title: ffpe-breast-tumor (14-07280)

description: breast tumor


title: Alone Replicate 4

status: Public on Apr 01 2018

type: SRA

city: Medford

first: Benjamin

last: Wolfe

state: MA

address: Tufts University - Biology, 200 Boston Ave, Suite 4700

department: Biology

country: USA

institute: Tufts University - Biology

description: GlutiPenRNAseqforGEO.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped and gene expression values were calculated using default parameters in Rockhopper version 2.0.3 (De novo assembly of bacterial transcriptomes from RNA-seq data. Brian Tjaden. Genome Biology, 16:1, 2015.)
Genome_build: ASM287867v1
Supplementary_files_format_and_content: Rockhopper output with raw and normalized expression values [GlutiPenRNAseqforGEO.txt]

molecule: total RNA

organism: Glutamicibacter arilaitensis

source_name: Biofilm of Glutamicibacter arilaitensis growing on cheese curd agar

growth_protocol: For each experimental unit, approximately 80,000 CFUs of G. arilaitensis JB182 were spread across the surface of a 100mm Petri dish containing 20 mL of cheese curd agar.

extract_protocol:
Rind biofilms were harvested by scraping the cheese curd surface and stored in RNAProtect Reagent (Qiagen) and RNA was extracted using a standard phenol-chloroform protocol.
To confirm that the samples were free of DNA contaminants, a PCR of the 16S rRNA gene was performed with standard primers (27f and 1492r). Overall quantity and quality of the RNA preps were confirmed by Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. RNA-seq libraries were constructed from purified mRNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Pooled library samples were be sequenced using paired-end 100bp reads on an Illumina HiSeq Rapid Run by the Harvard Bauer Core Sequencing Core Facility. Each library yielded 6.8-8.9 million forward reads that were used for analysis.

treatment_protocol: For the + Penicillium sp. #12 treatment, approximately 100,000 CFUs of Penicillium were co-inoculated onto the plates with G. arilaitensis JB182. Plates were at > 90% relative humidity at 24 °C for 5 days.

tag: strain

tag: treatment

value: growing alone

tag: tissue

value: experimental biofilm


title: ffpe-breast-tumor (14-07279)

type: RNA

city: Salt Lake City

first: Nicola

middle: J

last: Camp

state: UT

address: 2000 Cir of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah

description: breast tumor

data_processing: Each gene was normalized to the expression of the same gene in a within-run reference sample and then normalized to the geometric average of the 5 housekeeper genes (ACTB, MRPL19, PSMC4, RPLP0, SF3A1)

label: SYBR Green

organism: Homo sapiens

source_name: tumor FFPE

label_protocol: First-strand cDNA was synthesized using Superscript III reverse transcriptase (first Strand Kit; Invitrogen, Carlsbad, CA) and a mixture of random hexamers and gene-specific primers. PCR amplification and fluorescent melting curve analysis was done on the LightCycler 480 using SYBR Green I Master Mix (Roche Applied Science).

extract_protocol: Total RNA was extracted with High Pure RNA Paraffin Kit (Roche)

tag: Sex

value: F

tag: intrinsic subtype

value: Luminal B


title: ffpe-breast-tumor (14-07278)

description: breast tumor

value: Basal-like


title: px0494-AGCATCA

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
Basecalls performed using Illumina's CASAVA software, version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The first 6 bases were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.1 using the parameters --clip_R1 6 --clip_R2 6 –paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), –a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ≤ 20), and –u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17. Duplicates were marked with Picard V1.31 (http://picard.sourceforge.net).
Methylation of each cytosine was called using SAMtools mpileup (-B -C 0 -q 30 -d 500) followed by Novomethyl V1.01 (-o Consensus -%) (www.novocraft.com). Cytosine calls with Phred quality score ≤15 were discarded. Methylation percentage of each CpG di-nucleotide (found by searching the genome with a custom java script) was calculated by taking a weighted average of each cytosine using the map command from the bedtools suite (Quinlan and Hall, 2010). In most cases, only one base within a CpG dinucleotide had coverage; in these cases, the methylation information of the covered base was extrapolated to the other base.
Genome_build: hg19
Supplementary_files_format_and_content: bed file for CpG methylation. Columns are as follows: chr, start, end, fractional methylation, methylated C's, total C's, # of CpGs covered in the dinucleotide (1=just one, 2=both C and G covered)

molecule: genomic DNA

source_name: CD49f Hematopoetic stem cell

extract_protocol:
Sorted cells were lysed in 96 well plates in 4 uL of lysis buffer (20 mM Tris-HCl, pH 8.0, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL Qiagen Protease) for 30 minutes at 50 degrees.
The lysed cells were then spiked-in with 1 uL of 60 fg/uL purified T7 phage DNA (GeneON). The DNA mixture was then bisulfite converted with the MethylEdge Bisulfite Conversion kit (Promega) using a modified bead-based protocol which enables automation (Domanico et al., 2013): 5 uL of the lysis/spike-in mixture was combined with 32.5 uL of MethylEdge Conversion reagent and incubated at 98°C for 8 minutes and 54°C for 60 minutes in a PCR machine. After incubation, the plate was briefly spun down and placed on an Agilent Bravo robot for subsequent steps. The 37.5 uL of bisulfite converted DNA was mixed with 180 uL of MethylEdge Binding Buffer and 1.8 uL of 20 mg/mL MagSi-DNA allround magnetic silica beads (MagnaMedics) and incubated at room temperature for 15 minutes. The beads were then collected on a magnet for 3 minutes and washed twice with 220 uL of 80% ethanol for 30 seconds while on the magnet. 60 uL of MethylEdge desulfonation buffer was added and incubated for 15 minutes. The desulfonation buffer was then removed and the beads were washed twice with 100 uL of 80% ethanol. The beads were then air-dried for 1 minute, resuspended in 20 uL of Qiagen elution buffer, and incubated at 56°C in a shaking incubator at 2,000 rpm for 15 minutes. The beads were then collected on a magnet for 30 seconds and the supernatant containing the DNA was removed. The bisulfite-converted ssDNA from above was added directly into a mixture containing 1.25 uL of 10 mM dNTPs and 1 uL of 500 uM random hexamers (3’ phosphothioate). The reactions were incubated at 98°C for 1 minute and snap frozen on ice for 2 minutes. A mastermix of 0.5 uL of 50 U/uL Klenow fragment [3’→5’ exo-] (NEB M0212M), and 2.5 uL of 10X NEB Buffer 2 was added on ice and mixed well. The reactions incubated in a PCR machine as follows: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes. The entire reaction was denatured again at 98˚C for 1 minute and snap frozen on ice for 2 minutes. The reaction was transferred on a pre-chilled CoolRack by robot into a new plate containing 5 uL mixture of 20 uM random hexamers (3’ phosphothioate), 0.5 mM dNTPs, 1X NEB buffer and 25 U of Klenow fragment [3’→5’ exo-]. The wells were mixed well and the reaction was cycled once again: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes, and heat-inactivated at 70°C for 10 minutes. 20 uL of Qiagen Elution Buffer was added to each reaction to make it up to 50 uL, and each reaction was purified using 50 uL of Sera-Mag beads before proceeding to the standard illumina adapter ligation library construction protocol. The 25 uL of cleaned-up adapter-ligated fragments were PCR amplified in 50 uL containing 1 U of Phusion U Hot Start DNA Polymerase (Life Technologies F-555S), 1X HF buffer, 3% DMSO, 200 uM dNTPs, 0.5 uM PCR primer 1.0 (need sequence) (IDT), and corresponding 0.5 uM indexing PCR primer 2.0. The reactions were incubated in a PCR machine as follows: initial 98˚C for 1 minute; 10 cycles of 98˚C for 30 seconds, 65˚C for 15 seconds, 72˚C for 15 seconds; and a final extension of 72˚C for 5 minutes. The 50 uL reaction was cleaned up with 40 uL of Sera-Mag beads and eluted in 15 uL.

tag: type

value: single-cell

tag: donor

tag: markers


title: px0494-ACCCAGA


title: px0494-ACATCTA


title: ffpe-breast-tumor (14-07277)

description: breast tumor


title: px0494-ACAGTGA


title: Alone Replicate 1

description: GlutiPenRNAseqforGEO.txt


title: ffpe-breast-tumor (14-07276)

description: breast tumor

value: Luminal A


title: ffpe-breast-tumor (14-06544)

description: breast tumor


title: px0494-AATAGGA


title: px0494-ACTCTCA


title: ffpe-breast-tumor (14-06543)

description: breast tumor


title: ffpe-breast-tumor (14-06542)

description: breast tumor


title: S_71

city: Brussel

first: Yacine

last: Bareche

address: Rue Héger-Bordetstraat 1

country: Belgium

institute: Jules Bordet Institute

description: Gene expression data from breast tumor sample

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing: Gene expression data from the NanoString nCounter assay were analyzed after QC filtering and normalization by using the R package NanoStringQCPro (version 0.99.8.3). As recommended, the mean of the positive probes and the housekeeping genes were used in order to account for differences in sample input. Moreover, negative control probes were used for background correction and samples that did not pass QC control were removed.

source_name: Breast tumor

label_protocol: Not applicable

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: gender

value: Female

value: breast cancer tumor

tag: tumor type

value: HER2 Breast Cancer

tag: age

tag: estrogen receptor status

value: YES

tag: grade

tag: Stage

value: II

tag: progesterone receptor status

tag: pcr


title: S_55

value: NO


title: S_106

value: III


title: ffpe-breast-tumor (14-06541)

description: breast tumor


title: px0494-AAGACTA


title: Alone Replicate 2

description: GlutiPenRNAseqforGEO.txt


title: ffpe-breast-tumor (14-06540)

description: breast tumor


title: S_60


title: px0494-AACCCCA


title: px0494-AACTTGA


title: px0494-AAACATA


title: ffpe-breast-tumor (14-06535)

description: breast tumor


title: S_44


title: px0493-TTCTCCA


title: S_119


title: S_161


title: ffpe-breast-tumor (14-06534)

description: breast tumor


title: ffpe-breast-tumor (14-06539)

description: breast tumor


title: px0494-AAGGACA


title: ffpe-breast-tumor (14-06532)

description: breast tumor


title: ffpe-breast-tumor (14-06533)

description: breast tumor


title: px0493-TTAGGCA


title: px0494-AAGCGAA


title: ffpe-breast-tumor (14-06531)

description: breast tumor


title: px0493-TGCCATA


title: S_61


title: S_39


title: px0493-TGACCAA


title: S_28


title: S_15


title: ffpe-breast-tumor (14-06530)

description: breast tumor


title: ffpe-breast-tumor (14-06529)

description: breast tumor


title: px0493-TTCGAAA


title: px0493-TCGGCAA


title: px0493-TGAATGA


title: ffpe-breast-tumor (14-06528)

description: breast tumor


title: ffpe-breast-tumor (14-06527)

description: breast tumor


title: px0493-TACAGCA


title: px0493-TAATCGA


title: ffpe-breast-tumor (14-06526)

description: breast tumor


title: S_86


title: S_157


title: S_8


title: ffpe-breast-tumor (14-06524)

description: breast tumor


title: px0493-GTGGCCA


title: px0493-GTGAAAA


title: S_148


title: S_87


title: ffpe-breast-tumor (14-06523)

description: breast tumor


title: ffpe-breast-tumor (14-06522)

description: breast tumor


title: S_18


title: S_123


title: S_146


title: S_90


title: ffpe-breast-tumor (14-06521)

description: breast tumor

value: Unknown


title: S_112


title: ffpe-breast-tumor (14-06519)

description: breast tumor


title: ffpe-breast-tumor (14-06520)

description: breast tumor


title: px0493-GTAGAGA


title: S_79


title: ffpe-breast-tumor (14-06525)

description: breast tumor


title: px0493-GGCCTGA


title: px0493-GGCTACA


title: px0493-GGCACAA


title: ffpe-breast-tumor (14-06518)

description: breast tumor


title: px0493-GCCGCGA


title: S_12


title: S_130


title: px0493-GTCCGCA


title: px0493-GCACTTA


title: px0493-GCCAATA


title: px0493-GCAAGGA


title: ffpe-breast-tumor (14-06516)

description: breast tumor


title: S_97


title: px0493-GATCAGA


title: ffpe-breast-tumor (14-06514)

description: breast tumor


title: ffpe-breast-tumor (14-06515)

description: breast tumor


title: S_166


title: ffpe-breast-tumor (14-06517)

description: breast tumor


title: S_85


title: S_40


title: ffpe-breast-tumor (14-06512)

description: breast tumor


title: px0493-GAATAAA


title: px0493-CTTGTAA


title: S_53


title: ffpe-breast-tumor (14-06510)

description: breast tumor


title: px0493-CTATACA


title: ffpe-breast-tumor (14-06511)

description: breast tumor


title: px0493-CGAGAAA


title: px0493-CCTTAGA


title: S_143


title: S_114


title: ffpe-breast-tumor (14-06507)

description: breast tumor


title: S_95


title: px0493-CCGTCCA


title: ffpe-breast-tumor (14-06509)

description: breast tumor


title: S_21


title: ffpe-breast-tumor (14-06508)

description: breast tumor


title: ffpe-breast-tumor (14-06513)

description: breast tumor


title: px0493-CCCATGA


title: S_36


title: ffpe-breast-tumor (14-06505)

description: breast tumor


title: px0493-CGATGTA


title: S_81


title: px0493-CATGGCA


title: S_105


title: px0493-CAGGCGA


title: S_158


title: S_165


title: px0493-CACTCAA


title: ffpe-breast-tumor (14-06503)

description: breast tumor


title: ffpe-breast-tumor (14-06504)

description: breast tumor


title: ffpe-breast-tumor (14-06506)

description: breast tumor


title: px0493-CACGATA


title: ffpe-breast-tumor (14-06502)

description: breast tumor


title: S_42


title: S_70


title: px0493-CAAAAGA


title: px0493-ATTCCTA


title: ffpe-breast-tumor (14-06499)

description: breast tumor


title: ffpe-breast-tumor (14-06500)

description: breast tumor


title: ffpe-breast-tumor (14-06501)

description: breast tumor


title: S_76


title: S_126


title: ffpe-breast-tumor (14-06497)

description: breast tumor


title: px0493-ATGTCAA


title: ffpe-breast-tumor (14-06498)

description: breast tumor


title: ffpe-breast-tumor (14-06495)

description: breast tumor


title: px0493-CACCGGA


title: px0493-ATGAGCA


title: px0493-ATCTATA


title: px0493-CAACTAA


title: ffpe-breast-tumor (14-06494)

description: breast tumor


title: px0493-ATCCTAA


title: ffpe-breast-tumor (14-06496)

description: breast tumor


title: px0493-ATCACGA


title: S_144


title: S_121


title: S_78


title: S_77


title: S_108


title: ffpe-breast-tumor (14-06493)

description: breast tumor


title: S_57


title: S_149


title: px0493-ATAATTA


title: S_151


title: ffpe-breast-tumor (14-06492)

description: breast tumor


title: ffpe-breast-tumor (14-06491)

description: breast tumor


title: S_25


title: ffpe-breast-tumor (14-06490)

description: breast tumor


title: S_0


title: px0493-AGTTCCA


title: ffpe-breast-tumor (14-06489)

description: breast tumor


title: S_141


title: px0493-AGGTTTA


title: KG-9

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

label: biotin

source_name: HCC-cell line, Zerumbone treated

label_protocol: not provided

growth_protocol: MHCC-LM3 cells were maintained in Minimum Essential Media supplemented with L-glutamine (2 mM), 10% FBS, sodium pyruvate (0.11 g/L) and penicillin/streptomycin (100 U/mL) at 37°C with 5% CO2.

extract_protocol: Total RNA from the MHCC-LM3 cells was isolated using TRIzol (Invitrogen) and purified using RNeasy Mini columns (QIAGEN), and the integrity and quantity of the RNA were assessed using an Agilent Bioanalyzer and Nanodrop RNA 6000, respectively.

treatment_protocol: MHCC-LM3 cells treated with Zerumbone (50 µM) or DMSO for 24 hours.

value: Hepatocellular carcinoma (HCC)

tag: cell line


title: px0493-AGGCCGA


title: px0493-ATACGGA


title: ffpe-breast-tumor (14-06488)

description: breast tumor


title: KG-7

source_name: HCC-cell line, DMSO


title: px0493-AGCGCTA


title: S_117


title: px0493-AGCATCA


title: KG-8


title: ffpe-breast-tumor (14-06485)

description: breast tumor


title: ffpe-breast-tumor (14-06486)

description: breast tumor


title: S_138


title: S_22


title: KG-10


title: px0493-AGAAGAA


title: ffpe-breast-tumor (14-06483)

description: breast tumor


title: S_154


title: S_72


title: ffpe-breast-tumor (14-06487)

description: breast tumor


title: ffpe-breast-tumor (14-06482)

description: breast tumor


title: px0493-ACGATAA


title: S_102


title: ffpe-breast-tumor (14-06481)

description: breast tumor


title: CTC_129195_8CTC

type: genomic

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description:
Sample name: 129195_8CTC
Matched TLDA sample name: CTC.129195.20CTC.T2
Matched TLDA sample Accession Number: GSM998250

hyb_protocol: We combined and precipitated 30 µL Cy3 labeled test DNA, 30 µL Cy5 labeled reference DNA and 100 µg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ice-cold ethanol. We collected the precipitate by centrifugation  at 14000 rpm for 45 minutes at 4°C. We the final hybridization mixture containing 7ul dH20, 14µL  20% SDS, and 49 µL or Master Mix (5 mL ultra pure formamide from Invitrogen, 1g 500000MW Dextran Sulfate, 1mL 20xSSC, 1mL H20). We denatured the hybridization mixture at 73°C for 15 min and then incubated the samples at 37°C for 2hours to allow the Cot 1 DNA to anneal to repetitive DNA sequeces on both the sample and reference DNA. We exposed our printed arrays to 260000uJoules of UV using StrataLinker and applied a rubber cement ring around each array to form a well. After air drying the rubber cement we added our combined sample/reference hybridization solution onto the array. We placed a silicone gasket around the edge of the wells and laid a clean glass microscope slide on top of the gasket. We clamped the assembly together using binder clips to create an air tight environment. The arrays were incubated or 48-68 hours at 37°C on a slowly rocking table (1rpm). After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min. We removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: Arrays were imaged using a custom built CCD array imaging system  and analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios.

data_processing: The aCGH data from our cohort were processed by the custom program SPROC in order to automatically filter out data points with low DAPI intensity, low correlation between Cy3 and Cy5 within each spot, and low reference/DAPI signal intensity. Clones whose ratios were derived from only one of the triplicate spots or with a triplicate log2 SD >0.2 were set as missing. The tumor data was filtered for unmapped clones and poorly performing ones identified as those missing in more than 50% of the tumor samples. A second set of triplicate spots for 38 of these clones were averaged resulting in a total of 1965 clones remaining after processing. The data were mapped to the May 2004 freeze of the human DNA sequence.

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic  breast cancer patient

label_protocol: BioPrime Array CGH Labeling System (Invitrogen) was used to enzymatically label approximately 600ng of test or reference DNA with Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham), respectively.Briefly, DNA suspended in 11µL of water and 10µL of random prime mix was heated for 10mins at 100°C and snap cooled on ice. 2.5uL of 10x-dNTP mix (8µL of 100mM dATP, 8µL of 100mM dGTP, 8µL of 100mM dTTP, 4µL of 100mM dCTP, 2µL 1M Tris, 0.4µL of 0.5M EDTA, and water), 1µL of Cy3 or Cy5 labeled dCTP( 1mM) and 0.6µL Exo-Klenow (40 U/µL) were added to the denatured DNA and incubated for 12 -20 hours at 37°C. Unincorporated nucleotides were removed using a Sephadex G-50 spin-columns.

extract_protocol: Magnetic beads coated with EpCAM mAb are used to enrich for tumor cells and then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. Using this protocol, we isolated small pools of highly purified CTCs from breast cancer patients. DNA from Tumor cells sorted in 10µL of TE was amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) according to manufacturer’s protocol. The approach was evaluated using breast tumor cell model systems, BT474 and MCF7, and CTCs metastatic breast cancer (MBC) patients. Microdissection and DNA extraction of archival formalin-fixed paraffin-embedded (FFPE) primary tumor were done as previously described in Waldman FM, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000;92(4):313-20.

treatment_protocol: Array CGH experiments of Circulating Tumor, Primary Tumor, or cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

tag: diagnosis

value: Breast cancer

tag: tumor stage

value: Metastatic

value: Peripheral Blood

tag: cell type

value: Circulating Tumor Cells

source_name: Promega reference Male genomic DNA

tag: reference

value: Promega Human Genomic DNA  cat#G147A


title: px0493-ACCCAGA


title: ffpe-breast-tumor (14-06480)

description: breast tumor

tag: Sex

value: F

tag: intrinsic subtype


title: CTC_128914_20CTC

description:
Sample name: 128914_20CTC
Matched TLDA sample name: CTC.128914.20CTC.1
Matched TLDA sample Accession Number: GSM998241

tag: tissue


title: S_5


title: CTC_127923_6CTC

description:
Sample name: 127923_6CTC
Matched TLDA sample name: CTC.127923.20CTC
Matched TLDA sample Accession Number: GSM998225


title: ffpe-breast-tumor (14-06484)

description: breast tumor

value: Luminal B


title: px0493-ACATCTA

tag: type

value: single-cell

tag: donor

tag: markers


title: px0493-AGATAGA


title: ffpe-breast-tumor (14-06479)

description: breast tumor


title: S_67

tag: gender

value: Female

tag: tumor type

tag: age


title: CTC_127201_5CTC

description:
Sample name: 127201_5CTC
Matched TLDA sample name: CTC.127201.20CTC
Matched TLDA sample Accession Number: GSM998221


title: CTC_127268_20CTC

description:
Sample name: 127268_20CTC
Matched TLDA sample name: CTC.127268.20CTC.1
Matched TLDA sample Accession Number: GSM998223


title: S_30

value: breast cancer tumor

tag: estrogen receptor status

tag: grade

tag: Stage


title: px0493-ACTCTCA


title: px0493-ACAGTGA


title: S_84

value: HER2 Breast Cancer

tag: progesterone receptor status

tag: pcr


title: ffpe-breast-tumor (14-06478)

description: breast tumor


title: NRAS_Q61K

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: gene expression data from C2C12 myotubes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix mouse genome 430 2.0 array.

scan_protocol: GeneChips were scanned according to standard protocols at the Genomics Technology Laboaratory

data_processing: The data were normalized by Affymetrix Power Tool

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA

growth_protocol: C2C12 cells were transduced with retrovirus and selected with puromycin.  Expression of RAS was verified by immunoblot.

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Transduced cells were incubated in DMEM + 2% horse serum for 5 days prior to RNA extraction.  Media was replaced daily.

tag: days in differentiation media


title: KRAS_G12D


title: CTC_126976_20CTC

description:
Sample name: 126976_20CTC
Matched TLDA sample name: CTC.126976.16CTC
Matched TLDA sample Accession Number: GSM998217

tag: diagnosis

tag: tumor stage

tag: cell type


title: px0493-ACAAACA


title: px0493-AATAGGA


title: ffpe-breast-tumor (14-06477)

description: breast tumor

tag: Sex

tag: intrinsic subtype

value: Basal-like


title: pBABE


title: px0493-AAGGACA

tag: type


title: px0493-AAGCGAA

tag: donor


title: px0493-AAGACTA

tag: markers


title: S_129

tag: gender

tag: tissue

value: YES


title: ffpe-breast-tumor (14-06475)

description: breast tumor


title: S_100

tag: tumor type

tag: age

value: NO

value: II


title: ffpe-breast-tumor (14-06472)

description: breast tumor

value: Luminal A


title: CTC_126721_20CTC

description:
Sample name: 126721_20CTC
Matched TLDA sample name: CTC.126721.20CTC.1
Matched TLDA sample Accession Number: GSM998205

tag: reference


title: S_48

tag: estrogen receptor status

tag: grade

tag: Stage


title: S_65

tag: progesterone receptor status

tag: pcr


title: CTC_126703_20CTC

description:
Sample name: 126703_20CTC
Matched TLDA sample name: CTC.126703.20CTC.1
Matched TLDA sample Accession Number: GSM998203

tag: diagnosis

tag: tumor stage


title: CTC_126746_20CTC

description:
Sample name: 126746_20CTC
Matched TLDA sample name: CTC.126746.20CTC.1
Matched TLDA sample Accession Number: GSM998206

tag: cell type


title: ffpe-breast-tumor (14-06473)

description: breast tumor

tag: Sex

tag: intrinsic subtype


title: CTC_126423_20CTC

description:
Sample name: 126423_20CTC
Matched TLDA sample name: CTC.126423.20CTC.1
Matched TLDA sample Accession Number: GSM998189


title: CTC_126608_20CTC

description:
Sample name: 126608_20CTC
Matched TLDA sample name: CTC.126608.20CTC.1.A1
Matched TLDA sample Accession Number: GSM998193


title: CTC_126563_20CTC

description:
Sample name: 126563_20CTC
Matched TLDA sample name: CTC.126563.20CTC.1
Matched TLDA sample Accession Number: GSM998191


title: CTC_126624_20CTC

description:
Sample name: 126624_20CTC
Matched TLDA sample name: CTC.126624.20CTC.1
Matched TLDA sample Accession Number: GSM998195


title: S_27

value: III


title: px0493-AACCCCA

tag: type

tag: donor


title: ffpe-breast-tumor (14-06471)

description: breast tumor


title: px0493-AAAGCAA

tag: markers


title: S_73

tag: gender

tag: tissue


title: ffpe-breast-tumor (14-06470)

description: breast tumor


title: ffpe-breast-tumor (14-06474)

description: breast tumor


title: S_127

tag: tumor type

tag: age


title: HRAS_Q61L

tag: days in differentiation media


title: ffpe-breast-tumor (14-06469)

description: breast tumor


title: S_156

tag: estrogen receptor status

tag: grade


title: px0493-AAACATA


title: CTC_126149_20CTC

description:
Sample name: 126149_20CTC
Matched TLDA sample name: CTC.126149.20CTC.1.T3
Matched TLDA sample Accession Number: GSM998180

value: Breast cancer

tag: reference


title: CTC_126358_20CTC

description:
Sample name: 126358_20CTC
Matched TLDA sample name: CTC.126358.20CTC
Matched TLDA sample Accession Number: GSM998187

value: Metastatic


title: px0494-CGTACGA

value: negative


title: ffpe-breast-tumor (14-06468)

description: breast tumor


title: S_171

description: Gene expression data from breast tumor sample

tag: Stage

tag: progesterone receptor status

tag: pcr


title: S_134


title: px0494-ACTTGAA


title: ffpe-breast-tumor (14-06467)

description: breast tumor


title: CTC_125796_20CTC

description:
Sample name: 125796_20CTC
Matched TLDA sample name: CTC.125796.20CTC.1
Matched TLDA sample Accession Number: GSM998173

tag: diagnosis

tag: tumor stage

value: Peripheral Blood

tag: cell type

value: Circulating Tumor Cells


title: px0494-AAATGCA

tag: type


title: CTC_125263_20CTC

description:
Sample name: 125263_20CTC
Matched TLDA sample name: CTC.125263.20CTC.1
Matched TLDA sample Accession Number: GSM998167

value: Promega Human Genomic DNA  cat#G147A


title: px0493-AACTTGA

tag: donor


title: ffpe-breast-tumor (14-06466)

description: breast tumor

tag: Sex

value: F

tag: intrinsic subtype


title: S_109

tag: gender

tag: tissue


title: ffpe-breast-tumor (14-06465)

description: breast tumor

value: Luminal B


title: px0493-CGTACGA

tag: markers


title: ffpe-breast-tumor (14-06464)

description: breast tumor


title: px0493-ACTTGAA


title: S_136

value: Female

tag: tumor type

tag: age


title: CTC_125051_20CTC

description:
Sample name: 125051_20CTC
Matched TLDA sample name: CTC.125051.20CTC.1
Matched TLDA sample Accession Number: GSM998156


title: S_164

value: breast cancer tumor

tag: estrogen receptor status

tag: grade


title: CTC_124437_5CTC

description:
Sample name: 124437_5CTC
Matched TLDA sample name: CTC.124437.20CTC
Matched TLDA sample Accession Number: GSM998140

tag: reference


title: ffpe-breast-tumor (14-06463)

description: breast tumor


title: px0493-AAATGCA


title: ffpe-breast-tumor (14-06462)

description: breast tumor


title: CTC_124523_20CTC

description:
Sample name: 124523_20CTC
Matched TLDA sample name: CTC.124523.20CTC.1.T3
Matched TLDA sample Accession Number: GSM998145


title: S_118

value: HER2 Breast Cancer

tag: Stage

tag: progesterone receptor status


title: S_133

tag: pcr


title: CTC_124228_20CTC

description:
Sample name: 124228_20CTC
Matched TLDA sample name: CTC.124228.20CTC.2
Matched TLDA sample Accession Number: GSM998136

tag: diagnosis

tag: tumor stage


title: ffpe-breast-tumor (14-06461)

description: breast tumor


title: CTC_124088_20CTC

description:
Sample name: 124088_20CTC
Matched TLDA sample name: CTC.124088.20CTC.1
Matched TLDA sample Accession Number: GSM998133

tag: cell type


title: S_104


title: S_115


title: CTC_123834_20CTC

description:
Sample name: 123834_20CTC
Matched TLDA sample name: CTC.123834.20CTC.1.T2
Matched TLDA sample Accession Number: GSM998132


title: S_34


title: ffpe-breast-tumor (14-06459)

description: breast tumor


title: ffpe-breast-tumor (14-06460)

description: breast tumor


title: CTC_123625_13CTC

description:
Sample name: 123625_13CTC
Matched TLDA sample name: CTC.123625.20CTC
Matched TLDA sample Accession Number: GSM998123


title: ffpe-breast-tumor (14-06458)

description: breast tumor


title: S_64


title: ffpe-breast-tumor (14-06457)

description: breast tumor


title: CTC_123562_20CTC

description:
Sample name: 123562_20CTC
Matched TLDA sample name: CTC.123562.20CTC.1
Matched TLDA sample Accession Number: GSM998122


title: CTC_123547_20CTC

description:
Sample name: 123547_20CTC
Matched TLDA sample name: CTC.123547.20CTC.1
Matched TLDA sample Accession Number: GSM998120


title: S_38


title: S_6


title: S_128


title: ffpe-breast-tumor (14-06455)

description: breast tumor


title: S_132


title: ffpe-breast-tumor (14-06454)

description: breast tumor


title: CTC_124828_14CTC

description:
Sample name: 124828_14CTC
Matched TLDA sample name: CTC.124828.20CTC.T2
Matched TLDA sample Accession Number: GSM998155


title: CTC_123412_20CTC

description:
Sample name: 123412_20CTC
Matched TLDA sample name: CTC.123412.20CTC.1
Matched TLDA sample Accession Number: GSM998114


title: ffpe-breast-tumor (14-06453)

description: breast tumor


title: S_29


title: CTC_4043_10CTC

description:
Sample name: 4043_10CTC
Matched TLDA sample name: CTC.4043.20CTC.1.T2
Matched TLDA sample Accession Number: GSM998261


title: CTC_119982_20CTC

description:
Sample name: 119982_20CTC
Matched TLDA sample name: CTC.119982.20CTC.1
Matched TLDA sample Accession Number: GSM998058


title: S_49


title: S_167


title: CTC_123544_5CTC

description:
Sample name: 123544_5CTC
Matched TLDA sample name: CTC.123544.15CTC
Matched TLDA sample Accession Number: GSM998118


title: CTC_122306_20CTC

description:
Sample name: 122306_20CTC
Matched TLDA sample name: CTC.122306.20CTC.1.A1
Matched TLDA sample Accession Number: GSM998094


title: ffpe-breast-tumor (14-06450)

description: breast tumor


title: ffpe-breast-tumor (14-06452)

description: breast tumor


title: ffpe-breast-tumor (14-06456)

description: breast tumor


title: ffpe-breast-tumor (14-06451)

description: breast tumor


title: CTC_52582_20CTC

description:
Sample name: 52582_20CTC
Matched TLDA sample name: CTC.52582.20CTC
Matched TLDA sample Accession Number: GSM998263


title: CTC_4037_20CTC

description:
Sample name: 4037_20CTC
Matched TLDA sample name: CTC.4037.20CTC.1
Matched TLDA sample Accession Number: GSM998254


title: S_94

description: Gene expression data from breast tumor sample


title: CTC_4042_20CTC

description:
Sample name: 4042_20CTC
Matched TLDA sample name: CTC.4042.20CTC.1.T2.D1
Matched TLDA sample Accession Number: GSM998257


title: S_23


title: ffpe-breast-tumor (14-06448)

description: breast tumor


title: ffpe-breast-tumor (14-06449)

description: breast tumor


title: ffpe-breast-tumor (14-06447)

description: breast tumor

value: Basal-like


title: ffpe-breast-tumor (14-06446)

description: breast tumor


title: S_168


title: S_51


title: ffpe-breast-tumor (14-04753)

description: breast tumor


title: S_2


title: S_172


title: ffpe-breast-tumor (14-04752)

description: breast tumor


title: ffpe-breast-tumor (14-04750)

description: breast tumor


title: S_50


title: S_107

value: YES


title: ffpe-breast-tumor (14-04749)

description: breast tumor


title: ffpe-breast-tumor (14-04748)

description: breast tumor


title: S_125

value: NO


title: 20month-frontal-cortex[Q331K_Q331K]9

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced with 2x100bp paired-end reads on a HiSeq2500 platform.
Reads were trimmed using Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using hisat2 v2.0.5. BAM files were imported to Seqmonk v1.37.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline using opposite-stranded counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Genes were quantified as raw counts using SeqMonk. The report is in the following tab delimited format: (1) gene name; (2) Chromosome; (3) Start; (4) End; (5) Strand; …; (14-41) Raw Read Counts

molecule: polyA RNA

source_name: Frontal cortex

extract_protocol:
Total RNA was extracted from 20 month old frontal cortex tissue using TRIsure reagent (Bioline) and the RNeasy extraction kit (Qiagen).
Libraries were prepared using the TrueSeq Stranded mRNA kit (Illumina) following the low sample protocol. RNA fragmentation time was reduced to 3 minutes at 94°C.

treatment_protocol:
Frontal cortex tissues were collected from either wild type, heterozygous or homozygous TDP-43 Q331K knockin mice, at 20 months of age.
Tissues were snap frozen on liquid nitrogen and stored at -80°C until processing

tag: strain background

tag: genotype

value: 20 months

value: Frontal cortex


title: S_26

value: II


title: S_153


title: S_83


title: 20month-frontal-cortex[Q331K_Q331K]7


title: S_4


title: 20month-frontal-cortex[Q331K_Q331K]8


title: ffpe-breast-tumor (14-04745)

description: breast tumor

tag: Sex

tag: intrinsic subtype


title: S_101

tag: gender

tag: tissue

value: III


title: ffpe-breast-tumor (14-04746)

description: breast tumor


title: S_122

tag: tumor type


title: ffpe-breast-tumor (14-04743)

description: breast tumor

value: Luminal A


title: 20month-frontal-cortex[Q331K_Q331K]6

tag: age


title: ffpe-breast-tumor (14-04742)

description: breast tumor


title: 20month-frontal-cortex[Q331K_Q331K]5


title: ffpe-breast-tumor (14-04751)

description: breast tumor


title: S_82

tag: estrogen receptor status


title: ffpe-breast-tumor (14-04747)

description: breast tumor


title: 20month-frontal-cortex[Q331K_Q331K]4


title: ffpe-breast-tumor (14-04744)

description: breast tumor


title: ffpe-breast-tumor (14-04741)

description: breast tumor


title: 20month-frontal-cortex[Q331K_Q331K]1


title: ffpe-breast-tumor (14-04739)

description: breast tumor


title: S_1

tag: grade


title: S_46


title: S_47


title: ffpe-breast-tumor (14-04738)

description: breast tumor


title: ffpe-breast-tumor (14-04740)

description: breast tumor


title: 20month-frontal-cortex[Q331K_Q331K]10


title: 20month-frontal-cortex[Q331K_+]9


title: S_54


title: ffpe-breast-tumor (14-04736)

description: breast tumor


title: ffpe-breast-tumor (14-04737)

description: breast tumor


title: 20month-frontal-cortex[Q331K_+]8


title: S_92


title: ffpe-breast-tumor (14-06476)

description: breast tumor


title: S_140


title: S_16


title: S_33


title: 20month-frontal-cortex[Q331K_+]7


title: 20month-frontal-cortex[Q331K_Q331K]3


title: 20month-frontal-cortex[Q331K_Q331K]2


title: ffpe-breast-tumor (14-04734)

description: breast tumor

value: Unknown


title: ffpe-breast-tumor (14-04733)

description: breast tumor


title: 20month-frontal-cortex[Q331K_+]6


title: S_80


title: 20month-frontal-cortex[Q331K_+]5


title: S_10


title: 20month-frontal-cortex[Q331K_+]4


title: S_32


title: 20month-frontal-cortex[Q331K_+]3


title: S_31


title: 20month-frontal-cortex[Q331K_+]1


title: ffpe-breast-tumor (14-04730)

description: breast tumor


title: ffpe-breast-tumor (14-04735)

description: breast tumor


title: S_145


title: ffpe-breast-tumor (14-04728)

description: breast tumor


title: 20month-frontal-cortex[Q331K_+]10


title: ffpe-breast-tumor (14-04729)

description: breast tumor


title: S_103


title: S_135


title: 30 ppb lufenuron 10165_Block2_updatedBlock2.txt

city: Victoria

first: Ben

middle: F

last: Koop

address: PO Box 3020 STN CSC

institute: The University of Victoria

description: 30 ppb lufenuron

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).  hyb protocol

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery). scan protocol

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX11 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the three experiments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags. data processing

organism: Lepeophtheirus salmonis

source_name: Pool of approx. 500 copepodids (Atlantic Canada)

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.  label protocol

growth_protocol: Atlantic L. salmonis egg strings were obtained from adult female lice infecting Atlantic salmon in a salmon farm located in BMA-2a in the Bay of Fundy, New Brunswick. Eggs were hatched in a static sea water hatch system and grown to copepodids at Huntsman Marine Science Centre, St Andrew's, NB, Canada.   growth protocol

extract_protocol: Lice were flash frozen in pools of 500 and kept at -80 degrees Celcius until RNA extraction (n = 21 pools). Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.       extract protocol

treatment_protocol: Stock lufenuron (Elanco®) was prepared to 100 mg/L in 50% acetone, then diluted to working concentrations in seawater. Lufenuron dilutions were prepared to final concentrations of 0, 30, 300, 700, 1000, and 1500 parts per billion (n = 3 pools/treatment). Exposure time was 3 h before a 21 h holding in seawater. Pools of 500 copepodids were flash frozen post 24 h bioassay. treatment protocol

tag: treatment

value: 30 ppb lufenuron

source_name: all condition pool

tag: sample type

value: reference


title: S_169

tag: Stage

tag: progesterone receptor status


title: Acetone Control 10167_Block2_updatedBlock2.txt

description: Acetone Control

value: Acetone Control


title: S_152

tag: pcr


title: ffpe-breast-tumor (14-04732)

description: breast tumor

value: F


title: 20month-frontal-cortex[+_+]8


title: ffpe-breast-tumor (14-04727)

description: breast tumor


title: S_74


title: ffpe-breast-tumor (14-04726)

description: breast tumor


title: ffpe-breast-tumor (14-04731)

description: breast tumor


title: 30 ppb lufenuron 10163_Block3_updatedBlock3.txt

description: 30 ppb lufenuron


title: 20month-frontal-cortex[Q331K_+]2


title: ffpe-breast-tumor (14-04725)

description: breast tumor


title: 20month-frontal-cortex[+_+]7


title: 20month-frontal-cortex[+_+]6


title: 20month-frontal-cortex[+_+]5


title: S_69


title: 20month-frontal-cortex[+_+]4


title: ffpe-breast-tumor (14-04723)

description: breast tumor


title: 1000 ppb lufenuron 10162_Block1_updatedBlock1.txt

description: 1000 ppb lufenuron

value: 1000 ppb lufenuron


title: S_11

value: Female


title: ffpe-breast-tumor (14-04724)

description: breast tumor


title: S_62

value: breast cancer tumor


title: S_170

value: HER2 Breast Cancer


title: Seawater Control 10162_Block4_updatedBlock4.txt

description: Seawater Control

value: Seawater Control


title: 1000 ppb lufenuron 10163_Block4_updatedBlock4.txt

description: 1000 ppb lufenuron


title: 1500 ppb lufenuron 10158_Block1_updatedBlock1.txt

description: 1500 ppb lufenuron

value: 1500 ppb lufenuron


title: 20month-frontal-cortex[+_+]3


title: ffpe-breast-tumor (14-04721)

description: breast tumor

value: Luminal B


title: S_113

value: NO


title: S_150


title: ffpe-breast-tumor (14-04722)

description: breast tumor


title: 300 ppb lufenuron 10163_Block1_updatedBlock1.txt

description: 300 ppb lufenuron

value: 300 ppb lufenuron


title: 20month-frontal-cortex[+_+]1

value: 20 months

value: Frontal cortex


title: 1000 ppb lufenuron 10157_Block1_updatedBlock1.txt

description: 1000 ppb lufenuron


title: ffpe-breast-tumor (14-04720)

description: breast tumor


title: ffpe-breast-tumor (14-04719)

description: breast tumor

value: Luminal A


title: 1500 ppb lufenuron 10156_Block1_updatedBlock1.txt

description: 1500 ppb lufenuron


title: S_91

value: YES

value: III


title: Seawater Control 10156_Block4_updatedBlock4.txt

description: Seawater Control

value: reference


title: S_89


title: ffpe-breast-tumor (14-04718)

description: breast tumor


title: 300 ppb lufenuron 10155_Block4_updatedBlock4.txt

description: 300 ppb lufenuron


title: ffpe-breast-tumor (14-04717)

description: breast tumor


title: ffpe-breast-tumor (14-04715)

description: breast tumor


title: S_9


title: S_35

value: II


title: 20month-frontal-cortex[+_+]2


title: S_142


title: ffpe-breast-tumor (14-04714)

description: breast tumor

value: F


title: 30 ppb lufenuron 10155_Block1_updatedBlock1.txt

description: 30 ppb lufenuron

value: 30 ppb lufenuron


title: S_93

value: Female


title: ffpe-breast-tumor (14-04713)

description: breast tumor


title: S_99

value: breast cancer tumor


title: 700 ppb lufenuron 10151_Block4_updatedBlock4.txt

description: 700 ppb lufenuron

value: 700 ppb lufenuron


title: ffpe-breast-tumor (14-04716)

description: breast tumor


title: ffpe-breast-tumor (14-04712)

description: breast tumor


title: S_147

value: HER2 Breast Cancer


title: S_3


title: 300 ppb lufenuron 10152_Block3_updatedBlock3.txt

description: 300 ppb lufenuron


title: Acetone Control 10154_Block2_updatedBlock2.txt

description: Acetone Control

value: Acetone Control


title: Acetone Control 10154_Block4_updatedBlock4.txt

description: Acetone Control


title: 1500 ppb lufenuron 10151_Block2_updatedBlock2.txt

description: 1500 ppb lufenuron

value: 1500 ppb lufenuron


title: 700 ppb lufenuron 10116_Block3_updatedBlock3.txt

description: 700 ppb lufenuron


title: ffpe-breast-tumor (14-04710)

description: breast tumor

value: Luminal B


title: ffpe-breast-tumor (14-04711)

description: breast tumor


title: T41 tumor sample

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: mesothelioma FFPE sample

label_protocol: probe labeling used Agilent Technologies Genomic DNA Enzymatic Labeling Kit. Labelling was performed following manufacturer's instructions.

extract_protocol: chromosomal DNA were extracted using Qiagen DNA extraction Kit following manufacturer's instructions

value: mesothelioma

value: male

tag: age (years)

tag: histological properties

value: Epithelial

tag: asbestos

value: yes

tag: surviving (months)

source_name: T leukocytes

value: patient sample taken as reference


title: 700 ppb lufenuron 10116_Block2_updatedBlock2.txt

description: 700 ppb lufenuron


title: Seawater Control 10116_Block1_updatedBlock1.txt

description: Seawater Control

value: Seawater Control


title: T42 tumor sample


title: CLIP_Math1_P21_rep3

city: New York

first: Saša

last: Jereb

state: New York

address: 1230 York Ave

department: Laboratory of Molecular Neuro-Oncology

institute: The Rockefeller University

description:
PABPC1-bound RNA
p21_rep3
Math1_p0_p21_clusters.txt

data_processing:
Library strategy: cTag-PAPERCLIP
Analysis of cTag-PAPERCLIP datasets: The processing of raw reads was performed using the CIMS software package as previously described (Moore et al., 2014). Raw reads were filtered based on quality score. Filtered reads with the exact sequence were collapsed into one. Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin, 2011). Only reads that are at least 25-nt in length were mapped to mm10 reference genome. Mapping was performed using Novoalign (Novocraft) without trimming. Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single read as previously described (Moore et al., 2014). CIMS software package was then used to cluster overlapping collapsed reads from all biological replicates (for each condition) and to determine the number of reads in each cluster. To define a list of high confidence clusters we used the following criteria: clusters had to contain reads from all replicates in each condition, the number of reads in a cluster had to be at least 10% of gene total, clusters had to be located within 20 kb from 3′ ends annotated by RefSeq, clusters that were located upstream of a stretch of 6 or more adenines were excluded due to potential internal priming of the reverse transcription primer. To identify differences in APA between different conditions, Fisher’s exact test was performed comparing the ratio between reads in a particular cluster and the sum of reads in all other clusters in a gene in the two conditions. The output p-values were adjusted for multiple hypotheses testing using the Benjamini-Hochberg method.
Analysis of RNA-seq datasets: RNA-sequencing reads were mapped to the mouse genome (mm10) using Novoalign (Novocraft), reads overlapping genes were counted using HTSeq-count (Anders et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: Columns in tab-delimited files for CLIP datasets represent the following: name_cluster (name of a CLIP cluster), id_gene (Refseq gene ID), chr_cluster (chromosome where cluster is located), start_cluster (cluster start), end_cluster (cluster end), strand_cluster (strand), name2 (gene symbol) and number of reads from each replicate in a given cluster.
Supplementary_files_format_and_content: Tab-delimited text files for RNA-seq datasets represent Refseq gene ID and number of reads overlapping with exons.

source_name: Cerebellar granule cells

extract_protocol:
cTag-PAPERCLIP on dissected P21 cerebellar cortices. Mouse monoclonal anti-GFP clones 19F7 and 19C8 (Heiman et al., 2008) were used for immunoprecipitation.
The PAPERCLIP procedure was performed as previously described (Hwang et al., 2016). Individual cTag-PAPERCLIP libraries were multiplexed and sequenced on MiSeq (Illumina) to obtain 75-nt single-end reads. A barcode sequence was removed from the reads, so the final length of reads is 68-nt.

tag: cell type

value: Cerebellar granule cells

value: post-natal day 21

tag: genotype

value: Math1-Cre; Pabpc1-cTag


title: ffpe-breast-tumor (14-04709)

description: breast tumor

tag: Sex

value: F

tag: intrinsic subtype


title: S_131

tag: gender

value: Female

tag: tissue

tag: tumor type

value: NO

value: III


title: CLIP_Math1_P21_rep2

description:
PABPC1-bound RNA
p21_rep2
Math1_p0_p21_clusters.txt

tag: age


title: CLIP_Math1_P21_rep1

description:
PABPC1-bound RNA
p21_rep1
Math1_p0_p21_clusters.txt


title: T5 tumor sample

value: no


title: T40 tumor sample

value: Biphasic


title: S_110

value: breast cancer tumor

value: HER2 Breast Cancer

tag: estrogen receptor status

tag: grade


title: T37 tumor sample

tag: sample type

value: mesothelioma

value: female


title: S_160

value: YES

tag: Stage

value: II

tag: progesterone receptor status


title: CLIP_Math1_P0_rep3

description:
PABPC1-bound RNA
p0_rep3
Math1_p0_p21_clusters.txt

source_name: Cerebellar granule cell progenitors

extract_protocol:
cTag-PAPERCLIP on dissected P0 cerebellar cortices. Mouse monoclonal anti-GFP clones 19F7 and 19C8 (Heiman et al., 2008) were used for immunoprecipitation.
The PAPERCLIP procedure was performed as previously described (Hwang et al., 2016). Individual cTag-PAPERCLIP libraries were multiplexed and sequenced on MiSeq (Illumina) to obtain 75-nt single-end reads. A barcode sequence was removed from the reads, so the final length of reads is 68-nt.

value: Cerebellar granule cell progenitors

value: post-natal day 0


title: T38 tumor sample

value: male

tag: age (years)

value: Epithelial

value: yes

value: patient sample taken as reference


title: T4 tumor sample

tag: histological properties


title: T39 tumor sample

tag: asbestos


title: S_41

value: Female

tag: pcr


title: ffpe-breast-tumor (14-04707)

description: breast tumor

value: F

value: Luminal A


title: ffpe-breast-tumor (14-04708)

description: breast tumor


title: ffpe-breast-tumor (14-04706)

description: breast tumor

value: Basal-like


title: ffpe-breast-tumor (14-04384)

description: breast tumor


title: ffpe-breast-tumor (14-04383)

description: breast tumor


title: CLIP_Math1_P0_rep2

description:
PABPC1-bound RNA
p0_rep2
Math1_p0_p21_clusters.txt

tag: cell type

value: Math1-Cre; Pabpc1-cTag


title: S_98

value: breast cancer tumor

value: NO

value: III


title: S_43

value: HER2 Breast Cancer


title: S_96


title: T7 tumor sample

value: mesothelioma

tag: surviving (months)


title: ffpe-breast-tumor (14-04382)

description: breast tumor

tag: Sex


title: S_52


title: CLIP_Pcp2_P56_rep1

description:
PABPC1-bound RNA
pcp2_rep1
NeuroD1_Pcp2_clusters.txt

source_name: Cerebellar Purkinje cells

extract_protocol:
cTag-PAPERCLIP on dissected P56 cerebella. Mouse monoclonal anti-GFP clones 19F7 and 19C8 (Heiman et al., 2008) were used for immunoprecipitation.
The PAPERCLIP procedure was performed as previously described (Hwang et al., 2016). Individual cTag-PAPERCLIP libraries were multiplexed and sequenced on MiSeq (Illumina) to obtain 75-nt single-end reads. A barcode sequence was removed from the reads, so the final length of reads is 68-nt.

value: Cerebellar Purkinje cells

value: post-natal day 56

tag: genotype

value: Pcp2-Cre; Pabpc1-cTag


title: CLIP_Math1_P0_rep1

description:
PABPC1-bound RNA
p0_rep1
Math1_p0_p21_clusters.txt

value: Cerebellar granule cell progenitors

value: post-natal day 0


title: T35 tumor sample

tag: gender

value: female

value: Sarcomatoid

value: no


title: CLIP_Pcp2_P56_rep3

description:
PABPC1-bound RNA
pcp2_rep3
NeuroD1_Pcp2_clusters.txt


title: S_14

value: Female

tag: tissue

value: II


title: ffpe-breast-tumor (14-04381)

description: breast tumor

value: F

tag: intrinsic subtype

value: Luminal A


title: S_75

value: breast cancer tumor

tag: tumor type

tag: age

value: YES


title: ffpe-breast-tumor (14-04380)

description: breast tumor

value: Luminal B


title: T32 tumor sample

value: Epithelial

value: patient sample taken as reference


title: T34 tumor sample

value: mesothelioma


title: S_56

value: HER2 Breast Cancer

tag: estrogen receptor status

value: NO

tag: grade

value: III


title: CLIP_Neurod1_P56_rep4

description:
PABPC1-bound RNA
neurod1_rep4
NeuroD1_Pcp2_clusters.txt

value: Cerebellar granule cells

value: post-natal day 56

value: Neurod1-Cre; Pabpc1-cTag


title: CLIP_Neurod1_P56_rep3

description:
PABPC1-bound RNA
neurod1_rep3
NeuroD1_Pcp2_clusters.txt


title: T33 tumor sample

tag: sample type

value: male

value: no


title: ffpe-breast-tumor (14-04379)

description: breast tumor


title: CLIP_Neurod1_P56_rep2

description:
PABPC1-bound RNA
neurod1_rep2
NeuroD1_Pcp2_clusters.txt


title: S_63

value: Female

tag: Stage

value: II

tag: progesterone receptor status


title: CLIP_Pcp2_P56_rep2

description:
PABPC1-bound RNA
pcp2_rep2
NeuroD1_Pcp2_clusters.txt

value: Cerebellar Purkinje cells

value: Pcp2-Cre; Pabpc1-cTag


title: T36 tumor sample

tag: age (years)

tag: histological properties


title: S_120

value: breast cancer tumor

tag: pcr


title: CLIP_Neurod1_P56_rep1

description:
PABPC1-bound RNA
neurod1_rep1
NeuroD1_Pcp2_clusters.txt

tag: cell type


title: ffpe-breast-tumor (14-04377)

description: breast tumor

value: F

value: Luminal A


title: T30 tumor sample

value: Sarcomatoid

tag: asbestos

tag: surviving (months)

value: patient sample taken as reference


title: S_20

value: HER2 Breast Cancer

value: YES


title: T31 tumor sample

value: mesothelioma

value: Epithelial


title: Barcode_mapping_rep2

city: Los Angeles

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Plasmid DNA
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
barcode_mapping.txt

data_processing:
Counts for each unique barcode in the census files were complete in Unix as follows: Raw sequences were extracted from each fastq file and the first 20 bp (corresponding to the barcode) was extracted. This sequence was reverse complemented and the entire file was sorted before counting the number of counts of each barcode. Counts were normalized as a proportion of totals reads per sample and all samples aggregated together in R.
Barcode mapping was completed as follows: Demultiplexed reads were paired using Paired-End reAd mergeR (PEAR v0.9.1, default settings). Custom python code was used to identify reads corresponding to perfectly synthesized promoters and their respective barcodes. Briefly, this code searched the first 150 bp of each read for perfect matches to library variants. For reads with perfect matches, the last 20 bp of each read (the barcode) was extracted and a list was compiled mapping each barcode to the most frequently associated library variant. A single barcode appears many times in the sequencing data, and we took steps to ensure a barcode consistently mapped to the same variant. We required that all variants mapped to a single barcode be within an edit distance (Levenshtein distance) of 5 from one another (five single bp changes between the two sequences). We determined this number by bootstrapping a distribution of the edit distance between any two random sequences in our variant library, and setting the threshold to the first percentile (1%) of this bootstrapped distribution. Additionally, each barcode had to appear at least three times in order to be considered for downstream analysis. This step hopefully eliminates barcodes which contained sequencing errors. Promoter-barcode associations can be found in barcode_mapping.txt
Promoter variant expression was calculated in R by assigning barcodes to their mapped promoter and, for each promoter, dividing the sum of all RNA counts for all of its barcodes by the sum of all DNA counts for all of its barcodes. The result of this is in sigma70_variant_data.txt.
Genome_build: U00096.2
barcode_mapping.txt: columns: Barcode, Mapped Variant Sequence, Mapped Variant Name
barcode_counts_normalized.txt: columns: barcode, rLP5_min_DNA_rep1.1, rLP5_min_DNA_rep1.2, rLP5_min_RNA_rep1.1, rLP5_min_RNA_rep1.2, rLP5_min_DNA_rep2, rLP5_min_RNA_rep2, rLP5_min_DNA_rep3, rLP5_min_RNA_rep3
sigma70_variant_data.txt: columns: name, UP_element, Minus35, Spacer, Minus10, Background, RNA_exp_average

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: LB

extract_protocol: Qiagen Plasmid Plus Maxi Kit

tag: strain


title: ffpe-breast-tumor (14-04376)

description: breast tumor

tag: Sex

value: Basal-like


title: Barcode_mapping_rep1


title: T25 tumor sample

tag: gender

value: female

value: Biphasic


title: S_88

tag: tissue

value: NO


title: ffpe-breast-tumor (14-04375)

description: breast tumor

tag: intrinsic subtype


title: T24 tumor sample

value: no


title: T3 tumor sample

value: male

value: yes


title: ffpe-breast-tumor (14-04374)

description: breast tumor


title: S_111

value: Female

tag: tumor type

tag: age

value: II


title: T23 tumor sample


title: S_162

value: breast cancer tumor

tag: estrogen receptor status

tag: grade


title: S_17

tag: Stage


title: ffpe-breast-tumor (14-04372)

description: breast tumor

value: F


title: ffpe-breast-tumor (14-04371)

description: breast tumor

value: Luminal B


title: S_59

tag: progesterone receptor status


title: ffpe-breast-tumor (14-04373)

description: breast tumor

value: Luminal A


title: S_155

value: HER2 Breast Cancer

value: III


title: T22 tumor sample

tag: sample type

value: mesothelioma

tag: age (years)

value: patient sample taken as reference


title: S_68

tag: pcr


title: ffpe-breast-tumor (14-04370)

description: breast tumor


title: ffpe-breast-tumor (14-04369)

description: breast tumor


title: S_159

value: YES


title: ffpe-breast-tumor (14-04368)

description: breast tumor


title: S_66


title: S_19


title: ffpe-breast-tumor (14-04367)

description: breast tumor


title: T21 tumor sample

value: female

tag: histological properties

value: Epithelial


title: S_24

value: NO


title: T17 tumor sample

tag: asbestos

value: no


title: T15 tumor sample

value: male

tag: surviving (months)


title: T16 tumor sample

value: yes


title: ffpe-breast-tumor (14-04365)

description: breast tumor


title: T13 tumor sample


title: T18 tumor sample


title: S_37

value: Female


title: T10 tumor sample

value: Biphasic


title: S_163

value: breast cancer tumor

value: II


title: ffpe-breast-tumor (14-04363)

description: breast tumor

value: F

value: Basal-like


title: S_137

value: HER2 Breast Cancer


title: ffpe-breast-tumor (14-04362)

description: breast tumor


title: S_139

value: III


title: T14 tumor sample

value: mesothelioma


title: T2 tumor sample

value: patient sample taken as reference


title: ffpe-breast-tumor (14-04364)

description: breast tumor

value: Unknown


title: S_124

value: YES


title: T11 tumor sample

value: Epithelial


title: ffpe-breast-tumor (14-04366)

description: breast tumor


title: ffpe-breast-tumor (14-03739)

description: breast tumor

value: Luminal B


title: ffpe-breast-tumor (14-04361)

description: breast tumor


title: S_116


title: ffpe-breast-tumor (14-03738)

description: breast tumor


title: PA3381_F_KO

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

data_processing: GeneChip™ Mouse Gene 2.0 ST Array, Affymetrix console, RMA normalization

source_name: pancreatic cancer

growth_protocol: F12/DMEM supplemented with EGF

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: genotype

value: KDM6A KO

tag: cell type

value: pancreatic cancer


title: PA2006_F_KO

tag: Sex


title: ffpe-breast-tumor (14-03737)

description: breast tumor

source_name: tumor FFPE

value: Luminal A


title: HuR-KO RAW264.7

city: Ikoma, Takayama

first: Takuya

last: Sueyoshi

state: Nara

department: Biological Science

country: Japan

institute: Nara Institute of Science and Technology

description: gene expression in HuR-deficient RAW264.7

hyb_protocol: Following fragmentation, the samples were hybridized with for 16hr at 45C on Mouse Gene 2.0 ST Array (Affymetrix). GeneChips were washed and stained using Affymetrix Fluidics Station 450

scan_protocol: Genechip were sccaned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with RMA.

source_name: HuR-deficient RAW264.7 stimulated with poly(I:C) HMW using lipofectamine 2000 for 8 hours.

label_protocol: Samples were biotinylated using Encore Biotin Module (NuGEN) according to manufacturer's instructions.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS in a humidified 5% CO2/95% air atomosphere.

extract_protocol: Trizol was used to extract the RNA. Protocol is depends on manufacturer's instractions.

treatment_protocol: WT and HuR-deficient RAW264.7 cells stimulated with 1mg/ml high molecular weight of poly(I:C)  using lipofectamine 2000 for 8 hours.

tag: cell line

value: macrophage cell line

value: HuR-deficient


title: WT RAW264.7

description: gene expression in WT RAW264.7

source_name: WT RAW264.7 stimulated with poly(I:C) HMW using lipofectamine 2000 for 8 hours.

value: wildtype


title: S_7

description: Gene expression data from breast tumor sample

source_name: Breast tumor

tag: gender

value: Female

tag: tissue

value: breast cancer tumor

value: NO


title: PA3685_2_F_WT

value: KDM6A WT


title: T1 tumor sample

value: male

value: no


title: PA3685_1_F_WT


title: ffpe-breast-tumor (14-03736)

description: breast tumor

value: F

tag: intrinsic subtype


title: S_45

tag: tumor type

value: HER2 Breast Cancer

tag: age

tag: estrogen receptor status

value: III


title: S_58

tag: grade

tag: Stage

value: II

tag: progesterone receptor status


title: ffpe-breast-tumor (14-03734)

description: breast tumor


title: ffpe-breast-tumor (14-03732)

description: breast tumor


title: ffpe-breast-tumor (14-03735)

description: breast tumor

value: Basal-like


title: PA1582_M_KO

value: KDM6A KO

value: Male


title: ffpe-breast-tumor (14-03733)

description: breast tumor

value: Luminal B


title: WT3.rep3

city: Minneapolis

first: Jakub

last: Tolar

state: MN

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota, Twin Cities

data_processing:
Low quality bases were trimmed using Trimmomatic (enabled with the optional "--qualitycontrol" option and a 3bp sliding-window trimming from the 3' end requiring minimum Q16).
The remaining reads were mapped to hg19 using Tophat2.
The featureCounts program in the R SubRead package was used to generate a transcript abundance file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimted text file includes read counts

growth_protocol: iPSCs were maintained on Matrigel in E8 medium (Invitrogen).

extract_protocol:
Cells were detached with trypsin on day 10 of the protocol. Total RNA was extracted using an Rneasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA with a RIN score >8 was used for library generation.
RNA libraries were prepared for sequencing using a TruSeq Stranded mRNA Sample Preparation kit and standard Illumina protocols.

treatment_protocol: iPSCs were singularized and seeded on Matrigel in E8 medium with 10 µM Y-27632 (BD Biosciences) (Day -3). On Day 0 differentiation was induced by switching to unconditioned medium (UM): DMEM/F12 (Life Technologies) containing 20% Knockout Serum Replacement (Life Technologies), 1X MEM non-essential amino acids (Life Technologies), 1 mM L-Glutamine (Life Technologies), and 0.1 mM 2-mercaptoethanol (Sigma). Medium was changed every 24 hours. On Day 6, medium was changed from UM to endothelial cell (EC) medium: human endothelial serum free medium (Invitrogen) with 1% platelet-poor plasma derived serum (Biomedical Technologies) supplemented with 20 ng/mL basic fibroblast growth factor (bFGF; R&D Systems) and 10 µM all-trans retinoic acid (RA; Sigma). Medium was not changed for 48 h. On Day 8, cells were detached with Accutase (Invitrogen) and subcultured onto tissue culture polystyrene plates (Corning) coated with a water-based solution of 400 µg/mL collagen IV (Sigma) and 100 µg/mL fibronectin (Sigma). 24 h after subculture, medium was changed to EC medium without bFGF or RA.

value: wild-type

value: iPSC-derived Brain microvascular endothelial cells (BMECs)


title: WT3.rep2


title: PA1504_M_KO

value: pancreatic cancer


title: PA3210_M_WT


title: WT2.rep3


title: S_13

value: Female

value: YES

tag: pcr


title: WT3.rep1


title: WT2.rep2


title: WT2.rep1


title: ffpe-breast-tumor (14-03730)

description: breast tumor


title: ffpe-breast-tumor (14-03729)

description: breast tumor


title: PA1493_M_WT


title: ffpe-breast-tumor (14-03728)

description: breast tumor


title: WT1.rep3


title: ffpe-breast-tumor (14-03731)

description: breast tumor


title: WT1.rep2


title: PBMC-TC-sample16_vs_TC-PBMC-refpool

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

hyb_protocol: Microarrays used were chicken whole genome gene expression arrays V2 (Agilent, Santa Clara, CA, USA) representing 42034 Gallus gallus 60-mer probes in a 4x44K layout. Probe sequences were re-annotated by BLAST searching against the chicken genome version 76.4 at ENSEMBL. Microarray hydridization and washing was performed with a HS4800PRO system with QuadChambers (Tecan, Männedorf, Switzerland) using 1000 ng, 1-2% Cy5/Cy3 labeled cRNA per channel.

scan_protocol: Slides were scanned on an Agilent G2565BA scanner.

data_processing: Data was extracted using Imagene 8.0 (BioDiscovery, Hawthorne, CA, USA) and Loess normalization was performed on mean spot intensities50. Gene-specific dye bias was corrected by a within-set estimate. Differences in gene expression between treatment groups were analyzed by Linear Model for Microarray Analysis (LIMMA) with Benjamini-Hochberg FDR correction. Genes with p<0.05 and fold-change>2 were considered significantly changed. Because the Bioanalyzer results showed monospecific peaks in the cRNA pointing to contamination of the RNA, principal component analysis (PCA) was performed on log2 transformed expression values of genes with a >2-fold difference between samples. The principal component (PC2) with the highest correlation to the peaks from the Bioanalyzer results was then used as a covariate in LIMMA representing severity of contamination. Results of the corrected and uncorrected LIMMA analyses were compared to obtain significantly changed genes.

organism: Gallus gallus

label_protocol: An automated system (Caliper Life Sciences, Hopkinton, MA, USA) was used to perform cDNA synthesis, labeling, quantification, quality control by Bioanalyzer and fragmentation, starting with 3 µg total RNA from each samples as previously described. Per treatment, three samples were labeled with Cy5 and co-hybridized with reference RNA (pooled RNA from all experimental samples) labeled with Cy3. The remaining samples were labeled and hybridized the opposite way

growth_protocol: PBMCs were isolated from whole blood using a Ficoll gradient. Spleen and cecal tonsil single cell suspensions were made by gently pressing the tissue through a 70 µM cell strainer followed by a Ficoll gradient for spleen samples. Cells were frozen at -80 °C until further analysis.

extract_protocol: RNA (n=6/group) was isolated from PBMCs using Trizol (Ambion, Paisley, UK) precipitation and purified using RNeasy columns (Qiagen, Venlo, The Netherlands).

treatment_protocol: Peptide preparation and injection was similar to Cuperus et al. Briefly, D-CATH-2 was dissolved in PBS (1.48 mM NaH2PO4.H20, 8.06 mM Na2HPO4, 20 mM NaCl, pH 7.27, filter sterilized) to a concentration of 0.22 mg/ml, to which cholesterol (5% v/v, 2 mg/ml in absolute ethanol) was added. Three days before hatch (ed18, estimated embryo weight = 22 g), 1 mg/kg D-CATH-2 or buffer was administered in ovo into the amniotic cavity using a 1 inch, 21G needle injected up to the hilt. Posthatch, only male chickens were selected (n=6-8/group) and housed in separate isolators per experimental treatment. Animals were euthanized by electrocution followed by cardiac puncture and organs, blood and intestinal content were collected. Three separate in vivo experiments were conducted in which the same batch of chicken feed was used.

value: PBMC

tag: treatment

source_name: TC-PBMC-refpool

tag: sample type

value: referencepool


title: WT1.rep1


title: ffpe-breast-tumor (14-03727)

description: breast tumor

extract_protocol: Total RNA was extracted with High Pure RNA Paraffin Kit (Roche)

value: Luminal A


title: ccALD3.rep3

value: cerebral childhood adrenoleukodystrophy (ccALD)


title: ffpe-breast-tumor (14-04378)

description: breast tumor

value: F

value: Unknown


title: ffpe-breast-tumor (14-03726)

description: breast tumor


title: ccALD3.rep1


title: ccALD3.rep2


title: ffpe-breast-tumor (14-03725)

description: breast tumor


title: PBMC-TC-sample15_vs_TC-PBMC-refpool

value: placebo


title: PBMC-TC-PBMC-refpool_vs_TC-sample14


title: PBMC-TC-PBMC-refpool_vs_TC-sample13


title: ffpe-breast-tumor (14-03723)

description: breast tumor


title: ffpe-breast-tumor (14-03722)

description: breast tumor


title: ccALD2.rep2


title: ccALD2.rep3


title: ffpe-breast-tumor (14-03721)

description: breast tumor


title: PBMC-TC-sample12_vs_TC-PBMC-refpool


title: PBMC-TC-PBMC-refpool_vs_TC-sample10


title: PBMC-TC-PBMC-refpool_vs_TC-sample9


title: PBMC-TC-sample4_vs_TC-PBMC-refpool


title: PBMC-TC-sample11_vs_TC-PBMC-refpool


title: PBMC-TC-sample3_vs_TC-PBMC-refpool


title: ccALD1.rep3


title: ffpe-breast-tumor (14-03724)

description: breast tumor


title: ccALD2.rep1


title: ffpe-breast-tumor (14-03720)

description: breast tumor


title: ccALD1.rep2


title: ffpe-breast-tumor (14-03719)

description: breast tumor


title: ffpe-breast-tumor (14-03718)

description: breast tumor


title: ffpe-breast-tumor (14-03717)

description: breast tumor


title: ccALD1.rep1


title: T26 tumor sample

value: mesothelioma

value: male

tag: age (years)

tag: histological properties

value: Epithelial

tag: asbestos

value: no

tag: surviving (months)

value: patient sample taken as reference


title: T3

status: Public on Mar 31 2018

city: Luoyang

first: wei

middle: lan

last: lan

address: Kaiyuan avenue

country: China

institute: Henan University of Science and Technology

description:
Actinomycetes
All_sample_gene_expression_information.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NZ_JRKI00000000.1  whole genome using bowtie 2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
peaks were called using PeaksFind version 2.2
Genome_build: NZ_JRKI00000000.1(Streptomyces natalensis ATCC 27448)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Streptomyces natalensis

source_name: adding fungal elicitor

growth_protocol: The fungal elicitor was obtained from the fermentation broth of Penicillium chrysogenum AS 3.5163. P. chrysogenum AS 3.5163 was cultured at 28oC with the shaking of 180 r/min. After separation and purification to the broth, a compound was obtained and identified. Its molecular formula was C13H19N5O3 and it was named as 2-amino-N-(1-(2-aminopropyl)-4- oxo-1,2-diazetidin -3- yl)-2-(4-hydroxyphenyl)acetamide. To my knowledge, this compound was not reported. S. natalensis HW-2 was cultured at 28oC with the shaking of 180r/min for 24h. Then, the elicitor was added into the fermentation broth of S. natalensis HW-2 and continued to culture.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
Library was prepared according to Illumina's instructions with VAHTS Total RNA-Seq（H/M/R) Library PrepKit (NR603-02, Vazyme）. Briefly, RNA was extracted and rRNA was depleted with Ribo-Zero rRNA Removal Reagents(MRZB12424, Epicentre). mRNA was fragmented with Fragment High Mix. First Strand cDNA was synthesized with First Strand Synthesis Act D Mix and Second Strand cDNA was synthesized with Second Strand Marking Master Mix. Adenylate 3' Ends and Ligate Adapters were treated. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 520 bp were checked with an Agilent 2100 Bioanalyzer. Libraries were sequenced on Illumina Hiseq 2000 System following the manufacturer's protocols.

treatment_protocol: The fungal elicitor was added into the fermentation broth of Streptomyces natalensis HW-2 at 24h. The bacteria continued to culture. The broth was collected at 40 h and 80 h, respectively. Then, the bacteria were centrifuged at 10000 r/min for 10 min. CK1= 40h without the fungal elicitor, T1= 40h with the fungal elicitor, CK3= 80h without the fungal elicitor, T3= 80h with the fungal elicitor.

tag: strain

tag: duration

value: 80 hours with elicitor


title: CK3

source_name: without  fungal elicitor

value: 80 hours with no elicitor


title: ffpe-breast-tumor (14-03710)

description: breast tumor

tag: Sex


title: CK1

value: 40 hours with no elicitor


title: d-2d-TRT-psc-3_H7K7MCCXY_L4

city: Wuhan

first: Thuy Nhien

last: Tran Thi

state: Hubei

address: Shizishan

institute: Huazhong Agricultural University

data_processing:
The quality of RNA sequence data was controlled using FastQC software and trimmed using the Trimmomatic tool
The trimmed adapters and purified sequences were mapped and identified based on Ensembl Sus scrofa 11.1.90 set GTF annotation genome utilizing HISAT2
Stringtie was used to estimate gene expression and transcript levels via FPKM (fragments per kilobase of transcript per million mapped fragments) approach
Genome_build: Ensembl Sus scrofa 11.1.90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Sus scrofa

source_name: Muscle satellite cells

growth_protocol: Porcine satellite cells (PSCs) were isolated from the hindlimb muscle of 5-days-old male piglet.After isolating, PSCs were seeded at a density of (specific density/cm2), in 6-well plates pre-coated with gel, and incubated at 37°C under 5%CO2overnight with growth medium

extract_protocol:
At each time point, the poisoned effect of PSCs was harvested by TRIzol 0.25%.
A  total  amount  of  1.5μg  RNA  per  sample  was  used  as  input  material  for  the  RNA  sample preparations.  Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: After 24h of culturing, porcine satellite cells  were treated with 10 µg/mL of poly (I:C) within 12h and untreated PSCs as control. Next, the cells were washed once with PBS and entered into differentiation stages. The triplication of each sample at 4-time points, including0h and 12h of proliferation stage, at 24h and 48h of differentiation stage, was collected from poly (I:C) stimulation.

tag: cell type

value: Muscle satellite cells

tag: developmental stage

value: differentiation

tag: time

value: 48 hours

tag: untreated and treated poly (i


title: d-2d-TRT-psc-1_H7K7MCCXY_L4


title: d-2d-UN-psc-3_H7K7MCCXY_L4


title: PBMC-TC-PBMC-refpool_vs_TC-sample2

value: PBMC

value: referencepool


title: d-2d-UN-psc-2_H7JWVCCXY_L3


title: LSD1 × p53+/− #2

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

description: Gene expression data

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61 x 21.6 mm, Scan resolution 3 μm, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Spleen

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Splenic cells were isolated from 10-week old p53+/−, LSD1 × p53+/− #2, and LSD1 × p53+/− #3 mice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Isolated cells were used without treatment.

tag: genotype

value: LSD1 × p53+/−

tag: tissue

value: Splenic tumor

tag: gender

value: Male


title: LSD1 × p53+/− #3

description: Gene expression data


title: PBMC-TC-PBMC-refpool_vs_TC-sample1

value: placebo


title: T1

value: 40 hours with elicitor


title: d-1d-UN-psc-3_H7JWVCCXY_L3

value: 24 hours


title: d-1d-UN-psc-2_H7JN2CCXY_L2


title: d-1d-TRT-psc-3_H7JWVCCXY_L3


title: d-1d-UN-psc-1_H7JN2CCXY_L2


title: p-12h-TRT-psc-3_H7JWVCCXY_L3

value: proliferation

value: 12 hours


title: d-1d-TRT-psc-1_H7JWVCCXY_L3


title: p-12h-UN-psc-2_H7JN2CCXY_L2


title: p-0h-UN-psc-3_H7JWVCCXY_L3

value: 0 hour


title: p-0h-UN-psc-2_H7JN2CCXY_L2


title: d-2d-TRT-psc-2_H7K7MCCXY_L4


title: p-12h-UN-psc-1_H7JN2CCXY_L2


title: p53+/−

description: Gene expression data


title: d-2d-UN-psc-1_H7JWVCCXY_L3


title: SCA5

city: Irapuato

first: Sergio

middle: F.

last: Nigenda-Morales

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Unit of Advanced Genomics - National Laboratory of Genomics for Biodiversity

country: Mexico

institute: Center for Research and Advanced Studies

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA13_SCA3E

data_processing:
Filtering and quality:  Raw sequences were processed using Trim Galore! 0.3.6 to remove Illumina adapters and filter out sequences that did not meet the quality thresholds (q > 20, length > 50 bp).
Alignment : Reads alignment was performed on TOPHAT2 2.0.11 using the gray short-tailed opossum (Monodelphis domestica) as a reference genome (Ensembl release 74; ftp://ftp.ensembl.org/pub/release-74/fasta/monodelphis_domestica/dna/Monodelphis_domestica.BROADO5.74.dna.toplevel.fa.gz). To maximize the number of unique reads mapped to the reference genome, we used the following parameters: read-mismatches = 20, read-gap-length = 24, read-edit-dist = 28.
Counts: Aligned reads were converted to raw counts using HTSEQ (Anders  et al., 2014) with the “union” mode. 15,487 genes that have more than three read counts in all individuals mapped to the Monodelphis genome. From these , genes that were highly expressed in muscle were filtered out, resulting in 14,289 genes that were used in downstream analyses.
Normalization: Values for the remaining 14,289 genes were normalized applying the conditional quantile normalization and adjusted for gene length and GC content using the package CQN in R (Hansen et al., 2012).
Differential expression: Differential expression was calculated with an empirical Bayesian framework based on linear modeling implemented in the program limma-voom (Smyth 2005; Law et al. 2014; Ritchie et al. 2015). We adjusted our significance values to account for multiple hypothesis testing using the false discovery rate (FDR) method as implemented in the qvalue package in R (Storey  et al., 2015) and selected genes falling below Q < 0.1.
Genome_build: Monodelphis domestica (Ensembl release 74)
Supplementary_files_format_and_content: Tab-delimited text file including 14, 289 genes with more than three counts and Tab-delimited text file including the cqn normalized counts of 14,289 genes

organism: Didelphis virginiana

source_name: skin sample (ear punch)

extract_protocol:
Total RNA was extracted from each of the 13 skin samples using the TRIzol Plus RNA purification kit (Ambion, ThermoFisher) protocol. RNA was quantified on the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
To prepare the cDNA libraries we used the Illumina TruSeq RNA Sample Prep Kit (Illumina, San Diego, USA). Each sample was uniquely tagged with Illumina TruSeq tags. Individual sample libraries were then pooled in equimolar ratios, with 4 or 5 samples per pool and each pool sequenced in one lane of an Illumina HiSeq 2000 sequencer.

tag: pigmentation

value: depigmented

tag: sampling location

value: South Carolina, USA


title: SCA4

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA12_SCA3D


title: SCA3

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA11_SCA3C


title: p-12h-UN-psc-3_H7JN2CCXY_L2


title: YUC2

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA06_YUC2B

value: pigmented

value: Yucatan, Mexico


title: SCA1

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA09_SCA3A


title: YUC4

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA08_YUC2D


title: YUC1

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA05_YUC2A


title: MOR4

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA04_MOR1D

value: Morelos, Mexico


title: MOR3

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA03_MOR1C


title: p-0h-UN-psc-1_H7JWVCCXY_L3

value: Muscle satellite cells


title: MOR1

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA01_MOR1A


title: MOR2

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA02_MOR1B


title: Tachyzoites_T2

status: Public on Mar 30 2018

city: Zurich

first: Chandra

last: Ramakrishnan

address: Winterthurerstrasse 266a

department: Institute of Parasitology

country: Switzerland

institute: University of Zurich

description: Tachyzoites_T2 [FPKM]

data_processing:
Quality control with Fastqc and FastqScreen
Alignment with STAR-aligner (reference genome ME49 ToxoDB release 24)
Gene expression values (normalised counts) computed with featureCounts from the R package Rsubread
FPKM (fragments per kilobase of transcript per million mapped reads) calculatec using transcrpit lengths from ToxoDB
Genome_build: reference genome ME49 ToxoDB release 24
Supplementary_files_format_and_content: Excel table with FPKM values

organism: Toxoplasma gondii

source_name: Infected human foreskin fibroblasts

extract_protocol:
For enteroepithelial stages and tachyzoites: Q IAGEN Rneasy Mini Kit; for tissue cysts:Zymo Direct-zol RNA Miniprep kit
TruSeq RNA Sample Prep Kit v2 (Illumina)

value: CZ clone H3

value: Tachyzoites

tag: host

value: Homo sapiens

value: foreskin fibroblasts


title: Tissue_cysts_A

description: Tissue_cysts_A [FPKM]

source_name: Infected brain

value: Tissue cysts

value: Mus musculus


title: Tachyzoites_T4

description: Tachyzoites_T4 [FPKM]


title: Day7_CS9

description: Day7_CS9 [FPKM]

source_name: Infected intestine

value: Enteropithelial stages

value: Felis catus

tag: time point

value: day 7 post infection


title: Day7_CS8

description: Day7_CS8 [FPKM]


title: Day7_CS7_C

description: Day7_CS7 [FPKM]


title: Day7_CS7_A

description: Day7_CS7 [FPKM]


title: Day7_CS7_B

description: Day7_CS7 [FPKM]


title: SCA2

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA10_SCA3B


title: Day5_CS2_B

description: Day5_CS2 [FPKM]

value: day 5 post infection


title: Day5_CS2_A

description: Day5_CS2 [FPKM]


title: YUC3

description:
Final_Filtered_Counts_14289.txt
Voom_normalized_cqn_counts_14289.txt
DiviRNA07_YUC2C


title: Day3_CS6_B

description: Day3_CS6 [FPKM]

value: day 3 post infection


title: Day3_CS5_B

description: Day3_CS5 [FPKM]


title: Day3_CS4_B

description: Day3_CS4 [FPKM]


title: Day3_CS4_A

description: Day3_CS4 [FPKM]


title: IMR-90 40_36h

status: Public on Mar 27 2018

city: Beijing

first: Zhen

last: Zhao

address: Haidian District

department: Department of Automation

institute: Tsinghua University

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 36 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_36h

data_processing:
Sequenced reads were trimmed for adaptor sequence,then mapped to hg19 whole genome using bowtie2 v2.2.3.
Read quality was checked for each sample using FastQC v0.11.5.
High-quality reads were then imported into TopHat v2.0.12 for alignment into BAM files.
The mapped reads were counted for gene using HTSeq v0.6.1.The count data were normalized using DESeq. Gene counts values were log2-transformed after one was added to count values.
If a gene's count value was less than a millionth of the aligned read number, the gene was considered to be low expression. We filtered out genes with low expression in all samples.
Genome_build: hg19, reference sequence is gencode v24(https://www.gencodegenes.org/releases/24lift37.html)
Supplementary_files_format_and_content: ProcessedDataMatrix_Final.txt: tab-delimited text file includes gene count values (for log2-transformed after one was added to count values)

source_name: lung

growth_protocol: Human diploid IMR90 fibroblasts were cultured at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium, 10% fetal bovine serum and antibiotics.  The cells were plated at 20000/cm^2.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina was used with 1 ug of total RNA for the construction of sequencing libraries.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 20pM hybridization to a 2x125 paired end flow cell.

treatment_protocol: The cells were plated at 20000/cm^2. After two days, the cells were treated with the DNA-damaging agent bleomycin at 0 ug/ml, 2 ug/ml and 40 ug/ml for 2 h. The total RNA was extracted using TRIzol reagent (Invitrogen) at 12 time points (0 h, 2 h, 4 h, 8 h, 12 h, 24 h, 32 h, 2 days, 4 days, 6 days and 8 days) after exposure to bleomycin at 2 ug/ml and 40 ug/ml. The total RNA was extracted at 3 time points (0 h, 4 days and 8 days) after exposure to bleomycin at 0 ug/ml.

tag: cell line

value: fibroblast

tag: age

value: 16 weeks gestation

tag: agent

value: bleomycin

tag: dose

value: 40 ug/ml


title: IMR-90 40_4h

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 4 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_4h

value: 4 h


title: IMR-90 40_2h

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 2 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_2h

value: 2 h


title: IMR-90 2_12h

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 12 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_12h

value: 2 ug/ml


title: Tissue_cysts_B

description: Tissue_cysts_B [FPKM]

tag: strain

value: CZ clone H3


title: Day5_K4-14

description: Day5_K4-14 [FPKM]


title: Day3_CS6_A

description: Day3_CS6 [FPKM]


title: Day3_CS5_A

description: Day3_CS5 [FPKM]


title: p-12h-TRT-psc-2_H7JN2CCXY_L2

value: Muscle satellite cells

value: proliferation

value: 12 hours


title: HabenulaR1

status: Public on Mar 23 2018

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

description: 10X library for adult habenula R1

data_processing:
Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using "cellranger mkfastq"
FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read, aligned reads to a zebrafish reference transcriptome, and quantified transcript counts for each annotated gene within every cell. Here, the 10bp unique molecular identifier (UMI) on the left read was used to collapse PCR duplicates, and accurately quantify the number of transcript molecules captured for each gene in every cell.
Supplementary_files_format_and_content: text file with tab delimiters

organism: Danio rerio

source_name: adult habenula

extract_protocol:
polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.
Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/)

value: Adult

value: Brain

tag: tissue subtype

value: adult habenula


title: HabenulaR2

description: 10X library for adult habenula R2


title: larvalR2

description: 10X libraries for larval habenula

source_name: larval habenula

value: 10 days post fertilization

value: larval habenula


title: IMR-90 2_8h

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 8 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_8h

tag: cell type

value: 8 h


title: Y-651-B

status: Public on Mar 06 2018

city: Mainz

first: Matteo

middle: Antoine

last: Negroni

address: Joh.-von-Müller-Weg 6 Room 02-239

department: Institute of Organismic and Molecular Evolution

country: Germany

institute: Johannes Gutenberg, University, Mainz

description:
Table_S3_Differentially_expressed_within_brain_between_age_classes.xlsx
Table_S4_Differentially_expressed_within_fat_body_between_age_classes.xlsx
Table_S8_Differentially_expressed_within_young_between_tissues.xlsx
Table_S9_Differentially_expressed_within_old_between_tissues.xlsx
Table-S6.csv

data_processing:
FastQC-v0.11.5; default parameters
Trimmomatic-v0.36; default parameters
Trinityrnaseq-Trinity-v2.4.0; command: Trinity --seqType fq --max_memory 200G --left 03_R1_trimP.fastq.gz --right 03_R2_trimP.fastq.gz --CPU 32 --min_contig_length 300 --output Trinity_assembly --full_cleanup --no_bowtie
RSEM-v1.3.0; command: ./align_and_estimate_abundance.pl --transcripts Trinity_assembly.fasta --seqType fq --left sample-1-paired-forward-F --right sample-1-paired-reverse-F --thread_count 10 --est_method RSEM --prep_reference --aln_method bowtie2 --output_dir RSEM-output-sample-1
R package Deseq2-v1.2.10
Genome_build: de novo transcriptome assembly
Supplementary_files_format_and_content: Table_S3_Differentially_expressed_within_brain_between_age_classes.xlsx; Table_S4_Differentially_expressed_within_fat_body_between_age_classes.xlsx; Table-S6.csv (normalized read count output from RSEM); Table_S8_Differentially_expressed_within_young_between_tissues.xlsx; Table_S9_Differentially_expressed_within_old_between_tissues.xlsx ; Trinity_assembly.fasta

organism: Temnothorax rugatulus

source_name: brain

extract_protocol:
Each individual was killed by decapitation, and brain, fat body were immediately dissected on ice. Tissue dissection took less than 10 minutes for each individual. Brain and fat body were separately crushed in 50 μL of TRIZOL for storage at -20°C before RNA extraction. RNA was extracted from fat body and brain samples separately using the RNAeasy mini extraction kit (Qiagen)
Libraries were constructed by BGI (Hongkong, China) immediately prior to sequencing

tag: individual

value: Young

tag: specimen type

value: Queen

value: brain


title: Y-503-B


title: Y-594-B


title: Y-361-F

source_name: fat body

value: fat body


title: Y-453-F


title: Y-503-F


title: Y-651-F