title: PEGcaucasian: genomic DNA from whole blood of subject Sample218

description: genomic DNA from Blood

tag: Sex

tag: levodopaperdayincludingagonists


title: ChIP experiment with H3K9me3 antibody of HTT shRNA H9 hESCs (replicate 1)

status: Public on Sep 04 2018

type: SRA

city: Cologne

first: David

last: Vilchez

state: NRW

address: Joseph Stelzmann Strasse, 26

country: Germany

institute: CECAD - Cluster of Excellence

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
ChIP-seq reads were aligned to the  homo sapiens
peaks were called using macs version 2
Genome_build: homo_sapiens – Ensembl build 87 (hg38)

molecule: genomic DNA

organism: Homo sapiens

source_name: H9 hESCs (WA09)

growth_protocol: hESCs were grown on Geltrex (ThermoFisher Scientific) using mTeSR1 media (Stem Cell Technologies) after passaged using a solution of dispase (2 mg ml-1), and scraping the colonies with a glass pipette.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinked cells were quenched with 0,125M glycine for 10 min at room temperature and then scraped and transferred to a 15 ml conical tube on ice. Cells were centrifuged for 5 min at 4°C followed by two washing steps with 5 ml PBS 1x/ PMSF 1 mM. Cells were then resuspended sequentially in three different lysis buffers (lysis buffer 1: 50 mM Hepes, 140 mM NaCL, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 and protease inhibitor (Roche); lysis buffer 2: 10 mM Tris, 200 mM NaCL, 1 mM EDTA, 0.5 mM EGTA; lysis buffer 3: 10 mM Tris, 100 mM NaCL, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine). Chromatin was then sonicated for 20 cycles (30 s on, 45 s off) using Bioruptor (Diagenode). After sonication, the material was centrifuged at 16000g during 3 min at 4°C, with the supernatant representing the sonicated chromatin. 75 μl was not subject to immunoprecipitation, thus representing total input control for the ChIP reactions. 750 μl were incubated with 10 μg of anti-H3K9me3 antibody (Abcam, #8898, reported suitable for ChIP) overnight at 4°C. On day 2, magnetic Dynabeads G (Thermofisher) at 10x volume of H3K9me3 antibody were aliquoted into a new microtube. Magnetic beads were washed five times with cold RIPA wash buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Next, beads were washed once with 1 ml TE + 50 mM NaCl on ice and sample was centrifuged at 950g for 3 min at 4°C. After removing all liquid from beads, elution buffer (50 mM Tris, 10 mM EDTA, 1% SDS) was added for 15 min at 65°C. Finally, beads were centrifuged for 1 min at 1600g and placed on magnetholder to settle and the supernatant was transferred into a new tube. To reverse crosslinking, 3x volume of the elution buffer was added to the input and left to incubate together with the ChIP sample at 65°C overnight. On day 3, 1x volume of TE buffer and 0.2 mg ml-1 RNase were added and incubated for 1 h at 37°C. Afterwards, 0.2 mg ml-1 Proteinase K was added and incubated for 2 h at 55°C to digest proteins. Next, DNA was phenol-chloroform extracted at room temperature with 1x volume of 25:24:1 phenol-chloroform-isoamyl alcohol and centrifuged for 5 min to separate layers, followed by the addition of 1x volume chloroform. The DNA was then transferred to a new tube for precipitation with 1/10 of NaOAc 3 M, 1 μl 20 mg ml-1 glycogen, 2x volume of ice cold ethanol during 30 min at -80°C. After a centrifugation during 30 min at 4°C, the supernatant was removed and we added 0.5 ml ice cold 70% ethanol followed by 5 min centrifugation. After removing the ethanol, the pellet was air-dried at room temperature and resuspended in 40 μl dH2O.
Illumina ChIP Seq library Protocol

treatment_protocol: To obtain shRNA stable lines, hESC colonies growing on Geltrex were incubated with mTesR1 medium containing 10 μM ROCK inhibitor for 1 h and individualized using Accutase. Fifty thousand cells were infected with 20 µl of concentrated lentivirus in the presence of 10 μM ROCK inhibitor for 1 h. Cell suspension was centrifuged to remove virus, passed through a mesh of 40 μM to obtain individual cells, and plated back on a feeder layer of mitotically inactive mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% knockout serum replacement (ThermoFisher Scientific), 0.1 mM non-essential amino acids, 1 mM L-glutamine, β-mercaptoethanol and 10 ng ml−1 bFGF (Joint Protein Central) supplemented with 10 μM ROCK inhibitor. After several days in culture, small hESC colonies arose. Then, we performed 1 µg ml−1 puromycin selection during 2 days and colonies were manually passaged onto fresh MEFs to establish new hESC stable lines.

tag: antibody

value: H3K9me3 antibody (Abcam, #8898)

tag: expression

value: HTT shRNA


title: Input HTT shRNA H9 hESCs (replicate 1)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample217

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA from Blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values

label: Cy3 and Cy5

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from EDTA tubes using the RecoverEase DNA Isolation Kit.

value: male

tag: age

tag: ethnicity

value: Caucasian

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

value: PD

tag: levodopastatus

value: yes

tag: numberofyearsinschool

tag: smokingstatus

value: former

tag: packyearstotal

tag: familyhistoryofparkinsons


title: ChIP experiment with H3K9me3 antibody of HTT shRNA H9 hESCs (replicate 2)


title: Input HTT shRNA H9 hESCs (replicate 2)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample216

description: genomic DNA from Blood

tag: Sex

value: no

tag: levodopaperdayincludingagonists


title: PEGcaucasian: genomic DNA from whole blood of subject Sample215

description: genomic DNA from Blood

value: control


title: PEGcaucasian: genomic DNA from whole blood of subject Sample228

description: genomic DNA from Blood

value: never


title: PEGcaucasian: genomic DNA from whole blood of subject Sample226

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample214

description: genomic DNA from Blood

value: female


title: RNA seq of ATF7IP shRNA   NPC from H9 hESCs replicate #3

description:
NPCs from H9 hESCs expressing HTT shRNA to silence the expression of HTT
FPKM_dvilchez1.csv

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling
Sequenced reads mapped to
Fragment Per Kilobase of exon per Million (RPKM) were calculated using a Cufflinks
Genome_build: homo_sapiens (ensembl 87)
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample

molecule: polyA RNA

source_name: NPCs dervided from H9 hESCs

growth_protocol: iPSCs and hESCs were grown on Geltrex (ThermoFisher Scientific) using mTeSR1 media (Stem Cell Technologies) after passaged using a solution of dispase (2 mg ml-1), and scraping the colonies. We induced neural differentiation of hESCs/iPSCs with STEMdiff Neural Induction Medium (Stem Cell Technologies) following the monolayer culture method as previously described (97). Undifferentiated cells were rinsed once with PBS and then we added 1 ml of Gentle Dissociation Reagent (Stem Cell Technologies) for 10 min. After the incubation period, we gently dislodged hESCs/iPSCs and add 2 ml of Dulbecco’s Modified Eagle Medium (DMEM)-F12 (ThermoFisher Scientific) + 10 μM ROCK inhibitor (Abcam). Then, we centrifuged cells at 300g for 10 min. hESCs/iPSCs were resuspended on STEMdiff Neural Induction Medium + 10 μM ROCK inhibitor and plated on polyornithine (15 μg ml−1)/laminin (10 μg ml−1)-coated plates at a density of 200,000 cells cm−2 with a glass pipette.

extract_protocol:
Total RNA was extracted using RNAbee (Tel-Test Inc.).
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit. Library preparation started with 1 µg total RNA. After selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (20 µl template, 14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent 2100 Bioanalyzer), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina HiSeq 4000 sequencer with a paired- end (2 × 75bp) protocol.

treatment_protocol: To obtain shRNA stable lines, iPSCs/hESC colonies growing on Geltrex were incubated with mTesR1 medium containing 10 μM ROCK inhibitor for 1 h and individualized using Accutase. Fifty thousand cells were infected with 20 µl of concentrated lentivirus in the presence of 10 μM ROCK inhibitor for 1 h. Cell suspension was centrifuged to remove virus, passed through a mesh of 40 μM to obtain individual cells, and plated back on a feeder layer of mitotically inactive mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% knockout serum replacement (ThermoFisher Scientific), 0.1 mM non-essential amino acids, 1 mM L-glutamine, β-mercaptoethanol and 10 ng ml−1 bFGF (Joint Protein Central) supplemented with 10 μM ROCK inhibitor. After several days in culture, small hESC colonies arose. Then, we performed 1 µg ml−1 puromycin selection during 2 days and colonies were manually passaged onto fresh MEFs to establish new hESC stable lines.

tag: expression


title: PEGcaucasian: genomic DNA from whole blood of subject Sample212

description: genomic DNA from Blood

tag: age


title: pcr_wafergen_expt_original

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
Original single cell RNA seq library from the Wafergen iCell 8 platform. Human Breast Cancer xenograft into mice, cells isolated from a primary fatpad tumor, a brain metastasis, a bone metastasis, or the original primary cell line.
pcr_wafergen_expt_bcs.txt

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/rnabioco/scrna-subsets). Single cell RNA-Seq libraries were preprocessed to append the read 1 sequence to the paired read 2 read id (append_read_name) followed by quality trimming and poly(A) tail removal from read 2 using cutadapt (v. 1.8.3 -a 'A{{100}}' -O 6 -m 20 -q 10) (Martin 2011). Reads were next aligned with STAR (Dobin et al. 2013) to either the human genome assembly (hg38) for the PBMC experiments or a genome with both human (hg38) and mouse (mm38) sequences for all other experiments. Sequence headers in the human/mouse combined genome were prefixed with either an “H_” or “M_” to designate human or mouse references respectively.  Following alignment, BAM files were processed to extract the cell barcode and UMI sequences into tags (CN and BX) within the BAM file (barcode_tag_bam). The cell barcode was error corrected against a list of cell barcodes, either as known well barcodes (Wafergen experiments), or generated from the original 10x genomics single cell libraries processed with the 10x genomics software cellranger (v. 2.1.1). Cell barcodes within edit distance of 1 of the known barcodes were considered valid cell barcodes and corrected to the known barcode. Alignments not designated as multi-mapping that overlapped distinct exonic features were tagged in the BAM file (subread v. 1.6.0) (Liao et al. 2014). Gencode v25 annotations was used for human data, and a union reference containing Gencode v25 and mouse v11 was used for human/mouse datasets. UMIs per gene were enumerated per cell using umi-tools (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.
Genome_build: mm38, hg38
Supplementary_files_format_and_content: Text files containing cell barcode sequences, count matrices of UMIs per gene per cell are provided. For the TCR single cell libraries JSON files are provided with detailed annotations for each assembled contig per cell.

molecule: total RNA

source_name: Human Breast Cancer Xenograft

extract_protocol:
Tumor cells were purified and resuspended in a single cell suspension. Single cells were captured on the iCell8 wafergen platform. Live cells were selected after capture and further processed for single cell RNA-Seq.
Libraries were constructed using Wafergen Biosystems 3'end based RNA-Seq chemistry. Read 1 positions 1-11 contain the 11bp cell barcode, and positions 12-22 contain a 10bp UMI. Read 2 contains the cDNA.

tag: sample type

value: Human Breast Cancer Xenograft


title: PEGcaucasian: genomic DNA from whole blood of subject Sample213

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage


title: RNA seq of  NT  NPC from H9 hESCs replicate #3

description:
NPCs from H9 hESCs expressing NT shRNA as a control to compare with HTT shRNA-treated cells
FPKM_dvilchez1.csv


title: RNA seq of  NT  NPC from H9 hESCs replicate #2

value: NT shRNA as a control to compare with HTT shRNA-treated cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample222

description: genomic DNA from Blood

tag: plasmablast

tag: nk


title: RNA seq ATF7IP H9 hESCs replicate #2

description:
H9 hESCs expressing ATF7IP shRNA
FPKM_dvilchez1.csv

source_name: H9 hESCs

value: ATF7IP shRNA


title: PEGcaucasian: genomic DNA from whole blood of subject Sample211

description: genomic DNA from Blood

tag: bcell

tag: mono


title: RNA seq of  NT  NPC from H9 hESCs replicate #1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample210

description: genomic DNA from Blood

tag: gran

tag: diseasestatus


title: RNA seq of ATF7IP shRNA  NPC from H9 hESCs replicate #1

value: HTT shRNA to silence the expression of HTT


title: PEGcaucasian: genomic DNA from whole blood of subject Sample209

description: genomic DNA from Blood

tag: levodopastatus

tag: numberofyearsinschool


title: RNA seq of contrATF7IP shRNA   NPC from H9 hESCs replicate #2


title: PEGcaucasian: genomic DNA from whole blood of subject Sample208

description: genomic DNA from Blood

tag: smokingstatus

tag: packyearstotal


title: Input NT shRNA H9 hESCs (replicate 2)

tag: antibody

value: non-targeting (NT) shRNA


title: ChIP experiment with H3K9me3 antibody of NT shRNA H9 hESCs (replicate 2)


title: RNA seq ATF7IP H9 hESCs replicate #1


title: RNA seq NT H9 hESCs replicate #2

description:
H9 hESCs expressing NT shRNA as a control to compare with ATF7IP shRNA-treated cells
FPKM_dvilchez1.csv


title: RNA seq NT H9 hESCs replicate #1

value: NT shRNA as a control to compare with ATF7IP shRNA-treated cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample207

description: genomic DNA from Blood

tag: Sex

tag: levodopaperdayincludingagonists

tag: familyhistoryofparkinsons


title: RNA seq of HD ATF7IP shRNA  iNPC from  PSCs (Q180) replicate #3

description:
NPCs from HD (Q180) iPSCs expressing ATF7IP shRNA
FPKM_dvilchez1.csv

source_name: NPCs derived from Q180 iPSCs

tag: expression


title: RNA seq of HD ATF7IP shRNA NPC from iPSCs (Q180) replicate #1


title: RNA seq of HD ATF7IP shRNA  NPC from iPSCs (Q180) replicate #2


title: PEGcaucasian: genomic DNA from whole blood of subject Sample203

description: genomic DNA from Blood

tag: age

tag: ethnicity


title: PEGcaucasian: genomic DNA from whole blood of subject Sample204

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast


title: PEGcaucasian: genomic DNA from whole blood of subject Sample202

description: genomic DNA from Blood

tag: nk

tag: bcell


title: RNA seq of HD NT NPC from iPSCs (Q180) replicate #3

description:
NPCs from HD (Q180) iPSCs expressing NT shRNA as a control to compare with shRNA-treated cells
FPKM_dvilchez1.csv


title: PEGcaucasian: genomic DNA from whole blood of subject Sample201

description: genomic DNA from Blood

tag: mono

tag: gran


title: RNA seq of HD NT NPC from iPSCs (Q180) replicate #1

value: NT shRNA as a control to compare with shRNA-treated cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample200

description: genomic DNA from Blood

tag: diseasestatus

tag: levodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample199

description: genomic DNA from Blood

tag: numberofyearsinschool

tag: smokingstatus


title: RNA seq of HD NT NPC from iPSCs (Q180) replicate #2


title: PEGcaucasian: genomic DNA from whole blood of subject Sample198

description: genomic DNA from Blood

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample197

description: genomic DNA from Blood

tag: Sex


title: PEGcaucasian: genomic DNA from whole blood of subject Sample196

description: genomic DNA from Blood

tag: levodopaperdayincludingagonists


title: RNA seq of control NT  NPC from iPSCs (Q33) replicate #1

description:
NPCs from Control (Q33) iPSCs expressing NT shRNA as a control to compare with shRNA-treated cells
FPKM_dvilchez1.csv

source_name: NPCs derived from Q33 iPSCs


title: PEGcaucasian: genomic DNA from whole blood of subject Sample206

description: genomic DNA from Blood

tag: familyhistoryofparkinsons


title: RNA seq of control NT NPC from iPSCs (Q33) replicate #3

tag: expression


title: PEGcaucasian: genomic DNA from whole blood of subject Sample195

description: genomic DNA from Blood

tag: age


title: PEGcaucasian: genomic DNA from whole blood of subject Sample193

description: genomic DNA from Blood

tag: ethnicity


title: PEGcaucasian: genomic DNA from whole blood of subject Sample205

description: genomic DNA from Blood

tag: dnamage


title: PEGcaucasian: genomic DNA from whole blood of subject Sample194

description: genomic DNA from Blood

tag: plasmablast


title: PEGcaucasian: genomic DNA from whole blood of subject Sample192

description: genomic DNA from Blood

tag: nk


title: PEGcaucasian: genomic DNA from whole blood of subject Sample191

description: genomic DNA from Blood

tag: bcell


title: thymus_non-puberty_NF3_miRNA

type: RNA

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: microRNA expression from thymus explant

hyb_protocol: Dried Cy3-labelled miRNA sample was resuspended with 17uL of nuclease-free water and mixed to Hyb Spike-In and 10x GE Blocking Agent solutions, and 2x Hi-RPM Hybridization buffer. The final volume was incubated at 100°C for 5 minutes and hybridized to Human miRNA Microarray slides (8x60K) -  (G4872A) - Agilent Technologies, for 20 hours at 55°C in a rotating Agilent hybridization oven (20rpm).

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 8x60k miRNA microarrray slides.

data_processing: Data extraction was carried out with Feature Extraction Software 10.7.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected miRNA transcripts were used for analysis using the R software and considering up to 3 NA for each group (MM or MF) and the expression values in Log (base 2). NA converted to null in data table.  Data for identical probe names were averaged. Data not normalized.

source_name: thymus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the microRNA Complete Labeling and Hyb Kit (Agilent Technologies), without column purification, according to the manufacturer's instructions.

extract_protocol: Thymus explants (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: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

tag: tissue

value: thymus

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample190

description: genomic DNA from Blood

tag: mono

tag: gran

tag: diseasestatus

tag: levodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample188

description: genomic DNA from Blood

tag: Sex

tag: numberofyearsinschool

tag: smokingstatus

tag: packyearstotal


title: thymus_non-puberty_NF5_miRNA

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample186

description: genomic DNA from Blood

tag: age

tag: levodopaperdayincludingagonists

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample187

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

tag: plasmablast


title: RNA seq of control NT NPC from iPSCs  (Q33) replicate #2

tag: expression


title: PEGcaucasian: genomic DNA from whole blood of subject Sample189

description: genomic DNA from Blood

value: male

tag: nk

tag: bcell


title: PEGcaucasian: genomic DNA from whole blood of subject Sample184

description: genomic DNA from Blood

value: Caucasian

tag: mono


title: PEGcaucasian: genomic DNA from whole blood of subject Sample183

description: genomic DNA from Blood

tag: gran

value: PD


title: PEGcaucasian: genomic DNA from whole blood of subject Sample182

description: genomic DNA from Blood

tag: diseasestatus

value: current


title: thymus_non-puberty_NF6_miRNA

description: microRNA expression from thymus explant

tag: tissue

tag: gender

tag: age at surgery (yr/mo/d)


title: thymus_non-puberty_NF1_miRNA

description: microRNA expression from thymus explant


title: thymus_non-puberty_NF4_miRNA

description: microRNA expression from thymus explant


title: thymus_non-puberty_NM3_miRNA

description: microRNA expression from thymus explant


title: thymus_non-puberty_NM2_miRNA

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample181

description: genomic DNA from Blood

tag: Sex

tag: levodopastatus

value: yes

tag: numberofyearsinschool

tag: smokingstatus

value: former


title: thymus_minipuberty_MF4

description: microRNA expression from thymus explant

data_processing: Data extraction was carried out with Feature Extraction Software 10.7.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected miRNA transcripts were used for analysis using the R software and considering up to 3 NA for each group (MM or MF) and the expression values in Log (base 2). Data not normalized.


title: thymus_non-puberty_NM1_miRNA

description: microRNA expression from thymus explant


title: thymus_non-puberty_NM5_miRNA

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample180

description: genomic DNA from Blood

tag: age

value: control

value: no

tag: levodopaperdayincludingagonists

tag: packyearstotal

tag: familyhistoryofparkinsons


title: thymus_minipuberty_MF5

description: microRNA expression from thymus explant

value: female


title: thymus_minipuberty_MF3

description: microRNA expression from thymus explant


title: thymus_non-puberty_NM6_miRNA

description: microRNA expression from thymus explant


title: thymus_non-puberty_NF2_miRNA

description: microRNA expression from thymus explant


title: thymus_minipuberty_MF2

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample179

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

tag: plasmablast


title: PEGcaucasian: genomic DNA from whole blood of subject Sample177

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono


title: PEGcaucasian: genomic DNA from whole blood of subject Sample178

description: genomic DNA from Blood

tag: gran

tag: diseasestatus

value: never


title: PEGcaucasian: genomic DNA from whole blood of subject Sample176

description: genomic DNA from Blood


title: thymus_minipuberty_MF1

description: microRNA expression from thymus explant

tag: tissue

tag: gender

tag: age at surgery (yr/mo/d)


title: thymus_non-puberty_NM4_miRNA

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample185

description: genomic DNA from Blood

tag: Sex

tag: levodopastatus

tag: numberofyearsinschool


title: thymus_minipuberty_MM6

description: microRNA expression from thymus explant


title: thymus_minipuberty_MM5

description: microRNA expression from thymus explant


title: thymus_minipuberty_MM4

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample175

description: genomic DNA from Blood

tag: age

tag: levodopaperdayincludingagonists

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample174

description: genomic DNA from Blood

tag: ethnicity

tag: packyearstotal

tag: familyhistoryofparkinsons


title: Mir182mTg Basal rep2

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 and HT-seq
Counts Per Million (CPM) were calculated using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

organism: Mus musculus

source_name: Bone Marrow Macrophages

growth_protocol: Bone marrow was flushed from femur and tibia and cultured with M-CSF for 3 days to get bone marrow macrophages.

extract_protocol:
RNA was harvested using RLT buffer from Rneasy RNA extraction kit. mRNA was purified by poly-A+ selection. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow macropahges were treated with RANKL for 5days.

tag: strain

tag: genotype

tag: cell type

value: Bone Marrow Macrophages

tag: stimulation

value: none (basal)


title: thymus_minipuberty_MM3

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample173

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample172

description: genomic DNA from Blood

tag: Sex

tag: age

tag: levodopastatus

tag: numberofyearsinschool


title: Control Basal rep2

value: LysMcre(+)


title: Mir182ΔM/ΔM RANKL rep2

value: RANKL


title: Mir182ΔM/ΔM Basal rep2


title: PEGcaucasian: genomic DNA from whole blood of subject Sample170

description: genomic DNA from Blood

tag: ethnicity

tag: levodopaperdayincludingagonists

tag: smokingstatus

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample169

description: genomic DNA from Blood

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample168

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample167

description: genomic DNA from Blood


title: WT Basal rep2

tag: strain

tag: genotype

tag: cell type

tag: stimulation


title: WT RANKL rep2


title: thymus_minipuberty_MM2

description: microRNA expression from thymus explant

tag: tissue

tag: gender

tag: age at surgery (yr/mo/d)


title: Control Basal rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

treatment_protocol: Bone marrow macrophages were treated with RANKL for 5days.


title: Mir182mTg Basal rep1


title: Mir182ΔM/ΔM RANKL rep1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample165

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus


title: thymus_minipuberty_MM1

description: microRNA expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample164

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus


title: Mir182ΔM/ΔM Basal rep1

tag: strain

tag: genotype

tag: cell type

tag: stimulation


title: WT RANKL rep1


title: WT Basal rep1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample163

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample162

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample161

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

tag: diseasestatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample160

description: genomic DNA from Blood

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample171

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample159

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample158

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample157

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample156

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample155

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample166

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample154

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample153

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample152

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample150

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample151

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample148

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample146

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample147

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample144

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample145

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample149

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample142

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample143

description: genomic DNA from Blood


title: BH150464-1-1_14-477BS2Ca

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Ca-tumor

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 7.1

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tissues from  HIV associated lung cancer

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

treatment_protocol: Two types of samples from  3 pairs of tumor/adjacent normal tissue paraffin specimens and 1 pair of tumor/adjacent normal fresh tissue samples.

tag: disease

value: adenocarcinoma (AC)

tag: tissue

value: tumor

tag: tissue type

value: paraffin specimens


title: BH150464-1-1_13-1720BS5P

description: P-adjacent normal tissue

value: adjacent normal tissue


title: BH150464-1-1_14-477-8P

description: P-adjacent normal tissue


title: SiT3: Huh7 cells, Tryo3 siRNA

city: 台北市

first: 佳良

last: 蔡

state: TWN

address: 復興北路486號

country: Taiwan

institute: Chang Gung Memorial Hospital

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.4

source_name: Huh7 cells, Tryo3 siRNA

label_protocol: Standard Affymetrix protocol

growth_protocol: We cultured Huh7 cells in DMEM medium containing 10% FBS.

extract_protocol: Standard Qiagen Rneasy Mini Kit protocol

treatment_protocol: Standard Invitrogen Lipofectamine 3000 Transfection Reagent protocol

value: Huh7 cells

tag: cell type

value: hepatocellular carcinoma


title: SiNS: Huh7 cells, control siRNA

source_name: Huh7 cells, control siRNA


title: BH150464-2_JS70020 3-P

description: P-adjacent normal -fresh

value: squamous cell carcinoma (SCC)

value: fresh tissue


title: PEGcaucasian: genomic DNA from whole blood of subject Sample141

description: genomic DNA from Blood

value: male

value: Caucasian

tag: dnamage

tag: plasmablast

value: PD

value: yes

value: former

tag: packyearstotal

tag: familyhistoryofparkinsons


title: BH150464-2_JS70020 3-Ca

description: Ca-tumor-fresh


title: BH150464-2_15-1423-6P

description: P-adjacent normal tissue


title: BH150464-1-1_13-1720BS2Ca

description: Ca-tumor


title: PEGcaucasian: genomic DNA from whole blood of subject Sample140

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono

tag: gran

value: control

value: no

value: never


title: Patient_11_Varicose

city: Novosibirsk

first: Mariya

middle: Alexandrovna

last: Smetanina

address: 8 Lavrentiev Avenue

country: Russia

institute: Institute of Chemical Biology and Fundamental Medicine SB RAS

description: varicose vein sample (disease condition)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation27 Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scanning protocol, iScan System, iScan Control Software

data_processing: Illumina GenomeStudio V2011.1 software, Methylation Module

label: Cy5 and Cy3

source_name: large hollow vein

extract_protocol: genomic DNA was extracted from homogenized veins using TRIzol according to the manufacturer's protocol.

tag: gender

value: Female

tag: age

tag: stage of the disease, ceap


title: Patient_13_Varicose

value: Male


title: Patient_3_Varicose


title: Patient_26_Varicose


title: PEGcaucasian: genomic DNA from whole blood of subject Sample139

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: BH150464-2_15-1423-2Ca

description: Ca-tumor

tag: disease

value: adenocarcinoma (AC)

tag: tissue

value: tumor

tag: tissue type


title: Patient_27_Varicose


title: Patient_27_Control

description: normal vein sample (healthy condition)


title: Patient_5_Varicose


title: Patient_18_Varicose


title: Patient_19_Varicose


title: Patient_12_Varicose


title: Patient_26_Control

description: normal vein sample (healthy condition)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample138

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: smokingstatus

tag: packyearstotal

tag: familyhistoryofparkinsons


title: Patient_19_Control

description: normal vein sample (healthy condition)

tag: gender


title: PEGcaucasian: genomic DNA from whole blood of subject Sample136

description: genomic DNA from Blood

tag: age

tag: nk

tag: bcell

tag: mono

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample137

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: diseasestatus

tag: levodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample134

description: genomic DNA from Blood

value: female

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: PEGcaucasian: genomic DNA from whole blood of subject Sample133

description: genomic DNA from Blood

tag: dnamage


title: PEGcaucasian: genomic DNA from whole blood of subject Sample132

description: genomic DNA from Blood

tag: plasmablast


title: WT231  Rep3 [RNA]

city: Shanghai

first: Zhonghua

last: Tao

state: Shanghai

address: No.270, Dong'an Road, Xuhui.

country: China

institute: Fudan University Shanghai Cancer Center

description:
lncRNA.expression.xls
YD_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the cleandata were calculated. All the downstream analyses were based on the clean data with high quality.
RNA-sequencing reads were processed using Tophat-Cufflinks（cufflinks-2.2.1） workflows. And FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).Barcodes not matching correct length are filtered out. Besides, the transcript per million (TPM) was used to normalize the expression level of circRNAs.
Genome_build: Human genome version hg38
Supplementary_files_format_and_content: FPKM, TPM
For all generated raw reads, adaptor sequences, low-quality reads, contaminant reads, and reads that were shorter than 18 nt were eliminated and trimmed with the Fastx-Toolkit software.  The resulting set of trimmed reads were then mapped against the Homo sapiens of Ensembl (Release 80, http://www.ensembl.org/) using the program SOAP . Subsequently, by the same approach, the perfectly matched reads were screened against miRBase (Release 21, http://www.mirbase.org/) and human non-coding RNA sequence of Ensembl (Release 80, http://www.ensembl.org/) to obtain the annotation of known mature miRNAs and other small non-coding RNAs (allowing two mismatches)  To correct for the difference in tag counts between samples, the tag counts were scaled to the copy number of transcripts per million (TPM) based on the total number of tags aligned to known human mature miRNAs in miRBase 21.
Genome_build: miRBase 21
Supplementary_files_format_and_content: FPKM, TPM

growth_protocol: MDA-231 breast carcinoma cells (5x10^4 cells) were seeded in defined medium in the bottom of a 6-well Transwell culture dish and allowed to settle for 24 hours.

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer's protocols.
First, Total RNA was treated with the Epicentre Ribo-Zero kit (cat.#MRZH11124) to remove the all the rRNAs. The remaining RNAs were processed using the TruSeq RNA Sample Prep Kit according to the Illumina protocol. After cDNA synthesis, 6.5 pmol of DNA from each sample were clustered and sequenced on the Illumina HiSeq X-Ten (Illumina) in 150 bp paired-end reads.

treatment_protocol: Human adipose cells (5x10^5 cells) were added in Transwell inserts for 36 hours.

tag: cell line

value: MDA-231 breast carcinoma cells

tag: treatment


title: WT231  Rep2 [RNA]

description:
lncRNA.expression.xls
YD_2


title: WT231  Rep1 [RNA]

description:
lncRNA.expression.xls
YD_1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample129

description: genomic DNA from Blood

tag: smokingstatus

value: current

tag: packyearstotal

tag: familyhistoryofparkinsons


title: Patient_1_Varicose

tag: gender

tag: age

tag: stage of the disease, ceap


title: PEGcaucasian: genomic DNA from whole blood of subject Sample128

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono

tag: gran


title: GPY231 Rep3 [RNA]

description:
lncRNA.expression.xls
WT_3

value: co-culture:Human adipose cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample131

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: diseasestatus

tag: levodopastatus


title: GPY231 Rep2 [RNA]

description:
lncRNA.expression.xls
WT_2


title: PEGcaucasian: genomic DNA from whole blood of subject Sample127

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: PEGcaucasian: genomic DNA from whole blood of subject Sample130

description: genomic DNA from Blood

tag: smokingstatus

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample125

description: genomic DNA from Blood

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample126

description: genomic DNA from Blood

tag: age


title: Patient_18_Control

description: normal vein sample (healthy condition)

tag: gender

tag: stage of the disease, ceap


title: Patient_11_Control

description: normal vein sample (healthy condition)


title: GPY231 Rep1 [RNA]

description:
lncRNA.expression.xls
WT_1

tag: cell line

tag: treatment


title: PEGcaucasian: genomic DNA from whole blood of subject Sample135

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono

tag: gran


title: Patient_13_Control

description: normal vein sample (healthy condition)


title: Patient_12_Control

description: normal vein sample (healthy condition)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample123

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: diseasestatus

tag: levodopastatus


title: Patient_5_Control

description: normal vein sample (healthy condition)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample122

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: PEGcaucasian: genomic DNA from whole blood of subject Sample121

description: genomic DNA from Blood

tag: age

tag: smokingstatus

tag: packyearstotal

tag: familyhistoryofparkinsons


title: Patient_3_Control

description: normal vein sample (healthy condition)

tag: gender

tag: stage of the disease, ceap


title: PEGcaucasian: genomic DNA from whole blood of subject Sample120

description: genomic DNA from Blood

tag: nk

tag: bcell


title: PEGcaucasian: genomic DNA from whole blood of subject Sample118

description: genomic DNA from Blood

tag: mono

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample119

description: genomic DNA from Blood

tag: Sex

tag: ethnicity


title: WT vs quad at time 6 water_Rep2

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Background corrections, loess normalization within arrays. Quantile normalization across arrays

organism: Arabidopsis thaliana

source_name: Arabidopsis mature whole plant

label_protocol: not provided

growth_protocol: Seeds were sterilized with 35% bleach and sown in 0.5 MS agar medium without sucrose. Seedlings were grown for 7 days and then transfer to soil.  They were grown on soil for 16 days at LD conditions (16/8h light/dark) at 22ºC and approx. 60% relative humidity prior the treatment

extract_protocol: RNeasy Plant Mini Kit (Quiagen) according manufacturer instructions

treatment_protocol: Drought treatment were performed by shutting the watering for 6 days. Controls were watered normally

tag: genotype

value: quad mutant

tag: time and condition

value: 6 water

tag: tissue

value: mature whole plant

value: Col-0 WT


title: PEGcaucasian: genomic DNA from whole blood of subject Sample124

description: genomic DNA from Blood

value: male

value: Caucasian

tag: dnamage

tag: plasmablast

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists


title: PEGcaucasian: genomic DNA from whole blood of subject Sample116

description: genomic DNA from Blood

tag: age

value: PD

tag: numberofyearsinschool

tag: smokingstatus

value: former

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample117

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono

value: no

value: never


title: WT vs quad at time 4 drought_Rep2

value: 4 drought


title: WT vs quad at time 2 water_Rep2

value: 2 water


title: PEGcaucasian: genomic DNA from whole blood of subject Sample113

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: gran

value: yes


title: WT vs quad at time 6 drought_Rep2

tag: genotype

tag: time and condition

value: 6 drought

tag: tissue


title: WT vs quad at time 2 drought_Rep2

value: 2 drought


title: PEGcaucasian: genomic DNA from whole blood of subject Sample112

description: genomic DNA from Blood

value: female

tag: dnamage

tag: plasmablast

tag: diseasestatus


title: WT vs. quad at time 0_Rep2

value: 0 (control)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample109

description: genomic DNA from Blood

tag: age

tag: levodopastatus

tag: levodopaperdayincludingagonists


title: Patient_1_Control

description: normal vein sample (healthy condition)

tag: gender

value: Male

tag: stage of the disease, ceap


title: PEGcaucasian: genomic DNA from whole blood of subject Sample111

description: genomic DNA from Blood

tag: nk

value: control

tag: numberofyearsinschool

tag: smokingstatus

value: current

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample107

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: bcell

tag: mono

tag: gran


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 2_TC-Mɸ

city: Guangzhou

first: Zhao

last: Jinghua

address: 107 Yanjiang West Road

institute: SunYat-Sen Memorial Hospital, SunYat-Sen University

description: This sample was from donor 2 and treated with HER2 positive cell line for 24h

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Quantile normalization across multiple arrays, log 2 transformation of expression levels
High quality expression values was selected for analysis, then differentially expressed genes were identified.

source_name: Sample from indicated treatments

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Macrophages were obtained by culturing monocytes in DMEM medium (Gibco) supplemented with 10ng/ml M-CSF (Cat# 11792-HNAH, Sino Biological Inc.) and 10% FBS (Gibco) for 6 days.

extract_protocol: Total RNA was extracted from 3 donors with 3 indicated treatments (5 x 106 cells for each sample) using the TRIzol Reagent (Cat#A33251, Thermo Fisher).

treatment_protocol: HER2+ breast cancer cells pre-dyed by CellTtracker Deep Red Dye (Cat# C34565, Thermo Fisher) were co-cultured with macrophages pre-dyed by CellTracker CMFDA Dye (Cat# C7025, Thermo Fisher) with or without Trastuzumab (Roche). The ratio between tumor cells and macrophages was 1:5. After 24 hr, the cells were rigorously washed by PBS, digested by 10×TrypLE Selected Enzyme (Cat# A1217701, Gibco) diluted 5× in PBS with 1mM EDTA and sorted by CD14 Isolation Kit (Cat# 130-050-201, Miltenyi Biotec) to collect macrophages followed the instructions

tag: cell type

value: HER2+ breast cancer

tag: donor


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 3_ADCP-Mɸ

description: This sample was from donor 3 and treated with HER2 positive cell line for 24h in the presence of trastuzumab


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 2_Mɸ

description: This sample was from donor 2 and untreated


title: PEGcaucasian: genomic DNA from whole blood of subject Sample108

description: genomic DNA from Blood

tag: age

tag: dnamage

tag: plasmablast

tag: diseasestatus


title: WT vs quad at time 6 drought_Rep1

tag: genotype

value: Col-0 WT

tag: time and condition

tag: tissue

value: mature whole plant

value: quad mutant


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 3_Mɸ

description: This sample was from donor 3 and untreated


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 3_TC-Mɸ

description: This sample was from donor 3 and treated with HER2 positive cell line for 24h


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 2_ADCP-Mɸ

description: This sample was from donor 2 and treated with HER2 positive cell line for 24h in the presence of trastuzumab


title: thymus_control_non-puberty_NF6

description: Gene expression from thymus explant

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 (G4845A) 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 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering only one NA for each group (NM and NF). NA converted to null in data table. Data for identical probe names were averaged.  The expression values were log2 transformed and normalized by Lowess method.

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 RNeasy 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).

value: thymus

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample106

description: genomic DNA from Blood

value: Caucasian

tag: nk

tag: levodopastatus

value: no

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus

value: former

tag: packyearstotal

tag: familyhistoryofparkinsons


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 1_ADCP-Mɸ

description: This sample was from donor 1 and treated with HER2 positive cell line for 24h in the presence of trastuzumab

tag: cell type

tag: donor


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 1_Mɸ

description: This sample was from donor 1 and untreated


title: WT vs quad at time 4 water_Rep1

value: 4 water


title: PEGcaucasian: genomic DNA from whole blood of subject Sample105

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

tag: dnamage

tag: bcell

tag: mono

tag: gran


title: thymus_control_non-puberty_NF4

description: Gene expression from thymus explant

tag: tissue

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample104

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists


title: thymus_control_non-puberty_NF5

description: Gene expression from thymus explant


title: WT vs quad at time 4 water_Rep2

tag: genotype

tag: time and condition


title: PEGcaucasian: genomic DNA from whole blood of subject Sample103

description: genomic DNA from Blood

tag: Sex

tag: numberofyearsinschool

tag: smokingstatus

tag: packyearstotal

tag: familyhistoryofparkinsons


title: WT vs quad at time 6 water_Rep1

value: 6 water


title: WT vs quad at time 4 drought_Rep1

value: 4 drought


title: PEGcaucasian: genomic DNA from whole blood of subject Sample114

description: genomic DNA from Blood

value: male

tag: age

tag: ethnicity

tag: dnamage

tag: bcell

tag: mono


title: PEGcaucasian: genomic DNA from whole blood of subject Sample102

description: genomic DNA from Blood

value: female

tag: plasmablast

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample115

description: genomic DNA from Blood

tag: nk

tag: diseasestatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample110

description: genomic DNA from Blood

value: PD

tag: levodopastatus

tag: levodopaperdayincludingagonists


title: PEGcaucasian: genomic DNA from whole blood of subject Sample100

description: genomic DNA from Blood

value: never


title: PEGcaucasian: genomic DNA from whole blood of subject Sample99

description: genomic DNA from Blood


title: WT vs quad at time 2 water_Rep1

tag: genotype

tag: time and condition

value: 2 water

tag: tissue


title: PEGcaucasian: genomic DNA from whole blood of subject Sample98

description: genomic DNA from Blood

tag: Sex

tag: numberofyearsinschool

tag: smokingstatus


title: thymus_control_non-puberty_NF3

description: Gene expression from thymus explant

tag: gender

tag: age at surgery (yr/mo/d)


title: WT vs quad at time 2 drought_Rep1

value: 2 drought


title: thymus_control_non-puberty_NF8

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample96

description: genomic DNA from Blood

tag: age

tag: ethnicity

tag: dnamage

value: control

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample97

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis_donor 1_TC-Mɸ

description: This sample was from donor 1 and treated with HER2 positive cell line for 24h

tag: cell type

value: HER2+ breast cancer

tag: donor


title: PEGcaucasian: genomic DNA from whole blood of subject Sample95

description: genomic DNA from Blood

tag: Sex

tag: diseasestatus

tag: levodopastatus

value: yes

tag: levodopaperdayincludingagonists


title: WT vs. quad at time 0_Rep1

tag: genotype

value: Col-0 WT

tag: time and condition

value: 0 (control)

tag: tissue

value: mature whole plant

value: quad mutant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample91

description: genomic DNA from Blood

tag: age

tag: ethnicity

value: Caucasian

tag: dnamage

value: no

tag: numberofyearsinschool

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample92

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: bcell

value: former

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample101

description: genomic DNA from Blood

tag: Sex

tag: mono

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample90

description: genomic DNA from Blood

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists


title: PEGcaucasian: genomic DNA from whole blood of subject Sample89

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample93

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample87

description: genomic DNA from Blood


title: thymus_control_non-puberty_NF7

description: Gene expression from thymus explant

tag: tissue

value: thymus

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample86

description: genomic DNA from Blood

value: male

tag: age

tag: ethnicity

tag: dnamage


title: PEGcaucasian: genomic DNA from whole blood of subject Sample88

description: genomic DNA from Blood

tag: plasmablast

tag: numberofyearsinschool

tag: smokingstatus


title: thymus_control_non-puberty_NM9

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample85

description: genomic DNA from Blood

value: female

tag: nk

tag: bcell

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample84

description: genomic DNA from Blood

tag: Sex

tag: mono

value: PD

value: current

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample94

description: genomic DNA from Blood

tag: gran

tag: diseasestatus

tag: levodopastatus


title: thymus_control_non-puberty_NF2

description: Gene expression from thymus explant

tag: tissue

tag: gender


title: PEGcaucasian: genomic DNA from whole blood of subject Sample82

description: genomic DNA from Blood

tag: age

tag: levodopaperdayincludingagonists


title: PEGcaucasian: genomic DNA from whole blood of subject Sample80

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

value: never


title: PEGcaucasian: genomic DNA from whole blood of subject Sample83

description: genomic DNA from Blood

tag: plasmablast

tag: numberofyearsinschool


title: PEGcaucasian: genomic DNA from whole blood of subject Sample81

description: genomic DNA from Blood

tag: nk

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample77

description: genomic DNA from Blood

tag: bcell

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample76

description: genomic DNA from Blood

tag: Sex

tag: mono


title: PEGcaucasian: genomic DNA from whole blood of subject Sample74

description: genomic DNA from Blood

tag: gran

tag: familyhistoryofparkinsons


title: thymus_control_non-puberty_NF1

description: Gene expression from thymus explant

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample73

description: genomic DNA from Blood

tag: diseasestatus

tag: levodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample78

description: genomic DNA from Blood

tag: age


title: thymus_control_non-puberty_NM6

description: Gene expression from thymus explant

tag: tissue

tag: gender


title: PEGcaucasian: genomic DNA from whole blood of subject Sample72

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

tag: levodopaperdayincludingagonists


title: thymus_control_non-puberty_NM4

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample79

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: numberofyearsinschool


title: thymus_control_non-puberty_NM5

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample71

description: genomic DNA from Blood

tag: bcell

tag: smokingstatus

tag: packyearstotal


title: thymus_control_non-puberty_NM8

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample70

description: genomic DNA from Blood

tag: Sex

tag: mono

tag: gran


title: thymus_control_non-puberty_NM7

description: Gene expression from thymus explant

tag: age at surgery (yr/mo/d)


title: thymus_control_non-puberty_NM2

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample68

description: genomic DNA from Blood

tag: diseasestatus

tag: levodopastatus

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample69

description: genomic DNA from Blood

tag: age


title: PEGcaucasian: genomic DNA from whole blood of subject Sample66

description: genomic DNA from Blood

tag: ethnicity


title: PEGcaucasian: genomic DNA from whole blood of subject Sample67

description: genomic DNA from Blood

tag: dnamage


title: thymus_control_minipuberty_MF7

description: Gene expression from thymus explant

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering only one NA for each group (MM and MF). NA converted to null in data table. Data for identical probe names were averaged.  The expression values were log2 transformed and normalized by Lowess method.

tag: tissue

tag: gender


title: thymus_control_minipuberty_MF5

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample63

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: levodopaperdayincludingagonists


title: thymus_control_minipuberty_MF6

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample65

description: genomic DNA from Blood

tag: bcell

tag: numberofyearsinschool

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample62

description: genomic DNA from Blood

tag: Sex

tag: mono

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample61

description: genomic DNA from Blood

tag: gran

tag: diseasestatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample59

description: genomic DNA from Blood

tag: levodopastatus

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample58

description: genomic DNA from Blood

tag: age

tag: ethnicity


title: PEGcaucasian: genomic DNA from whole blood of subject Sample56

description: genomic DNA from Blood

tag: dnamage


title: thymus_control_minipuberty_MF4

description: Gene expression from thymus explant

tag: tissue

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample75

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: levodopaperdayincludingagonists


title: PEGcaucasian: genomic DNA from whole blood of subject Sample55

description: genomic DNA from Blood

tag: bcell

tag: numberofyearsinschool

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample60

description: genomic DNA from Blood

tag: Sex

tag: mono

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample54

description: genomic DNA from Blood

tag: gran

tag: diseasestatus

tag: levodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample57

description: genomic DNA from Blood

tag: age

tag: ethnicity

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample64

description: genomic DNA from Blood

tag: dnamage


title: W_6: 35S:BRL3_Water_Rep3

data_processing:
Trimming of 5bp at 3’
Quality filter with FastQC. Minimum quality cut-off of 28 in at least 80% of the bases of the read
Reads mapped against TAIR10 genome with HISAT2 aligner v2.1.0
Quantification at gene level with HtSeq-count v0.9.1 (union mode)
Genome_build: TAIR10
Supplementary_files_format_and_content: Raw counts at gene level

source_name: Arabidopsis mature roots

extract_protocol:
RNeasy Plant Mini Kit (Quiagen) according manufacturer instructions
TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: Drought treatment were performed by shutting the watering for 5 days. Controls were watered normally

tag: genotype

tag: condition

value: watered control

tag: tissue

value: mature roots


title: PEGcaucasian: genomic DNA from whole blood of subject Sample53

description: genomic DNA from Blood

tag: plasmablast

tag: nk

value: control

tag: levodopaperdayincludingagonists


title: thymus_control_minipuberty_MF2

description: Gene expression from thymus explant

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample51

description: genomic DNA from Blood

tag: Sex

tag: bcell

tag: mono

tag: numberofyearsinschool

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample52

description: genomic DNA from Blood

tag: age

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: packyearstotal


title: W_3: Col-0_WT_Water_Rep3

tag: genotype

tag: condition


title: thymus_control_minipuberty_MM8

description: Gene expression from thymus explant

tag: tissue


title: thymus_control_minipuberty_MM7

description: Gene expression from thymus explant


title: thymus_control_minipuberty_MM1

description: Gene expression from thymus explant


title: thymus_control_minipuberty_MF1

description: Gene expression from thymus explant


title: W_4: 35S:BRL3_Water_Rep1


title: thymus_control_minipuberty_MM9

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample50

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

tag: plasmablast

tag: nk

value: yes

tag: familyhistoryofparkinsons


title: thymus_control_non-puberty_NM1

description: Gene expression from thymus explant

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample49

description: genomic DNA from Blood

tag: Sex

tag: bcell

tag: mono

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: PEGcaucasian: genomic DNA from whole blood of subject Sample47

description: genomic DNA from Blood

tag: age

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: smokingstatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample48

description: genomic DNA from Blood

tag: ethnicity

tag: packyearstotal


title: W_2: Col-0_WT_Water_Rep2

tag: genotype

tag: condition

tag: tissue


title: W_1: Col-0_WT_Water_Rep1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample45

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: nk

tag: familyhistoryofparkinsons


title: thymus_control_minipuberty_MF3

description: Gene expression from thymus explant

tag: gender

tag: age at surgery (yr/mo/d)


title: thymus_control_minipuberty_MM2

description: Gene expression from thymus explant


title: PEGcaucasian: genomic DNA from whole blood of subject Sample43

description: genomic DNA from Blood

tag: Sex

tag: bcell

tag: mono

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: PEGcaucasian: genomic DNA from whole blood of subject Sample42

description: genomic DNA from Blood

tag: age

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: smokingstatus


title: D_5: 35S:BRL3_Drought_Rep2

tag: genotype

tag: condition

value: 5 days drought

tag: tissue


title: PEGcaucasian: genomic DNA from whole blood of subject Sample40

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

tag: plasmablast

tag: nk

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample41

description: genomic DNA from Blood

tag: Sex

tag: bcell

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample38

description: genomic DNA from Blood

tag: mono

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: D_4: 35S:BRL3_Drought_Rep1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample46

description: genomic DNA from Blood

tag: age

tag: gran

tag: diseasestatus


title: D_3: Col-0_WT_Drought_Rep3

tag: genotype


title: PEGcaucasian: genomic DNA from whole blood of subject Sample37

description: genomic DNA from Blood

tag: levodopastatus

tag: smokingstatus


title: D_2: Col-0_WT_Drought_Rep2

tag: condition

tag: tissue


title: PEGcaucasian: genomic DNA from whole blood of subject Sample44

description: genomic DNA from Blood

tag: ethnicity

tag: dnamage

tag: plasmablast


title: PEGcaucasian: genomic DNA from whole blood of subject Sample35

description: genomic DNA from Blood

tag: Sex

tag: nk

tag: packyearstotal


title: D_6: 35S:BRL3_Drought_Rep3


title: thymus_control_minipuberty_MM5

description: Gene expression from thymus explant

tag: gender

tag: age at surgery (yr/mo/d)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample33

description: genomic DNA from Blood

tag: bcell

tag: mono

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: familyhistoryofparkinsons


title: D_1: Col-0_WT_Drought_Rep1

tag: genotype


title: SKO-AT90ES-UV-2

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

hyb_protocol: Fragmented and Labeled products were hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix part# 902500). Washing and staining of arrays took place on the GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G system

data_processing: Data were analyzed using the robust multi-array average (RMA) method from R package “affy”

label_protocol: 300ng of Total RNA per sample was prepared using the GeneChip WT PLUS Reagent Kit (Affymetrix part#902280) and yielded cDNA product for fragmentation and labeling

growth_protocol: Bone Marrow Derived Macrophages were isolated from hind-limb femurs of 8-10 weeks old Wild type (WT) and STING knockout (SKO) mice. The hematopoietic cells from the bone marrow were cultured in complete DMEM (Invitrogen) including 10 ng/ml of Mouse Recombinant Colony-Stimulating Factor (M-CSF) for 14 days.

extract_protocol: RNeasy Mini Kit (Quiagen)

treatment_protocol: We next fed UV treated double-strand DNA containing HEK293 cells to the Wild type or STING KO macrophages for 6 hours.

value: STING Knock out

tag: cell type

value: Bone-marrow derived macrophages

tag: protocol

value: SKO macrophages phagocyting UV treated HEK293 cells containing AT90ES


title: B16-Mock-1

growth_protocol: B16-OVA cells were cultured in DMEM containing 10% FBS.

treatment_protocol: The B16-OVA cells were treated with 90mer double strand DNA using Lipofectamine 2000 for 6 hours.

tag: cell line

value: B16-OVA melanoma cells

value: Mock transfected


title: B16-AT90ES-2

value: AT90ES transfected


title: PEGcaucasian: genomic DNA from whole blood of subject Sample32

description: genomic DNA from Blood

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values

tag: age

tag: ethnicity

value: Caucasian

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: smokingstatus

value: former


title: PEGcaucasian: genomic DNA from whole blood of subject Sample36

description: genomic DNA from Blood

tag: Sex

value: female

tag: dnamage

tag: plasmablast

tag: nk

value: no

tag: packyearstotal


title: SKO-AT90ES-UV-1


title: B16-AT90ES-1


title: WT231  Rep2 [miRNA]

description:
all_miRNA_exp.xls
YD_2

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer's protocols.
For small RNA librarires, 18-30 nt RNAs were isolated from total RNA of dissected ovaries using 15% polyacrylamide gels and libraries were constructed using the Illumina TruSeq smallRNA Library Kit. And the libraries were sequenced with an Illumina HiSeq2500 in 50-bp single-end fashion.

value: MDA-231 breast carcinoma cells

tag: treatment


title: PEGcaucasian: genomic DNA from whole blood of subject Sample31

description: genomic DNA from Blood

value: male

tag: bcell

tag: mono

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

value: current

tag: familyhistoryofparkinsons


title: WT231  Rep3 [miRNA]

description:
all_miRNA_exp.xls
YD_3

tag: cell line


title: B16-Mock-2

tag: protocol


title: PEGcaucasian: genomic DNA from whole blood of subject Sample30

description: genomic DNA from Blood

tag: age

tag: ethnicity

tag: gran


title: WT-AT90ES-UV-2

tag: genotype

value: Wild type

tag: cell type

value: WT macrophages phagocyting UV treated HEK293 cells containing AT90ES


title: SKO-Mock-2

source_name: SKO-Mock

value: SKO macrophages only


title: PEGcaucasian: genomic DNA from whole blood of subject Sample28

description: genomic DNA from Blood

tag: Sex

tag: dnamage

tag: diseasestatus

value: PD

tag: levodopastatus

value: yes

tag: smokingstatus


title: SKO-UV-2

source_name: SKO-UV

value: STING Knock out

value: Bone-marrow derived macrophages

value: SKO macrophages phagocyting UV treated HEK293 cells


title: SKO-Mock-1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample26

description: genomic DNA from Blood

tag: plasmablast

tag: nk

tag: bcell

tag: packyearstotal


title: PEGcaucasian: genomic DNA from whole blood of subject Sample39

description: genomic DNA from Blood

tag: mono

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample34

description: genomic DNA from Blood

tag: age

tag: ethnicity


title: SKO-UV-1

tag: genotype

tag: protocol


title: WT231  Rep1 [miRNA]

description:
all_miRNA_exp.xls
YD_1

tag: cell line

tag: treatment


title: PEGcaucasian: genomic DNA from whole blood of subject Sample27

description: genomic DNA from Blood

tag: Sex

tag: dnamage

tag: gran

tag: diseasestatus

value: control


title: WT-UV-1

source_name: WT-UV

tag: cell type

value: WT macrophages phagocyting UV treated HEK293 cells


title: GPY231 Rep3 [miRNA]

description:
all_miRNA_exp.xls
WT_3

value: co-culture:Human adipose cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample24

description: genomic DNA from Blood

source_name: Whole Blood

value: Caucasian

tag: plasmablast

tag: nk

tag: bcell

tag: levodopastatus

tag: smokingstatus

value: former


title: GPY231 Rep2 [miRNA]

description:
all_miRNA_exp.xls
WT_2


title: PEGcaucasian: genomic DNA from whole blood of subject Sample25

description: genomic DNA from Blood

value: female

tag: mono

value: no

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample29

description: genomic DNA from Blood

tag: age

tag: ethnicity

value: never


title: PEGcaucasian: genomic DNA from whole blood of subject Sample23

description: genomic DNA from Blood

tag: Sex


title: WT-AT90ES-UV-1

tag: genotype

tag: protocol


title: WT-Mock-2

source_name: WT-Mock

value: WT macrophages only


title: PEGcaucasian: genomic DNA from whole blood of subject Sample21

description: genomic DNA from Blood

tag: dnamage

tag: gran

tag: diseasestatus


title: KO-BKC rep1

city: Oklahoma City

first: Lerin

last: Luckett-Chastain

state: OK

address: 1110 N. Stonewall

department: Pharmaceutical Science

institute: OUHSC

description: BKC Treated (7 Days)

data_processing:
Qiagen's CLC Genomic Workbench version 10.0.1 was used for alignment and analysis.
CLC's standard RNA-Seq Analysis pipeline was used to align with the Mus musculus (GRCm38) genome. Differential expression analyses were performed using CLC's RNA-Seq Analysis workflow.
Differential expression settings were as follows: 3 samples per group. Data were normalized to reads per million (RPKM), and statistical analysis run with minimum fold change of 5 and FDR pvalue cutoff of 0.1
Genome_build: Mus musculus build 37.2
Supplementary_files_format_and_content: RPKM, TPM

source_name: Skin

growth_protocol: Mice were obtained from Jackson Laboratory at 4-5 weeks old. Mice were allowed to acclimate for 2 weeks and treatments began at 6 weeks old.

extract_protocol:
Skin was isolated after 7 consecutive days of treatment (or non for control), RNA was isolated using Tri-Reagent.
RNAseq libraries were prepared using total RNA and standard Illumina protocols for TruSeq library construction kit.

treatment_protocol: 6 C57 and 6 IL-6KO mice were shaved on Day 0. 3 C57 and 3 IL-6KO were left untreated for 7 days, 3 C57 and 3 IL-6KO were treated with 50μl .02% BKC for 7 days,  On Day 8 all mice were euthanized and skin was isolated.

tag: strain

tag: tissue

value: Skin

tag: agent

value: BKC


title: KO-BKC rep2

description: BKC Treated (7 Days)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample20

description: genomic DNA from Blood

value: male

tag: plasmablast

tag: nk

tag: bcell

tag: levodopastatus

tag: smokingstatus


title: C57-BKC rep3

description: BKC Treated (7 Days)

value: wild type


title: PEGcaucasian: genomic DNA from whole blood of subject Sample19

description: genomic DNA from Blood

tag: mono

value: PD

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: packyearstotal

tag: familyhistoryofparkinsons


title: C57-BKC rep2

description: BKC Treated (7 Days)

tag: genotype


title: 32-0018

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
The preprocessing of RNA-Seq data started with filtering unqualified reads, followed by trimming Illumina universal adapter using Trimmomatic-0.32.
the preprocessed reads were aligned to genome build hg38 using Tophat-21.0/Bowtie2-2.2.6.
To profile the gene expression, the gene features and annotation were first obtained from GENCODE, version 24.
Gene counts were then estimated by using Bioconductor function GenomicAlignment::summarizeOverlap() with IntersectionStrict mode, which restrict read-counts to those that fall completely within the range of exons.
Genome_build: hg38
Supplementary_files_format_and_content: (1) biopsy.dds.rda is an RDA file storing a DESeqDataSet instance containing sample info, phenotype data, gene futures, gene counts and FPKM. (2) biopsy_FPKM.csv biopsy_genecounts.csv and bopsy_normalized_genegoutns.csv contain FPKM, gene counts and normalized gene counts, respectively.

growth_protocol: Muscle biopsy samples extracted from 34 of the 36 FSHD subjects, and on 9 control quadriceps muscle biopsies from unaffected individuals.

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.

tag: subject status

value: Facioscapulohumeral muscular dystrophy (FSHD)

tag: age

tag: gender

tag: inflam

tag: active

tag: stir

value: muscle biopsy

tag: batch

value: IV


title: 32-0017

tag: tissue


title: 32-0019


title: C57-BKC rep1

description: BKC Treated (7 Days)

tag: strain

tag: agent


title: GPY231 Rep1 [miRNA]

description:
all_miRNA_exp.xls
WT_1

tag: cell line

value: MDA-231 breast carcinoma cells

tag: treatment


title: PEGcaucasian: genomic DNA from whole blood of subject Sample18

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: smokingstatus


title: 32-0016

tag: subject status

tag: age

tag: gender

tag: stir

tag: tissue

tag: batch


title: PEGcaucasian: genomic DNA from whole blood of subject Sample17

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

value: control

tag: numberofyearsinschool

tag: packyearstotal

tag: familyhistoryofparkinsons


title: 32-0015

tag: inflam

tag: active


title: KO rep3

description: No Treatment

tag: strain

tag: genotype

tag: agent


title: 01-0038


title: WT-UV-2

value: Wild type

tag: cell type

value: Bone-marrow derived macrophages

tag: protocol

value: WT macrophages phagocyting UV treated HEK293 cells


title: PEGcaucasian: genomic DNA from whole blood of subject Sample22

description: genomic DNA from Blood

tag: age

value: Caucasian

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: smokingstatus

value: former


title: TEAD4_ChIP

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Mapping fastq on mm10 using BWA 0.7.12 aligner  using default settings implemented in docker4seq package, https://github.com/kendomaniac/docker4seq
Histon mark peaks were detected with SICER 1.1 using default settings and transcription factors peaks were detected with MACS 1.4.3, implemented in docker4seq package, https://github.com/kendomaniac/docker4seq
Genome_build: mm10
Supplementary_files_format_and_content: bigwig generated with bedtools 2.17.0

source_name: BCC

extract_protocol:
Chromatin was fragmaneted with sonicaiton and precleared prior to overnight incubation with specific antibodies
Library was prepared using NEBNext® Ultra DNA Library Prep Kit and NEBNext® Multiplex Oligos for Illumina (NEB) according to the manufacturer’s recommendations
DNA extraction and chromatin immunoprecipitation were performed  as previously described in Galli et al., 2012 doi 10.1016/j.molcel.2015.09.001
Libraries for ChIP-sequencing were generated by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and barcoding added using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB) according to the manufacturer’s recommendation.

treatment_protocol: BCC tumors were induced with Tamoxifen administration in 4-week old mice with R26-SmoM2/+ K14CreER or R26-SmoM2/+ Yapfl/fl K14CreER.  The BCC tumor cells were isolated 6 or 9 weeks post tamoxifen.

value: BCC from tail epidermis

tag: tumor stage

value: 9 weeks post tamoxifen

value: R26-SmoM2/+ K14CreER

tag: chip antibody

value: Anti-Tead4 (ab58310 – Abcam)


title: TEAD1_ChIP

tag: genotype

value: Anti-Tead1 (BD 610922)


title: H3K27Ac_ChIP

value: Anti-H3K27Ac (ab4729 – Abcam)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample16

description: genomic DNA from Blood

extract_protocol: genomic DNA was extracted and purified from EDTA tubes using the RecoverEase DNA Isolation Kit.

tag: Sex

value: female

tag: ethnicity

value: PD

value: yes

tag: numberofyearsinschool

value: current

tag: packyearstotal

tag: familyhistoryofparkinsons


title: KO rep2

description: No Treatment

tag: strain

tag: tissue

value: Skin

tag: agent


title: Input_ChIP

tag: cell type


title: KO-BKC rep3

description: BKC Treated (7 Days)

value: BKC


title: PEGcaucasian: genomic DNA from whole blood of subject Sample15

description: genomic DNA from Blood

value: male

tag: age

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran


title: 01-0049

tag: subject status

value: Control

value: muscle biopsy

tag: batch

value: IV


title: KO rep1

description: No Treatment

tag: genotype


title: C57 rep3

description: No Treatment

value: wild type


title: DM2242_BCC_Ko_2

data_processing:
Mapping fastq on mm10 using STAR aligner version 2.5 using default settings
Gene symbol annotation based EMSEMBL GRCm38.92
Genome_build: mm10
Supplementary_files_format_and_content: DEseq2 (1.18.1) library  normalized counts

growth_protocol: BCC tumors were induced with Tamoxifen administration in 4-week old mice with R26-SmoM2/+ K14CreER or R26-SmoM2/+ Yapfl/fl K14CreER.  The BCC tumor cells were isolated 6 or 9 weeks post tamoxifen.

extract_protocol:
Total RNA was purified using Qiagen Rneasy Plus Mini Kit
Library was prepared using TruSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s protocol

value: ear epidermis

value: basal cell carcinoma (BCC)

tag: tumor stage

value: 6 weeks post tamoxifen

tag: genotype/variation

value: R26-SmoM2/+ Yapfl/fl K14CreER


title: PEGcaucasian: genomic DNA from whole blood of subject Sample14

description: genomic DNA from Blood

tag: Sex

tag: ethnicity

value: Caucasian

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus

value: never

tag: packyearstotal

tag: familyhistoryofparkinsons


title: DM2437_BCC_Ko_3

tag: tissue

tag: cell type


title: WT-Mock-1

value: Wild type

value: Bone-marrow derived macrophages

tag: protocol

value: WT macrophages only


title: 01-0046

tag: subject status


title: H9 with P4 passage group

city: Seoul

first: Hyuk-Jin

last: Cha

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: WA09 (H9) cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: human embryonic stem cell (hESCs) line

tag: passages


title: PEGcaucasian: genomic DNA from whole blood of subject Sample13

description: genomic DNA from Blood

tag: age

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

value: PD

value: yes

value: former


title: C57 rep2

description: No Treatment

tag: strain

value: Skin

tag: genotype

tag: agent


title: 01-0032

value: Facioscapulohumeral muscular dystrophy (FSHD)

tag: gender

value: male

tag: inflam

tag: active

tag: stir

value: muscle biopsy

tag: batch


title: DM2241_BCC_Ko_1

tag: tissue

value: ear epidermis

tag: cell type

tag: tumor stage

tag: genotype/variation


title: DM2447_BCC_Wt_3

value: basal cell carcinoma (BCC)

value: R26-SmoM2/+ K14CreER


title: PEGcaucasian: genomic DNA from whole blood of subject Sample12

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

tag: dnamage

tag: plasmablast

tag: diseasestatus

tag: levodopastatus

value: no

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus

tag: packyearstotal

tag: familyhistoryofparkinsons


title: 01-0021

tag: subject status

tag: gender

value: female

tag: inflam

tag: active

tag: stir

tag: batch

value: IV


title: C57 rep1

description: No Treatment

tag: strain

tag: tissue

tag: genotype

value: wild type

tag: agent


title: DM2278_BCC_Wt_1

tag: cell type

tag: tumor stage

value: 6 weeks post tamoxifen

tag: genotype/variation


title: PEGcaucasian: genomic DNA from whole blood of subject Sample11

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

value: Caucasian

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

value: control

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool


title: DM2279_BCC_Wt_2

tag: tissue


title: tgf_SIS3_1

city: Houston

first: yu

last: xiang

state: Texas

address: 6431 Fannin

institute: UTHealth McGovern Medical School

data_processing:
Hisat2 v2.0.5 was used for aligning to the hg19 genome.
Four circRNA identification methods, CIRI2, CIRCexplorer2, circRNA_finder and find_circ are used to identify circRNAs profile.
Genome_build: hg19
Supplementary_files_format_and_content: xls file contains circRNAs profile for each sample.

source_name: A549 cells

extract_protocol:
Cells treated by TGF-β and SIS3 and RNA are extracted by using Quick-RNA MiniPrep kit from ZYMO Research. Each sample contains 2 biological replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were pre-treated with 5uM of SIS3 for 1 hour followed by TGF-β treatment at 5 ng/mL in the presence or absence of SIS3 for 30 min.

tag: treatment

value: tgf-beta+ inhibitor


title: tgf_SIS3_2


title: 01-0047

tag: subject status

value: Control

tag: batch


title: LK_PRMT5_KO_C

last: Nimer

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

data_processing:
Base calling using Illumina RTA 2.4.11
Reads mapped to GRCm38/mm10 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Estimated counts were obtained from RSEM.gene.results
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file contains aggragated raw RSEM expected gene level counts for all samples .

source_name: sorted LK cells from Mx1-cre;PRMT5fl/fl (KO)

extract_protocol:
RNA was harvested using Qiagen Rneasy Plus Micro Kit (Cat# 74034)
RNA-Seq library prep was carried out using the Illumina TruSeq Total Stranded kit following manufacturer’s standard protocol without modification.

tag: genotype/variation

value: PRMT5fl/fl KO

tag: cell type

value: sorted LK cells


title: tgf_2

value: tgf-beta


title: tgf_1


title: LK_PRMT5_WT_C

source_name: sorted LK cells from PRMT5fl/fl (WT)

value: PRMT5fl/fl wild type


title: con1


title: PEGcaucasian: genomic DNA from whole blood of subject Sample8

last: Horvath

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

tag: smokingstatus

value: never

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample7

description: genomic DNA from Blood

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample10

description: genomic DNA from Blood

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

value: former


title: PEGcaucasian: genomic DNA from whole blood of subject Sample9

description: genomic DNA from Blood

value: male

value: PD

value: yes


title: H9 with P3 passage group

tag: cell line

tag: cell type

value: human embryonic stem cell (hESCs) line

tag: passages


title: PEGcaucasian: genomic DNA from whole blood of subject Sample6

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity


title: con2

tag: treatment


title: H9 with P1 passage group


title: LK_PRMT5_WT_B

tag: genotype/variation


title: 32-0014

tag: subject status

value: Facioscapulohumeral muscular dystrophy (FSHD)

tag: gender

value: female

tag: inflam

tag: active

tag: stir

tag: tissue

value: muscle biopsy

tag: batch

value: III


title: 32-0012


title: 32-0010


title: 01-0048


title: H9 with P2 passage group


title: PEGcaucasian: genomic DNA from whole blood of subject Sample4

description: genomic DNA from Blood

value: Caucasian

tag: dnamage

tag: plasmablast

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: smokingstatus

tag: packyearstotal

tag: familyhistoryofparkinsons


title: 32-0013

tag: subject status

tag: age

tag: gender

tag: inflam


title: 32-0011

tag: stir

tag: tissue

tag: batch


title: 01-0044


title: LK_PRMT5_WT_A

tag: genotype/variation

tag: cell type


title: NY15_input_ChIP_2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Reads were mapped to the reference genome (canonical chromosomes only) using bowtie v.1.1.1 and parameters -n 3 -k 1 -m 1.
Peaks were called using MACS v.1.4.2, using paired "input" samples as control and parameters --bw 300 --keep-dup 1.
BigWig files were generated using deepTools bamCoverage v.2.4.0 and parameters --binSize -normalizeTo1x hs --normalizeUsingRPKM --ignoreForNormalization chrX chrM --ignoreDuplicates --blackListFileName.  Blacklist file contained the ENCODE DAC blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/).
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the ChIP-seq peaks files (generated by MACS) indicate: (1) chromosome; (2) start; (3) end; (4) peak name; (5) peak score
Supplementary_files_format_and_content: ChIP-seq coverage files are in the bigWig format

growth_protocol: NY8 and NY15 cells were grown in RPMI 1640 media with GlutaMAX-I, 10% FBS, antibiotic-antimycotic, and 100µg/ml gentamicin. Cells were cultured at 37˚C with 5% carbon dioxide.

extract_protocol:
A confluent 15cm culture plate of cells (NY8 or NY15) was used per immunoprecipitation. Cells were fixed with 1% formaldehyde for 10 minutes. Nuclei were collected and chromatin sheared to 1-10 nucleosomes using the SimpleChIP Plus Enzymatic Chromatin IP kit and protocol (Cell Signaling). HNF1A was immunoprecipitated overnight with goat polyclonal antibody C-19 (Santa Cruz) and 60µL magnetic protein G beads. Beads were washed and immunoprecipitated DNA was reverse crosslinked/purified per the SimpleChIP Plus Enzymatic Chromatin kit protocol.
10 to 500 ng of ChIPped DNA was prepared as a standard Illumina library using IntegenX Prep X (was Wafergen now Takara) reagents on the Apollo 324 instrument, where the fragments are end-repaired, A-tailed, and adapter ligated. Then the samples are PCR amplified and pooled. Final libraries were checked for quality and quantity by TapeStation (Agilent, Santa Clara, CA) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).  They were clustered on the cBot (Illumina) and sequenced on a 50 cycle single end run on a HiSeq 2500 in High Output mode using version 4 reagents according to manufacturer’s protocols.

treatment_protocol: NY8 and NY15 cells were grown to confluency in 15cm cell culture plates prior to ChIP.

value: pancreatic cancer-derived cells

tag: cell line

tag: chip antibody


title: 01-0045

value: Control


title: LK_PRMT5_KO_B

value: PRMT5fl/fl KO