precursor cell

value: early (<1 week)


title: UC Sample 3


title: 100 minutes after rapamycin addition, biological replicate 2

description:
Sample 14
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 100 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: rapamycin

value: 100 minutes


title: Sample 1

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Sample and reference were pooled together, after which cot-1, 10xblocking buffer and hybridization buffer (Agilent) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent US22502676 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: parseAgilent R script was used for background subtraction and normalization.

source_name: lymphoma

label_protocol: 500 ng of genomic DNA was labeled using the CGH labeling kit for oligo arrays (ENZO). Initially, the DNA and random primer were mixed together which was then denatured at 99ºC for 10 minutes in a thermocycler.. Samples were cooled to 4ºC and transferred to ice after which dNTP-cy3 mix and klenow were added. Incubation was for 4 hours in a thermocycler. After incubation the unincorporated nucleotides were removed using the QIAquick PCR purification column (Qiagen) and the labeled probe was eluted with 2x10ul washes.

extract_protocol: Genomic DNA was isolated using QIAamp DNA Micro Kit according to the manufacter instructions (QIAamp)

tag: disease state

value: lymphome

value: female

value: healthy

source_name: reference


title: 80 minutes after rapamycin addition, biological replicate 2

description:
Sample 13
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 80 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: 80 minutes


title: UC Sample 29

value: Male


title: UC Sample 37

value: Female

value: Chinese


title: UC Sample 32


title: 60 minutes after rapamycin addition, biological replicate 2

description:
Sample 12
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 60 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: 60 minutes


title: cortex_adult_treated AV2

value: Han Wistar

value: brain cortex

value: adult


title: UC Sample 23


title: UC Sample 27


title: UC Sample 30


title: 40 minutes after rapamycin addition, biological replicate 2

description:
Sample 11
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 40 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: 40 minutes


title: EPC-Control mRNA

source_name: PB-EPC, High glucose, Control

value: Endothelial precursor cell

value: Control


title: Late EPC rep1

value: Late endothelial precursor cell

value: late (2-4 weeks)


title: 20 minutes after rapamycin addition, biological replicate 2

description:
Sample 10
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 20 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: rapamycin

value: 20 minutes


title: UC Sample 22


title: Time 0 (immediately before rapamycin addition), biological replicate 2

description:
Sample 9
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.
Note: GSM1262423 raw data file is identical to GSM1154250 raw data file.

value: control


title: cortex_adult_control AC5

description: adult (22 months) animals,  control


title: cortex_adult_control AC3

description: adult (22 months) animals,  control


title: 120 minutes after rapamycin addition, biological replicate 1

description:
Sample 7
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

value: 120 minutes


title: UC Sample 24


title: UC Sample 19

value: Indian


title: LMBtestis_48h_cadmium_rep3

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description: Gene expression profiling after 48h exposure to 20ug CdCl2/kg

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity  > 8 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto  custom-designed fathead minnow (15K oligonulceotide) arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 min with GE Wash Buffer 1 (Agilent), GE Wash buffer 2 (Agilent) kept at 37°C , then 30 sec in Stabilization and Drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k 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-v5_10and Grid: 019597_D_F_20080305) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Micropterus salmoides

source_name: testis, 48h, cadmium, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000 ng RNA using the One-Color Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).  Cy3 dye incorporation and cRNA yield were measured with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted, DNase-treated and purified using Qiagen RNeasy Mini kit following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: After excision, liver and testis samples were cut in small pieces and snap-frozen in liquid nitrogen. Smples were kept at -80C until RNA extraction

value: testis

tag: Stage

value: adult male

value: 48h exposure to 20ug CdCl2/kg


title: LMBtestis_48h_cadmium_rep2

source_name: testis, 48h, cadmium, replicate 2


title: cortex_adult_control AC4

description: adult (22 months) animals,  control


title: cortex_adult_control AC2

description: adult (22 months) animals,  control


title: LMBtestis_48h_cadmium_rep4

source_name: testis, 48h, cadmium, replicate 4


title: LMBtestis_48h_cadmium_rep1

source_name: testis, 48h, cadmium, replicate 1


title: LMBtestis_48h_control_rep2

description: Gene expression profiling after 48h exposure to saline solution

source_name: testis, 48h, saline solution, replicate 2

value: 48h exposure to saline solution


title: UC Sample 20

source_name: Umbilical cord

value: Female

value: Chinese


title: UC Sample 21

value: Male


title: UC Sample 18


title: cortex_adult_control AC1

description: adult (22 months) animals,  control

source_name: cortex

value: Han Wistar

value: brain cortex

value: adult


title: LMBtestis_48h_control_rep3

source_name: testis, 48h, saline solution, replicate 3


title: 80 minutes after rapamycin addition, biological replicate 1

description:
Sample 5
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

value: 80 minutes


title: 60 minutes after rapamycin addition, biological replicate 1

description:
Sample 4
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

value: 60 minutes


title: UC Sample 17


title: LMBtestis_48h_control_rep1

source_name: testis, 48h, saline solution, replicate 1


title: 100 minutes after rapamycin addition, biological replicate 1

description:
Sample 6
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 100 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: rapamycin

value: 100 minutes


title: cortex_young_treated YV4

description: young (3-4 months) animals, VSL#3 treated

value: young


title: 20 minutes after rapamycin addition, biological replicate 1

description:
Sample 2
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

value: 20 minutes


title: LMBliver_48h_cadmium_rep3

source_name: liver, 48h, cadmium, replicate 3

value: liver


title: cortex_adult_treated AV1

description: adult (22 months) animals, VSL#3 treated


title: UC Sample 16


title: 40 minutes after rapamycin addition, biological replicate 1

description:
Sample 3
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

value: 40 minutes


title: LMBliver_48h_cadmium_rep4

source_name: liver, 48h, cadmium, replicate 4

value: adult male


title: LMBliver_48h_cadmium_rep2

source_name: liver, 48h, cadmium, replicate 2

value: 48h exposure to 20ug CdCl2/kg


title: cortex_young_treated YV1


title: Time 0 (immediately before rapamycin addition), biological replicate 1

description:
Sample 1
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

value: control


title: cortex_young_treated YV5


title: cortex_young_control YC5

description: young (3-4 months) animals, control


title: cortex_young_treated YV3


title: LMBliver_48h_control_rep4

source_name: liver, 48h, saline solution, replicate 4

value: 48h exposure to saline solution


title: cortex_young_control YC4

description: young (3-4 months) animals, control


title: LMBliver_48h_cadmium_rep1

source_name: liver, 48h, cadmium, replicate 1


title: UC Sample 12

value: Female

value: Indian


title: 150 minutes after rapamycin addition, biological replicate 1

description:
Sample 8
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.

source_name: 150 minutes after rapamycin addition to induce depletion of Rpb1 from the nucleus

value: 150 minutes


title: cortex_young_control YC3

description: young (3-4 months) animals, control

value: Han Wistar

value: brain cortex


title: UC Sample 15

value: Male

value: Malay


title: UC Sample 14


title: LMBliver_48h_control_rep3

source_name: liver, 48h, saline solution, replicate 3


title: UC Sample 13

value: Chinese


title: UC Sample 9


title: UC Sample 11


title: Day 8_3

status: Public on Apr 01 2014

city: LUND

first: Magnus

last: Ellström

address: Sölvegatan 37

department: MEMEG

country: Sweden

institute: Lund University

description:
Day 8; Replicate 3 (subarray 06)
array:  527890A09

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).

scan_protocol: Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 20% PMT.

data_processing: The bursted and gridded tif-files (.tif file) were directly subjected data extraction, background reduction and quantile normalization using the RMA (Robust Multi-Chip Average) algoritm as implemented by the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.)(www.nimblegen.com).

organism: Paxillus involutus

source_name: mycelium patch_day8

label_protocol: Single-color labeling was performed using the Roche/NimbleGen One-Color DNA Labeling kit (# 05 223 55 001) following their Gene Expression v5.0 protocol (www.nimblegen.com).

growth_protocol: Paxillus involutus (Batsch) Fr. (ATCC 200175) was grown axenically in Petri dishes on a layer of glass beads immersed in Minimum Melin Norkrans medium amended witn ammonium to a C/N ratio of 3. The fungus was first grown for 10 days on a Minimum Melin Norkrans (MMN) medium and then starved for N during 24 h.

extract_protocol: Total RNA was extracted using the Plant RNeasy Mini kit (www.qiagen.com) and concentrated using RNA MinElute kit (www.qiagen.com). RNA quality/integrity and concentration was assessed by analysis on a RNA 6000 Nano chip using the 2100 Bioanalyzer (Agilent). From total RNA, cDNA was produced using the SuperScript double-stranded cDNA Synthesis kit (Invitrogen, #11917-0xx) according to the NimbleGen Gene Expression v5.0 protocol (www.nimblegen.com).

treatment_protocol: The fungal cultures was incubated for 13 days. At day 2, 6, 8 and 13 RNA was extracted from three biological replicates each consisting of 2 pooled fungal cultures.

value: mycelium


title: Day 8_2

description:
Day 8; Replicate 2 (subarray 05)
array:  527890A08


title: cortex_young_control YC1

description: young (3-4 months) animals, control

value: young


title: Day 6_3

description:
Day 6; Replicate 3 (subarray 09)
array:  527890A06

source_name: mycelium patch_day6


title: Day 13_3

description:
Day 13; Replicate 3 (subarray 12)
array:  527890A12

source_name: mycelium patch_day13


title: UC Sample 7


title: UC Sample 8


title: LMBliver_48h_control_rep2

source_name: liver, 48h, saline solution, replicate 2


title: Day 13_1

description:
Day 13; Replicate 1 (subarray 10)
array:  527890A10


title: LMBliver_48h_control_rep1

source_name: liver, 48h, saline solution, replicate 1


title: Day 13_2

description:
Day 13; Replicate 2 (subarray 11)
array:  527890A11


title: LMBtestis_48h_control_rep4

source_name: testis, 48h, saline solution, replicate 4

value: testis


title: UC Sample 5

source_name: Umbilical cord


title: Day 8_1

description:
Day 8; Replicate 1 (subarray 04)
array:  527890A07


title: cortex_young_control YC2

description: young (3-4 months) animals, control

source_name: cortex


title: Day 2_3

description:
Day 2; Replicate 3 (subarray 03)
array:  527890A03

source_name: mycelium patch_day2


title: Day 2_2

description:
Day 2; Replicate 2 (subarray 02)
array:  527890A02


title: Day 2_1

description:
Day 2; Replicate 1 (subarray 01)
array:  527890A01


title: Day 6_1

description:
Day 6; Replicate 1 (subarray 07)
array:  527890A04


title: UC Sample 6


title: Day 6_2

description:
Day 6; Replicate 2 (subarray 08)
array:  527890A05


title: UC Sample 4


title: UC Sample 10


title: UC Sample 3


title: UC Sample 2


title: UC Sample 1


title: cortex_young_treated YV2

description: young (3-4 months) animals, VSL#3 treated


title: M102 rep1

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

hyb_protocol: 20ug (30ug if possible) of labeled DNAs (30ug input DNA + 30ug IP DNA) were hybridized to the 12x270K arrays according to the array manufacturer protocol (42°C, 72hrs). Arrays were then washed according to the array manufacturers protocol.  (NimbleGen Arrays User’s Guide: CGH and CGH/LOH Arrays v9.1 chap. 4,5).

scan_protocol: Arrays were scanned according to the NimbleScan User Guide using the  MS 200 scanner.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files expored from Nimblescan were imported into the R statistical environment. Samples were frist normalized within arrays to minimize dye-bias,  and then normalized across arrays to achieve consistency between arrays. The normalized log2 (IP/input) ratio was used for downstream analyses.

organism: Zea mays

source_name: M102 rep1 input

label_protocol: Amplified input and methylated DNA samples were labeled (.666 ug per subarray sample), hybridized to the 12x270K  feature array. Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5. (NimbleGen Arrays User’s Guide: CGH and CGH/LOH Arrays v9.1 chap. 3).

growth_protocol: The NIL was grown in a controlled environment with a light cycle of 15 hours of light and 9 hours of dark.

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation.  2ug of genomic DNA were sheared using a Covaris S220 Focused-ultrasonicator. Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of corresponding sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-50RXN).

treatment_protocol: genomic DNAs were sonicated, amplified, and fluorophore-labeled

tag: background inbred line

value: B73 and Mo17

tag: nil line

value: seedling leaf (L3)

tag: molecule subtype

value: input DNA

source_name: M102 rep1 IP

treatment_protocol: genomic DNAs were sonicated, methylated DNAs were isolated, amplified, and fluorophore-labeled

value: methylated DNA


title: M100 rep1

source_name: M100 rep1 input

source_name: M100 rep1 IP


title: M054 rep1

source_name: M054 rep1 input

source_name: M054 rep1 IP


title: M062 rep1

source_name: M062 rep1 input

source_name: M062 rep1 IP


title: M083 rep1

source_name: M083 rep1 input

source_name: M083 rep1 IP


title: M097 rep1

source_name: M097 rep1 input

source_name: M097 rep1 IP


title: M081 rep1

source_name: M081 rep1 input

source_name: M081 rep1 IP


title: M072 rep1

source_name: M072 rep1 input

source_name: M072 rep1 IP


title: M058 rep1

source_name: M058 rep1 input

source_name: M058 rep1 IP


title: M099 rep1

source_name: M099 rep1 input

source_name: M099 rep1 IP


title: M040 rep1

source_name: M040 rep1 input

source_name: M040 rep1 IP


title: M049 rep1

source_name: M049 rep1 input

source_name: M049 rep1 IP


title: M051 rep1

source_name: M051 rep1 input

source_name: M051 rep1 IP


title: M052 rep1

source_name: M052 rep1 input

source_name: M052 rep1 IP


title: M098 rep1

source_name: M098 rep1 input

source_name: M098 rep1 IP


title: M093 rep1

source_name: M093 rep1 input

source_name: M093 rep1 IP


title: M078 rep1

source_name: M078 rep1 input

source_name: M078 rep1 IP


title: M055 rep1

source_name: M055 rep1 input

source_name: M055 rep1 IP


title: M079 rep1

source_name: M079 rep1 input

source_name: M079 rep1 IP


title: M038 rep1

source_name: M038 rep1 input

source_name: M038 rep1 IP


title: M037 rep1

source_name: M037 rep1 input

source_name: M037 rep1 IP


title: M082 rep1

source_name: M082 rep1 input

source_name: M082 rep1 IP


title: M073 rep1

source_name: M073 rep1 input

source_name: M073 rep1 IP


title: M046 rep1

source_name: M046 rep1 input

source_name: M046 rep1 IP


title: M035 rep1

source_name: M035 rep1 input

source_name: M035 rep1 IP


title: M016 rep1

source_name: M016 rep1 input

source_name: M016 rep1 IP


title: M032 rep1

source_name: M032 rep1 input

source_name: M032 rep1 IP


title: M022 rep1

source_name: M022 rep1 input

source_name: M022 rep1 IP


title: M024 rep1

source_name: M024 rep1 input

source_name: M024 rep1 IP


title: M030 rep1

source_name: M030 rep1 input

source_name: M030 rep1 IP


title: M017 rep1

source_name: M017 rep1 input

source_name: M017 rep1 IP


title: M008 rep1

source_name: M008 rep1 input

source_name: M008 rep1 IP


title: M007 rep1

source_name: M007 rep1 input

source_name: M007 rep1 IP


title: M014 rep1

source_name: M014 rep1 input

source_name: M014 rep1 IP


title: B189 rep1

source_name: B189 rep1 input

source_name: B189 rep1 IP


title: M011 rep1

source_name: M011 rep1 input

source_name: M011 rep1 IP


title: M012 rep1

source_name: M012 rep1 input

source_name: M012 rep1 IP


title: B185 rep1

source_name: B185 rep1 input

source_name: B185 rep1 IP


title: B117 rep1

source_name: B117 rep1 input

source_name: B117 rep1 IP


title: B139 rep1

source_name: B139 rep1 input

source_name: B139 rep1 IP


title: B081 rep1

source_name: B081 rep1 input

source_name: B081 rep1 IP


title: B126 rep1

source_name: B126 rep1 input

source_name: B126 rep1 IP


title: B141 rep1

source_name: B141 rep1 input

source_name: B141 rep1 IP


title: B183 rep1

source_name: B183 rep1 input

source_name: B183 rep1 IP


title: B069 rep1

source_name: B069 rep1 input

source_name: B069 rep1 IP


title: B154 rep1

source_name: B154 rep1 input

source_name: B154 rep1 IP


title: B152 rep1

source_name: B152 rep1 input

source_name: B152 rep1 IP


title: B149 rep1

source_name: B149 rep1 input

source_name: B149 rep1 IP


title: B164 rep1

source_name: B164 rep1 input

source_name: B164 rep1 IP


title: B057 rep1

source_name: B057 rep1 input

source_name: B057 rep1 IP


title: B086 rep1

source_name: B086 rep1 input

source_name: B086 rep1 IP


title: B094 rep1

source_name: B094 rep1 input

source_name: B094 rep1 IP


title: B125 rep1

source_name: B125 rep1 input

source_name: B125 rep1 IP


title: M031 rep1

source_name: M031 rep1 input

source_name: M031 rep1 IP


title: B133 rep1

source_name: B133 rep1 input

source_name: B133 rep1 IP


title: B157 rep1

source_name: B157 rep1 input

source_name: B157 rep1 IP


title: B102 rep1

source_name: B102 rep1 input

source_name: B102 rep1 IP


title: B054 rep1

source_name: B054 rep1 input

source_name: B054 rep1 IP


title: B046 rep1

source_name: B046 rep1 input

source_name: B046 rep1 IP


title: B121 rep1

source_name: B121 rep1 input

source_name: B121 rep1 IP


title: B043 rep1

source_name: B043 rep1 input

source_name: B043 rep1 IP


title: B040 rep1

source_name: B040 rep1 input

source_name: B040 rep1 IP


title: B037 rep1

source_name: B037 rep1 input

source_name: B037 rep1 IP


title: B050 rep1

source_name: B050 rep1 input

source_name: B050 rep1 IP


title: mCherry+ mantle cell 11 hpCu rep3

city: New York

first: Aaron

middle: B

last: Steiner

state: NY

address: 1230 York Ave, Box 314

department: Laboratory of Sensory Neuroscience

institute: The Rockefeller University

description: polyA RNA amplified

hyb_protocol: Biotin-labeled cDNA libraries were hybridized to Affymetrix Zebrafish Gene 1.0 ST Arrays for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). After hybridization, Gene Chips were stained with streptavidin-phycoerythrin, followed by an antibody solution (anti-streptavidin) and a second streptavidin-phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using AGCC, Affymetrix GeneChip Command Console 3.1 core software according to standard protocols.

data_processing: Data processing was performed using the Partek Genomics Suite, v6.6 (Partek, Inc.). Probeset data were imported using RMA background correction, and were normalized by quantile normalization. Data for comparison of all untreated cell types to each other were imported separately from the time course experiment data (for which untreated mCherry+ and NF cells were re-imported). This was done to prevent cell types not included in the time course (i.e. GFP+ hair cells and mCherry+/GFP+ mantle cells) from affecting quantile normalization of treated samples. In the accompanying submission, data for all untreated samples is as imported for comparison between untreated cell types. Probeset summarization was done by median polish. Imported array data were subjected to principal component analysis, and outliers discarded (not included in this submission). Batch effects due to different sample collection and processing dates were then identified by ANOVA and removed. Probeset data were summarized to transcript-level data for gene-expression analysis; Transcript-level data are included in the accompanying submission. Lists of differentially-expressed genes were compiled according to set cut-offs (i.e. 2-fold up- or down-regulation between sample classes) with Benjamini-Hochberg-adjusted ANOVA-derived P values of less than 0.05.

label: Biotin

organism: Danio rerio

source_name: mCherry+ sorted mantle cells, 11 h after copper sulfate treatment

label_protocol: Amplified cDNA libraries were fragmented and biotin-labeled using a standard protocol (Encore Biotin Module, NuGEN, Inc.).

growth_protocol: Fish embryos were produced by natural mating and maintained in system water at 27 degrees Celsius until 3 days post-fertilization, at which point they were moved into E3 medium and shifted to 28.5 degrees Celsius. Samples were collected 4 days post-fertilization.

extract_protocol: Total RNA was isolated by a standard protocol (RNeasy Micro Kit, Qiagen). The yield and quality of the product were measured with respectively a spectrophotometer (NanoDrop 1000, NanoDrop Technologies) and a bioanalyzer (Agilent 2100). Only samples with an RNA integrity score greater than 8.0 were selected for the preparation of cDNA libraries. One nanogram of total RNA from each sample was amplified to several micrograms of cDNA (Pico WTA System V2, NuGEN, Inc.) before labeling. In the cases of GFP+ hair cells and mCherry+/GFP+ mantle cells, cells from several sorts were pooled to provide sufficient RNA for each amplification reaction.

treatment_protocol: Larvae were either left untreated or treated with 5 µM CuSO4 for 1 h at 28.5 degrees Celsius. Untreated larvae or copper-treated larvae at specified times post-treatment were anaesthetized in Ringer's solution with 600 μM 3 aminobenzoic acid ethyl ester methanesulfonate and their skins removed with fine forceps. Approximately 50 skins were collected for each sample. Skins were placed on ice, and their cells dissociated by incubation with 0.25% trypsin-EDTA (Life Technologies) for 15 min in a water bath at 28.5 ˚C. The samples were then triturated with a P1000 pipet five times or until visibly homogenized. After the trypsin digestion had been quenched with 30% fetal bovine serum and 6 mM CaCl2 in phosphate-buffered saline solution (PBS), the liberated cells were recovered by centrifugation (400 x g for 5 min at 4 ˚C). The pellet was rinsed once with Ca2+-free Ringer’s solution containing 0.5 mg/mL DNaseI (Sigma), resedimented by centrifugation, and resuspended in 100 μl of the same solution. The suspension was kept on ice until just prior to sorting, when it was passed once through a 40 μm filter. Cells were sorted in a flow cytometer equipped with an 85 μm nozzle and 488 nm and 561 nm lasers (FACSAria II, BD Biosciences). Distinct populations of cells were isolated on the basis of forward scattering, lateral scattering, and the intensity of mCherry or GFP fluorescence. Sorted cells were collected in a lysis-buffer solution (RNeasy Micro Kit, Qiagen) supplemented with 130 mM β mercaptoethanol and were stored at  80 ˚C until RNA extraction.

tag: hours post-treatment

value: mCh+ Mantle


title: mCherry+ mantle cell 5 hpCu rep4

description: polyA RNA amplified

source_name: mCherry+ sorted mantle cells, 5 h after copper sulfate treatment


title: mCherry+ mantle cell 5 hpCu rep3

description: polyA RNA amplified


title: mCherry+ mantle cell 3 hpCu rep4

description: polyA RNA amplified

source_name: mCherry+ sorted mantle cells, 3 h after copper sulfate treatment


title: B041 rep1

source_name: B041 rep1 input

source_name: B041 rep1 IP


title: mCherry+ mantle cell 3 hpCu rep2

description: polyA RNA amplified


title: mCherry+ mantle cell 5 hpCu rep2

description: polyA RNA amplified


title: mCherry+ mantle cell 5 hpCu rep1

description: polyA RNA amplified


title: mCherry+ mantle cell 11 hpCu rep2

description: polyA RNA amplified


title: B027 rep1

source_name: B027 rep1 input

source_name: B027 rep1 IP


title: mCherry+ mantle cell 3 hpCu rep3

description: polyA RNA amplified


title: mCherry+ mantle cell 1 hpCu rep2

description: polyA RNA amplified

source_name: mCherry+ sorted mantle cells, 1 h after copper sulfate treatment


title: Non-fluorescent 11 hpCu rep4

description: polyA RNA amplified

source_name: Non-fluorescent sorted cells, 11 h after copper sulfate treatment

value: NF


title: mCherry+ mantle cell 11 hpCu rep1

description: polyA RNA amplified


title: mCherry+ mantle cell 3 hpCu rep1

description: polyA RNA amplified


title: B018 rep1

source_name: B018 rep1 input

source_name: B018 rep1 IP


title: mCherry+ mantle cell 1 hpCu rep4

description: polyA RNA amplified


title: mCherry+ mantle cell 1 hpCu rep3

description: polyA RNA amplified


title: B039 rep1

source_name: B039 rep1 input

source_name: B039 rep1 IP


title: B032 rep1

source_name: B032 rep1 input

source_name: B032 rep1 IP


title: mCherry+ mantle cell 1 hpCu rep1

description: polyA RNA amplified


title: Non-fluorescent 11 hpCu rep3

description: polyA RNA amplified


title: Non-fluorescent 5 hpCu rep3

description: polyA RNA amplified

source_name: Non-fluorescent sorted cells, 5 h after copper sulfate treatment


title: Non-fluorescent 3 hpCu rep2

description: polyA RNA amplified

source_name: Non-fluorescent sorted cells, 3 h after copper sulfate treatment


title: Non-fluorescent 1 hpCu rep5

description: polyA RNA amplified

source_name: Non-fluorescent sorted cells, 1 h after copper sulfate treatment


title: Non-fluorescent 5 hpCu rep2

description: polyA RNA amplified


title: Non-fluorescent 11 hpCu rep2

description: polyA RNA amplified


title: Non-fluorescent 5 hpCu rep1

description: polyA RNA amplified


title: Non-fluorescent 1 hpCu rep4

description: polyA RNA amplified


title: Non-fluorescent 1 hpCu rep6

description: polyA RNA amplified


title: Non-fluorescent 1 hpCu rep7

description: polyA RNA amplified


title: Non-fluorescent 5 hpCu rep4

description: polyA RNA amplified


title: Non-fluorescent 3 hpCu rep4

description: polyA RNA amplified


title: Non-fluorescent 1 hpCu rep3

description: polyA RNA amplified


title: B011 rep1

source_name: B011 rep1 input

source_name: B011 rep1 IP


title: Non-fluorescent 11 hpCu rep1

description: polyA RNA amplified


title: GFP+ Hair cell untreated rep1

description: polyA RNA amplified

source_name: GFP+ Hair cells (from alpl:mCherry;pou4f3:GFP), untreated

value: Untreated

value: GFP+ Hair


title: mCherry+/GFP+ mantle cell untreated rep3

description: polyA RNA amplified

source_name: mCherry+/GFP+ sorted mantle cells (from alpl:mCherry;Et20), untreated

value: mCh+/GFP+ Mantle


title: Non-fluorescent 1 hpCu rep2

description: polyA RNA amplified


title: Non-fluorescent 3 hpCu rep1

description: polyA RNA amplified


title: Non-fluorescent 1 hpCu rep1

description: polyA RNA amplified


title: mCherry+ mantle cell untreated rep4

description: polyA RNA amplified

source_name: mCherry+ sorted mantle cells, untreated


title: mCherry+/GFP+ mantle cell untreated rep4

description: polyA RNA amplified


title: mCherry+/GFP+ mantle cell untreated rep2

description: polyA RNA amplified


title: Non-fluorescent 3 hpCu rep3

description: polyA RNA amplified


title: GFP+ Hair cell untreated rep2

description: polyA RNA amplified


title: mCherry+ mantle cell untreated rep5

description: polyA RNA amplified


title: RNA-Seq on Rnase R treated RNA

city: Stanford

first: Julia

last: Salzman

address: 279 West Campus Drive, MC: 5307

institute: Stanford University

data_processing:
The genome and transcriptome were downloaded from ftp://ftp.ensemblgenomes.org/pub/protists/release-18/fasta/dictyostelium_discoideum/  . Aligning reads are in the file
Reads failing alignment to the genome and  http://dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=blast_databases&ID=dicty_primary_cds.gz ([39])were aligned to the junctional database; read length = 150; read length: 150; bowtie flags –trim5 5 –trim3 5 –v 3.  See methods from publication Wang et al.  Circular RNA is Expressed Across the Eukaryotic Tree of Life.
Genome_build: hg19; ucsc knowngene19
Supplementary_files_format_and_content: bowtie output

organism: Dictyostelium discoideum

source_name: Rnase R treated RNA

extract_protocol:
Total RNA was extracted using TRIZOL from wildtype Dictyostelium discoideum cells (orfj) grown axenically in 1.5xHL+FM medium. RNA was treated with DNase I, digested twice with RNase R, combined with similarly treated Neurospora crassa RNA, and then processed to a barcoded paired-end Illumina sequencing library using 1/4th of a normal ScriptSeq reaction (Epicentre). This library was included as 1/15th of a pool of libraries for a single Illumina MiSeq 150 nt paired-end run.
Nextera

value: whole organism


title: mCherry+/GFP+ mantle cell untreated rep1

description: polyA RNA amplified


title: PTCL50

city: Nagoya

first: Miyuki

middle: Suguro

last: Katayama

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

department: Division of Molecular Medicine

country: Japan

institute: Aichi Cancer Center Research Institute

description: file with raw data for this sample: PTCL50.txt

hyb_protocol: Labeled 1 μg of tested and reference DNA samples was mixed with 100 μg of Human Cot-1 DNA (Invitrogen) and precipitated, after which the pellet was resuspended in the 45-μl hybridization mixture, which consisted of 50% form amide, 10% dextran sulfate, 2× SSC, 4% SDS, and 10 μg/μl yeast tRNA (Invitrogen Life Technologies, Inc.) Hybridization was performed for 48 h in a container placed on a slowly rocking table containing 200 μl of 50% form amide and 2× SSC to control moisture.    It was followed by 15 min post hybridization washing in 50% form amide/2× SSC at 50°C, 30 min in 2× SSC/0.1% SDS at 50°C, 15 min in PN buffer consisting of 0.1 M NaH2PO4, 0.1 M Na2HPO4 at (pH 8.0), and 0.1% NP40 at room temperature, rinsing in 2× SSC at room temperature, and finally dehydration in 70%, 85%, 100% ethanol at room temperature for 2 min each and air-drying.

scan_protocol: Scanning analysis was carried out with the Agilent Micro Array Scanner (Agilent Technologies).

data_processing: Acquired array images were analyzed using Genepix Pro 4.1 (Axon Instruments, Inc., Foster City, CA). DNA spots were automatically segmented, the local background was subtracted, and the total intensities and fluorescence intensity ratio of the two dyes for each spot were calculated. Fluorescence intensity ratio of the two dyes (Cy3 intensity/Cy5 intensity) were converted into log2 intensity ratios (log2 ratio).  In order to remove the so-called probe effect, we first selected a subset of the samples whose Pearson's correlation coefficient r > 0.5 (p=2E-155), where correlation was computed after removing obvious genomic aberrations manually.   Then, at each probe, we considered the median value of those selected samples as the probe specific bias, and it was subtracted from the log2 ratios of the entire samples.

source_name: A tumor biopsy sample of a PTCL patient at diagnosis

label_protocol: Tested and reference(mixture of 10 healthy male) DNA (1 μg each) was digested with DpnII and labeled with the Bio prime DNA labeling system (Invitrogen) using cyanine3-dUTP and cyanine5-dUTP (GE Healthcare Life Sciences), respectively. Unincorporated fluorescent nucleotides were removed with the aid of Sephadex G-50 spin columns (GE Healthcare Life Sciences).

extract_protocol: Genomic DNA was extracted according to standard procedures using proteinase K digestion and phenol chloroform extraction. Normal DNA was prepared by using peripheral-blood lymphocytes from a normal male.

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (-)

tag: international prognostic index

value: high / high intermediate

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

value: loss / deletion

tag: genomic loss for 17p13.1 (tp53 locus)

value: loss

tag: follow up years

tag: dead or alive at the end of follow-up

value: Dead

source_name: healthy males

value: male


title: mCherry+ mantle cell untreated rep1

description: polyA RNA amplified

tag: cell type


title: PTCL51

description: file with raw data for this sample: PTCL51.txt

value: clonal heterogeneity (+)

value: low / low intermediate

value: Alive

tag: gender


title: Non-fluorescent untreated rep6

description: polyA RNA amplified

source_name: Non-fluorescent sorted cells, untreated


title: Non-fluorescent untreated rep3

description: polyA RNA amplified


title: PTCL45

description: file with raw data for this sample: PTCL45.txt


title: PTCL49

description: file with raw data for this sample: PTCL49.txt


title: PTCL46

description: file with raw data for this sample: PTCL46.txt


title: PTCL48

description: file with raw data for this sample: PTCL48.txt


title: Non-fluorescent untreated rep5

description: polyA RNA amplified


title: PTCL43

description: file with raw data for this sample: PTCL43.txt


title: PTCL44

description: file with raw data for this sample: PTCL44.txt


title: Non-fluorescent untreated rep4

description: polyA RNA amplified


title: PTCL40

description: file with raw data for this sample: PTCL40.txt


title: PTCL41

description: file with raw data for this sample: PTCL41.txt


title: PTCL47

description: file with raw data for this sample: PTCL47.txt


title: B019 rep1

source_name: B019 rep1 input

value: B73 and Mo17

tag: tissue

value: seedling leaf (L3)

value: input DNA

source_name: B019 rep1 IP


title: mCherry+ mantle cell untreated rep3

description: polyA RNA amplified

value: mCh+ Mantle


title: mCherry+ mantle cell untreated rep2

description: polyA RNA amplified

value: Untreated


title: Non-fluorescent untreated rep1

description: polyA RNA amplified

value: NF


title: mCherry+ mantle cell 11 hpCu rep4

description: polyA RNA amplified

source_name: mCherry+ sorted mantle cells, 11 h after copper sulfate treatment


title: PTCL42

description: file with raw data for this sample: PTCL42.txt


title: Normal hepatocyte cell line_HL-7702_rep1

city: Xi'an

first: Wei-Hua

last: Xu

state: Shaanxi

address: No. 127 West Changle Road

department: Hepatobiliary Surgery

country: China

institute: Xijing Hospital, Fourth Military Medical University

description: Gene expression of HL-7702 human HCC cell lines

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit in Hybridization Oven (Agilent Technologies) according to the manufacturer’s instructions. After a 17-hour hybridization, the arrays were washed in staining dishes with a Gene Expression Wash Buffer Kit (Agilent Technologies), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent Technologies) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies).

source_name: Normal hepatocyte cell line, HL-7702, replicate 1

label_protocol: Total RNA was amplified and transcribed into fluorescent cRNA using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). The labeled cRNA was purified using an RNeasy Mini Kit (QIAGEN) and hybridized to the Agilent Human LncRNA Microarray

growth_protocol: The  SMMC7721, HepG2 and Huh7 human HCC cell lines and the HL-7702 human immortalized normal hepatocyte cells were maintained in our lab. All of the cell lines were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco, Gaithersburg, MD, USA) containing 10% fetal bovine serum (Gibco) and incubated at 37 °C in a humidified environment containing 5% CO2.

extract_protocol: Total RNA was extracted from the cells or tissue samples using TRIzol (Life Technologies, Carlsbad, CA, USA) reagent according to the manufacturer’s recommended instructions. RNA purity and integrity were analyzed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Quantified total RNA was further purified using an RNeasy Mini Kit (QIAGEN, GmBH, Germany) and an RNase-free DNase set (QIAGEN).

tag: cell line

value: hepatocyte


title: Hepatoma cell line_Huh7_rep1

description: Gene expression of Huh7 human HCC cell lines

source_name: Hepatoma cell line, Huh7, replicate 1


title: PTCL39

description: file with raw data for this sample: PTCL39.txt


title: Hepatoma cell line_HepG2_rep 1

description: Gene expression of HepG2 human HCC cell lines

source_name: Hepatoma cell line, HepG2, replicate 1


title: PTCL38

description: file with raw data for this sample: PTCL38.txt


title: Hepatoma cell line_SMMC7721_rep1

description: Gene expression of SMMC7721 human HCC cell lines

source_name: Hepatoma cell line, SMMC7721, replicate 1


title: PTCL34

description: file with raw data for this sample: PTCL34.txt


title: PTCL32

description: file with raw data for this sample: PTCL32.txt


title: PTCL36

description: file with raw data for this sample: PTCL36.txt


title: PTCL33

description: file with raw data for this sample: PTCL33.txt


title: PTCL31

description: file with raw data for this sample: PTCL31.txt


title: PTCL35

description: file with raw data for this sample: PTCL35.txt


title: PTCL25

description: file with raw data for this sample: PTCL25.txt


title: PTCL30

description: file with raw data for this sample: PTCL30.txt


title: PTCL27

description: file with raw data for this sample: PTCL27.txt


title: PTCL23

description: file with raw data for this sample: PTCL23.txt


title: PTCL28

description: file with raw data for this sample: PTCL28.txt


title: PTCL37

description: file with raw data for this sample: PTCL37.txt


title: PTCL22

description: file with raw data for this sample: PTCL22.txt


title: PTCL21

description: file with raw data for this sample: PTCL21.txt


title: PTCL24

description: file with raw data for this sample: PTCL24.txt


title: PTCL20

description: file with raw data for this sample: PTCL20.txt


title: PTCL29

description: file with raw data for this sample: PTCL29.txt


title: PTCL26

description: file with raw data for this sample: PTCL26.txt


title: PTCL19

description: file with raw data for this sample: PTCL19.txt


title: PTCL16

description: file with raw data for this sample: PTCL16.txt


title: PTCL18

description: file with raw data for this sample: PTCL18.txt


title: PTCL14

description: file with raw data for this sample: PTCL14.txt


title: PTCL15

description: file with raw data for this sample: PTCL15.txt


title: PTCL13

description: file with raw data for this sample: PTCL13.txt


title: PTCL11

description: file with raw data for this sample: PTCL11.txt


title: PTCL17

description: file with raw data for this sample: PTCL17.txt


title: PTCL12

description: file with raw data for this sample: PTCL12.txt


title: PTCL08

description: file with raw data for this sample: PTCL08.txt


title: PTCL10

description: file with raw data for this sample: PTCL10.txt


title: PTCL09

description: file with raw data for this sample: PTCL09.txt


title: PTCL07

description: file with raw data for this sample: PTCL07.txt


title: PTCL06

description: file with raw data for this sample: PTCL06.txt


title: PTCL05

description: file with raw data for this sample: PTCL05.txt


title: PTCL04

description: file with raw data for this sample: PTCL04.txt


title: PTCL03

description: file with raw data for this sample: PTCL03.txt


title: PTCL02

description: file with raw data for this sample: PTCL02.txt


title: 83_254451610095

city: Dummerstorf

first: Klaus

last: Wimmers

state: Mecklenburg-Vorpommern

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology

hyb_protocol: Hybridization were made in house using Tecan HS400 Pro (Tecan Group Ltd., Switzerland) according to Agilent's protocol.

scan_protocol: Processed arrays were scanned using Tecan PowerScanner (Tecan Group Ltd., Switzerland). Array signal intensities  and local backgrounds were then summarized using Array-Pro Analyzer 6.3 (Meida Cybernetics Inc., USA), with potentially unreliable spots marked for removal.

data_processing: Previously marked spots were first removed across samples. Then local background were subtracted before vsn normalization using spike-in controls. As the last step, signals are corrected for batch effect using ComBat.

organism: Sus scrofa

source_name: M. longissimus dorsi_LO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, May 2010), followed by ? RNAeasy column purification (Qiagen, 4106)

extract_protocol: RNA was prepared using the miRNeasy Kit (Qiagen, 217004) following the manufacturer's recommendations. The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies)

tag: drip loss phenotype

value: low (LO)

tag: Sex

value: female

tag: batch

value: muscle sample of M. longissimus dorsi


title: 424_254451610100


title: 434_254451610093

source_name: M. longissimus dorsi_HI

value: high (HI)


title: Non-fluorescent untreated rep2

description: polyA RNA amplified


title: 579_254451610098


title: 234_254451610091


title: 261_254451610094


title: 82_254451610099


title: MCL29

description: file with raw data for this sample: MCL01_to_MCL29.txt

source_name: A tumor biopsy sample of a Mantle Cell lymphoma patient at diagnosis

value: loss / deletion

value: loss


title: 234_254451610084


title: 82_254451610090


title: 579_254451610066

value: male


title: MCL28

value: clonal heterogeneity (+)

value: Dead


title: MCL27

value: low / low intermediate


title: 204_254451610092


title: 83_254451610087


title: MCL26

value: clonal heterogeneity (-)

value: high / high intermediate


title: 261_254451610096


title: 205_254451610089


title: MCL25


title: MCL24


title: 559_254451610065


title: MCL23


title: 434_254451610082


title: 204_254451610068


title: MCL22


title: 424_254451610081


title: 205_254451610043


title: PTCL01

description: file with raw data for this sample: PTCL01.txt

value: Alive


title: 559_254451610097


title: MCL21


title: MCL19


title: 199_254451610042


title: 36_254451610083


title: MCL20


title: 204_254451610088


title: 424_254451610085


title: MCL18


title: 82_254451610080


title: MCL15


title: 83_254451610067


title: MCL12


title: MCL13


title: MCL10


title: MCL14


title: MCL11


title: MCL17


title: MCL08


title: MCL09


title: MCL07


title: D027039_254451610072

source_name: M. longissimus dorsi

tag: type

value: LO

value: M


title: D027038_254451610073

value: HI


title: MCL06


title: IgMhigh vs IgMlow B cells in cattle numbered 384

city: Sapporo

first: Ryoyo

last: Ikebuchi

state: Hokkaido

address: Kitaku Kita18jou Nishi9tyoume

department: Disease Control

institute: Graduate School of Veterinary Medicine, Hokkaido University

description: IgMhigh and IgMlow B cells were sorted from peripheral blood mononuclear cells cultivated overnight

hyb_protocol: Hybridization was performed by Gene Expression Hybridization Kit following manufacturer's instructions.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

organism: Bos taurus

source_name: IgMhigh B cells

label_protocol: 100 ng of total RNA were labeled by Low Input Quick Amp Labeling Kit following manufacturer's instructions.

growth_protocol: Peripheral blood mononuclear cells from bovine leukemia virus-infected cattle were cultivated overnight in RPMI-1640.  Then, IgMhigh and IgMlow B cells were sorted by cell sorter.

extract_protocol: Total RNA extracted using Rneasy Plus Mini following manufacturer's instructions.

value: Blood

tag: disease stage

value: Persistent lymphocytosis

source_name: IgMlow B cells


title: D036046_254451610075


title: D026053_254451610076


title: MCL05


title: MCL16


title: 36_254451610041


title: IgMhigh vs IgMlow B cells in cattle numbered 651


title: IgMhigh vs IgMlow B cells in cattle numbered 827


title: D036029_254451610078

value: F


title: MCL02


title: MCL03


title: miR-17-92_TG2_25.5hr

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

organism: Mus musculus

source_name: FoB cells_miR-17-92TG_25.5

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

extract_protocol: Total RNA was extracted using RNeasy kit (QIAGEN).

tag: strain

tag: genotype

value: CD19-Cre;miR-17~92 Tg/Tg mice

value: Follicular B cells

tag: stimulation duration


title: D026048_254451610077


title: FL80

description: file with raw data for this sample: Follicular_lymphoma_3.txt

source_name: A tumor biopsy sample of a Follicular Lymphoma patient at diagnosis

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index


title: D023016_254451610046


title: FL79

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

source_name: healthy males


title: miR-17~92_TG3_13.5hr

source_name: FoB cells_miR-17-92TG_13.5

tag: cell type


title: miR-17-92_TG2_13.5hr


title: MCL04

value: loss / deletion

tag: dead or alive at the end of follow-up

tag: gender


title: MCL01

value: loss


title: FL78

value: male


title: WT3_25.5hr

source_name: FoB cells_WT_25.5

value: WT


title: miR-17-92_TG3_25.5hr


title: D036029_254451610057


title: D026030_254451610045


title: FL77

value: clonal heterogeneity (+)


title: D036028_254451610079


title: FL76


title: D026048_254451610060


title: FL75

description: file with raw data for this sample: Follicular_lymphoma_1.txt

value: Dead


title: WT1_25.5hr


title: FL74


title: miR-17-92_TG1_25.5hr


title: D027038_254451610050


title: D027039_254451610049


title: FL72

description: file with raw data for this sample: Follicular_lymphoma_2.txt

value: clonal heterogeneity (-)


title: WT2_25.5hr


title: FL71


title: D036058_254451610048


title: D049051_254451610055


title: S. mutans ∆nox mutant pH5 replicate 4

city: Rochester

first: Roberta

last: Faustoferri

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

hyb_protocol: The slides were hybridized in a mixture containing equal amounts of labeled test and reference cDNA as described by the protocol from the Pathogen Functional Genomics Research Center (PFGRC) for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Hybridized slides were washed and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were washed using the method described by the Pathogen Functional Genomics Research Center (PFGRC) and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  MIDAS software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting, followed by in-slide replicate analysis.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P-value of 0.01 and a ≥2-fold change of expression.

organism: Streptococcus mutans UA159

source_name: RNA from ∆nox mutant strain, steady-state pH5

label_protocol: Once RNA was purified as described above, cDNA was generated from 2µg RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Life Technologies, Carlsbad, CA) to increase cDNA yields.  Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: S. mutans UA159 (parent strain) and MU1020 (∆nox) were grown in continuous culture to steady-state pH values of 5 with or without supplemented oxygen in a BioFlo2000 fermentor at a dilution rate of 0.24h-1 in non-limiting glucose concentrations.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in continuous culture in TY + 1% glucose medium to steady-state pH value of 5 with or without supplemented oxygen, by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined spectrophotometrically.

value: nox null

tag: treatment

value: steady-state pH5

value: mutant

source_name: RNA from parent strain, mid-log

value: control

value: wild type

tag: growth phase

value: mid-log


title: WT3_13.5hr

source_name: FoB cells_WT_13.5


title: WT2_13.5hr


title: WT1_13.5hr


title: S. mutans ∆nox mutant pH5 replicate 2


title: D026053_254451610059

value: HI

tag: Sex

value: M

tag: batch


title: miR-17-92_TG1_13.5hr

value: CD19-Cre;miR-17~92 Tg/Tg mice


title: D036058_254451610056

tag: type


title: S. mutans ∆nox mutant pH5 replicate 1


title: S. mutans ∆nox mutant pH5 replicate 3


title: FL67


title: FL68


title: FL69


title: D036028_254451610058

value: F


title: D027039_254451610063

value: LO


title: D049051_254451610047


title: FL66


title: D026030_254451610061


title: FL64


title: FL65


title: FL61


title: FL62

value: Alive


title: FL60

value: loss / deletion

value: loss

value: male


title: D027038_254451610064


title: S. mutans UA159 parent strain + 8.4% O2 pH5 replicate 4

source_name: RNA from parent strain with oxygen, steady-state pH5

value: oxygen, steady-state pH5

value: supplemented


title: FL63

value: clonal heterogeneity (-)


title: S. mutans UA159 parent strain + 8.4% O2 pH5 replicate 3


title: S. mutans UA159 parent strain pH5 replicate 3

source_name: RNA from parent strain, steady-state pH5

value: steady-state pH5

value: parental


title: S. mutans UA159 parent strain pH5 replicate 4

value: control


title: S. mutans UA159 parent strain + 8.4% O2 pH5 replicate 1

value: wild type


title: S. mutans UA159 parent strain pH5 replicate 2

value: mid-log


title: S. mutans UA159 parent strain pH5 replicate 1


title: FL59


title: FL55


title: FL56

value: clonal heterogeneity (+)


title: FL53


title: D023016_254451610062


title: FL52


title: FL58


title: FL57


title: FL49

value: Dead


title: FL50


title: FL51


title: FL48


title: FL44


title: FL42


title: FL41


title: FL46


title: FL47


title: FL54


title: FL43


title: FL45


title: FL40


title: FL73


title: FL39


title: FL38


title: FL37


title: Twin36-1

city: Choongchung-Buk-do

first: Hyo-Jeong

last: Ban

address: OHTAC, Yeonje-ree 643, Osong-eup, Chungwon-Koon

department: bioinformatics

country: South Korea

institute: KCDC

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was log transformed and then VST-quantile normalized based on R packages (lumi v.14.01, affy v.1.41.2).

source_name: lymphoblastoid cells

label_protocol: standard as recommended by illumina

extract_protocol: Cells were lysed and RNA extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser and Nanodrop

tag: twin pairing

value: MZ twin pair 2 sibling 1

value: lymphoblastoid cells


title: Twin33-1


title: FL35


title: Twin36-2

value: MZ twin pair 2 sibling 2


title: FL33

value: Alive


title: FL34


title: FL32


title: Twin35-2


title: Twin31-1

value: MZ twin pair 1 sibling 1


title: Twin33-2


title: Twin32-1


title: Twin34-1


title: Twin34-2


title: Twin32-2


title: Twin30-2


title: Twin31-2

value: MZ twin pair 1 sibling 2


title: S. mutans UA159 parent strain + 8.4% O2 pH5 replicate 2

tag: genotype


title: Twin28-1


title: Twin30-1


title: Twin29-2


title: Twin28-2


title: FL36

value: male


title: Twin27-2


title: Twin27-1


title: FL29

value: loss / deletion


title: FL28


title: FL30


title: FL31


title: Twin29-1


title: Twin26-1


title: FL22


title: FL23


title: FL21


title: FL27


title: FL26


title: Twin25-2


title: Twin24-2


title: Twin23-2


title: FL19


title: Twin25-1


title: FL20


title: Twin24-1


title: Twin22-2


title: Twin23-1


title: FL18


title: FL16


title: FL15


title: FL13


title: FL12


title: FL14


title: Twin21-2


title: Twin20-2


title: FL17


title: FL11


title: Twin19-2


title: FL10


title: Twin17-2


title: FL09


title: FL08


title: FL07


title: FL04


title: FL05


title: FL06


title: Twin26-2


title: FL03


title: Twin18-2


title: FL02


title: FL01


title: DLBCL118

description: file with raw data for this sample: DLBCL_1.txt

source_name: A tumor biopsy sample of a DLBCL patient at diagnosis

value: loss


title: DLBCL117


title: Twin19-1


title: DLBCL116

value: clonal heterogeneity (-)


title: Twin16-1


title: DLBCL115


title: Twin22-1


title: Twin15-1


title: Twin21-1


title: Twin18-1


title: Twin15-2


title: Twin14-1


title: Twin20-1


title: Twin13-1


title: DLBCL114


title: Twin14-2


title: Twin17-1


title: Twin12-2


title: Twin35-1


title: Twin13-2


title: Twin11-1


title: Twin10-1


title: Twin11-2


title: FL24


title: Twin12-1


title: FL25


title: DLBCL110


title: DLBCL108


title: DLBCL113


title: DLBCL111


title: DLBCL109


title: DLBCL107


title: DLBCL106


title: DLBCL105


title: DLBCL112


title: DLBCL103


title: DLBCL104


title: DLBCL102


title: Twin9-2


title: Twin8-2


title: Twin10-2


title: DLBCL100


title: Twin7-1


title: Twin8-1


title: Twin7-2


title: Twin6-2


title: Twin5-2


title: Twin5-1


title: Twin9-1


title: Twin4-2


title: Twin3-1


title: DLBCL097

value: high / high intermediate


title: DLBCL096


title: DLBCL098


title: DLBCL101


title: Twin3-2


title: Twin4-1


title: Twin2-2


title: Twin1-2


title: Twin2-1


title: DLBCL095

description: file with raw data for this sample: DLBCL_2.txt


title: Twin1-1


title: DLBCL099


title: Twin6-1


title: Mec1_CD38M vitro_rep2_clone2

city: Turin

first: SILVIA

last: DEAGLIO

address: Via Nizza 52

department: Medical Sciences

institute: University of Torino & Human Genetics Foundation

description:
7018852051_L
vitro_rep2_clone2

hyb_protocol: Standard Illumina hybridization protocol using Whole-Genome Expression Direct Hybridization kit

scan_protocol: Standard Illumina scanning protocol (iScan System)

data_processing: Detection call for each probe set of the array were obtained with the GenomeStudio Gene Expression Module Software (Illumina) applying a standard quantile normalization.

source_name: cell culture

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted from purified leukemic cells with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: cell type (grown in vitro)


title: DLBCL092

tag: total number of genomic aberrations


title: DLBCL091

tag: with or without clonal heterogeneity

value: low / low intermediate


title: DLBCL090

description: file with raw data for this sample: DLBCL_4.txt

tag: international prognostic index


title: DLBCL088

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)


title: DLBCL086

tag: genomic loss for 17p13.1 (tp53 locus)


title: DLBCL087

description: file with raw data for this sample: DLBCL_3.txt

tag: follow up years


title: DLBCL089


title: DLBCL093


title: DLBCL085


title: DLBCL094


title: DLBCL084


title: Mec1_CD38M vitro_rep3_clone1

description:
7018852051_K
vitro_rep3_clone1


title: Mec1_CD38WT vitro_rep2_clone2

description:
7018852051_J
vitro_rep2_clone2


title: DLBCL083


title: Mec1_CD38M vivo_rep2_clone1

description:
7018852051_E
vivo_rep2_clone1

tag: cell type (grown in vivo)

value: Mec1_CD38M (purified leukemic cells recovered from kidney metastases)


title: DLBCL082

tag: dead or alive at the end of follow-up


title: Mec1_CD38WT vivo_rep3_clone2

description:
5937345101_F
vivo_rep3_clone2

value: Mec1_CD38WT (purified leukemic cells recovered from kidney metastases)


title: Mec1_GFP vivo_rep3

description:
7018852051_A
vivo_rep3

value: Mec1_GFP (purified leukemic cells recovered from kidney metastases)


title: Mec1_GFP vivo_rep4

description:
7018852051_B
vivo_rep4

source_name: purified leukemic cells recovered from kidney metastases


title: Mec1_CD38WT vivo_rep3_clone1

description:
7018852051_C
vivo_rep3_clone1


title: Mec1_CD38WT vivo_rep4_clone1

description:
7018852051_D
vivo_rep4_clone1


title: Mec1_CD38M vitro_rep1_clone2

description:
5937345101_E
vitro_rep1_clone2


title: DLBCL081

value: clonal heterogeneity (+)

tag: gender


title: Mec1_GFP vitro_rep3

description:
7018852051_I
vitro_rep3


title: Mec1_CD38M vivo_rep1_clone1

description:
5937345101_G
vivo_rep1_clone1


title: Mec1_CD38WT vivo_rep2_clone2

description:
5937311008_L
vivo_rep2_clone2


title: DLBCL080


title: Mec1_CD38WT vivo_rep2_clone1

description:
5937311008_K
vivo_rep2_clone1


title: Mec1_GFP vivo_rep2

description:
5937311008_J
vivo_rep2


title: DLBCL079


title: DLBCL073


title: DLBCL077


title: DLBCL076


title: DLBCL074


title: Mec1_CD38WT vitro_rep1_clone2

description:
5937345101_D
vitro_rep1_clone2


title: DLBCL075


title: Twin16-2

tag: cell type


title: DLBCL069


title: DLBCL070


title: Mec1_GFP vitro_rep2

description:
5937311008_G
vitro_rep2


title: Mec1_CD38M vitro_rep1_clone1

description:
5937311007_I
vitro_rep1_clone1


title: DLBCL068


title: Mec1_CD38WT vitro_rep2_clone1

description:
5937311008_H
vitro_rep2_clone1


title: Mec1_CD38WT vivo_rep1_clone1

description:
5937311007_K
vivo_rep1_clone1


title: Mec1_CD38M vitro_rep2_clone1

description:
5937311008_I
vitro_rep2_clone1


title: Mec1_CD38WT vivo_rep1_clone2

description:
5937311007_L
vivo_rep1_clone2


title: Mec1_GFP vivo_rep1

description:
5937311007_J
vivo_rep1


title: DLBCL067


title: Mec1_GFP vitro_rep1

description:
5937311007_G
vitro_rep1


title: Mec1_CD38WT vitro_rep1_clone1

description:
5937311007_H
vitro_rep1_clone1


title: DLBCL064


title: DLBCL078


title: DLBCL063


title: PE PREGNANCY [101379-24]

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

institute: Amsterdam UMC

description: Delivery by C section at 30 weeks + 2 days of gestation

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was analysed using Genespring GX12.6. RAW data were subject to quantile normalization and baseline transformation was performed to the median of all.

source_name: pregnancy complicated with preeclampsia

label_protocol: Biotinylated cRNA was prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted with Trizol reagent from tissue stored at -80 degrees Celcius in RNALater. After clean-up with the QIAGEN RNeasy MinElute Cleanup Kit in accordance with the protocol described by the manufactorer  and DNase I treatment, quality control was performed with the Agilent Bioanalyser.

tag: tissue

value: Placenta


title: DLBCL066


title: PE PREGNANCY [101379-23]

description: Vaginal delivery at 38 weeks + 0 days of gestation


title: DLBCL062


title: NORMOTENSIVE PREGNANCY [101379-22]

description: Vaginal delivery at 31 weeks + 3 days of gestation

source_name: normotensive pregnancy


title: DLBCL061


title: NORMOTENSIVE PREGNANCY [101379-21]

description: Delivery by C section at 31 weeks + 5 days of gestation


title: DLBCL060


title: DLBCL065


title: PE + HELLP PREGNANCY [101379-20]

description: Delivery by C section at 28 weeks + 4 days of gestation

source_name: pregnancy complicated with preeclampsia and HELLP syndrome


title: DLBCL059


title: DLBCL058


title: NORMOTENSIVE PREGNANCY [101379-19]

description: Delivery by C section at 33 weeks + 6 days of gestation


title: DLBCL056


title: DLBCL055


title: NORMOTENSIVE PREGNANCY [101379-16]

description: Vaginal delivery at 26 weeks + 2 days of gestation


title: NORMOTENSIVE PREGNANCY [101379-09]

description: Delivery by C section at 40 weeks + 0 days of gestation


title: PE + HELLP PREGNANCY [101379-17]

description: Vaginal delivery at 34 weeks + 4 days of gestation


title: DLBCL053


title: PE + HELLP PREGNANCY [101379-18]

description: Delivery by C section at 33 weeks + 1 day of gestation


title: NORMOTENSIVE PREGNANCY [101379-10]

description: Delivery by C section at 40 weeks + 1 day of gestation


title: PE + HELLP PREGNANCY [101379-15]

description: Delivery by C section at 29 weeks + 1 day of gestation


title: PE + HELLP PREGNANCY [101379-11]


title: NORMOTENSIVE PREGNANCY [101379-13]

description: Delivery by C section at 34 weeks + 5 days of gestation


title: DLBCL050

description: file with raw data for this sample: DLBCL_1.txt


title: DLBCL049

description: file with raw data for this sample: DLBCL_2.txt


title: DLBCL051


title: DLBCL052


title: DLBCL054


title: DLBCL046

value: Dead


title: DLBCL047


title: DLBCL048

description: file with raw data for this sample: DLBCL_4.txt


title: NORMOTENSIVE PREGNANCY [101379-08]

description: Delivery by C section at 39 weeks + 3 days of gestation


title: NORMOTENSIVE PREGNANCY [101379-07]

description: Delivery by C section at 35 weeks + 5 days of gestation


title: PE PREGNANCY [101379-12]

description: Delivery by C section at 35 weeks + 3 days of gestation


title: DLBCL045


title: NORMOTENSIVE PREGNANCY [101379-06]

description: Delivery by C section at 38 weeks + 5 days of gestation


title: NORMOTENSIVE PREGNANCY [101379-05]

description: Vaginal delivery at 39 weeks + 2 days of gestation


title: PE PREGNANCY [101379-03]

description: Delivery by C section at 30 weeks + 5 days of gestation


title: DLBCL044


title: DLBCL043


title: PE PREGNANCY [101379-14]

description: Delivery by C section at 34 weeks + 1 day of gestation


title: DLBCL042


title: DLBCL041


title: NORMOTENSIVE PREGNANCY [101379-01]

description: Vaginal delivery at 36 weeks + 5 days of gestation


title: DLBCL039


title: DLBCL040


title: PE + HELLP PREGNANCY [101379-02]

description: Delivery by C section at 28 weeks + 1 day of gestation


title: DLBCL037


title: PE + HELLP PREGNANCY [101379-04]

description: Vaginal delivery at 36 weeks + 3 days of gestation


title: DLBCL035


title: mda_mb_231_treated_repli3

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

country: Belgium

institute: University Of Antwerp

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in limma 3.14.1 for R

source_name: cell line ATCC

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: The MDA-MB-231 and MCF-7 cell lines, purchased from American Type Culture Collection (Manassas, VA, USA), were cultivated in high glucose (4,5 g/L) Dulbecco’s Modified Eagle Medium with 10% Foetal Bovine Serum, 2 mM L-Glutamine, 1 mM Sodium Pyruvate MEM, 50 IU/mL Penicillin and 50 µg/mL Streptomycin. The MDA-MB-231 cell line was additionally supplemented with 1% MEM Non-Essential Amino Acids. Each cell line was maintained at 37°C in the humidified atmosphere containing 5% CO2 until 80-90% confluence.

extract_protocol: RNA was extracted using TRI reagent (Sigma-Aldrich)  and Rneasy Mini kit (Qiagen)

treatment_protocol: Induction experiments with WA, 2 x 10^4 viable MDA-MB-231 cells/cm2 and 5.3 x 10^3 viable MCF-7 cells/cm2 were plated in an appropriate cell culture flask/plate 24 hours before the treatment. Every 24 hours, compounds or DMSO controls (final concentration 0,0035% if not otherwise stated) diluted in a fresh medium were added for a total time of 72 hours. At that time point, cells were harvested with 0.05% Trypsin/EDTA solution, washed with 1x PBS and collected for further analysis.

tag: cell line

tag: treatment

value: treated with 700 nM WA


title: DLBCL034

description: file with raw data for this sample: DLBCL_5.txt


title: DLBCL038


title: mcf7_treated_repli3

description: replicate 3


title: mda_mb_231_repli1

description: replicate 1

value: untreated


title: mcf7_repli3

description: replicate 3


title: mcf7_treated_repli1

description: replicate 1


title: DLBCL033


title: mda_mb_231_repli2

description: replicate 2


title: mda_mb_231_treated_repli2

description: replicate 2


title: mcf7_repli2

description: replicate 2


title: mda_mb_231_repli3

description: replicate 3


title: mda_mb_231_treated_repli1

description: replicate 1


title: DLBCL032


title: DLBCL031


title: DLBCL030


title: mcf7_treated_repli2

description: replicate 2


title: DLBCL029


title: DLBCL028


title: DLBCL027

description: file with raw data for this sample: DLBCL_3.txt


title: DLBCL036


title: mcf7_repli1

description: replicate 1


title: DLBCL026


title: DLBCL023


title: DLBCL024


title: DLBCL071


title: DLBCL072

value: Alive


title: DLBCL020


title: DLBCL019


title: DLBCL021


title: DLBCL022


title: DLBCL018


title: C2PL15V2

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT12 V4 beadchips (Illumina, San Diego, CA)

scan_protocol: Following hybridization each chip was washed, blocked, stained, and scanned on an Illumina BeadStation 500 following the manufacturer’s protocols.

data_processing: Illumina GenomeStudio software was used for each sample to subtract background and scale average signal intensity to the global average signal intensity for all samples.

source_name: Whole Blood

label_protocol: 250 ng of RNA from all samples passing quality control were then amplified and labeled using the Illumina TotalPrep-96 RNA amplification kit (Ambion, Austin, TX)

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: group

value: SLE

tag: age

value: F

tag: race

value: White

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

value: Y

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL27V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d


title: DLBCL025

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

value: high / high intermediate

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

source_name: healthy males

value: male


title: DLBCL017

value: clonal heterogeneity (-)

tag: gender


title: C2PL7V2

tag: group

tag: age

tag: race

value: Black

tag: country of origin

value: Comorres

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL6V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d


title: DLBCL016

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL20V4

tag: group

tag: age

tag: gender

value: M

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL23V1

tag: group

tag: age

tag: gender

tag: race

value: Asian

tag: country of origin

value: China

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL34V2

tag: group

tag: age

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C1PL13V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL4V1

tag: group

tag: age

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL19V3

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL11V1

tag: group

tag: age

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: DLBCL013

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (+)

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

value: Dead

tag: gender


title: DLBCL014

value: low / low intermediate


title: C1PL14V2

tag: group

value: SLE

tag: age

value: F

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd


title: C2PL2V4

tag: group

tag: age

tag: gender

tag: race

value: White

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: DLBCL012

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

value: loss / deletion

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL42V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: Vietnam

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: Y

tag: joints

value: N

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb


title: C2PL34V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL38V1

tag: group

tag: age

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb


title: C2PL3V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C3VS20n1

tag: group

value: Healthy control of SLE

tag: age


title: DLBCL011

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

value: high / high intermediate

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender

value: male


title: DLBCL010


title: DLBCL015

value: clonal heterogeneity (-)


title: DLBCL007


title: DLBCL008


title: C2PL22V3

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils


title: DLBCL006

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: DLBCL009

value: loss


title: C3VS19n1

tag: group

tag: age

tag: race

tag: country of origin


title: DLBCL005


title: DLBCL003


title: DLBCL004


title: C2PL11V2

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: lymphocytes

tag: eosino


title: C3VS14n1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin


title: BL26

description: file with raw data for this sample: Burkitt_lymphoma01_to_26.txt

source_name: A tumor biopsy sample of a Burkitt lymphoma patient at diagnosis

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (+)

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: DLBCL001

value: Dead


title: DLBCL002


title: C2PL29V2

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL7V3

tag: group

tag: age

tag: gender

tag: race

value: Black

tag: country of origin

value: Comorres

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: low c3

tag: low c4

tag: lymphocytes

tag: eosino


title: C2PL28V3

tag: group

value: SLE

tag: age

value: F

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL24V2

tag: group

tag: age

tag: gender

tag: race

value: White

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: low c3

tag: low c4

tag: lymphocytes

tag: eosino


title: C3VS29

tag: group

tag: age


title: C2PL43V2

tag: gender

tag: race

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL4V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: low c3

tag: low c4

tag: eosino


title: BL24

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL38V3

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL36V3

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: Cuba

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: low c3

tag: low c4

tag: eosino


title: C1PL5V1

tag: group

tag: age

value: M

value: Y

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL9V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

value: N

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: low c3

tag: low c4

tag: eosino


title: BL25

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL42V2

tag: group

tag: age

tag: gender

tag: race

value: Asian

tag: country of origin

value: Vietnam

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: BL23

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (-)

tag: international prognostic index

value: high / high intermediate

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

value: Alive

tag: gender

value: male


title: C1PL11V3

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: low c3

tag: low c4

tag: eosino


title: C2PL44V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL12V1

tag: group

tag: age

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: low c3

tag: low c4

tag: eosino