title: ATAC-seq for patient CLL7 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL7 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL9 during Ibrutinib treatment

status: Public on Jan 26 2019

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL9 during Ibrutinib treatment

library_source: genomic

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair created
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair; narrowPeak files contain peaks called by MACS2

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary peripheral blood mononucleated cells (PBMC) from chronic lymphocytic leukemia patient

extract_protocol:
Heparinized peripheral blood was obtained from CLL patients after signed informed consent. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Hypaque (GE Healthcare, Uppsala, Sweden) centrifugation. Patients were screened for CLL characteristic chromosomal aberrations including deletions on 13q14, 11q22, and 17p13 and for trisomy 12 by FISH analysis. The IGHV and TP53 mutational status was determined by sequencing (LGC Genomics, Berlin, DE). PBMCs from CLL patients were cryopreserved in RPMI 1640 supplemented with 40% FCS and 10 % DMSO.
~10^5 cells were pelleted by centrifuging for 5 min at 4 °C at 300 x g. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 ml 2xTD buffer, 2 ml TDE1 (Illumina) and 10.25 ml nuclease-free water, 0.25 µl 5% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11 µl, 1 µl of the eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 25-bp paired-end configuration.

tag: patient id

tag: library

value: ATAC-seq

tag: cell type

value: CLL

tag: processing batch

value: Vienna General Hospital

tag: sample type

tag: clinical status

value: disease

tag: disease

tag: timepoint name

value: M

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment


title: ATAC-seq for patient CLL7 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL7 before Ibrutinib treatment

tag: clinical centre

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

value: FALSE

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

value: TRUE

tag: sample tp53 mutation description

value: SD


title: ATAC-seq for patient CLL6 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL6 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

value: F

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: DEXTGFbeta_1

status: Public on Jan 27 2019

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University of Belfast

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC hg38 whole genome using Rsubread v1.22 with parameters Type =0 nthreads= 16 nTrim5 13 nTrim3=3
Counts were calculated using FeatureCounts function within the Rssubread package
Genome_build: UCSC hg38
Supplementary_files_format_and_content: A single tab delimited file contains the raw counts for the 18 samples analysed

molecule: total RNA

source_name: BEAS-2B cell line

growth_protocol: Human A549 lung adenocarcinoma cells (ATCC, Manassas, VA, USA) were grown in phenol red-free Dulbecco's modified Eagle's media (DMEM) containing 5% vv−1 heat-inactivated fetal calf serum (FCS), 15 mM HEPES, 0.2% vv−1 sodium bicarbonate, 2 mM L-glutamine, 1% vv−1 non-essential amino acids, 1% vv−1 sodium pyruvate, 5 IU·mL−1 penicillin and 50 µg·mL−1 streptomycin and maintained at 37°C in a humidified 5% CO2/95% air atmosphere

extract_protocol:
Total RNA was extracted using RNeasy miniprep kit (Qiagen)
RNA-Seq libraries were prepared from 500ng total RNA (RIN>8 according to Agilent Bioanalyzer 2100) using NEBNext Ultra RNA library prep kit for Illumina (#E7530) with NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490).

treatment_protocol: Human BEAS-2B bronchial epithelial cells (ATCC, Manassas, VA, USA) were seeded at a density of 25,000 cells/cm2 in 24 well tissue culture plates and allowed to adhere overnight in complete growth medium (LHC-9 media containing 2% v/v heat-inactivated fetal calf serum, 2 mM L-glutamine, 50 IU/mL penicillin and 50 µg/mL streptomycin). Cells were then starved in serum- and steroid-free medium (RPMI medium containing 0.25% bovine serum albumin, 2 mM L-glutamine, 1% v/v sodium pyruvate and 1% v/v non-essential amino acids, 15 mM HEPES, 0.2% v/v sodium bicarbonate, 50 IU/mL penicillin and 50 µg/mL streptomycin) for 24 h prior to treatment with TGF-β1 (40 pM) for 24 h then dexamethasone (30 nM) stimulation for a further 4 h.

tag: cell type

value: BEAS-2B bronchial epithelial cells

tag: treatment

value: Dexamethasone and TGF-beta1


title: Dex_1

value: Dexamethasone


title: ATAC-seq for patient CLL3 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL3 during Ibrutinib treatment

tag: patient id

tag: library

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: blood platelets

tag: sample viability percentage

value: PR


title: control_2


title: ATAC-seq for patient CLL4 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL4 during Ibrutinib treatment

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL5 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL5 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status


title: ATAC-seq for patient CLL21 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL21 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL20 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL20 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description

value: c.845delGinsCCTC, p.(Asp281_Arg282insPro;Arg282Ser); Exon 8


title: ATAC-seq for patient CLL3 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL3 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL21 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL21 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage


title: TGF-Beta_3

tag: cell type

tag: treatment


title: ATAC-seq for patient CLL20 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL20 before Ibrutinib treatment

tag: patient id

tag: library

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample clone number

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL19 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL19 before Ibrutinib treatment

tag: cell type

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description


title: ATAC-seq for patient CLL17 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL17 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL17 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL17 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description

value: c.215G>C pArg72Pro


title: ATAC-seq for patient CLL19 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL19 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment


title: ATAC-seq for patient CLL4 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL4 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL2 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL2 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment


title: ATAC-seq for patient CLL14 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL14 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL15 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL15 before Ibrutinib treatment

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description


title: ATAC-seq for patient CLL13 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL13 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL16 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL16 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage


title: ATAC-seq for patient CLL14 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL14 before Ibrutinib treatment

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage


title: ATAC-seq for patient CLL15 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL15 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: blood hemoglobin

tag: blood platelets

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: ATAC-seq for patient CLL13 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL13 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description

value: c.215G>C pArg72Pro Homozygot


title: ATAC-seq for patient CLL11 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL11 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: Gamma150.S19

status: Public on Jan 25 2019

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

country: USA

institute: University of Pennsylvania

description: master_list_gene_counts_MIN.sense.Gamma_Proton_radiation.txt.gz

data_processing:
CASAVA-1.8.1 was used to demultiplex pooled samples and convert BCL to FASTQ.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR_2.5.2a.
Data were normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

organism: Mus musculus

source_name: aorta

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap

extract_protocol:
RNA was extracted using Trizol and Qiagen Rneasy Mini kit.
Library construction was carried out using Illumina TruSeq RNA Sample Prep kit and SBS kit v3. Samples were handled in a blinded fashion. Selection strategy: polyA

treatment_protocol: 10 mice were treated with ten different centigrays of gamma radiation and 10 mice were treated with ten different centigrays of high energy protons (0 cGy, 5 cGy, 10 cGy, 25 cGy, 50 cGy, 75 cGy, 100 cGy, 125 cGy, 150 cGy, 200 cGy). Treated at the same time, same day. Sacrificed 4 hours after irradiation.

tag: strain

tag: developmental stage

value: adult

tag: Sex

value: male

tag: age

value: 10 to 12 week

tag: genetic alteration

value: wildtype

tag: radiation

value: Gamma

tag: radiation dose

value: 150 cGy


title: Gamma125.S18

value: 125 cGy


title: ATAC-seq for patient CLL1 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL1 during Ibrutinib treatment

tag: patient id

tag: library

value: ATAC-seq

tag: cell type

value: CLL

tag: processing batch

tag: clinical centre

value: Vienna General Hospital

tag: sample type

tag: clinical status

value: disease

tag: disease

tag: timepoint name

tag: patient gender

value: M

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood granulocyte percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+cd5- percentage


title: ATAC-seq for patient CLL10 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL10 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: blood monocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19-cd5+ percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

value: FALSE

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation

value: SD


title: Gamma50.S15

tag: strain

tag: developmental stage

tag: Sex

tag: age

tag: genetic alteration

tag: radiation

tag: radiation dose

value: 50 cGy


title: Gamma25.S14

value: 25 cGy


title: ATAC-seq for patient CLL16 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL16 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

value: TRUE


title: Gamma5.S12

tag: strain

tag: developmental stage

value: adult

tag: Sex

tag: age

tag: genetic alteration

tag: radiation

tag: radiation dose

value: 5 cGy


title: ATAC-seq for patient CLL12 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL12 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample ighv mutation status

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: Gamma100.S17

tag: strain

tag: developmental stage

tag: Sex

value: male

tag: age

value: 10 to 12 week

tag: genetic alteration

tag: radiation

tag: radiation dose

value: 100 cGy


title: ATAC-seq for patient CLL1 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL1 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

value: PR


title: ATAC-seq for patient CLL11 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL11 during Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

value: F

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation


title: Gamma200.S20

tag: strain

tag: developmental stage

tag: Sex

tag: age

tag: genetic alteration

value: wildtype

tag: radiation

value: Gamma

tag: radiation dose

value: 200 cGy


title: ATAC-seq for patient CLL10 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL10 during Ibrutinib treatment

tag: patient id

tag: library

value: ATAC-seq

tag: cell type

value: CLL

tag: processing batch

tag: clinical centre

value: Vienna General Hospital

tag: sample type

tag: clinical status

value: disease

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage


title: Proton125.S8

tag: strain

tag: developmental stage

tag: Sex

tag: age

tag: genetic alteration

tag: radiation

value: Proton

tag: radiation dose

value: 125 cGy


title: ATAC-seq for patient CLL12 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL12 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

value: M

tag: patient years at diagnosis

tag: patient leukocyte count (10e3/ul)

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample cd38+ percentage in viable cd19+cd5+

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

value: FALSE

tag: sample del11q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

value: TRUE

tag: sample tp53 mutation description

value: c.215G>C pArg72Pro

tag: sample days since ibrutinib treatment

tag: patient preliminary response evaluation

value: SD


title: mRNAseq_CD_0_Ins_metformin_replicate1

status: Public on Jan 31 2019

city: Bethesda

first: Anthony

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

description: mRNA_CD_0_Ins_metformin_allReps_gene_raw_read_counts.txt

data_processing:
Raw sequencing reads were aligned to known mouse RefSeq gene transcripts obtained from the UCSC table browser (accessed on January 25, 2012) and the mouse genome (build mm9) with the splice junction-aware short-read alignment tool TopHat (version 1.4.0). We restricted TopHat to only align to known transcript splice junctions. Gene-level read counts were quantified using the python package HTSeq. We used the Bioconductor package conditional quantile normalization (CQN, version 1.6.0) to remove systematic biases due to GC-content and gene length coverage and used DESeq2 (version 1.0.18) to perform differential expression analyses. We considered a gene to be differentially expressed if it possessed an absolute log2 fold-change between conditions ≥ 0.5, an FDR-adjusted p-value (q-value) ≤ 0.05, and was expressed in at least one tested condition (i.e. ≥ 0.1 FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: *_raw_read_counts.txt files were generated with the HTSeq count python program using BAM files against mouse RefSeq gene models (included in *.gtf file) with, column 1 containing gene names and the remaining containing read count values for each labeled condition; *_normalized_read_counts.txt files contain conditional quantile normalization (CQN) and DESeq2 normalized counts for all samples in the same format as the raw read count files

molecule: polyA RNA

extract_protocol:
All livers were removed using clamps cooled in liquid nitrogen. Frozen liver were then pulverized using a CryoPREP impactor (Covaris).
We extracted total RNA from the pulverized frozen livers of mice using the miRNeasy Mini kit (Qiagen). We prepared mRNA-Seq libraries using the TruSeq RNA Sample Prep Kit v1 (Illumina) and size-selected using 2% agarose gel electrophoresis for 180 +/- 25 base-pairs of insert. We multiplexed mRNA-Seq libraries and paired-end sequenced samples for 40-50 base-pairs on an Illumina Hi-Seq 2000 machine.

treatment_protocol: We fed mice a standard chow diet (Prolab Isopro RMH 3000, Purina) or a high-fat diet (S3282, Bioserve) for 6 or 16 weeks. HFD feeding was initiated when mice were 8 weeks of age for the 16 week time point or at 18 weeks of age for the 6 week time point. All mice were sacrificed at 24 weeks of age following overnight starvation. Some mice were administered 1 U/kg of insulin (Novolin R, Novo Nordisk) diluted in PBS via intraperitoneal injection. These mice were sacrificed at variable times post insulin injection. Other mice were treated with metformin (Sigma, PHR1084), initiated at 8 or 18 weeks, dissolved in drinking water to attain a dose of 270 mg/kg/day lean body mass by dilution of a freshly prepared 10 mg/ml stock solution.

tag: strain

tag: tissue

value: liver

tag: diet

value: chow diet

tag: age

value: 24 weeks

tag: genotype

value: wild type

tag: treatment

value: Metformin treatment


title: Proton25.S4

tag: developmental stage

value: adult

tag: Sex

value: male

value: 10 to 12 week

tag: genetic alteration

value: wildtype

tag: radiation

tag: radiation dose

value: 25 cGy


title: Proton10.S3

value: Proton

value: 10 cGy


title: Gamma75.S16

value: Gamma

value: 75 cGy


title: Proton0.S1

value: 0 cGy


title: Gamma0.S11


title: Proton100.S7

value: 100 cGy


title: Gamma10.S13


title: Proton150.S9

value: 150 cGy


title: Proton200.S10

value: 200 cGy


title: Proton75.S6


title: ATAC-seq for patient CLL2 during Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL2 during Ibrutinib treatment

tag: patient id

tag: library

value: ATAC-seq

tag: cell type

value: CLL

tag: processing batch

tag: clinical centre

value: Vienna General Hospital

tag: sample type

tag: clinical status

value: disease

tag: disease

tag: timepoint name

tag: patient gender

value: M

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

value: SD


title: Proton50.S5

tag: strain

tag: developmental stage

value: adult

tag: Sex

value: male

tag: age

value: 10 to 12 week

tag: genetic alteration

tag: radiation

tag: radiation dose

value: 50 cGy


title: KO Bone-3

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts (.txt)

extract_protocol:
Bone & marrow fraction were separated from tibia, femur and humeri of WT and Gfra2KO mice. After RBC lysis, mature hematopoietic cells were depleted using the EasyStep Mouse Hematopoietic Progenitor Cell Isolation Cocktail (Stem cell Technologies, 19756) according to the manufacturer’s protocol. The depleted cell population was stained for 20 minutes in PBS with 2 % FCS for LSK CD48-CD150+ markers. After dead cell exclusion using DAPI, pools of 30 viable LSK CD48-CD150+ cells were sorted using BD Influx™ cell sorter into 4 µl lysis buffer (0.5 U/µl SUPERase In RNase Inhibitor in 0.2 % (v/v) Triton-X-100) containing 12.5 mM DTT and 2.5 mM dNTP. RNAseq was performed following Smart-seq2 protocol (Picelli 2014)
Pooled libraries of 4 replicates per sample were prepared using the Illumina Nextera XT DNA preparation kit & sequencing was performed on the Illumina HiSeq 4000

treatment_protocol: no treatment

tag: tissue

value: Bone marrow - Bone fraction

tag: genotype

value: Gfra2 KO


title: WT Bone-2

value: Gfra2 WT


title: KO Bone-4


title: WT Bone-4


title: KO Marrow-2

value: Bone marrow - Marrow fraction


title: Proton5.S2

value: wildtype

value: Proton

value: 5 cGy


title: WT Marrow-3


title: KO Marrow-3


title: KO Bone-2


title: WT Marrow-2


title: KO Marrow-1


title: KO Bone-1


title: WT Bone-1


title: WT Marrow-1


title: Control240

city: Bronx

first: Maureen

middle: J

last: Charron

state: NY

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

description:
HpaII test for HELP-tagging
C15_240

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (ELAND - 1.7.0).  Initial data processing was performed using the default read length of 37 or 42 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions. To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Illumina Casava was used for basecalling.
After the sequence data was obtained from Illumina HiSeq 2500, we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again  (ELAND - 1.7.0) on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: Format: wiggle track; content: methylation level for each CpG site

source_name: control_human CD3+ T-cell

extract_protocol:
High molecular weight genomic DNA was extracted fromCD3+ T-cell from human cord blood.
Custom adapters were created for HELP-tagging, referred to as AE and AS Index. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence, and adapter AS contains index sequences for multiplexing .  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure XP (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

tag: subject status

value: control

tag: maternal age (years)

tag: weight at term (lbs)

tag: bmi at term

tag: gestational age (weeks)

tag: birth weight (g)

value: cord blood

tag: cell type

value: CD3+ T-cell


title: IUGR126

description:
HpaII test for HELP-tagging
CB126

source_name: IUGR_human CD3+ T-cell

value: Intrauterine Growth Restricted (IUGR) Newborns


title: IUGR357

description:
HpaII test for HELP-tagging
IU10_357


title: WT Marrow-4


title: Control253

description:
HpaII test for HELP-tagging
C3_253


title: IUGR373

description:
HpaII test for HELP-tagging
IU12_373


title: IUGR127

description:
HpaII test for HELP-tagging
CB127


title: Control160

description:
HpaII test for HELP-tagging
CB160


title: Control234

description:
HpaII test for HELP-tagging
C1_234


title: IUGR168

description:
HpaII test for HELP-tagging
CB168


title: Control199

description:
HpaII test for HELP-tagging
CB199


title: IUGR158

description:
HpaII test for HELP-tagging
CB158


title: Control268

description:
HpaII test for HELP-tagging
C4_268


title: IUGR399

description:
HpaII test for HELP-tagging
IU14_399


title: WT Bone-3


title: Control139

description:
HpaII test for HELP-tagging
CB139


title: Subc. adipose tissue Healthy control subject-6 at ZT D3:1115

status: Public on Jan 24 2019

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

data_processing:
Alignment of sequence reads was performed in colorspace for the individual samples against the GRCh37/hg19 reference genome using the Lifescope aligner (v2.5.1) from Applied Biosystems (Thermo Fisher Scientific) applying the “whole transcriptome mapping” workflow with a mapping quality cut-off (bamgen.mqv.threshold) set to 20.
Counts were obtained using the corresponding genome annotation (as provided by Applied Biosystems) and applying the default values of the Lifescope workflow (only primary alignments, mapping quality above 10, only reads exceeding the provided feature boundaries with less than 3 bases in total).
The obtained counts were used as input for the consecutive analysis using the statistical computing environment R (version 3.1.0). Only features with CPM (counts per million mapped reads) of more than 1 in 2 or more samples were retained in the analysis (16818 genes).
Counts were normalized by applying the trimmed mean of M-values method.
Dispersion estimation and differential expression analyses were performed using edgeR (v3.6.7).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file contains raw count data as obtained using Lifescope workflow; rownames contain genename, chromosome and RefSeq accession numbers; one column per sample.

source_name: Subcutaneous adipose tissue

extract_protocol:
RNA isolation was performed according to the RNeasy-Mini protocol for animal tissues and cells on the Qiacube (Qiagen) including an RNAse-free-DNAse digestion step. RNA concentrations were measured with a Nanodrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and quality was checked on a RNA 6000 Nanochip with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Subsequently cDNA was constructed with the Ovation RNA-Seq System V2 (NuGen, Manchester, UK) and the product was purified with the MinElute PCR Purification kit (Qiagen). cDNAconcentration was determined by fluormetric measurement with Qubit dsDNA BR (Invitrogen, Thermo Fisher Scientific) and quality checked with the Bioanalyser  DNA1000 (Agilent Technologies). 2 ug cDNA was sheared by sonication (Covaris, Woburn, MA, USA)  using the following settings: 7 cycles, frequency sweeping, 10% duty cycle, intensity 5, 100 cycles/burst, 60 seconds. Size distribution after shearing was checked using the Bioanalyser. Sheared cDNA was size selected to maintain fragments in the size range of 140 to 180 bp, by double ampure purification (Agencourt, Beckman Coulter, Brea, CA, USA) on a Biomek FX automated liquid handler (Beckman Coulter) according to the manufacturer’s recommendations, an ampure:sample ratio of 1.0 for the first bead capture, and a ratio of 1.5 for the second bead capture. Sizing and concentration were checked using Bioanalyser and Qubit.
Barcoded adaptor ligated library construction, from the size selected cDNA, was performed using the Biomek FX automated liquid handler, and the Solid fragment Library preparation kit (Lifetech, pn 4464412), and Solid barcoded adaptors following manufacturer’s protocol. Each sample was generated using a separate 10bp barcode incorporated in the adaptor sequence. After 8 cycles of amplification using the library prep kit supplied PCR primers, PCR mix, and PCR protocol, samples were purified twice using ampure (ratio of 1.5) and pooled equimolar based on concentration and average sample size. Sequencing of this equimolar pool was performed on the Solid 5500 Wildfire sequencer (Life technologies, Thermo Fisher Scientific) generating an average of 40 million 50bp fragment and 10bp barcode reads per sample.

value: Healthy

tag: subject id #

tag: gender

tag: bmi (kg/m2)

tag: hba1c (mmol/mol)

tag: timepoint


title: Subc. adipose tissue Healthy control subject-6 at ZT D3:545

tag: age


title: Subc. adipose tissue Healthy control subject-6 at ZT D3:015


title: Subc. adipose tissue Healthy control subject-5 at ZT D3:1115


title: Subc. adipose tissue Healthy control subject-5 at ZT D2:1530


title: Subc. adipose tissue Healthy control subject-5 at ZT D3:015


title: Subc. adipose tissue Healthy control subject-4 at ZT D3:545


title: Subc. adipose tissue Healthy control subject-4 at ZT D3:015


title: Subc. adipose tissue Healthy control subject-4 at ZT D3:1115


title: Subc. adipose tissue Healthy control subject-5 at ZT D3:545


title: Control138

description:
HpaII test for HELP-tagging
CB138


title: KO Marrow-4

tag: strain


title: Subc. adipose tissue Healthy control subject-1 at ZT D3:1115


title: Subc. adipose tissue Healthy control subject-1 at ZT D3:015


title: Subc. adipose tissue Healthy control subject-2 at ZT D2:1530


title: Subc. adipose tissue Healthy control subject-2 at ZT D3:1115


title: Subc. adipose tissue Healthy control subject-4 at ZT D2:1530


title: Subc. adipose tissue Type 2 diabetes patient-6 at ZT D3:1115

value: Type 2 diabetes


title: Subc. adipose tissue Healthy control subject-3 at ZT D3:015


title: Subc. adipose tissue Healthy control subject-6 at ZT D2:1530


title: Subc. adipose tissue Healthy control subject-2 at ZT D3:015


title: Subc. adipose tissue Healthy control subject-3 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-6 at ZT D3:545


title: Subc. adipose tissue Healthy control subject-3 at ZT D3:1115


title: Subc. adipose tissue Healthy control subject-3 at ZT D2:1530


title: Subc. adipose tissue Type 2 diabetes patient-5 at ZT D3:1115


title: Subc. adipose tissue Type 2 diabetes patient-6 at ZT D2:1530


title: Subc. adipose tissue Type 2 diabetes patient-5 at ZT D3:015


title: Subc. adipose tissue Type 2 diabetes patient-5 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-5 at ZT D2:1530


title: Subc. adipose tissue Type 2 diabetes patient-4 at ZT D3:1115


title: Subc. adipose tissue Type 2 diabetes patient-4 at ZT D3:015


title: Subc. adipose tissue Type 2 diabetes patient-4 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-4 at ZT D2:1530


title: Subc. adipose tissue Healthy control subject-2 at ZT D3:545


title: Subc. adipose tissue Healthy control subject-1 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-6 at ZT D3:015


title: Subc. adipose tissue Type 2 diabetes patient-3 at ZT D3:1115


title: Subc. adipose tissue Healthy control subject-1 at ZT D2:1530


title: iPSCs(serum)

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
Reads were aligned to the UCSC mm10 transcriptome (using RNA-Seq genome-aligner  STAR), and a matrix of UMI counts was obtained using CELLRANGER from the 10X Genomics pipeline  (v1.1.0) with default parameters
All cells with less than 1000 UMIs detected per cell in total and all  genes that were expressed in less than 50 cells were discarded, leaving 65,781 cells and 16,339  genes for further analysis. The elements of expression matrix were normalized by dividing UMI count  by the total UMI counts detected in a cell, multiplied by 10,000, and log-transformed after adding a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: txt file contains normalized and log-transformed expression matrix

source_name: iPSCs

growth_protocol: For the reprogramming assay, 20,000 low passage MEFs (no greater than 3-4 passages from isolation) were seeded in a 6-well plate. These cells were cultured at 37°C and 5% CO2 in reprogramming medium containing KnockOut DMEM (GIBCO), 10% knockout serum replacement (KSR, GIBCO), 10% fetalbovine serum (FBS, GIBCO), 1% GlutaMAX (Invitrogen), 1% nonessential amino acids (NEAA, Invitrogen), 0.055 mM 2-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Invitrogen) and 1,000 U/ml leukemia inhibitory factor (LIF, Millipore). Day 0 medium was supplemented with 2g/mL doxycycline Phase-1(Dox) to induce the polycistronic OKSM expression cassette. Medium was refreshed every other day. At day 8, doxycycline was withdrawn, and cells were transferred to either serum-free 2i medium containing 3 M CHIR99021, 1 M PD0325901, and LIF (Phase-2(2i)) (25) or maintained in reprogramming medium (Phase-2(serum)). Fresh medium was added every other day until the final time point on day 16. Oct4-EGFP positive iPSC colonies should start to appear on day 10, indicative of successful reprogramming of the endogenous Oct4 locus.

extract_protocol:
We collected a total of 66,000 cells from twelve time points over a period of 16 days in two different culture conditions. Single or duplicate samples were collected at day 0 (before and after Dox addition), 2, 4, 6, and 8 in Phase-1(Dox); day 9, 10, 11, 12, 16 in Phase-2(2i); and day 10, 12, 16 in Phase-2(serum). Cells were also collected from established iPSCs cell lines reprogrammed from the same MEFs, maintained either in Phase-2(2i) conditions or in Phase-2(serum) medium. For all time points, selected wells were trypsinized for 5 mins followed by inactivation of trypsin by addition of MEF medium. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps. Cell count was determined using Neubauer chamber hemocytometer to a final concentration of 1000 cells/ul.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3’ Reagent Kits v1 (PN-120230, PN-120231, PN-120232) according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, Atailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry.

tag: cell types

value: iPSCs (OKSM)

tag: time point:


title: Subc. adipose tissue Type 2 diabetes patient-3 at ZT D2:1530

value: male


title: Subc. adipose tissue Type 2 diabetes patient-2 at ZT D3:1115


title: Subc. adipose tissue Type 2 diabetes patient-2 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-1 at ZT D3:015


title: Subc. adipose tissue Type 2 diabetes patient-1 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-1 at ZT D3:1115


title: Subc. adipose tissue Type 2 diabetes patient-2 at ZT D3:015


title: Subc. adipose tissue Type 2 diabetes patient-1 at ZT D2:1530


title: Subc. adipose tissue Type 2 diabetes patient-3 at ZT D3:545


title: Subc. adipose tissue Type 2 diabetes patient-2 at ZT D2:1530


title: FA_rep1

first: Aalim

middle: M

last: Weljie

address: 3400 Civic Center Blvd

data_processing:
CASAVA was used to demultiplex pooled samples and convert BCL to FASTQ.
Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-Seq data were aligned to the rat genome build rn6 by STAR 2.4.1d.
Data were normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization
Read resampling and quantification steps were performed 10 times and the average of ten normalized counts was calculated.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was isolated by trizol extraction of liver samples
Library preparation was performed using Illumina kit following the manufacturer prescribed protocol. mRNA was purified and fragmented followed by cDNA synthesis. The 3' ends were adenylated and adapters were ligated followed by PCR amplification. The quality and quantitiy of library was validated using bioanalyzer followed by normalization and pooling of libraries.

tag: tissue

value: liver

tag: sleep restriction

value: Forced activity control


title: SR_rep2

value: Sleep restriction


title: SR_rep1


title: JLDDC2NT4 Biological Replicate #2

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
Illumina Casava1.8 software used for basecalling.
The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%.
Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2).
Genome_build: version 5.5 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii hmox1 complemented strain

growth_protocol: All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness.

extract_protocol: Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina.

treatment_protocol: Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit.

tag: treatment

value: 0 mM

tag: light

value: 4h white light


title: FA_rep2


title: Subc. adipose tissue Type 2 diabetes patient-3 at ZT D3:015

tag: subject status


title: JLDDC1NT05 Biological Replicate #2

value: 0.5h white light


title: JLDDC2NT4 Biological Replicate #1


title: JLDDC2NT0 Biological Replicate #2

value: dark


title: JLDDC1NT4 Biological Replicate #1


title: JLDDC1NT05 Biological Replicate #1


title: JLDDC2NT05 Biological Replicate #1


title: JLDDC2NT0 Biological Replicate #1


title: JLDDC2NT05 Biological Replicate #2


title: JLDDC1NT0 Biological Replicate #2


title: JLDD4ABV4 Biological Replicate #2

source_name: Chlamydomonas reinhardtii 4A+ wild-type


title: JLDDhoNT4 Biological Replicate #1

source_name: Chlamydomonas reinhardtii hmox1 mutant


title: JLDDhoNT4 Biological Replicate #2


title: JLDDhoBV4 Biological Replicate #2


title: JLDDC1NT0 Biological Replicate #1


title: JLDD4ABV4 Biological Replicate #1


title: JLDD4ANT4 Biological Replicate #2


title: 3131_benign_prostate_TABseq

status: Public on Jan 23 2019

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Library strategy: TAB-seq
Sequencing reads from TAB-seq data were aligned to the human genome  using version 1.0 of an internally developed pipeline,  publicly available for download from https://github.com/luuloi/WGBSX10.
Adaptor sequences and poor-quality bases were removed using cutadapt  (https://github.com/marcelm/cutadapt) in paired-end mode with  default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: prostate biopsy DNA from a single donor

growth_protocol: Five 2 mm core biopsies were taken from 1) each of the dominant nodule in areas of >90% cancer cell density, and 2) adjacent benign prostate tissue.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen, USA)
β-Glucosetransferase (GT)-mediated 5hmC protection and TET1-mediated 5mC oxidation were performed using the 5hmC TAB-seq Kit (WiseGene, USA, cat no K001).  Bisulphite treatment of TET1-oxidised DNA followed by the library preparation was performed using the TrueMethyl Whole-Genome kit from Cambridge Epigenetix according to the manufacturer’s instructions. Paired-end 150bp sequencing was performed for each library on the Illumina HiSeqX platform using the HiSeq X™ Ten Reagent Kit v2.

tag: sample id

value: adjacent benign normal prostate


title: JLDD4ANT4 Biological Replicate #1


title: 3640_tumor_prostate_TABseq

value: prostate tumor


title: 3640_benign_prostate_TABseq


title: 3131_tumor_prostate_TABseq


title: 24023_tumor_prostate_TABseq


title: mouseStriatum_wtHTT_AGO2RIP_S13_smallRNA

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description:
small RNA
wtHTT-RIP1_S13_L001_R1_001
small RNA seq

data_processing:
Adaptors were trimmed using Cutadapt and qualtiy of reads were checked using FASTQC
Data was aligned either to the human (hg38) or to the mouse (mm10) genome using StarAligner 2.5.0a.
For analysis of small RNAs 1 mismatch per 22nt were allowed, for mRNA analyses default setting were used.
For the analyses of small RNAs deriving from transposable elements, we uniquely aligned the data to the human genome (hg38) using StarAligner 2.5.0a (0 mismatches). For the analysis of transposable elements in total RNA samples data was uniquely aligned, allowing for 2 mismatches in 50bp (--outFilterMismatchNoverLmax 0.04).
mRNA and non-coding RNAs were quantified using the subread package FeatureCoutns (primary reads) using annotation files from Ensembl and iGenomes NCBI annotations. Transposable elements were quantified using the RepeatMasker Track from UCSC.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: featC.3UTR.txt.gz [Tab-delimited table with quantification of reads mapping to 3UTR annotation of Ensembl. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.linc.txt.gz [Tab-delimited table with quantification of reads mapping to lncRNA annotation of NCBI igenomes. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.refseq.txt.gz [Tab-delimited table with quantification of reads mapping to igenomes NCBI annotation. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.RNR.txt.gz [Tab-delimited table with quantification of reads mapping to RNR from NCBI annotation. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.repeatsONLYminOverlap.txt.gz [Tab-delimited table with quantification of reads mapping to repeats from UCSC genome browser RepeatMasker track annotations. Column 1: RepName, Column2: Total length of all elements of the given element subfamily. Column 3-: each column correspond to one sample, identified in header]
featC.repeatsONLYminOverlap2024.txt.gz [Tab-delimited table with quantification of 20-24 nt long reads mapping to repeats from UCSC genome browser RepeatMasker track annotation. Column 1: RepName, Column2: Total length of all elements of the given element subfamily. ]
featC.piRNA2024minOverlap.txt.gz [Tab-delimited table with quantification of 20-24 nt long reads mapping to piRNAs from piRNAbank annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.piRNAminOverlap.txt.gz [Tab-delimited table with quantification of reads mapping to piRNAs from piRNAbank annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.miRbaseminoverlap.txt.gz [Tab-delimited table with quantification of reads mapping to miRNAs from miRbase annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.miRbase2024_minoverlap.txt.gz [Tab-delimited table with quantification of 20-24nt long reads mapping to miRNAs from miRbase annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.hg38tRNA_minO.txt.gz [Tab-delimited table with quantification of reads mapping to tRNAs from UCSC genome browser RepeatMasker track annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.small.hg38tRNAminO.txt.gz [Tab-delimited table with quantification of 20-24nt  reads mapping to tRNAs from UCSC genome browser RepeatMasker track annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.3UTRCells.txt.gz [Tab-delimited table with quantification of reads mapping to 3UTR annotation of Ensembl. Column 1 contains transcriptID. Column 2: reads of RIP and input samples]
Bigwigs

source_name: brain

extract_protocol:
Brain biopsies were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NEBNext Multiplex Small RNA Library Prep Set for Illumina

value: striatal tissue

tag: rip antibody

value: AGO2 antibody Sigma-Aldrich 2E12-1C9

tag: ago protein


title: mouseStriatum_wtHTT_AGO2RIP_S17_smallRNA

description:
small RNA
wtHTT-RIP3_S17_L001_R1_001
small RNA seq


title: mouseStriatum_wtHTT_AGO2RIP_S15_smallRNA

description:
small RNA
wtHTT-RIP2_S15_L001_R1_001
small RNA seq


title: Mutant CD4 SP cells, rep1

city: Freiburg

first: Andreas

middle: S.

last: Richter

address: Stuebeweg 51

department: Bioinformatics Unit

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Processed data file: mouse_CD4SP_diff_expr_genes_edgeR.tsv.gz
Processed data file: mouse_CD4SP_exon_skipping_rMATS.tsv.gz

data_processing:
Basecalling was performed with Illumina RTA version 1.18.64.
Mouse reads were aligned to GRCm38 genome assembly using TopHat 2.0.13 with the following settings: transcriptome alignment to GENCODE release M4 gene annotation first, library type fr-firststrand, fragment length mean and standard deviation set to sample-specific values. The fragment length metrics was determined by mapping a 1 million read pair subsample to the mouse transcriptome using Bowtie 2.2.3. Zebrafish reads were aligned with the same strategy to Zv9 genome assembly and Ensembl 78 gene annotation.
The numbers of sequenced fragments per annotated gene (based on GENCODE M4 mouse or Ensembl 78 zebrafish annotation, respectively) were quantified with featureCounts version 1.4.5-p1. Fragments were only counted if both ends aligned to the same chromosome with a minimum mapping quality of 10 and in agreement with the strand orientation of the annotated gene.
Differential gene expression analysis for mouse was performed with the Bioconductor package edgeR version 3.12.0 using the quasi-likelihood (QL) method, robustified against potential outlier genes. Weakly expressed genes with less than 0.2 counts-per-million (CPM) in at least 3 samples were filtered out. The FDR threshold was 1%. Differentially expressed genes in zebrafish were called using the Bioconductor package DESeq2 version 1.6.3 at 5% FDR. As the mutant and wild-type fish were different mixtures of genetic backgrounds, the linear regression formula used was modified accordingly ("~background+condition").
Differential alternative splicing events were analysed with rMATS 3.0.9. Aligned reads were filtered to include only reads overlapping with annotated transcripts in the same strand orientation based on GENCODE M4 mouse or Ensembl 78 zebrafish annotation, respectively. Fragment size mean and standard deviation were set to sample-specific values as described for the read alignment step. Alternative splicing events supported by reads spanning splice junctions were reported.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include significant differentially expressed genes as reported by edgeR and DESeq2 for mouse and zebrafish, respectively. Tab-delimited text files include exon skipping events generated by rMATS.

source_name: thymocytes, CD4+, Tnpo3 mutant

extract_protocol:
Total RNA was extracted from purified mouse thymocytes using RNeasy Mini kit (Qiagen), including a DNaseI treatment step. For the analysis of mutant zebrafish, RNA was extracted from 4 dpf embryos using Tri-Reagent (Sigma), treated with DNaseI and re-extracted with Tri-Reagent. RNA quality was determined using the 2100 Bioanalyzer instrument (Agilent) and RNA concentration was determined using Qbit 2.0 Fluorometer (Life Technologies).
RNA libraries were prepared for sequencing using the TruSeq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat (RS-122-2203, Illumina).

tag: genotype/variation

value: Tnpo3fl/fl; Lck:Cre

tag: strain/background

tag: cell type

value: thymocytes

tag: surface phenotype


title: Control CD4 SP cells, rep1

source_name: thymocytes, CD4+, control

value: Tnpo3fl/+; Lck:Cre


title: Control CD4 SP cells, rep2


title: Mutant DP cells, rep3

source_name: thymocytes, CD4+CD8+, Tnpo3 mutant


title: Mutant CD4 SP cells, rep2


title: Mutant CD4 SP cells, rep3


title: Mutant DP cells, rep2


title: JLDDC1NT4 Biological Replicate #2


title: JLDDhoBV4 Biological Replicate #1


title: LNCaP Repli-Seq S3 rep2

city: Darlinghurst

first: Qian

last: Du

address: 384 Victoria St

institute: Garvan Institute of Medical Research

data_processing:
Repli-Seq reads were aligned to hg19 using bowtie v1.1.0 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
To avoid bias from duplications or repeats, read densities were calculated in 150 bp intervals and intervals were excluded from further analysis if they contained greater than 20 reads per 150 bp window. Read densities were calculated in 50 kb sliding windows at 1 kb intervals across the remaining genomic regions, excluding chrY and chrM. Read densities were normalised to reads/counts per million and 50kb windows with low coverage (5 reads/counts per million) were removed.
To account for variation in sequencing coverage, mapability and cell-type specific copy-number variations, the remaining 50 kb window reads/counts per million values in all 6 fractions of a given sample were converted to a percentage of total signal at each 1kb locus called Percent-normalised Density Values (PNDV).
PNDV values were then converted into a single replication timing weighted average score per 1kb loci using the following formula: Weighted Average = (0.917*G1)+(0.750*S1)+(0.583*S2)+(0.417*S3)+(0.250*S4)+(0*G2). The formula for this transformation was obtained from the ENCODE method for “Replication Timing by Repli-Seq”.
Replicate WA values per cell line were averaged and used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: LNCaP prostate cancer cell

growth_protocol: Cell lines were cultured according to manufacturer's instructions.

extract_protocol:
Cells were labeled with BrdU (50uM, Sigma, #B5002) for two hours. Labeled cells were sorted into 6 fractions across the cell cycle (G1b, S1, S2, S3, S4, G2M) on the FACSAriaII based on DNA content labeling using propidium iodide. DNA extraction and BrdU-labeled DNA immunoprecipitation were performed with anti-BrdU antibody (BD Pharmingen, #555627). Validation of BrdU immunoprecipitation was carried out using qPCR on known Early (BMP1) and Late (DPPA2) loci (primers from Ryba et. al. (2011)).
ssDNA was reconstituted for the complementary DNA strand using Klenow extension with random hexamers (Random Primers DNA Labeling System, Invitrogen #18187-013) using 10 ng of ssDNA input and a 2hr incubation. Reconstituted dsDNA was rechecked for enrichment of known Early and Late loci using qPCR. Klenow-treated products were sonicated using a Sonifer 250 probe sonicator. Klenow-treated dsDNA was sent to University of Southern California Epigenome Centre Data Production Facility for 50 bp single-end sequencing on the Illumina HiSeq 2000.

value: Prostate

tag: cell line

value: LNCaP


title: LNCaP Repli-Seq S4 rep2


title: Control DP cells, rep2

source_name: thymocytes, CD4+CD8+, control


title: Mutant DP cells, rep1


title: LNCaP Repli-Seq G2 rep1


title: LNCaP Repli-Seq S4 rep1


title: 24023_benign_prostate_TABseq


title: LNCaP Repli-Seq G1 rep2


title: Control DP cells, rep1


title: LNCaP Repli-Seq G2 rep2


title: LNCaP Repli-Seq S1 rep1


title: LNCaP Repli-Seq S3 rep1


title: Control CD4 SP cells, rep3


title: LNCaP Repli-Seq S2 rep1


title: LNCaP Repli-Seq G1 rep1


title: Control DP cells, rep3


title: PrEC Repli-Seq S2 rep2

source_name: PrEC normal prostate cell

value: PrEC


title: PrEC Repli-Seq G1 rep2


title: PrEC Repli-Seq S4 rep2


title: PrEC Repli-Seq S3 rep2


title: PrEC Repli-Seq G2 rep1


title: PrEC Repli-Seq G2 rep2


title: LNCaP Repli-Seq S1 rep2


title: PrEC Repli-Seq S1 rep2


title: PrEC Repli-Seq S2 rep1


title: PrEC Repli-Seq S3 rep1


title: PrEC Repli-Seq G1 rep1


title: PrEC Repli-Seq S1 rep1


title: PrEC Repli-Seq S4 rep1


title: LNCaP Repli-Seq S2 rep2


title: A9195A

city: East Lansing

first: Stephanie

last: Valberg

state: MI

address: 736 Wilson Road, D202

department: LACS

institute: Michigan State University

data_processing:
Fastqc, sickle for trimming with min 100 bp, N 's removed, STAR to align and get counts using version 2.86 of horse transcriptome, Edge R  to get DE
Picard tools used for calculating insert size and other stats
Genome_build: EquCab2 and release version was 86 from Ensembl (http://www.ensembl.org/Equus_caballus/Info/Index?db=core)
Supplementary_files_format_and_content: Included raw count file

organism: Equus caballus

source_name: muscle_After exercise

extract_protocol:
Total RNA extracted using a modified trizol method
Using Illumina Stranded True-Seq kit
Strand specific, RNA-Seq, paired

tag: breed

value: Arabian horse

value: After exercise

value: Gluteal muscle


title: A9199B

source_name: muscle_Before exercise

value: Before exercise


title: A9197A


title: A9202A


title: A9197B


title: A9191B


title: A9194A


title: A9194B


title: A9196B


title: A9195B


title: A9196A


title: A9190B


title: A9188B


title: A9202B


title: A9187A


title: A9185B


title: A9187B


title: A9185A


title: A9184B


title: A9184A


title: Glioblastoma_AGO2IN_B9_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B9IN
total RNA seq

extract_protocol:
Brain biopsies were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NuGen Ovation RNAseq V2 kit, followed by the Ovation® Ultralow V2 Library or Ovation® Rapid Library Systems

value: Glioblastoma

value: AGO2 IN


title: Glioblastoma_AGO2IN_B10_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B10IN
total RNA seq


title: HumanCortex_AGO2IN_B8_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B8IN
total RNA seq

value: cortex


title: Glioblastoma_AGO2IN_B6_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B6IN
total RNA seq


title: HumanCortex_AGO2IN_B14_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B14_AGO2IN_T_S74_L005_R1_001
total RNA seq


title: hESC_AGO2RIP_totalRNA

description:
featC.3UTRCells.txt.gz [3utr]
Cells
total RNA seq

source_name: ESCs

growth_protocol: Human ESC H9 (WA09, passage 31-45) was expanded and maintained on γ-irradiated mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% KSR, 0.05 mM 2-mercaptoethanol, 0.5% pen/strep, 0.5% glutamate and 10 ng/ml FGF-2 (R&D Systems). The cells were passaged once weekly with EDTA (0.5 mM).Differentiation was initiated by detaching the hESC colonies with EDTA and grown as free-floating aggregates in DMEM/F12:Neurobasal (1:1) supplemented with N2 (1:100), B27 (without vitamin A) (1:50) for 4 days and Y-27632 (10 mM, Tocris Bioscience) for the initial 2 days. The formed EBs were thereafter plated in DMEM/F12:Neurobasal (1:1), N2 (1:200) and B27 (without vitamin A) (1:100) onto a surface coated with polyornithine (PO), fibronectin (FN) and laminin (lam). From d0 to d9, SB431542 (10 mM, Tocris Bioscience) and noggin (200 ng/ml, R&D) were present in the medium for neuralisation.  At day 11, the attached cell clusters were dissociated to a single-cell suspension with Accutase, and were replated in 20 μl droplets of 10,000-15,000 cells/μl onto dry PO/FN/lam-coated plates in Neurobasal, B27 (without vitamin A) (1:50), brain-derived neurotrophic factor (BDNF) (20 ng/ml), glial-derived neurotrophic factor (GDNF) (10 ng/ml) and ascorbic acid (200 mM).

extract_protocol:
Cells were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NuGen Ovation RNAseq V2 kit, followed by the Ovation® Ultralow V2 Library or Ovation® Rapid Library Systems

value: ESC-derived neurons


title: A9191A


title: Glioblastoma_AGO2RIP_B10_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B10
total RNA seq


title: A9190A


title: Glioblastoma_AGO2RIP_B6_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B6
total RNA seq


title: Glioblastoma_AGO2RIP_B9_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B9
total RNA seq


title: HumanCortex_AGO1IN_B8_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B8AGO1IN
small RNA seq

value: AGO1 IN


title: Glioblastoma_AGO2IN_B7_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B7AGO2IN
small RNA seq


title: Glioblastoma_AGO1IN_B7_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B7AGO1IN
small RNA seq


title: Glioblastoma_AGO2IN_B10_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B10AGO2IN
small RNA seq


title: Glioblastoma_AGO1IN_B9_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B9AGO1IN
small RNA seq


title: Glioblastoma_AGO1IN_B6_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B6AGO1IN
small RNA seq


title: HumanCortex_AGO2RIP_B8_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B8
total RNA seq


title: Glioblastoma_AGO2IN_B2_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
Sample_B2NsmallRNA
small RNA seq


title: Glioblastoma_AGO2IN_B9_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B9AGO2IN
small RNA seq


title: hESC_AGO2IN_totalRNA

description:
featC.3UTRCells.txt.gz [3utr]
CellsIN
total RNA seq


title: Glioblastoma_AGO2IN_B6_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B6AGO2IN
small RNA seq


title: A9188A


title: HumanCortex_AGO2IN_B5_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
Sample_B5NsmallRNA
small RNA seq


title: HumanCortex_AGO2IN_B8_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B8AGO2IN
small RNA seq


title: HumanCortex_AGO2IN_B14_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B14_AGO2IN_S_S20_L005_R1_001
small RNA seq


title: Glioblastoma_AGO2IN_B1_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
Sample_B1NsmallRNA
small RNA seq


title: hESC_AGO2IN_smallRNA

description:
small RNA
CellsAGO2IN
small RNA seq

extract_protocol:
Cells were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NEBNext Multiplex Small RNA Library Prep Set for Illumina

value: ES-derived neurons


title: Glioblastoma_AGO1RIP_B10_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B10AGO1
small RNA seq

value: AGO1 antibody:Active Motif, 61071


title: Glioblastoma_AGO2RIP_B9_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B9AGO2
small RNA seq


title: Glioblastoma_AGO1RIP_B7_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B7AGO1
small RNA seq


title: Glioblastoma_AGO1RIP_B9_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B9AGO1
small RNA seq


title: Glioblastoma_AGO2RIP_B10_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B10AGO2
small RNA seq


title: Glioblastoma_AGO2RIP_B7_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B7AGO2
small RNA seq


title: Glioblastoma_AGO1RIP_B8_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B8AGO1
small RNA seq


title: Glioblastoma_AGO1RIP_B6_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B6AGO1
small RNA seq


title: Glioblastoma_AGO2RIP_B2_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
Sample_B2smallRNA
small RNA seq


title: HumanCortex_AGO2RIP_B8_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B8AGO2
small RNA seq


title: Glioblastoma_AGO2RIP_B6_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B6AGO2
small RNA seq


title: HumanCortex_AGO2RIP_B5_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
Sample_B5smallRNA
small RNA seq


title: Glioblastoma_AGO2RIP_B1_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
Sample_B1smallRNA
small RNA seq


title: 3030_CD8_antiCD3_IFNgpos

city: La JOLLA

first: Alba

last: Grifoni

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Insitute for allergy and immunology

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: Cryopreserved PBMC

growth_protocol: Cells were isolated post thawing of cryopreserved PBMC samples and lysed after 3 hrs of stimulaton and  IFN-gamma capture assay.

extract_protocol:
Cryopreserved PBMC were thawed, stimulated with ZIKA pool of peptides or anti-CD3/CD28 stimulation or with no stimuli. After 3 hr of stimulation cells were stained with antibodies and IFNg capture assay, 200 cells of CD8 T cells were sorted using BD Aria 3 or BD Aria Fusion cell sorter for each condition, multiple of 200  cells were collected when possible.  CD8 responding and non responding  cells were defined with the expression of the followiing antibodies CD3+CD8+IFNg+ and CD3+CD8+IFNg- respectively.
Microscaled cDNA amplification of purified total RNA (1 to 5 ng) following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: Cells were pulsed for 3 hrs with no stimuli or ZIKV pool of peptides or anti-CD3/CD28 beads.

tag: individual

value: subject 3030

tag: stimulation

value: CD8 T cells

tag: cell subset

value: CD3+CD8+ T cells


title: 3052_CD8_antiCD3_IFNgpos

value: subject 3052


title: 3047_CD8_antiCD3_IFNgpos

value: subject 3047


title: 3045_CD8_antiCD3_IFNgpos

value: subject 3045


title: 3053_CD8_antiCD3_IFNgpos

value: subject 3053


title: 3031_CD8_antiCD3_IFNgpos

value: subject 3031


title: 3039_CD8_antiCD3_IFNgpos

value: subject 3039


title: 3038_CD8_antiCD3_IFNgpos

value: subject 3038


title: 3043_CD8_antiCD3_IFNgpos

value: subject 3043


title: 3028_CD8_antiCD3_IFNgpos

value: subject 3028


title: 3027_CD8_antiCD3_IFNgpos

value: subject 3027


title: hESC_AGO2RIP_smallRNA

description:
small RNA
CellsAGO2
small RNA seq


title: 2894_CD8_ZK_IFNgpos

value: subject 2894

value: CD3+CD8+IFNg+ T cells


title: 3054_CD8_ZK_IFNgpos

value: subject 3054


title: 3052_CD8_ZK_IFNgpos


title: 2653_CD8_ZK_IFNgpos

value: subject 2653


title: 3047_CD8_ZK_IFNgpos


title: 2692_CD8_antiCD3_IFNgpos

value: subject 2692


title: 3045_CD8_ZK_IFNgpos

value: CD8 T cells


title: 3038_CD8_ZK_IFNgpos


title: 3054_CD8_antiCD3_IFNgpos

value: CD3+CD8+ T cells


title: 2653_CD8_antiCD3_IFNgpos


title: 3031_CD8_ZK_IFNgpos


title: 3043_CD8_ZK_IFNgpos