title: xenografted ARD cells

city: Chengdu

first: Juan

last: Xu

address: Guo Xue Xiang #37

institute: West China Hospital, Sichuan University

description: Single cell RNA-seq

data_processing:
MacoskoDropSeq pipeline was used to generate the single-cell transcriptome profile.
The raw pair-end sequencing data was first processed using DropSeq Core computation protocol developed at McCarrll’s lab.
The derived digital expression matrix was then used to generate Seurat object using Seurat R package.
The downstream analyses and data visualization were performed using Seurat functions. The following Seurat functions were used in the Seurat pre-processing pipeline: NormalizeData, ScaleData were used for calculate the comparable expression values; FindVariableFeatures were used to include the variable genes that contribute to the overall similarity/variability of cellular transcriptomic profiles; RunPCA, FindNeighbors, FindClusters, RunTSNE, and RunUMAP were used to calculate the dimension-reduction coordinates for visualization and to perform unsupervised clustering. In the downstream analyses, we used Uniform Manifold Approximation and Projection (UMAP) coordinates to visualize the layout of the cells.
We used monocle2 software to explore the possible differentiation path of these xenografted plasma cells and identify the subclusters using the default software parameters.
We used top 10 principle components to represent the digital expression profiles of each cells, and calculate the median values of these 10 principle components of each putative clusters. Then we calculate the overall dissimilarity using the cosine distances algorithm. The abovementioned dissimilarity measure was defined in TooManyCells method. The hierarchical cluster was plotted based on the dissimilarity matrix of each clusters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.
Supplementary_files_format_and_content: matrix.mtx: gene-barcode counts
Supplementary_files_format_and_content: features.tsv: gene file
Supplementary_files_format_and_content: barcodes.tsv: cell barcode file

source_name: xenografted ARD cells in spleen

extract_protocol:
Splenic cells were collected from a tumor-bearing mouse xenografted with ARD cells. CD138-positive MM cells were then sorted by PE-conjugated CD138 antibody (BD, Biosciences, Cat.# 552026) using flow cytometry technology.
Libraries were prepared using Illumina Nextera XT DNA Sample Preparation Kit.

tag: xenografted cells

value: human MM cell line ARD

tag: genotype

value: wild type

tag: strain

value: immunocompromised B-NDG mouse (NOD-Prkdcscid IL2rgtm1/Bcgen)

tag: age

value: six weeks

tag: disease state

value: extramedullary multiple myeloma

value: spleen

tag: cell type

value: CD138+ MM cells

tag: treatment

value: untreated


title: TBI_7d_Rep2_Lib1

status: Public on Jul 20 2021

type: SRA

city: Philadelphia

first: Nancy

middle: M

last: Bonini

address: 433 South University Ave

country: USA

institute: University of Pennsylvania

description: Severe TBI injured males, 7 d post-injury, biological replicate 2

library_source: transcriptomic

data_processing:
demultiplexed fastq files were obtained from Illumina's BaseSpace and quality checked with fastqc/multiqc
sequenced reads were were mapped to the fly genome (FlyBase d. mel build 6.17) using HISAT2 with parameter --rna-strandness R; index reference was created using hisat2-build
aligned reads were converted to  bam files sorted by aligned position
sample bam files were merged across sequencing runs using Picard
Htseq-count was used to generate unnormalized read count table (with parameters: htseq-count --format bam --order pos --mode union --stranded reverse --minaqual 1 --type exon --idattr gene_id --nonunique=none) for differential expression analysis with DESeq2
Genome_build: Flybase dmel r6.17
Supplementary_files_format_and_content: matrix table (.csv) with raw gene counts for every gene (FlyBase gene ID) and every sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole heads

growth_protocol: reared at 25C; 12 hour light-dark cycle; standard medium

extract_protocol:
whole flies were flash frozen in liquod nitrogen; heads (n=20/sample) were dissociated by vortexing then collected. Total RNA was extracted by TRIzol/chloroform.
sample libraries were prepared in two batches (separate days) using the same Illumina TruSeq Stranderd Sample Kit (Cat# RS-122-2103)
RNA-seq; sequenced on Illumina NextSeq using NextSeq® 500/550 High Output Kit v2 (75 cycles; FC-404-2005)

treatment_protocol: 3d old male flies were subjected to sham or severe dTBI injury. control animals are 3d old males.

value: w[1118]; Bloomington stock 5905

tag: post-injury timepoint

tag: condition

value: TBI

tag: library

value: library 1

tag: tissue

value: whole heads


title: Organoid, AMC-17CT-008

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description: gene expression

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normaliztion for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: colorectal cancer

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
cDNA library was constructed using the TruSeq RNA Access Library Prep Kit (Illumina)

treatment_protocol: Fresh tissue

tag: cancer site

value: Large intestine

value: Colorectal cancer organoids (CCOs)


title: Organoid, AMC-17CT-047

description: gene expression


title: sham_7d_Rep3_Lib1

description: Sham injured males, 7 d post-injury, biological replicate 3

value: sham


title: KS79 grown to post-exponential phase not exposed to H2O2, biological replicate 2

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch2/Ch1 was calculated. We used gDNA for data normalization accross slides, as described in Talaat, 2002, NAR.

label: Alexa Fluor 546

molecule: genomic DNA

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: genomic DNA, reference channel

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

growth_protocol: Aces-buffered yeast extract (AYE) broth at 37°C shaking.

extract_protocol: RNA: TRIzol reagent (Invitrogen), reverse-transcribed into cDNA. Genomic DNA: QIAamp kit (QIAgen).

treatment_protocol: Grown to post-exponential phase, treated or not (control) with 10 mM H2O2

tag: growth

value: AYE broth, 37°C shaking

label: Alexa Fluor 647


title: Organoid, AMC-17CT-056

description: gene expression


title: KS79 grown to post-exponential phase not exposed to H2O2, biological replicate 1


title: SC-derived neurons_25 [Sample_43]

city: Neuherberg

first: Pawel

last: Smialowski

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
Raw reads were demultiplex using Je (version 2.0.2).
Raw reads were aligned to Ensembl GRCm38 mouse reference genome using STAR aligner (version 2.7.10) with GeneCounts paramter on.
Genome_build: Ensembl GRCm38 mouse reference genome
Supplementary_files_format_and_content: NormCount

organism: Mus musculus

source_name: Reprogrammed astrocyte

growth_protocol: Reprogrammed cells were maintained for 3-to-4 weeks in differentiation medium (DMEM/F12, 2% B27, P/S)

extract_protocol:
Single cells were sucked with an electrophysiological tip after being analyzed by ephys
SmartSeq2 + illumina protocols

treatment_protocol: Cells were treated every 3rd day with BDNF, GDNF, cAMP, N2, NT-3

tag: isolation

value: MACS-sorted

tag: transcription factor

tag: ephys property

value: immature


title: sham_7d_Rep2_Lib1

description: Sham injured males, 7 d post-injury, biological replicate 2


title: CSU-046 tumor pre-treatment replicate A

type: RNA

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Gene expression data from osteosarcoma sample CSU-046A

hyb_protocol: Fragmented and labeled cRNA were frozen at -20°C and overnight shipped on dry ice to the University of Colorado Cancer Center Genomics and Miroarray Shared Resource (University of Colorado, Anschutz Medical Campus, Aurora, CO) where Hybridized chips were washed, stained and scanned using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The Affymetrix GeneChip scanner 3000 7G was used to acquire images

data_processing: The data were analyzed  in R using RMA and COMBAT normalization methods for batch correction.

label: biotin

organism: Canis lupus familiaris

source_name: Osteosarcoma

label_protocol: Reverse transcription of cRNA as well as cRNA in vitro transcription, amplification, purification, biotin-labeling, and fragmentation were performed using a GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix, Cat. 902416) following manufacturer instructions.

growth_protocol: Following diagnosis and amputation of the affected limb, biopsy material was collected using a Michele Trephine bone biopsy instrument and collected biopsies reviewed by a veterinary pathologist for assessment of the percent of viable tumor present within each sample.  Two samples from each tumor with the highest percent viable tumor were selected for mRNA isolation and subsequent Affymetrix Canine 2.0 microarray analysis

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, total RNA was further purified using Qiagen RNeasy Purification Kits.

treatment_protocol: Tumor samples were frozen in liquid N2, pulverized to a powder by freeze-fracture using a manual Bio-Pulverizer

tag: breed

value: Airedale

tag: Sex

value: Male

tag: neutered status

value: Yes

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: CSU-046 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-046C


title: Organoid, AMC-17CT-123

description: gene expression

tag: age

tag: tissue


title: CSU-045 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-045C

value: Great Dane


title: sham_7d_Rep1_Lib1

description: Sham injured males, 7 d post-injury, biological replicate 1

tag: strain

tag: post-injury timepoint

tag: condition

tag: library


title: CSU-045 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-045A

tag: breed


title: CSU-043 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-043C

tag: Sex


title: SC-derived neurons_24 [Sample_42]

tag: isolation

tag: transcription factor

tag: ephys property

value: firing


title: CSU-050 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-050B

value: Malamute

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)


title: Organoid, AMC-17CT-099

description: gene expression

tag: cancer site


title: CSU-043 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-043A

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: TBI_3d_Rep3_Lib1

description: Severe TBI injured males, 3 d post-injury, biological replicate 3

tag: strain

tag: post-injury timepoint

tag: condition

tag: tissue


title: SC-derived neurons_23 [Sample_41]

tag: isolation


title: Organoid, AMC-17CT-079

description: gene expression

tag: age


title: TBI_3d_Rep2_Lib1

description: Severe TBI injured males, 3 d post-injury, biological replicate 2

tag: library


title: SC-derived neurons_22 [Sample_40]

tag: transcription factor

tag: ephys property


title: CSU-042 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-042A

tag: breed

value: Golden Ret

tag: Sex

value: Female

tag: neutered status

tag: age (years)

tag: time to progression (days)


title: TBI_3d_Rep1_Lib1

description: Severe TBI injured males, 3 d post-injury, biological replicate 1

value: w[1118]; Bloomington stock 5905

value: TBI


title: Organoid, AMC-17CT-107

description: gene expression

tag: cancer site


title: CSU-042 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-042C

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: sham_3d_Rep3_Lib1

description: Sham injured males, 3 d post-injury, biological replicate 3

tag: strain

tag: post-injury timepoint

tag: condition

value: library 1

tag: tissue

value: whole heads


title: SC-derived neurons_20 [Sample_38]

tag: isolation

tag: transcription factor


title: Primary cancer, AMC-17CT-044

description: gene expression

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normalization for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.

treatment_protocol: Formalin-fixed paraffin-embedded tissue

value: Large intestine

tag: age

value: colorectal cancer


title: Primary cancer, AMC-17CT-147

description: gene expression


title: SC-derived neurons_21 [Sample_39]

tag: ephys property


title: sham_3d_Rep1_Lib1

description: Sham injured males, 3 d post-injury, biological replicate 1

value: sham

tag: library


title: SC-derived neurons_19 [Sample_37]

value: MACS-sorted


title: SC-derived neurons_18 [Sample_33]

value: immature


title: Organoid, AMC-17CT-095

description: gene expression

value: Colorectal cancer organoids (CCOs)


title: sham_3d_Rep2_Lib1

description: Sham injured males, 3 d post-injury, biological replicate 2


title: TBI_24h _Rep3_Lib1

description: Severe TBI injured males, 24 h post-injury, biological replicate 3


title: SC-derived neurons_16 [Sample_31]

value: DsRed

value: no


title: SC-derived neurons_17 [Sample_32]


title: Primary cancer, AMC-17CT-058

description: gene expression


title: Primary cancer, AMC-17CT-051

description: gene expression


title: CSU-041 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-041B

tag: breed

tag: Sex

value: Male

tag: neutered status

value: Yes

tag: age (years)

tag: number of carboplatin treatments


title: CSU-040 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-040C

value: Great Dane

tag: time to progression (days)

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels


title: TBI_24h _Rep2_Lib1

description: Severe TBI injured males, 24 h post-injury, biological replicate 2

tag: strain

tag: post-injury timepoint


title: CSU-041 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-041C

value: Golden Ret

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: CSU-040 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-040B


title: TBI_24h _Rep1_Lib1

description: Severe TBI injured males, 24 h post-injury, biological replicate 1

tag: condition

tag: tissue


title: Primary cancer, AMC-17CT-093

description: gene expression

tag: cancer site

tag: age


title: CSU-039 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-039A

tag: breed

value: Mix

value: Female


title: Primary cancer, AMC-17CT-146

description: gene expression


title: SC-derived neurons_14 [Sample_29]

tag: isolation

tag: transcription factor

tag: ephys property


title: sham_24h _Rep3_Lib1

description: Sham injured males, 24 h post-injury, biological replicate 3

value: w[1118]; Bloomington stock 5905

tag: library


title: sham_24h _Rep2_Lib1

description: Sham injured males, 24 h post-injury, biological replicate 2

value: library 1


title: Primary cancer, AMC-17CT-065

description: gene expression


title: CSU-038 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-038C

tag: Sex

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: number of carboplatin treatments


title: SC-derived neurons_13 [Sample_28]

value: firing


title: sham_24h _Rep1_Lib1

description: Sham injured males, 24 h post-injury, biological replicate 1

tag: strain

tag: post-injury timepoint

value: whole heads


title: CSU-038 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-038A

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: CSU-036 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-036C

tag: breed

value: Greyhound


title: SC-derived neurons_12 [Sample_27]

tag: isolation


title: CSU-037 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-037B

value: Bernese Mtn Dog


title: control_0_Rep3_Lib1

description: Uninjured 3d old males, biological replicate 3

tag: condition

value: control

tag: tissue


title: SC-derived neurons_15 [Sample_30]

value: MACS-sorted

tag: transcription factor

tag: ephys property


title: control_0_Rep2_Lib1

description: Uninjured 3d old males, biological replicate 2

tag: library


title: Primary cancer, AMC-17CT-039

description: gene expression

tag: cancer site

value: Large intestine

tag: age

value: colorectal cancer


title: SC-derived neurons_11 [Sample_26]

value: immature


title: SC-derived neurons_9 [Sample_24]


title: SC-derived neurons_10 [Sample_25]

value: Control

value: no


title: Primary cancer, AMC-17CT-043

description: gene expression


title: control_0_Rep1_Lib1

description: Uninjured 3d old males, biological replicate 1


title: CSU-036 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-036B

tag: Sex

tag: neutered status

value: Yes

tag: age (years)

tag: time to progression (days)

tag: number of carboplatin treatments


title: CSU-035 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-035C

value: Great Pyrenees

value: Male

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels


title: Primary cancer, AMC-17CT-078

description: gene expression


title: Primary cancer, AMC-17CT-031

description: gene expression


title: SC-derived neurons_8 [Sample_23]


title: Primary cancer, AMC-17CT-063

description: gene expression


title: SC-derived neurons_7 [Sample_22]


title: CSU-034 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-034C

tag: breed

value: Vizsla

value: Female

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: Primary cancer, AMC-17CT-125

description: gene expression

tag: tissue


title: SC-derived neurons_6 [Sample_21]

tag: isolation

tag: transcription factor


title: HPV QVD specific CD8 TILS VDJ Patient 37_metastatic lymph node

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

data_processing:
Library strategy: VDJ-seq
Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1
Supplementary_files_format_and_content: Cell Ranger output and contig annotations

source_name: metastatic lymph node

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. RNA was extracted using qiagen all-prep kits. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

tag: subject id

tag: disease state

value: HPV+ HNSCC

tag: treatment

value: previously untreated disease

tag: tetramer

value: QVD

tag: sample type

value: TCR VDJ


title: Primary cancer, AMC-17CT-059

description: gene expression

tag: cancer site

tag: age


title: HPV QVD specific CD8 TILS GEX Patient 37_metastatic lymph node

data_processing:
Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1
Supplementary_files_format_and_content: Cell Ranger output and contig annotations

value: RNA


title: CSU-032 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-032C

value: Australian Heeler

tag: Sex

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: number of carboplatin treatments


title: CSU-034 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-034B

tag: breed

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: CSU-035 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-035A

tag: number of doxorubicin treatments


title: SC-derived neurons_5 [Sample_20]

tag: isolation

value: MACS-sorted

tag: transcription factor

tag: ephys property


title: CSU-032 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-032B


title: Primary cancer, AMC-17CT-033

description: gene expression

value: Large intestine

tag: tissue


title: CSU-031 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-031C

value: Border Collie


title: HPV QVD specific CD8 TILS CITE Patient 42_primary tumor

description:
hashtag1 = beta2-microglobulin and CD298
CITE-seq processed data included in RNA-seq data matrix on GSM5456941

data_processing:
Library strategy: ADT(CITE)
Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1
Supplementary_files_format_and_content: Cell Ranger output and contig annotations

source_name: primary tumor

tag: subject id

tag: disease state

tag: treatment

tag: tetramer

tag: feature barcode

value: Biolegend TotalSeq-C:Sample ID and antibodies

tag: sample type

value: ADT (antibody derived tags)


title: CSU-031 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-031B

tag: Sex

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: number of carboplatin treatments


title: HPV QVD specific CD8 TILS GEX Patient 42_primary tumor

description: Data matrix includes CITE-seq data for GSM5456942


title: Primary cancer, AMC-17CT-012

description: gene expression

tag: cancer site

tag: age

value: colorectal cancer


title: SC-derived neurons_3 [Sample_18]

tag: isolation

value: firing


title: Primary cancer, AMC-17CT-091

description: gene expression


title: PD1+ CD8 TILS VDJ Patient 7_metastatic lymph node

value: none bulk PD1+


title: CSU-030 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-030C

tag: breed

value: Doberman

value: Male

value: Yes

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: HPV QVD specific CD8 TILS VDJ Patient 42_primary tumor

tag: subject id

tag: disease state

value: HPV+ HNSCC

tag: treatment

tag: tetramer


title: SC-derived neurons_2 [Sample_17]

tag: transcription factor

tag: ephys property


title: Primary cancer, AMC-17CT-106

description: gene expression

tag: tissue


title: CSU-030 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-030A

tag: Sex

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: number of carboplatin treatments


title: PD1+ CD8 TILS GEX Patient 7_metastatic lymph node

value: previously untreated disease

tag: sample type


title: PD1+ CD8 TILS VDJ Patient 7_primary tumor


title: SC-derived neurons_1 [Sample_16]

tag: isolation


title: Primary cancer, AMC-17CT-072

description: gene expression

tag: cancer site

tag: age


title: PD1+ CD8 TILS GEX Patient 7_primary tumor


title: Primary cancer, AMC-17CT-049

description: gene expression


title: Primary cancer, AMC-17CT-062

description: gene expression


title: HPV KSA specific CD8 TILS VDJ Patient 7_metastatic lymph node

value: KSA


title: Tg7a2 scRNA-seq

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
The data was de-multiplexed and analysed using CellRanger v3.0.2 and bcl2fastq v2.17.1.14.
Briefly, libraries were de-multiplexed using CellRanger mkfastq based on sample indices.
CellRanger count pipeline was used to perform alignment against mouse genome mm10 (using STAR), filtering and counting UMIs.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and matrix files

source_name: Tg7, 12 week of age

extract_protocol: Pancreatic islets were isolated from 12 week of age Tg7 mice (and litter controls) using Liberase digestion and Histopaque gradient

tag: cell type

value: pancreatic islets

tag: strain

value: 12 week of age

tag: genotype

value: male


title: Tg7_12w_3 bulkRNA-seq

data_processing:
The Illumina bcl2fastq (2.20.0) Conversion Software was used for demultiplexing.
Raw RNA-Seq reads were trimmed with trimmomatic to remove adaptors and low-quality reads (v.0.33)
Trimmed reads were mapped to Ensembl Mus musculus genome reference sequence assembly (NCBIM37) whole genome using tophat2 (2.0.11) with argument  “--library-type fr-firststrand"
Gene annotations were obtained from iGenome NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Tg7 , 12 weeks of age

extract_protocol:
Trizol followed by Qiagen RNA purification columns
RNA-seq libraries were prepared from a minimum of 10ng of total RNA using the NEB Ultra II RNA librairy kit (Illumina, San Diego, USA) according to the manufacturer’s protocol.

treatment_protocol: Pancreatic islets were isolated from 2 and 12 week of age Tg7 mice (and litter controls) using Liberase digestion and Histopaque gradient

value: 12 weeks of age


title: SC-derived neurons_4 [Sample_19]

value: MACS-sorted


title: HPV KSA specific CD8 TILS GEX Patient 7_metastatic lymph node

tag: subject id

tag: disease state

tag: treatment

value: RNA


title: Primary cancer, AMC-17CT-083

description: gene expression

value: Large intestine


title: CSU-029 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-029B

tag: breed

value: Mix

tag: overall survival (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: Tg7_12w_2 bulkRNA-seq

tag: Sex


title: CSU-027 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-027C

value: Lab

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: number of carboplatin treatments


title: Primary cancer, AMC-17CT-113

description: gene expression

tag: cancer site

tag: age

tag: tissue

value: colorectal cancer


title: HPV QVD specific CD8 TILS VDJ Patient 7_metastatic lymph node

tag: subject id

tag: tetramer

value: QVD

tag: sample type

value: TCR VDJ


title: HPV QVD specific CD8 TILS GEX Patient 7_metastatic lymph node

tag: disease state

tag: treatment


title: Primary cancer, AMC-17CT-086

description: gene expression


title: Primary cancer, AMC-17CT-018

description: gene expression


title: CSU-029 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-029C

tag: breed

value: Male

tag: overall survival (days)

tag: body weight (kgs)


title: Tg7_12w_1 bulkRNA-seq

tag: cell type

tag: strain

tag: genotype


title: HPV KSA specific CD8 TILS VDJ Patient 7_primary tumor


title: Wt_12w_4 bulkRNA-seq

source_name: Wild-type, 12 weeks of age

value: Wild-type

tag: Sex


title: CSU-026 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-026C

value: Golden Ret

tag: neutered status

value: Yes

tag: age (years)

tag: time to progression (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: CSU-026 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-026B

tag: number of carboplatin treatments


title: WT scRNA-seq

source_name: Wild-type, 12 week of age

tag: age


title: HPV KSA specific CD8 TILS GEX Patient 7_primary tumor

tag: subject id

tag: disease state

value: HPV+ HNSCC

value: previously untreated disease

tag: tetramer

value: KSA

tag: sample type


title: Wt_12w_2 bulkRNA-seq

value: pancreatic islets

value: male


title: Primary cancer, AMC-17CT-085

description: gene expression

tag: cancer site

tag: tissue


title: PD1+ CD8 TILS VDJ Patient 51_metastatic lymph node

tag: treatment

value: none bulk PD1+


title: CSU-025 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-025B

tag: breed

tag: overall survival (days)

tag: body weight (kgs)


title: CSU-024 tumor pre-treatment replicate E

description: Gene expression data from osteosarcoma sample CSU-024E

tag: Sex

value: Female

tag: neutered status

tag: age (years)


title: Wt_12w_1 bulkRNA-seq

tag: cell type

tag: strain

value: 12 weeks of age

tag: genotype


title: Primary cancer, AMC-17CT-046

description: gene expression

value: Large intestine

tag: age


title: CSU-024 tumor pre-treatment replicate D

description: Gene expression data from osteosarcoma sample CSU-024D

value: Mix

tag: time to progression (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: Primary cancer, AMC-17CT-068

description: gene expression

tag: cancer site

tag: tissue

value: colorectal cancer


title: PD1+ CD8 TILS VDJ Patient 51_primary tumor

tag: subject id

tag: disease state

tag: treatment

tag: tetramer

tag: sample type


title: Tg7_2w_3 bulkRNA-seq

source_name: Tg7 , 2 weeks of age

value: 2 weeks of age

tag: Sex


title: PD1+ CD8 TILS GEX Patient 51_metastatic lymph node

value: RNA


title: SC-derived neurons_26 [Sample_44]

tag: isolation

value: MACS-sorted

tag: transcription factor

tag: ephys property

value: firing


title: CSU-023 tumor pre-treatment replicate E

description: Gene expression data from osteosarcoma sample CSU-023E

tag: breed

value: Lab

value: Male

tag: neutered status

tag: age (years)

tag: overall survival (days)

tag: body weight (kgs)


title: Tg7_2w_2 bulkRNA-seq

tag: cell type

tag: strain

tag: age

tag: genotype


title: Primary cancer, AMC-17CT-131

description: gene expression

tag: cancer site

tag: tissue


title: Tg7_2w_1 bulkRNA-seq


title: Primary cancer, AMC-17CT-055

description: gene expression


title: Wt_2w_3 bulkRNA-seq

source_name: Wild-type, 2 weeks of age

value: Wild-type


title: Primary cancer, AMC-17CT-080

description: gene expression


title: Wt_2w_2 bulkRNA-seq


title: PD1+ CD8 TILS GEX Patient 51_primary tumor

tag: subject id

tag: disease state

value: HPV+ HNSCC

tag: treatment

value: previously untreated disease

tag: tetramer


title: Primary cancer, AMC-17CT-009

description: gene expression


title: CSU-023 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-023B

tag: Sex

value: Yes

tag: time to progression (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: HPV QVD specific CD8 TILS VDJ Patient 51_metastatic lymph node

value: QVD

tag: sample type

value: TCR VDJ


title: HPV KSA specific CD8 TILS VDJ Patient 51_primary tumor

value: KSA


title: Primary cancer, AMC-17CT-109

description: gene expression


title: Wt_2w_1 bulkRNA-seq

tag: cell type

value: pancreatic islets

value: male


title: HPV QVD specific CD8 TILS GEX Patient 51_metastatic lymph node


title: CSU-025 tumor pre-treatment replicate E

description: Gene expression data from osteosarcoma sample CSU-025E

tag: breed

value: Mix

tag: neutered status

tag: age (years)

tag: overall survival (days)

tag: body weight (kgs)


title: CSU-022 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-022C

value: Mix breed

value: Female


title: CSU-022 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-022A


title: Primary cancer, AMC-17CT-108

description: gene expression

tag: cancer site

value: Large intestine

tag: age

tag: tissue

value: colorectal cancer


title: Primary cancer, AMC-17CT-082

description: gene expression


title: Methylseq D-OSKM ESCs -1

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

library_source: genomic

data_processing:
Library strategy: MethylC-seq
For RNA-seq analysis, after trimming of adaptor sequences and low-quality bases with cutadapt-1.18, sequenced reads were mapped to the mouse reference genome (mm10) and expression levels were calculated as TPM using RSEM 1.3.1 with STAR (v. 2.6.0c) aligner and the GENCODE version M23 annotation gtf file.
For WGBS and MethylC-seq analyses, bases with low-quality scores and the adapters in all sequenced reads were trimmed with cutadapt-1.18. Trimmed reads were mapped to mouse reference genomes (mm10) using the Bismark software-v0.20.1 with bowtie2 (version 2.3.5). Methylated cytosines were extracted from reads using the Bismark methylation extractor with the following options: --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5.
Genome_build: mm10

source_name: ES cells

extract_protocol:
RNAeasy plus Mini or Micro Kit (QIAGEN) for RNA and PureLink Genomic DNA mini kit (invitrogen) for genomic DNA.
For RNA-seq library, RNA (in vitro and in vivo samples; 200 ng, FACS-sorted mCherry-positive tumor cells; 50 ng) was prepared for library construction. RNA-seq libraries were generated using the TruSeq Stranded mRNA LT sample prep kit (Illumina) or NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The libraries were sequenced on a NextSeq500 (Illumina) as 86 bp single reads. For whole genome bisulfite sequencing library, 500ng of DNA was fragmented by sonication (Covaris) and ligated with methylated adapters using TruSeq™ Nano DNA Library Prep Kit and TruSeq™ ChIP Libary Preparation Kit (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold Kit™ (ZYMO RESEARCH). Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). For methyl-seq library, 1μg of DNA was fragmented by sonication. Subsequently, library preparation was performed using the SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). DNA was bisulfite-treated using the EZ DNA Methylation-Gold Kit™. The libraries were then sequenced on a Hiseq 2500 (Illumina) in a rapid mode as paired-end reads (Read1:109 bp, Read2:108bp). For ATAC-seq library, cells were lysed with a lysis buffer (10mM Tris-HCl pH7.4, 3mM MgCl2, 10mM NaCl and 0.1% IGEPAL CA-630). Yielded nuclei were suspended in the transposase reaction mix (25 µl of 2X TD Buffer (Illumina), 2.5 µl of TD Enzyme 1 (Illumina), and 22.5 µl of nuclease-free water), and incubated for 30 minutes at 37 ℃. Fragmented DNA was then purified using MinElute PCR purification kit (QIAGEN). After that, fragmented DNA was amplified by PCR to obtain ATAC-seq libraries. The libraries were paired-end sequenced with a length of 50 bp on Hiseq 1500 (Illumina).

value: ES cells

tag: experimental type

value: in vitro

tag: treatment

value: Not applicable


title: HPV QVD specific CD8 TILS VDJ Patient 51_primary tumor

tag: subject id

tag: disease state

tag: tetramer


title: Methylseq D-OSKM pancreatic tumor DoxON14dplusOFF7d -6

source_name: Pancreas tumors

value: Pancreas tumors

value: in vivo

value: Dox treatement for 14days, followed by withdrawal for 7days


title: CSU-021 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-021A

value: Golden Ret

tag: Sex

value: Male

value: Yes

tag: time to progression (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: Primary cancer, AMC-17CT-088

description: gene expression


title: HPV QVD specific CD8 TILS GEX Patient 51_primary tumor

value: HPV+ HNSCC

value: previously untreated disease

value: QVD

tag: sample type

value: RNA


title: Methylseq D-OSKM pancreatic tumor DoxON14dplusOFF7d -4

tag: cell type


title: Primary cancer, AMC-17CT-036

description: gene expression


title: PD1+ CD8 TILS VDJ Patient 34_metastatic lymph node

value: none bulk PD1+

value: TCR VDJ


title: CSU-021 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-021C

tag: breed

tag: neutered status

tag: age (years)

tag: overall survival (days)

tag: number of carboplatin treatments


title: Methylseq Normal pancreas -2

source_name: Pancreas tissues

value: Pancreas tissues

tag: experimental type


title: CSU-019 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-019B

value: Standard Poodle

value: Female

tag: body weight (kgs)


title: Primary cancer, AMC-17CT-069

description: gene expression

tag: cancer site

value: Large intestine

tag: age

tag: tissue

value: colorectal cancer


title: CSU-018 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-018B

value: Akbash

tag: Sex


title: Methylseq Normal pancreas -1

value: in vivo

tag: treatment

value: Not applicable


title: WGBS D-OSKM ESCs -1

data_processing:
For RNA-seq analysis, after trimming of adaptor sequences and low-quality bases with cutadapt-1.18, sequenced reads were mapped to the mouse reference genome (mm10) and expression levels were calculated as TPM using RSEM 1.3.1 with STAR (v. 2.6.0c) aligner and the GENCODE version M23 annotation gtf file.
For WGBS and MethylC-seq analyses, bases with low-quality scores and the adapters in all sequenced reads were trimmed with cutadapt-1.18. Trimmed reads were mapped to mouse reference genomes (mm10) using the Bismark software-v0.20.1 with bowtie2 (version 2.3.5). Methylated cytosines were extracted from reads using the Bismark methylation extractor with the following options: --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5.
Genome_build: mm10

value: ES cells

value: in vitro


title: CSU-017 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-017C

value: Mix breed

value: Yes

tag: time to progression (days)

tag: alkaline phosphatase levels


title: PD1+ CD8 TILS VDJ Patient 34_primary tumor

tag: subject id

tag: disease state

value: HPV+ HNSCC

value: previously untreated disease

tag: tetramer


title: CSU-020 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-020C

tag: breed

value: Golden Ret

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: PD1+ CD8 TILS GEX Patient 34_metastatic lymph node

value: none bulk PD1+

tag: sample type

value: RNA


title: Primary cancer, AMC-17CT-096

description: gene expression


title: Primary cancer, AMC-17CT-004

description: gene expression


title: WGBS D-OSKM pancreatic tumor DoxON14dplusOFF7d -6

tag: cell type

value: Pancreas tumors

value: Dox treatement for 14days, followed by withdrawal for 7days


title: PD1+ CD8 TILS GEX Patient 34_primary tumor


title: HPV KSA specific CD8 TILS VDJ Patient 34_metastatic lymph node

value: KSA

value: TCR VDJ


title: Primary cancer, AMC-17CT-139

description: gene expression

value: Large intestine

value: colorectal cancer


title: CSU-020 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-020A

value: Female

tag: neutered status

tag: age (years)

tag: overall survival (days)

tag: number of carboplatin treatments


title: WGBS D-OSKM pancreatic tumor DoxON14dplusOFF7d -4

tag: experimental type

value: in vivo


title: HPV KSA specific CD8 TILS GEX Patient 34_metastatic lymph node


title: Primary cancer, AMC-17CT-120

description: gene expression

tag: cancer site

tag: age

tag: tissue


title: WGBS Normal pancreas -2

value: Pancreas tissues

tag: treatment

value: Not applicable


title: HPV QVD specific CD8 TILS VDJ Patient 34_metastatic lymph node

tag: subject id

value: QVD


title: Primary cancer, AMC-17CT-075

description: gene expression


title: WGBS Normal pancreas -1

value: in vitro


title: HPV QVD specific CD8 TILS GEX Patient 34_metastatic lymph node

tag: disease state

value: HPV+ HNSCC


title: HPV QVD specific CD8 TILS VDJ Patient 34_primary tumor

value: previously untreated disease

tag: tetramer


title: A549-BRG1_rep3

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

description: A549 cell line transfected with pcDNA4-SMARCA4

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Raw sequences were trimmed in order to remove adapter sequences and random nucleotides introduced during the library preparation.
Reads shorter than 15 nucleotides (nt) and larger than 28 nt after trimming were discarded.
We used QuickMIRSeq to align not against reference miRNAs
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file with counts normalized by TMM for each miRNA (rows) and all samples (columns)

source_name: Lung adenocarcinoma derived cell line

growth_protocol: A549 was grown under standard conditions (humidified 5% CO2 atmosphere at 37 °C) in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin/amphotericin

extract_protocol:
Total RNA was extracted using the mirVana RNA Isolation Kit (Thermo Scientific).
Illumina TruSeq® Small RNA Library Prep Kit (Illumina Inc) was used to generate sequencing libraries, according to the manufacturer's instructions.

treatment_protocol: Restoration of SMARCA4 was performed with Lipofectamine 2000 (Thermo Scientific) and pcDNA4 or pcDNA4-SMARCA4 following the manufacturer's protocol.

tag: cell line

value: Lung

value: Epithelial

value: Adenocarcinoma

value: 48h after transfection with pcDNA4-SMARCA4


title: A549-BRG1_rep2


title: Primary cancer, AMC-17CT-112

description: gene expression


title: Primary cancer, AMC-17CT-054

description: gene expression


title: HPV QVD specific CD8 TILS GEX Patient 34_primary tumor

value: RNA


title: A549-BRG1_rep1


title: CSU-017 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-017B

tag: breed

value: Mix breed

tag: Sex

value: Yes

tag: time to progression (days)

tag: body weight (kgs)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: CSU-014 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-014C

value: Rottweiler

tag: neutered status

tag: age (years)

tag: overall survival (days)

tag: number of doxorubicin treatments


title: CSU-016 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-016B

value: Newfoundland

value: Male

tag: number of carboplatin treatments


title: A549-EV_rep3

description: A549 cell line transfected with pcDNA4

tag: tissue

tag: cell type

value: 48h after transfection with pcDNA4


title: Primary cancer, AMC-17CT-097

description: gene expression

tag: cancer site

value: Large intestine

tag: age

value: colorectal cancer


title: Primary cancer, AMC-17CT-114

description: gene expression


title: HPV KSA specific CD8 TILS VDJ Patient 15_primary tumor

tag: subject id

tag: disease state

tag: treatment

tag: tetramer

value: KSA

tag: sample type

value: TCR VDJ


title: CSU-016 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-016C

tag: breed

tag: Sex

tag: time to progression (days)

tag: body weight (kgs)


title: CSU-013 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-013C

value: Female

tag: neutered status

tag: age (years)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)


title: CSU-014 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-014B

tag: overall survival (days)

tag: number of doxorubicin treatments

tag: number of carboplatin treatments


title: CSU-012 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-012C

value: Lab


title: CSU-012 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-012A


title: A549-EV_rep2

description: A549 cell line transfected with pcDNA4

tag: cell line

tag: tissue

value: Lung

tag: cell type


title: Primary cancer, AMC-17CT-028

description: gene expression

tag: cancer site

tag: age


title: Primary cancer, AMC-17CT-048

description: gene expression


title: HPV KSA specific CD8 TILS GEX Patient 15_primary tumor

tag: subject id

tag: disease state

value: HPV+ HNSCC

tag: treatment

value: previously untreated disease

tag: tetramer

tag: sample type


title: HPV QVD specific CD8 TILS VDJ Patient 15_primary tumor

value: QVD


title: A549-EV_rep1

description: A549 cell line transfected with pcDNA4

value: Epithelial

value: Adenocarcinoma


title: HPV QVD specific CD8 TILS GEX Patient 15_primary tumor

value: RNA


title: CSU-013 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-013A

tag: breed

value: Mix breed

tag: Sex

tag: neutered status

value: Yes

tag: time to progression (days)

tag: body weight (kgs)


title: CSU-011 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-011B

value: Australian Shep

value: Male

tag: age (years)

tag: overall survival (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: Primary cancer, AMC-17CT-057

description: gene expression

tag: cancer site

value: Large intestine

tag: tissue


title: CSU-011 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-011C

tag: number of carboplatin treatments


title: Primary cancer, AMC-17CT-052

description: gene expression

tag: age

value: colorectal cancer


title: ChIP_input_30min_salt_rep2

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

data_processing:
Standard Illumina Sequencing Pipeline
C-TALE Processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest was embedded, using Bowtie2 v2.3.5. The data were processed using the hiclib pipeline (https://github.com/mirnylab/hiclib-legacy). Statistics for the C-TALE data processing can be found in the table. 10kb-binned HDF5 files were converted to cool format matrices using cooler v0.8.7. Data from three biological replicates for each experimental condition (control and high salt treated chromatin) were merged in two matrices which were then iteratively normalized using publicly available script (https://github.com/Phlya/C-TALE-Normalization) (“--mult_factor 2” option). Weights in a few poorly covered bins were reduced to NA during the normalization procedure; rhdf5 R package was used to manually replace these NA weights with the values of the highest weight found in each matrix.
ChIP-seq processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest (hg19, chr21: 28,981,189-30,260,402) was embedded, using Bowtie2 v2.3.5. Illumina TruSeq adapters were trimmed with cutadapt. Read pairs with at least one non-uniquely mapped read as well as PCR and optical duplicates were filtered using samtools v1.7. Bedtools v2.25.0 and bedGraphToBigWig utility (from UCSC) were used to generate bigwig coverage files. All bigwig files were scaled to 1 mln uniquely mapped read pairs with deeptools v3.4.3. Corresponding input bigwig files were subtracted from each immunoprecipitation bigwig file and then mean profiles were calculated from pairs of biological replicates. Both operations were performed with deeptools v3.4.3.
Genome_build: hg19 (chr21:27,922,688-32,028,897 region)
Supplementary_files_format_and_content: .cool files contain C-TALE contact matrices in an easy to visualize and access format (see https://cooler.readthedocs.io/en/latest/schema.html)
Supplementary_files_format_and_content: bigwig files are binary files containing ChIP-seq profiles in an easy to visualize and access format

source_name: HeLa cells

growth_protocol: Human HeLa cells were cultured in a DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin at 37°C in 5% CO2 in a humidified atmosphere. For G1 synchronization, cells were treated with 2 mM thymidine for 20 hours, washed twice with DPBS, and released into a complete medium. After 6 h, nocodazole (Sigma) was added (100 ng/ml) for 8 h. Mitotic cells were collected by shake-off and centrifugation. Cells were washed twice with DPBS and released into a fresh complete medium.Mitotic cells were seeded in poly-L-lysine-coated dishes. For coating, dish bottoms were covered with 0.1 mg/mL solution of poly-L-lysine (Sigma, P6282) in DPBS and incubated for 1 h at room temperature; after the solution was discarded dishes were rinsed twice with DPBS and dried for 45 min under the hood. G1 cells were harvested for experiments after 5 h of release from mitotic arrest.

extract_protocol:
C-TALE was performed as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan). For ChIP-seq experiments, fixed chromatin pellets were resuspended in 600 uL of ice cold RIPA buffer supplemented with protease inhibitors. Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 10 30-sec pulses on “15” power setting, separated with 3 min periods of recovery. Input DNA was isolated from 1/10 aliquots of sonicated samples. Sheared chromatin from approximately 1 mln of cells and 1 ug of antibodies (against either CTCF, Smc3, or Rad21) were used in each immunoprecipitation reaction. Chromatin immunoprecipitation was performed as described in Abcam X-ChIP manual (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor modifications. 25 ul of protein A/G magnetic beads (Thermo Scientific, 26162) was used per reaction instead of agarose beads, thus a magnet was used instead of a centrifuge to reclaim beads. Beads were blocked with 1% BSA solution in RIPA overnight, while chromatin was incubated with antibodies. BSA-blocked beads were mixed with antibody-bound chromatin for 6 h. Immunoprecipitated DNA was separated from beads by overnight treatment with proteinase K (Thermo Scientific, EO0491) in PBS supplemented with 1% SDS at 65C. Solution was then cleared from beads with a magnet and DNA was isolated with standard phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries from 3C-seq material, immunoprecipitated DNA and ChIP inputs were generated as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan).

treatment_protocol: G1 synchronized HeLa cells in 10-cm dishes were washed once with PBS and dishes were cooled on ice for several minutes. 5 mL of ice cold isotonic lysis buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2, 1% NP-40, 1x protease inhibitors) were added to each dish, cells were permeabilized for 10 min on ice, then the buffer was removed. 5 mL of either ice cold isotonic buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1x protease inhibitors) or high salt buffer (10 mM Hepes pH 8.0, 500 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1x protease inhibitors) was added to permeabilized cells. Dishes were incubated at 4°C for 30 min. In one series of ChIP-seq experiments incubation time was shortened to 1 min. After the incubation, permeabilized cells  were rinsed three times with 5 mL of ice cold wash buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2). Each washing was performed on ice and lasted for 10 min. After the final portion of wash buffer was discarded, chromatin was fixed for 10 min at room temperature with 9 ml of 2% formaldehyde solution in the wash buffer. Fixation was quenched by adding 1 ml of 2 M glycine for 10 min. Fixed chromatin was washed once with PBS and scraped in 7 mL of ice cold Farnham lysis buffer (5 mM Hepes pH 8.0, 85 mM KCl, 0.5% NP-40 ) supplemented with protease inhibitors. Chromatin was collected with centrifugation at 1,000 g for 5 min at 4°C.

tag: cell line

value: HeLa

tag: cell type

value: cervical carcinoma cells

tag: chip antibody

tag: treatment

value: high salt buffer


title: Primary cancer, AMC-17CT-089

description: gene expression

source_name: colorectal cancer


title: BRP283R

city: Leeds

first: Panagiotis

last: Ntostis

address: Clarendon Way

department: Medicine and Health

institute: University of Leeds

data_processing:
Trim galore was used to trim paired-end reads and remove adapters and poor quality sequence.
HISAT2 aligner (version 2.0.4) was used to map read mates to the Human reference genome (hg38), using  the following parameters -p 8 -k 1 --dta --rna-strandness FR --no-mixed --no-discordant.
Incorrectly paired and unmapped reads were removed. The remaining reads converted to bam format with the view function of samtools (version 1.3).
Picard MarkDuplicates (version 2.1.1) was emloyed to tag potential PCR duplicates.
Using the UCSC hg38 annotation of the human genome as a guide, StringTie was used to identify potential novel transcripts.
Rsubread's featureCounts function and Python script prepDE.py (https://ccb.jhu.edu/software/stringtie/dl/prepDE.py) were used to count assigned reads to genomic features. Only correctly paired-end, uniquely mapped, non-duplicated reads were considered.
The libraries were normalised for library sizes using the edgeR function calcNormFactors, that is based on the trimmed mean M value (TMM). The threshold of copies-per-million (cpm) was set at 1 for at least half of the libraries to be included in the analysis. The differential gene expression between blastocysts deriving from young and advanced maternal age women, was statistically tested by the edgeR Exact test (FDR 0.05).
Genome_build: hg38
Supplementary_files_format_and_content: Trophectoderm_GEO_refSeq_submission.xlsx: Excel file includes raw counts.

source_name: middle

growth_protocol: Intracytoplasmic sperm injection (ICSI) was used to fertilise human oocytes. The embryos were cultured to the blastocyst stage, in continuous single culture media with 5% Human Serum Albumin (HSA) (IrvineScientific, CA, USA).

extract_protocol:
A small hole was opened in the zona pellucida opposite the inner cell mass, using a non-contact laser. Six to eight trophectoderm cells were biopsied, inserted into lysis buffer with RNase Inhibitor (Clontech, USA) and frozen at -80°C.
RNA libraries were prepared for sequencing using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA library preparation kit (Illumina), according to the manufacturer's instructions.

value: Trophectoderm

tag: developmental stage

value: Blastocyst

tag: day of development

value: Day 5

tag: maternal age

value: between 30 and 39 years


title: BRP282R


title: Primary cancer, AMC-17CT-116

description: gene expression


title: BRP281R


title: CSU-010 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-010A

tag: breed

value: Belgian Tervuren

tag: Sex

value: Female

tag: neutered status

tag: time to progression (days)

tag: body weight (kgs)


title: Primary cancer, AMC-17CT-053

description: gene expression


title: ChIP_input_30min_control_rep2

value: isotonic buffer


title: CSU-010 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-010C

tag: age (years)

tag: overall survival (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: Primary cancer, AMC-17CT-101

description: gene expression

tag: cancer site

tag: age

tag: tissue


title: C-TALE_control_rep1

tag: cell line

tag: cell type

tag: treatment


title: C-TALE_salt_rep1


title: Primary cancer, AMC-17CT-011

description: gene expression


title: BRP232R

tag: developmental stage

tag: day of development

tag: maternal age


title: Primary cancer, AMC-17CT-040

description: gene expression


title: CD16Int, replicate 1

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Base calling: raw .bcl files were converted to fastq files using bcl2fastq v2.20.0.422.
Demultiplexing: reads were demultiplexed based on the 8-base NuGen sample barcode using a custom Perl script.
Removal of PCR duplicates: PCR duplicates were removed by collapsing sequences with 100% identity over all 92 bases (76 sequenced bases plus 8 base sample index plus 8 base UMI) using a custom Perl script.
Quality Assurance/Quality Control: QA/QC was performed using FastQC v0.10.1.  No issues were found, so no further trimming or other QA/QC steps were deemed necessary.
Alignment: Raw fastq sequences were aligned to the human reference genome (hg38.p12) using STAR v2.6 guided by an ENSEMBL v93 gtf with mitochondrial and ribosomal RNAs removed.
Count extraction: Raw read counts were obtained from the STAR aligned bam files using HTSeq v0.10.0.
Genome_build: hg38.p12
Supplementary_files_format_and_content: htseq_rawCounts.txt

source_name: CD16Int, replicate 1

extract_protocol:
RNA was extracted using Qiagen's RNAeasy Plus Microkit.
Library Preparation: Libraries were prepared using the Universal Plus mRNA-Seq with (NuGEN Cat# 0520-24).  a. Poly(A) Selection: 8-30 ng of RNA samples (in a volume of 50 μl) were mixed with  Oligo (dT) Beads and incubated at 65oC for 5 minutes, mixed, then at room  temperature for 10 mins. The supernatant was discarded and the beads were  washed with wash buffer. Captured polyadenylated RNA was eluted using Elution  buffer at 80°C for 2 min. mRNA is further purified in a second bead clean-up.  b. RNA Fragmentation: Beads were mixed with 20 μl Fragmentation Buffer and  incubated for 8 minutes at 94oC. 20 μl of supernatant was removed from the beads  and proceeded immediately to First Strand cDNA Synthesis.  c. First Strand cDNA Synthesis: 5 μl of First Strand Master Mix was added to each  sample and placed on a thermal cycler to run preprogrammed thermal conditions.  d. Second Strand cDNA Synthesis: 50 μl Second Strand Master Mix was added to  each sample, mixed well and incubated in a thermal cycler at 16oC for one hour. e. cDNA Purification: cDNA was purified using Agencourt AMPure XP Beads (1.8  volumes), eluted in 10 μl of H2O, and stored at -20oC.  f. End Repair: End Repair Mix was added to the purified samples from step e and the  samples were incubated in a preprogrammed thermal cycler.  g. Adaptor Ligation: Samples were mixed with 3 μl adaptor mix, then 12 μl Ligation  Mix, and incubated in a thermal cycler at 25oC for 30 minutes.  Sample and Barcode Information: Samples were barcoded with NuGEN Unique  Dual Indexes. Strand Selection: 70 μl of Strand Selection Master Mix was added to 30 μl of each  sample, incubated in a pre-heated thermal cycler at 72oC for 10 minutes. Strand Selection Purification: Strand selected cDNA was purified using  Agencourt AMPure XP Beads (0.8 volumes), eluted in 15 μl of H2O, and stored at -  20oC.  j. Library Amplification: 76.5 μl of Library Amplification Master Mix was added to  13.5 μl of each sample and incubated in a preprogrammed thermal cycler, for 13-  16 cycles, which was pre-optimized with qPCR.  k. Amplified Library Purification: Amplified libraries were purified using 90 μl  Agencourt AMPure XP Beads (1.0 volumes). 25 μl of eluted libraries were collected  and stored at -20oC.  l. Validate Library: The concentration of libraries were measured by Qubit dsDNA  HS Assay Kit (Invitrogen Q32851). Libraries were diluted and normalized to the  optimal range for Agilent Bioanalyzer analysis using the DNA High Sensitivity Kit  (Agilent Technologies, Cat# 5067-4626).  m. Normalize and Pool Libraries: Same amount of libraries were pooled based on  the molar concentration from Bioanalyzer measurements. Library Denaturing and Diluting for MiSeq Nano 300: Pooled library was run on MiSeq  to test quantity and quality, using the MiSeq Reagent Nano Kit V2 300 cycles (Illumina, Cat.  No. MS-103-1001). Library and PhiX control (Illumina, Cat. No. FC-110-3001) were  denatured and diluted using the standard normalization method following manufacturer's  directions, to a final concentration of 6pM. Equal volume of library and PhiX were combined and  sequenced on Illumina MiSeq.  (https://basespace.illumina.com/run/196126950/JY_Xiaoling07072020_test)  3. Library Denaturing and Diluting for Nextseq 500: Library and PhiX were denatured and  diluted using the standard normalization method following manufacturer's directions. The  loading of library pool was 1.3 ml at 1.8 pM, with 1% PhIX spike in.  Sequencing Run: Sequencing was performed on the University of Louisville Brown Cancer  Center Genomics Core Illumina NextSeq 500 using the NextSeq 500/550 75 cycle High  Output Kit v2.5 (20024906).

treatment_protocol: CD16High and CD16Int neutrophils were sorted by FACSAria III from three severe COVID-19 patients and NDN were purified from healthy donor peripheral blood.

tag: disease

tag: neutrophils

value: peripheral blood


title: CD16High, replicate 3

source_name: CD16High, replicate 3


title: CD16Int, replicate 3

source_name: CD16Int, replicate 3


title: BRP113


title: CD16Int, replicate 2

source_name: CD16Int, replicate 2


title: CSU-007 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-007C

source_name: Osteosarcoma

tag: breed

value: Malamute

tag: Sex

tag: neutered status

tag: time to progression (days)

tag: body weight (kgs)

tag: number of carboplatin treatments


title: CSU-008 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-008C

value: Akita

value: Yes

tag: age (years)

tag: overall survival (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: BRP273

tag: tissue


title: CSU-009 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-009A

value: Elkhound


title: CSU-008 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-008A

value: Male


title: CSU-007 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-007B


title: BRP112

tag: developmental stage


title: CSU-006 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-006C

value: Mix breed


title: Primary cancer, AMC-17CT-073

description: gene expression

tag: cancer site

value: Large intestine

tag: age

value: colorectal cancer


title: BRP111

tag: day of development

tag: maternal age


title: Primary cancer, AMC-17CT-074

description: gene expression


title: Primary cancer, AMC-17CT-121

description: gene expression


title: CD16High, replicate 1

source_name: CD16High, replicate 1

tag: disease

tag: neutrophils


title: BRP92R


title: CSU-006 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-006A

tag: breed

tag: Sex

tag: neutered status


title: Primary cancer, AMC-17CT-103

description: gene expression


title: Healthy donor, normal density neutrophils (NDN), replicate 3

value: Healthy

value: NDN


title: BRP91R

value: Trophectoderm

value: Blastocyst


title: Healthy donor, normal density neutrophils (NDN), replicate 1


title: BRP72

value: Day 5

value: between 30 and 39 years


title: CD16High, replicate 2

source_name: CD16High, replicate 2


title: Primary cancer, AMC-17CT-084

description: gene expression


title: Primary cancer, AMC-17CT-111

description: gene expression


title: Primary cancer, AMC-17CT-060

description: gene expression


title: BRP71


title: CSU-005 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-005A

value: Golden Ret

tag: time to progression (days)

tag: body weight (kgs)

tag: number of carboplatin treatments


title: BRP132


title: CSU-005 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-005B

tag: age (years)

tag: overall survival (days)

tag: alkaline phosphatase levels


title: CSU-004 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-004B

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: Primary cancer, AMC-17CT-066

description: gene expression

tag: cancer site

tag: tissue


title: CSU-004 tumor pre-treatment replicate A

description: Gene expression data from osteosarcoma sample CSU-004A


title: CEM-C7_RNAseq_rep2

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description:
RNAseq Sample 6
C7-UVA.minus.norm.bigWig
C7-UVA.plus.norm.bigWig

data_processing:
RNAseq:Align with tophat
RNAseq:Merge bam files for all replicates
RNAseq:Normalize and create bigWig
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq:bigWig file for merged replicates

source_name: T-ALL cell line

growth_protocol: CEMC1 and CEmC7 cells were cultured in RPMI media (Invitrogen) with 10% FBS (Invitrogen), 1% penicillin/streptomycin (Invitrogen). Cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cell lysis in hypotonic solution
nextera kit and truseq.

treatment_protocol: baseline

tag: cell line

tag: number of cells

value: Healthy cells with passage number < 30


title: CEM-C7_RNAseq_rep3

description:
RNAseq Sample 7
C7-UVA.minus.norm.bigWig
C7-UVA.plus.norm.bigWig


title: Primary cancer, AMC-17CT-010

description: gene expression

tag: age


title: CSU-009 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-009B

value: Female


title: CSU-002 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-002C

value: Lab


title: CEM-C7_RNAseq_rep1

description:
RNAseq Sample 5
C7-UVA.minus.norm.bigWig
C7-UVA.plus.norm.bigWig


title: BRP122R

tag: developmental stage

tag: day of development

tag: maternal age


title: CSU-003 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-003C

tag: breed

value: Anatolian Shep

tag: Sex

tag: neutered status


title: Healthy donor, normal density neutrophils (NDN), replicate 2

tag: disease

tag: neutrophils

value: peripheral blood


title: CSU-003 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-003B

value: Yes

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)

tag: body weight (kgs)

tag: number of carboplatin treatments


title: BRP253R

source_name: mature

tag: tissue

value: at least 40 years old


title: Primary cancer, AMC-17CT-081

description: gene expression

tag: cancer site


title: CEM-C1_RNAseq_rep4

description:
RNAseq Sample 4
C1-UVA.minus.norm.bigWig
C1-UVA.plus.norm.bigWig

tag: cell line

tag: number of cells


title: CEM-C7_RNAseq_rep4

description:
RNAseq Sample 8
C7-UVA.minus.norm.bigWig
C7-UVA.plus.norm.bigWig

extract_protocol:
Cell lysis in hypotonic solution
nextera kit and truseq.
Cell lysis in hypotonic solution
nextera kit and truseq.


title: CSU-002 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-002B

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: BRP242R

tag: developmental stage

tag: day of development

tag: maternal age


title: HPV KSA specific CD8 TILS GEX Patient 51_primary tumor

source_name: primary tumor

tag: subject id

tag: disease state

value: HPV+ HNSCC

tag: treatment

value: previously untreated disease

tag: tetramer

value: KSA

tag: sample type

value: RNA


title: Primary cancer, AMC-17CT-138

description: gene expression

value: Large intestine

tag: age

value: colorectal cancer


title: CEM-C1_RNAseq_rep3

description:
RNAseq Sample 3
C1-UVA.minus.norm.bigWig
C1-UVA.plus.norm.bigWig


title: BRP131

value: Trophectoderm

value: Blastocyst


title: Primary cancer, AMC-17CT-019

description: gene expression


title: BRP241R

value: Day 5


title: Primary cancer, AMC-17CT-050

description: gene expression


title: CEM-C1_RNAseq_rep2

description:
RNAseq Sample 2
C1-UVA.minus.norm.bigWig
C1-UVA.plus.norm.bigWig


title: CEM-C1_RNAseq_rep1

description:
RNAseq Sample 1
C1-UVA.minus.norm.bigWig
C1-UVA.plus.norm.bigWig


title: CSU-001 tumor pre-treatment replicate B

description: Gene expression data from osteosarcoma sample CSU-001B

tag: breed

value: Mix breed

tag: Sex

tag: neutered status

tag: age (years)

tag: time to progression (days)

tag: overall survival (days)

tag: body weight (kgs)

tag: number of carboplatin treatments


title: BRP43R

tag: tissue

tag: developmental stage


title: A375

city: Albany

first: Ariel

last: Jaitovich

email: balnisj@amc.edu, jaitova@amc.edu

state: NY

address: 47 New Scotland Ave.

department: MCP

institute: Albany Medical College

data_processing:
Quality filtering for sequencing error, contamination, or PCR artifact - FastQC 0.11.2
Remove adapter and primer sequences - Trimmomatic 0.36
Alignment and read mapping - STAR 2.6.0c
Quality control step looks at read distribution over genome features (intron, exon, UTR, etc.) - RseQC 2.6.4
Raw read counts, normalized read count per sample, and differential expression - DESeq2 1.16.1 and edgeR_3.16.5
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in .txt files

source_name: Skeletal muscle stem cells

growth_protocol: Animal littermates, both with type and IL13TG (COPD) are induced for two months with doxycycline in drinking water. IL13TG developed a COPD-like phenotype. Animals are used at 22 weeks of age.

extract_protocol:
Animals hind leg skeletal muscles from both legs were enzymatically digested. Mononuclear cells were stained and sorted with FACS to collect alpha7 integrin positive skeletal muscle satellite cells. After sorting RNA was isolated from cells using Arcturus PicoPure RNA isolation kit.
Library construction was performed using Takara Bio SMART-Seq stranded kit for low input library generation following manufacturers recommended protocols.

treatment_protocol: IL13TG animals contain an inducible transgene that when expressed, causes development of COPD upon induction with doxycycline.

tag: strain

tag: genotype

tag: cell type

value: Skeletal muscle stem cells

value: Doxycycline induction


title: A361

tag: treatment


title: Primary cancer, AMC-17CT-117

description: gene expression

tag: cancer site


title: CEM-C7_ATACseq_rep3

description:
ATACseq Sample 7
C7_merged.bigWig
C7_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed

data_processing:
ATAC:Align with bowtie2
ATAC:Merge bam files for all replicates
ATAC:Normalize and create bigWig
ATAC:Peak calling with hotspot (standard paramters)
Genome_build: hg38
Supplementary_files_format_and_content: ATAC:bigWig file for merged replicates, Single nucleotide resolution (SNR) bigWig file for all replicates, hotspot file for merged replicates.

extract_protocol:
Cell lysis in hypotonic solution
nextera kit and truseq.
Varying amount of NP40 was a step in library preparation: 0.00% NP40

tag: cell line

tag: number of cells

value: Healthy cells with passage number < 30


title: A371


title: A360


title: BRP41R

tag: day of development

tag: maternal age


title: CEM-C7_ATACseq_rep2

description:
ATACseq Sample 6
C7_merged.bigWig
C7_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed


title: Primary cancer, AMC-17CT-045

description: gene expression

tag: age


title: A359


title: Primary cancer, AMC-17CT-035

description: gene expression


title: BRP233R

value: between 30 and 39 years


title: Primary cancer, AMC-17CT-037

description: gene expression


title: CEM-C7_ATACseq_rep1

description:
ATACseq Sample 5
C7_merged.bigWig
C7_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed

extract_protocol:
Cell lysis in hypotonic solution
nextera kit and truseq.
Varying amount of NP40 was a step in library preparation: 0.1% NP40


title: A373

value: wild-type


title: BRP223R

source_name: young

value: below 30 years old


title: CEM-C1_ATACseq_rep4

description:
ATACseq Sample 4
C1_merged.bigWig
C1_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed

extract_protocol:
Cell lysis in hypotonic solution
nextera kit and truseq.
Varying amount of NP40 was a step in library preparation: 0.02% NP40


title: A364


title: Primary cancer, AMC-17CT-115

description: gene expression

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
cDNA library was constructed using the TruSeq RNA Access Library Prep Kit (Illumina)


title: BRP221R


title: BRP44R

value: at least 40 years old


title: CEM-C1_ATACseq_rep3

description:
ATACseq Sample 3
C1_merged.bigWig
C1_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed


title: A362


title: A374


title: CEM-C1_ATACseq_rep2

description:
ATACseq Sample 2
C1_merged.bigWig
C1_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed


title: Primary cancer, AMC-17CT-135

description: gene expression


title: BRP171R


title: A353


title: BRP101R


title: thymic portal endothelial cells

city: Beijing

first: Suijuan

last: Zhong

state: Haidian

address: No.19 Xinjiekouwai Street

country: China

institute: Beijing Normal University

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to mm10 mouse genome by Cellranger(v2.0.1)
Filtered count matrix was merged by Seurat R Package(v2.3.4)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: Adult mouse

extract_protocol: NOT PROVIDED; REQUESTED

tag: week

value: thymic portal endothelial cells


title: Primary cancer, AMC-17CT-032

description: gene expression


title: BRP222R


title: CEM-C1_ATACseq_rep1

description:
ATACseq Sample 1
C1_merged.bigWig
C1_merged_minushg38andlifted.rmdup.fdr0.01.hot.bed


title: Primary cancer, AMC-17CT-008

description: gene expression


title: 8h Of2-3

city: IRAPUATO

first: Alfredo

last: Herrera-Estrella

state: GUANAJUATO

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: LANGEBIO

country: Mexico

institute: CINVESTAV

description:
8Of3
processed data file/column: 8h AF2-3 (raw-counts.txt)

data_processing:
RNA sequencing trought the Illumina NextSeq500 platform in the 1x75 single-end mode
Raw RNA-seq data were first processed with FastQC Version 0.11.6  to clean adapter contamination and quality analysis. Around 14 millions of high-quality reads per library were obtained. After quality analysis read were aligned to the T. atroviride IMI 206040 genome (JAEAGS000000000)  using HISAT2 version 2.1.0 . For mapping reads counting to each gene HTseq version 0.14.1  was used
For differential expression analysis, counted reads were processed with Edge R,  only those with at least two counts in at least five libraries were consider as transcribed
To analyze if there exist differences in gene expression between controls, these were fist compared using contrast between the time point control T0 and control T8 using a cutoff of False Discovery Rate <0.05 and <0.005 using glmQLF Test. Replicate number two of the Time C0 was discarded for the noise at moment to performed differential expresion analysis (DE).
Five libraries of control conditions (T0 and T8) were taken as Control condition for contrasts against injury and fungivory libraries. FDR >0.005 was selected to perform the DE analysis, to find those genes that specifically respond in each condition and time point
After DEG analysis, Gene Ontology (GO) enrichment analysis were performed using topGO from package from R  and a cutoff of Fisher test P>0.05 for significant enriched Biological process
The GO terms before plotting were filter for redundancy using REVIGO
Genome_build: T. atroviride IMI 206040 genome (JAEAGS000000000)
Supplementary_files_format_and_content: A matrix teble "raw-counts.txt" including Counts per million (CPM),  of all conditions and replicates. Counts per gene (rows) and condition (columns) are included. A data datriz containing all Diferential expressed genes against  control condition is included in the file (DEG.txt).  ID Genes (rows) and LogFC values (columns).

organism: Trichoderma atroviride

source_name: 8h after fungivory by O. folsomi

growth_protocol: 1x10^6 fresh conidia of T. atroviride were inoculated in plates with PDA media and sterile cellophane circles, plates were incubated during 36h in dark at 27C. After treatment, fungi were incubated 30, 90 min, 4 and 8 h.

extract_protocol:
After each incubation times, mycelium was collected and frozen using liquid nitrogen. For the RNA extraction TRIZOL method was performed.
Libraries for RNA sequencing were prepared following the Illumina® TruSeq® Stranded Total RNA Sample Preparation kit instructions.

treatment_protocol: Interactions between T. atroviride WT and insects were performed placing the insects on fungus mycelia during 10 minutes in dark. After 10 minutes, insects were immediately carefully withdrawn using a sterile dissection forceps. After fungivory, mycelium was incubated during 30 min, 90 min, 4 h and 8 h. After incubation times, mycelia were collected and frozen using liquid nitrogen. For mechanical injury conditions, mycelium was cut using a sterile scalpel, cuts were performed in all mycelia in the less time possible. After cuts, mycelium was incubated during 30 min, 90 min, 4 h and 8 h. After each incubation times, mycelia were collected and frozen using liquid nitrogen. For control conditions untreated mycelia plates were open for 2 minutes in dark and incubated during 30 min and 8 h

value: mycelia


title: Primary cancer, AMC-17CT-047

description: gene expression

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normalization for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.


title: 8h Of2-2

description:
8Of2
processed data file/column: 8h AF2-2 (raw-counts.txt)


title: BRP32R


title: BRP33R


title: Primary cancer, AMC-17CT-056

description: gene expression


title: BRP172R


title: BRP31R


title: Primary cancer, AMC-17CT-042

description: gene expression


title: 8h Of2-1

description:
8Of1
processed data file/column: 8h AF2-1 (raw-counts.txt)


title: input_DNA

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

address: 21111 Lakeshore road

department: Animal Science

data_processing:
Raw reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads. Trimming and clipping were performed using Trimmomatic version 0.36 (Bolger et al., 2014).
Each read was mapped against the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) downloaded from UCSC genome browser (Haeussler et al., 2019) using Bowtie 2 version 2.3.4.1 (Langmead and Salzberg, 2012).
We excluded reads that exhibited more than 3 mismatches. SAMtools version 1.9 (Li et al., 2009) was then used to sort and convert SAM files.
Genome_build: hg19
Supplementary_files_format_and_content: Coverage tracks were generated from aligned reads using deepTools2 (Ramirez et al., 2016). The coverage was calculated as the number of reads extended to 150bp fragment size per 25 bp bin and normalized using Reads Per Kilobase per Million mapped reads (RPKM) not located in chromosome X.

source_name: human sperm

extract_protocol:
Semen samples were collected by masturbation after at least 3 days of abstinence. Following semen liquefaction (20-30min at room temperature), an aliquot was used for sperm count and the remaining sample was immediately frozen.
ChIP-seq libraries were prepared using the Kapa HTP Library Preparation Kit (Roche) as per the manufacturer's recommendations except that the size selection was performed after the PCR step.

value: sperm

value: spermatozoa


title: 4h Of2-3

description:
4Of3
processed data file/column: 4h AF2-3 (raw-counts.txt)

source_name: 4h after fungivory by O. folsomi


title: Primary cancer, AMC-17CT-090

description: gene expression

source_name: colorectal cancer

value: Large intestine


title: BRP102R


title: 4h Of2-2

description:
4Of2
processed data file/column: 4h AF2-2 (raw-counts.txt)


title: NHEK_mock_rep2

city: Nagasaki

first: Sayaka

last: Kuwatsuka

department: Dermatology

institute: Nagasaki University Graduate School of Biomedical Sciences

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed　at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1  (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014850_D_20070820).

source_name: keratinocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low RNA fluorescent linear amplification kit plus(1 color) (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).   Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Standard Agilent Protocol


title: CSU-001 tumor pre-treatment replicate C

description: Gene expression data from osteosarcoma sample CSU-001C

data_processing: The data were analyzed  in R using RMA and COMBAT normalization methods for batch correction.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, total RNA was further purified using Qiagen RNeasy Purification Kits.

tag: breed

tag: Sex

value: Female

tag: neutered status

value: Yes

tag: age (years)

tag: time to progression (days)

tag: alkaline phosphatase levels

tag: monocyte counts (1000 cells/μl)

tag: number of doxorubicin treatments


title: NHEK_Pitavastatin 0.1 µM treated_rep1

value: HMG-CoA reductase inhibitor


title: Primary cancer, AMC-17CT-123

city: Seoul

first: Chang Ohk

last: Sung

description: gene expression

tag: tissue

value: colorectal cancer


title: NHEK_Pitavastatin 0.1 µM treated_rep2

tag: treatment


title: PCV2

city: New York

first: Yingli

last: Shang

address: 535E 70th Street

institute: Hospital for Special Surgery

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Hisat2 (v2.0.1) was used to index reference genome sequence, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene.To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BMDMs

growth_protocol: Murine BMDMs were obtained and maintained in DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor.

extract_protocol:
Total RNA was then extracted with a total RNA purification kit (GeneMarkbio).
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

treatment_protocol: BMDMs were left untreated or infected with PCV2 for 12 h.

tag: cell type

value: Bone marrow derived macrophages

tag: strain

value: PCV2 infection for 12 h


title: Primary cancer, AMC-17CT-079

address: Song-Pa gu,Pung-nap dong

institute: Asan Medical Center

description: gene expression

tag: cancer site


title: P8_2_R1_RNA

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Using the Kallisto aligner78 v. 0.46, reads were aligned to the hg38 ENSEMBL release 7979 transcripts, with a transcript support level between 1 and 3
Read summation onto genes and differential expression analysis was performed by sleuth v. 0.3080
Differential expression p-values and Bonferroni corrected q-values were calculated using a likelihood ratio test comparing a model containing only participant information (~ Participant) to a model with participant and training status information (~ Participant + Training)
Fold changes were calculated using a Wald-test, as described in the Sleuth manual.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with estimated abundances

source_name: vastus lateralis

extract_protocol:
20-30 mg of human skeletal muscle tissue was used for purification of total RNA. After lysis of muscle tissue in RLT buffer (Qiagen) by the use of a Tissuelyzer II (Qiagen, 30 hertz for 3x30sec), total RNA was purified using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). The quality of recovered RNA was assessed by the Agilent RNA 6000 Nano Kit (Agilent Technologies) and RNA concentration was determined by spectrophotometry using a NanoDrop 2000 (Thermo Scientific).
For RNA-sequencing, 0.5 microgram of total RNA was depleted of rRNA and subsequently used to generate libraries using the TruSeq standard total RNA with Ribo-Zero Gold kit (Illumina). The PCR cycle number for each library amplification was optimized by running 10% of the library DNA in a real-time PCR reaction using Brilliant III Ultra-fast SYBR Green QPCR Master Mix (AH Diagnostic) and a C1000 Thermal cycler (Bio-Rad)

value: vastus lateralis

tag: participant

tag: training

value: Trained


title: 4h Of2-1

description:
4Of1
processed data file/column: 4h AF2-1 (raw-counts.txt)


title: H3K4me3_ChIP_seq

institute: McGill University

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology 9751S)


title: Mock

value: Uninfected


title: NHEK_mock_rep1


title: P7_2_R1_RNA


title: C2C12D_Membrane_Monosome_rep2

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

department: Program in Gene Expression and Regulation; Center for Systems and Computational Biology

institute: Wistar Institute

description:
C2C12D_Membrane_Monosome_rep2
3pREADS_counts_in_pA_sites.txt

data_processing:
Library strategy: 3'READS+
Adpter trimming performed using Cutadapt
3'READs reads were aligned to mm9 using bowtie2
reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered.
RNA-seq:  Reads were mapped to the genome using STAR (version 2.5.2) and APAlyzer was used to interrogate APA.
Genome_build: mm9
Supplementary_files_format_and_content: txt files include all cluster sites (chromosome, strand, position) with count values for each sample.
Supplementary_files_format_and_content: RNAseq read counts
Supplementary_files_format_and_content: 3'READS+ clusters with read counts

source_name: Differentiating C2C12 Cells

extract_protocol:
Phenol/Choloroform
RNAseq libraries: 250 ng of total RNA was used for library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®. 3'READS+ libraries: The READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 0.1 ~ 2.5 µg of total-cell RNA was captured using 10 µl of oligo(dT)25 magnetic beads (NEB) in 100 µl of 1x Binding Buffer (10 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl of RNase III Buffer (10 mM Tris-Cl pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) for 15 min at 37 °C. After washing away unbound RNA fragments using Binding Buffer, polyA+ fragments were eluted from the beads using TE Buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated using ethanol, followed by ligation to 3 pmol of heat-denatured 5'-adapter (5'-CCUUGGCACCCGAGAAUUCCANNNN-3') in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (ThermoFisher Scientific), and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 hr. Ligation products were captured using 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific). After washing with Washing Buffer (10 mM Tris-Cl pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) for 30 min at 37 °C in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H Buffer, RNA fragments were eluted from the beads in Elution Buffer (1 mM NaCl, 1 mM EDTA pH7.5, and 0.05% TWEEN 20) at 50 °C, precipitated using ethanol, and then ligated to 3 pmol of heat-denatured 5'-adenylated 3'-adapter (5'-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC-3') using 0.25 µl of T4 RNA ligase 2 (truncated KQ version) for 1 hr at 22 °C in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. Ligation products were precipitated and reverse-transcribed using M-MLV reverse transcriptase, and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers (Sigma-Aldrich) for 15 cycles. Both RT primer (5'-GTTCAGAGTTCTACAGTCCGACGATC-3') and PCR primers with indexes have been described previously (Hoque et al., 2013). PCR products were size-selected twice using 0.6 volume of AMPure XP beads (Beckman Coulter) relative to the PCR reaction volume to remove large DNA molecules, followed by an additional 0.4 volume of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The sizes of the libraries eluted from the AMPure beads were examined using a high-sensitivity DNA kit (Agilent) and an Agilent Bioanalyzer. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Equal amounts of libraries were mixed and sequenced using an Illumina NextSeq 500 (1x75 bases).

tag: cell line

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Differentiating

tag: fraction

value: Membrane Monosome


title: P8_1_R1_RNA

value: Untrained


title: Primary cancer, AMC-17CT-107

description: gene expression

tag: age


title: P7_1_R1_RNA


title: C2C12D_Cytosol_Monosome_rep2

description:
C2C12D_Cytosol_Monosome_rep2
3pREADS_counts_in_pA_sites.txt

value: Cytosol Monosome


title: 90 Of2-2

description:
90Of2
processed data file/column: 90 AF2-2 (raw-counts.txt)

source_name: 90 min after fungivory by O. folsomi

value: mycelia


title: 90 Of2-1

description:
90Of1
processed data file/column: 90 AF2-1 (raw-counts.txt)


title: C2C12D_Membrane_Monosome_rep1

description:
C2C12D_Membrane_Monosome_rep1
3pREADS_counts_in_pA_sites.txt


title: C2C12D_Cytosol_Monosome_rep1

description:
C2C12D_Cytosol_Monosome_rep1
3pREADS_counts_in_pA_sites.txt


title: Primary cancer, AMC-17CT-095

description: gene expression

value: Large intestine


title: C-TALE_salt_rep3

source_name: HeLa cells

extract_protocol:
C-TALE was performed as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan). For ChIP-seq experiments, fixed chromatin pellets were resuspended in 600 uL of ice cold RIPA buffer supplemented with protease inhibitors. Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 10 30-sec pulses on “15” power setting, separated with 3 min periods of recovery. Input DNA was isolated from 1/10 aliquots of sonicated samples. Sheared chromatin from approximately 1 mln of cells and 1 ug of antibodies (against either CTCF, Smc3, or Rad21) were used in each immunoprecipitation reaction. Chromatin immunoprecipitation was performed as described in Abcam X-ChIP manual (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor modifications. 25 ul of protein A/G magnetic beads (Thermo Scientific, 26162) was used per reaction instead of agarose beads, thus a magnet was used instead of a centrifuge to reclaim beads. Beads were blocked with 1% BSA solution in RIPA overnight, while chromatin was incubated with antibodies. BSA-blocked beads were mixed with antibody-bound chromatin for 6 h. Immunoprecipitated DNA was separated from beads by overnight treatment with proteinase K (Thermo Scientific, EO0491) in PBS supplemented with 1% SDS at 65C. Solution was then cleared from beads with a magnet and DNA was isolated with standard phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries from 3C-seq material, immunoprecipitated DNA and ChIP inputs were generated as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan).

value: HeLa

value: cervical carcinoma cells

value: high salt buffer


title: P6_1_R1_RNA


title: P6_2_R1_RNA


title: P5_2_R1_RNA