title: Raw 264.7 monocytes treated with IL-33_rep3

city: Shanghai

first: Yunlong

last: Yang

address: Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Dong'an road 130

institute: Fudan University

description:
Gene expression data of RAW cells treated with IL-33
BH13040_2_YY_P_3_NS

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization,Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix,Santa Clara, CA, US) .

data_processing:
Data command Console Software 3.1 (Affymetrix, Santa Clara, CA,US) with default settings. Raw data were normalized by Gene Spring Software 11.0 Agilent technologies, Santa Clara, CA, US).
The dataset was normalized using the Robust Multi Array Average (RMA) method.

source_name: Raw 264.7 monocytes treated with IL-33

label_protocol: Total RNA were amplified, labeled and purified by using Ambion WT Expression Kit(Cat#411973， Ambion, US) and GeneChip WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Cells were grown in DMEM mudium with 10% FBS.

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

treatment_protocol: After starvation, Cells were treated with 2% FBS DMEM with or without 50 ng/ml IL-33

value: Raw 264.7 monocytes

tag: agent


title: SAMPLE 260_Effector Th1 (ACC1 KO-1)

status: Public on Nov 30 2018

type: RNA

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

country: Japan

institute: Chiba University

description: Effector Th1

data_processing: raw data was collected from the Fluidigm Real-Time PCR Analysis software single cell data could be furthor analized in R software with the Package SINGuLAR™ 3.0

label: Eva Green

molecule: total RNA

organism: Mus musculus

source_name: cultured primary CD4 T cells from spleen

label_protocol: qRT-PCR was performed on the 96.96 IFC using the pre-amplified product on the Fluidigm Biomark platform according to the manufacture's instructions

extract_protocol: single cells were lysed and preamplified with the kit (CellsDirect™ One-Step qRT-PCR Kit, Thermo, 11753100)

treatment_protocol: Splenic CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro.

tag: strain

value: BALB/c

tag: tissue

value: spleen

tag: cell type

value: CD4 T cells


title: SAMPLE 259_Effector Th1 (TOFA-92)

description: Effector Th1


title: SAMPLE 257_Effector Th1 (TOFA-90)

description: Effector Th1


title: SAMPLE 258_Effector Th1 (TOFA-91)

description: Effector Th1


title: SAMPLE 261_Effector Th1 (ACC1 KO-2)

description: Effector Th1


title: SAMPLE 262_Effector Th1 (ACC1 KO-3)

description: Effector Th1


title: SAMPLE 256_Effector Th1 (TOFA-89)

description: Effector Th1


title: Raw 264.7 monocytes treated with IL-33_rep2

country: China

description:
Gene expression data of RAW cells treated with IL-33
BH13040_2_YY_P_2_NS

label: biotin

tag: cell line


title: Raw 264.7 monocytes treated with PBS_rep3

description:
Gene expression data of RAW cells treated with PBS
BH13040_2_YY_IL_3_NS

source_name: Raw 264.7 monocytes treated with PBS

value: control


title: Raw 264.7 monocytes treated with IL-33_rep1

description:
Gene expression data of RAW cells treated with IL-33
BH13040_2_YY_P_1_NS


title: SAMPLE 254_Effector Th1 (TOFA-87)

description: Effector Th1


title: SAMPLE 253_Effector Th1 (TOFA-86)

description: Effector Th1


title: SAMPLE 252_Effector Th1 (TOFA-85)

description: Effector Th1


title: SAMPLE 251_Effector Th1 (TOFA-84)

description: Effector Th1


title: SAMPLE 250_Effector Th1 (TOFA-83)

description: Effector Th1


title: SAMPLE 249_Effector Th1 (TOFA-82)

description: Effector Th1


title: SAMPLE 248_Effector Th1 (TOFA-81)

description: Effector Th1


title: SAMPLE 247_Effector Th1 (TOFA-80)

description: Effector Th1


title: Raw 264.7 monocytes treated with PBS_rep2

description:
Gene expression data of RAW cells treated with PBS
BH13040_2_YY_IL_2_NS


title: SAMPLE 245_Effector Th1 (TOFA-78)

description: Effector Th1


title: Raw 264.7 monocytes treated with PBS_rep1

description:
Gene expression data of RAW cells treated with PBS
BH13040_2_YY_IL_1_NS


title: NTN_CD4xNEMO_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: NTN_CD4xNEMO_CD4 lymphocyte

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice expressing Cre recombinase under the CD4 promoter were crossed with floxed IKK2 or NEMO mice. The mice were generously provided by Dr. M. Karin (San Diego) for IKK2fl/fl mice, Dr. C. Wilson (Seattle) for CD4cre mice and Dr. Manolis Pasparakis (Cologne) for NEMOfl/fl mice. Efficiency and specificity of the IKK2 or NEMO deletion were assessed by PCR from FACS-sorted CD4+ and CD4− splenocytes (BD ARIAIII Cytometer, Becton Dickinson, Germany). All animals were housed at the animal facility of the University Medical Center Hamburg-Eppendorf.

extract_protocol: CD4+ splenocyte was isolated with CD4+ T cell isolation kit (Miltenyi Biotec) in accordance with the instruction of the manufacturer. CD4+ T cell was purified with FACS ARIA. RNA of CD4+ cell (≤ 5×106 cells) was extracted by NucleoSpin® RNA kit (MACHEREY-NAGEL, Germany), or (≤ 5×105 cells) by RNeasy micro kit 50 (QIAGEN, Germany). The RNA quality of the collected CD4+ T cell was assessed by Agilent RNA 6000 Nano Kit (Agilent Technologies, Germany) as the instruction of the manufacturer. The total amount of RNA should be ≥ 200ng and the RNA integrity number (RIN) should be ≥ 8.0.

treatment_protocol: NTN was induced in 8- to 10-week-old male mice by i.p. injection of 2.5 mg of nephrotoxic sheep serum per gram body weight. Organs were harvested on day 10 after injection.

tag: strain  background

value: NEMOfl/f

tag: age

value: 8- to 10-week-old

tag: gender

value: male

tag: infammation

value: nephrotoxic serum nephritis (NTN)

value: CD4 Lymphocyte


title: NTN_CD4xNEMO_1


title: SAMPLE 246_Effector Th1 (TOFA-79)

description: Effector Th1


title: CD4xNEMO_1

source_name: CD4xNEMO_CD4 lymphocyte

value: no inflammation


title: NTN_CD4xIKK2_3

source_name: NTN_CD4xIKK2_CD4 lymphocyte


title: CD4xNEMO_2


title: SAMPLE 244_Effector Th1 (TOFA-77)

description: Effector Th1


title: SAMPLE 242_Effector Th1 (TOFA-75)

description: Effector Th1


title: SAMPLE 241_Effector Th1 (TOFA-74)

description: Effector Th1


title: SAMPLE 243_Effector Th1 (TOFA-76)

description: Effector Th1


title: SAMPLE 240_Effector Th1 (TOFA-73)

description: Effector Th1


title: SAMPLE 237_Effector Th1 (TOFA-70)

description: Effector Th1


title: SAMPLE 236_Effector Th1 (TOFA-69)

description: Effector Th1


title: SAMPLE 239_Effector Th1 (TOFA-72)

description: Effector Th1


title: SAMPLE 235_Effector Th1 (TOFA-68)

description: Effector Th1


title: SAMPLE 234_Effector Th1 (TOFA-67)

description: Effector Th1


title: SAMPLE 233_Effector Th1 (TOFA-66)

description: Effector Th1


title: benign nodule 581B

type: SRA

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

country: USA

institute: Beckman Research Institute

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq2-2.18
Reads were trimmed by trim_galore (v0.3.1) with the --rrbs parameter
Reads were aligned to the hg19 genome assembly using bismark (v0.8.3) with default parameters
Methylation information was extracted using bismark_methylation_extractor with the setting -s --comprehensive --report --bedGraph --counts for single-end reads, and with the setting -p --no_overlap --comprehensive --report --bedGraph --counts for pair-end reads
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using bismark (v0.8.3)

molecule: genomic DNA

organism: Homo sapiens

source_name: Thyroid

growth_protocol: Retrospective surgical human specimens from thyroidectomy

extract_protocol:
DNA from fresh frozen samples was isolated by using the phenol/chloroform extraction approach. For DNA isolation from FFPE samples, QIAamp DNA FFPE Tissue Kit was used (Qiagen Inc., Valencia, CA)
The RRBS procedure was previously described (Hahn et. al., 2015; PMID: 25421665). DNA sequencing was performed on an HiSeq Illumina instrument and aligned to the human genome at the City of Hope Integrative Genomics Core.

value: Thyroid

tag: tissue type

value: benign nodule

tag: cohort

value: testing cohort


title: benign nodule 583B


title: SAMPLE 232_Effector Th1 (TOFA-65)

description: Effector Th1


title: SAMPLE 231_Effector Th1 (TOFA-64)

description: Effector Th1


title: benign nodule 580B


title: SAMPLE 238_Effector Th1 (TOFA-71)

description: Effector Th1


title: benign nodule 579B


title: SAMPLE 230_Effector Th1 (TOFA-63)

description: Effector Th1


title: SAMPLE 229_Effector Th1 (TOFA-62)

description: Effector Th1


title: NTN_CD4xIKK2_1


title: NTN_CD4xIKK2_2


title: SAMPLE 228_Effector Th1 (TOFA-61)

description: Effector Th1


title: CD4xIKK2_3

source_name: CD4xIKK2_CD4 lymphocyte


title: CD4xIKK2_2


title: NTN_CD4cre_3

source_name: NTN_CD4cre_CD4 lymphocyte


title: NTN_CD4cre_1


title: CD4xIKK2_1


title: CD4cre_3

source_name: CD4cre_CD4 lymphocyte


title: benign nodule 576B


title: benign nodule 578B


title: SAMPLE 225_Effector Th1 (TOFA-58)

description: Effector Th1


title: SAMPLE 226_Effector Th1 (TOFA-59)

description: Effector Th1


title: CD4cre_2


title: SAMPLE 224_Effector Th1 (TOFA-57)

description: Effector Th1


title: benign nodule 575B


title: SAMPLE 222_Effector Th1 (TOFA-55)

description: Effector Th1


title: SAMPLE 220_Effector Th1 (TOFA-53)

description: Effector Th1


title: SAMPLE 221_Effector Th1 (TOFA-54)

description: Effector Th1


title: SAMPLE 227_Effector Th1 (TOFA-60)

description: Effector Th1


title: NTN_CD4cre_2


title: benign nodule 574B


title: SAMPLE 223_Effector Th1 (TOFA-56)

description: Effector Th1


title: SAMPLE 219_Effector Th1 (TOFA-52)

description: Effector Th1


title: benign nodule 572B


title: benign nodule 571B


title: CD4cre_1


title: SAMPLE 218_Effector Th1 (TOFA-51)

description: Effector Th1


title: SAMPLE 217_Effector Th1 (TOFA-50)

description: Effector Th1


title: SAMPLE 215_Effector Th1 (TOFA-48)

description: Effector Th1


title: SAMPLE 216_Effector Th1 (TOFA-49)

description: Effector Th1


title: benign nodule 570B


title: SAMPLE 214_Effector Th1 (TOFA-47)

description: Effector Th1


title: SAMPLE 212_Effector Th1 (TOFA-45)

description: Effector Th1


title: SAMPLE 255_Effector Th1 (TOFA-88)

description: Effector Th1


title: SAMPLE 213_Effector Th1 (TOFA-46)

description: Effector Th1


title: polII_H2O_DRB5m_1

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
Chromatin IP of RNA pol II
polII_H2O_DRB5m.bw

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7. Custom software was used to remove duplicates from NET-seq libraries: https://github.com/sheridar/TFIISdn_paper.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: BigWig

source_name: HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 5 min

tag: growth conditions

value: DMEM 10% FCS, +hygromycin, +blasticidin, +DRB

tag: antibody

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

tag: molecule

value: Genomic DNA


title: SAMPLE 211_Effector Th1 (TOFA-44)

description: Effector Th1


title: polII_H2O_DRB20m_1

description:
Chromatin IP of RNA pol II
polII_H2O_DRB20m.bw

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 20 min


title: malignant nodule 179T

description: PE100; SE50

value: malignant nodule


title: benign nodule 582B


title: malignant nodule 181T


title: polII_H2O_DRB0m_1

description:
Chromatin IP of RNA pol II
polII_H2O_DRB0m.bw

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs


title: malignant nodule 175T


title: polII_H2O_DRB10m_1

description:
Chromatin IP of RNA pol II
polII_H2O_DRB10m.bw

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min


title: SAMPLE 206_Effector Th1 (TOFA-39)

description: Effector Th1

value: BALB/c


title: SAMPLE 210_Effector Th1 (TOFA-43)

description: Effector Th1

value: spleen


title: malignant nodule 178T


title: SAMPLE 205_Effector Th1 (TOFA-38)

description: Effector Th1

value: CD4 T cells


title: SAMPLE 207_Effector Th1 (TOFA-40)

description: Effector Th1


title: SAMPLE 208_Effector Th1 (TOFA-41)

description: Effector Th1


title: SAMPLE 209_Effector Th1 (TOFA-42)

description: Effector Th1


title: polII_Dox_DRB5m_1

description:
Chromatin IP of RNA pol II
polII_Dox_DRB5m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 5 min

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB


title: malignant nodule 182T


title: polII_Dox_DRB20m_1

description:
Chromatin IP of RNA pol II
polII_Dox_DRB20m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 20 min


title: SAMPLE 203_Effector Th1 (TOFA-36)

description: Effector Th1


title: malignant nodule 172T


title: SAMPLE 204_Effector Th1 (TOFA-37)

description: Effector Th1


title: SAMPLE 201_Effector Th1 (TOFA-34)

description: Effector Th1


title: malignant nodule 170T


title: SAMPLE 202_Effector Th1 (TOFA-35)

description: Effector Th1


title: SAMPLE 200_Effector Th1 (TOFA-33)

description: Effector Th1


title: polII_Dox_DRB10m_1

description:
Chromatin IP of RNA pol II
polII_Dox_DRB10m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min


title: SAMPLE 199_Effector Th1 (TOFA-32)

description: Effector Th1


title: SAMPLE 198_Effector Th1 (TOFA-31)

description: Effector Th1


title: malignant nodule 168T


title: SAMPLE 197_Effector Th1 (TOFA-30)

description: Effector Th1


title: polII_Dox_DRB0m_1

description:
Chromatin IP of RNA pol II
polII_Dox_DRB0m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs


title: SAMPLE 196_Effector Th1 (TOFA-29)

description: Effector Th1


title: malignant nodule 169T


title: SAMPLE 195_Effector Th1 (TOFA-28)

description: Effector Th1


title: SAMPLE 189_Effector Th1 (TOFA-22)

description: Effector Th1


title: SAMPLE 194_Effector Th1 (TOFA-27)

description: Effector Th1


title: SAMPLE 193_Effector Th1 (TOFA-26)

description: Effector Th1


title: SAMPLE 191_Effector Th1 (TOFA-24)

description: Effector Th1


title: SAMPLE 192_Effector Th1 (TOFA-25)

description: Effector Th1


title: SAMPLE 190_Effector Th1 (TOFA-23)

description: Effector Th1


title: SAMPLE 187_Effector Th1 (TOFA-20)

description: Effector Th1


title: SAMPLE 181_Effector Th1 (TOFA-14)

description: Effector Th1


title: SAMPLE 182_Effector Th1 (TOFA-15)

description: Effector Th1


title: SAMPLE 183_Effector Th1 (TOFA-16)

description: Effector Th1


title: SAMPLE 184_Effector Th1 (TOFA-17)

description: Effector Th1


title: malignant nodule 167T


title: SAMPLE 186_Effector Th1 (TOFA-19)

description: Effector Th1


title: SAMPLE 180_Effector Th1 (TOFA-13)

description: Effector Th1


title: benign nodule 567B


title: benign nodule 620B


title: Lymph node (LN)

source_name: Lymph node

value: Lymph node


title: SAMPLE 185_Effector Th1 (TOFA-18)

description: Effector Th1


title: benign nodule 568B


title: benign nodule 565B


title: benign nodule 564B


title: benign nodule 614B


title: SAMPLE 188_Effector Th1 (TOFA-21)

description: Effector Th1


title: benign nodule 563B


title: benign nodule 559B


title: SAMPLE 176_Effector Th1 (TOFA-9)

description: Effector Th1


title: SAMPLE 179_Effector Th1 (TOFA-12)

description: Effector Th1


title: SAMPLE 177_Effector Th1 (TOFA-10)

description: Effector Th1


title: SAMPLE 178_Effector Th1 (TOFA-11)

description: Effector Th1


title: benign nodule 556B


title: SAMPLE 172_Effector Th1 (TOFA-5)

description: Effector Th1


title: SAMPLE 174_Effector Th1 (TOFA-7)

description: Effector Th1


title: benign nodule 558B


title: SAMPLE 171_Effector Th1 (TOFA-4)

description: Effector Th1


title: SAMPLE 169_Effector Th1 (TOFA-2)

description: Effector Th1


title: benign nodule 555B


title: SAMPLE 170_Effector Th1 (TOFA-3)

description: Effector Th1


title: SAMPLE 167_Effector Th1 (ACC1Lo-67)

description: Effector Th1


title: SAMPLE X - LE1: Light drinkers striatum

city: Belo Horizonte

first: Ana Lúcia

last: Brunialti Godard

state: Minas Gerais

address: Avenida Antonio Carlos, 6627

department: Biologia Geral

country: Brazil

institute: UFMG

description:
Chip number: 10
Pool concentration 580,84 ng/µL

hyb_protocol: For both striatum and prefrontal cortex array, equal amounts of RNA of four animals of light group and four animals of inflexible group were pooled. Each pool was hybridized in three different chips in technical triplicates. The microarray assays were performed using GeneChip®Mouse Genome 430 2.0Array (Affymetrix, São Paulo, Brazil). In vitro transcription was per-formed using 200 ng of total RNA and all subsequent steps were carried out according to the 3IVT Express Kit (Affymetrix, SãoPaulo, Brazil) manual. For the hybridization and scanning step was prepared the hybridization solution, wich 80 ul was pipetted in each chip hole. Chip remained incubated for a 17h at 45°C and 60 RPM. After, hibridization reagente was clean up and replaced by the Wash Buffer. Chips were sealed and placed in the Affymetrix scaning station to fluorescence capture. The stain cocktail 1 (hibridization reagente), stain cokctail 2 (washing) and array holding buffer (buffer) were pipetted in three tub of 1.5 mL e placed in their respective spots inside the Affymetrix washing station.

scan_protocol: Hybridized microarray slides were scanned using Affymetrix Scanner Station

data_processing:
All the microarray data analyses were performed in R environ-ment (www.R-project.org). Hybridization intensities of the imageswere normalized using the RMA (Robust Multi-array Average)method through the affy package, available at http://bioconductor.org/biocLite.R. Differential gene expression (DEG) investigationwas performed with RankProd with a significance level set at99% (p < 0.01). Data integration was evaluated through enrichmentanalyses in the MetaCore®systems biology analysis suite (Thom-son Reuters, New York, USA), which categorized the list of DEGs indifferent molecular pathways.
Differential gene expression (DEG) investigation was performed with RankProd with a significance level set at99% (p < 0.01).

label: Biotin

source_name: Striatum of mice with an avarage of blood ethanol concentration of  48 ± 13.3 mg/dL

label_protocol: After the acquisition of diferencial regulated identifiers between groups, was performed a data-mining, a post-processing analysis to relate gene name, chromossomal loci and function to numerical ID of each probe.

extract_protocol: Total RNA was extracted from the whole striatum and Prefrontal cortex using TRIzol reagent in accordance with manufacture's instructions.

treatment_protocol: 6-week-old Swiss male were subjected to a three-bottle free-choice treatment: a 10% and a 5%(v/v) ethanol solution, and water. The experimental design consisted of four steps: (1) acquisition/free-choice (AC: 10 weeks) with simultaneous access to water and ethanol solutions 5 and 10% (v/v); (2) withdrawal of ethanol solutions (2 weeks); (3) reinstatement of ethanol solutions (RE: 2 weeks); (4) adulteration of ethanol solutions 5 and 10% with 0.005 g/L quinine (AD: 2 weeks). The Control group had access only to tap water throughout the experiment (Ribeiro et al., 2012). At the end of the exposition to the three-bottle free-choice paradigm, mice were classified based on individual ethanol consumption and preference: “Light Drinkers” (significant higher water consumption levels than the ethanol consumption); “Heavy Drinkers” (preference for ethanol decreased after adulteration of the ethanol solution with quinine), and “Inflexible Drinkers” (preference for ethanol at all experimental stages even after addition of quinine to the ethanol solution). Animals that did not meet any of the classification criteria were excluded. At the end of AD phase mice from Inflexible, Heavy and Light groups were exposed to the same free-choice task for one more week, allowing the return to their previous ethanol intake profiles.

value: Swiss

tag: age (at end of experiment)

value: 22 weeks

value: striatum


title: SAMPLE XI - LE2: Light drinkers striatum

description:
Chip number: 11
Pool concentration 580,84 ng/µL

value: male


title: SAMPLE 9 - AE3: Inflexible Drinkers striatum

description:
Chip number: 9
Pool concentration 574,36 ng/µL

source_name: Striatum of mice with an avarage of blood ethanol concentration of  113 ± 11.3 mg/dL


title: SAMPLE 8 - AE2: Inflexible Drinkers striatum

description:
Chip number: 8
Pool concentration 574,36 ng/µL


title: SAMPLE 168_Effector Th1 (TOFA-1)

description: Effector Th1


title: SAMPLE XII - LE3: Light drinkers striatum

description:
Chip number: 12
Pool concentration 580,84 ng/µL


title: benign nodule 554B


title: SAMPLE 166_Effector Th1 (ACC1Lo-66)

description: Effector Th1


title: SAMPLE 7 - AE1: Inflexible Drinkers striatum

description:
Chip number: 7
Pool concentration 574,36 ng/µL


title: SAMPLE 175_Effector Th1 (TOFA-8)

description: Effector Th1


title: benign nodule 557B


title: SAMPLE 6 - LC3: Light drinkers pre-frontal cortex

description:
Chip number: 5
Pool concentration 395,72 ng/µL

source_name: PFC of mice with an avarage of blood ethanol concentration of  48 ± 13.3 mg/dL

value: pre-frontal cortex


title: SAMPLE 164_Effector Th1 (ACC1Lo-64)

description: Effector Th1


title: SAMPLE 173_Effector Th1 (TOFA-6)

description: Effector Th1


title: benign nodule 548B

value: Thyroid


title: SAMPLE 163_Effector Th1 (ACC1Lo-63)

description: Effector Th1


title: SAMPLE 4 - LC1: Light drinkers pre-frontal cortex

description:
Chip number: 17
Pool concentration 395,72 ng/µL


title: SAMPLE 5 - LC2: Light drinkers pre-frontal cortex

description:
Chip number: 4
Pool concentration 395,72 ng/µL


title: SAMPLE 162_Effector Th1 (ACC1Lo-62)

description: Effector Th1


title: SAMPLE 160_Effector Th1 (ACC1Lo-60)

description: Effector Th1


title: benign nodule 546B

value: benign nodule


title: TOFA effector Th1 cells

description: Gene expression data from effector CD4 T cells

hyb_protocol: RNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according to the manufacture's protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing:
Expression values were determined using GeneChip Operating Software (GCOS) v1.2 software.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.19935

label_protocol: Total RNA was extracted usin the IVT Labeling kit from Affymetrix.

extract_protocol: Total cellular RNA was extracted with TRIzol reagent (Invitrogen).

tag: cell subtype

value: TOFA effector Th1 cells


title: SAMPLE 3 - AC3 : Inflexible Drinkers pre-frontal cortex

description:
Chip number: 3
Pool concentration 1034,04 ng/µL

source_name: PFC of mice with an avarage of blood ethanol concentration of  113 ± 11.3 mg/dL


title: SAMPLE 2 - AC2 : Inflexible Drinkers pre-frontal cortex

description:
Chip number: 2
Pool concentration 1034,04 ng/µL


title: SAMPLE 1 - AC1: Inflexible Drinkers pre-frontal cortex

description:
Chip number: 1
Pool concentration 1034,04 ng/µL


title: SAMPLE 165_Effector Th1 (ACC1Lo-65)

description: Effector Th1


title: benign nodule 547B

value: testing cohort


title: SAMPLE 161_Effector Th1 (ACC1Lo-61)

description: Effector Th1


title: benign nodule 545B


title: benign nodule 542B


title: benign nodule 534B


title: benign nodule 531B


title: SAMPLE 159_Effector Th1 (ACC1Lo-59)

description: Effector Th1


title: benign nodule 522B


title: SAMPLE 158_Effector Th1 (ACC1Lo-58)

description: Effector Th1


title: benign nodule 525B


title: SAMPLE 150_Effector Th1 (ACC1Lo-50)

description: Effector Th1


title: SAMPLE 148_Effector Th1 (ACC1Lo-48)

description: Effector Th1


title: SAMPLE 146_Effector Th1 (ACC1Lo-46)

description: Effector Th1


title: SAMPLE 152_Effector Th1 (ACC1Lo-52)

description: Effector Th1


title: SAMPLE 155_Effector Th1 (ACC1Lo-55)

description: Effector Th1


title: SAMPLE 149_Effector Th1 (ACC1Lo-49)

description: Effector Th1


title: SAMPLE 154_Effector Th1 (ACC1Lo-54)

description: Effector Th1


title: SAMPLE 151_Effector Th1 (ACC1Lo-51)

description: Effector Th1


title: SAMPLE 147_Effector Th1 (ACC1Lo-47)

description: Effector Th1


title: benign nodule 519B


title: SAMPLE 157_Effector Th1 (ACC1Lo-57)

description: Effector Th1


title: SAMPLE 156_Effector Th1 (ACC1Lo-56)

description: Effector Th1


title: SAMPLE 153_Effector Th1 (ACC1Lo-53)

description: Effector Th1


title: Memory Th1 cells

description: Gene expression data from memory CD4 T cells

source_name: primary CD4 T cells from spleen

value: Memory Th1 cells


title: benign nodule 516B


title: SAMPLE 145_Effector Th1 (ACC1Lo-45)

description: Effector Th1


title: SAMPLE 144_Effector Th1 (ACC1Lo-44)

description: Effector Th1


title: SAMPLE 143_Effector Th1 (ACC1Lo-43)

description: Effector Th1


title: SAMPLE 142_Effector Th1 (ACC1Lo-42)

description: Effector Th1


title: benign nodule 514B


title: Rap effecrot Th1 cells

value: Rap effecrot Th1 cells


title: malignant nodule 619T

value: malignant nodule


title: SAMPLE 141_Effector Th1 (ACC1Lo-41)

description: Effector Th1

value: BALB/c


title: SAMPLE 140_Effector Th1 (ACC1Lo-40)

description: Effector Th1

value: spleen


title: malignant nodule 617T


title: SAMPLE 136_Effector Th1 (ACC1Lo-36)

description: Effector Th1

value: CD4 T cells


title: SAMPLE 135_Effector Th1 (ACC1Lo-35)

description: Effector Th1


title: SAMPLE 137_Effector Th1 (ACC1Lo-37)

description: Effector Th1


title: SAMPLE 138_Effector Th1 (ACC1Lo-38)

description: Effector Th1


title: SAMPLE 139_Effector Th1 (ACC1Lo-39)

description: Effector Th1


title: malignant nodule 616T


title: Control effector Th1 cells

value: Control effector Th1 cells


title: Naïve CD4 T cells

description: Gene expression data from naïve CD4 T cells

value: Naïve CD4 T cells


title: substantia-nigra Braak4 2

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from substantia nigra

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D__F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: brain, substantia_nigra

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Brain tissue explants from substantia nigra (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Post-mortem substrantia nigra explants from patients were obtained and immediately preserved with 600 uL of RNAlater (Qiagen).

tag: disease state

value: Parkinson's disease

value: Male

tag: disease stage

value: Braak 4

value: substantia nigra


title: substantia-nigra Braak4 3

description: Gene expression from substantia nigra


title: substantia-nigra Braak4 1

description: Gene expression from substantia nigra

value: Female


title: substantia-nigra Braak3 3

description: Gene expression from substantia nigra

value: Braak 3


title: malignant nodule 615T

value: Thyroid


title: substantia-nigra Braak3 4

description: Gene expression from substantia nigra


title: SAMPLE 133_Effector Th1 (ACC1Lo-33)

description: Effector Th1

source_name: cultured primary CD4 T cells from spleen

tag: strain


title: SAMPLE 134_Effector Th1 (ACC1Lo-34)

description: Effector Th1

tag: tissue


title: malignant nodule 613T


title: SAMPLE 132_Effector Th1 (ACC1Lo-32)

description: Effector Th1

tag: cell type


title: SAMPLE 131_Effector Th1 (ACC1Lo-31)

description: Effector Th1


title: malignant nodule 612T


title: malignant nodule 611T


title: substantia-nigra Braak3 2

description: Gene expression from substantia nigra


title: substantia-nigra Braak3 1

description: Gene expression from substantia nigra


title: SAMPLE 130_Effector Th1 (ACC1Lo-30)

description: Effector Th1


title: SAMPLE 127_Effector Th1 (ACC1Lo-27)

description: Effector Th1


title: SAMPLE 129_Effector Th1 (ACC1Lo-29)

description: Effector Th1


title: malignant nodule 610T


title: SAMPLE 128_Effector Th1 (ACC1Lo-28)

description: Effector Th1


title: SAMPLE 126_Effector Th1 (ACC1Lo-26)

description: Effector Th1


title: substantia-nigra control 6

description: Gene expression from substantia nigra

value: control


title: SAMPLE 125_Effector Th1 (ACC1Lo-25)

description: Effector Th1


title: malignant nodule 609T

value: testing cohort


title: substantia-nigra Braak4 5

description: Gene expression from substantia nigra


title: substantia-nigra Braak4 4

description: Gene expression from substantia nigra


title: substantia-nigra control 3

description: Gene expression from substantia nigra


title: malignant nodule 607T


title: SAMPLE 124_Effector Th1 (ACC1Lo-24)

description: Effector Th1


title: malignant nodule 608T


title: substantia-nigra control 5

description: Gene expression from substantia nigra


title: SAMPLE 122_Effector Th1 (ACC1Lo-22)

description: Effector Th1


title: SAMPLE 120_Effector Th1 (ACC1Lo-20)

description: Effector Th1


title: SAMPLE 121_Effector Th1 (ACC1Lo-21)

description: Effector Th1


title: substantia-nigra control 4

description: Gene expression from substantia nigra


title: substantia-nigra control 2

description: Gene expression from substantia nigra


title: malignant nodule 606T


title: SAMPLE 123_Effector Th1 (ACC1Lo-23)

description: Effector Th1


title: substantia-nigra control 1

description: Gene expression from substantia nigra


title: SAMPLE 118_Effector Th1 (ACC1Lo-18)

description: Effector Th1


title: SAMPLE 117_Effector Th1 (ACC1Lo-17)

description: Effector Th1


title: SAMPLE 119_Effector Th1 (ACC1Lo-19)

description: Effector Th1


title: malignant nodule 605T


title: malignant nodule 603T


title: malignant nodule 602T


title: SAMPLE 116_Effector Th1 (ACC1Lo-16)

description: Effector Th1


title: malignant nodule 601T


title: SAMPLE 115_Effector Th1 (ACC1Lo-15)

description: Effector Th1


title: SAMPLE 114_Effector Th1 (ACC1Lo-14)

description: Effector Th1


title: malignant nodule 164T


title: SAMPLE 113_Effector Th1 (ACC1Lo-13)

description: Effector Th1


title: malignant nodule 163T


title: malignant nodule 162T


title: SAMPLE 111_Effector Th1 (ACC1Lo-11)

description: Effector Th1


title: dim5_DD_rep2

city: New Brunswick

first: William

middle: J.

last: Belden

state: NJ

address: 59 Dudley Rd

department: Animal Sciences

institute: Rutgers, The State University of New Jersey

library_source: transcriptomic

data_processing:
HISAT2 (version 2.1.0) and StringTie( version 1.3.3b) for mapping and transcripts discovery. The 100bp pair-end reads were mapped to the Neurospora NC12 reference genome using the existing GTF file as a guide. The Neurospora transcriptome created by Hisat2 was assembled and merged using StringTie to generate the merged GTF file. Next, we used Cuffdiff  for differential expression analysis.
Genome_build: NC12

organism: Neurospora crassa

source_name: mycelia

growth_protocol: For the growth, Neurospora conidia were inoculated in 2% liquid culture media (2% LCM) and grown in 100-mm Petri dishes overnight at 30 °C to generate mycelia mats. Plugs were cut from the mycelia and used to inoculate flasks containing 100 ml of 2% LCM and grown for a total of 2 days at 25 °C.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) following manufacturer’s instructions.  The total RNA was sent to the Columbia Genome Center for library preparation and RNA-seq.
Ribosomal RNAs were depleted and the remaining RNA was for cDNA library preparation using the TrueSeq library preparation kit version 2. A total of 60 million 100bp paired-ended reads were sequenced on the Illumina 2500 instrument.

treatment_protocol: For DD24 cultures were grown in the light for 24 hours then transferred to constant dark for 24 hours and harvested.  The LP30 were grown in a similar fashion but just prior to harvesting the cultures were placed in constant light for 30 min prior to harvesting.  The tissue was immediately snap frozen.

tag: harvest time


title: dim5_DD_rep1


title: set1_LP30_rep2


title: set1_DD_rep1


title: set1_LP30_rep1


title: dim5_LP30_rep2


title: malignant nodule 161T


title: SAMPLE 110_Effector Th1 (ACC1Lo-10)

description: Effector Th1


title: SAMPLE 112_Effector Th1 (ACC1Lo-12)

description: Effector Th1


title: WT_LP30_rep2

value: WT


title: malignant nodule 158T


title: SAMPLE 109_Effector Th1 (ACC1Lo-9)

description: Effector Th1


title: WT_LP30_rep1


title: WT_DD_rep2


title: malignant nodule 155T


title: dim5_LP30_rep1


title: SAMPLE 107_Effector Th1 (ACC1Lo-7)

description: Effector Th1


title: malignant nodule 154T


title: WT_DD_rep1


title: SAMPLE 106_Effector Th1 (ACC1Lo-6)

description: Effector Th1


title: SAMPLE 108_Effector Th1 (ACC1Lo-8)

description: Effector Th1


title: malignant nodule 153T


title: malignant nodule 152T


title: SAMPLE 105_Effector Th1 (ACC1Lo-5)

description: Effector Th1


title: set1_DD_K4_rep2

data_processing:
ChIP-seq reads were mapped to NC12 genome using Burroghs Wheeler Aligner (BWA) . The resulting Bam files were processed using macs2  to call peaks (broad peaks function was used for H3K9me3).
Genome_build: NC12

extract_protocol:
Tissue was crosslinked with 1% formaldehyde.
The purified DNA was sent to Beijing Genome Institute (BGI) for library preparation and sequencing. The samples were sequenced to a depth of 50 million 50-bp single-end read.

tag: genotype/variation


title: set1_DD_K4_rep1


title: SAMPLE 104_Effector Th1 (ACC1Lo-4)

description: Effector Th1


title: dim5_LP_K4_rep2


title: malignant nodule 150T


title: malignant nodule 141T


title: malignant nodule 148T


title: dim5_DD_K4_rep1


title: dim5_DD_K4_rep2


title: malignant nodule 138T


title: dim5_LP_K4_rep1


title: malignant nodule 137T


title: WT_LP_K4_rep2


title: WT_LP_K4_rep1


title: SAMPLE 101_Effector Th1 (ACC1Lo-1)

description: Effector Th1


title: SAMPLE 100_Effector Th1 (ACC1Hi-100)

description: Effector Th1


title: SAMPLE 99_Effector Th1 (ACC1Hi-99)

description: Effector Th1


title: SAMPLE 102_Effector Th1 (ACC1Lo-2)

description: Effector Th1


title: adjacent tissues 117N

value: adjacent tissues

value: developing cohort


title: WT_DD_K4_rep2


title: adjacent tissues 116N


title: malignant nodule 146T

value: malignant nodule


title: WT_DD_K4_rep1


title: SAMPLE 103_Effector Th1 (ACC1Lo-3)

description: Effector Th1

value: BALB/c

value: spleen


title: SAMPLE 98_Effector Th1 (ACC1Hi-98)

description: Effector Th1

value: CD4 T cells


title: adjacent tissues 113N


title: SAMPLE 97_Effector Th1 (ACC1Hi-97)

description: Effector Th1


title: SAMPLE 96_Effector Th1 (ACC1Hi-96)

description: Effector Th1


title: dim5_DD_K9_rep2


title: SAMPLE 95_Effector Th1 (ACC1Hi-95)

description: Effector Th1


title: adjacent tissues 112N


title: SAMPLE 94_Effector Th1 (ACC1Hi-94)

description: Effector Th1


title: set1_LP_K9_rep2


title: dim5_DD_K9_rep1


title: adjacent tissues 109N


title: set1_LP_K9_rep1


title: adjacent tissues 107N


title: adjacent tissues 106N


title: SAMPLE 93_Effector Th1 (ACC1Hi-93)

description: Effector Th1


title: set1_DD_K9_rep2


title: WT_LP_K9_rep2


title: adjacent tissues 105N


title: set1_DD_K9_rep1


title: adjacent tissues 103N


title: SAMPLE 91_Effector Th1 (ACC1Hi-91)

description: Effector Th1


title: adjacent tissues 102N


title: adjacent tissues 101N


title: SAMPLE 90_Effector Th1 (ACC1Hi-90)

description: Effector Th1


title: adjacent tissues 80N


title: SAMPLE 92_Effector Th1 (ACC1Hi-92)

description: Effector Th1


title: WT_LP_K9_rep1


title: SAMPLE 89_Effector Th1 (ACC1Hi-89)

description: Effector Th1


title: WT_DD_K9_rep2


title: adjacent tissues 79N


title: WT_DD_K9_rep1


title: SAMPLE 87_Effector Th1 (ACC1Hi-87)

description: Effector Th1


title: SAMPLE 86_Effector Th1 (ACC1Hi-86)

description: Effector Th1


title: adjacent tissues 75N


title: SAMPLE 88_Effector Th1 (ACC1Hi-88)

description: Effector Th1


title: SAMPLE 85_Effector Th1 (ACC1Hi-85)

description: Effector Th1


title: GMR_PRP8-RNAi_GD_15-22-SampleB_S3

city: Philadelphia

first: Iryna

last: Shakhmantsir

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
gene_quant.txt
junction_counts.txt
exon_counts.txt

data_processing:
Raw RNA-Seq reads were aligned to the BDGP6.v88 build of the fruitfly genome using STAR v2.5.3a. STAR was provided with gene models from the Ensembl v88 genome annotation.
The Pipeline of RNA-Seq Transformations (PORT) v0.8.2a-beta was used to perform gene-level and exon-level normalization and quantification of the aligned data. PORT is an implementation of the re-sampling approach for normalization proposed by Li and Tibshirani. Briefly, PORT accounts for potential confounding factors like reads mapping to rRNA and mitochondrial DNA. Next, PORT determines the input samples with the fewest number of gene-mapping reads and re-samples all datasets to the same number of reads. Lastly, PORT quantifies the normalized gene-level reads counts for each sample.
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

organism: Drosophila melanogaster

source_name: fly head

growth_protocol: 3-5 day old flies were entrained for at least 3 full cycles in 12h:12h light:dark conditions and all frozen at ZT12 for subsequent RNA isolation

extract_protocol:
Fly heads were then collected on dry ice and homogenized with Trizol (Life Technologies) on ice using standard protocols. Following the phase separation, the aqueous phase was transferred into a new tube, mixed with an equal volume of 70% ethanol and loaded directly onto the RNeasy mini kit columns (Qiagen). The rest of RNA isolation was done according to the manufacturer’s protocol. On-column DNase digestion (Qiagen) for 15 minutes at RT was always included.
Samples were prepared with Lexogen’s SENSE mRNA-Seq library Prep Kit. Illumina Next-Generation Sequencing (NextSeq 500) with 300pb paired-end high output run (at ~50M reads per sample) was performed by the Genomics Facility at the Wistar Institute.

value: adult head

value: prp8 knockdown sample (GMR>prp8-RNAi (GD))


title: adjacent tissues 73N


title: adjacent tissues 71N


title: GMR_PRP8-RNAi_GD_13-19-SampleB_S15


title: GMR_PRP8-RNAi_GD_12-18-SampleB


title: GMR_PRP8-RNAi_GD_14-20-SampleB_S6


title: GMR_PRP8-RNAi_GD_11-17-SampleB_S12


title: adjacent tissues 66N


title: adjacent tissues 69N


title: SAMPLE 83_Effector Th1 (ACC1Hi-83)

description: Effector Th1


title: SAMPLE 84_Effector Th1 (ACC1Hi-84)

description: Effector Th1


title: SAMPLE 82_Effector Th1 (ACC1Hi-82)

description: Effector Th1


title: adjacent tissues 64N


title: GMR_PRP4-RNAi_GD_10-16-SampleA_S14

value: prp4 knockdown sample (GMR>prp4-RNAi (GD))


title: SAMPLE 81_Effector Th1 (ACC1Hi-81)

description: Effector Th1


title: GMR_PRP4-RNAi_GD_9-15-SampleA_S1


title: adjacent tissues 63N


title: GMR_PRP4-RNAi _GD_8-13-SampleA_S5


title: GMR_PRP4-RNAi_GD_7-12-SampleA_S10


title: adjacent tissues 62N


title: adjacent tissues 61N


title: SAMPLE 79_Effector Th1 (ACC1Hi-79)

description: Effector Th1


title: SAMPLE 78_Effector Th1 (ACC1Hi-78)

description: Effector Th1


title: SAMPLE 80_Effector Th1 (ACC1Hi-80)

description: Effector Th1


title: adjacent tissues 58N


title: SAMPLE 77_Effector Th1 (ACC1Hi-77)

description: Effector Th1


title: GMR_PRP4-RNAi_GD_6-9-SampleA_S4


title: GMR_+_5-8-CTRL_S7

value: GMR/+


title: adjacent tissues 56N


title: SAMPLE 76_Effector Th1 (ACC1Hi-76)

description: Effector Th1


title: GMR_+_4-7-CTRL_S9


title: adjacent tissues 55N


title: set1_DD_rep2


title: SAMPLE 75_Effector Th1 (ACC1Hi-75)

description: Effector Th1


title: SAMPLE 73_Effector Th1 (ACC1Hi-73)

description: Effector Th1


title: adjacent tissues 19N


title: GMR_+_3-6-CTRL_S13


title: GMR_+_2-5-CTRL_S8


title: adjacent tissues 18N


title: SAMPLE 74_Effector Th1 (ACC1Hi-74)

description: Effector Th1


title: adjacent tissues 17N


title: SAMPLE 72_Effector Th1 (ACC1Hi-72)

description: Effector Th1


title: adjacent tissues 16N


title: GMR_+_1-3-CTRL_S2


title: CCR7loCD137hi-2_ RNA

description: Splenic CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 4 days in vitro. These cells were separated according to the expression of CCR7 and CD137 by Aria cell sorter.

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Sorted subpopulation (CCR7loCD137hi) of five-day cultured Th1 cells.

growth_protocol: See "description".

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

value: CCR7loCD137hi CD4 T


title: SAMPLE 71_Effector Th1 (ACC1Hi-71)

description: Effector Th1


title: CCR7hiCD137lo-2_ RNA

source_name: Sorted subpopulation (CCR7hiCD137lo) of five-day cultured Th1 cells.

value: CCR7hiCD137lo CD4 T


title: SAMPLE 70_Effector Th1 (ACC1Hi-70)

description: Effector Th1


title: CCR7loCD137hi-1_ RNA


title: adjacent tissues 13N

source_name: Thyroid


title: adjacent tissues 15N


title: adjacent tissues 11N


title: CCR7hiCD137lo-1_ RNA


title: SAMPLE 69_Effector Th1 (ACC1Hi-69)

description: Effector Th1


title: SAMPLE 67_Effector Th1 (ACC1Hi-67)

description: Effector Th1


title: adjacent tissues 12N


title: adjacent tissues 10N


title: SAMPLE 68_Effector Th1 (ACC1Hi-68)

description: Effector Th1


title: adjacent tissues 9N


title: SAMPLE 66_Effector Th1 (ACC1Hi-66)

description: Effector Th1


title: adjacent tissues 8N


title: SAMPLE 63_Effector Th1 (ACC1Hi-63)

description: Effector Th1


title: SAMPLE 64_Effector Th1 (ACC1Hi-64)

description: Effector Th1


title: adjacent tissues 7N


title: adjacent tissues 6N


title: SAMPLE 65_Effector Th1 (ACC1Hi-65)

description: Effector Th1


title: adjacent tissues 4N


title: adjacent tissues 2N


title: L. bicolor T4 3

city: Lund

first: Anders

last: Tunlid

address: Sölvegatan 37

department: Biology

country: Sweden

institute: Lund University

description: Prolonged glucose depletion

data_processing:
FastQC (ver. 0.11.2) (Andrews, 2010) was used for quality control of raw RNA-Seq reads and ribosomal RNA-like sequences were removed using riboPicker (standalone ver. 0.4.3, SILVA database ver. 119) (Schmieder et al., 2012). RNA-Seq reads were aligned to the transcriptome using TopHat2 (ver. 2.0.13) (Kim et al., 2013) with Bowtie2 (ver. 2.2.3.0) (Langmead et al., 2012) and the following parameters: -T -x 1 -I 5000 --library-type 'fr-firststrand'  SAMtools (ver. 0.1.19) (Li et al., 2009) was used to sort and convert the BAM files to SAM files. Transcript abundances were measured as read counts in CDS using htseq-count (ver. 0.6.1) (Anders et al., 2015) with the following parameters: -s 'reverse' -t 'CDS' -i 'gene_id' -m 'intersection-nonempty'   Genes with mean count below 11 across all samples were removed. Read count normalization factors were calculated for each fungus using EDASeq (ver. 2.8.0) with 50 strata and full quantile normalization to correct for transcript length and G/C-content within each sample (Risso et al., 2011), and combined with sample size factors to adjust for different sequencing depths using DESeq2 (ver. 1.14.1) (Love et al., 2014). Principal component analysis (PCA) was performed on normalized and regularized log-transformed (DESeq2) RNAseq data blinded to the experimental design for quality assurance.
Genome_build: Paxillus involutus ATCC 200175 v1.0 (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html)
Genome_build: Laccaria bicolor v2.0 (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html)
Supplementary_files_format_and_content: The tab-delimited Lac_rawCounts.tab and Pax_rawCounts.tab files contain the Joint Genome Institute (JGI) gene model names and raw read counts for each sample.
Supplementary_files_format_and_content: The tab-delimited Lac_normalizationFactors.tab and Pax_normalizationFactors.tab files contain the matrix of normalization factors for each gene and sample. Used in DESeq2 with the raw counts file to correct for gene-specific effects and sample-specific sequencing depths. For correct dispersion estimation the matrix of normalization factors needs first to be scaled to geometric mean near 1 for each row (gene) for correct dispersion estimation (see DESeq2::normalizationFactors).
Supplementary_files_format_and_content: The tab-delimited Lac_rlog_normalizedCounts.tab and Pax_rlog_normalizedCounts.tab files contain the gene model names and DESeq2 regularized log (rlog) transformed normalized counts for each sample.

organism: Laccaria bicolor

source_name: Mycelium

growth_protocol: Cultures of P. involutus (Batsch Fr., strain ATCC 200175) and L. bicolor (strain Maire P.D.Orton) were grown in petri dishes on a glass bead layer containing liquid minimum Melin-Norkrans (MMN) medium for 9 and 18 days, respectively. The medium was replaced with MMN medium without N to induce an N-deprived mycelium.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) with the RLC buffer and on-column DNase treatment, according to the manufacturer’s instructions. Total RNA was eluted in H2O.
After reverse transcription into double-stranded cDNA and barcoding by means of the massively parallel signature sequencing protocol, libraries were sequenced (RNA-Seq) using a HiSeq2000 instrument (Illumina Inc.) in single-read mode and with a read length of 50 bp (IGA Technology Services, Italy; www.igatechnology.com).

treatment_protocol: After 24 h of nitrogen starvation, the mycelium was washed with sterile water and the SOM extract was added. The extract was supplemented with glucose to a final concentration similar to that in the MMN medium (Rineau et al., 2012). For the production om extract forest litter material was collected from the upper 10-cm soil layer in a 61-year-old Norway spruce stand growing in a N-poor site in central Sweden (soil pH, 5.0) and was extracted using hot water.

value: Maire P.D.Orton

tag: days

tag: time point

tag: biological replicate


title: SAMPLE 62_Effector Th1 (ACC1Hi-62)

description: Effector Th1


title: adjacent tissues 3N

value: Thyroid

tag: tissue type


title: SAMPLE 61_Effector Th1 (ACC1Hi-61)

description: Effector Th1


title: SAMPLE 58_Effector Th1 (ACC1Hi-58)

description: Effector Th1


title: SAMPLE 59_Effector Th1 (ACC1Hi-59)

description: Effector Th1


title: SAMPLE 60_Effector Th1 (ACC1Hi-60)

description: Effector Th1


title: benign nodule 511B

value: benign nodule

tag: cohort


title: SAMPLE 57_Effector Th1 (ACC1Hi-57)

description: Effector Th1


title: adjacent tissues 1N


title: L. bicolor T4 2

description: Prolonged glucose depletion


title: SAMPLE 56_Effector Th1 (ACC1Hi-56)

description: Effector Th1


title: benign nodule 510B


title: L. bicolor T4 1

description: Prolonged glucose depletion


title: L. bicolor T3 3

description: Glucose depletion


title: L. bicolor T3 2

description: Glucose depletion


title: benign nodule 509B


title: SAMPLE 54_Effector Th1 (ACC1Hi-54)

description: Effector Th1


title: SAMPLE 55_Effector Th1 (ACC1Hi-55)

description: Effector Th1


title: benign nodule 508B


title: SAMPLE 53_Effector Th1 (ACC1Hi-53)

description: Effector Th1


title: Control Mouse 3

city: Malaga

first: James

middle: R

last: Perkins

state: Malaga

address: Bulevar Louis Pasteur

department: Molecular Biology and Biochemistry

country: Spain

institute: CIBERER / Universidad de Malaga

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10) using the TopHat software (-r 200; -g 1)
Expression was quantified using HTSeq
Differential expression (DE) analysis was performed using DESeq2
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited file showing genes and aligned reads

molecule: polyA RNA

source_name: Lymph node derived dendritic cells

extract_protocol:
SMARTer Ultra low input RNA library kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: female

value: Balb/c

tag: age

value: 4-5 weeks

tag: treatment

value: Intranasally administered vehicle + Pr p 3 challenge


title: Control Mouse 4


title: Control Mouse 5


title: benign nodule 507B

value: developing cohort


title: L. bicolor T3 1

description: Glucose depletion


title: Control Mouse 2


title: L. bicolor T2 3

description: Ammonium depletion


title: SAMPLE 51_Effector Th1 (ACC1Hi-51)

description: Effector Th1

value: BALB/c


title: SAMPLE 52_Effector Th1 (ACC1Hi-52)

description: Effector Th1

value: spleen


title: benign nodule 506B


title: Control Mouse 1


title: L. bicolor T2 2

description: Ammonium depletion


title: Anaphylactic Mouse 5

value: intranasally administered Pru p 3 in combination with LPS + Pru p 3 challenge to induced anaphylaxis


title: SAMPLE 50_Effector Th1 (ACC1Hi-50)

description: Effector Th1

value: CD4 T cells


title: SAMPLE 49_Effector Th1 (ACC1Hi-49)

description: Effector Th1


title: L. bicolor T2 1

description: Ammonium depletion


title: benign nodule 504B


title: L. bicolor T1 3

description: Active growth


title: benign nodule 505B


title: benign nodule 502B


title: Anaphylactic Mouse 3


title: L. bicolor T1 2

description: Active growth


title: SAMPLE 48_Effector Th1 (ACC1Hi-48)

description: Effector Th1


title: Anaphylactic Mouse 2


title: Anaphylactic Mouse 4


title: SAMPLE 47_Effector Th1 (ACC1Hi-47)

description: Effector Th1


title: L. bicolor T1 1

description: Active growth


title: benign nodule 501B


title: benign nodule 19B


title: SAMPLE 46_Effector Th1 (ACC1Hi-46)

description: Effector Th1


title: benign nodule 18B


title: SAMPLE 44_Effector Th1 (ACC1Hi-44)

description: Effector Th1


title: benign nodule 16B


title: MII stage embryo

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

description: MII

data_processing:
Illumina HiSeq 2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MII stage embryo

growth_protocol: GV oocytes from Hybrid B6D2F1 (C57BL/6 x DBA) female mice (6-8 weeks old) were selected and maintained in M16 medium.

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

treatment_protocol: Tubastatin A HCl (Catalogue no. 27108) was obtained from BPS Bioscience (San Diego, USA). The compound was dissolved in DMSO and further diluted in saline to the 10 and 20uM concentration.

value: non-treated

value: Hybrid B6D2F1 (C57BL/6 x DBA)

tag: gender


title: benign nodule 17B


title: SAMPLE 43_Effector Th1 (ACC1Hi-43)

description: Effector Th1


title: 20uM tubastatin A- treated oocytes

source_name: 20uM tubastatin A- treated oocytes

value: 11uM tubastatin A- treated


title: GV stage oocytes

description: GV

source_name: GV stage oocytes


title: benign nodule 503B


title: benign nodule 15B


title: SAMPLE 41_Effector Th1 (ACC1Hi-41)

description: Effector Th1


title: benign nodule 14B


title: SAMPLE 40_Effector Th1 (ACC1Hi-40)

description: Effector Th1


title: wildtype_SM_3weeksDex_rep2 [GAR0290]

city: Neuherberg

first: Henriette

last: Uhlenhaut

state: Munich

address: Ingolstaedter Landstr 1

department: HDC

institute: Helmholtz

description:
GAR0290
PolyA RNA-Seq from skeletal muscle of 3 weeks Dexamethason-treated male, E47+/+  C57BL/6 mice

data_processing:
The reads were mapped to the mouse genome mm10 (Ensembl build 38.91) and reads per gene counted using STAR version 2.4.2a and/or HTSeq-cout version 0.7.0. Raw count data is available as _STAR_count.txt or _STARReadsPerGene.out.tab. See: https://github.com/FranziG/E47KO-liver for all the codebooks and scripts.
Counts were filtered for their expression strength by selecting only genes with counts above 25th percentile as expressed. Gene count normalization and differential expression analysis was performed with DESeq2. See: https://github.com/FranziG/E47KO-liver for all the codebooks and scripts.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt version 2.32.1 and information from Ensembl (build 38.91). See: https://github.com/FranziG/E47KO-liver for all the codebooks and scripts.
Genome_build: mm10
Supplementary_files_format_and_content: *_unfiltered.txt files contain the unfiltered results from the DESeq2 analysis for differential expression on E47-/- versus E47+/+ or Albcre/+;E47fl/fl versus  Alb+/+;E47fl/fl, respectively.

growth_protocol: Mice were housed in a controlled SPF facility with a 12 hr dark/light cycle in groups of 4 animals per cage. The cages were individually ventilated and the room was kept at 23°C with constant humidity. They were fed ad libitum with regulator chow diet. Mice were sacrificed by cervical dislocation and the liver was immediately snap-frozen in liquid nitrogen.

extract_protocol:
For longterm Cort-treated liver tissue and longterm Dex-treated liver, skeletal muscle and white adipose tissue, RNA was extracted using the Qiazol protocol. For acute Dex-injected liver tissue RNA was extracted using the RNeasy minikit (Qiagen). All samples were DNAse-treated using the Ambion DNase I kit (Thermo Fisher Scientific).
The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies). Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) or unstranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: GR-ligand (dexamethasone or corticosterone) was supplemented in the drinking water of mice for 3 consecutive weeks. Mice had free access to water and food for the entire treatment period. For the acute response, mice were injected with 1mg/kg Dex and sacrificed 1 hour later with free access to food and water the entire time.

tag: strain background

value: male

tag: diet

value: chow

value: 3 weeks 10 ug/ml concentration Dexamethasone in drinking water

tag: sacrifice condition

value: sacrificed after GTT

value: skeletal muscle; quadriceps

tag: library

value: unstranded


title: wildtype_SM_3weeksDex_rep1 [GAR0288]

description:
GAR0288
PolyA RNA-Seq from skeletal muscle of 3 weeks Dexamethason-treated male, E47+/+ C57BL/6 mice

tag: tissue


title: E47KO_SM_3weeksDex_rep2 [GAR0287]

description:
GAR0287
PolyA RNA-Seq from skeletal muscle of 3 weeks Dexamethason-treated male, E47-/- C57BL/6 mice


title: SAMPLE 39_Effector Th1 (ACC1Hi-39)

description: Effector Th1

tag: strain

tag: cell type


title: SAMPLE 37_Effector Th1 (ACC1Hi-37)

description: Effector Th1


title: SAMPLE 38_Effector Th1 (ACC1Hi-38)

description: Effector Th1


title: SAMPLE 45_Effector Th1 (ACC1Hi-45)

description: Effector Th1


title: Anaphylactic Mouse 1

value: female

value: Balb/c


title: E47KO_SM_3weeksDex_rep1 [GAR0285]

description:
GAR0285
PolyA RNA-Seq from skeletal muscle of 3 weeks Dexamethason-treated male, E47-/- C57BL/6 mice

tag: genotype/variation


title: benign nodule 9B

value: Thyroid

value: benign nodule


title: 10uM tubastatin A- treated oocytes

source_name: 10uM tubastatin A- treated oocytes

value: 20uM tubastatin A- treated


title: SAMPLE 42_Effector Th1 (ACC1Hi-42)

description: Effector Th1

value: BALB/c

value: spleen


title: E47KO_SM_3weeksDex_rep3 [GAR0289]

description:
GAR0289
PolyA RNA-Seq from skeletal muscle of 3 weeks Dexamethason-treated male, E47-/- C57BL/6 mice


title: benign nodule 13B

value: developing cohort


title: benign nodule 6B


title: benign nodule 12B


title: wildtype_WAT_3weeksDex_rep2 [GAR0294]

description:
GAR0294
PolyA RNA-Seq from white adipose tissue of 3 weeks Dexamethason-treated male, E47+/+  C57BL/6 mice

value: epididymal white adipose tissue


title: wildtype_WAT_3weeksDex_rep1 [GAR0292]

description:
GAR0292
PolyA RNA-Seq from white adipose tissue of 3 weeks Dexamethason-treated male, E47+/+  C57BL/6 mice


title: wildtype_liver_3weeksDex_rep2 [GAR0184]

description:
GAR0184
PolyA RNA-Seq from liver tissue of 3 weeks Dexamethason-treated male, E47+/+ C57BL/6 mice

value: liver tissue


title: benign nodule 10B


title: benign nodule 3B


title: E47KO_liver_3weeksDex_rep3 [GAR0183]

description:
GAR0183
PolyA RNA-Seq from liver tissue of 3 weeks Dexamethason-treated male, E47-/- C57BL/6 mice


title: SAMPLE 36_Effector Th1 (ACC1Hi-36)

description: Effector Th1

value: CD4 T cells


title: wildtype_liver_3weeksDex_rep1 [GAR0182]

description:
GAR0182
PolyA RNA-Seq from liver tissue of 3 weeks Dexamethason-treated male, E47+/+  C57BL/6 mice

value: male


title: SAMPLE 29_Effector Th1 (ACC1Hi-29)

description: Effector Th1


title: SAMPLE 35_Effector Th1 (ACC1Hi-35)

description: Effector Th1


title: E47KO_WAT_3weeksDex_rep3 [GAR0295]

description:
GAR0295
PolyA RNA-Seq from white adipose tissue of 3 weeks Dexamethason-treated male, E47-/-  C57BL/6 mice

value: chow


title: benign nodule 8B


title: E47KO_liver_3weeksDex_rep2 [GAR0181]

description:
GAR0181
PolyA RNA-Seq from liver tissue of 3 weeks Dexamethason-treated male, E47-/- C57BL/6 mice

value: 3 weeks 10 ug/ml concentration Dexamethasone in drinking water


title: benign nodule 1B


title: SAMPLE 34_Effector Th1 (ACC1Hi-34)

description: Effector Th1


title: benign nodule 7B


title: SAMPLE 28_Effector Th1 (ACC1Hi-28)

description: Effector Th1


title: E47KO_WAT_3weeksDex_rep2 [GAR0293]

description:
GAR0293
PolyA RNA-Seq from white adipose tissue of 3 weeks Dexamethason-treated male, E47-/- C57BL/6 mice

value: sacrificed after GTT


title: SAMPLE 33_Effector Th1 (ACC1Hi-33)

description: Effector Th1


title: benign nodule 4B


title: E47KO_liver_3weeksDex_rep1 [GAR0179]

description:
GAR0179
PolyA RNA-Seq from liver tissue of 3 weeks Dexamethason-treated male, E47-/-  C57BL/6 mice


title: malignant nodule 136T

value: malignant nodule


title: SAMPLE 31_Effector Th1 (ACC1Hi-31)

description: Effector Th1


title: SAMPLE 32_Effector Th1 (ACC1Hi-32)

description: Effector Th1


title: SAMPLE 30_Effector Th1 (ACC1Hi-30)

description: Effector Th1


title: benign nodule 2B


title: SAMPLE 27_Effector Th1 (ACC1Hi-27)

description: Effector Th1


title: malignant nodule 131T


title: SAMPLE 24_Effector Th1 (ACC1Hi-24)

description: Effector Th1


title: SAMPLE 23_Effector Th1 (ACC1Hi-23)

description: Effector Th1


title: malignant nodule 130T


title: malignant nodule 127T


title: malignant nodule 126T


title: malignant nodule 134T


title: SAMPLE 22_Effector Th1 (ACC1Hi-22)

description: Effector Th1


title: malignant nodule 125T


title: SAMPLE 21_Effector Th1 (ACC1Hi-21)

description: Effector Th1


title: malignant nodule 132T


title: malignant nodule 122T


title: SAMPLE 20_Effector Th1 (ACC1Hi-20)

description: Effector Th1


title: malignant nodule 119T


title: SAMPLE 26_Effector Th1 (ACC1Hi-26)

description: Effector Th1


title: SAMPLE 25_Effector Th1 (ACC1Hi-25)

description: Effector Th1


title: SAMPLE 19_Effector Th1 (ACC1Hi-19)

description: Effector Th1


title: SAMPLE 18_Effector Th1 (ACC1Hi-18)

description: Effector Th1


title: SAMPLE 17_Effector Th1 (ACC1Hi-17)

description: Effector Th1


title: malignant nodule 118T


title: malignant nodule 116T


title: malignant nodule 113T


title: SAMPLE 15_Effector Th1 (ACC1Hi-15)

description: Effector Th1


title: SAMPLE 16_Effector Th1 (ACC1Hi-16)

description: Effector Th1


title: malignant nodule 112T


title: SAMPLE 14_Effector Th1 (ACC1Hi-14)

description: Effector Th1


title: malignant nodule 109T


title: SAMPLE 13_Effector Th1 (ACC1Hi-13)

description: Effector Th1


title: SAMPLE 12_Effector Th1 (ACC1Hi-12)

description: Effector Th1


title: malignant nodule 117T


title: malignant nodule 107T


title: SAMPLE 11_Effector Th1 (ACC1Hi-11)

description: Effector Th1


title: malignant nodule 106T


title: SAMPLE 9_Effector Th1 (ACC1Hi-9)

description: Effector Th1


title: SAMPLE 10_Effector Th1 (ACC1Hi-10)

description: Effector Th1


title: malignant nodule 103T


title: DNA extracted from peripheral blood from C11

type: genomic

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

institute: Boldrini Children's Hospital

description: DNA extracted from peripheral blood

hyb_protocol: As per Illumina protocol

scan_protocol: iScan SQ scanner (Illumina) using  GenomeStudio software (v.2011.1)

data_processing: Normalized data (FunNorm) were corrected for technical replicates

label: Cy5 and Cy3

source_name: male control

label_protocol: As per Illumina protocol

extract_protocol: QIAamp DNA BloodMidi Kit as per protocol

treatment_protocol: DNA treated with sodium bisulfite


title: ARCI skin biopsy P5

city: Uppsala

first: Hans

last: Törmä

address: Dag Hammarskjölds väg 20

department: Dept of Medical Sciences

institute: Uppsala University

hyb_protocol: GeneChip® Clariom D Human Arrays were hybridized for 16 hours in a 45°C incubator, followed by washing and staining

scan_protocol: The GeneChip® Array-plates were scanned with GeneTitan® Multi-Channel (MC) Instrument

data_processing: The raw data was normalized in Expression Console provided by Affymetrix, using the robust multi-array average (RMA) method.

source_name: ARCI skin biopsy

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual ( P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA)

extract_protocol: Total RNA was isolated using TriReagent (Ambion) according to the protocol.

value: Male

tag: disease state

value: ARCI

value: Skin biopsy (mainly epidermis)


title: DNA extracted from peripheral blood from C6

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C12

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C7

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C10

description: DNA extracted from peripheral blood


title: ARCI skin biopsy P4


title: DNA extracted from peripheral blood from A2

description: DNA extracted from peripheral blood

source_name: female relative without KDM5C mutation

value: female


title: malignant nodule 105T

value: Thyroid


title: DNA extracted from peripheral blood from P2-r2

description: DNA extracted from peripheral blood

source_name: male with KDM5C mutation


title: malignant nodule 80T


title: DNA extracted from peripheral blood from C8

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C3

description: DNA extracted from peripheral blood


title: malignant nodule 102T


title: DNA extracted from peripheral blood from M

description: DNA extracted from peripheral blood

source_name: female relative with KDM5C mutation


title: DNA extracted from peripheral blood from A1

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from P3-r2

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from P1-r2

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C4

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C2

description: DNA extracted from peripheral blood


title: malignant nodule 78T


title: DNA extracted from peripheral blood from C1

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from P2-r1

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from C5

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from P3-r1

description: DNA extracted from peripheral blood


title: DNA extracted from peripheral blood from P1-r1

description: DNA extracted from peripheral blood


title: malignant nodule 75T


title: SAMPLE 7_Effector Th1 (ACC1Hi-7)

description: Effector Th1

data_processing: raw data was collected from the Fluidigm Real-Time PCR Analysis software single cell data could be furthor analized in R software with the Package SINGuLAR™ 3.0

source_name: cultured primary CD4 T cells from spleen

extract_protocol: single cells were lysed and preamplified with the kit (CellsDirect™ One-Step qRT-PCR Kit, Thermo, 11753100)

treatment_protocol: Splenic CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro.


title: malignant nodule 101T


title: malignant nodule 73T


title: DNA extracted from peripheral blood from C9

description: DNA extracted from peripheral blood


title: SAMPLE 6_Effector Th1 (ACC1Hi-6)

description: Effector Th1


title: malignant nodule 72T


title: SAMPLE 8_Effector Th1 (ACC1Hi-8)

description: Effector Th1


title: SAMPLE 5_Effector Th1 (ACC1Hi-5)

description: Effector Th1


title: malignant nodule 79T


title: SAMPLE 4_Effector Th1 (ACC1Hi-4)

description: Effector Th1


title: SAMPLE 3_Effector Th1 (ACC1Hi-3)

description: Effector Th1


title: malignant nodule 62T


title: 8_FL-14.5-Fancg-/--HSC

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

description: 8_KO E14.5 FANCG LSA #2.CEL

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MTA1.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V20 was used for annotation.

source_name: HSC LSA FL-14.5-Fancg-/-

label_protocol: 2 ng of total RNA is reverse transcribed  following the Ovation Pico System V2  (Nugen) Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MTA1.0  (Affymetrix) at 45°C for 17 hours.

extract_protocol: RNeasy Plus Micro Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: Fancg-/-

tag: developmental stage

value: fetal liver

tag: cell line

value: Sorted Hematopoietic stem cells (HSCs)


title: 7_FL-14.5-Fancg-/--HSC

description: 7_KO E14.5 FANCG LSA #1.CEL


title: SAMPLE 2_Effector Th1 (ACC1Hi-2)

description: Effector Th1

value: BALB/c

value: spleen


title: malignant nodule 61T

data_processing:
Basecalls performed using bcl2fastq2-2.18
Reads were trimmed by trim_galore (v0.3.1) with the --rrbs parameter
Reads were aligned to the hg19 genome assembly using bismark (v0.8.3) with default parameters
Methylation information was extracted using bismark_methylation_extractor with the setting -s --comprehensive --report --bedGraph --counts for single-end reads, and with the setting -p --no_overlap --comprehensive --report --bedGraph --counts for pair-end reads
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using bismark (v0.8.3)

extract_protocol:
DNA from fresh frozen samples was isolated by using the phenol/chloroform extraction approach. For DNA isolation from FFPE samples, QIAamp DNA FFPE Tissue Kit was used (Qiagen Inc., Valencia, CA)
The RRBS procedure was previously described (Hahn et. al., 2015; PMID: 25421665). DNA sequencing was performed on an HiSeq Illumina instrument and aligned to the human genome at the City of Hope Integrative Genomics Core.

tag: tissue type

value: developing cohort


title: ARCI skin biopsy P3


title: SAMPLE 1_Effector Th1 (ACC1Hi-1)

description: Effector Th1

value: CD4 T cells


title: malignant nodule 71T

tag: cohort


title: 9_FL-14.5-Fancg-/--HSC

description: 9_KO E14.5 FANCG LSA #3.CEL


title: malignant nodule 58T


title: 3_FL-14.5-WT-HSC

description: 3_WT E14.5 FANCG LSA #3.CEL

source_name: HSC LSA FL-14.5-WT

value: WT


title: malignant nodule 66T


title: 1_FL-14.5-WT-HSC

description: 1_WT E14.5 FANCG LSA #1.CEL


title: ARCI skin biopsy P1


title: ANT rep3

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
BGISEQ-500 platform
SOAPnuke, Version: v1.5.2, Parameter: -l 15 -q 0.2 -n 0.05, Webstite: https://github.com/BGI-flexlab/SOAPnuke
Bowtie2, Version: v2.2.5, Parameter: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, Website: http://bowtie-bio.sourceforge.net/Bowtie2/index.shtml
HISAT2, Version: v2.0.4, Parameter: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000, Website: http://www.ccb.jhu.edu/software/hisat
Genome_build: hg18
Supplementary_files_format_and_content: FPKM

source_name: NCCIT tumor cell line

growth_protocol: The human pluripotent embryonic carcinoma cell line NCCIT was purchased from ATCC (CRL-2073). NCCIT cells were cultured in RPMI 1640 (Invitrogen, Beijing, China) containing 10% fetal bovine serum (Invitrogen), 1% penicillin/stretomycin (Invitrogen) at 37oC with 5% CO2.

extract_protocol:
Total RNA (including microRNAs) was extracted using miRcute miRNA Isolation Kit (Tiangen, Beijing, China).
Performed by BGI (Shenzhen, China)
RNA-Seq, 20M clean reads

treatment_protocol: NCCIT cells were transfected with the miR-125b antagomir (50 nM) or miR-125b agomir (25 nM) or non-targeting control (NC) oligonucleotides (25 nM) using EntransterTM-R4000 transfection reagent (Engreen, Beijing, China).

value: TGCT cell line

value: Testis-derived

tag: passage


title: Control skin biopsy 4

source_name: Control skin biopsy

tag: age

value: control


title: Control skin biopsy 3

value: Female


title: Control skin biopsy 2

value: Male


title: malignant nodule 64T

source_name: Thyroid

value: malignant nodule


title: malignant nodule 63T


title: ARCI skin biopsy P2

value: ARCI

value: Skin biopsy (mainly epidermis)


title: malignant nodule 11T

value: Thyroid


title: Control skin biopsy 1


title: malignant nodule 60T


title: malignant nodule 56T


title: ANT rep1


title: ANT rep2


title: 21_FL-12.5-Fancg-/--HSC

description: 21-ko FL 34 KLSA.CEL

source_name: HSC LSA FL-12.5-Fancg-/-

value: Fancg-/-


title: 20_FL-12.5-Fancg-/--HSC

description: 20-ko FL 34 KLSA.CEL

value: fetal liver


title: 14_FL-12.5-WT-HSC

description: 14-wt FL 34K LSA.CEL

source_name: HSC LSA FL-12.5-WT

value: Sorted Hematopoietic stem cells (HSCs)


title: 2_FL-14.5-WT-HSC

description: 2_WT E14.5 FANCG LSA #2.CEL


title: 19_FL-12.5-Fancg-/--HSC

description: 19-ko FL 34 KLSA.CEL


title: AGO rep3


title: NC rep3


title: H37Rv_INH-2

city: Newark

first: Pradeep

last: Kumar

address: 185 So Orange Avenue, MSB/A920A

department: Medicine

institute: Rutgers-New Jersey Medical SChool

description: mRNA

data_processing:
CLC Genomics Workbench 9.0.1 version (http:// www.clcbio.com/products/clc-genomics-workbench/; Qiagen) was utilized for RNA-seq analysis.
De-multiplexed fastq files from RNA-Seq libraries were imported into the CLC software. Bases with low quality were trimmed and reads were mapped to the reference genome, Mycobacterium tuberculosis H37Rv (NCBI Reference Sequence: NC_000962.3). The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench.
RPKM values were calculated for each gene to quantify absolute expression. Statistical analysis of differentially expressed genes was carried out with the Empirical analysis of Digital Gene Expression data tool in CLC Genomic Workbench. Replicates were averaged, and genes with FDR adjusted p value <0.05 and fold change was calculated.

organism: Mycobacterium tuberculosis H37Rv

source_name: Whole cell

growth_protocol: M. tuberculosis H37Rv was grown to OD595 to ~0.4 in 7H9-Glycerol-Tween-OADC media in tissue culture flasks (50 mL each) and pooled.

extract_protocol:
The cultures were harvested by centrifugation and total RNA was extracted using TRIzol® LS reagent (ThermoFisher Scientific) and bead beating followed by extraction with the RNeasy® Mini Kit (Qiagen).
rRNA was removed, and the cDNA library was prepared using illumina library prep kit.
The sequencing of the cDNA libraries was performed on the Illumina NextSeq 500 platform (Illumina, San Diego, CA) using the high output 1X75 cycles configuration.

treatment_protocol: The cultures (10 mL) were redistributed into flasks containing each compound (10x MIC) or compound combination or vehicle (DMSO) control. The final concentration of DMSO was kept constant in each flask. After 4 h incubation at 37 °C with shaking.

tag: start od595

tag: growth phase

value: log

value: Whole cell


title: H37Rv_INH-3

description: mRNA


title: H37Rv_DG167+INH-3

description: mRNA


title: RNA from RPTEC cells treated with aMD5-BMH 2

city: Kanazawa

first: Kunio

last: Matsumoto

address: Kakuma

institute: Kanaawa University

description: Gene expression in RPTEC cells treated with aMD5-BMH

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Processed Signal intensity. Normalization was performed by GeneSpring GX ver.12.5 as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array; 4, per-gene normalization, in which the data were normalized to control (mock; cells treated with vehicle) samples.

source_name: RPTEC cells treated with aMD5-BMH, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RPTEC cells was cultured in Cellmatrix type I-A collagen at 3D condition with Renal Epithelial Cell Basal Medium supplemented with 0.5% FBS, 10 nM triiodothyronine, 10 ng/ml recombinant human EGF, 100 ng/ml hydrocortisone hemisuccinate, 5 μg/ml recombinant human insulin, 1 μM epinephrine, 5 μg/ml transferrin and 2.4 mM L-alanyl-L-glutamine on the uplayer.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared using Sepazol reagent (Nakarai Tesque).

treatment_protocol: RPTEC cells were treated with/without 1.2nM HGF, 120nM aMD5-PEG11 and 120nM aMD5-BMH for 8 hr.

value: Primary Renal Proximal Tubule Epithelial Cells

tag: treatment


title: H37Rv_DG167+INH-2

description: mRNA


title: 15_FL-12.5-WT-HSC

description: 15-wt FL 34K LSA.CEL

tag: strain background


title: 13_FL-12.5-WT-HSC

description: 13-wt FL 34K LSA_2.CEL


title: NC rep1


title: AGO rep2


title: H37Rv_DG167+INH-1

description: mRNA


title: RNA from RPTEC cells treated with aMD5-PEG11 2

description: Gene expression in RPTEC cells treated with aMD5-PEG11

source_name: RPTEC cells treated with aMD5-PEG11, replicate 2


title: AGO rep1


title: H37Rv_INH-1

description: mRNA


title: NC rep2


title: H37Rv_DG167-3

description: mRNA


title: RNA from RPTEC cells treated with HGF 2

description: Gene expression in RPTEC cells treated with HGF

source_name: RPTEC cells treated with HGF, replicate 2

value: HGF


title: H37Rv_DG167-2

description: mRNA


title: H37Rv_DG167-1

description: mRNA


title: H37Rv_DMSO-2

description: mRNA


title: H37Rv_DMSO-3

description: mRNA


title: NET_H2O_r2_2

description:
anti-pol II mNET-seq
NET_H2O_r2.F.bw
NET_H2O_r2.R.bw

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7. Custom software was used to remove duplicates from NET-seq libraries: https://github.com/sheridar/TFIISdn_paper.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: BigWig

source_name: HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN

extract_protocol:
Pol II-associated nascent RNA was isolated by IP
10-20ng of RNA was used with the Lexogen small RNA-seq kit (#052)

treatment_protocol: Uninduced control cells

tag: growth conditions

value: DMEM 10% FCS, +hygromycin, +blasticidin

tag: antibody

value: Mouse 8WG16 anti-pol II (Thompson et al, 1990)

tag: molecule

value: Nascent RNA


title: NET_H2O_r1_3

description:
anti-pol II mNET-seq
NET_H2O_r1.F.bw
NET_H2O_r1.R.bw


title: The crz1/crz1 mutant with 0.2M CaCl2 treatment

city: Zibo

first: Linghuo

last: Jiang

address: 266 West Road Xincun

institute: Shandong University of Technology

data_processing:
Clean reads from RNA-Seq data were assembled into full-length transcriptome with the reference genome (http://www.candidagenome.org/).
Gene expression levels were measured as numbers of reads, and normalized with TPF.
Genome_build: http://www.candidagenome.org/
Supplementary_files_format_and_content: SuppInfo 1.xlsx: TPM values for each sample
SuppInfo 2.xlsx: List of 219 genes whose expression is positively regulated by CaCrz1#
SuppInfo 3.xlsx: List of 59 genes whose expression is negatively regulated by CaCrz1

organism: Candida albicans

source_name: Log-phase cells in YPD medium containing 0.2M CaCl2 at 30oC.

growth_protocol: Two strains were grown to log phase in YPD medium at 30oC.

extract_protocol:
Total RNA samples were extracted using the Qiagen RNeasy minikit (USA) according to the manufacturer’s instructions. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA sequencing, data analysis and sequence assembly were performed by the Quebec Genome Innovation Center at McGill University (Montreal, Canada). Preparation of the paired-end libraries and sequencing were performed following standard Illumina methods and protocols. The mRNA-seq library was sequenced using an Illumina miSEQ sequencing platform.

treatment_protocol: With or without 0.2M CaCl2 treatment

tag: genotype

value: SN148 crz1/crz1


title: The wild type SN148 with 0.2M CaCl2 treatment

value: SN148  wildtype


title: H37Rv_DMSO-1

description: mRNA

tag: strain

tag: tissue


title: RNA from RPTEC cells treated with vehicle 2

description: Gene expression in RPTEC cells treated with vehicle

source_name: RPTEC cells treated with vehicle, replicate 2

value: mock


title: RNA from RPTEC cells treated with HGF 1

source_name: RPTEC cells treated with HGF, replicate 1


title: RNA from RPTEC cells treated with aMD5-PEG11 1

source_name: RPTEC cells treated with aMD5-PEG11, replicate 1


title: NET_H2O_r2_3


title: The crz1/crz1 mutant

source_name: Log-phase cells in YPD medium at 30oC.


title: RNA from RPTEC cells treated with aMD5-BMH 1

source_name: RPTEC cells treated with aMD5-BMH, replicate 1


title: NET_Dox_r1_3

description:
anti-pol II mNET-seq
NET_Dox_r1.F.bw
NET_Dox_r1.R.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline


title: NET_H2O_r1_4


title: older cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: NHDF at passage 23 as older cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given gene was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: NHDF

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: FBM Fibroblast Basal Medium with FGM-2 growth factors

extract_protocol: Standard Trizol Reagent for the RNA extraction.

treatment_protocol: Passages were done every three days

tag: cell type

value: Normal fibroblast


title: The wild type SN148

value: SN148 wildtype


title: NET_Dox_r2_3

city: Aurora

first: Ryan

last: Sheridan

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
anti-pol II mNET-seq
NET_Dox_r2.F.bw
NET_Dox_r2.R.bw


title: younger cells

description: NHDF at passage 5 as younger cells


title: NET_Dox_r1_4


title: NET_Dox_r2_2


title: TFIISwt_Dox_polII

description:
Chromatin IP of RNA pol II
TFIISwt_Dox_polII.bw

source_name: HMLE RAS pCW57bla Avitag TFIISWT

growth_protocol: DMEM/F-12(50/50), +10 ng/ml hEGF, +0.5 ug/ml hydrocortisone, +10 ug/ml insulin, +8 ug/ml blasticidin, +0.5 ug/ml puromycin

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: TFIISwt expression was induced with 2ug/ml doxycycline for 24 hrs

value: DMEM/F-12(50/50), +hEGF, +hydrocortisone, +insulin, +blasticidin

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: Genomic DNA


title: Phagocytes + Apoptotic Cells 2

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

description:
Apoptotic Cells from human (Jurkat Lymphoma)
LR73_AC_results.xls

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GCF_000223135.1_CriGri_1.0_genomic
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

organism: Cricetulus griseus

source_name: Fibroblast

growth_protocol: alpha-MEM + 10% FBS + 1% PSQ

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform

treatment_protocol: Jurkat lymphoma cells were UV C treated at 1500mJ then cultured for 4h prior to co-culture with phagocytes

tag: condition

value: in vitro cultured

value: LR73 co-cultured with apoptotic Jurkat lymphoma cells


title: Phagocytes + Apoptotic Cells 4


title: Phagocytes + Apoptotic Cells 3


title: TFIISwt_Dox_input

description:
Input
TFIISwt_Dox_input.bw

value: Input


title: Phagocytes + Apoptotic Cells 1


title: Phagocytes alone 1


title: Phagocytes alone 3


title: TFIISdn_Dox_avi

description:
Chromatin IP of avi-tagged TFIISDN
TFIISdn_Dox_avi.bw

source_name: HMLE RAS pCW57bla Avitag TFIISDN

value: Rabbit anti-avi-tag (GenScript A00674)


title: HSC3-shScr

address: 10-1 tebiro 6-chome

description: human  tongue cancer cell line with GFP transfection

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: human  tongue cancer cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented by 10% FBS. For HSC-3 shScr and HSC-3 shDKK3, 10µg/µl of puromycin was supplemented.

extract_protocol: RNA samples were extracted by Nucleospin RNA (Macherey-Nagel).

treatment_protocol: DKK3-Human shRNA constructs in  Lentiviral GFP Vector or non-effective shRNA cassette  in pGFP-C-shLenti Vector were transfected to HEK293 cell. Then, mediiu containing virus was collected and added to HSC-3 cells.

tag: cell line

tag: shRNA

value: scramble


title: HSC3 parental cell

description: human  tongue cancer cell line


title: HSC3-shDKK3

description: human  tongue cancer cell line with DKK3 transfection


title: RNA from RPTEC cells treated with vehicle 1

source_name: RPTEC cells treated with vehicle, replicate 1

value: Primary Renal Proximal Tubule Epithelial Cells


title: TFIISwt_Dox_avi

description:
Chromatin IP of avi-tagged TFIISWT
TFIISwt_Dox_avi.bw


title: TFIISdn_Dox_polII

description:
Chromatin IP of RNA pol II
TFIISdn_Dox_polII.bw


title: HuFL HSC control1

description: fetal liver 13WG

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® HumanGene2.0ST (Affymetrix) at 45°C for 17 hours

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V21 was used for annotation.

source_name: HSC CD117hi FL CT 13WG

label_protocol: 2 ng of total RNA is reverse transcribed  following the Ovation Pico System V2  (Nugen) Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

tag: sample group

value: control

value: fetal liver

value: Sorted Hematopoietic stem cells (HSCs)


title: Phagocytes alone 2


title: TFIISdn_Dox_input

description:
Input
TFIISdn_Dox_input.bw


title: Phagocytes alone 4


title: malignant nodule 69T

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

institute: Beckman Research Institute

source_name: Thyroid

value: Thyroid

tag: tissue type

value: malignant nodule

tag: cohort

value: developing cohort


title: HuFL HSC control2

description: fetal liver 17.7WG

source_name: HSC CD117hi FL CT 17.7WG


title: HeLa_spermine_3mM_day1

status: Public on Nov 29 2018

source_name: HeLa, spermine 3mM, day3

growth_protocol: HeLa cells were incubated in DMEM which contains 10% dialized FBS and penicillin/ streptomycin.

extract_protocol: ISOGEN was used for extracting total RNA

treatment_protocol: HeLa cells were exposed to 0mM, 3mM and 5mM spermine. Cell collection was performed at 24 hours.

value: HeLa

tag: treated with

value: Spermine 3mM

tag: time point

value: 24 hrs


title: HuFL HSC FA

description: fetal liver 13WG

source_name: HSC CD117hi FL FA 13WG

value: Fanconi anemia


title: HeLa_spermine_0mM_day1

source_name: HeLa, control, day3

value: Spermine 0mM


title: HeLa_putrescine_5mM_day3

description: HeLa P5d3

source_name: HeLa, putrescine 5mM, day3

treatment_protocol: HeLa cells were exposed to 0mM, 3mM and 5mM putrescine. Cell collection was performed at 24 hours and 72 hours.

value: Purtersine 5mM

value: 72 hrs


title: CD8T.5

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
Haemopedia-Human-RNASeq_raw.txt
Haemopedia-Human-RNASeq_rpkm.txt

data_processing:
Sequence reads were alligned using the R Subread aligner
Genewise counts were obtained using FeatureCounts
Counts were converted to counts per million mapped reads per kilobase of transcript
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: raw_counts file is the counts as given by FeatureCounts
Supplementary_files_format_and_content: norm_Log2RPKM files give the normalized Log2 reads per kilobase of transcript, per million mapped reads

source_name: CD8:+ T Cell

extract_protocol:
Buffy pack from adult donors
PBMCs were isolated with Ficoll Density Gradient
RNA was isolated from two biological repliates (RNAeasy plus micro kit, QIagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8:+ T Cell

tag: cell lineage

value: T Cell Lineage

tag: antibodies

value: Peripheral Blood


title: HeLa_putrescine_5mM_day1

description: HeLa P5d1

source_name: HeLa, putrescine 5mM, day1


title: pDC.2

source_name: Plasmacytoid DC

value: Plasmacytoid DC

value: Dendritic Cell Lineage

value: CD14:- BDCA1:- BDCA2:+ CD123:Hi


title: myDC.3

source_name: Myeloid DC

value: Myeloid DC


title: HeLa_putrescine_0mM_day3

description: HeLa P0d3

value: Purtersine 0mM


title: HeLa_spermine_5mM_day1

source_name: HeLa, spermine 5mM, day3

value: Spermine 5mM


title: HeLa_putrescine_3mM_day3

description: HeLa P3d3

source_name: HeLa, putrescine 3mM, day3

value: Purtersine 3mM


title: CD4T.5

source_name: CD4:+ T Cell

value: CD4:+ T Cell


title: NK.5

source_name: NK Cell

value: NK Cell

value: NK Cell Lineage