title: pol2MG_rnh202_24hr_NT

description:
TAK_1314
TAK_1314-pol2MG_rnh202_24hr_NT

value: pol2-M644G rnh202{delta}


title: HI.3965.006.RPI14.19-2_R1

status: Public on Jul 01 2019

type: SRA

city: Grafton

first: FARHA

last: RAMZAN

state: AUCKLAND

address: 85 Park road

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: miRNA

library_source: transcriptomic

data_processing:
Cutadapt - 3’ adapter sequences removed, aligning the reads to miRBase (version21), reads are tallied to generate total counts for each miRNA, statistical significance (p-value) between 2 or more samples is calculated to generate differential expression profiles
Genome_build: miRBase (version21)
Supplementary_files_format_and_content: 58_samples_Readcount.tab- Readcounts of all samples for differential expression

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Plasma/Serum RNA Purification Kit using  Norgen Biotek (Cat#55000)
a standard library preparation workflow using Norgen's Small RNA Library Prep Kit for Illumina (Cat# 63600). Six microliter of each RNA sample was used as input. The workflow includes the following steps in sequence -  3' adapter ligation, 5' adapter ligation, reverse transcription/cDNA synthesis and then the indexing PCR. The final library is then subjected to column clean-up before resolving on a 6% TBE PAGE gel for size selection. The target band (~141-144 bp) is then excised from PAGE gel and purified

tag: subject id

tag: time

tag: diet

value: Protein diet-2xRDA; 1.6g/kg/day

tag: tissue

value: plasma

tag: age

value: >70 years

tag: Sex

value: male


title: LNCaP-RT_ENZA_MTH038G03G03_01, biological rep3

type: RNA

city: Montreal

first: Thierry

last: Muanza

address: 3755 Chemin de la Côte-Sainte-Catherine,

country: Canada

institute: McGill Univeristy

description: Enzalutamide added 2h before radiation and tRNA extracted 4h after radiation

hyb_protocol: After fragmentation and labeling, 2.8 µg DNA target was hybridized on Clariom™S HT, Human (Thermo Fisher Scientific) and process on the GeneTitan® Instrument (Thermo Fisher Scientific) for Hyb-Wash-Scan automated workflow. For hybridization on the Gene Titan we use the GeneTitan™ Hybridization, Wash, and Stain Kit for WT Array Plates.

scan_protocol: The imaging device in GeneTitan MC Instrument uses an external, high-intensity xenon lamp and dual excitation and emission filters to capture images from array plates for use in expression.

data_processing: The primary analysis was completed using the R/Bioconductor package. The data was normalized using the 'rma' method in the bioconductor package 'oligo'.

label: biotin

label_protocol: Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).  Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss-cDNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific).

growth_protocol: LNCaP and C4-2 cells are cultured in RPMI media containing 10%FBS

extract_protocol: The toal RNA was isolated by the Rneasy Mini Kit (Qiagen) according to the manufactures' instructions.

treatment_protocol: LNCaP and C4-2 cells maintained in 6 well plates for 24 hours. After 24 hours the cells were treated with either 10 uM Enzalutamide (celleckchem) or ADT (charcopl phenol free media) or the combination of both, 2 hours later,  the cells were radiated (4Gy). 4 hours after radiation, tRNA was extracted

tag: cell line

value: LNCaP (hormone-sensitive PCa cells)

value: prostate

tag: protocol


title: flag_c_input

city: Madison

first: Elena

last: Sorokin

state: WI

address: 433 Babcock Drive

department: Biochemistry

country: USA

institute: UW-Madison

description: chip antibody: M2 Flag antibody (F1804 Sigma)

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the ce10 genome assembly using bowtie with the following configurations: -q -m 1 -v 3 -sam -best -strata
Peak density, scaled to a total library size of 10 million reads, was visualized using IGV
We specified the minimum fold change of IP to input of four-fold minimum and FDR < 0.01 for the peak call in Homer, for at least two biological replicates.
Genome_build: ce10
Supplementary_files_format_and_content: bedgraph files were generated using Homer where tag densities were scaled to 10 million tags.
Supplementary_files_format_and_content: Peak calling was performed using Homer and MACS, and tag density under each peak was assessed using Homer.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: ~104 L4 stage worms were crosslinked and used for chromatin immunoprecipitation (ChIP) of DNAs preferentially bound to LAG-1(N-tag), GLP-1 (C-tag) or Control worms using established protocols.  Modifications include: using 4 mg/mL extract, omission of the wash with FA buffer containing 1 M NaCl.

extract_protocol:
Immunocomplexes, from each sample, were collected using 10 µg of M2 Flag antibody (F1804 Sigma) or 10 µg of 9E10 Myc antibody (Sigma M4439) overnight at 4 °C.  Then each sample was incubated for 1-2hr at 4 °C with 75 µL Dynabeads-Protein G (Novex 10003D).  Lysate samples and immunoprecipated protein samples were analyzed by immunoblot analysis using standard protocols.
ChIP-Seq DNA libraries were prepared using standard protocols and assessed for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  DNA sequencing was performed on four lanes of an Illumina HiSeq2000 at the University of Wisconsin-Madison Biotechnology Center (Madison, WI).

tag: developmental stage

value: L4 larva

tag: growth temperature ('c)

tag: strain


title: flag_c_chip


title: HI.3965.006.RPI13.19-1_R1

description: miRNA

value: Baseline


title: LNCaP-RT_MTH021D05D02_01, biological rep2

description: tRNA extracted 4h after radiation

value: tRNA extracted 4h after radiation


title: HI.3965.006.RPI12.18-2_R1

description: miRNA

value: protein diet-RDA; 0.8 g/kg/day)


title: LNCaP-RT_ENZA_ADT_MTH040H05H02_01, biological rep3

description: Enzalutamide+ADT added 2h before radiation and tRNA extracted 4h after radiation


title: LNCaP-ADT_ENZA_MTH036C06C03_01, biological rep3

description: tRNA extracted 6h after Enzalutamide+ADT treatment


title: 22-2_S3_L001_R1_001

description: miRNA


title: LNCaP-RT_ADT_MTH039A01A01_01, biological rep3

description: ADT added 2h before radiation and tRNA extracted 4h after radiation


title: LNCaP-N3-RT_MTH037B02B02_01, biological rep3

description: tRNA extracted 4h after radiation


title: LNCaP-RT_ENZA_ADT_MTH024A03A03_01, biological rep2

value: Enzalutamide+ADT added 2h before radiation and tRNA extracted 4h after radiation


title: flag_b_input


title: LNCaP-ADT_MTH035B03B03_01, biological rep3

description: tRNA extracted 6h after ADT treatment

value: tRNA extracted 6h after ADT treatment


title: pol2MG_rnh202_0hr_NT

city: Durham

first: Zhi-Xiong

last: Zhou

address: 111 TW Alexander Dr.

institute: National Institute of Envinromental Health Sciences

description:
TAK_1311
TAK_1311-pol2MG_rnh202_0hr_NT

data_processing:
library strategy: HydEn-seq
Base calling and generation of FASTQ files performed by Illumina Hiseq standard pipeline
Reads trimmed for adapter sequence using cutadapt 1.12, discarding pairs with one or both reads shorter than 15 nt
Align end 1 to index of oligos used during library prep, exclude successful pairs from further analysis (bowtie 1.2 -k1 -v2, see supplementary file oligos.fa)
Align remaining pairs to reference sequence (Ch_10_before_BIR.fa/Ch_10_after.fa), trim single nt from 3' end of reads to allow mapping of 100% overlapping pairs (bowtie 1.2 -m1 -v2 -X10000 -3 1)
Align end 1 of unmapped pairs to reference (bowtie 1.2 -m1 -v2)
Retain 5' end only for all single- and paired-end unique alignments, combine
Determine counts of ends mapped to PmeI restriction sites, calculate size factors using method applied in DESeq, Anders et al., 2010
Filter ends mapping within 2 nt of an PmeI restrition site or site with 1 bp mismatch relative to PmeI motif, divide by previously determined size factors
Genome_build: Ch_10_before_BIR.fa, Ch_10_after_BIR.fa
Supplementary_files_format_and_content: bigWig, count of HydEn-seq 5' ends per position

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown to log phase at 30°C in YPR medium before treated with 0.1 μg/ml doxycycline, 20 μg/ml nocodazole for 2 hours, followed by 50 μg/ml doxycycline and 2.5 mM IAA for 1 hours before HO induction. Samples were taken at various time points.

extract_protocol:
DNA was isolated using the MasterPure™ Yeast DNA Purification Kit (Epicentre) without RNase A treatment.
HydEn-seq libraries are constructed as previously described (Clausen, et al. 2015 NSMB) with modifications by the following steps. Briefly, extract yeast genomic DNA (gDNA) using Epicenter MasterPure Yeast DNA Purification Kit. Treat 200 ng gDNA with Shrimp Alkaline Phosphatase (rSAP, New England Biolabs). Denature rSAP and restriction digest with PmeI at 37 °C for 1 hour. Split the DNA into two fractions. Treat one fraction with RNase HII (NEB) at 37 °C for 2 hours and designate the other fraction as non-treatment control. Denature the DNA by incubation at 90 °C for 2 min and ligate to adaptor ARC140 by T4 RNA ligase 1 (NEB) overnight at 25 °C. Denature DNA and anneal to the duplex adaptor ARC76/77. Synthesize the second strand using T7 DNA polymerase (NEB). Amplify the library for 20 cycles by primer ARC49 and an indexing primer using KAPA HiFi HotStart Ready Mix (KAPA Biosystems). 0.8 volumes of MagBio HighPrep PCR beads were used to purify DNA between steps that require changing buffers and/or removal of oligo adaptors and in the final library cleanup. The library was sequenced on an Illumina HiSeq 4000 machine for paired end 50 bp reads. The rSAP, SfbI-HF and RNase HII treatments are the main modifications to the original protocol to improve on signal-to-noise ratio, quantitation and specificity.

tag: genotype/variation

tag: growth phase

value: Log phase cell culture


title: HI.3965.006.RPI9.17-1_R1

description: miRNA


title: LNCaP-ENZA_MTH034H04H01_01, biological rep3

description: tRNA extracted 6h after Enzalutamide treatment


title: pol2MG_rnh202_6hr_NT

description:
TAK_1312
TAK_1312-pol2MG_rnh202_6hr_NT


title: LNCaP-CTR_MTH033D04D01_01, biological rep3

description: No treatment

value: No treatment


title: LNCaP-RT_ENZA_MTH022C02C02_01, biological rep2

value: Enzalutamide added 2h before radiation and tRNA extracted 4h after radiation


title: flag_b_chip


title: flag_a_input


title: HI.3965.006.RPI8.16-2_R1

description: miRNA


title: HI.3965.006.RPI7.16-1_R1

description: miRNA


title: LNCaP-RT_ADT_MTH023A04A01_01, biological rep2

value: ADT added 2h before radiation and tRNA extracted 4h after radiation


title: pol1YA_rnh202_24hr_NT

description:
TAK_1310
TAK_1310-pol1YA_rnh202_24hr_NT

value: pol1-Y869A rnh202{delta}


title: HI.3965.006.RPI10.17-2_R1

description: miRNA


title: HI.3965.006.RPI4.14-2_R1

description: miRNA


title: flag_a_chip


title: pol1YA_rnh202_12hr_NT

description:
TAK_1309
TAK_1309-pol1YA_rnh202_12hr_NT


title: pol1YA_rnh202_6hr_NT

description:
TAK_1308
TAK_1308-pol1YA_rnh202_6hr_NT


title: mTN14

city: Stockholm

first: Martin

last: Bergö

address: Hälsovägen 7C (Neo building)

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Paired-end reads  were mapped to mouse genome with STAR (version 2.5.0a) aligner
Genes were quantified with the featureCount tool (version 1.5.2)
Differential gene expression was performed by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files including log2fold chnages of differtial experssion of genes
Supplementary_files_format_and_content: Raw read counts

organism: Mus musculus

source_name: Lung tumor

growth_protocol: Cells were grown in DMEM medium glutaMAX, glucose 1g/L containing 10% FBS, supplemented with NEAA (1%), penicillin/streptomycin (1%)

extract_protocol:
Total RNA were extracted using RNEasy mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: no specific treatment was applied

value: mixed C57BL/6-129/Sv

value: Lung tumor

tag: group

value: NAC-treated (drinking water of mice)


title: pol1YA_rnh202_0hr_NT

description:
TAK_1307
TAK_1307-pol1YA_rnh202_0hr_NT


title: HI.3965.006.RPI3.14-1_R1

description: miRNA

value: plasma

value: >70 years

value: male


title: mTN12


title: HI.3965.006.RPI6.15-2_R1

description: miRNA

value: Protein diet-2xRDA; 1.6g/kg/day


title: HI.3965.006.RPI5.15-1_R1

description: miRNA

value: Baseline


title: rnh202_24hr_NT

description:
TAK_1306
TAK_1306-rnh202_24hr_NT


title: mTN11


title: LNCaP-CTR_MTH017D06D03_01, biological rep2

description: No treatment

value: LNCaP (hormone-sensitive PCa cells)

value: prostate


title: LNCaP-ENZA_MTH018E01E01_01, biological rep2

value: tRNA extracted 6h after Enzalutamide treatment


title: LNCaP-RT_MTH005F06F03_01, biological rep1

description: tRNA extracted 4h after radiation

value: tRNA extracted 4h after radiation


title: mTN13


title: rnh202_12hr_NT

description:
TAK_1305
TAK_1305-rnh202_12hr_NT

value: Log phase cell culture


title: LNCaP-ADT_MTH019F05F02_01, biological rep2

description: tRNA extracted 6h after ADT treatment

value: tRNA extracted 6h after ADT treatment


title: rnh202_6hr_NT

description:
TAK_1304
TAK_1304-rnh202_6hr_NT


title: pol2MG_rnh202_12hr_NT

description:
TAK_1313
TAK_1313-pol2MG_rnh202_12hr_NT

value: pol2-M644G rnh202{delta}


title: HI.3965.006.RPI2.13-2_R1

description: miRNA

value: protein diet-RDA; 0.8 g/kg/day)


title: mTC31

value: Control


title: LNCaP-ADT_ENZA_MTH020E03E03_01, biological rep2

value: tRNA extracted 6h after Enzalutamide+ADT treatment


title: BIR_pol3LG_rnh202_24hr_RII_2

description:
TAK_2066
TAK_2066-BIR_pol3LG_rnh202_24hr_RII
processed data file: TAK_2050_2066-BIR_pol3LG_rnh202_24hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2050_2066-BIR_pol3LG_rnh202_24hr_RII_after_reverse_normalized.bw

value: pol3-L612G rnh202{delta}


title: LNCaP-RT_ENZA_ADT_MTH008A06A03_01, biological rep1

value: Enzalutamide+ADT added 2h before radiation and tRNA extracted 4h after radiation


title: mTC11

value: mixed C57BL/6-129/Sv

value: Lung tumor


title: HI.3965.005.RPI18.9-2_R1

description: miRNA

value: plasma

value: >70 years

value: male


title: mTC14


title: BIR_pol2MG_rnh202_24hr_RII_2

description:
TAK_2064
TAK_2064-BIR_pol2MG_rnh202_24hr_RII
processed data file: TAK_2048_2064-BIR_pol2MG_rnh202_24hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2048_2064-BIR_pol2MG_rnh202_24hr_RII_after_reverse_normalized.bw


title: HI.3965.005.RPI17.9-1_R1

description: miRNA

value: Baseline


title: BIR_pol1YA_rnh202_24hr_RII_2

description:
TAK_2062
TAK_2062-BIR_pol1YA_rnh202_24hr_RII
processed data file: TAK_2046_2062-BIR_pol1YA_rnh202_24hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2046_2062-BIR_pol1YA_rnh202_24hr_RII_after_reverse_normalized.bw

value: pol1-Y869A rnh202{delta}


title: BIR_pol2MG_rnh202_12hr_RII_2

description:
TAK_2063
TAK_2063-BIR_pol2MG_rnh202_12hr_RII
processed data file: TAK_2047_2063-BIR_pol2MG_rnh202_12hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2047_2063-BIR_pol2MG_rnh202_12hr_RII_after_reverse_normalized.bw


title: HI.3965.006.RPI24.12-2_R1

description: miRNA


title: LNCaP-RT_ENZA_MTH006C03C03_01, biological rep1

value: LNCaP (hormone-sensitive PCa cells)

value: prostate

value: Enzalutamide added 2h before radiation and tRNA extracted 4h after radiation


title: HI.3965.006.RPI23.12-1_R1

description: miRNA


title: HI.3965.005.RPI16.8-2_R1

description: miRNA

value: Protein diet-2xRDA; 1.6g/kg/day


title: 8-1_S2_L001_R1_001

description: miRNA


title: BIR_rnh202_24hr_RII_2

description:
TAK_2060
TAK_2060-BIR_rnh202_24hr_RII
processed data file: TAK_2044_2060-BIR_rnh202_24hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2044_2060-BIR_rnh202_24hr_RII_after_reverse_normalized.bw

value: Log phase cell culture


title: rnh202_0hr_NT

description:
TAK_1303
TAK_1303-rnh202_0hr_NT


title: HI.3965.006.RPI22.11-2_R1

description: miRNA

value: protein diet-RDA; 0.8 g/kg/day)


title: BIR_pol1YA_rnh202_12hr_RII_2

description:
TAK_2061
TAK_2061-BIR_pol1YA_rnh202_12hr_RII
processed data file: TAK_2045_2061-BIR_pol1YA_rnh202_12hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2045_2061-BIR_pol1YA_rnh202_12hr_RII_after_reverse_normalized.bw


title: BIR_pol3LG_rnh202_12hr_RII_2

description:
TAK_2065
TAK_2065-BIR_pol3LG_rnh202_12hr_RII
processed data file: TAK_2049_2065-BIR_pol3LG_rnh202_12hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2049_2065-BIR_pol3LG_rnh202_12hr_RII_after_reverse_normalized.bw


title: HI.3965.005.RPI14.7-2_R1

description: miRNA


title: BIR_pol3LG_rnh202_24hr_NT_2

description:
TAK_2058
TAK_2058-BIR_pol3LG_rnh202_24hr_NT
processed data file: TAK_2042_2058-BIR_pol3LG_rnh202_24hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2042_2058-BIR_pol3LG_rnh202_24hr_NT_after_reverse_normalized.bw


title: BIR_pol3LG_rnh202_12hr_NT_2

description:
TAK_2057
TAK_2057-BIR_pol3LG_rnh202_12hr_NT
processed data file: TAK_2041_2057-BIR_pol3LG_rnh202_12hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2041_2057-BIR_pol3LG_rnh202_12hr_NT_after_reverse_normalized.bw


title: LNCaP-ADT_MTH003C05C02_01, biological rep1

description: tRNA extracted 6h after ADT treatment

value: tRNA extracted 6h after ADT treatment


title: HI.3965.005.RPI13.7-1_R1

description: miRNA


title: LNCaP-ENZA_MTH002A02A02_01, biological rep1

value: tRNA extracted 6h after Enzalutamide treatment


title: C4-2-RT_ENZA_ADT_MTH048E05E02_01, biological rep3

value: C4-2 (hormone-resistant PCa cells)


title: C4_2_ENZA_MTH042H01H01_01, biological rep3


title: LNCaP-ADT_ENZA_MTH004B01B01_01, biological rep1

value: tRNA extracted 6h after Enzalutamide+ADT treatment


title: HI.3965.005.RPI20.10-2_R1

description: miRNA


title: BIR_pol2MG_rnh202_24hr_NT_2

description:
TAK_2056
TAK_2056-BIR_pol2MG_rnh202_24hr_NT
processed data file: TAK_2040_2056-BIR_pol2MG_rnh202_24hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2040_2056-BIR_pol2MG_rnh202_24hr_NT_after_reverse_normalized.bw

value: pol2-M644G rnh202{delta}


title: BIR_pol2MG_rnh202_12hr_NT_2

description:
TAK_2055
TAK_2055-BIR_pol2MG_rnh202_12hr_NT
processed data file: TAK_2039_2055-BIR_pol2MG_rnh202_12hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2039_2055-BIR_pol2MG_rnh202_12hr_NT_after_reverse_normalized.bw


title: C4-2-RT_MTH045F04F01_01, biological rep3

description: tRNA extracted 4h after radiation

value: tRNA extracted 4h after radiation


title: LNCaP-RT_ADT_MTH007G02G02_01, biological rep1

value: ADT added 2h before radiation and tRNA extracted 4h after radiation


title: C4-2-CTR_MTH041B05B02_01, biological rep3

description: No treatment

value: No treatment


title: C4-2-RT_ENZA_MTH046H06H03_01, biological rep3

description: Enzalutamide added 2h before radiation and tRNA extracted 4h after radiation


title: C4-2-ADT_MTH043F01F01_01, biological rep3

description: tRNA extracted 6h after ADT treatment


title: LNCaP-CTR_MTH001C04C01_01, biological rep1

description: No treatment


title: HI.3965.005.RPI19.10-1_R1

description: miRNA

value: plasma

value: >70 years

value: male


title: BIR_rnh202_12hr_RII_2

description:
TAK_2059
TAK_2059-BIR_rnh202_12hr_RII
processed data file: TAK_2043_2059-BIR_rnh202_12hr_RII_after_reverse_normalized.bw
processed data file: processed data file: TAK_2043_2059-BIR_rnh202_12hr_RII_after_reverse_normalized.bw


title: 6-2_S1_L001_R1_001

description: miRNA


title: HI.3965.006.RPI21.11-1_R1

description: miRNA

value: Baseline


title: C4-2-ADT_ENZA_MTH044F02F02_01, biological rep3

value: prostate


title: BIR_pol1YA_rnh202_12hr_NT_2

description:
TAK_2053
TAK_2053-BIR_pol1YA_rnh202_12hr_NT
processed data file: TAK_2037_2053-BIR_pol1YA_rnh202_12hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2037_2053-BIR_pol1YA_rnh202_12hr_NT_after_reverse_normalized.bw

value: pol1-Y869A rnh202{delta}


title: HI.3965.005.RPI11.6-1_R1

description: miRNA


title: C4-2-RT_MTH029B04B01_01, biological rep2

description: tRNA extracted 4h after radiation


title: C4-2-RT_ENZA_MTH030B06B03_01, biological rep2

value: Enzalutamide added 2h before radiation and tRNA extracted 4h after radiation


title: BIR_pol1YA_rnh202_24hr_NT_2

description:
TAK_2054
TAK_2054-BIR_pol1YA_rnh202_24hr_NT
processed data file: TAK_2038_2054-BIR_pol1YA_rnh202_24hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2038_2054-BIR_pol1YA_rnh202_24hr_NT_after_reverse_normalized.bw

value: Log phase cell culture


title: BIR_rnh202_24hr_NT_2

description:
TAK_2052
TAK_2052-BIR_rnh202_24hr_NT
processed data file: TAK_2036_2052-BIR_rnh202_24hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2036_2052-BIR_rnh202_24hr_NT_after_reverse_normalized.bw


title: BIR_rnh202_12hr_NT_2

description:
TAK_2051
TAK_2051-BIR_rnh202_12hr_NT
processed data file: TAK_2035_2051-BIR_rnh202_12hr_NT_after_reverse_normalized.bw
processed data file: processed data file: TAK_2035_2051-BIR_rnh202_12hr_NT_after_reverse_normalized.bw


title: BIR_pol3LG_rnh202_24hr_RII_1

description:
TAK_2050
TAK_2050-BIR_pol3LG_rnh202_24hr_RII

value: pol3-L612G rnh202{delta}


title: HI.3965.005.RPI5.3-1_R1

description: miRNA


title: HI.3965.005.RPI6.3-2_R1

description: miRNA

value: protein diet-RDA; 0.8 g/kg/day)


title: HI.3965.005.RPI10.5-2_R1

description: miRNA

value: Protein diet-2xRDA; 1.6g/kg/day


title: HI.3965.005.RPI9.5-1_R1

description: miRNA


title: HI.3965.005.RPI3.2-1_R1

description: miRNA


title: HI.3965.005.RPI8.4-2_R1

description: miRNA


title: HI.3965.005.RPI4.2-2_R1

description: miRNA


title: BIR_pol2MG_rnh202_24hr_RII_1

description:
TAK_2048
TAK_2048-BIR_pol2MG_rnh202_24hr_RII


title: BIR_pol3LG_rnh202_12hr_RII_1

description:
TAK_2049
TAK_2049-BIR_pol3LG_rnh202_12hr_RII


title: BIR_pol1YA_rnh202_24hr_RII_1

description:
TAK_2046
TAK_2046-BIR_pol1YA_rnh202_24hr_RII


title: BIR_pol2MG_rnh202_12hr_RII_1

description:
TAK_2047
TAK_2047-BIR_pol2MG_rnh202_12hr_RII


title: BIR_pol1YA_rnh202_12hr_RII_1

description:
TAK_2045
TAK_2045-BIR_pol1YA_rnh202_12hr_RII


title: HI.3965.005.RPI7.4-1_R1

description: miRNA


title: C4-2-ENZA_MTH026G01G01_01, biological rep2

description: tRNA extracted 6h after Enzalutamide treatment

value: C4-2 (hormone-resistant PCa cells)


title: C4-2-CTR_MTH025G06G03_01, biological rep2

description: No treatment


title: C4-2-ADT_MTH027C01C01_01, biological rep2

description: tRNA extracted 6h after ADT treatment

value: tRNA extracted 6h after ADT treatment


title: C4-2-ADT_ENZA_MTH028A05A02_01, biological rep2

description: tRNA extracted 6h after Enzalutamide+ADT treatment


title: C4-2-RT_ENZA_ADT_MTH032H03H03_01, biological rep2

description: Enzalutamide+ADT added 2h before radiation and tRNA extracted 4h after radiation


title: C4-2-RT_ADT_MTH031E02E02_01, biological rep2

description: ADT added 2h before radiation and tRNA extracted 4h after radiation


title: HI.3965.005.RPI2.1-2_R1

description: miRNA


title: C4-2-RT_MTH013D01D01_01, biological rep1

description: tRNA extracted 4h after radiation


title: C4-2-RT_ENZA_MTH014D02D02_01, biological rep1


title: HI.3965.005.RPI1.1-1_R1

description: miRNA


title: BIR_rnh202_12hr_RII_1

description:
TAK_2043
TAK_2043-BIR_rnh202_12hr_RII


title: BIR_pol3LG_rnh202_24hr_NT_1

description:
TAK_2042
TAK_2042-BIR_pol3LG_rnh202_24hr_NT


title: LD1

city: Cardiff

first: Natalia

last: Sevane

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

data_processing:
Quality assessment and control was performed using the Trim Galore software (Babraham bioinformatics, UK). For adapter trimming the minimum required adapter overlap was 1 bp. To remove potential methylation-biased bases from the MspI digestion end-repair reaction, RRBS reads were trimmed a further 2 bp when adapter contamination was detected and by 2 bp at the start when read started with CAA or CGA. Trimming was performed on all reads using a minimum Phred quality score of 20.
Sequences were mapped using single end mapping to the bovine genome assembly UMD3.1.1 using Bismark. Following optimisation, a seed length of 20 bp was chosen and only one mismatch was allowed. The minimum alignment score function was set at L,0,-0.6.
For CpG level comparison, percent methylation of individual CpGs was calculated using MethylKit package in R and the coverage files from Bismark aligner.
DMRs were determined using the R package dispersion shrinkage for sequencing data (DSS), which outperforms other methods when sample size per group is small owing to the adoption of Wald test with shrinkage for determining differentially methylated cytosines (DMC). We identified DMRs using the coverage files from Bismark and the callDMR function with a p-value threshold of 0.01, delta=0.1 and otherwise default parameters. To be considered significant, a DMR was required to contain at least 3 CpG sites (default parameter, although the smallest significant DMR included 4 CpGs) within a distance of 200 bp, and with an absolute mean methylation difference greater than 25% when comparing Creole and Spanish samples.
Annotation with the closest/overlapping TSS (±100 kb) and CpGI was performed using the identgenloc program from the DMAP package.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: Bismark coverage files (.cov); Tab-delimited text file including DMRs between Creole and Spanish samples.

organism: Bos taurus

source_name: Blood

extract_protocol:
DNA was extracted from blood samples of adult males using the UltraClean BloodSpin DNA Isolation Kit (MO BIO Laboratories, Inc) for the Creole samples and the QIAamp DNA Blood Mini Kit (Qiagen) for the Spanish samples.
Genomic DNA (0.5-1.0 ug) from each sample was restricted with MspI enzyme (New England Biosciences), cleaned using DNA Clean and concentrator-25 columns (Zymo Research), and eluted in 60 ul for library preparation. The sticky ends produced by MspI digestion were filled with CG nucleotides and Illumina sequencing adapters. The TruSeq Nano DNA LT Library Prep Kit (Illumina) was used for 3’adenylation and adapter ligation. The end-repaired samples were purified using 2.5X AMpure XP Beads (Beckman Coulter) and eluted in 20 ul resuspension buffer. After adapter ligation, samples were again purified using 1.0X AMpure XP Beads and eluted in 40 ul resuspension buffer. Size-selection of DNA fragments (175-225 bp) was performed using a 2% Agarose gel (Invitrogen), and the selected fragments were purified twice using 1.0X AMpure XP Beads and finally eluted in 22 ul resuspension buffer. Bisulfite conversion of non-methylated cytosines was performed on 20 ul size-selected fragments using the EZ DNA Methylation-Lightning Kit (Zymo Research). PCR (20 cycles) was performed to enrich the sequencing library by using a TruSeq Nano DNA LT Library Prep Kit (Illumina). The Pfu Turbo Cx Hotstart DNA polymerase (Agilent Technologies) and 10 mM dNTP mix (Life Technologies) were used for PCR reactions.  After enrichment, the library was purified twice using 1X AMpure XP Beads (Beckman Coulter) and quantified using the Qubit dsDNA HS Assay Kit (Life Technologies). The average library size (270 pb) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies). The libraries were then pooled in equimolar ratios of 2 nM, and 6.0 pM of the pool was clustered and sample tracked using the cBot (Illumina) and sequenced following a 2 x 150 bp protocol for 300 cycles using the HiSeq 2500 system (Illumina).

tag: breed

value: Lidia breed


title: BIR_pol3LG_rnh202_12hr_NT_1

description:
TAK_2041
TAK_2041-BIR_pol3LG_rnh202_12hr_NT


title: RAV

value: Asturiana de los Valles


title: BIR_pol2MG_rnh202_24hr_NT_1

description:
TAK_2040
TAK_2040-BIR_pol2MG_rnh202_24hr_NT

value: pol2-M644G rnh202{delta}


title: BIR_pol2MG_rnh202_12hr_NT_1

description:
TAK_2039
TAK_2039-BIR_pol2MG_rnh202_12hr_NT


title: CCC2

description: breed: Costeño con Cuernos

value: Costeno con Cuernos


title: RET

value: Retinta


title: C4-2-RT_ENZA_ADT_MTH016E06E03_01, biological rep1

value: Enzalutamide+ADT added 2h before radiation and tRNA extracted 4h after radiation


title: BIR_rnh202_24hr_RII_1

description:
TAK_2044
TAK_2044-BIR_rnh202_24hr_RII


title: C4-2-RT_ADT_MTH015E04E01_01, biological rep1

value: ADT added 2h before radiation and tRNA extracted 4h after radiation


title: C4-2-ENZA_MTH010G05G02_01, biological rep1

value: tRNA extracted 6h after Enzalutamide treatment


title: C4-2-RT_ADT_MTH047D03D03_01, biological rep3

value: prostate


title: CCC1

description: breed: Costeño con Cuernos


title: C4-2-CTR_MTH009G04G01_01, biological rep1

description: No treatment

value: No treatment


title: C4-2-ADT_ENZA_MTH012F03F03_01, biological rep1

value: tRNA extracted 6h after Enzalutamide+ADT treatment


title: C4-2-ADT_MTH011H02H02_01, biological rep1

description: tRNA extracted 6h after ADT treatment


title: BIR_pol1YA_rnh202_24hr_NT_1

description:
TAK_2038
TAK_2038-BIR_pol1YA_rnh202_24hr_NT

value: pol1-Y869A rnh202{delta}

value: Log phase cell culture


title: BIR_pol1YA_rnh202_12hr_NT_1

description:
TAK_2037
TAK_2037-BIR_pol1YA_rnh202_12hr_NT


title: SM1

value: Sanmartinero


title: BIR_rnh202_12hr_NT_1

description:
TAK_2035
TAK_2035-BIR_rnh202_12hr_NT


title: BIR_rnh202_24hr_NT_1

description:
TAK_2036
TAK_2036-BIR_rnh202_24hr_NT


title: 0.1% Tween 24hr Control rep3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: 0.1% Tween

data_processing:
Raw fastq reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32
Genome_build: Z. mays AGPv4.34
Supplementary_files_format_and_content: tab delimited text file, see "RNA_column_header_descriptions.txt" for column headers

organism: Zea mays

source_name: Emergent but non-fully-expanded 4th leaf

growth_protocol: Zea mays Var. Golden Queen seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).

extract_protocol:
RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
Stranded mRNA-seq

tag: cultivar

value: Var. Golden Queen

value: Leaf


title: 0.1% Tween 24hr Control rep4

description: 0.1% Tween


title: 0.1% Tween 24hr Control rep2

description: 0.1% Tween


title: SLB 24hr leaf treatment rep4

description: SLB spore suspension (1X106)


title: 0.1% Tween 24hr Control rep1

description: 0.1% Tween


title: SLB 24hr leaf treatment rep3

description: SLB spore suspension (1X106)


title: Median nodes cultivated 1 day in vitro in the presence of 100mM sucrose and 10mM nitrate H01

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

data_processing:
Illumina MiSeq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
An RNA-Seq de novo transcriptome assembly was perform using the Trinity assembler v2.2.0 (params :  --min_contig_length 100 --KMER_SIZE 31) and an additional round of assembly with iAssembler-v1.3.2.x64 (params : -u Rosa_BI_20160929). The 3 fastq files were used for the de novo transcriptome.
RNAseq reads counts of A01 and H01 samples for each previously obtained sequences were generated using Bowtie (v1.1.1) and samtools (v1.3.1) and read counts were normalized using edgeR (version: 3.24.3)
Genome_build: Rosa_BI_20160929_unigene_seq.fasta
Supplementary_files_format_and_content: fasta file : multi-fasta with the name of the de novo sequence previously obtained. Count files : tab-delimited text file with respectively : sequence name, sequence length, number of  reads aligned, number of reads unaligned.

organism: Rosa hybrid cultivar

extract_protocol:
RNA from median nodes was extracted, from 50 to 100 mg FW, using a lysing buffer (80°C) composed of guanidine isothiocyanate (4 M), EDTA (25 mM), PVP40 (2.5 %), sarcosyl (2 %) and sodium acetate (0.2 M), pH 5.5 (MacKenzie et al., 1997; Gambino & Gribaudo, 2006). Samples were heated at 70°C for 10 min before chloroform / isoamyl alcohol (24 / 1; v / v) step. The aqueous phase was recovered and transferred in violet column of RNeasy Plant Mini Kit (Qiagen) following the supplier’s protocol. A DNase treatment (Qiagen) was performed. RNA was quantified using Qubit® (fluorometer, InVitrogen) technology and quality was verified using Experion® (LabChip Caliper, BioRad) which creates a virtual electrophoresis profile, according to the steps defined by the protocol of the Biorad supplier (Kappa).
Library construction was performed following the Agilent protocol for Illumina Miseq technology.

tag: tissus

value: Median nodes

tag: genetic background

value: radrazz

tag: genotype

value: Wild-type

tag: phenotype

tag: treatment

value: 1 day in vitro on an agar basic medium in the presence of 100mM sucrose and 10mM nitrate (hight light)

value: 5 weeks after potting  as decribed on Le Moigne et al. 2018

tag: growth protocol

value: in glasshouse during 5 weeks and in control condition during one day


title: SLB 24hr leaf treatment rep1

description: SLB spore suspension (1X106)

tag: tissue

tag: age


title: L41_g3_cervical_s91

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description:
rawcounts.txt
normcounts.txt
RNA-seq - 4 animals per age category (i.e. p18/p28).

data_processing:
Illumina Casava2.2 software used for basecalling.
Sequenced reads were mapped to rn6 whole genome using STAR v2.5.3a with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.16.5
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text file includes rawcount values for each Sample
Supplementary_files_format_and_content: tab-delimited text file includes normalized expression values(cpm = count per millions) for each Sample

organism: Rattus norvegicus

source_name: cervical

growth_protocol: normal growth

extract_protocol:
Laser micro-dissection
RNA libraries were prepared for sequencing using SMARTer Ultra Low input RNA kit

treatment_protocol: no treatment

tag: subject

value: 28 days

value: PDL

tag: region

value: cervical


title: Median nodes cultivated 1 day in vitro in the presence of 100mM sucrose A01

value: 1 day in vitro on an agar basic medium in the presence of 100mM sucrose (hight ligth)


title: HI.3965.006.RPI1.13-1_R1

description: miRNA

tag: subject id

tag: time

tag: diet

value: Baseline

value: plasma

value: >70 years

tag: Sex

value: male


title: L33_g1_cervical_s49

value: 18 days


title: SLB 24hr leaf treatment rep2

description: SLB spore suspension (1X106)

value: Var. Golden Queen

tag: developmental stage


title: Median nodes cultivated 1 day in vitro in the presence of 100mM sucrose A


title: OB_WT_2M_R1

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

description:
WT_2M_T2_8682_S18
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Mouse Clariom S Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Olfactory bulb, WT, 2m

label_protocol: The sense cDNA was prepared from 1 ng of total RNA using the Affymetrix GeneChip® WT Pico Kit (PN902623). The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

growth_protocol: Not applicable.

extract_protocol: For olfactory bulb mRNA extraction, the Maxwell 16 simplyRNA kit (Promega) was used.

treatment_protocol: Not applicable.

tag: genotype/variation

value: WT

value: Olfactory bulb

tag: gender

value: Female

value: 2 months


title: OB_WT_6M_R3

description:
WT_6M_T2_8672_S11
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

source_name: Olfactory bulb, WT, 6m

value: 6 months


title: OB_WT_6M_R2

description:
WT_6M_T2_8637_S12
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).


title: OB_WT_2M_R2

description:
WT_2M_T2_8683_S17
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).


title: OB_TG2576_6M_R3

description:
TG2576_6M_T2_8662_S7
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

source_name: Olfactory bulb, Tg2576, 6m

value: Tg2576 transgenic


title: OB_WT_6M_R1

description:
WT_6M_T2_8609_S10
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).


title: OB_WT_2M_R3

description:
WT_2M_T2_8684_S16
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).


title: mKO_4

city: Barcelona

first: Ana

last: Martín-Pardillos

address: Passeig de la Vall d'Hebron, 119-129

institute: Vall d´Hebron Institut de Recerca

description: Gene expression from clonal cell line derived from MDA-MB231 parental cell line

hyb_protocol: Sense ssDNA was fragmented, labelled and hybridized to the arrays with the GeneChip WT Plus Terminal Labeling and Hybridization Kit from Thermofisher-Affymetrix.

scan_protocol: Microarrays service was carried out at High Technology Unit (UAT) at Vall d’Hebron Research Institut (VHIR), Barcelona (Spain). Affymetrix GeneTitan microarray platform and the Genechip Human Clariom D array cartridges were used for this experiment.

data_processing:
Robust Multi-array Average (RMA) algorithm was used for pre-processing microarray data. Background adjustment, normalization and summarization of raw core probe expression values were defined so that the exon level values were averaged to yield one expression value per gene. Data were subjected to non-specific filtering to remove low variability genes. Conservative thresholds were used to reduce possible false negative results.
Selection of differentially expressed genes was based on a linear model analysis with empirical Bayes modification for the variance estimates

label: Biotin

source_name: mKO E10 (CLONE 2)

label_protocol: Starting material was 200 ng of total RNA of each sample. Briefly, sense ssDNA suitable for labelling was generated from total RNA with the GeneChip WT Plus Reagent Kit from Affymetrix (Thermofisher-Affymetrix) according to the manufacturer’s instructions.  Labelled and hybridized to the arrays with the GeneChip WT Plus Terminal Labeling and Hybridization Kit from Thermofisher-Affymetrix.

growth_protocol: 1.5 million cells were seeded in 100x17mm-dish in triplicate. After 72 hours cells were trypsinized and centrifugated.

extract_protocol: RNA was extracted using the PureLink™ RNA Mini Kit (ThermoFisher), quantification and assessment of RNA purity was performed using a NanoDrop™ 2000/2000c Spectrophotometer and confirmed according to the value RIN (RNA Integrity Number) using RNA 6000 Nano Kit and 2100 Bioanalyzer (Agilent).

treatment_protocol: No treatment

tag: cell line

value: MDA-MB231 breast cancer cell line

tag: fluorescent protein expression

value: mKO expression

tag: growth rate in vitro

value: 0.6 (relative to control, MDA-MB231)

tag: clone properties when injected in mice [morphology (in vivo, tumors)]

value: More rhabdoid and plasmacytoid shape

tag: clone properties when injected in mice [%-age of lung area occupied by metastasis (after 36 days post-injection)]


title: Sap_3

source_name: Sapphire D7 (CLONE 3)

value: Sapphire expression

value: 0.7 (relative to control, MDA-MB231)

value: Cells particularly small and rounded


title: L29_g1_cervical_s47

value: PDL

value: cervical


title: Sap_2


title: L21_g3_cervical_s85

value: 28 days


title: RoaR_2 [MEW514_2]

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

description:
100031_CCGTCC_S11
MEW514_2_sort.bam

data_processing:
Alignment with BWA v 0.7.8-r455
Differential expression analyses were perfomed with limma and edgeR packages in R
Genome_build: Streptococcus pyogenes MEW123, GenBank accession #: CP014139
Supplementary_files_format_and_content: txt file with cpm values for each gene in each sample, key to match MEW and AWM59 locus tags

organism: Streptococcus pyogenes

source_name: RoaR deficient

growth_protocol: Cells were grown in C-media at 37C under anaerobic conditions to mid-log phase (OD600 of 0.6)

extract_protocol:
RiboPure RNA Purification Kit, bacteria (AM1925)
Library construction was performed by the University of Michigan Sequencing Core using the Ribo-Zero Magnetic Kit, bacteria for rRNA depletion and the Illumina TruSeq Sample Prep Kit

treatment_protocol: Cell pellets were resuspended in RNAlater and stored at -20C

tag: strain

value: RoaR deficient


title: mKO_1


title: Sap_1


title: RoaR_1 [MEW514_1]

description:
100030_CTTGTA_S10
MEW514_1_sort.bam


title: mKO_2


title: GFP_3

source_name: GFP C3 (CLONE 1)

value: GFP expression

value: 1 (relative to control, MDA-MB231)

value: Epithelial cells


title: mKO_3


title: WT_3 [MEW123_3]

description:
100029_ATGTCA_S9
MEW123_3_sort.bam

source_name: wild type

value: wild type


title: OB_TG2576_6M_R2

description:
TG2576_6M_T2_8629_S8
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

tag: tissue

value: Olfactory bulb

value: Female

value: 6 months


title: RoaR_3 [MEW514_3]

description:
100032_TTAGGC_S12
MEW514_3_sort.bam


title: OB_TG2576_6M_R1

description:
TG2576_6M_T2_8628_S9
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

value: Tg2576 transgenic

tag: age


title: OB_TG2576_2M_R3

description:
TG2576_2M_T2_8685_S13
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

source_name: Olfactory bulb, Tg2576, 2m

value: 2 months


title: L5_g3_cervical_s89

tag: subject


title: L13_g1_cervical_s43

value: 18 days

tag: region


title: GFP_1

value: MDA-MB231 breast cancer cell line


title: WT_1 [MEW123_1]

description:
100027_ACAGTG_S7
MEW123_1_sort.bam


title: OB_TG2576_2M_R2

description:
TG2576_2M_T2_8680_S14
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).


title: S5_deeper_sequencing

status: Public on Jun 30 2019

city: New Orleans

first: YiPing

last: Chen

address: 6400 Freret Street

institute: Tulane University

description: single-cell RNA-seq

data_processing:
cells were loaded for capture onto 10x genomics Chromium single cell 3' library & gel bead kit v2
construct an Illumina sequencing library and sequenced on NextSeq 500 with 150 cycle sequencing
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger/2.1.0
FASTQ files were then aligned to mm10 mouse reference genome and transcriptome using the CellRanger/2.1.0 software pipeline with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

source_name: SAN cells including atrial cells

extract_protocol:
RNA was extracted from SAN (including atrium) single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit V2
Library construction was performed according to 10X v2 kit protocol.

tag: Stage

value: SAN cells including atrial cells

tag: genotype


title: S1_first_sequencing

description: single-cell RNA-seq


title: KO-hESC-H3k27ac

first: Carissa

middle: L

last: Sirois

address: 1500 Highland Ave T515

department: Waisman Center

institute: University of Wisconsin-Madison

data_processing:
Align to genome using bowtie2: Vesion 2.2.9
Sort with samtools: Version 1.7
Index with samtools: Version 1.7
Convert to tag align format for size estimation: PhantompeakqualTools
Peak calling with MACS2: Version 2.1.2
ENCODE IDR analysis pipeline: https://github.com/nboley/idr/archive/2.0.0.tar.gz
Genome_build: hg19
Supplementary_files_format_and_content: bigBed for peak calls: bigWig for p-value ChIP-Seq Signals

source_name: hESCs

growth_protocol: hESCs were grown and maintained as previously described (Chamberlain SJ, et al. (2010), Proc Natl Acad Sci U S A 107(41):17668-17673); hESC-derived neural progenitors and neurons were differentiated as previously described (Germain, ND, et al. (2014) Mol Autism 5:44)

extract_protocol:
hESCs, NPCs, and neurons were processed for ChIP-seq as previously described (Cotney & Noonan (2015), Cold Spring Harb Protoc 2015(4): 419
Libraries were prepared from ChIPed DNA using the Takara ThruPLEX DNA-seq library preparation kit according to manufacturer's instructions. Libraries were quantified with the NEBNext Library Quant Kit for Illumina

treatment_protocol: UBE3A-null hESCs were obtained by editing H9 hESCs with CRISPR sgRNAs

tag: cell type

value: H9 hESCs with homozygous UBE3A deletion

tag: weeks of differentiation

value: no differentiation

value: UBE3A KO

tag: antibody

tag: antibody catalog number and manufacturer

value: C15410196 (Diagenode)


title: S5_first_sequencing

description: single-cell RNA-seq


title: L1_g1_cervical_s45

value: PDL

value: cervical


title: KO-hESC-UBE3A-352-2

description:
overlapped peak file:
UBE3A-null-352_1_VS_UBE3A-null-352_2-overlapped-peaks.txt
input file:
UBE3A_null_input_2_trim_merge.fastq.gz
input file md5sum: b5ac90e78bcf772e548d47f02da758c5


title: KO-hESC-UBE3A-352-1

description:
overlapped peak file:
UBE3A-null-352_1_VS_UBE3A-null-352_2-overlapped-peaks.txt
input file:
UBE3A_null_input_1_trim_merge.fastq.gz
input file md5sum: 5c1fd05903de4d496e478a94bceacabb


title: GFP_2

value: GFP expression

value: 1 (relative to control, MDA-MB231)


title: MDA-MB231_3

description: Gene expression from MDA-MB231 parental cell line

source_name: MDA-MB231 (CONTROL)

value: No expression

value: Epithelial cells.High grade of vascular invasion


title: KO-hESC-UBE3A-351-2

description:
overlapped peak file:
UBE3A-null-351_1_VS_UBE3A-null-351_2-overlapped-peaks.txt
input file:
UBE3A_null_input_2_trim_merge.fastq.gz
input file md5sum: b5ac90e78bcf772e548d47f02da758c5


title: MDA-MB231_4


title: KO-hESC-UBE3A-351-1

description:
overlapped peak file:
UBE3A-null-351_1_VS_UBE3A-null-351_2-overlapped-peaks.txt
input file:
UBE3A_null_input_1_trim_merge.fastq.gz
input file md5sum: 5c1fd05903de4d496e478a94bceacabb


title: H9-Neuron-UBE3A-352-2

description:
overlapped peak file:
H9-Neuron-352_1_VS_H9-Neuron-352_2-overlapped-peaks.txt
input file:
H9_Neuron_input_2_trim_merge.fastq.gz
input file md5sum: 6bf6a12e473dcc74a0ac3d9f8d527f8d

source_name: Neurons

value: H9 hESC-derived neurons

value: 10 weeks

value: wildtype


title: H9-Neuron-UBE3A-352-1

description:
overlapped peak file:
H9-Neuron-352_1_VS_H9-Neuron-352_2-overlapped-peaks.txt
input file:
H9_Neuron_input_1_trim_merge.fastq.gz
input file md5sum: 087f1fabfffbebf5da59a449d48416a3


title: H9-Neuron-UBE3A-351-2

description:
overlapped peak file:
H9-Neuron-351_1_VS_H9-Neuron-351_2-overlapped-peaks.txt
input file:
H9_Neuron_input_2_trim_merge.fastq.gz
input file md5sum: 6bf6a12e473dcc74a0ac3d9f8d527f8d


title: H9-Neuron-UBE3A-351-1

description:
overlapped peak file:
H9-Neuron-351_1_VS_H9-Neuron-351_2-overlapped-peaks.txt
input file:
H9_Neuron_input_1_trim_merge.fastq.gz
input file md5sum: 087f1fabfffbebf5da59a449d48416a3


title: H9-NPC-UBE3A-352-1

description:
overlapped peak file:
H9-NPC-352_1_VS_H9-NPC-352_2-overlapped-peaks.txt
input file:
H9_NPC_input_1_trim_merge.fastq.gz
input file md5sum: 9ee7cdf91047bd58fda35623515dd94c

source_name: Neural progenitor cells

value: H9 hESC-derived neural progenitors

value: 5 weeks


title: H9-NPC-UBE3A-351-2

description:
overlapped peak file:
H9-NPC-351_1_VS_H9-NPC-351_2-overlapped-peaks.txt
input file:
H9_NPC_input_2_trim_merge.fastq.gz
input file md5sum: 2d2d50d10f593d4df13d8733a00b65d5


title: H9-NPC-UBE3A-352-2

description:
overlapped peak file:
H9-NPC-352_1_VS_H9-NPC-352_2-overlapped-peaks.txt
input file:
H9_NPC_input_2_trim_merge.fastq.gz
input file md5sum: 2d2d50d10f593d4df13d8733a00b65d5


title: MDA-MB231_2

value: MDA-MB231 breast cancer cell line


title: MDA-MB231_1


title: WT_2 [MEW123_2]

description:
100028_GCCAAT_S8
MEW123_2_sort.bam

tag: genotype/variation

value: wild type


title: L25_g3_cervical_s87

description:
rawcounts.txt
normcounts.txt
RNA-seq - 4 animals per age category (i.e. p18/p28).

value: 28 days


title: Brain_Tumor1679_FeIR

type: genomic

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Tumor tissue derived from a NesCre p53 f/+ Pten f/+ mouse irradiated with Fe ions

hyb_protocol: Hybridization was automated using an Agilent Hybridization SureHyb chamber kit and gasket slide kit (Agilent)

scan_protocol: The arrays were scanned at 2 µm resolution using a fluorescence scanner (Tecan)

data_processing:
Feature extraction of raw signals was performed using the ImaGene 9.0 program.
Raw signals were imported in Partek (Partek Inc.), and raw copy number calls from Partek were used as input for cghFlasso R package

source_name: Brain/glioma

label_protocol: Labeling followed the Agilent Oligonucleotide Array-based CGH labeling protocol, specifically the Direct Labeling  protocol using the SureTag Complete DNA Laeling kit, with fluors Cyanine 3-dUTP and Cyanine 5-dUTP.

growth_protocol: Colonies of mixed strain mice (FVB/NJ-C57BL6 mixed background) with brain-specific Nestin-Cre (NesCre) driven LoxP-excision of p53 (exons 2-10) and Pten (exon 5) alleles were bred and maintanied for the purposes of this study.

extract_protocol: Genomic DNA was extracted from 25 mg of flash frozen glioma tissue using the Qiagen Blood and Tissue Kit (Qiagen). DNA was quantified using Nanodrop (IsoGen Life Science) and quailified using Bioanalyzer 2100 (Agilent).

treatment_protocol: Cohorts of 40 4-8 weeks old mixed gender, mixed strain mice (FVB/NJ-C57BL6 mixed background) with brain-specific monoallelic deletions of p53 and Pten were mock-irradiated or irradiated with a single intracranial dose of 0.5 Gy of X-ray or Hydrogen, Carbon, Silicon or Iron ions. Mice were monitored daily up to 15 months post-IR for neurological symptoms (lack of clasp reflex, ataxia, and seizures) and for additional symptoms such as hydrocephalus, lethargy, or weight loss. For glioma resection, mice were deeply anesthetized and killed by decapitation. Fresh brain tissue was sectioned using a brain matrix and the tumor tissue was resected under a microscope. Tumor tissue was flash frozen in liquid nitrogen and kept in -80oC until DNA extraction.

value: brain

tag: disease state

value: glioma

value: FVB/NJ-C57BL6 mixed

value: 7-15 months

tag: treatment

value: particulate radiation 0.5 Gy

value: mock-irradiation

source_name: Brain/normal

value: normal


title: pre-school age_mild/moderate wheeze_285

city: Stevenage

first: Adam

last: Taylor

address: Medicine Research Center

institute: GalxoSmithKline

description: pre-school age mild/moderate wheeze

hyb_protocol: Standard procedure for Affymetrix GeneTitan running Affymetrix GeneChip Command Console 2.0.

data_processing: Scans were imported into ArrayStudio V8.0 and pre-processed using the default RMA pipeline

molecule: polyA RNA

source_name: Blood sample collected at baseline

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation RNA amplification system V2 with OvationWB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: RNA was extracted from blood collected in PAXgene tubes using the PAXgene blood miRNA kit

tag: cohort

tag: disease

value: mild/moderate wheeze

tag: age group

value: pre-school age


title: pre-school age_mild/moderate wheeze_282

description: pre-school age mild/moderate wheeze

scan_protocol: Standard procedure for Affymetrix GeneTitan running Affymetrix GeneChip Command Console 2.0.


title: pre-school age_severe wheeze_290

description: pre-school age severe wheeze

value: severe wheeze


title: school age_severe asthma_286

description: school age severe asthma

value: severe asthma

value: school age


title: school age_mild/moderate asthma_292

description: school age mild/moderate asthma

value: mild/moderate asthma


title: pre-school age_mild/moderate wheeze_291

description: pre-school age mild/moderate wheeze


title: Brain_Tumor2250_SiR

description: Tumor tissue derived from a NesCre p53 f/+ Pten f/+ mouse irradiated with Si ions

tag: strain


title: pre-school age_severe wheeze_279

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_281

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_276

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_295

description: school age mild/moderate asthma


title: H9-NPC-UBE3A-351-1

description:
overlapped peak file:
H9-NPC-351_1_VS_H9-NPC-351_2-overlapped-peaks.txt
input file:
H9_NPC_input_1_trim_merge.fastq.gz
input file md5sum: 9ee7cdf91047bd58fda35623515dd94c

value: H9 hESC-derived neural progenitors

value: 5 weeks

value: wildtype


title: school age_severe asthma_278

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_280

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_287

description: school age severe asthma


title: Brain_Tumor1035_FeIR

tag: tissue


title: school age_severe asthma_275

description: school age severe asthma


title: Brain_Tumor1022_FeIR

tag: age


title: school age_mild/moderate asthma_288

description: school age mild/moderate asthma


title: pre-school age_mild/moderate wheeze_277

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_269

description: pre-school age severe wheeze


title: school age_severe asthma_283

description: school age severe asthma


title: school age_mild/moderate asthma_271

description: school age mild/moderate asthma


title: Brain_Tumor2089_SiR


title: pre-school age_severe wheeze_268

description: pre-school age severe wheeze


title: Brain_Tumor999_FeIR


title: Brain_Tumor2634_HIR

description: Tumor tissue derived from a NesCre p53 f/+ Pten f/+ mouse irradiated with H ions


title: pre-school age_severe wheeze_260

description: pre-school age severe wheeze


title: school age_severe asthma_261

description: school age severe asthma


title: pre-school age_severe wheeze_266

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_258

description: school age mild/moderate asthma


title: OB_TG2576_2M_R1

description:
TG2576_2M_T2_8679_S15
Affymetrix Mouse Clariom S chip with bioconductor (pd.clariom.s.mouse).

value: Tg2576 transgenic

value: Olfactory bulb

tag: gender

value: Female

value: 2 months


title: pre-school age_mild/moderate wheeze_256

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_254

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_252

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_244

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_245

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_248

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_263

description: school age mild/moderate asthma


title: school age_severe asthma_249

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_272

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_243

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_257

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_247

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_232

description: pre-school age severe wheeze


title: pre-school age_mild/moderate wheeze_238

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_240

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_242

description: school age mild/moderate asthma


title: school age_severe asthma_241

description: school age severe asthma


title: school age_severe asthma_237

description: school age severe asthma


title: school age_severe asthma_230

description: school age severe asthma


title: school age_severe asthma_229

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_231

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_262

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_264

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_226

description: school age mild/moderate asthma


title: school age_severe asthma_259

description: school age severe asthma


title: pre-school age_severe wheeze_216

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_215

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_220

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_219

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_202

description: school age mild/moderate asthma


title: school age_severe asthma_201

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_213

description: pre-school age mild/moderate wheeze


title: school age_mild/moderate asthma_208

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_206

description: pre-school age severe wheeze


title: school age_severe asthma_214

description: school age severe asthma


title: school age_severe asthma_225

description: school age severe asthma


title: school age_mild/moderate asthma_223

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_199

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_207

description: pre-school age severe wheeze


title: school age_severe asthma_200

description: school age severe asthma


title: pre-school age_severe wheeze_198

description: pre-school age severe wheeze


title: school age_severe asthma_196

description: school age severe asthma


title: school age_severe asthma_192

description: school age severe asthma


title: school age_mild/moderate asthma_195

description: school age mild/moderate asthma


title: school age_severe asthma_191

description: school age severe asthma


title: school age_severe asthma_203

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_212

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_267

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_182

description: pre-school age severe wheeze


title: school age_severe asthma_217

description: school age severe asthma


title: school age_mild/moderate asthma_185

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_172

description: pre-school age severe wheeze


title: school age_severe asthma_173

description: school age severe asthma


title: pre-school age_severe wheeze_188

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_184

description: pre-school age severe wheeze


title: pre-school age_mild/moderate wheeze_169

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_170

description: school age severe asthma


title: pre-school age_severe wheeze_164

description: pre-school age severe wheeze


title: school age_severe asthma_176

description: school age severe asthma


title: pre-school age_severe wheeze_167

description: pre-school age severe wheeze


title: school age_severe asthma_174

description: school age severe asthma


title: pre-school age_severe wheeze_158

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_181

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_157

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_151

description: school age mild/moderate asthma


title: school age_severe asthma_183

description: school age severe asthma


title: school age_severe asthma_175

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_150

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_179

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_154

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_178

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_146

description: pre-school age mild/moderate wheeze


title: school age_mild/moderate asthma_161

description: school age mild/moderate asthma


title: pre-school age_mild/moderate wheeze_153

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_152

description: school age severe asthma


title: school age_mild/moderate asthma_171

description: school age mild/moderate asthma


title: school age_severe asthma_160

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_144

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_131

description: school age severe asthma


title: school age_severe asthma_135

description: school age severe asthma


title: school age_severe asthma_126

description: school age severe asthma


title: school age_mild/moderate asthma_140

description: school age mild/moderate asthma


title: school age_severe asthma_142

description: school age severe asthma


title: school age_severe asthma_124

description: school age severe asthma


title: school age_severe asthma_138

description: school age severe asthma


title: school age_severe asthma_221

description: school age severe asthma


title: pre-school age_severe wheeze_123

description: pre-school age severe wheeze


title: school age_severe asthma_120

description: school age severe asthma


title: school age_severe asthma_118

description: school age severe asthma


title: pre-school age_severe wheeze_143

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_139

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_137

description: school age mild/moderate asthma


title: sdsR-8

city: Daejeon

first: Younghoon

last: Lee

address: KAIST 291 Daehak-ro, Yuseong-gu

department: Chemistry

country: South Korea

institute: KAIST

data_processing:
The sequence data for the reference genome were retrieved from the NCBI database.
Qualityfiltered reads were aligned to the reference‐genome sequence using Bowtie2.
The relative transcript abundance was measured in RLE.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: For all processed data files, the relative transcript abundance was measured in RLE.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: sdsR promoter mutant

growth_protocol: E. coli cells with mutation on the -10 promoer region of ryeA or sdsR were grown for 3 h and 8 h post-inoculation.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: sdsR -10 mutation; sdsR promoter mutant

tag: time point

value: 8 h post-inoculation


title: WT8_2

value: wild type


title: pre-school age_mild/moderate wheeze_117

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_116

description: school age severe asthma


title: school age_mild/moderate asthma_125

description: school age mild/moderate asthma


title: pre-school age_mild/moderate wheeze_119

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_136

description: pre-school age mild/moderate wheeze


title: sdsR-3

value: 3 h post-inoculation


title: WT3_2


title: pre-school age_mild/moderate wheeze_127

description: pre-school age mild/moderate wheeze

value: mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_115

description: pre-school age mild/moderate wheeze

value: pre-school age


title: ryeA-8

source_name: ryeA promoter mutant

value: ryeA -10 mutation;  ryeA promoter mutant


title: ryeA-3


title: WT8_1


title: pre-school age_severe wheeze_112

description: pre-school age severe wheeze

value: severe wheeze


title: pre-school age_severe wheeze_113

description: pre-school age severe wheeze


title: school age_mild/moderate asthma_110

description: school age mild/moderate asthma

value: school age


title: pre-school age_severe wheeze_111

description: pre-school age severe wheeze


title: school age_severe asthma_114

description: school age severe asthma

value: severe asthma


title: WT3_1


title: Thioridazine NF Stage 47 Rep 3

city: Medford

first: Kelly

last: McLaughlin

state: MA

address: 200 Boston Avenue

department: Biology

institute: Tufts University

description: X. laevis with thioridazine-induced craniofacial abnormalities at NF stage 47, Biological Replicate 3

data_processing:
Reads were trimmed to remove adapter sequences and filtered to remove any low-quality reads with Trimmomatic.
Trimmed reads were mapped to the Xenopus laevis genome v9.1 with HISAT2.
Transcript count tables were generated with HTSeq-count.
Differential gene analysis was carried out using the DESeq2 package in R (Love et al., 2014).
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Excel sheet, differential gene expression list.

organism: Xenopus laevis

source_name: Whole-head tissue

growth_protocol: All experiments utilizing Xenopus laevis were conducted in accordance with the guide for Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee at Tufts University. Embryo culturing was carried out as previously described (Caine and McLaughlin, 2013). Embryos and tadpoles were reared in 0.1x Marc’s Modified Ringer’s solution (MMR, 10mM NaCl, 0.2 mM KCl, 0.1 mM CaCl, 0.2 mM MgCl2, 0.5 MM HEPES, 1 µM EDTA, pH 7.5) at 14-23 ˚C. The 0.1x MMR rearing media was refreshed at least three times a week. Feeding stage tadpoles were fed Sera Micron powdered growth food three times a week. Embryos and tadpoles were staged based on Nieuwkoop and Faber (P.D. Nieuwkoop and J. Faber, 1994).

extract_protocol:
RNA libraries were generated with the Qiagen RNeasy Mini kit and DNAse treated prior to generating cDNA libraries for RNAseq.
RNAseq cDNA libraries were constructed with the Illumina Truseq RNA Library Preparation Kit v2, following the manufacturer’s protocol. We applied Quibit analysis to quantify the RNAseq cDNA libraries, which were then pooled and run on Illumina Hi-Seq 2500 at the Tufts University Core Facility to generate 100-bp single end reads.

treatment_protocol: Pharmacological exposures to induce craniofacial defects were conducted on neurula stage embryos (NF stage 14-26) that had been reared at 14 ˚C prior to exposure. During the exposure windows, experimental and controls embryos were kept at 18 ˚C, after the exposure they were returned to 14 ˚C until they reached feeding-tadpole stages. Pharmacological treatments included: 90 µM thioridazine (Tocris). Plate densities during exposures were kept at 50 embryos per 10 mL of media.

value: Whole-head

tag: group (control/thioridazine)

value: Thioridazine

tag: developmental stage

value: NF stage 47

tag: biological replicate


title: Thioridazine NF Stage 47 Rep 2

description: X. laevis with thioridazine-induced craniofacial abnormalities at NF stage 47, Biological Replicate 2


title: Thioridazine NF Stage 47 Rep 1

description: X. laevis with thioridazine-induced craniofacial abnormalities at NF stage 47, Biological Replicate 1


title: Thioridazine NF Stage 45 Rep 2

description: X. laevis with thioridazine-induced craniofacial abnormalities at NF stage 45, Biological Replicate 2

value: NF stage 45


title: school age_severe asthma_101

description: school age severe asthma


title: pre-school age_severe wheeze_106

description: pre-school age severe wheeze


title: school age_severe asthma_099

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_105

description: pre-school age mild/moderate wheeze


title: Thioridazine NF Stage 45 Rep 1

description: X. laevis with thioridazine-induced craniofacial abnormalities at NF stage 45, Biological Replicate 1


title: school age_severe asthma_108

description: school age severe asthma


title: school age_severe asthma_098

description: school age severe asthma


title: Control NF Stage 47 Rep 3

description: Wildtype X. laevis at NF stage 47, Biological Replicate 3

value: Control


title: Control NF Stage 47 Rep 2

description: Wildtype X. laevis at NF stage 47, Biological Replicate 2


title: pre-school age_mild/moderate wheeze_096

description: pre-school age mild/moderate wheeze


title: school age_mild/moderate asthma_228

description: school age mild/moderate asthma

value: mild/moderate asthma


title: Control NF Stage 47 Rep 1

description: Wildtype X. laevis at NF stage 47, Biological Replicate 1


title: pre-school age_mild/moderate wheeze_107

description: pre-school age mild/moderate wheeze


title: school age_mild/moderate asthma_093

description: school age mild/moderate asthma


title: school age_severe asthma_095

description: school age severe asthma


title: Thioridazine NF Stage 45 Rep 3

description: X. laevis with thioridazine-induced craniofacial abnormalities at NF stage 45, Biological Replicate 3


title: pre-school age_severe wheeze_091

description: pre-school age severe wheeze


title: Control NF Stage 45 Rep 3

description: Wildtype X. laevis at NF stage 45, Biological Replicate 3


title: school age_severe asthma_087

description: school age severe asthma


title: school age_severe asthma_092

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_102

description: pre-school age mild/moderate wheeze


title: pre-school age_severe wheeze_090

description: pre-school age severe wheeze


title: Control NF Stage 45 Rep 2

description: Wildtype X. laevis at NF stage 45, Biological Replicate 2


title: pre-school age_mild/moderate wheeze_089

description: pre-school age mild/moderate wheeze


title: pre-school age_mild/moderate wheeze_088

description: pre-school age mild/moderate wheeze


title: ASO control of UPF1

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

institute: Hanyang University

data_processing:
RNA-seq data were trimmed by 9 nt for the first fragment of paired-end reads and 6nt for the second of paired-end reads to remove adaptor sequence using seqtk version 1.0. All RNA-seq reads were trimmed with the criterion of the minimum quality 20 and, then, reads with less than 20 nt in length were removed using Sickle version 1.2 (parameters: -q 20 -l 20)
Reads were mapped to the hg19 genomes using Tophat version 2.0.6 (Trapnell et al., 2009), allowing at most five genomic loci mapping, two nucleotide mismatches, and novel introns within one to 99 percentile length of known introns, but not allowing any mismatch at splice sites (parameters: --solexa1.3-quals --splice-mismatches 0 --min-intron-length 61 --max-intron-length 265006 --max-multi hits 5--read-mismatches 2)
Expression level, fragments per kilobase of transcript per million mapped reads (FPKM), were calculated by Cufflinks version 2.1.1 (Trapnell et al., 2010)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa cell line

growth_protocol: HeLa cells were maintained in DMEM media supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Cells were seeded one day before transfection with ASO/siRNA using Lipofectamine3000 (Invitrogen)

tag: sample type

value: Cell line

tag: cell line

value: HeLa

tag: cell origin

value: HeLa cervical cancer cell

value: transfected with random sequence ASO


title: ASO-SMG7

value: transfected with ASOs targeting SMG7


title: ASO-UPF1

value: transfected with ASOs targeting UPF1


title: pre-school age_mild/moderate wheeze_085

description: pre-school age mild/moderate wheeze

value: mild/moderate wheeze

value: pre-school age


title: Control NF Stage 45 Rep 1

description: Wildtype X. laevis at NF stage 45, Biological Replicate 1


title: school age_mild/moderate asthma_103

description: school age mild/moderate asthma


title: school age_mild/moderate asthma_084

description: school age mild/moderate asthma


title: school age_severe asthma_097

description: school age severe asthma


title: ASO control of SMG7


title: school age_severe asthma_086

description: school age severe asthma


title: pre-school age_severe wheeze_082

description: pre-school age severe wheeze

value: severe wheeze


title: pre-school age_severe wheeze_083

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_081

description: pre-school age severe wheeze


title: RHKO_IFNB_RepC

city: St. Louis

first: Sumit

middle: Kumar

last: Matta

state: MO

address: 660 S. Euclid

department: Molecular Microbiology

institute: Washington University in St. Louis

description: run_2057_s_1_withindex_sequence.txt_TGTTTGT

data_processing:
Reads were sequenced on Illumina HiSeq 2500 sequencer and base calling was performed with Illumina RTA ver 1.18.64. Demultiplexing of the lane level fastq files into individual fastq files for each sample was performed with Illumina bcl2fastq2.
RNA-Seq-Analysis built-in tool of  CLCGenomics Workbench ver 9.5.3 was used to map the reads to Homo sapiens hg19 reference genome resulting in gene expression (GE) and transcript expression (TE) tracks for each sample. Expression levels were calculated as total counts of genes and transcripts using these tracks.
Differentail expression for RNA-Seq built-in tool of CLCGenomics Workbench ver 9.5.3 was used to calculate fold difference in total counts between different samples (using gene expression tracks or (GE).clc files).
Differentially expressed genes or transcripts between samples were used for downstream Ingenuity Pathway Analysis (IPA).
Gene expression and transcript expression tracks ((GE).clc and (TE).clc) were generated using RNA-Seq-Analysis tool in CLCGenomics Workbench ver 9.5.3
Genome_build: hg19
Supplementary_files_format_and_content: Expression_Values.csv is the expression table for all 57,773 annotated human genes across all samples and replicates.

growth_protocol:
HFFs were maintained in Dulbecco's modified eagle medium (DMEM) with 10% v/v fetal bovine serum (FBS) at 37 ⁰C and 5% CO₂.
Parasites were grown as tachyzoites in HFFs (obtained from the laboratory of Dr. John Boothroyd, Stanford University) in DMEM with 10% v/v FBS at 37 ⁰C and 5% CO₂. Briefly, the tachyzoites were passed after every 48 hours of infection cycle in HFFs at 1:125. Parasites for all experiments were harvested shortly after natural egress and purified by passage through 20 g needle and separated from host cell debris using 3.0 micron polycarbonate nucleopore filters (Whatman).

extract_protocol:
Samples were lysed, and RNA was extracted using QIAGEN RNeasy mini kit per manufacturer’s instructions. Total RNA was then submitted to Genome Technology Access Center (GTAC), Washington University in St. Louis, School of Medicine for Next generation mRNA sequencing.
Briefly, mRNA was extracted from the total RNA using Oligo-dT beads binding poly-A-tail. mRNA was then fragmented, and reverse transcribed to cDNA using random primers followed by addition of sample specific adaptors. 1X50 bp single end reads were sequenced using Illumina HiSeq 2500 sequencer.

treatment_protocol: HFFs were cultured without infection or infected with parasites for 12 h follow with treatment with human IFN-β (100 Units/ml), or left untreated for additional 6 h.

value: HFF

tag: cell type

value: Fibroblasts (Skin)

tag: infection

value: TgIST knockout (RH KO) T. gondii parasites for 12 hrs

value: IFN-β

tag: replicate

value: C


title: RHKO_UT_RepC

description: run_2057_s_1_withindex_sequence.txt_GGTCCTC

tag: treatment

value: Untreated


title: pre-school age_severe wheeze_077

description: pre-school age severe wheeze

tag: cohort

tag: disease

tag: age group


title: pre-school age_severe wheeze_078

description: pre-school age severe wheeze


title: RH_IFNB_RepC

description: run_2057_s_1_withindex_sequence.txt_GCTTAGA

value: wild type (RH) T. gondii parasites for 12 hrs


title: pre-school age_mild/moderate wheeze_073

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_074

description: school age severe asthma

value: severe asthma

value: school age


title: RH_UT_RepC

description: run_2057_s_1_withindex_sequence.txt_GTCGATA


title: school age_mild/moderate asthma_072

description: school age mild/moderate asthma

value: mild/moderate asthma


title: UI_UT_RepC

description: run_2057_s_1_withindex_sequence.txt_GGGTCAA

value: Uninfected


title: UI_IFNB_RepC

description: run_2057_s_1_withindex_sequence.txt_AGATACT


title: CSD21

city: Shanghai

first: Xinzhi

last: Zhao

address: No. 138, Yixueyuan Rd.

department: Fudan University

country: China

institute: Institutes of Biomedical Sciences

description: control

hyb_protocol: Bisulfate conversion was performed using an EZ-96 DNA Methylation-GoldTM Kit, DNA templates were then used for PCR amplification and the products were dissolved and dispensed on the Illumina Infinium HumanMethylation450 (450k) BeadChip and assayed on the Illumina HiScanSQ system

scan_protocol: In Methylation NXT mode

data_processing: IDAT files were analyzed with R package minfi for Beta value using Illumina's formula. Methylated, unmethylated signal and detection P value were also computed with minfi.

label: Cy5 and Cy3

source_name: placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted with a QIAGEN DNAeasy blood & tissue kit (Hilden, Germany) from the placental tissue.

tag: gestational age (weeks+days)


title: PSD60

description: case


title: PSD59

description: case


title: school age_mild/moderate asthma_070

description: school age mild/moderate asthma


title: PSD61

description: case


title: PSD55

description: case


title: PSD63

description: case


title: CSD17

description: control


title: CSD20

description: control


title: pre-school age_mild/moderate wheeze_069

description: pre-school age mild/moderate wheeze


title: PSD57

description: case


title: RHKO_IFNB_RepB

description: run_2056_s_2_withindex_sequence.txt_CAATATC

value: B


title: PSD25

description: case


title: PSD64

description: case


title: school age_mild/moderate asthma_067

description: school age mild/moderate asthma


title: PSD56

description: case


title: pre-school age_severe wheeze_068

description: pre-school age severe wheeze


title: RHKO_UT_RepB

description: run_2056_s_2_withindex_sequence.txt_ACCCACT


title: PSD24

description: case


title: PSD26

description: case


title: RH_IFNB_RepB

description: run_2056_s_2_withindex_sequence.txt_TCAACTG


title: PSD21

description: case


title: PSD28

description: case


title: PSH4

description: case


title: CSD16

description: control


title: RH_UT_RepB

description: run_2056_s_2_withindex_sequence.txt_TTTAACT


title: pre-school age_severe wheeze_066

description: pre-school age severe wheeze


title: UI_IFNB_RepB

description: run_2056_s_2_withindex_sequence.txt_TGAGGTT


title: PSD58

description: case


title: PSD2

description: case


title: PSD3

description: case


title: CSD53

description: control


title: RHKO_IFNB_RepA

description: run_2056_s_1_withindex_sequence.txt_GCAGGGG

value: A


title: PSD19

description: case


title: UI_UT_RepB

description: run_2056_s_2_withindex_sequence.txt_ACGTCTG


title: RHKO_UT_RepA

description: run_2056_s_1_withindex_sequence.txt_CAAGCCG


title: school age_severe asthma_065

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_062

description: pre-school age mild/moderate wheeze


title: RH_IFNB_RepA

description: run_2056_s_1_withindex_sequence.txt_GTCTGAT


title: CSH5

description: control

value: :NA


title: school age_mild/moderate asthma_063

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_061

description: pre-school age severe wheeze


title: UI_IFNB_RepA

description: run_2056_s_1_withindex_sequence.txt_CGTCGCT


title: RH_UT_RepA

description: run_2056_s_1_withindex_sequence.txt_TTTTGTC


title: pre-school age_mild/moderate wheeze_059

description: pre-school age mild/moderate wheeze

value: mild/moderate wheeze


title: pre-school age_severe wheeze_060

description: pre-school age severe wheeze

value: pre-school age


title: CSD52

description: control


title: UI_UT_RepA

description: run_2056_s_1_withindex_sequence.txt_GAGGCGT


title: CSD49

description: control


title: PSD18

description: case


title: pre-school age_severe wheeze_054

description: pre-school age severe wheeze

value: severe wheeze


title: school age_severe asthma_058

description: school age severe asthma


title: school age_severe asthma_052

description: school age severe asthma


title: CSD43

description: control


title: CSD51

description: control


title: CSD50

description: control


title: pre-school age_severe wheeze_051

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_064

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_050

description: pre-school age severe wheeze


title: school age_severe asthma_053

description: school age severe asthma


title: CSD42

description: control


title: CSD46

description: control


title: PSD14

description: case


title: dermis_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

source_name: dermis of the retroauricular skin

extract_protocol:
Total RNAs were extracted from the cells with miRNeasy FFPE Kit (QIAGEN), according to the manufacturer’s protocol.
NGS library preparation was performed using the SMARTer® Stranded Total RNA Sample Prep Kit-Pico Input Mammalian (Clontech, TaKaRa) according to the manufacturer’s instructions.

value: dermis cut by laser micro dissection from cholesteatoma


title: CSD47

description: control


title: school age_severe asthma_047

description: school age severe asthma


title: CSD22

description: control


title: CSD2

description: control


title: PSD62

description: case


title: permatrix_rep3

source_name: prematrix of cholesteatoma

value: permatrix of cholesteatoma cut by laser micro dissection from cholesteatoma


title: dermis_rep2


title: CSD48

description: control


title: CSD45

description: control


title: school age_severe asthma_041

description: school age severe asthma


title: school age_severe asthma_036

description: school age severe asthma


title: pre-school age_severe wheeze_033

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_044

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_043

description: pre-school age severe wheeze


title: school age_severe asthma_032

description: school age severe asthma


title: pre-school age_mild/moderate wheeze_038

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_049

description: school age severe asthma


title: permatrix_rep2


title: school age_severe asthma_035

description: school age severe asthma


title: school age_severe asthma_026

description: school age severe asthma


title: school age_mild/moderate asthma_030

description: school age mild/moderate asthma


title: CSD25

description: control


title: school age_mild/moderate asthma_039

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_031

description: pre-school age severe wheeze


title: dermis_rep1


title: permatrix_rep1


title: CSD41

description: control


title: PSD20

description: case


title: pre-school age_mild/moderate wheeze_025

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_021

description: school age severe asthma


title: pre-school age_severe wheeze_009

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_018

description: pre-school age severe wheeze


title: pre-school age_severe wheeze_022

description: pre-school age severe wheeze


title: school age_severe asthma_055

description: school age severe asthma


title: pre-school age_severe wheeze_020

description: pre-school age severe wheeze


title: school age_severe asthma_023

description: school age severe asthma


title: school age_severe asthma_016

description: school age severe asthma


title: school age_severe asthma_010

description: school age severe asthma


title: school age_severe asthma_013

description: school age severe asthma


title: pre-school age_severe wheeze_011

description: pre-school age severe wheeze


title: DC from mice fed HFD and  treated with IMQ, biological rep3

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

institute: INSERM

description: Gene expression data from GM-DC treated with mock in the presence of PA during 24 hr

hyb_protocol: Following fragmentation, 5.5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Microarray data were background-corrected and normalized using the robust multi-array average (RMA) algorithm by using affy R package

source_name: DC sorted from  inguinal lymph nodes

label_protocol: Biotinylated ssDNA were prepared using  5 ng RNA from sorted cDC, amplified and labeled with Ovation Pico WTA Systems V2.

growth_protocol: Animals were housed within the specific pathogen-free facility at the Institut Pasteur de Lille with ad libitum access to water and food. CD3−CD19−CD64−Ly6G−CD11c+MHCII+ DCs were sorted from mouse iLN using BD Influx Cell Sorter (BD Biosciences).

extract_protocol: Total RNA was isolated from sorted cDC with Arcturus Picopure RNA isolation Kit

treatment_protocol: Mice were treated with a daily topical dose (62.5 mg) of IMQ cream (Aldara 5%) on the shaved abdominal skin for 5 days and sacrificed 24 hr later.

tag: gender

value: male

tag: genotype


title: school age_severe asthma_008

description: school age severe asthma


title: pre-school age_severe wheeze_024

description: pre-school age severe wheeze


title: school age_severe asthma_014

description: school age severe asthma


title: DC from mice fed HFD and  treated with IMQ, biological rep4


title: school age_severe asthma_045

description: school age severe asthma


title: school age_mild/moderate asthma_015

description: school age mild/moderate asthma


title: school age_mild/moderate asthma_019

description: school age mild/moderate asthma


title: pre-school age_mild/moderate wheeze_002

description: pre-school age mild/moderate wheeze


title: school age_severe asthma_001

description: school age severe asthma


title: school age_mild/moderate asthma_005

description: school age mild/moderate asthma


title: school age_mild/moderate asthma_048

description: school age mild/moderate asthma


title: pre-school age_severe wheeze_000

description: pre-school age severe wheeze


title: DC from mice fed HFD and  treated with IMQ, biological rep1

description: Gene expression data from DC isolated from mice treated with IMQ and fed CD


title: DC from mice fed CD and  treated with IMQ, biological rep4


title: Uninvolved epidermis from AD skin, sample 5, set 2

description: Gene expression in human epidermis

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was hybridized with Human Gene Expression Microarray 8x60K chip (Agilent Technologies) according to manufacturer's protocol

scan_protocol: Slides were scanned with the Agilent G2505B scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1). Data were background-corrected with 'normexp' option and quantile normalized using limma R package

source_name: Human uninvolved epidermis from AD skin, sample 5 (laser capture microdissection)

label_protocol: 10 ng RNA were amplified with ExpressArt Kit and labeled (Cy3) with One-color microarray-based Gene Expression Analysis Low Input Quick Amp WT Labeling (Agilent Technologies) according to manufacturer's protocol

extract_protocol: RNA was isolated with Arcturus Picopure RNA isolation Kit according to manufacturer's protocol

treatment_protocol: Epidermis and dermis were obtained from human skin biopsies by laser capture microdissection using Arcturus XT (MDS Analytical Technologies) system

tag: tissue

value: epidermis

value: atopic dermatitis


title: Uninvolved epidermis from AD skin, sample 3, set 1

description: Gene expression in human epidermis

source_name: Human uninvolved epidermis from AD skin, sample 3 (laser capture microdissection)


title: Involved epidermis from AD skin, sample 7, set 2

description: Gene expression in human epidermis

source_name: Human involved epidermis from AD skin, sample 7 (laser capture microdissection)


title: DC from mice fed CD and  treated with IMQ, biological rep2


title: GM-DC treated with IMQ in the presence of PA, biological rep2

description: Gene expression data from GM-DC treated with IMQ in the presence of PA during 24 hr

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: GM-DC were differentiated from bone marrow in DMEM containing 20 ng/ml mouse recombinant GM-CSF,  10% FCS, 2 mM L-glutamine, 4.5 g/L glucose, and 10 g/ml gentamycin during 10 days.

extract_protocol: RNeasy Micro Kit was used to extract total RNA according to the manufacturer's instructions

treatment_protocol: GM-DC were treated with 3 ug/ml IMQ with or without PA or OA conjugated with BSA (0.5 mM, molar ratio PA:BSA 6:1) during 24 hr in DMEM containing 10% FCS, 2 mM L-glutamine, 4.5 g/L glucose, and 10 ug/ml gentamycin


title: Involved epidermis from AD skin, sample 5, set 2

description: Gene expression in human epidermis

source_name: Human involved epidermis from AD skin, sample 5 (laser capture microdissection)


title: Uninvolved epidermis from AD skin, sample 2, set 1

description: Gene expression in human epidermis

source_name: Human uninvolved epidermis from AD skin, sample 2 (laser capture microdissection)


title: GM-DC treated with IMQ in the presence of PA, biological rep1

source_name: GM-DC treated with IMQ in the presence of PA during 24 hr


title: Involved epidermis from AD skin, sample 4, set 1

description: Gene expression in human epidermis

source_name: Human involved epidermis from AD skin, sample 4 (laser capture microdissection)


title: Involved epidermis from AD skin, sample 2, set 1

description: Gene expression in human epidermis

source_name: Human involved epidermis from AD skin, sample 2 (laser capture microdissection)


title: GM-DC treated with IMQ in the presence of PA, biological rep3


title: GM-DC treated with IMQ, biological rep2

description: Gene expression data from GM-DC treated with IMQ during 24 hr

source_name: GM-DC treated with IMQ during 24 hr


title: GM-DC treated with mock in the presence of PA, biological rep1

source_name: GM-DC treated with mock in the presence of PA during 24 hr


title: GM-DC treated with IMQ, biological rep3


title: DC from mice fed CD and  treated with IMQ, biological rep1


title: GM-DC treated with IMQ, biological rep1


title: GM-DC treated with IMQ in the presence of PA, biological rep4


title: GM-DC treated with mock in the presence of PA, biological rep2


title: GM-DC treated with mock in the presence of PA, biological rep4


title: Involved epidermis from AD skin, sample 3, set 1

description: Gene expression in human epidermis

source_name: Human involved epidermis from AD skin, sample 3 (laser capture microdissection)


title: GM-DC treated with IMQ, biological rep4


title: Uninvolved epidermis from AD skin, sample 4, set 1

description: Gene expression in human epidermis

source_name: Human uninvolved epidermis from AD skin, sample 4 (laser capture microdissection)


title: DC from mice fed CD and  treated with IMQ, biological rep3


title: GM-DC treated with mock, biological rep4

description: Gene expression data from GM-DC treated with mock during 24 hr

source_name: GM-DC treated with mock during 24 hr


title: GM-DC treated with mock in the presence of PA, biological rep3


title: LN_2: Lung tissue rep2

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

institute: Seoul National University

data_processing:
TopHat alignment coupled with Cufflinks assembly was used to generate the final transcriptome assembly and examine gene expression levels
The number of reads aligned to each gene was normalized to fragments per kilobase of exon per million (FPKM)
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text files include FPKM for each sample

source_name: Lung

extract_protocol:
Total RNA was extracted from adipose or lung tissue of two randomly selected mice using the RNeasy Mini kit (Qiagen) with DNase I (Qiagen) treatment
RNA sequencing libraries were generated using the TruSeq RNA sample Preparation kit (Illumina)

tag: strain

value: Lung

tag: age

value: 4 weeks old

value: wild type

tag: Sex

value: female


title: F_2: Adipose tissue rep2

source_name: Adipose

value: Adipose


title: F_1: Adipose tissue rep1


title: Spc-Cre;LSL-KrasG12D/+_Lung tissue

city: Guangzhou

first: junchao

last: Cai

address: zhongshan er road

institute: Sun-yat sen university

description: lung tissue from the Spc-Cre;LSL-KrasG12D/+ mice at 9 months

hyb_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai biochip corporation.

growth_protocol: The lung tissues from indicated mice were directly resected and washed with PBS, without primary culture.

extract_protocol: Total RNA was isolated using Trizol RNA isolation kit (Thermo Fisher, Waltham, MA) following supplier’s protocol.

treatment_protocol: LSL-KrasG12D/+ mice purchased from the Jackson Labrotory were normally bred.  At 9 months,  LSL-KrasG12D/+ mice were anesthetized and resected for lung tissue, followed by PBS wash for 3 times.  KrasLSL-G12D/+ and Spc-Cre mice were intercrossed to generate Spc-Cre;KrasLSL-G12D/+ mice, which were normally bred.   At 9 months,  Spc-Cre;KrasLSL-G12D/+ mice were anesthetized and resected for lung tissue, followed by PBS wash for 3 times.

value: lung tissue with cancerous nodules

tag: genotype/variation

value: Spc-Cre;LSL-KrasG12D/+ mice


title: LSL-KrasG12D/+_Lung tissue

description: lung tissue from the LSL-KrasG12D/+ mice at 9 months

scan_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

value: normal lung tissue without cancerous lesion

value: LSL-KrasG12D/+ mice


title: school age_severe asthma_034

description: school age severe asthma

source_name: Blood sample collected at baseline

value: severe asthma

value: school age


title: LN_1: Lung tissue rep1