title: human_spleen

description:
human_spleen_counts_normalized_4465x12476.tsv
human_spleen_cell_metadata_4465x9.tsv

source_name: spleen

extract_protocol:
Fresh spleen tissue was obtained from patients undergoing surgical resection of tumors in other organs. Patients were not receiving treatment at the time of surgery and had not received prior chemotherapy or immunotherapy. Spleen tissue was dissociated by manual mincing followed by an incubation of 45 min at 37°C, 250 rpm,  in RPMI1640 supplemented with 5% fetal calf serum, 1% L-glutamine, 1% penicillin–streptomycin, 10 mM HEPES, 1 mg/ml collagenase A (Sigma, 11088793001) and 1U/mL DNase I (Sigma, 10104159001). Cells were then washed and filtered with a 100 μm filter. Human DCs from spleen were enriched with Dynabeads™ Human DC Enrichment kit (Thermofisher). Lin(CD3, CD19, CD56)–CD14–CD11c+MHCII+ cells were then FACS-isolated into RPMI-2% FBS for single cell RNA-seq.
The scRNA-seq libraries were prepared following the user guide manual (CG00052 Rev E) provided by the 10X Genomics and Chromium™ Single Cell 3' Reagent Kit (v2). Briefly, samples were encapsulated in microfluidic droplets at a dilution of ~70 cells/µl (doublet rate ~3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53ºC for 60 min. After RT step, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by 14-cycles of PCR-amplification (98 °C for 180 s; [98 °C for 15 s, 67 °C for 20 s, 72 °C for 60 s] x 12-cycles; 72 °C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adapter followed by indexing PCR (98 °C for 45 s; [98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s] x 10 cycles; 72 °C for 60 s). The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform  (R1 – 26 cycles, i7 – 8 cycles, R2 – 96 cycles) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14).

value: spleen


title: EC ALE-4_2

status: Public on Oct 25 2019

type: SRA

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

department: Bioengineering

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode
Estimated the dispersion of each gene using DESeq2
Transcript per Million (TPM) were calculated by DESeq2
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: csv file includes TPM values for each Sample

molecule: total RNA

organism: Escherichia coli K-12

source_name: EC ALE-4_mid-log phase bacteria culture

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol: KAPA Stranded RNA-Seq Kit

tag: strain

tag: media

value: M9 minimal media w/ 4g/L glucose


title: CITE_BMMC_D1T1

city: Stanford

first: Jeffrey

middle: Michael

last: Granja

address: 87 Hulme Ct Apt 101

department: Genetics

institute: Stanford University

data_processing:
Library strategy: CITE-seq
The Cell Ranger RNA Software Suite (version 3.0.0) was used for processing sequencing information and single cell barcodes
Matrix was filtered for mitochondrial and ribosomal RNA.
Cells were filtered unique molecular identifies greater than 1000 and number of genes greater than 400.
genome build: hg19/Grhc37
processed data files format and content: scRNA-rds files are a binary R file that contain a scRNA-seq counts sparse matrix; scADT-rds files are a binary R file that contain a scADT-seq counts matrix associated with the scRNA-seq sparse matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: Healthy Human Bone Marrow

extract_protocol:
All cells used in this study were cryopreserved (fresh frozen in either Bambanker freezing media or 10% DMSO with 90% serum). Thawed cells were not filtered for viability prior to loading into droplets.
10X Genomics Single Cell RNA version 2

tag: disease state

value: Healthy

tag: tissue

value: Bone Marrow

tag: Sex

value: F

tag: age

tag: molecule subtype

value: polyA RNA + ADT


title: 101-LPS-D1

city: Copenhagen

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

country: Denmark

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using Tophat.
The annotated gene information of porcine genome was downloaded from Ensembl.
The script htseq-count was used to generate gene count matrix.
The gene count was normalized using DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: A matrix table of normalized gene count from DESeq2.

organism: Sus scrofa

source_name: Distal small intestine

extract_protocol:
Total RNA from the distal small intestines was isolated with RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed using NEBNext Ultra RNA library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. RNA libraries were sequenced on the Illumina HiSeq 4000 platform with paired-end 150-bp reads production.

tag: group

tag: litter

value: M


title: EC ALE-4_1


title: scATAC_MPAL1_T1

library_source: genomic

data_processing:
The Cell Ranger ATAC Software Suite (version 1.0.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the Tn5 transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified with MACS2
Barcodes likely associated with whole cells were identified by analyzing the number of fragments (1000) mapped near TSS regions (8) and a peak-barcode matrix is defined
genome build: hg19/Grhc37
processed data files format and content: fragments-tsv files contain aligned scATAC-seq fragments

molecule: genomic DNA

source_name: MPAL Donor Peripheral Blood

extract_protocol:
Nuclei were extracted from cells that were cryopreserved (fresh frozen in either Bambanker freezing media or 10% DMSO with 90% serum). Thawed cells were not filtered for viability prior to loading into droplets.
10X Genomics Single Cell ATAC Kit version 2

value: mixed-phenotype acute leukemia (MPAL)

value: Peripheral Blood


title: 103-LPS-D1


title: BCSCs_tumor

city: Hangzhou

first: sen

last: ye

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

country: China

institute: Zhejiang University

data_processing:
The library of each samples was sequenced on an Illumina Hiseq PE150 platform with a 150 bp paired-end module
The raw reads were filtered by removing reads containing adapter, ploy-N and low-quality reads for subsequent analysis.
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, UMI counting and clustering for cells. All barcodes whose total UMI counts exceed m/10 are called as cells.
Supplementary_files_format_and_content: tab-delimited text files of the list of differential gene expression between the six clusters in BCSCs from solid tumors taken from NOD/SCID mice.

source_name: homo sapiens

growth_protocol: BCSCs were plated at a density of 4000-8000 cells/well in the 6-well ultra-low-attachment plates and cultured in tumorspheres formation conditions (DMEM/F12 (Corning; 10-092-cv) supplemented with 10% serum replacement (SR; Thermo Fisher Scientific; 10828028), human recombinant epidermal growth factor (EGF 20 ng/ml), heparin sodium of 5 ng/ml (MedChemExpress; 9041-08-1), human recombinant basic fibroblast growth factor of bFGF (20 ng/ml) (PeproTech; 96-100-18B-500) at 37℃ in a humidified 5% CO2 incubator). The medium was replaced every 2 days. After culturing for two weeks, tumorspheres could be visualized using an inverted phase-contrast microscope.

extract_protocol:
Cellular suspensions were loaded on a Single-cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs.
Single cell was reverse-transcribed using the Discover-scTM WTA Kit V2 (Vazyme, N711) and incorporated into the cDNA library using TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, TD503). Sequencing libraries were loaded on an Illumina Hiseq PE150 a 150 bp paired-end module. The raw reads were filtered by removing reads containing adapter, ploy-N and low-quality reads for subsequent analysis. The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing and UMI counting. All barcodes whose total UMI counts exceed m/10 are called as cells.

treatment_protocol: To obtain a single cell suspension, solid tumors of mouse xenografts were cut up into small pieces and then minced completely by using sterile blades prior to digestion, the resulting tumor pieces were then mixed with ultra-pure collagenase III (Worthington; LS004180) in DMEM (250 units of collagenase per ml) and allowed to incubate at 37°C for 3-4 hrs. During the incubation, mixing it by pipetting every 15-20 mins. After incubation, cells were filtered through a 45-mm nylon mesh and washed with DMEM containing 10% FBS, then washed twice with HBSS. Antibodies of CD24-PE and CD44-FITC (diluted in 200 μl HBSS containing 2% FBS per 1μl antibody) were then added and incubated for 20 mins on ice, followed by washing twice with HBSS. Dead cells stained with propidium iodide (PI) were eliminated by gating. Flow cytometry was performed on a FACS Vantage (BD). Side scatter and forward scatter profiles were used to eliminate cell doublets. Cells were routinely sorted twice and reanalyzed for purity of 90%. Four populations of CD44high/CD24low, CD44high/CD24high, CD44low/CD24high, and CD44low/CD24low were discriminated. The population of CD44high/CD24low was used as BCSCs in this study.

value: breast cancer solid tumors

tag: cell markers


title: EC ALE-3_H2O2_2

source_name: EC ALE-3_H2O2_mid-log phase bacteria culture

tag: treatment

value: 2 mM Hydrogen peroxide


title: scATAC_PBMC_D12T2

source_name: Healthy Human Peripheral Blood


title: BCSCs_MCF7

description:
single cells
BCSCs

data_processing:
The library of each samples was sequenced on an Illumina Hiseq PE150 platform with a 150 bp paired-end module
The raw reads were filtered by removing reads containing adapter, ploy-N and low-quality reads for subsequent analysis.
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, UMI counting and clustering for cells. All barcodes whose total UMI counts exceed m/10 are called as cells.
Supplementary_files_format_and_content: tab-delimited text files of the list of differential gene expression between the six clusters in BCSCs from MCF7 cell line

source_name: MCF7 cell line

treatment_protocol: Antibodies of CD24-PE and CD44-FITC (diluted in 200 μl HBSS containing 2% FBS per 1μl antibody) were then added and incubated for 20 mins on ice, followed by washing twice with HBSS. Dead cells stained with propidium iodide (PI) were eliminated by gating. Flow cytometry was performed on a FACS Vantage (BD). Side scatter and forward scatter profiles were used to eliminate cell doublets. Cells were routinely sorted twice and reanalyzed for purity of 90%. Four populations of CD44high/CD24low, CD44high/CD24high, CD44low/CD24high, and CD44low/CD24low were discriminated. The population of CD44high/CD24low was used as BCSCs in this study.

tag: cell line

tag: cell marker signature


title: 537-CON-D5


title: 540-CON-D5


title: BCSCsGFP [RNA-seq]

description: overexpression of GFP in BCSCs

data_processing:
The library of each samples was sequenced on an Illumina PE150 platform with a 150 bp paired-end module
Clean reads were aligned to the reference genome using Bowtie2 (v2.2.9) and TopHat (v2.1.1).
Cuffdiff (v2.2.1) was used to calculate FPKMs for coding genes in each sample
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKMs values for each Sample ...

growth_protocol: BCSCsSETD4 or BCSCsGFP were plated at a density of 4000-8000 cells/well in the 6-well ultra-low-attachment plates and cultured in tumorspheres formation conditions (DMEM/F12 (Corning; 10-092-cv) supplemented with 10% serum replacement (SR; Thermo Fisher Scientific; 10828028), human recombinant epidermal growth factor (EGF 20 ng/ml), heparin sodium of 5 ng/ml (MedChemExpress; 9041-08-1), human recombinant basic fibroblast growth factor of bFGF (20 ng/ml) (PeproTech; 96-100-18B-500) at 37℃ in a humidified 5% CO2 incubator). The medium was replaced every 2 days. After culturing for two weeks, tumorspheres could be visualized using an inverted phase-contrast microscope.

extract_protocol:
The RNAs of bulk cells (either BCSCsGFP or BCSCsSETD4) were extracted using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SETD4 gene cloning: to obtain the full length ORF of human SETD4 gene, primers (GFP-SETD4F: GCCGCGATCGCCATGCAGAAAGGAAAAGG, GFP-SETD4R: CGTACGCGTTCAGGTAAAAGCTGTTTG) were designed and PCR was performed. Total RNA was extracted from Artemia by using TRIzol reagent (Invitrogen; 15596018), according to the manufacturer’s instructions, and then quantified by using a Genova UV-visible spectrophotometer at 260 nm. First-strand cDNA was synthesized from 1 ug of total RNA by using the SuperScript/First-Strand cDNA synthesis kit (Invitrogen; 11904018), according to the manufacturer’s protocol, and was used as a template for PCR. Victor and overexpression of SETD4 gene: Based on the sequence of the human SETD4 gene (NM_017438.4) in GenBank, the pLent-EF1a-SETD4-CMV-GFP-P2A-Puro overexpression plasmid (Vigene biosciences; LT88002) was synthesized and transfected with a viral packaging plasmid of 10 μg of plasmid containing the vector of SETD4, 10 μg of pMD2.G (Addgene; 12259) and 15 μg of psPAX2 (Addgene; 12260) by Lipo 3000 (Invitrogen; L3000015) into HEK293T cells overnight, and the viral supernatant was collected 48 hours later. The viral supernatant was filtered through a 0.45 μm filter, and the freshly sorted BCSCs were used for infection in the presence of 5 μg/ml Polybrene (Sigma-Aldrich; 107689-10G).

tag: genotype/variation

value: SETD4 low

value: MCF7 cell line


title: scATAC_PBMC_D12T1


title: EC ALE-3_2

source_name: EC ALE-3_mid-log phase bacteria culture


title: 536-CON-D5


title: BCSCsSETD4 [RNA-seq]

description: overexpression of SETD4 in BCSCs

value: SETD4 high


title: EC ALE-3_1


title: BCSCsGFP

description: ChIP-SEQ of H4K20me3 in overexpressed GFP in BCSCs

data_processing:
The library of each samples was sequenced on an Illumina PE150 platform with a 150 bp paired-end module
Reads were aligned to the human genome using Bowtie2 (v2.2.9). Peaks were called for aligned reads using MACS2
Different enriched peaks were analyzed using differential peaks and notated using notate peaks.pl in the homer software.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H4K20me3 (Abcam; ab9053).
The DNA samples were constructed for the library and sequenced on an Illumina Hiseq pe150 platform.

treatment_protocol: SETD4 gene cloning: to obtain the full length ORF of human SETD4 gene, primers (GFP-SETD4F: GCCGCGATCGCCATGCAGAAAGGAAAAGG, GFP-SETD4R: CGTACGCGTTCAGGTAAAAGCTGTTTG) were designed and PCR was performed. Total RNA was extracted from Artemia by using TRIzol reagent (Invitrogen; 15596018), according to the manufacturer’s instructions, and then quantified by using a Genova UV-visible spectrophotometer at 260 nm. First-strand cDNA was synthesized from 1 ug of total RNA by using the SuperScript/First-Strand cDNA synthesis kit (Invitrogen; 11904018), according to the manufacturer’s protocol, and was used as a template for PCR. Victor and overexpression of SETD4 gene: Based on the sequence of the human SETD4 gene (NM_017438.4) in GenBank, the pLent-EF1a-SETD4-CMV-GFP-P2A-Puro overexpression plasmid (Vigene biosciences; LT88002) was synthesized and transfected with a viral packaging plasmid of 10 μg of plasmid containing the vector of SETD4, 10 μg of pMD2.G (Addgene; 12259) and 15 μg of psPAX2 (Addgene; 12260) by Lipo 3000 (Invitrogen; L3000015) into HEK293T cells overnight, and the viral supernatant was collected 48 hours later. The viral supernatant was filtered through a 0.45 μm filter, and the freshly sorted BCSCs were used for infection in the presence of 5 μg/ml Polybrene (Sigma-Aldrich; 107689-10G). Chromatin immuno-precipitation sequencing (ChIP-seq) was performed from the BCSCsGFP and BCSCsSETD4. ChIP procedures were modified from the Millipore EZ ChIP kit (Millipore; 17-371) according to the manufacturer’s instructions. Briefly, Cells were cross-linked in culture media (with 1% formaldehyde) with gentle shaking for 10 min at room temperature and stopped by adding glycine to a final concentration of 0.125 M. Nuclei were then lysed in lysis buffer with proteinase inhibitor cocktails and sonicated shear genomic DNA, to a range of 200–1,000 bp. The samples were centrifuged at 12,000 g at 4°C for 10 min and incubated overnight with 10 μg of H4K20me3 antibody at 4°C with rotation. The immuno-complexes were collected with 60 μl of A/G-agarose, sequentially washed and then eluted by addition of 200 μl of ChIP direct elution buffer, and reverse crosslinks of protein/DNA complexes to free DNA. The DNA was directly recovered by gel extraction kit (Omega; D2500-02).

tag: antibody


title: scATAC_PBMC_D11T1


title: 105-LPS-D1


title: BCSCsSETD4

description: ChIP-SEQ of H4K20me3 in overexpressed SETD4 in BCSCs


title: 532-CON-D5


title: scATAC_PBMC_D10T1


title: EC ALE-2_H2O2_2

source_name: EC ALE-2_H2O2_mid-log phase bacteria culture


title: scATAC_CD34_D9T1

data_processing:
The Cell Ranger RNA Software Suite (version 3.0.0) was used for processing sequencing information and single cell barcodes
Matrix was filtered for mitochondrial and ribosomal RNA.
Cells were filtered unique molecular identifies greater than 1000 and number of genes greater than 400.
genome build: hg19/Grhc37
processed data files format and content: scRNA-rds files are a binary R file that contain a scRNA-seq counts sparse matrix; scADT-rds files are a binary R file that contain a scADT-seq counts matrix associated with the scRNA-seq sparse matrix

source_name: Healthy Human CD34+ Bone Marrow

value: CD34+ Bone Marrow


title: EC ALE-2_H2O2_1


title: activated qBCSCs 3

description: quiescent BCSCs from quiescence into activation

data_processing:
The library of each samples was sequenced on an Illumina Hiseq PE150 platform with a 150 bp paired-end module
Clean reads were aligned to the reference genome using Bowtie2 (v2.2.9) and TopHat (v2.1.1).
Cuffdiff (v2.2.1) was used to calculate FPKMs for coding genes in each sample
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: BCSCs (either BCSCs, qBCSCs or activated qBCSCs) were plated at a density of 4000-8000 cells/well in the 6-well ultra-low-attachment plates and cultured in tumorspheres formation conditions (DMEM/F12 (Corning; 10-092-cv) supplemented with 10% serum replacement (SR; Thermo Fisher Scientific; 10828028), human recombinant epidermal growth factor (EGF 20 ng/ml), heparin sodium of 5 ng/ml (MedChemExpress; 9041-08-1), human recombinant basic fibroblast growth factor of bFGF (20 ng/ml) (PeproTech; 96-100-18B-500) at 37℃ in a humidified 5% CO2 incubator). The medium was replaced every 2 days. After culturing for two weeks, tumorspheres could be visualized using an inverted phase-contrast microscope.

extract_protocol:
The RNAs of bulk cells (either BCSCs, qBCSCs or activated qBCSCs) were extracted using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The population of PKH26+ cells was used as qBCSCs in this study. The labeled cells were cultured under tumorspheres formation conditions (described above) for 2 weeks, and the medium was changed every 2 days. After two weeks’ incubation, the tumorspheres were dissociated by accutase (Gibco; A1110501), then the single cell suspension was washed by HBSS and subjected to FACS Vantage (BD). Cells with the signal of PKH26 (Ex:551nm, Em:567nm) were harvested. For activation of qBCSCs obtained above, FACS-sorted qBCSCs were plated in 6-well ultra-low-attachment plates (Corning; 3471) and cultured in tumorspheres formation conditions (described above) plus 50 ng/ml exosomes that has been isolated form MCF7 cells culture supernatants by cell medium exosome isolation kit (Life technology; 4478359) according to the manufacturer’s instructions for 20 hrs, which is the time that just before one cell dividing into two cells.

tag: signature


title: scATAC_PBMC_D12T3


title: 513-CON-D5


title: scATAC_CD34_D8T1


title: EC ALE-2_2

source_name: EC ALE-2_mid-log phase bacteria culture


title: 510-CON-D5


title: EC ALE-2_1


title: scATAC_CD34_D7T1


title: activated qBCSCs 1


title: EC ALE-1_H2O2_2

source_name: EC ALE-1_H2O2_mid-log phase bacteria culture


title: 113-CON-D5


title: CITE_MPAL5R_T2


title: qBCSCs 3

description: quiescent BCSCs


title: CITE_MPAL5R_T1


title: EC ALE-1_H2O2_1


title: 16071_0002

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

country: Germany

institute: Ruhr-University Bochum

description:
genomic DNA and total RNA
BCC 2

data_processing:
Library strategy: DNA-seq
Furthermore, annotations were added in order to identify known pathogenic variants or explore novel variants that are predicted to have a deleterious effect by virtue of a change in amino acid, disruption of a regulatory motif, or the disease- or pathway-association of the affected gene. Therefore, the databases HGMD (Human Gene Mutation Database), EVS (Exome Variant Server) and ClinVar (public archive of relationships among sequence variation and human phenotype) were accessed. The initially generated quality filtered variant lists were finally filtered in order to reduce the number of reported variants to those with possible clinical relevant or pathological effects. In addition, we conducted a second variant analysis of all 16 samples starting from the aligned BAM-files. Variants were called using the FreeBayes algorithm (14). Called were both SNPs and InDel variants reaching as low as a minimal detection rate of 1%. Resulting variant candidates have been PHRED-quality filtered in order to remove sites with a high chance of being polymorphic.
Genome_build: hg19
Supplementary_files_format_and_content: excel file showing all Dicer mutations . Variants were called using the FreeBayes algorithm. Called were both SNPs and InDel variants reaching as low as a minimal detection rate of 1%. Resulting variant candidates have been PHRED-quality filtered in order to remove sites with a high chance of being polymorphic.

source_name: epithelial skin tumor

extract_protocol:
Genomic DNA (gDNA) and total RNA were isolated in parallel from the same sample using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. The final volume of the eluate was 50 μl for gDNA and 30 μl for total RNA. The total RNA samples were isolated for RNA and miRNA sequencing analysis. An aliquot of each total RNA sample was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). All samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) using RNA 6000 Nano LabChip Kits (Agilent Technologies, Santa Clara, USA) and RNA integrity number (RIN) was determined.   An aliquot of each gDNA sample was used to determine purity and approximate DNA concentration on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). The TruSeq Custom Amplicon Low Input (TSCA) library preparation protocol was followed. The gDNA samples were additionally quantified using the highly sensitive fluorescent dye-based Qubit® dsDNA HS Assay Kit (ThermoFisherScientific, Karlsruhe, Germany).
The microRNA maturing enzyme Dicer 1 (ribonuclease III, Gene ID 23405 on Chromosome 14) was defined as the target gene. The online tool Illumina Design Studio (http://designstudio.illumina.com/) was used to design an amplicon-based enrichment panel (TruSeq Custom Amplicon Low Input) that targets the DICER1 gene. The design strategy was based on human reference genome hg19 including the coding sequence of DICER1 with a targeted amplicon size of 175 bp (13).
Library preparation was performed with the TruSeq Custom Amplicon Low Input Library Kit (Illumina, San Diego, USA) using a dual pool approach according to the manufacturer´s protocol (1).
Hybridization of oligos to genomic DNA was performed in a 96-well plate, followed by extension and ligation to form DNA templates consisting of the regions of interest flanked by universal primer sequences. Using indexed primers, DNA templates were amplified by PCR and elongated with barcodes and sequencing adapters. In addition to the 16 gDNA samples, resulting in 32 DNA-oligo-pool samples, a control DNA (2800M) and a non-template control (NTC) were processed in parallel in order to control the complete library preparation process. Identification of each sample was ensured by an unique index sequence combination allowing identification of each sample. The DNA 1000 and High Sensitivity LabChip Kit (Agilent Technologies, Santa Clara, USA) were used on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) to analyze the quality and fragment distribution of the generated libraries. The expected PCR product size including adapter sequences was ~ 280 bp for the targeted amplicon size of 175 bp.
bidirectional sequencing was performed, starting first at the end of the sense strand (read 1) and subsequently at the end of the complementary strand (read 2). Both reads had a length of 150 bases, finally producing 300 bases of sequence information in 2 x 150 bp paired-end (PE) reads.

tag: diagnosis

value: basal cell carcinoma

tag: patient id

value: BCC 2

tag: tumor type

value: nodular

tag: cell type

value: epidermal skin tumor


title: qBCSCs 1

description: quiescent BCSCs


title: scATAC_MPAL2_T2

source_name: MPAL Donor Bone Marrow Aspirate

tag: disease state

tag: tissue


title: 526-CON-D1

tag: Sex


title: CITE_MPAL5_T1

tag: age

tag: molecule subtype


title: 111-CON-D5

tag: group

tag: litter


title: qBCSCs 2

description: quiescent BCSCs


title: 516-CON-D5


title: BCSCs 3

description: BCSCs


title: 107-CON-D5


title: CITE_MPAL4_T2


title: CITE_MPAL4_T1


title: EC ALE-1_1

source_name: EC ALE-1_mid-log phase bacteria culture

tag: strain

tag: media

value: M9 minimal media w/ 4g/L glucose


title: BCSCs 2

description: BCSCs


title: activated qBCSCs 2


title: GMOS_H2O2_2

source_name: GMOS_H2O2_mid-log phase bacteria culture

tag: treatment


title: 523-CON-D1


title: 524-CON-D1


title: CITE_MPAL3_T2


title: 509-CON-D1


title: GMOS_H2O2_1


title: GMOS_2

source_name: GMOS_mid-log phase bacteria culture


title: CITE_MPAL3_T1


title: EC ALE-1_2


title: 508-CON-D1


title: 500-CON-D1


title: WT_H2O2_2

source_name: WT_H2O2_mid-log phase bacteria culture


title: Normalized SNCs-exposed sample 2 of 3 (0.05mg/L SNCs)

type: RNA

city: Itakura

first: Shosaku

last: Kashiwada

state: Gunma

address: 1-1-1 Izumino

department: Department of Life Sciences

country: Japan

institute: Toyo University

description: 12,000 spots of Oryzias latipes (medaka fish) oligo DNA probes are present on the microarray.

hyb_protocol: 5μg of the purified Cy5-cRNA sample was dissolved in 100μl of hybridization solution ( 25% formamide/6x SSPE/0.04% SDS/0.05% Tween-20/20mM EDTA solution), and hybridization reaction was carried out at 45ºC for 16hours.  Post-hybridization washes were performed using the following solutions in listed order: two washes in 6x SSPE/0.05% Tween-20 at 45°C for 5 minutes each, two washes in 3x SSPE/0.05% Tween-20 at ambient temperature for 1 minute each, two washes in 0.5x SSPE/0.05% Tween-20 at ambient temperature for 1 minute each, two washes in 2x PBS/0.1% Tween-20 at ambient temperature for 1 minute each, and two final washes in 2x PBS at ambient temperature for 1 minute each.

scan_protocol: The microarrays were scaned by Axon Instruments GenePix 4000B scanner (5μm resolution, PMT gain at 450-650, Laser power at 100%).

data_processing: Raw data (Kashiwada-CTL-1_PMT600_635.txt, Kashiwada-CTL-2_PMT600_635.txt, Kashiwada-CTL-3_PMT600_635.txt, Kashiwada-EXP-1_PMT550_635.txt, Kashiwada-EXP-2_PMT550_635.txt, and Kashiwada-EXP-3_PMT550_635.txt) were obtained from the scanned images using MicroarrayImager ver.6.0.1(CombiMatrix Corp.), and were background-subtracted and median-normalized for each of the microarray.  We employed statistical analysis by arraySTAT z-test (Imaging Research Inc., St. Catharines, ON, Canada) with significance determination at p < 0.05 to obtain differentiated transcriptional expression ratio (also called “fold difference” or “FD”) for each of the gene probes on the microarray.

organism: Oryzias latipes

source_name: whole embryo

label_protocol: 1μg from each of the extracted total RNA was reverse-transcribed with T7-oligo dT primer to synthesize single-stranded cDNA (ss-cDNA).  Subsequently, double-stranded cDNA was synthesized from the ss-cDNA, and in vitro transcription with T7 RNA polymerase and Cy5-CTP to generate fluorochrome-labeled cRNA target samples was performed.  The Cy5-cRNA samples were purified and spin column-purified for microarray hybridization.  All of the processes from reverse-transcription of the total RNA to Cy5-cRNA purification were carried out with QuickAmp Labeling Kit (Cy5-dye), Agilent Technologies Inc., Cat. No. 5190-0442.

growth_protocol: 15 embryos at stage 21 were exposed in triplicate to 0mg/L and 0.05mg/L of SNC for 48 hours at 25±0.1ºC in 6-well polystyrene plates protected from light. Test solutions were renewed every 24 hours.

extract_protocol: After control/exposure test fifteen medaka embryos (per set) were pooled and homogenized in RLT lysis buffer (QIAGEN), and total RNA was extracted by RNeasy Micro kit according to the manufacturer's protocol provided in the kit (QIAGEN, cat#74004).

treatment_protocol: Silver content of the purified silver nanocolloids which we used in our experiment contained approximately 15-20% ionic silver and 80-85% particle silver.  Mean particle diameter of SNCs was about 28.4 ± 8.5 nm.   SNCs were purchased from Utopia silver supplements (Utopia, Texas, USA).  For the DNA microarray gene expression analysis, each of the six sets of fifteen medaka embryos at stage 21 were exposed to 5 mL of 0.05 mg/L SNCs (dissolved in dH2O) solution in embryo-rearing medium at pH7.0 in 6-well plate at 25℃ in the dark for 48 hours.  No-exposure (control) experiment was also carried out in the same way except that the SNCs solution was replaced by 5 mL of dH2O.

tag: organ/tissue

value: whole embryo

tag: developmental stage


title: GMOS_1


title: CITE_MPAL1_T1

source_name: MPAL Donor Peripheral Blood


title: CITE_MPAL1_T2


title: CITE_CD34_D3T1

value: Healthy

value: F


title: 104-CON-D1

source_name: Distal small intestine


title: Normalized SNCs-exposed sample 3 of 3 (0.05mg/L SNCs)


title: CITE_CD34_D2T1

extract_protocol:
All cells used in this study were cryopreserved (fresh frozen in either Bambanker freezing media or 10% DMSO with 90% serum). Thawed cells were not filtered for viability prior to loading into droplets.
10X Genomics Single Cell RNA version 3

value: M

value: polyA RNA + ADT


title: 106-CON-D1


title: WT_2

source_name: WT_mid-log phase bacteria culture


title: WT_1


title: 100-CON-D1


title: Normalized SNCs-exposed sample 1 of 3 (0.05mg/L SNCs)


title: Normalized control sample 2 of 3 (0mg/L SNC)


title: Normalized control sample 3 of 3 (0mg/L SNC)


title: Normalized control sample 1 of 3 (0mg/L SNC)


title: CITE_MPAL2_T1

value: mixed-phenotype acute leukemia (MPAL)

value: Bone Marrow


title: GD4_Uterus_2

status: Public on Oct 24 2019

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
raw sequence files were first chekced for quality by FASTQC.
quality trimmed with fqtrim (v 0.9.4) phred 30, min length 20
mapped with hisat2 (v 2.0.3)
counted mapped reads with featureCounts and Ensembl version 89 annotation
edgeR-robust DE analysis
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text file with raw read counts for each gene

organism: Mus musculus

source_name: Mouse uterus on day 4 of pregnancy

growth_protocol: Adult (6–10 week old) C57BL/6 J wild-type female mice were mated with fertile males to induce pregnancy. The vaginal plug was observed on day 1 of the mating. Pregnancy was confirmed by the presence of blastocysts in the uterine flush on GD4. Mice were necropsied and the whole brain and uterus (n = 4 mice each) were collected on GD4, trimmed of connective tissue, washed in PBS and snap frozen in liquid nitrogen for downstream analysis.

extract_protocol:
Qiagen rneasy kit
Illumina Tru-seq Stranded Ribo-zero kit

treatment_protocol: No treatment

tag: gestation day

tag: organ

value: Uterus


title: GD4_Uterus_1


title: GD4_Uterus_4


title: TES_D4_F_mu3_S5

description: FAIRE DNA

data_processing:
raw sequence files were first chekced for quality by FASTQC.
quality trimmed with fqtrim (v 0.9.4) phred 30, min length 20
mapped with bowtie2
The post-alignment quality control was performed by using the Homer tools (http://homer.ucsd.edu/homer/).(Zhang et al. 2008) to predict peaks with default parameters.
The uniquely mapped reads were used with the MACS algorithm (v2.1.0) to predict peaks with default parameters.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text file of FAIRE peaks with peak position in the genome and peak calling statistics generated by MACS2.

growth_protocol: Adult (6–10 week old) C57BL/6 J wild-type female mice were mated with fertile males to induce pregnancy. The vaginal plug was observed on day 1 of the mating. Pregnancy was confirmed by the presence of blastocysts in the uterine flush on GD4. Mice were necropsied and the whole uterus (n = 3 mice each) were collected on GD4, trimmed of connective tissue, washed in PBS and snap frozen in liquid nitrogen for downstream analysis.

extract_protocol:
Frozen GD4 uteri (100 mg) were pulverized and crosslinked for 9 min with 1% formaldehyde, and the formaldehyde was quenched with 125 mM glycine. Following crosslinking, the tissue was washed, pelleted, and resuspended in cold lysis buffer (10 mM Tris-HCl pH 8.0, 2% Triton X-100, 1% SDS, 100 mM NaCl, 1 mM EDTA). The mixture was then subjected to bead beating with 2.38 mm metal beads at 4°C (five two-minute cycles followed by two minutes of rest on ice) and sonication to achieve an average fragment length of 300 bp. The fragmented chromatins were recovered by centrifugation at 15,000g for 5 min at 4 °C. and purified with phenol-chloroform extractions. The recovered chromatin from the aqueous phase was further treated with RNase A and proteinase K and then purified through Zymo-I spin columns before using them to prepare sequencing libraries.
Illumina Tru-seq Stranded kit


title: TES_D4_F_mu2_S6

description: FAIRE DNA


title: GD4_Uterus_3


title: GD4_Brain_M3

source_name: Mouse brain on day 4 of pregnancy

value: Maternal brain


title: WT_H2O2_1

value: 2 mM Hydrogen peroxide


title: GD4_Brain_M4


title: 102-CON-D1


title: GD4_Brain_M1


title: GD4_Brain_M2


title: High-dup2

city: ROCKVILLE

first: Eric

last: Long

state: MD

address: 5625 FISHERS LN RM 4S-12A

department: Molecular & Cellular Immunology Section

institute: National Institute of Allergy and Infectious Diseases

description:
Amplified gRNA library from genomic DNA of transfected K562 cells.
processed data file: HighSelection_Gene_Summary.txt

data_processing:
Library strategy: CRISPR-Screen
Adapter sequences were removed from raw sequencing read FASTQ files using cutadapt version 1.17 and options -e 0.1 -m 20 -l 20 (M. Marcel, EMBnet. Journal 17.1, 2011; DOI: 10.14806/ej.17.1.200).
Counts were made with MAGeCK version 0.5.7 based on the GeCKO sgRNA library via the "count" function with the follow options: --norm-method control --trim-5 0 (Li, Wei, et al., Genome Biology 15.12, 2014; DOI: 10.1186/s13059-014-0554-4).
Gene essentiality was calculated using the MAGeCK version 0.5.7 "mle" algorithm and the following options: --norm-method control --genes-var 0 --update-efficiency
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_Gene_Summary.txt: Gene summary text files processed using MAGeCK version 0.5.7. These files contain significance tests of gene essentiality (columns) for each gene (rows).

source_name: K562 cells

extract_protocol:
Genomic DNA was extracted using the QIAGEN Blood & Cell DNA mini kit (13323).
Library construction was carried out as described previously (Joung et al., Nat Protoc, 2017; PMID: 28333914).

tag: cell line

value: Human acute leukemia cell line

value: Treated

tag: nk-killing pressure

value: Higher

tag: transfection

value: Cas9 and guide RNA library


title: High-dup1

tag: cell type


title: Low-Ctrl-rep2

description:
Amplified gRNA library from genomic DNA of transfected K562 cells.
processed data file: LowSelection_Gene_Summary.txt

value: Control

value: Lower


title: High-Ctrl


title: Low-Surv-rep2


title: Low-Ctrl-rep1


title: Low-Surv-rep1


title: TES_D4_F_mu1_S7

description: FAIRE DNA


title: A549 cells, R8A_mock_3

city: New York

first: Meike

last: Dittmann

state: NY

address: 430 East 29th Street, room 313

institute: NYU Medical School

data_processing:
Reads were mapped to the human genome reference (hg19) supplemented with the pSCRPSY plasmid sequence (containing EGFP gene),  using the HISAT2 (v2.1.0) alignment tool with Ensembl v75 gene annotations (supplemented with pSCRPSY gene annotation) and the "--rna-strandness R" and "--dta" parameters
Read counts per gene were quantified against Ensembl (v75) transcript reference annotations (appended with gene annotation for pSCRPSY, "MSTRG.1") using featureCounts (v1.6.3) in the subread package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes read counts per gene for each sample

source_name: A549 cells transduced with pSCRPSY ELF1 R8A

growth_protocol: A549 cells were mainained in DMEM, 10% FBS, NEAA, Pen/Strep.

extract_protocol:
All collections were made in buffer RLT supplied with RNeasy mini kit from Qiagen. Total RNA was obtained from all samples simultaneously following RNeasy mini kit protocol.
All libraries were constructed simultaneously with Illumina TruSeq Stranded mRNA Library Preparation kit. 500 ng of input RNA sample was used with 11 cycles of final amplificaiton.

treatment_protocol: A549 cells were either transduced with lentivirus containing empty vector, ELF1, or ELF1 R8A mutant and collected for total RNA isolation. In parallel, collections were done for A549 cells transduced with empty vector lentivirus and treated with 500 U/mL IFN-beta for 6 hours or 48 hours.

value: lung epithelial adenocarcinoma cells

tag: passages

tag: elf1 construct transduction

tag: replicate batch

tag: ifn treatment

value: mock


title: A549 cells, R8A_mock_2


title: A549 cells, empty_mock_2

source_name: A549 cells transduced with pSCRPSY empty

value: empty


title: A549 cells, empty_IFN6_3

source_name: A549 cells transduced with pSCRPSY empty treated with IFN for 6 hours


title: A549 cells, empty_IFN6_1


title: A549 cells, empty_mock_1


title: A549 cells, empty_IFN6_2


title: A549 cells, empty_IFN48_2

source_name: A549 cells transduced with pSCRPSY empty treated with IFN for 48 hours


title: A549 cells, empty_IFN48_3


title: alpha_2A_1

city: Houston

first: Yongji

last: Zeng

state: Texas

address: One Baylor Plaza

department: Medicine

institute: Baylor Collge of Medicine

data_processing:
Fastq files were generated using the bc12fastq software, version 1.8.4 and provided to the UNMC Bioinformatics Core facility for further analysis.
The original fastq format reads were trimmed and filtered using the fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by our facility’s newly developed standard pipeline utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels.
Genome_build: Human NCBI genome build 36
Supplementary_files_format_and_content: xlsx files include TPM values, which were used for comparison results (student’s t-test) for all the available genes. The Benjamini-Hochberg (BH)adjusted p values were also provided to adjust for multiple testing-caused false discovery rate (FDR) with significant level of adjusted p value of ≤ 0.05.

source_name: Osteosarcoma cells

growth_protocol: U2OS cell line was purchased from American Type Culture Collection (ATCC) and cultured as ATCC instructed.The cell line was authenticated at ATCC and were used at low (< 25) passages.

extract_protocol:
The RNA was extracted by using the Direct-zol™ RNA Miniprep Plus Kit (Zymo Research) and evaluated the purity and concentration of the RNA by ultraviolet spectroscopy (NanoDrop). RNA  integrity numbers (RIN) were evaluated using the Agilent 2100 Bioanalyzer.
RNA sequencing libraries were constructed using 1000 ng of total RNA from each sample and the TruSeqV2 kit  from Illumina following manufacturer’s protocol.

tag: tissue

value: Osteosarcoma cells

value: Derived from moderately differentiated sarcoma of the tibia of a 15 year old girl.

tag: genotype


title: U_20S_3

value: wild type


title: alpha_2A_3


title: alpha_2A_2


title: 21-22_KO_1

value: AMPK[alpha]-KO


title: U_20S_1


title: 21-22_KO_2


title: U_20S_2


title: A549 cells, mock_2

source_name: A549 cells


title: A549 cells, mock_1


title: A549 cells, ELF1_mock_3

source_name: A549 cells transduced with pSCRPSY ELF1 WT


title: EC ALE-3_H2O2_1

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode
Estimated the dispersion of each gene using DESeq2
Transcript per Million (TPM) were calculated by DESeq2
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: csv file includes TPM values for each Sample

source_name: EC ALE-3_H2O2_mid-log phase bacteria culture

tag: strain

value: M9 minimal media w/ 4g/L glucose


title: A549 cells, empty_IFN48_1


title: 21-22_KO_3


title: A549 cells, ELF1_mock_2


title: A549 cells, ELF1_mock_1


title: A549 cells, mock_3


title: A549 cells, empty_mock_3


title: X9_OA

city: Newcastle

first: Catharien

last: Hilkens

state: Tyne and Wear

address: Framlington Place

department: Institute of Cellular Medicine

country: United Kingdom

institute: Newcastle University

description:
9_OApos
9-NBJS-6747-Catharien-Hilkens_S3

data_processing:
Data quality was examined with FASTQC (v0.11.5)
Raw FASTA files were trimmed with Trimmomatic (v0.33), with parameters at a trailing length of 20, and a minimum length of 60 to remove low quality reads
STAR (v2.4.0j) was used for alignment, default parameters were used with read length set at 75.
SAM files produced by STAR were converted into BAM files with SAMtools (v1.3) before conversion from aligned transcripts into gene counts with HTSEQ (v0.6.1)
Data was analysed with R (v3.4.2)
Genome_build: GRCh38.p7 version 25
Supplementary_files_format_and_content: Comma delimited matrix of transcript counts (.txt)

source_name: Synovial Tissue

extract_protocol:
RNA was extracted using Qiagen RNEasy isolation kit according to manufacturers protocol
SMART-Seqv4 plus Nextera XT Sequencing

tag: disease

value: Osteoarthritis

tag: isolation method

value: Total knee arthroplasty

value: Synovial Tissue


title: X10_RA

description:
10_RA
10-EA3273-Catharien-Hilkens_S2

value: Rheumatoid arthritis

value: Ultrasound guided wrist biopsy


title: X12_RA

description:
12_RA
12-EA7095-Catharien-Hilkens_S12


title: X8_OA

description:
8_OAneg
8-NBJS-6743-Catharien-Hilkens_S10


title: X11_PSA

description:
11_PSA
11-EA3312-Catharien-Hilkens_S9

value: Psoriatic arthritis


title: X4_OA

description:
4_OApos
4-NBJS-6668-Catharien-Hilkens_S11


title: X3_OA

description:
3_OAneg
3-NBJS-6601-Catharien-Hilkens_S5


title: X2_OA

description:
2_OAneg
2-NBJS-6550-Catharien-Hilkens_S4


title: X7_OA

description:
7_OAneg
7-NBJS-6742-Catharien-Hilkens_S6


title: X1_OA

description:
1_OApos
1-NBJS-6547-Catharien-Hilkens_S1


title: input CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
CHIP-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files
Genome_build: hg19
Supplementary_files_format_and_content: CHIP-seq signal in bigwig format

source_name: HCT116 colorectal cancer cells

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 0.18 M Glycine for 5 minutes. Cells were harvested and chromatin was extracted
10 ng of DNA from Inputs and IPs were used to prepare libraries using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, MI) following manufacturer’s protocol with an additional wash at the end using SPRIselect beads (Beckman Coulter, IN) to remove any larger libraries that could interfere with clustering on the instrument

tag: factor

value: input

tag: usp22 status

value: KO

tag: shRNA

tag: treatment

value: u

tag: replicate

tag: antibody


title: input CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 1

tag: cell line

value: wt

value: shLuc

value: T


title: input CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 1


title: USP22 CHIP-seq in USP22 wild type, untreated cells, replicate 1

value: no

value: Novus Biologicals cat# NBP1-49644


title: input CHIP-seq in USP22 wild type, untreated cells, replicate 1


title: input CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 1


title: input CHIP-seq in USP22 wild type, Thaps treated cells, replicate 1


title: X6_OA

description:
6_OAneg
6-NBJS-6721-Catharien-Hilkens_S8


title: USP22 CHIP-seq in USP22 wild type, untreated cells, replicate 2


title: ubH2B CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 2

value: Millipore cat# 05-1312


title: ubH2B CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 1


title: MED16 CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 2

value: Abcam cat# ab130996


title: USP22 CHIP-seq in USP22 wild type, Thaps treated cells, replicate 2


title: MED16 CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 1


title: MED16 CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 2


title: USP22 CHIP-seq in USP22 wild type, Thaps treated cells, replicate 1


title: MED16 CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 1


title: MED16 CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 1


title: ubH2B CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 1


title: ubH2B CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 2


title: ubH2B CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 2


title: ubH2B CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 2


title: MED16 CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 1


title: MED1 CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 1

value: Bethyl Labs cat# A300-793A


title: MED1 CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 1


title: MED1 CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 2


title: X5_OA

description:
5_OApos
5-NBJS-6681-Catharien-Hilkens_S7

value: Osteoarthritis


title: BCSCs 1

description: BCSCs

source_name: MCF7 cell line

tag: signature


title: ubH2B CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 1


title: MED16 CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 2


title: MED16 CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 2


title: MED1 CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 1


title: MED1 CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 2


title: ubH2B CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 1


title: ATXN7L3 CHIP-seq in USP22 wild type, untreated cells, replicate 1

value: Bethyl Labs cat# A302-800A


title: ATXN7L3 CHIP-seq in USP22 wild type, Thaps treated cells, replicate 1


title: GCN5 CHIP-seq in USP22 wild type, untreated cells, replicate 2

value: Santa Cruz cat# sc-20698


title: ATXN7L3 CHIP-seq in USP22 wild type, untreated cells, replicate 2


title: MED1 CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 2


title: GCN5 CHIP-seq in USP22 wild type, untreated cells, replicate 1


title: Pol2 CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 1

value: Santa Cruz cat# sc-899


title: GCN5 CHIP-seq in USP22 wild type, Thaps treated cells, replicate 2


title: GCN5 CHIP-seq in USP22 wild type, Thaps treated cells, replicate 1


title: ATXN7L3 CHIP-seq in USP22 wild type, Thaps treated cells, replicate 2


title: MED1 CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 2


title: Pol2 CHIP-seq in USP22 wild type (shLuc), untreated cells, replicate 2


title: Pol2 CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 1


title: Pol2 CHIP-seq in USP22 wild type (shLuc), Thaps treated cells, replicate 2


title: Pol2 CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 2


title: Pol2 CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 1


title: Pol2 CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 2


title: Pol2 CHIP-seq in USP22 knockdown (shUSP22), Thaps treated cells, replicate 1


title: C-12W

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.1.1
The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: Reads count for each gene

source_name: Mouse lung

extract_protocol:
Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.
Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

tag: stress

value: control

value: Lung


title: C-12W-BS

data_processing:
Reads were aligned to the mm10 genome assembly using meRanTK v1.2.0
m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed.
Genome_build: mm10
Supplementary_files_format_and_content: m5C sites in one biological replicate

extract_protocol: Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

tag: age

value: 4 weeks


title: PM-12W-BS

value: particulate matter 2.5 (PM2.5) exposure


title: DT-8 (Blastocyst-281)

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

data_processing:
Raw fastq data were trimmed using Trim-Galore 0.4.3 in pair-end mode with default parameters to remove adaptor seqeunces and low quality bases.
Trimmed data were mapped to human reference genome hg38 using STAR 2.7 aligner in pair-end mode, with default parameters.
Mapped results (bam files) were inputted to featureCounts 1.6.4, to generate the read count matrix for each gene and each cell.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text table for read count matrix.

source_name: embryo

growth_protocol: Human embryos collection was performed as described previously. Briefly, embryos were cultured in Cleavage Medium (SAGE, USA) in a low-oxygen humidified atmosphere containing 5% CO2, 5% O2, and 90% N2 at 37℃. Stages of human embryo development were assessed through microscopy and collected separately. 3PN embryos were collected based on observing three pronuclei in fertilized oocytes via phase-contrast microscropy.

extract_protocol:
Human embryos at different stages were treated with Tyrode’s acidic solution to remove the zona pellucida then seperated by 0.25% typsin digestion. Single blastomeres were washed twice with 1xPBS containing 0.1% BSA and transferred to 0.2ul of lysis buffer (0.5% NP40, 1U RNase inhibitor) by mouth pipetting.
Whole-transcript amplification for single blastomeres was done using the Quartz-seq method. Briefly, cDNA was first generated by reverse transcription with SuperScript III (Life technologies, 18080-044); After the digestion of the redundant RT-primer with exonuclease I (TAKARA, 2650A), first strand of cDNA was poly-A tailed with terminal transferase (Roche Applied Science, 3333574); After synthesis of the second strand of cDNA with tagging primer and Mighty DNA polymerase (TAKARA, R071A), the whole transcriptome was amplified usingsuspension PCR. PCR products were purified with Qiagen MinElute PCR purification kit (QIAGEN, 28004) and Library construction was performed following Illumina’s instruction. Libraries were sequenced on the Illumina Hiseq 2000 platform.

value: embryo

tag: embryo day

value: Blastocyst


title: DT-7 (Blastocyst-280)


title: DT-4 (Blastocyst-278)


title: DT-20 (Blastocyst-275)


title: DT-17 (Blastocyst-274)


title: DI-4 (Blastocyst-272)


title: DT-10 (Blastocyst-273)


title: DT-2 (Blastocyst-276)


title: CT-7 (Blastocyst-270)


title: DI-3 (Blastocyst-271)


title: CT-1 (Blastocyst-268)


title: CT-17 (Blastocyst-267)


title: CT-20 (Blastocyst-269)


title: CT-11 (Blastocyst-265)


title: CT-14 (Blastocyst-266)


title: BT-7 (Blastocyst-264)


title: PM-12W


title: BT-19 (Blastocyst-263)


title: BT-18 (Blastocyst-262)


title: MED1 CHIP-seq in USP22 knockdown (shUSP22), untreated cells, replicate 1

value: KO

value: u


title: DT-6 (Blastocyst-279)


title: DT-3 (Blastocyst-277)


title: BT-13 (Blastocyst-260)


title: BT-11 (Blastocyst-258)


title: AT-9 (Blastocyst-257)


title: BT-16 (Blastocyst-261)


title: AT-19 (Blastocyst-256)


title: AT-18 (Blastocyst-255)


title: AT-17 (Blastocyst-254)


title: AT-15 (Blastocyst-252)


title: Th9 transcriptome

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

description: Biological replicate 1

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

source_name: Naïve

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Splenic CD4 T cells were isolated from 6-8-week-old C57BL/6 mice. Naïve CD4 T cells were sorted based on surface marker expression by MACS. Naïve CD4 T cells were stimulated by plate-bound anti-CD3e (10 microgram/ml) and soluble anti-CD28 (10 microgram/ml) in the presence of polarizing cytokines for 3 days. For Th2, mouse recombinant IL-2 (1 ng/ml), mouse recombinant IL-4 (5 ng/ml), and an anti-IFNγ antibody (2 μg/ml) were used. For Th9 cells mouse recombinant IL-2 (0.2 ng/ml), mouse recombinant IL-4 (1 ng/ml), human recombinant TGF-β1 (2 ng/ml), and anti-IFN-γ (5 μg/ml; XMG1.2) were used. For Treg, mouse recombinant IL-2 (0.4 ng/ml), human recombinant TGF-β1 (5 ng/ml), anti-IFN-γ (5 μg/ml), and anti-IL-4 (5 μg/ml; 11B11) were used. Cells were harvested for RNA extraction.

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

value: spleen


title: AT-16 (Blastocyst-253)


title: AT-13 (Blastocyst-251)


title: 8H-2 (8-248)


title: iTreg transcriptome

description: Biological replicate 1

source_name: Treg


title: Th2 transcriptome

description: Biological replicate 1


title: 8A-17 (8-244)


title: 11Q-4 (11-239)


title: AT-11 (Blastocyst-250)


title: AI-1 (Blastocyst-249)


title: 11P-4 (11-237)


title: 8C-3 (8-246)


title: 8H-1 (8-247)


title: 11P-3 (11-236)


title: 8A-11 (8-243)


title: 11P-1 (11-234)


title: 11Q-5 (11-240)


title: BT-12 (Blastocyst-259)


title: 11N-9 (11-228)


title: 11O-11 (11-229)


title: 8A-9 (8-245)


title: 11P-2 (11-235)


title: 11Q-7 (11-241)


title: 11O-16 (11-233)


title: 11O-15 (11-232)


title: 11N-1 (11-222)


title: 11N-2 (11-223)


title: 11O-14 (11-231)


title: 11M-3 (11-214)


title: 11N-3 (11-224)


title: 11N-10 (11-217)


title: 11M-15 (11-213)


title: 11Q-2 (11-238)


title: 11M-14 (11-212)


title: 11M-12 (11-211)


title: 11N-7 (11-227)


title: 11N-16 (11-221)


title: 11N-15 (11-220)


title: 11I-2 (11-209)


title: 11N-6 (11-226)


title: 11N-14 (11-219)


title: 11H-4 (11-208)


title: 11E-4 (11-202)


title: 11N-12 (11-218)


title: 11M-9 (11-216)


title: 11M-7 (11-215)


title: 11D-10 (11-200)


title: 11B-5 (11-199)


title: 11K-3 (11-210)


title: 11O-13 (11-230)


title: 11N-4 (11-225)


title: FI-5 (Blastocyst-192)


title: FT-1 (Blastocyst-193)


title: CT-2 (Blastocyst-189)


title: 11H-3 (11-207)


title: CT-4 (Blastocyst-190)


title: 11G-2 (11-205)


title: BT-8 (Blastocyst-186)


title: 11F-1 (11-204)


title: 11E-5 (11-203)


title: 11D-9 (11-201)


title: BT-17 (Blastocyst-181)


title: BI-1 (Blastocyst-179)


title: 11A-6 (11-198)


title: AT-12 (Blastocyst-175)


title: CT-6 (Blastocyst-191)


title: 11A-5 (11-197)


title: 11A-4 (11-196)


title: 11A-2 (11-195)


title: 14I-9 (14-172)


title: 14I-7 (14-170)


title: FT-4 (Blastocyst-194)


title: 11H-1 (11-206)


title: 14I-16 (14-163)


title: CT-18 (Blastocyst-187)


title: CT-19 (Blastocyst-188)


title: 14I-14 (14-161)


title: 14I-13 (14-160)


title: 14I-15 (14-162)


title: BT-3 (Blastocyst-184)


title: BT-20 (Blastocyst-182)


title: 14H-3 (14-156)


title: 14H-2 (14-155)


title: 14I-11 (14-158)


title: BT-1 (Blastocyst-180)


title: AT-5 (Blastocyst-178)


title: AT-2 (Blastocyst-177)


title: AT-14 (Blastocyst-176)


title: AI-3 (Blastocyst-174)


title: 14G-1 (14-153)


title: 14F-5 (14-149)


title: AI-2 (Blastocyst-173)


title: 14I-8 (14-171)


title: 14F-2 (14-146)


title: 14I-6 (14-169)


title: BT-6 (Blastocyst-185)


title: 14I-5 (14-168)


title: 14I-4 (14-167)


title: BT-2 (Blastocyst-183)


title: 14E-42 (14-139)


title: 14E-5 (14-140)


title: 14E-4 (14-138)


title: 14I-3 (14-166)


title: 14E-39 (14-135)


title: 14I-2 (14-165)


title: 14I-17 (14-164)


title: 14E-36 (14-132)


title: 14I-12 (14-159)


title: 14F-8 (14-152)


title: 14E-33 (14-129)


title: 14E-32 (14-128)


title: 14F-7 (14-151)


title: 14E-3 (14-127)


title: 14F-6 (14-150)


title: 14E-29 (14-124)


title: 14E-28 (14-123)


title: 14E-27 (14-122)


title: 14E-26 (14-121)


title: 14E-30 (14-125)


title: 14E-25 (14-120)


title: 14F-3 (14-147)


title: 14F-1 (14-145)


title: 14E-9 (14-144)


title: 14I-10 (14-157)


title: 14F-4 (14-148)


title: 14E-19 (14-113)


title: 14E-20 (14-114)


title: 14E-18 (14-112)


title: 14E-8 (14-143)


title: 14E-7 (14-142)


title: 14E-6 (14-141)


title: 14G-2 (14-154)


title: 14E-41 (14-137)


title: Co-cultured Bovine Endometrial 3

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

data_processing:
Alignment of reads and gene specific analysis was performed in Partek® Flow® software, version 5.0 Copyright ©; 2018 Partek Inc., St. Louis, MO, USA. Human cells data was aligned to reference genome (hg38) using STAR alignment (in Partek Flow) and bovine data was aligned using Bos Taurus assembly UMD_3.1.1/bosTau8.
Quantification was performed using quantify to annotation model (Partek E/M) using Ensemble Transcripts release 85 (humans) or Ensemble-UMD3.1 gene annotation model
Normalization was performed using TPM (Transcripts Per Kilobase Million77).
Genome_build: Human (hg38), Cow (UMD_3.1.1/bosTau8)
Supplementary_files_format_and_content: TPM values in Excel file

organism: Bos taurus

source_name: Endometrial Stromal Fibroblasts

growth_protocol: Human ESFs were grown in phenol-red free DMEM/F12with high glucose(25 mM), supplemented with 10% charcoal stripped calf serum (Hyclone), and 1% antibiotic/antimycotic (Gibco).

extract_protocol:
RNA was isolated using RNeasy micro kit (QIAGEN, Germany) and resuspended in 10 μL water. SuperScript IV VILO Master Mix (ThermoFisher, USA) was used to synthesize cDNA from 1μg mRNA and ezDNase was used to remove DNA after reverse transcription.
Agilent Bioanalyzer 2100 was used to determine RNA quality and RIN number of over 8 was observed in the samples. TruSeq RNA Library from illumina was used to prepare mRNA library.
These libraries were sequenced on illumina HiSeq to generate 30-40million reads per sample (Single end 75 bp reads) and a high Q score was observed (Q>30) for the sequenced data.

tag: cell type

value: Endometrial Stromal Fibroblasts


title: Co-cultured Bovine Endometrial 1


title: Bovine Endometrial 3


title: 14E-11 (14-104)

tag: tissue


title: 14E-40 (14-136)


title: 14E-38 (14-134)


title: 14E-34 (14-130)


title: 14E-35 (14-131)


title: 14E-10 (14-103)


title: Bovine Endometrial 1


title: 14E-31 (14-126)


title: 14E-12 (14-106)


title: 14E-24 (14-119)


title: 14E-2 (14-116)


title: 14E-22 (14-117)


title: 14E-37 (14-133)


title: 14E-21 (14-115)


title: GTL-16_F crizotinib resistant clone, RNA, replicate 1

city: South San Francisco

first: Kenneth

last: Finn

state: CA

address: 1170 Veterans Blvd

institute: Calico Labs

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5).
Transcript expression was then quantified using Salmon (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing transcript-per-million (TPM) estimates, using the Ensembl GRCh38 human transcriptome.
Differential expression analysis was performed in R using the Sleuth package (v0.29.0), producing gene-level effect sizes and Q-values for each comparison considered (e.g., parental GTL-16 cells versus resistant clone)
Genome_build: GRCh38
Supplementary_files_format_and_content: GTL-16_crizotinib_resistance_matrix_full_gene.csv

source_name: GTL-16_F cell line (crizotinib resistant isolate)

growth_protocol: GTL-16 cells were maintained at 37C in a humidified atmosphere at 5% CO2 in RPMI-1640 media supplemented with 4 mM GlutaMax, 1mM Sodium Pyruvate, 5% Fetal Bovine Serum, 100 U/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL Amphotericin B (all components from Gibco).  Crizotinib-resistant clones were maintained in the same manner, with 1 uM crizotinib added to the medium.  Prior to collection of cells for RNA extraction, resistant subclones were cultured in the absence of crizotinib for 7-10 days.

extract_protocol:
Total RNA was isolated from GTL-16 cells and each of the resistant clones using a RNeasy Kit (Qiagen), according to the manufacturer’s instructions.  RNA sample quality was assessed using the RNA kit (DNF-471) from Agilent (formerly Advanced Analytical Technologies, Inc.) on a Fragment Analyzer (Advanced Analytical Technologies, Inc.).
Sequencing libraries were prepared as directed using an Illumina TruSeq Stranded mRNA kit, using 1000 ng of input material and the TruSeq RNA CD Index Plate.  Quality assessment of the individual prepared libraries was carried out using a HS NGS Fragment Kit (DNF-474) from Agilent (formerly Advanced Analytical Technologies, Inc.) on a Fragment Analyzer (Advanced Analytical Technologies, Inc.).  All libraries were pooled using an Echo 550 (Labcyte).  Quality assessment of the pooled libraries was performed on a Bioanalyzer (Agilent) using a High Sensitivity DNA chip.  Samples were loaded onto a HiSeq 4000 Illumina sequencer at 3 nM, and a 2 x 150 bp paired-end protocol was run, with an 8-cycle index read.

treatment_protocol:
untreated
None.  Cells were harvested following culture under growth conditions listed above, with no additional perturbation.

tag: cell line of origin

tag: group

value: GTL-16_F crizotinib resistant clone


title: GTL-16_E crizotinib resistant clone, RNA, replicate 3

source_name: GTL-16_E cell line (crizotinib resistant isolate)

value: GTL-16_E crizotinib resistant clone


title: 14C-8 (14-97)


title: 14C-7 (14-96)


title: GTL-16_E crizotinib resistant clone, RNA, replicate 1


title: GTL-16_E crizotinib resistant clone, RNA, replicate 2


title: 14E-17 (14-111)


title: 14E-16 (14-110)


title: 14E-15 (14-109)


title: GTL-16_D crizotinib resistant clone, RNA, replicate 2

source_name: GTL-16_D cell line (crizotinib resistant isolate)

value: GTL-16_D crizotinib resistant clone


title: 14C-5 (14-94)


title: Bovine Endometrial 2


title: 14E-1 (14-105)


title: 14E-23 (14-118)


title: GTL-16_D crizotinib resistant clone, RNA, replicate 1


title: GTL-16_C crizotinib resistant clone, RNA, replicate 2

source_name: GTL-16_C cell line (crizotinib resistant isolate)

value: GTL-16_C crizotinib resistant clone


title: GTL-16_C crizotinib resistant clone, RNA, replicate 1


title: 14E-13 (14-107)


title: 14D-4 (14-102)


title: GTL-16_B crizotinib resistant clone, RNA, replicate 3

source_name: GTL-16_B cell line (crizotinib resistant isolate)

value: GTL-16_B crizotinib resistant clone


title: 14C-1 (14-90)


title: GTL-16_F crizotinib resistant clone, RNA, replicate 3


title: GTL-16_B crizotinib resistant clone, RNA, replicate 2


title: 14B-8 (14-87)


title: GTL-16_B crizotinib resistant clone, RNA, replicate 1


title: GTL-16_F crizotinib resistant clone, RNA, replicate 2


title: 14D-2 (14-100)


title: 14D-3 (14-101)


title: Co-cultured Bovine Endometrial 2


title: 14C-9 (14-98)


title: 14D-1 (14-99)


title: 14C-6 (14-95)


title: 14B-7 (14-86)


title: 14C-4 (14-93)


title: 14B-6 (14-85)


title: 14C-3 (14-92)


title: GTL-16_A crizotinib resistant clone, RNA, replicate 2

source_name: GTL-16_A cell line (crizotinib resistant isolate)

value: GTL-16_A crizotinib resistant clone


title: GTL-16 parental cell line, RNA, replicate 3

source_name: GTL-16 cell line

value: GTL-16 parental cell line


title: 14C-2 (14-91)


title: 14B-4 (14-83)


title: 14C-10 (14-89)


title: 14B-9 (14-88)


title: GTL-16_D crizotinib resistant clone, RNA, replicate 3


title: GTL-16_C crizotinib resistant clone, RNA, replicate 3


title: GTL-16_A crizotinib resistant clone, RNA, replicate 3


title: GTL-16_A crizotinib resistant clone, RNA, replicate 1


title: ENSA_Input

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

data_processing:
Single-end BMAL1 ChIP-seq reads were trimmed using Trim Galore v0.4.3 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and cutadapt 1.14 (http://cutadapt.readthedocs.io/en/stable/guide.html). Reads were aligned to the hg19 human genome with BWA-MEM v0.7.17. BAM files were processed using SAMtools and PCR duplicates were removed with PicardTools (http://broadinstitute.github.io/picard/). BMAL1 peaks were called using MACS2 (v2.1.1) using a ChIP input file as a control using default settings. Replicate sample BAM files were merged using SAMBAMBA (v0.6.6, http://lomereiter.github.io/sambamba/). BIGWIG track coverage files were generated from merged BAM files using the DeepTools (v2.4.1) bamCoverage command with RPKM normalization (http://deeptools.readthedocs.io/en/latest/index.html). DiffBind was used to identify differential BMAL1 ChIP-seq peaks between GSC and NSC samples and to perform principal component analysis. Differential BMAL1 peaks (GSC or NSC specific BMAL1 peaks) were defined using the DESeq2 method within Diffbind, which selects differential regions based on an FDR-corrected q-value of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: NARROWPEAK, BIGWIG, BED

source_name: Non-malignant Neural Stem Cell

growth_protocol: Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

extract_protocol:
BMAL1 ChIP assays were performed with 107 cells using Magna ChIP-seq kit (Millipore, 17-10085) according to manufacturer’s instruction. Briefly, cells were fixed with 1% formaldehyde at room temperature for 10 minutes, and subsequently quenched with 0.125M glycine. Then, the cells were washed with cold PBS and suspended with lysis buffer supplemented with Protease Inhibitor Cocktail II. Chromatin was sonicated to obtain DNA fragments with an average length of 200-500 bp for sequencing by Bioruptor Plus sonication device (Diagenode) followed by centrifugation for clearing. Soluble fraction of sheared chromatin was diluted 10-fold with ChIP dilution buffer and incubated with BMAL1 antibody (Cell Signaling Technology) and EZ-Magna ChIP A/G magnetic beads overnight at 4°C with rotation. Chromatin-captured beads were washed once with low salt wash buffer, once with high salt wash buffer, once with LiCl wash buffer and twice with TE buffer for 5 min each by rotation at 4°C. Beads were resuspended in elution buffer and removed by magnet. Proteinase K was added to the eluted DNA followed by incubation at 62°C for 4 hours with shaking. Then the eluted DNA was incubated at 95°C for 10 min to remove RNA. Reverse-crosslinked DNA was purified by using purification columns. Eluted DNA was used to do quantitative PCR (qPCR) or sequencing library preparation. ChIP quantitative RT-PCR was performed by using SYBR Green PCR Master Mix (ABI, 4309155). qPCR primers were listed as Table S1. Then sequencing libraries were prepared by using ThruPLEX® NGS Library Preparation Kits (Rubicon Genomics, R400427) according to manufacturer’s instruction. ChIP-seq libraries were sequenced on Illumima HiSeq platform by Genewiz.
Then sequencing libraries were prepared by using ThruPLEX® NGS Library Preparation Kits (Rubicon Genomics, R400427) according to manufacturer’s instruction. ChIP-seq libraries were sequenced on Illumima HiSeq platform by Genewiz.

tag: tumor type


title: 14B-22 (14-77)


title: 14B-5 (14-84)


title: GTL-16 parental cell line, RNA, replicate 2


title: GTL-16 parental cell line, RNA, replicate 1


title: NSC_ENSA_Rep2

description:
BMAL1 ChIP-seq from patient derived glioblastoma stem cell specimens
ENSA_BMAL1_R1_R2_Merged.sorted.rmdup.bam.rpkm.bw
BMAL1_PeaksGainedinNSC.bed

treatment_protocol: Cells were passaged in vitro


title: NSC_hNP1_Rep1

description:
BMAL1 ChIP-seq from patient derived glioblastoma stem cell specimens
hNP1_BMAL1_R1_R2_Merged.sorted.rmdup.bam.rpkm.bw
BMAL1_PeaksGainedinNSC.bed


title: 14B-21 (14-75)


title: 14B-3 (14-82)


title: HNP1_Input


title: NSC_hNP1_Rep2


title: 14B-24 (14-79)


title: 14B-26 (14-81)


title: 14B-25 (14-80)


title: 14B-2 (14-76)


title: 14B-17 (14-71)


title: GSC_387_Rep2

description:
BMAL1 ChIP-seq from patient derived glioblastoma stem cell specimens
387_BMAL1_R1_R2_Merged.sorted.rmdup.bam.rpkm.bw
BMAL1_PeaksGainedinGSC.bed

source_name: Patient Derived Glioma Stem Cell

treatment_protocol: Cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.

value: Glioblastoma


title: GSC_3565_Rep2

description:
BMAL1 ChIP-seq from patient derived glioblastoma stem cell specimens
3565_BMAL1_R1_R2_Merged.sorted.rmdup.bam.rpkm.bw
BMAL1_PeaksGainedinGSC.bed


title: GSC_3565_Rep1


title: 387_Input


title: 14B-20 (14-74)


title: 14B-18 (14-72)


title: 14B-19 (14-73)


title: GSC_387_Rep1


title: 3565_Input


title: Hypoxia

first: Miao

last: Liu

address: Xitoutiao No.10, Youanmen Waidajie

institute: Capital Medical University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official database information, then to calculate FPKM the gene or transcript level separately and to find the difference using Ballgown software.
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome HG19, by Hisat2 software（v2.0.4）
Genome_build: HG19
Supplementary_files_format_and_content: Xlsx include FPKM values for all sample

source_name: cervical cells

growth_protocol: HeLa cells were were maintained in high glucose DMEM supplemented with 10% fetal bovine serum in a humidiﬁed atmosphere with 5% CO2 at 37℃.

extract_protocol:
The whole RNA of HeLa cell lines was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000.1-2 ug of total RNA was selected for each sample for sequencing library construction.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.

treatment_protocol: Cells were treated without or with 1μM of antimycin A or hypoxia (0.5% oxygen) for 8h.

value: HeLa


title: 14B-16 (14-70)


title: 14B-13 (14-67)


title: control


title: 14B-15 (14-69)


title: AntA


title: 14B-1 (14-65)


title: 14B-11 (14-64)


title: 14B-14 (14-68)


title: NSC_ENSA_Rep1


title: 14B-12 (14-66)


title: 14A-6 (14-62)


title: 14B-10 (14-63)


title: 14A-5 (14-61)


title: 14A-4 (14-60)


title: 14A-3 (14-59)


title: 14A-1 (14-57)


title: 14A-2 (14-58)


title: Rad21 Si CTCF Ab

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
Reads were aligned to hg19 + kshv (GQ994935) using Novoalign.
Coverage tracks (reads per million mapped) were generated using USeq 8.8.1.
Enriched peaks were called using MACS2
Peaks were annotated with USeq FindNeighboringGenes
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig coverage files from Useq

source_name: SLK cell line

growth_protocol: Bac16 KSHV infected iSLK cells (iSLK/Bac16) were maintained in 1.2 mg/ml hygromycin, 250µg/ml G-418 and 1µg/ml puromycin, inDMEM containing 10% charcoal stripped FBS (Sigma) and 1% glutamine.

extract_protocol:
Qiagen DNA isolation kit after immunoprecipitation with each antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: knockdown

value: Rad21 KD

value: CTCF Ab IP


title: Rad21 Si Rad21 Ab

value: Rad21 IP


title: 12323X8 RAD21 si KD

data_processing:
Reads were aligned to hg19 and KSHV (NC_009333.1) using Novoalign.
Spliced alignments were converted back to genomic space using Useq SamTranscriptomeParser.
Per gene read counts were generated using USeq DefinedRegionDifferentialSeq
Differently expressed genes were identified using DESeq2 with FDR < 0.01
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts from DefinedRegionDifferentialSeq

extract_protocol:
Qiagen miRNA isolation kit
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit. Briefly, oligo-dT beads were used to capture RNA species containing a polyA tail. Following polyA RNA enrichment, the RNA was chemically fragmented and random primed for reverse transcription. The average insert size of libraries constructed with the TruSeq Stranded mRNA Library Prep Kit is 200 bp.

tag: hci id

value: SLK

tag: infection

value: KSHV

value: RAD21 si KD


title: 12323X9 RAD21 si KD


title: 12323X5 CTCF si KD

value: CTCF si KD


title: 12323X4 CTCF si KD


title: 12323X6 CTCF si KD


title: 12323X7 RAD21 si KD


title: 11Q-3 (11-56)

value: embryo


title: 12323X2 Control si KD

value: Control si KD


title: CTCF Si Rad21 Ab

value: CTCF KD


title: 11O-9 (11-54)


title: 12323X3 Control si KD


title: 11Q-1 (11-55)


title: 11O-7 (11-53)


title: CTCF Si CTCF Ab


title: Control Si Rad21 Ab

value: control KD


title: 11O-5 (11-51)


title: Rad21 Si input

value: input


title: 14B-23 (14-78)


title: CTCF Si input


title: 11O-4 (11-50)


title: 11O-3 (11-49)


title: Control Si input


title: 12323X1 Control si KD


title: 11O-2 (11-48)


title: HT-1080 cells, Licochalcone A repeat 2

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

description: HT-1080 cells treated with Licochalcone A repeat 2

data_processing:
tophat2 with default parameters
samtools to sort and convert the file format
cufflinks with default parameters
cuffmerge with default parameters
cuffdiff with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene_Exp_UM20.diff, normalized expression values for Licochalcone A of 20uM

source_name: sarcoma

growth_protocol: density 5x10e6 HT-1080 cells in 15cm dish, 24 hours, to 70% confluence

extract_protocol:
2100 Bioanalyzer for quality check, DNaseI (Takara, Japan) for digestion at 37 C and 30 mins
100ng purified RNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: treatment with Licochalcone A or DMSO, after 48 hours

tag: agent

value: Licochalcone A


title: 11O-1 (11-47)


title: HT-1080 cells, Licochalcone A repeat 1

description: HT-1080 cells treated with Licochalcone A repeat 1


title: 11N-8 (11-46)


title: HT-1080 cells, DMSO repeat 2

description: HT-1080 cells treated with DMSO repeat 2

value: control


title: A549 cells, Input_rep2

state: New York

address: 430 E 29th Street

department: Microbiology

institute: NYU School of Medicine

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.3.4.1 with default parameters for local alignment.
SAM file generated with bowtie2 was converted to BAM file using samtools version 1.9; unmapped reads and mapped reads with a quality score below 30 were removed.
Duplicate reads were removed using picard-tools version 1.88.
BAM files converted to BED files and mitochondrial mapped reads were removed using bedtools version 2.27.1 bamToBed function with default parameters.
bigWig generation: End coordinates for all mapped reads were extended by 250 bp using bedtools slopbed function. Genome coverage was calculated using genomeCoverageBed function and resulting values were scaled for total mapped reads. hg19 chromosome size metric obtained from UCSC. Resulting bedgraph file was converted to bigWig format using ucscutils version 374.
Peaks were called using MACS2 version 2.1.1 with q-value cut off of 0.0001.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: A549 cells

growth_protocol: A549 cells were maintained in DMEM, 10% FBS, NEAA, Pen/Strep.

extract_protocol:
Lysates were clarified from sonicated nuclei and ELF1-DNA complexes were isolated with antibody.
Input or ChIPped DNA was end-repaired and "A" bases were subsequently added to the DNA. After purification, Illumina/Solexa PE adapters were ligated to DNA fragments. The DNA fragments were then purified and subjected to PCR using Illumina/Solexa primers PE 1.0 and 2.0. These final ChIP-Seq libraries were then purified with the QIAGEN MinElute kit.

treatment_protocol: A549 cells were left untreated and collected for ChIP-seq.

value: lung epithelial adenocarcinoma cell line

tag: passages

tag: chip antibody


title: 11N-13 (11-44)

source_name: embryo


title: 11M-6 (11-41)


title: 11N-5 (11-45)


title: 11M-8 (11-42)


title: Co-cultured Human Endometrial 3

value: Endometrial Stromal Fibroblasts


title: 11O-6 (11-52)


title: 11M-5 (11-40)


title: Control Si CTCF Ab

tag: antibody


title: HT-1080 cells, DMSO repeat 1

description: HT-1080 cells treated with DMSO repeat 1

tag: cell line


title: A549 cells, Input_rep1


title: 11M-4 (11-39)


title: A549 cells, ELF1_rep1

value: anti-ELF1 antibody, Cat# sc-631; RRID:AB_631428;Clone:C-20


title: A549 cells, ELF1_rep2


title: Co-cultured Human Endometrial 1


title: Co-cultured Human Endometrial 2


title: 11M-2 (11-38)


title: 11M-16 (11-37)


title: 11M-13 (11-36)


title: Human Endometrial 2


title: 11M-1 (11-35)


title: Human Endometrial 1


title: CD14+ monocytes, Young Control, 13555X28

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 87.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.16.0.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

source_name: CD14+ monocytes

extract_protocol:
Mononuclear cells (MNCs) were isolated from blood samples using Ficoll (GE Healthcare, Little Chalfont, UK), followed by NH4Cl-based red blood cell lysis according to standard procedures. CD14+ cells were purified from MNCs using an AutoMACS Pro Separator and CD14 microbeads (Miltenyi Biotech, Bergisch Gladbach, Germany) according to the manufacturer’s protocol.
The Illumina TruSeq Stranded Total RNA Sample Prep with Ribo-Zero™ Gold rRNA removal kit (Illumina, San Diego, CA) was used for RNA library preparation.

value: blood

value: CD14+ monocytes

tag: disease state

value: Young Control


title: 11N-11 (11-43)


title: CD14+ monocytes, Young Control, 13555X24


title: 11K-2 (11-32)


title: CD14+ monocytes, Young Control, 13555X23


title: CD14+ monocytes, Young Control, 13555X19


title: 11J-5 (11-30)


title: 11J-4 (11-29)


title: CD14+ monocytes, Young Control, 13555X21


title: 11J-3 (11-28)


title: CD14+ monocytes, Young Control, 13555X20


title: 11J-2 (11-27)


title: CD14+ monocytes, Young Control, 13555X22


title: 11I-1 (11-25)


title: 11J-1 (11-26)


title: CD14+ monocytes, Young Control, 13555X18


title: Human Endometrial 3


title: CD14+ monocytes, Young Control, 13555X16


title: CD14+ monocytes, Young Control, 13555X14


title: 11H-2 (11-24)


title: CD14+ monocytes, Young Control, 13555X13


title: 11M-11 (11-34)


title: 11E-3 (11-21)


title: 11F-2 (11-22)


title: 11M-10 (11-33)


title: CD14+ monocytes, Old Control, 13555X11

value: Old Control


title: 11F-3 (11-23)


title: 11E-2 (11-20)


title: CD14+ monocytes, Old Control, 13555X10


title: CD14+ monocytes, Old Control, 13555X9


title: 11E-1 (11-19)


title: CD14+ monocytes, Young Control, 13555X17


title: 11D-7 (11-17)


title: 11D-8 (11-18)


title: CD14+ monocytes, Old Control, 13555X8


title: CD14+ monocytes, Old Control, 13555X7


title: CD14+ monocytes, Old Control, 13555X6


title: 11D-4 (11-15)


title: 11D-5 (11-16)


title: CD14+ monocytes, Old Control, 13555X12


title: CD14+ monocytes, Old Control, 13555X5


title: 11D-2 (11-13)


title: 11D-3 (11-14)


title: CD14+ monocytes, Old Control, 13555X4


title: 11D-11 (11-11)


title: 11B-6 (11-10)


title: CD14+ monocytes, Old Control, 13555X3


title: CD14+ monocytes, CMML, 10650X24

value: CMML


title: 11B-2 (11-8)


title: CD14+ monocytes, Old Control, 13555X2


title: 11D-1 (11-12)


title: 11B-1 (11-7)


title: CD14+ monocytes, Young Control, 10650X19


title: CD14+ monocytes, CMML, 10650X18


title: 11A-9 (11-6)


title: CD14+ monocytes, CMML, 10650X14


title: CD14+ monocytes, Young Control, 10650X16


title: 11A-8 (11-5)


title: CD14+ monocytes, CMML, 10650X13


title: 11A-7 (11-4)


title: 11A-3 (11-3)


title: 11A-1 (11-2)


title: CD14+ monocytes, CMML, 10650X11


title: CD14+ monocytes, CMML, 10650X10


title: 11A-10 (11-1)


title: AC8975

city: Barcelona

first: Joan

middle: Anton

last: Puig-Butillé

state: Spain

address: Villarroel 170

department: Department of Biochemical and Molecular Genetics

country: Spain

institute: IDIBAPS-Hospital Clinic of Barcelona

data_processing:
RNA-seq reads were processed with STAR-fusion version 0.80 with default parameters
with Gencode 25 annotation
The processed files data files included the analyses of putative fusion transcripts detected in whole gene expression captured by RNA-sequencing in congenital melanocytic nevi. Each file includes the putative fusion transcripts of each biopsy.
Files include common parameters obtained in the analyses:
The "JunctionReads" column indicates the number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction.
The "SpanningFrags" column indicates the number of RNA-Seq fragments that encompass the fusion junction such that one read of the pair aligns to a different gene than the other paired-end read of that fragment.
The "SpliceType" indicates whether the proposed breakpoint occurs at reference exon junctions as provided by the reference transcript structure annotations (ex. gencode).
The following columns: Left Gene, LeftBreakpoint, right Gene and Right Breakpoint; indicate genes and its genomic breakpoint involved in the fusion transcript.
The "LargeAnchorSupport" column indicates whether there are split reads that provide 'long' (set to length of 25 bases) alignments on both sides of the putative breakpoint. Those fusions supported only by split reads (no spanning fragments) and lack LargeAnchorSupport are often highly suspicious and tend to be false positives. Those with LargeAnchorSupport are labeled as 'YES_LDAS' (where LDAS = long double anchor support.... yes, more jargon).
Additional information about the analyses can be found in https://github.com/STAR-Fusion/STAR-Fusion/wiki
Genome_build: GRCh38
Supplementary_files_format_and_content: candidate fusions xls

source_name: human skin biopsies

extract_protocol:
Skin lesions were biopsied, stabilized in RNA-later and frozen at 80ºC . Total RNA was isolated from fresh tissue with Trizol (Invitrogen, USA) followed by purification with the RNeasy mini kit (Qiagen, USA). RNASeq libraries were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: lesion type

value: CMN

tag: nras status

value: Wild-Type


title: CD14+ monocytes, Young Control, 10650X9

tag: age


title: CD14+ monocytes, CMML, 10650X21

tag: cell type


title: 11B-3 (11-9)

tag: tissue

value: embryo

tag: embryo day


title: AC8974


title: CD14+ monocytes, Old Control, 13555X1


title: AC8972


title: AC8971


title: CD14+ monocytes, CMML, 10650X7


title: CD14+ monocytes, CMML, 10650X4


title: CD14+ monocytes, CMML, 10650X5


title: AC8973


title: CD14+ monocytes, CMML, 10650X1


title: AC8970

value: acquired nevi


title: AC8969


title: 11K-1 (11-31)


title: AC8968


title: 387_shBMAL1.1536

description: RNA-seq from patient derived glioblastoma stem cell specimens following treatment with an shRNA targeting BMAL1

data_processing:
The Fastq files of the RNA-seq data were processed to read quality control by running ‘FastQC’ (Galaxy version 0.72) in Galaxy (usegalaxy.org) and then to remove the adapters by running ‘Trim Galore!’ (Galaxy version 0.4.3.1). The trimmed reads were mapped to human genome 38 by ‘HISAT2’ (Galaxy version 2.1.0+galaxy 4) and the mapped reads were then counted with ‘featureCounts’ (Galaxy version 1.6.3+galaxy 2). The counts were processed to differentially expressed gene analysis with R package ‘DESeq2’ (Version 1.14.1).
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts

growth_protocol:
Cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.
Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

extract_protocol: Cellular RNA was isolated using RNeasy kit and as described in the methods

value: Glioblastoma

tag: shRNA

value: shRNA targeting BMAL1


title: AC8967


title: 3565_shBMAL1.689

tag: tumor type


title: AC8966


title: AC8965


title: 387_shCONT

description: RNA-seq from patient derived glioblastoma stem cell specimens following treatment with a non-targeting shRNA

value: non-targeting shRNA


title: 3565_shBMAL1.1536


title: 3565_shCONT


title: sample20 120h infected, cord blood CD34+ cells

city: Florianopolis

first: Edgar

middle: Ernesto

last: Gonzalez Kozlova

state: Santa Catarina

address: Corrego Grande s/n

department: Farmacologia

country: Brazil

institute: Universidade Federal de Santa Catarina

description:
counts_matrix_RNAseq_data.tsv
AB20

data_processing:
Phred, Read Quality filter
Trimmomatic, Trimming and removing adaptors
STAR, aligment to hg38 genome
FeatureCounts
Genome_build: Hg38
Supplementary_files_format_and_content: Raw count matrix from FeatureCounts output

source_name: Purified cord blood CD34+ cells

growth_protocol: StemSpan Expantion Media – SFEM II (STEMCELL Technologies)

extract_protocol:
Trizol LS Invitrogen; 10296010
Nugen Ovation Trio input RNA Library Systems V2
Illumina HiSeq 2500 adaptors for v4 chemistry

treatment_protocol: Optimal cell density for replication was 5 x 10e4 CD34+ cell/mL. Following 4 days of expansion, cells were washed and diluted in SFEM II media without cytokine cocktail to the desired concentration. Culture purity was assessed by FACS and showed more than 90% of CD34+ events after expansion.

value: TB-infected

tag: time

tag: individual

value: purified CD34+ Cells


title: CD14+ monocytes, CMML, 10650X6


title: AC8962


title: AC8961


title: CD14+ monocytes, Youing Control, 10650X3


title: AC8960


title: AC8959


title: sample18 72h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB18

tag: infection


title: AC8958

value: Satellite


title: AC8956


title: AC8957


title: sample16 24h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB16


title: sample15 24h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB15

value: uninfected


title: sample14 120h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB14


title: sample19 120h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB19


title: AC8955

value: Healthy skin


title: sample12 72h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB12


title: 387_shBMAL1.689


title: AC8954


title: sample13 120h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB13


title: AC8953


title: AC8964


title: sample10 24h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB10


title: sample11 24h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB11


title: AC8952


title: AC8963


title: sample6 120h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB6


title: AC8951


title: AC8950


title: sample5 120h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB5


title: sample17 72h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB17


title: sample4 72h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB4


title: AC8949


title: AC8948


title: sample3 72h uninfected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB3


title: sample2 24h infected, cord blood CD34+ cells

description:
counts_matrix_RNAseq_data.tsv
AB2


title: AC8947


title: AC8946


title: AC8944


title: AC8945


title: AC8943


title: AC8942


title: AC8941


title: AC8940