title: 6_3D16-18_Needling_5d

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

hyb_protocol: Hybridization cocktails containing 5.5 Ig of fragmented, end-labelled cDNA were prepared and applied to GeneChip Human Gene 2.0 ST arrays. Hybridization was performed in 45°C hybridization oven at 60 rpm for 16 hours. Using the GeneChip® Fluidics Station 450 the hybridized GeneChip® Human Gene 2.0 ST Arrays were washed and stained (Fluidics Protocol FS450_0001).

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip®Operating Software (GCOS) version 1.4 to produce CEL intensity files.

data_processing:
Data analysis from the exon arrays were processed using GeneSpring GX 14.9 software (Agilent Technologies).
HuGene-2_0-st
Affymetrix.ExonExprChip.HuGene-2_0-st_na35_hg19_2015-04-15

source_name: fibroblasts and keratinocytes

label_protocol: 300µg total RNA from each model were processed using the WT Expression Kit (Ambion)  to generate amplified sense-strand cDNA. Fragmentation and labeling was done using the Affymetrix® GeneChip® WT Terminal Labeling Kit Assay (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: normal human epidermal keratinocytes (NHEK) and normal human dermal fibroblasts (NHDF) were isolated from biopsies of three different donors after cutaneous surgery. The epidermis was separated from the dermis by digestion with dispase (BD Biosciences, Franklin Lakes, NY) and trypsin (Lonza, Basel, Switzerland). Trypsin Neutralization Solution (Lonza) was used for pH-neutralization. The dermal portion of the biopsy was incubated in collagenase 1A (Sigma, Taufkirchen, Germany) to yield a single cell suspension of NHDF. Matriderm® (Medskin Solutions, Suwelack A.G., Billerbeck, Germany) is a 3D bovine collagen–elastin matrix consisting of bovine collagen types I, III, and V. In this study, matrices of 148 x 105 x 1 mm were used. The collagen–elastin matrix was sliced into circular 22 mm punches and transferred into six-well cell culture inserts (BD Falcon, Bedford, MA, USA), then stored under sterile conditions in six-well plates until use. Matriderm scaffolds were inoculated with 3 x 105 NHDF per cm2 in Tisseel (Baxter, Derfield, IL, USA) and submersed with fibroblast growth medium used for dermal scaffold skin equivalents. After three days, 3 x 106 NHEK were seeded on top of each dermal equivalent. Skin equivalents were submersed in equal volumes of DMEM and keratinocyte growth medium with 5% fetal calf serum (FCS), 50 µg ascorbic acid, and 5 µg/ml aprotinin (Applichem, Chicago, IL, USA). On the following day, skin equivalents were lifted to the air–liquid interface. The calcium concentration of the culture medium was increased to 1.0 mM and medium was changed every other day.

extract_protocol: Total RNA was isolated using the Nucleo Spin II RNA Mini Kit, (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions, including on-column digestion of DNA with RNase-free DNase I.

treatment_protocol: 3D skin models were treated with an eDermastamp® (Dermaroller GmbH, Wolfenbüttel, Germany) using a six needle plate (1.5 NM615LS16309, Amiea Med). One hundred insertions were made per second at a penetration depth of 1.0 mm and with three passes, according to the manufacturer´s and clinical treatment recommendations. After treatment, the models were cultivated in fresh culture medium and harvested on day 5 for histological analysis and detection of gene expression. Untreated models were maintained as negative controls.

value: skin model


title: 1004-Effector_memory_CD8pos_T-U

status: Public on Sep 05 2018

type: SRA

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Tn5 transposase adapters were trimmed with cutadapt version 1.13 with a minimum length of 20 and an overlap of 5 in paired-end mode.
RNA-seq reads were pseudoaligned using Kallisto version 0.43.0 (Bray et al., 2016). The Kallisto index was made with default parameters and the gencode v25lift37 fasta file (Harrow et al., 2012) and was run in quant mode with default parameters.
Gene abundances were computed using tximport version 1.2.0 (Soneson et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including gene abundance estimate for protein coding genes

molecule: polyA RNA

organism: Homo sapiens

source_name: primary blood

extract_protocol: RNA sequencing libraries were prepared according to the Smart-seq2 protocol (Picelli et al. ,2014). Custom Nextera barcoded PCR primers (Buenrostro et al., 2015) were used for dual indexing. Amplified libraries were purified using AMPure XP beads (Beckman Coulter) using a 1:1 ratio.

treatment_protocol:
Treatment 1: T lymphocytes were activated for 24 hours with dynabead conjugated CD3/CD28 antibodies at 1:1 ratio, supplemented with 50 unit/ml of human IL-2  or 300 unit/ml for regulatory T cells. B lymphocytes were activated for 24 hours with 10µg/ml  anti-IgG/IgM antibodies and 20ng/ml of human IL-4. Monocytes were activated with 1µg/ml of LPS for 24 hours. NK cells were activated with 200 unit/ml of human IL2 for 24 hours.
Treatment 2: Monocytes were activated with 100ng/ml of LPS for 6 hours. NK cells were activated with CD2 and CD355 coated beads at 1:2 cell to bead ratio supplemented with 500 unit/ml IL-2 for 48 hours.

tag: donor

tag: cell type

tag: lineage

tag: treatment


title: 5_3D16-18_Kontrolle_5d

type: RNA

country: Germany

label: biotin

molecule: total RNA

tag: tissue


title: 3_3D16-18_Kontrolle_5d


title: 1_3D16-18_Kontrolle_5d


title: 2_3D16-18_Needling_5d


title: 1004-Central_memory_CD8pos_T-S


title: 4_3D16-18_Needling_5d


title: 1008-pDCs-U

library_source: genomic

data_processing:
Tn5 transposase adapters were trimmed with cutadapt version 1.13 with a minimum length of 20 and an overlap of 5 in paired-end mode.
Trimmed reads were aligned using bowtie2 version 2.2.9
Following removal of chrM reads we filtered with samtools version 1.4 and-f 2 and -F 1804 and MAPQ > 30, and removed duplicate reads with picard version 1.134
Used get_count function from nucleoATAC
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including read count for each sample in each peak

molecule: genomic DNA

extract_protocol: ATAC-seq libraries were prepared following the Fast-ATAC protocol (Corces et al., 2016). Briefly, frozen cells were thawed, washed in media, aliquoted and resuspended in Tn5 reaction buffer and incubated at 37℃ for 30 min. Transposed samples were purified using MinElute PCR purification columns according to the manufacturer’s protocol (Qiagen, Germany). Purified samples were amplified and indexed using custom Nextera barcoded PCR primers as described in Buenrostro et al (Buenrostro et al., 2013). Amplified libraries were purified using MinElute PCR purification columns followed by gel-based size selection to remove free PCR primers.

value: pDCs

value: MYELOID


title: 1003-Effector_CD4pos_T-U

description:
Additional sequencing was performed on a NextSeq 500 and merged with this library.
ATAC_counts.txt.gz


title: 1003-Effector_CD4pos_T-S


title: 1003-Gamma_delta_T-S

value: GD


title: HeLa_rep20_6N

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

description: 3'READS human samples used in PolyA_DB version 3.2

data_processing:
Adpter trimming by Cutadapt:  cutadapt -a NNNNTGGAATTCTCGGGTGCCAAGG -n 1 -O 10 -m 25 -f fastq -q 10
3'READs and 3'READS+ reads were aligned to hg19 using bowtie2:
For the sample name ends with "3N":
bowtie2 --local --threads 24 -5 3 -x IndexFiles/bowtie2/hg19 -U sample_3N.trimmed.fastq -S sample_3N.sam
For the sample name ends with "4N":
bowtie2 --local --threads 24 -5 4 -x IndexFiles/bowtie2/hg19 -U sample_4N.trimmed.fastq -S sample_4N.sam
For the sample name ends with "6N":
bowtie2 --local --threads 24 -5 6 -x IndexFiles/bowtie2/hg19 -U sample_6N.trimmed.fastq -S sample_6N.sam
For 3'READs data, reads with a mapping quality score (MAPQ) >=10 were kept for further analysis. Reads with >=2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads count for each PAS position coverved by PolyA_DB version 3.2

extract_protocol:
TRIzol
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).

value: HeLa

tag: protocol

tag: purpose

tag: molecule type

value: total RNA


title: HeLa_rep21_6N

value: 3'READS human samples used in PolyA_DB version 3.2


title: LNCaP_rep6_6N

value: LNCaP


title: 1003-Naive_CD8_T-U


title: 293T_rep7_6N


title: 1004-Naive_B-U

value: B


title: 1004-CD8pos_T-U


title: 1004-Central_memory_CD8pos_T-U


title: 1004-CD8pos_T-S


title: 1004-Mem_B-U


title: A549_HT 44

city: Busan

first: Beomseok

last: Son

address: 322 Biology Building, 2 Busandaehakro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan National University

description: Gene expression data from HT(44 degrees celsius)-treated A549 cells

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: A549 cells, HT 44 degrees celsius

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: 3x105 A549 cells were subcultured and incubated for 24 h in RPMI-1640 medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin at 37°C in 95% air/5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: For HT treatment, cells were maintained in a humidified 5% CO2 temperature set at 41.5°C or 44°C for 1 h, and then incubated at 37°C for 3 h. For IR treatment, cells were irradiated with 3 Gy of X-ray using M-150WE (Softex Co., Ltd., Tokyo, Japan), and then incubated for 3 h at 37°C. For HT+IR combinatory treatment group, HT was treated to cells, and then, they were immediately irradiated.

tag: cell line


title: A549_IR_HT 41.5

description: Gene expression data from irradiated and HT(41.5 degrees celsius)-treated A549 cells

source_name: A549 cells, irradiated and HT 41.5 degrees celsius


title: SAP CONJ1

city: Chennai

first: Narayanan

last: Janakiraman

state: Tamil nadu

address: College Road

department: Nanobiotechnology

country: India

institute: Vision Research Foundation

description: MCF-7 with Saporin-EpCAM conjugate treatment for 24 h (1)

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45 °C on Affymetrix Human Primeview Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Stained arrays were scanned using Affymetrix Genechip scanner (3000 7G) at 570nm.

data_processing: The data analysis was done using RMA algorithm in Gene Spring Software ( Version13.0 GX).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ngs of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 Breast cancer cell line (ATCC) was maintained with DMEM culture media supplemented with 10% FBS, in a humidified Co2 incubator.

extract_protocol: RNA was extracted frm the cells using Qiagen RNAeasy mini kit

treatment_protocol: Cells were treated with Saporin (Sigma) and Saporin-EpCAM Antibody conjugate (using EDC-NHS cross linker) and incubated for 24 h, cells with out treatment was maintained as a control

value: MCF7 cells with same passage number


title: SAP 1

description: MCF-7 with saporin treatment for 24 h (1)


title: 1003-Effector_memory_CD8pos_T-S


title: A549_IR_HT 44

description: Gene expression data from irradiated and HT(44 degrees celsius)-treated A549 cells

source_name: A549 cells, irradiated and HT 44 degrees celsius


title: A549_IR

description: Gene expression data from irradiated A549 cells

source_name: A549 cells, irradiated


title: A549_HT 41.5

description: Gene expression data from HT(41.5 degrees celsius)-treated A549 cells

source_name: A549 cells, HT 41.5 degrees celsius


title: SAP CONJ2

description: MCF-7 with Saporin-EpCAM conjugate treatment for 24 h (2)


title: Control 1

description: Control sample of MCF-7 breast cancer cell line without treatment (1)


title: SAP 2

description: MCF-7 with saporin treatment for 24 h (2)


title: A549_control

description: Gene expression data from control A549 cells

source_name: A549 cells, control


title: Control 2

description: Control sample of MCF-7 breast cancer cell line without treatment (2)


title: NCS Conj 1

description:
sample 5 PR_(PrimeView).CEL
MCF-7 with the NCS-CONJ treatment post 24h incubation (1)

data_processing: The RMA normalization was done using Gene Spring Software (v.13.0 GX) following Affymetrix default workflow

treatment_protocol: Cells were treated with Neocarzinostatin (Sigma) and Neocarzinostatin-EpCAM aptamer conjugate (using Sulfo-LC-SPDP cross linker) and incubated for 24 h, cells with out treatment was maintained as a control

value: breast cancer cells (with same passage number)

tag: treated with

value: Neocarzinostatin-EpCAM Aptamer conjugate (NCS-CONJ) for 24 hrs


title: NCS Conj 2

description:
Sample 6 PR_(PrimeView).CEL
MCF-7 with the NCS-CONJ treatment post 24h incubation (2)


title: 1004-Bulk_B-U


title: LNCaP_rep5_6N


title: 1003-Effector_memory_CD8pos_T-U


title: 1003-Monocytes-S

value: Monocytes


title: 1003-Naive_CD8_T-S


title: 1003-Gamma_delta_T-U


title: LNCaP_rep4_6N


title: 1003-Central_memory_CD8pos_T-S


title: LNCaP_rep3_6N


title: LNCaP_rep2_3N


title: 1003-Mature_NK-S

value: NK


title: 1003-Monocytes-U


title: 1003-CD8pos_T-U


title: 1003-Th2_precursors-S


title: 1003-Th2_precursors-U


title: HeLa_rep19_3N

value: Nucleus


title: 1003-CD8pos_T-S


title: 1003-Mature_NK-U


title: NCS2

description:
Sample 4 PR_(PrimeView).CEL
MCF-7 with the NCS treatment for 24 h (2)

value: Neocarzinostatin (NCS) for 24 hrs


title: C2

description:
Sample 2 PR_(PrimeView).CEL
Control sample of MCF-7 breast cancer cell line without treatment (2)

value: none (untreated control)


title: NCS1

description:
sample 3 PR_(PrimeView).CEL
MCF-7 with the NCS treatment for 24 h (1)


title: NSC_rep16_3N

description: 3'READS human samples used in PolyA_DB version 3.2

value: NSC


title: C1

description:
sample 1 PR_(PrimeView).CEL
Control sample of MCF-7 breast cancer cell line without treatment (1)


title: NSC_rep17_3N


title: NSC_rep15_3N


title: 1003-Naive_B-U


title: NSC_rep14_3N


title: 1003-Th17_precursors-U


title: 1003-Naive_B-S

description:
Additional sequencing was performed on a NextSeq 500 and merged with this library.
ATAC_counts.txt.gz


title: Sinorhizobium meliloti CL150 pCAP11, biological rep 6

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: Affymetrix CEL files were analyzed using R and BIOCONDUCTOR software packages (Gentleman et al. 2004, Genome Biol 5:R80). Probe summarization and normalization were carried out with the AFFY package and the RMA algorithm (Irizarry et al. 2003, Biostatistics 4: 249-264).

organism: Sinorhizobium meliloti

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pCAP11 (empty vector control)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Bacteria were cultured in M9 medium with 0.4% glycerol as a carbon source, and supplemented with 50 ug/ml spectinomycin and 500 ug/ml streptomycin. When cultures reached an OD-600 of 0.5, melibiose was added to 0.4% for 30 minutes.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 (Proc Natl Acad Sci USA 101:16636-16641).

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: genotype/variation

value: wild type

tag: strain

value: CL150 pCAP11


title: Sinorhizobium meliloti CL150 pCAP11, biological rep 4


title: NSC_rep13_3N

value: cytoplasm


title: 1003-Central_memory_CD8pos_T-U


title: Sinorhizobium meliloti CL150 overexpressing FecI, biological rep 2

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1082 (FecI)

value: overexpressing FecI


title: 1003-Th17_precursors-S


title: Sinorhizobium meliloti CL150 pCAP11, biological rep 5


title: Sinorhizobium meliloti CL150 overexpressing FecI, biological rep 3


title: Sinorhizobium meliloti CL150 overexpressing FecI, biological rep 1


title: NSC_rep11_3N

value: total RNA


title: 1003-Mem_B-S


title: LNCaP_rep1_3N

value: 3'READS human samples used in PolyA_DB version 3.2


title: 1003-Regulatory_T-U


title: 1002-Myeloid_DCs-U

value: MYELOID


title: 1003-Mem_B-U

value: B


title: Sinorhizobium meliloti CL150 overexpressing RpoE10, biological rep 2

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pCL139 (RpoE10)

value: overexpressing RpoE10


title: 1002-Monocytes-S


title: 1003-Bulk_B-S


title: 1003-Th1_precursors-U


title: NSC_rep9_3N


title: 1003-Memory_Tregs-S


title: NSC_rep8_3N


title: Sinorhizobium meliloti CL150 overexpressing RpoE10, biological rep 3


title: NSC_rep12_3N


title: 1003-Regulatory_T-S


title: 1002-pDCs-U

value: pDCs


title: 1003-Memory_Tregs-U


title: 1003-Th1_precursors-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE9, biological rep 1

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1077 (RpoE9)

value: overexpressing RpoE9


title: Sinorhizobium meliloti CL150 overexpressing RpoE9, biological rep 2


title: 1002-Immature_NK-U


title: NSC_rep6_3N


title: 1003-Naive_Teffs-S


title: NSC_rep10_3N


title: 1002-Th2_precursors-U


title: 1003-Bulk_B-U


title: Sinorhizobium meliloti CL150 overexpressing RpoE10, biological rep 1


title: 1003-Naive_Teffs-U


title: 1003-Follicular_T_Helper-S


title: 1002-Memory_NK-U


title: Sinorhizobium meliloti CL150 overexpressing RpoE9, biological rep 3


title: 1002-Mature_NK-S


title: 1003-Follicular_T_Helper-U


title: NSC_rep3_3N


title: NSC_rep7_3N


title: 1003-Memory_Teffs-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE8, biological rep 1

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1086 (RpoE8)

value: overexpressing RpoE8


title: 1003-Effector_CD4pos_T-S


title: 1002-Th2_precursors-S


title: NSC_rep2_3N


title: Sinorhizobium meliloti CL150 overexpressing RpoE7, biological rep 3

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1080 (RpoE7)

value: overexpressing RpoE7


title: 1002-Th17_precursors-S


title: NSC_rep5_3N


title: NSC_rep4_3N


title: Sinorhizobium meliloti CL150 overexpressing RpoE8, biological rep 2


title: Sinorhizobium meliloti CL150 overexpressing RpoE8, biological rep 3


title: 1002-Th1_precursors-S


title: 1002-Th17_precursors-U


title: 1003-Memory_Teffs-U


title: Sinorhizobium meliloti CL150 overexpressing RpoE7, biological rep 2


title: 1003-Effector_CD4pos_T-U


title: 1002-Th1_precursors-U


title: 1003-Gamma_delta_T-S

value: GD


title: 293T_rep4_3N


title: 1003-Naive_CD8_T-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE6, biological rep 3

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1088 (RpoE6)

value: overexpressing RpoE6


title: 1003-Naive_CD8_T-U


title: Sinorhizobium meliloti CL150 overexpressing RpoE7, biological rep 1


title: 1002-Regulatory_T-U


title: 1002-Naive_Teffs-U


title: 293T_rep6_3N

value: Nucleus


title: 1002-Regulatory_T-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE6, biological rep 2


title: 1003-Gamma_delta_T-U


title: 1003-Effector_memory_CD8pos_T-U


title: 293T_rep5_3N


title: 293T_rep1_3N


title: 1003-Central_memory_CD8pos_T-S


title: 293T_rep3_3N

value: polysome


title: 1003-Effector_memory_CD8pos_T-S


title: 293T_rep2_3N


title: 1002-Memory_Tregs-S


title: 1003-Central_memory_CD8pos_T-U


title: HeLa_rep15_3N

value: HeLa


title: 1003-CD8pos_T-S


title: NSC_rep1_3N

value: NSC


title: HeLa_rep14_3N


title: Sinorhizobium meliloti CL150 overexpressing RpoE5, biological rep 1

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1074 (RpoE5)

value: overexpressing RpoE5


title: 1002-Memory_Teffs-U


title: cerebellum_rep4_3N

value: cerebellum


title: Sinorhizobium meliloti CL150 overexpressing RpoE5, biological rep 2


title: 1003-CD8pos_T-U


title: Sinorhizobium meliloti CL150 overexpressing RpoE5, biological rep 3


title: Sinorhizobium meliloti CL150 overexpressing RpoE6, biological rep 1


title: 1002-Follicular_T_Helper-U


title: 1002-Memory_Teffs-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE4, biological rep 3

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1085 (RpoE4)

value: overexpressing RpoE4


title: 1003-Naive_B-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE4, biological rep 1


title: 1002-Memory_Tregs-U


title: Sinorhizobium meliloti CL150 overexpressing RpoE4, biological rep 2


title: 1003-Mem_B-S


title: 1002-Naive_Teffs-S


title: 1002-Gamma_delta_T-S


title: 1002-Myeloid_DCs-U


title: HeLa_rep18_3N

value: 3'READS human samples used in PolyA_DB version 3.2

value: total RNA


title: JEG3_rep3_3N

value: free ribosomal


title: 1002-Follicular_T_Helper-S


title: HeLa_rep16_3N


title: 1002-Effector_CD4pos_T-S


title: 1002-Monocytes-U

value: Monocytes

value: MYELOID


title: Sinorhizobium meliloti CL150 overexpressing RpoE2, biological rep 3

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1084 (RpoE2)

value: overexpressing RpoE2


title: Sinorhizobium meliloti CL150 overexpressing RpoE2, biological rep 2


title: Sinorhizobium meliloti CL150 overexpressing RpoE3, biological rep 1

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1071 (RpoE3)

value: overexpressing RpoE3


title: Sinorhizobium meliloti CL150 overexpressing RpoE3, biological rep 3


title: cerebellum_rep2_3N


title: Sinorhizobium meliloti CL150 overexpressing RpoE1, biological rep 2

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pF1087 (RpoE1)

value: overexpressing RpoE1


title: 1002-Effector_CD4pos_T-U

source_name: primary blood


title: 1003-Bulk_B-S

value: B


title: cerebellum_rep1_3N


title: Sinorhizobium meliloti CL150 overexpressing RpoE3, biological rep 2


title: 1002-Memory_NK-U

value: NK


title: 1002-Effector_memory_CD8pos_T-S


title: 1002-Effector_memory_CD8pos_T-U


title: 1003-Bulk_B-U


title: JEG3_rep5_3N


title: 1002-Gamma_delta_T-U

value: GD


title: 1002-Mature_NK-S


title: HTR8_rep3_3N


title: cerebellum_rep3_3N


title: 1002-Naive_CD8_T-S


title: JEG3_rep4_3N

value: monosome


title: Sinorhizobium meliloti CL150 overexpressing RpoE2, biological rep 1


title: Sinorhizobium meliloti CL150 overexpressing RpoE1, biological rep 3


title: Sinorhizobium meliloti CL150 pCAP11, biological rep 2

value: wild type

value: CL150 pCAP11


title: 1002-Naive_CD8_T-U


title: JEG3_rep2_3N


title: Sinorhizobium meliloti Rm1021 pCAP11, biological rep 3

source_name: wild type strain Rm1021 carrying pCAP11 (empty vector control)

value: Rm1021 pCAP11


title: 1002-Monocytes-S


title: Sinorhizobium meliloti CL150 overexpressing RpoE1, biological rep 1


title: HTR8_rep5_3N

value: polysome


title: HTR8_rep4_3N


title: 1002-Central_memory_CD8pos_T-S


title: 1002-Central_memory_CD8pos_T-U


title: 1002-Th2_precursors-S


title: 1002-Mature_NK-U


title: HTR8_rep2_3N


title: MeWo_rep6_3N

value: MeWo


title: 1002-CD8pos_T-S


title: MeWo_rep4_3N

value: 3'READS human samples used in PolyA_DB version 3.2


title: MeWo_rep3_3N

value: total RNA


title: 1002-CD8pos_T-U


title: Sinorhizobium meliloti CL150 pCAP11, biological rep 1


title: MeWo_rep5_3N


title: Sinorhizobium meliloti CL101 pCAP11, biological rep 3

source_name: wild type strain CL101 (ecfR1 mutation corrected) carrying pCAP11 (empty vector control)

value: CL101 pCAP11


title: Sinorhizobium meliloti Rm1021 pCAP11, biological rep 2


title: 1002-Th17_precursors-U


title: 1002-Plasmablasts-U

value: Plasmablasts


title: 1002-Th2_precursors-U


title: 1002-Naive_B-U


title: 1002-Th1_precursors-S


title: 1002-Naive_B-S


title: Sinorhizobium meliloti Rm1021 pCAP11, biological rep 1


title: MeWo_rep2_3N


title: 1002-Mem_B-S


title: 1002-Mem_B-U


title: 1002-Regulatory_T-S


title: MeWo_rep1_3N


title: Sinorhizobium meliloti CL101 pCAP11, biological rep 1


title: IgG-CLIP-seq low RNase I

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

institute: Sejong University

description: CLIP-seq for AGO2

data_processing:
Reads were demuliplexed by using codes in the id of each reads by using the ShortRead package in BioConductor. Identical sequences were collapsed using the occurrenceFilter function in the ShortRead package.
3' adapter sequences were trimmed using the trimLRPatterns function in the ShortRead package. The 3' adapter sequences trimmed were sequences containing CCTGTGGTCGTAGCATCAGCTA.
The trimmed sequences were collapsed and converted to reverse complementary sequences.
CLIP-seq reads were sequentially mapped to rRNA, snRNA, snoRNA, tRNA and microRNA precursors sequences using Bowtie verions 1.12.7  with the following configurations -q –m 70 -n 2 -l 44 -5 1 -3 5 -a --best --strata -p 11 --sam --norc for noncoding RNAs. The remaining reads were aligned with the hg19 human genome  with the configuration -q –m 1 -n 0 -l 70 -5 1 -3 5 -a --best --strata -p 11 --sam  unique genomic sequences to generate bedGraph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph. Scores stand for CLIP-seq read coverage

source_name: Osteoblast differentiated from H1 hES cells

growth_protocol: H1 hESCs were differentiated to osteoblast as described by Kang et. al.

extract_protocol:
Two million cells were resuspended in 250 μl lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing EDTA-free protease inhibitor cocktail (Roche) and RNase inhibitor (Ambion) and briefly sonicated by using the Bioruptor.
The lysates were treated with 5 μl of Turbo DNase (Ambion) and 10 μl of 10 U/μl or 1 U/μl RNase I (Ambion) at 37°C for 3 min. Cellular debris was removed by centrifugation at 13,000 rpm for 15 min. Protein-RNA complexes were immunopurified with anti-AGO2 (ProteinTech) or IgG antibody (Bethyl laboratories) bound to Protein A/G Dynabeads. Beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS) followed by two washes with PNK buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20). For dephosphorylation of 3’ ends, 1U of FastAP alkaline phosphatase (Fermentas) was added to the beads and incubated at 37°C for 20 min. After washing the beads twice with PNK buffer, protein-bound RNAs were ligated to a pre-adenylylated 3’ adaptor overnight at 16°C. Beads were washed twice with PNK buffer again and labeled with [γ- 32P] ATP for visualization. The labeled RNAs were separated by 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane, and excised from the membrane. The protein was degraded by proteinase K treatment, and RNA was recovered by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Protein-associated RNAs purified by IP or CLIP were ligated to a pre-adenylylated 3’ adaptor that contains a 2-nt adapter code for de-multiplexing and a 3-nt random sequence to minimize the loss of information after collapsing identical sequences. The RNA-adapter hybrids were converted into cDNAs with RT primer and SuperScript III reverse transcriptase (Invitrogen). The cDNAs were size-fractionated by electrophoresis on a 12% denaturing polyacrylamide gel and circularized by single-stranded DNA ligase (Epicentre). Circularized cDNAs were amplified with PCR primers, in which one of them contained a 6-nt primer code for de-multiplexing. PCR products were purified by agarose gel elution and subjected to next-generation sequencing.

treatment_protocol: For CLIP experiments osteoblasts were irradiated with 300 mJ/cm2 of UVC light (254 nm) by using the CL-1000 ultraviolet crosslinker (UVP).

tag: antibody

value: rabbit IgG (Bethyl)

value: Osteoblast

tag: differentiated from

value: H1 hES cells


title: 1002-Naive_Teffs-U


title: 1002-Bulk_B-S


title: AGO2-CLIP-seq replicate 2 high RNase I

description: CLIP-seq for AGO2

value: anti-AGO2 (Proteintech, 10686-1)


title: 1002-Naive_Teffs-S


title: 1002-Th17_precursors-S


title: AGO2-CLIP-seq replicate 2 low RNase I

description: CLIP-seq for AGO2


title: Sinorhizobium meliloti CL101 pCAP11, biological rep 2


title: 1001-pDCs-U

value: pDCs

value: MYELOID


title: 1002-Regulatory_T-U


title: 1002-Bulk_B-U

value: B


title: Sinorhizobium meliloti RFF625c, biological rep 1

hyb_protocol: Amplifed RNA samples (20 ug) were hybridized to our chips at 45 degrees centigrade as described by Barnett et al 2004 (Proc Natl Acad Sci USA 101:16636-16641). GeneChips were washed and stained in the Affymetrix Fluidics Station 400

source_name: M. truncatula root nodules elicited by S. meliloti wild type strain RFF625c

label_protocol: Template RNA (1 μg) was amplified and was biotin-labeled, using the MessageAmp Bacteria kit (Ambion). Amplified RNA (20 μg) was fragmented in 40 μl of 200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate at 94 C for 35 min (Lang and Long 2015).

growth_protocol: We grew Medicago truncatula [Gaertn.] cvs. Jemalong on Buffered Nodulation Medium (BNM) agar plates as described previously (Mitra & Long, 2004 Plant Physiol 134:595-604). Four days after planting the plants were inoculated with either the wild type strain CL150; the all ECF sigma factor deletion strain (RFF625c); the rpoE8-SMb20593 deletion mutant (RFF465), the rpoE3-ecfR3 deletion mutant (RFF716) or the rpoH1 deletion mutant (RFF157). For the inoculation, S. meliloti cells were grown in LB medium, pelleted and resuspended in 10 mM MgSO4 to an OD of 0.5, and 1.5 µL of this cell suspension was spotted on the tip of the root of each plant.  For each of 4 replicates, we inoculated 22 plants.

extract_protocol: Nodules were ground with a microcentrifuge tube pestle as the buffer thawed. The lysate was brought to a volume of 450 μl with RLT buffer and processed through a Qiashredder column (Qiagen) and an RNeasy Mini spin column (Qiagen). The RNA was DNase-treated (DNase I; Thermo Fisher Scientific) in the presence of RNase inhibitor (SuperaseIN). The DNase-treated RNA was repurified using RNeasy MinElute columns (RNeasy MinElute kit, Qiagen). RNA quality and quantity were assayed using Bioanalyzer RNA Nano chips (Agilent) (Lang and Long 2015, Mol Plant Microbe Interact 28:856-868).

treatment_protocol: Root nodules elicited by wild type and sigma factor gene mutants were harvested at 25 days post inoculation and placed in 30 μl of RLT buffer (RNeasy mini kit; Qiagen), frozen in liquid nitrogen, and stored at -80 degrees centigrade.

tag: strain/genotype


title: AGO2-CLIP-seq replicate 1 low RNase I

description: CLIP-seq for AGO2


title: Sinorhizobium meliloti RFF625c, biological rep 3

value: all ECF sigma factor deletion strain (RFF625c)


title: 1001-Myeloid_DCs-U


title: 1002-Th1_precursors-U


title: Sinorhizobium meliloti RFF625c, biological rep 4


title: 1002-Memory_Tregs-S


title: Sinorhizobium meliloti RFF625c, biological rep 2


title: 1002-Memory_Teffs-S


title: AGO2-CLIP-seq replicate 1 high RNase I

description: CLIP-seq for AGO2


title: 1002-Follicular_T_Helper-U


title: 1001-Mature_NK-S

value: NK


title: Sinorhizobium meliloti RFF465, biological rep 2

source_name: M. truncatula root nodules elicited by S. meliloti wild type strain RFF465

value: rpoE8-SMb20593 deletion mutant (RFF465)


title: Sinorhizobium meliloti RFF465, biological rep 3


title: Sinorhizobium meliloti RFF465, biological rep 4


title: #20 CCl4 Study 2-4 CCl4+CCl4/EtOH 20D

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

institute: TEXAS A&M UNIVERSITY

data_processing:
Pair-end (100bp) sequencing was carried out using the Illumina HiSeq 2500 platform.
RNA-seq reads were aligned to appropriate reference genomes (NCBI mm10) using the “SNP-tolerant” GSNAP software
Differential gene expression analysis was then performed on the complete list of 18,965 genes using R package DESeq2 (v 1.12.3) [20].
A log2 fold-change (compared to Control group) and false discovery rate (FDR)-adjusted p-value (q-value) cut off at ±0.58 and <0.1, respectively, were applied
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample.

organism: Mus musculus

source_name: liver

extract_protocol:
Tissues were excised and snap-frozen in liquid nitrogen.
Libraries for RNA-seq were prepared from total liver RNA using the Illumina TruSeq mRNA Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: Adult male C57BL6/J mice were treated with CCl4 (0.2 ml/kg, 2×weekly by intraperitoneal injections for 6 weeks) to induce chronic liver fibrosis. Then, ethyl alcohol (EtOH) (up to 25 g/kg/day, for 3 weeks) was administered continuously to mice via a gastric feeding tube, with or without one-half dose of CCl4.

tag: developmental stage

value: adult

tag: gender

value: male

tag: time

value: liver


title: Sinorhizobium meliloti CL150 pCAP11, biological rep 3

source_name: wild type strain CL150 (ecfR1 pstC mutations corrected) carrying pCAP11 (empty vector control)

value: wild type

value: CL150 pCAP11


title: 1002-Gamma_delta_T-U

tag: donor

tag: cell type

value: GD


title: Sinorhizobium meliloti RFF716, biological rep 4

source_name: M. truncatula root nodules elicited by S. meliloti wild type strain RFF716

value: rpoE3-ecfR3 deletion mutant (RFF716)


title: Sinorhizobium meliloti RFF465, biological rep 1


title: Sinorhizobium meliloti RFF716, biological rep 3


title: 1001-Mature_NK-U

tag: lineage

tag: treatment


title: 1001-Immature_NK-U


title: #19 CCl4 Study 2-4 CCl4+CCl4/EtOH 20D

tag: tissue


title: 1002-Naive_CD8_T-S


title: 1002-Memory_Teffs-U


title: 1001-Monocytes-S

value: Monocytes


title: 1001-Monocytes-U


title: #18 CCl4 Study 2-4 CCl4+CCl4/EtOH 20D


title: 1001-Th2_precursors-U


title: 1002-Naive_CD8_T-U


title: 1002-Follicular_T_Helper-S


title: 1002-Effector_CD4pos_T-S


title: Sinorhizobium meliloti RFF716, biological rep 1


title: 1001-Memory_NK-U


title: Sinorhizobium meliloti RFF157, biological rep 4

source_name: M. truncatula root nodules elicited by S. meliloti wild type strain RFF157

value: rpoH1 deletion mutant (RFF157)


title: 1002-Effector_memory_CD8pos_T-S


title: Sinorhizobium meliloti RFF716, biological rep 2


title: #16 CCl4 Study 2-4 CCl4+CCl4/chow 20D


title: Sinorhizobium meliloti RFF157, biological rep 3


title: 1001-Th17_precursors-S


title: 1002-Effector_memory_CD8pos_T-U


title: 1001-Th2_precursors-S


title: #15 CCl4 Study 2-4 OO+OO/EtOH 20D

value: OO

value: OO/HFD/Etoh


title: 1002-CD8pos_T-S


title: 1001-Th17_precursors-U


title: 1001-Th1_precursors-S


title: 1001-Th1_precursors-U


title: 1002-CD8pos_T-U


title: 1002-Central_memory_CD8pos_T-S


title: #17 CCl4 Study 2-4 CCl4+CCl4/chow 20D


title: 1002-Mem_B-S


title: Sinorhizobium meliloti RFF157, biological rep 1


title: 1001-Regulatory_T-U


title: 1002-Naive_B-U


title: Sinorhizobium meliloti CL150, biological rep 4

source_name: M. truncatula root nodules elicited by S. meliloti wild type strain CL150

value: CL150, a wild type strain corrected for mutations in pstC and ecfR1


title: #12 CCl4 Study 2-4 OO+OO/chow 20D

value: OO/chow


title: 1001-Regulatory_T-S


title: #5 CCl4 Study 2-3 OO+chow 23D

value: chow


title: Sinorhizobium meliloti RFF157, biological rep 2


title: #6 CCl4 Study 2-3 OO+EtOH 23D

value: HFD/Etoh


title: 1001-Naive_Teffs-S


title: 1002-Bulk_B-S

value: B


title: #4 CCl4 Study CCl4 0D


title: Sinorhizobium meliloti CL150, biological rep 3


title: #2 CCl4 Study OO 0D


title: #14 CCl4 Study 2-4 OO+OO/EtOH 20D


title: 1001-Memory_Tregs-S


title: #13 CCl4 Study 2-4 OO+OO/EtOH 20D


title: 1002-Bulk_B-U


title: Sinorhizobium meliloti CL150, biological rep 2


title: #3 CCl4 Study CCl4 0D


title: Sinorhizobium meliloti CL150, biological rep 1


title: 1001-Memory_Tregs-U


title: 1002-Mem_B-U


title: 1001-Naive_Teffs-U


title: 1001-Memory_Teffs-S


title: #1 CCl4 Study OO 0D


title: 1001-Monocytes-S

value: MYELOID


title: 1001-Monocytes-U


title: 1001-Follicular_T_Helper-S


title: 1001-Memory_Teffs-U


title: 1001-Follicular_T_Helper-U


title: 1001-pDCs-U

value: pDCs


title: 24h_3

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

data_processing:
Sequencing software: HiSeq Control Software 2.2.58 Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64 fastq-file generation: CASAVA BCL2FASTQ Conversion Software 1.8.3
Sequenced reads with masked adaptor sequence were mapped to the murine genome, NCBI build 38, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM).
Genome_build: murine NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

source_name: interscapular brown adipose tissue

extract_protocol:
Interscapular BAT was excised and flash frozen. Total RNA was prepared from frozen tissue with Trisue (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were constructed from total RNA (TruSeq RNA Sample Prep kit v2 (Illumina)).

value: interscapular brown adipose tissue

tag: ambient temperature

tag: duration of cold exposure

value: 24 hours

value: male


title: 1001-Effector_CD4pos_T-S


title: 48h_1

value: 48 hours


title: 1001-Myeloid_DCs-U


title: 48h_2


title: 48h_3


title: 1001-Mature_NK-S

value: NK


title: 24h_2


title: 1001-Effector_CD4pos_T-U


title: 24h_1


title: 1001-Th2_precursors-S


title: 1001-Gamma_delta_T-U

value: GD


title: 1001-Mature_NK-U


title: 1001-Naive_CD8_T-S


title: 1001-Th17_precursors-S


title: 1001-Naive_CD8_T-U


title: 1001-Th2_precursors-U


title: 6h_2

value: 6 hours


title: 1001-Th17_precursors-U


title: 1001-Th1_precursors-S


title: 6h_1


title: 1001-Effector_memory_CD8pos_T-S


title: ctrl4


title: 6h_3


title: ctrl3


title: 1001-Th1_precursors-U


title: 1001-Effector_memory_CD8pos_T-U


title: SUM149 cell line treated with CX4945 Replicate 4

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

hyb_protocol: Samples were labeled and hybridized in Human Transcriptome arrays (HTA) by the Genomics Core Facility of the Center for Applied Medical Research (CIMA) following manufacturers instructions

scan_protocol: Affymetrix protocol

data_processing: Data preprocessed using aroma.affymetrix R package. Cel files where background corrected, quantile normalized and summarized using RMA.

source_name: SUM-149 Cell Line

growth_protocol: All cell lines were grown according to the suppliers’ recommendation

extract_protocol: Total RNAs were isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD) according to the manufacturer's protocol

treatment_protocol: To induce splicing events, cells were grown to ~70% confluence and treated with 1µM CX-4945  or DMSO during 12 hours in a total of 5 replicates per condition

tag: cell line

tag: agent


title: 1001-Central_memory_CD8pos_T-S


title: SUM149 cell line treated with CX4945 Replicate 1

label_protocol: Samples were labeled and hybridized in Human Transcriptome arrays (HTA) by the Genomics Core Facility of the Center for Applied Medical Research (CIMA) following manufacturers instructions


title: 1001-Central_memory_CD8pos_T-U


title: SUM149 cell line treated with CX4945 Replicate 3


title: SUM149 cell line treated with DMSO Replicate 5

value: DMSO


title: MDA468 cell line treated with CX4945 Replicate 5

source_name: MDA-MB-231 Cell Line


title: SUM149 cell line treated with CX4945 Replicate 2


title: ctrl2


title: ctrl1


title: 1001-Regulatory_T-S


title: 1001-CD8pos_T-U


title: 1001-CD8pos_T-S


title: 1001-Regulatory_T-U


title: 1001-Naive_Teffs-S


title: MDA468 cell line treated with DMSO Replicate 5


title: 1001-Naive_Tregs-U


title: SUM149 cell line treated with DMSO Replicate 4


title: 1001-Naive_B-S


title: 1001-Memory_Tregs-S


title: SUM149 cell line treated with DMSO Replicate 3


title: 1001-Memory_Tregs-U


title: 1001-Naive_B-U


title: 1001-Naive_Teffs-U


title: MDA468 cell line treated with CX4945 Replicate 1


title: 1001-Mem_B-S


title: 1001-Memory_Teffs-S


title: 1001-Mem_B-U


title: MDA468 cell line treated with DMSO Replicate 2


title: MDA468 cell line treated with DMSO Replicate 3


title: 1001-Bulk_B-S


title: MDA468 cell line treated with CX4945 Replicate 4


title: 1001-Plasmablasts-U

value: Plasmablasts


title: 1001-Memory_Teffs-U


title: 1001-Follicular_T_Helper-S


title: 1001-Follicular_T_Helper-U


title: 1011-Monocytes-S

value: Monocytes


title: 1001-Bulk_B-U


title: MDA468 cell line treated with CX4945 Replicate 3


title: MDA468 cell line treated with DMSO Replicate 1

source_name: MDA-MB-468 Cell Line


title: MDA468 cell line treated with DMSO Replicate 4


title: 1001-Effector_CD4pos_T-S


title: MDA468 cell line treated with CX4945 Replicate 2


title: 1001-Effector_CD4pos_T-U


title: 1011-Naive_Teffs-S


title: 1001-Gamma_delta_T-S


title: SUM149 cell line treated with DMSO Replicate 2


title: 1011-Naive_B-S


title: 1010-Monocytes-S


title: H5_methylation

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description: bisulfite converted genomic DNA

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4).
Reads were mapped to the reference genome (UMD3.1) using the software package Bismark (version: 0.17.0).
Methylation calls were performed for the alignment files using Bismark methylation extractor.
Genome_build: Cow genome assembly: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files including chromosome, genomic start position, genomic end position, percentage of methylation at that position, number of Cs methylated, and number of Cs non-methylated

organism: Bos taurus

source_name: Bull calf ID: 5 TRT: HT

extract_protocol:
Total DNA was extracted from liver and mammary gland samples for reduced representation bisulfite sequencing analysis. Extraction, library construction, bisulfite treatment and sequencing were performed by Epigentek. DNA was isolated from 50 mg of tissue with the FitAmpTM General Tissue Section DNA Isolation Kit.
DNA was digested with MspI restriction enzyme for 2 hrs at 37°C followed by digestion with TaqαI restriction endonuclease at 65°C. DNA fragments < 300 bp were selected and used for bisulfite treatment with the Methylamp DNA Conversion Kit. Standard lllumina sequencing adaptors were ligated onto the bisulfite treated DNA fragments using a random probing method. Library amplification was achieved using indexed primers and analyzed on a Bioanalyzer and with a KAPA Library Quantification Kit according to the manufacturer’s protocol. Purified DNA (15 nM of sample) libraries were sequenced using the Illumina HiSeq 4000 system generating 50 bp single-end reads.

value: Liver

tag: breed

value: Holstein

tag: animal id

value: Bull calf ID:5

value: HT


title: 1001-Gamma_delta_T-U


title: H4_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 4 TRT: HT

value: Bull calf ID:4


title: 1001-Naive_CD8_T-S

source_name: primary blood


title: 1010-Immature_NK-U


title: 1001-Naive_CD8_T-U


title: 1001-Effector_memory_CD8pos_T-S


title: 1010-Th2_precursors-U


title: H2_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 2 TRT: HT

value: Bull calf ID:2


title: 1010-Th17_precursors-U


title: MDA 231 cell line treated with CX4945 Replicate 4

value: MDA 231


title: 1001-Effector_memory_CD8pos_T-U


title: 1010-Mature_NK-S


title: C5_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 5 TRT: CL

value: CL


title: 1010-Th1_precursors-U


title: 1001-Central_memory_CD8pos_T-S


title: MDA 231 cell line treated with CX4945 Replicate 3


title: 1010-Naive_Tregs-S


title: C4_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 4 TRT: CL


title: 1001-Central_memory_CD8pos_T-U


title: MDA 231 cell line treated with CX4945 Replicate 2


title: C3_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 3 TRT: CL

value: Bull calf ID:3


title: 1010-Effector_CD4pos_T-U


title: 1010-Naive_B-U

value: B


title: C2_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 2 TRT: CL


title: MDA231 cell line treated with DMSO Replicate 4


title: MDA231 cell line treated with DMSO Replicate 3


title: 1010-Mem_B-U


title: MDA231 cell line treated with DMSO Replicate 5


title: H9204_methylation

description: bisulfite converted genomic DNA

source_name: Heifer ID: 9204 TRT: HT

value: Mammary gland

value: Heifer ID:9204


title: 1001-Plasmablasts-U


title: 1001-Naive_B-S


title: 1009-Monocytes-S

value: MYELOID


title: MDA 231 cell line treated with CX4945 Replicate 1


title: 1009-Mature_NK-S

value: NK


title: MDA231 cell line treated with CX4945 Replicate 5


title: H9196_methylation

description: bisulfite converted genomic DNA

source_name: Heifer ID: 9196 TRT: HT

value: Heifer ID:9196


title: 1001-Naive_B-U


title: 1001-CD8pos_T-U


title: 1001-CD8pos_T-S


title: 1001-Mem_B-S


title: 1009-Naive_Tregs-S


title: C9223_methylation

description: bisulfite converted genomic DNA

source_name: Heifer ID: 9223 TRT: CL

value: Heifer ID:9223


title: H9203_methylation

description: bisulfite converted genomic DNA

source_name: Heifer ID: 9203 TRT: HT

value: Heifer ID:9203


title: MDA231 cell line treated with DMSO Replicate 2

value: DMSO


title: MDA231 cell line treated with DMSO Replicate 1


title: SUM149 cell line treated with CX4945 Replicate 5


title: 1001-Mem_B-U


title: 1009-Naive_Teffs-S


title: SUM149 cell line treated with DMSO Replicate 1

scan_protocol: Affymetrix protocol Affymetrix protocol


title: 1009-Naive_B-S


title: 1008-Monocytes-S

value: Monocytes


title: 1001-Bulk_B-U


title: 1001-Bulk_B-S


title: C9214_methylation

description: bisulfite converted genomic DNA

source_name: Heifer ID: 9214 TRT: CL

value: Holstein

value: Heifer ID:9214


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

status: Public on Sep 04 2018

type: genomic

city: Los Angeles

first: Steve

last: Horvath

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

department: Human Genetics

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.

tag: Sex

value: male

tag: age

tag: ethnicity

value: Hispanic

tag: dnamage

tag: plasmablast

tag: natural killer cell

tag: b cell

tag: monocyte

tag: granulocyte

tag: disease status

value: PD

tag: pdstudylevodopastatus

value: no


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

description: genomic DNA from Blood

value: yes


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

description: genomic DNA from Blood

value: female


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


title: C9202_methylation

description: bisulfite converted genomic DNA

source_name: Heifer ID: 9202 TRT: CL

tag: tissue

value: Mammary gland

value: Heifer ID:9202

tag: treatment

value: CL


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


title: C1_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 1 TRT: CL

value: Liver

value: Bull calf ID:1


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


title: H3_methylation

description: bisulfite converted genomic DNA

source_name: Bull calf ID: 3 TRT: HT

value: Bull calf ID:3

value: HT


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood

value: control


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


title: PEGhispanic: genomic DNA from whole blood of subject Sample5

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


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

description: genomic DNA from Blood


title: PEGhispanic: genomic DNA from whole blood of subject Sample3

description: genomic DNA from Blood


title: PEGhispanic: genomic DNA from whole blood of subject Sample1

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample505

description: genomic DNA from Blood

value: Caucasian

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

tag: levodopastatus

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus

value: never

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample506

description: genomic DNA from Blood

tag: Sex

tag: age

tag: ethnicity

tag: dnamage

tag: plasmablast

value: former


title: PEGcaucasian: genomic DNA from whole blood of subject Sample508

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample504

description: genomic DNA from Blood

value: male


title: PEGcaucasian: genomic DNA from whole blood of subject Sample507

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample500

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample501

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample499

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample495

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample497

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample498

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample491

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample492

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample496

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample489

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample494

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample487

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample488

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample484

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample482

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample481

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample480

description: genomic DNA from Blood


title: PEGhispanic: genomic DNA from whole blood of subject Sample2

description: genomic DNA from Blood

value: Hispanic

tag: natural killer cell

tag: b cell

tag: monocyte

tag: granulocyte

tag: disease status

tag: pdstudylevodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample483

description: genomic DNA from Blood

tag: nk

tag: bcell

tag: mono

tag: gran

tag: diseasestatus

tag: levodopastatus


title: PEGcaucasian: genomic DNA from whole blood of subject Sample503

description: genomic DNA from Blood

tag: Sex

value: PD

tag: levodopaperdayincludingagonists

tag: numberofyearsinschool

tag: smokingstatus

tag: packyearstotal

tag: familyhistoryofparkinsons


title: PEGcaucasian: genomic DNA from whole blood of subject Sample502

description: genomic DNA from Blood

tag: age

tag: ethnicity

tag: dnamage

tag: plasmablast

value: no


title: PEGcaucasian: genomic DNA from whole blood of subject Sample478

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample476

description: genomic DNA from Blood

value: current


title: PEGcaucasian: genomic DNA from whole blood of subject Sample479

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample473

description: genomic DNA from Blood

value: female

value: yes


title: PEGcaucasian: genomic DNA from whole blood of subject Sample474

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample493

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample490

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample472

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample468

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample471

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample486

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample470

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample485

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample469

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample466

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample455

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample465

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample461

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample458

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample457

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample456

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample454

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample462

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample467

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample459

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample463

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample464

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample475

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample460

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample452

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample477

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample453

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample450

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample449

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample451

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample448

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample447

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample446

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample444

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample445

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample443

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample442

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample440

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample441

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample439

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample438

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample430

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample431

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample426

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample436

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample433

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample427

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample434

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample435

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample428

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample425

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample432

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample424

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample423

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample421

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample418

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample417

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample420

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample415

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample412

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample413

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample414

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample411

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample429

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample437

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample410

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample409

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample408

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample405

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample422

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample403

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample397

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample396

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample402

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample419

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample393

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample400

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample404

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample398

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample395

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample394

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample392

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample391

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample416

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample390

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample389

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample388

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample387

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample386

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample384

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample385

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample383

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample381

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample406

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample407

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample399

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample401

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample380

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample377

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample379

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample375

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample376

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample374

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample373

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample378

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample367

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample365

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample366

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample370

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample368

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample369

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample363

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample371

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample364

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample362

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample361

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample382

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample357

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample359

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample358

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample356

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample355

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample372

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample352

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample353

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample345

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample344

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample346

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample348

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample347

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample350

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample349

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample351

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample354

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample340

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample342

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample341

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample339

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample338

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample336

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample337

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample360

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample343

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample334

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample335

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample333

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample328

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample331

description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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title: PEGcaucasian: genomic DNA from whole blood of subject Sample295

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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample251

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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample237

description: genomic DNA from Blood


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description: genomic DNA from Blood


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description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample236

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample233

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample234

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample257

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample232

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample231

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample235

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample247

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample229

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample230

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample227

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample225

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample223

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample248

description: genomic DNA from Blood


title: PEGcaucasian: genomic DNA from whole blood of subject Sample224

description: genomic DNA from Blood


title: Input NT shRNA H9 hESCs (replicate 1)

city: Cologne

first: David

last: Vilchez

state: NRW

address: Joseph Stelzmann Strasse, 26

institute: CECAD - Cluster of Excellence

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)

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

tag: expression

value: non-targeting (NT) shRNA


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

value: H3K9me3 antibody (Abcam, #8898)


title: PEGcaucasian: genomic DNA from whole blood of subject Sample221

description: genomic DNA from Blood

tag: nk

tag: bcell


title: PEGcaucasian: genomic DNA from whole blood of subject Sample220

description: genomic DNA from Blood

tag: mono

tag: gran


title: PEGcaucasian: genomic DNA from whole blood of subject Sample219

description: genomic DNA from Blood

tag: diseasestatus

tag: levodopastatus