title: koala_WGBS_PC_skeletal_muscle

city: ATLANTA

first: Devika

last: Singh

state: Georgia

address: North Ave NW

institute: Georgia Institute of Technology

data_processing:
Paired-end raw fastq files were processed for quality control and adapter trimming using Trim Galore! (version 0.3.7) with a Phred score threshold of 20. To remove contaminating reads, the trimmed reads were mapped to the phi-X174 (NC_001422.1) reference assembly with Bismark version 0.18.1 using Bowtie 2 (Krueger and Andrews 2011) and only unmapped reads were retained for downstream analyses.
Final QC reads were then mapped to the koala reference assembly (phaCin_unsw_v4.1; (Johnson, et al. 2018)) using Bismark with the Bowtie 2 setting.
Two sequencing runs were performed per tissue sample which were merged following the read mapping step. All merged mapped files were deduplicated using Bismark’s deduplicate_bismark
Reports containing per-CpG-site methylation calls were subsequently generated using bismark_methylation_extractor, bismark2bedGraph, and coverage2cytosine in series for each sample.
Genome_build: phaCin_unsw_v4.1
Supplementary_files_format_and_content: Bismark cytosine report tab-delimited text files including chromosome, position, strand, methylated read count, unmethylated read count, cytosine context, and trinucleotide context

organism: Phascolarctos cinereus

source_name: skeletal muscle

extract_protocol:
All genomic DNA was extracted using a Bioline Isolate II Genomic DNA Extraction Kit (Cat#. BIO-52067) following the recommended protocol with an additional DNAse free RNaseA (100mg/ml) (Qiagen cat. #19101) treatment before column purification.
The bisulfite conversion was carried out by using the EX DNA Methylation-Lightning Kit (Zymo cat. #D5030) and the WGBS libraries were constructed using the TruSeq DNA methylation kit (Illumina cat.# EGMK81213).

tag: australian museum registration

tag: tissue

value: skeletal muscle


title: koala_WGBS_PC_pancreas

status: Public on Feb 27 2021

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

source_name: pancreas

tag: Sex

value: female

value: pancreas


title: koala_WGBS_Ben_skeletal_muscle

value: male


title: koala_WGBS_Ben_pancreas


title: koala_WGBS_Ben_lung

source_name: lung

value: lung


title: koala_WGBS_PC_lung


title: koala_WGBS_PC_kidney

source_name: kidney

value: kidney


title: koala_WGBS_Ben_kidney


title: koala_WGBS_Ben_brain

source_name: Right hemisphere cerebral lobe

value: brain


title: h+ rpb1-CTD-WT29::NatMX [WT2]

status: Public on Feb 25 2021

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: control for GSM4880428; GSM4880429; GSM4880430; GSM4880431; GSM4880432; GSM4880433; GSM4880434; GSM4880435, GSM4880436

library_source: transcriptomic

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: h+ rpb1-CTD-WT29::NatMX

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

tag: genotype/variation

value: h+ rpb1-CTD-WT29::NatMX

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: h+ rpb1-CTD-WT29::NatMX [WT3]


title: koala_WGBS_PC_brain


title: Control ChIP-seq from HAP-1 (ENCLB805IAS)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR771IOP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HAP-1
experiment encode accession: ENCSR771IOP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB805IAS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens HAP-1 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: dev stage

value: adult

tag: age

value: 44 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Haplogen Genomics

tag: link

value: ENCBS501QZV at ENCODE; https://www.encodeproject.org/ENCBS501QZV/

value: Derived from ENCODE donor ENCDO763VKT; https://www.encodeproject.org/ENCDO763VKT/


title: h+ rpb1-CTD-WT29::NatMX [WT1]


title: Histone ChIP-seq from SJCRH30 (ENCLB669RIG)

description:
https://www.encodeproject.org/experiments/ENCSR769CSE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human SJCRH30
experiment encode accession: ENCSR769CSE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR672UXO
encode release date: 2020-08-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB669RIG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SJCRH30 cell line originated from SJCRH30

tag: antibody

value: child

value: 17 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS386GKH at ENCODE; https://www.encodeproject.org/ENCBS386GKH/

value: Derived from ENCODE donor ENCDO339AAA; https://www.encodeproject.org/ENCDO339AAA/


title: Histone ChIP-seq from SJCRH30 (ENCLB282YBL)

description:
https://www.encodeproject.org/experiments/ENCSR022MBN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on human SJCRH30
experiment encode accession: ENCSR022MBN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR672UXO
encode release date: 2020-08-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB282YBL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: ENCBS696NDF at ENCODE; https://www.encodeproject.org/ENCBS696NDF/


title: CD4 single positive (CD4SP)  thymocytes from W131AOTII mice [TWO_1]

status: Public on Feb 22 2021

city: San Francisco, Room S-1024

first: Trang

middle: T. T

last: Nguye

state: California

address: 513 Parnassus

department: Department of Medicine

institute: University of California, San Francisco

data_processing:
Reads were aligned to the Mouse genome GRCm38 using the STAR alignment software version 2.7.2.
Differential expression analysis was done using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Sequencing Counts Matrix

molecule: total RNA

organism: Mus musculus

extract_protocol:
CD25neg Va2+ CD4SP thymocytes or peripheral naïve (CD44low CD62L+) CD25neg Va2+ CD4 T cells were sorted from OTII (n=3 mice), W131AOTII (n=12 mice, 4 mice/group), Cbl-b−/− (n=3 mice), or Cbl-b−/−W131AOTII (n=6 mice, 2 mice/group) and washed with PBS. Total RNA was isolated from 106 cells per sample using RNeasy (Qiagen) following the manufacturer’s protocol.
Libraries were prepared using the Nugen/Nextera XT kit (Illumina) and single-end 50pb RNA sequencing was performed using a HiSeq 4000 (Illumina).

tag: strain background

tag: genotype

value: Thymus

tag: cell type

value: Thymocytes


title: CD4 single positive (CD4SP)  thymocytes from OTII mice [TO_2]

value: OTII

tag: tissue


title: Peripheral naïve Cbl-b-/- OTII CD4 T cells [PCO_1]

value: Cbl-b-/-OTII

value: Spleens + Lymph nodes

value: T cells


title: Peripheral naïve Cbl-b-/- OTII CD4 T cells [PCO_3]


title: CD4 single positive (CD4SP)  thymocytes from W131AOTII mice [TWO_2]


title: Peripheral naïve W131AOTII CD4 T cells [PWO_3]

source_name: Peripheral naïve W131AOTII CD4 T cells


title: CD4 single positive (CD4SP)  thymocytes from OTII mice [TO_1]


title: Peripheral naïve W131AOTII CD4 T cells [PWO_2]


title: Peripheral naïve Cbl-b-/-W131AOTII CD4 T cells [PCWO_1]


title: Peripheral naïve Cbl-b-/-W131AOTII CD4 T cells [PCWO_3]


title: CD4 single positive (CD4SP)  thymocytes from OTII mice [TO_3]


title: Peripheral naïve Cbl-b-/- OTII CD4 T cells [PCO_2]


title: CD4 single positive (CD4SP)  thymocytes from W131AOTII mice [TWO_3]


title: Peripheral naïve W131AOTII CD4 T cells [PWO_1]


title: Peripheral naïve OTII CD4 T cells [PO_3]

source_name: Peripheral naïve OTII CD4 T cells


title: Peripheral naïve Cbl-b-/-W131AOTII CD4 T cells [PCWO_2]


title: Peripheral naïve OTII CD4 T cells [PO_2]


title: Peripheral naïve OTII CD4 T cells [PO_1]


title: AS95192-whole blood

status: Public on Feb 19 2021

type: genomic

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: amples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.  Processed data file includes average Beta values.
Normalised (dasen) Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: whole blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturerÔÇÖs standard protocol.

extract_protocol: Genomic DNA was extracted from frozen whole blood samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: Sex

value: F

tag: patientid


title: AS95192-Granulocytes

source_name: Granulocytes


title: AS95192-CD8 T-cells

source_name: CD8 T-cells


title: AS95192-CD4 T-cells

source_name: CD4 T-cells


title: AS95191-Buccal

source_name: Buccal


title: AS95192-B-cells

source_name: B-cells


title: AS95191-Nasal

source_name: Nasal


title: AS95191-Granulocytes


title: AS95191-whole blood


title: AS95191-Monocytes

source_name: Monocytes


title: AS95191-CD4 T-cells


title: AS95192-Buccal


title: AS95191-CD8 T-cells


title: AS94092-B-cells


title: AS94092-CD8 T-cells


title: AS81182-whole blood


title: AS81182-Buccal


title: AS94092-Buccal


title: AS94092-CD4 T-cells


title: AS94092-Granulocytes


title: AS94092-whole blood


title: AS94091-whole blood


title: AS94091-Granulocytes


title: AS94091-Buccal


title: AS95191-B-cells


title: AS81182-B-cells


title: AS94092-Monocytes


title: AS95192-Monocytes


title: AS81182-Granulocytes


title: AS81182-Monocytes


title: AS81182-CD4 T-cells


title: AS81181-Monocytes


title: AS81181-Granulocytes


title: AS81181-whole blood


title: AS81181-CD8 T-cells


title: AS81181-Buccal


title: AS81181-B-cells


title: AS81181-CD4 T-cells


title: AS66752-Buccal

value: M


title: AS81182-CD8 T-cells


title: AS66752-Granulocytes


title: AS66752-whole blood


title: AS66752-Nasal


title: AS66752-Monocytes


title: AS66752-CD4 T-cells


title: AS66751-Nasal


title: AS66752-B-cells


title: AS66751-Granulocytes


title: AS66751-whole blood


title: AS66751-Buccal


title: AS66752-CD8 T-cells


title: AS66751-CD8 T-cells


title: AS58662-whole blood


title: AS66751-CD4 T-cells


title: AS58662-Granulocytes


title: AS58662-Nasal


title: AS58662-CD8 T-cells


title: AS58661-Monocytes


title: AS58661-Buccal


title: AS58661-Granulocytes


title: AS58662-CD4 T-cells


title: AS58662-B-cells


title: AS58662-Monocytes


title: AS58661-whole blood


title: AS58661-CD8 T-cells


title: AS58661-CD4 T-cells


title: AS58661-B-cells


title: AS66751-Monocytes


title: AS66751-B-cells


title: AS58662-Buccal


title: AS57542-whole blood


title: AS57542-Granulocytes


title: AS57542-Nasal


title: AS57542-Monocytes


title: AS57542-CD8 T-cells


title: AS57541-whole blood


title: AS57541-Nasal


title: AS57542-CD4 T-cells


title: AS57541-Monocytes


title: AS57541-CD8 T-cells


title: AS47232-whole blood


title: AS57541-B-cells


title: AS47232-Granulocytes


title: AS57541-CD4 T-cells


title: AS57541-Granulocytes


title: AS47232-Monocytes


title: AS47232-B-cells


title: AS47231-Granulocytes


title: AS47232-CD4 T-cells


title: AS47232-CD8 T-cells


title: AS47231-whole blood


title: AS47231-Nasal


title: AS47231-CD4 T-cells


title: AS47231-CD8 T-cells


title: AS47231-Monocytes


title: AS47231-B-cells


title: AS44582-Nasal


title: AS44582-Monocytes


title: AS57542-B-cells


title: AS44582-Granulocytes


title: AS44582-whole blood


title: AS44582-CD4 T-cells


title: AS44582-B-cells


title: AS44581-Nasal


title: AS44581-CD8 T-cells


title: AS44581-whole blood


title: AS44581-Monocytes


title: AS44581-CD4 T-cells


title: AS44581-B-cells


title: AS42092-Monocytes


title: AS42092-Buccal


title: AS42092-Granulocytes


title: AS42092-CD8 T-cells


title: AS42092-whole blood


title: AS42092-CD4 T-cells


title: AS42091-Buccal


title: AS42092-B-cells


title: AS42091-Granulocytes


title: AS42091-Nasal


title: AS42091-Monocytes


title: AS42091-CD8 T-cells


title: AS44582-CD8 T-cells


title: AS42091-B-cells


title: AS42091-CD4 T-cells


title: AS38762-Granulocytes


title: AS38762-whole blood


title: AS38762-Monocytes


title: AS38762-CD8 T-cells


title: AS38762-CD4 T-cells


title: AS38761-Nasal


title: AS38761-Granulocytes


title: AS38761-CD8 T-cells


title: AS44581-Granulocytes


title: AS38761-whole blood


title: AS134932-Monocytes


title: AS38761-CD4 T-cells


title: AS134932-Buccal


title: AS38761-Monocytes


title: AS134931-Buccal


title: AS134932-B-cells


title: AS134932-Nasal


title: AS134932-Granulocytes


title: AS134931-Granulocytes


title: AS134932-CD8 T-cells


title: AS42091-whole blood


title: AS134932-CD4 T-cells


title: AS134931-Monocytes


title: AS134931-whole blood


title: AS134931-CD4 T-cells


title: AS134931-CD8 T-cells


title: AS125212-Nasal


title: AS125212-Buccal


title: AS125212-Monocytes


title: AS125212-CD4 T-cells


title: AS125212-Granulocytes


title: AS134931-B-cells


title: AS134932-whole blood


title: AS125211-Buccal


title: AS125212-B-cells


title: AS125211-Nasal


title: AS125211-Granulocytes


title: AS125211-whole blood


title: AS125212-CD8 T-cells


title: AS125211-Monocytes


title: AS125211-CD8 T-cells


title: AS125211-CD4 T-cells


title: AS122802-Nasal


title: AS125211-B-cells


title: AS122802-Granulocytes


title: AS122802-Monocytes


title: AS122802-whole blood


title: AS122801-Nasal


title: AS122802-CD4 T-cells


title: AS122802-B-cells


title: AS122801-Granulocytes


title: AS125212-whole blood


title: AS122801-whole blood


title: AS122801-Monocytes


title: AS122801-CD8 T-cells


title: AS122801-CD4 T-cells


title: AS119842-Nasal


title: AS119842-Granulocytes


title: AS119842-whole blood


title: AS119842-Monocytes


title: AS119842-B-cells


title: AS119841-Granulocytes


title: AS119841-Monocytes


title: AS119841-whole blood


title: AS119842-CD4 T-cells


title: AS119841-CD8 T-cells


title: AS122802-CD8 T-cells


title: AS122801-B-cells


title: AS119841-CD4 T-cells


title: AS119032-Nasal


title: AS119031-whole blood


title: AS119031-Granulocytes


title: AS119841-B-cells


title: AS119031-Monocytes


title: AS119031-CD8 T-cells


title: AS47232-Buccal


title: AS119031-Nasal


title: AS119842-CD8 T-cells


title: AS119031-CD4 T-cells


title: AS47231-Buccal


title: AS44582-Buccal


title: AS57542-Buccal


title: AS57541-Buccal


title: AS122801-Buccal


title: AS38762-B-cells


title: AS38761-Buccal


title: AS38761-B-cells


title: AS44581-Buccal


title: AS119842-Buccal


title: AS119032-Buccal


title: AS119841-Buccal


title: AS119031-Buccal


title: Treatment2_region5

status: Public on Feb 16 2021

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

data_processing:
The quality of all sequenced samples was analyzed using FastQC.The assessment results were summarized and visualized using MultiQC 1.6.
Reads were mapped to the Rnor6. Mapping and transcript assembly were performed with TopHat v2.1.0 and Cufflinks v2.2.1 respectively using default parameters.
We removed genes with FPKM <1 across all samples, as these genes were not expressed or were expressed at very low levels in all samples. To avoid inflation ratio, gene FPKM values < 0.1 were set to 0.1.
Genome_build: Rnor6
Supplementary_files_format_and_content: Matrix table with FPKM value for every gene and every sample

organism: Rattus norvegicus

source_name: section of spinal cord caudal to injury (~cervical level 4-6), including gray and white matter

growth_protocol: Four adult female Long-Evans rats weighing 275-350 grams were kept on 12 hour light/dark cycle with ad limbitum access to food and water.

extract_protocol:
Animals were euthanized and sections (outlined above) were quickly dissected out and snap frozen in liquid nitrogen. Tissue was homogenized and complete RNA was isolated using an RNAeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
Weill Cornell Epigenomics Core constructed the library per their standard Illumina methods for TruSeq Stranded Total-RNA protocol (citation: STAR: ultrafast universal RNA-seq aligner. Dobin, A. et al. Bioinformatics. 2012. 29 (1): 15-21.)

treatment_protocol: All animals (control and treatment) were given a hemicontusion injury at cervical level 4 using an Ohio State Impact Device calibrated to cause a displacement of 0.7mm. This incomplete injury causes a deficit in the use of the animal’s forelimb. Two weeks after injury all animals were implanted with an electrode array into motor cortex on the contralateral side to the injury. Approximate coordinates of the craniotomy were 5mm anterior to 1mm posterior of bregma, and 1-4mm lateral to the midline. One week after implantation, the efficacy of the electrodes to activate CST neurons was determined by measuring the threshold current for evoking forelimb movements on the lesioned side. Experimental animals were stimulated though the cortical channel that elicited the clearest forelimb movement at the lowest current threshold. Stimulation lasted for one week; control animals received sham stimulation (e.g. hooked up to stimulator with no current). Animals were stimulated for 5 hours a day at a frequency of 10 Hz for cycles of 5 minutes on/2 minutes off at 80% of movement threshold.

tag: strain

value: Long-Evans

value: spinal cord

value: ~6-8 months

value: WT

tag: treatment

value: spinal cord injury, electrode implant, 1 week of cortical electrical stimulation


title: Treatment2_region3

source_name: section of spinal cord rostral to injury (~cervical level 2-4) including gray and white matter


title: Treatment2_region2

source_name: 5mm^3 cube of subcortical white matter subcortical white matter below motor cortex on contralateral side to implant/stimulation; this region includes axons, and glia of many corticofugal and corticopetal pathways

value: subcortical white matter


title: Treatment2_region4

source_name: spinal cord at lesion (~cervical level 4), including gray and white matter


title: AS119031-B-cells


title: Treatment2_region1

source_name: 5mm^3 cube of subcortical white matter directly below implant/stimulation site; this region includes axons, and glia of many corticofugal and corticopetal pathways


title: Treatment1_region5


title: Control2_region5

value: spinal cord injury, electrode implant


title: Treatment1_region3


title: Treatment1_region2


title: Control2_region1

source_name: 5mm^3 cube of subcortical white matter directly below implant site; this region includes axons, and glia of many corticofugal and corticopetal pathways


title: Control2_region3


title: Control1_region2


title: Control1_region3


title: Control1_region1


title: K562 pooled_2

status: Public on Feb 15 2021

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie
Quantified gene expression levels in counts using RSEM v1.2.44
Genomic mappings(GM) performed with TopHat 2 v2.0.135 and GM percentages calculated using resulting alignments
Raw sequencing read data aligned to the human rRNA sequences using bowtie 2 v2.2.46, and calculated percentage of reads aligned to rRNA as reads aligned to sequences divided by the total reads
Genome_build: hg19
Supplementary_files_format_and_content: bulk_count.csv contains gene expression estimates of the bulk samples, whereas the single_count.csv contains expression data of the single cells.

extract_protocol:
Two single cell dataset are included: (1) 150 single human foreskin BJ fibroblast cells (2) 352 single K562 cells were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of two phenotypically divergent cells. In addition, RNA expression profiling of bulk cells (3 replicates for BJ and 4 replicates for K562) were performed in tubes. Polaris integrated fluidic circuit (IFC) was used to sequester up to 48 single cells per cell type per one IFC run using Polaris system. The captured single cells were processed for cell lysis, reverse transcription (RT), and full-length transcriptome amplification using template-switching chemistry.
Following harvest from the IFC, sequencing libraries are generated using a modified Nextera® protocol and sequenced on Illumina® NextSeq 500 platform.

tag: sample type

value: Pooled


title: BJ pooled_4

source_name: BJ

value: BJ


title: BJ pooled_1


title: BJ pooled_2


title: BJ pooled_3


title: K562 pooled_3


title: Treatment1_region4


title: BJ single cell 502

value: Single Cell


title: Treatment1_region1


title: Control2_region4


title: BJ single cell 498


title: BJ single cell 497


title: BJ single cell 500


title: BJ single cell 499


title: BJ single cell 494


title: BJ single cell 493


title: Control2_region2


title: BJ single cell 495


title: Control1_region5


title: Control1_region4


title: BJ single cell 490


title: BJ single cell 492


title: BJ single cell 489


title: BJ single cell 488


title: BJ single cell 486


title: BJ single cell 501


title: K562 pooled_1


title: BJ single cell 496


title: BJ single cell 483


title: BJ single cell 477


title: BJ single cell 478


title: BJ single cell 480


title: BJ single cell 485


title: BJ single cell 484


title: BJ single cell 476


title: BJ single cell 479


title: BJ single cell 473


title: BJ single cell 482


title: BJ single cell 468


title: BJ single cell 471


title: BJ single cell 475


title: BJ single cell 466


title: BJ single cell 491


title: BJ single cell 463


title: BJ single cell 472


title: BJ single cell 462


title: BJ single cell 465


title: BJ single cell 487


title: BJ single cell 469


title: BJ single cell 460


title: BJ single cell 467


title: BJ single cell 481


title: BJ single cell 458


title: BJ single cell 474


title: BJ single cell 470


title: BJ single cell 457


title: BJ single cell 459


title: BJ single cell 456


title: BJ single cell 455


title: BJ single cell 453


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title: K562 single cell 1


title: scATAC for Thymus cells, T-28-1073

status: Public on Feb 13 2021

city: Hefei

first: Kun

last: Qu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

country: China

description:
scATAC for Thymus cells
scATAC_Accesson.txt

data_processing:
Sequences were aligned using Cell Ranger version 1.3.1 from 10x Genomics with default parameters.
The GRCm38.p5 assembly was used as the reference genome, and ribosomal RNA, mitochondrial RNA (Mt-RNA) and pseudogenes were removed.
Cells with fewer than 500 detected genes and more than 4500 detected genes for which total mitochondrial gene expression exceeded 40% were removed. Genes that were expressed in fewer than three cells were also removed.
Quantile normalization was performed using qnorm in R.
Genome_build: hg38
Supplementary_files_format_and_content: 10x_log2_q_norm.txt - tab-delimited text file includes quantile normalized gene expression values for each cell
Supplementary_files_format_and_content: scATAC_Accesson.txt - tab delimited text file includes normalized accesson count values predicted by APEC for each cell

source_name: Thymocytes

extract_protocol:
Thymus tissues were harvested from mice aged 6 - 8 weeks and gently ground in 1 mL of RPMI-1640.
Single cells were captured in droplet emulsions using a GemCode Single-Cell Instrument (10x Genomics), and scRNA-seq libraries were constructed with the 10x Genomics protocol using a GemCode Single-Cell 3′ Gel Bead and Library V2 Kit. The libraries were sequenced using a HiSeq X-10 Sequencing System (Illumina). scATAC-seq experiments were performed as previously described by Li B et al, Genome Biology, 2020.

value: 7 weeks

value: male

value: Thymus


title: K562 single cell 12


title: Patient_One_A

status: Public on Feb 11 2021

city: Dunedin

first: Amber

last: Helliwell

address: 710 Cumberland Road

department: Biochemistry Department

country: New Zealand

institute: University of Otago

data_processing:
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with  the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs  to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
Genome_build: hg19
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
DNA was extracted from 200ul of PBMCs
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)

tag: disease state

value: myalgic encephalomyelitis/chronic fatigue syndrome

tag: individual

tag: time point

value: A

value: Peripheral Blood Mononuclear Cells


title: MP14: DLBCL tissue RNA

status: Public on Jan 21 2021

first: Maria

middle: Victoria

last: Revuelta

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Illumina Casava-1.8.2 software used for basecalling
Supplementary_files_format_and_content: Tab-delimited csv file includes Kallisto TPM values for protein-coding genes for RNA-sequenced samples

source_name: DLBCL tumor sample

extract_protocol: trizol extraction and llumina RNA Prep with enrichment, tagmentation kit

value: DLBCL tumor sample


title: MP12: DLBCL tissue RNA


title: MP13: DLBCL tissue RNA


title: Mutant_clone1_ATACseq

status: Public on Feb 04 2021

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: ATAC-seq

data_processing:
Two mutant clones and Hupde1 and Hudep2 samples were mapped to hg19 using BWA mem (v0.7.16a).
Duplicated reads were removed with samtools (v0.17). ATAC-seq peaks were called using MACS2 (v2.1.1) with the following parameters: macs2 callpeak --nomodel --shift --100 --extsize 200. BigWiggle files were generated using DeepTools (v3.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

extract_protocol:
The ATAC-seq library was prepared according to the published omni-ATAC protocol, using 50,000 live cells per sample
Libraries were pair-end 100-bp sequenced using an Illumina HiSeq 4000 system.

tag: cell line

value: Hudep2 mutant


title: MP10: DLBCL tissue RNA


title: fwa_r2_ATACseq

status: Public on Jan 25 2021

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
ATAC-seq read adaptors were removed with trim_galore and then mapped to the Arabidopsis thaliana reference genome TAIR10 using Bowtie (-X 2000 -m 1).
Reads aligned to chloroplast and mitochondrial DNA were filtered out and duplicated reads were removed using SAMtools.
ATAC-seq peaks were called by HMMRATAC with minlength 50 bp.
Paired-end Hi-C reads were aligned to tair10 with HiC-Pro (v2.11.1). Whole genome Hi-C heatmap was converted with juicer_tools (v1.13.02) and visualized with Juicebox (v1.11.08). Hi-C loops were called with analyzeHiC in Homer2 with 200 bp resolution and pvalue < 1e-10. The WashU EpiGenome Browser v46.2 (https://epgg-test.wustl.edu/browser/) was used to visualize Hi-C loops and ATAC-seq data. PC1 value of Hi-C data was calculated with Homer2. Regional Hi-C visualization was performed by hicexplorer (v3.4.3).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: ATAC-seq mapping file hic: Hi-C interaction file

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown at 22 °C in a long day (16 hour light, 8 hour dark) growth room. Flowers and leaves were collected from 4-5 week-old plants. For Hi-C, plants grown on agar plates at 21◦C under constant light for 14 days before seedling tissues (without roots) were harvested. Then, nuclei were isolated and flow–sorted from seedlings after formaldehyde fixation using a FACS Aria (BD Biosciences) according to their 2C and 4C ploidy level.

extract_protocol:
Inflorescence tissues were collected for nuclei extraction as follows. About 5 g of inflorescence tissue was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer at 4 °C and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was repeated once and the nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, 5 mM β-mercaptoethanol).  Hi-C libraries for Illumina sequencing were generated53. The libraries were sequenced on HiSeq 2000 DNA sequencers obtaining paired-end 50- or 51-nucleotide reads following manufacturer instructions (Illumina).
Nuclei were subjected to transposition reaction with Tn5 (Illumina, cat. no. FC-121-1030). For transposition reaction, 25 µl of 2x DMF (66mM Tris-acetate (pH=7.8), 132 mM K-Acetate, 20mM Mg-Acetate, 32 % DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37 °C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo, cat. no. D5205). Libraries were preparated with Phusion High-Fidelity DNA Polymerase (NEB, cat. no. M0530S) (12.5µl 2x Phusion, 1.25µl 10 mM Ad1 primer, 1.25µl 10 mM Ad2 primer, 4 µl ddH2O and 6µl purified transposed DNA fragments).

tag: ecotype background

tag: genotype/variation

value: fwa

tag: developmental stage

value: 4 weeks

value: flowers


title: Mutant_clone2_ATACseq

description: ATAC-seq


title: MP09: DLBCL tissue RNA


title: fwa_r1_ATACseq


title: MP08: DLBCL tissue RNA


title: MP07: DLBCL tissue RNA


title: MP06: DLBCL tissue RNA


title: uninfected_4_1

status: Public on Feb 12 2021

type: RNA

city: Bonn

first: Denna

last: Tabari

address: Kurt-Georg-Kiesinger Allee 3

country: Germany

institute: Federal Institute for Drugs and Medical Devices

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.025ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute 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 Microarray Scanner using one color scan setting for 8x60k array slides. Dye channel was set to Green.

data_processing: The scanned images were analyzed with GeneSpring Software (v.14.1.9, Agilent). Signal quality was maintained by filtering probes with compromised flags out. Differential gene expression was calculated in fold-change (FC) in sets of infected vs. uninfected cells at the same timepoints.

source_name: uninfected A549/D3 cells; 4 days of culture

label_protocol: RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies) according to the kit manual. 100 ng RNA were reversely transcribed to cDNA, from which Cy3-labeled cRNA was transcribed, purified and hybridized to the expression microarray.

growth_protocol: Cultivation of A549/D3 cells occurred in Dulbecco’s Modified Eagle’s Medium (DMEM; supplemented with 2 mM L-glutamine, 100 µg/mL streptomycin, 100 U/mL penicillin and 10 % v/v fetal bovine serum) at 37 °C  with 95 % relative humidity and 5 % CO2.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer’s instructions.

treatment_protocol: Persistently HEV-infected A549 cells (HEV genotype 3c isolate 47832c, derived from chronically infected German patient) or uninfected A549/D3 cells were harvested after 4 and 12 days of culturing.

value: uninfected

tag: timepoint

value: 4 days

value: A549/D3 cells


title: uninfected_4_3


title: MP04: DLBCL tissue RNA


title: HEV_12_2

source_name: A549/D3 cells infected with HEV; 12 days of culture

value: HEV infection

value: 12 days


title: uninfected_12_1

source_name: uninfected A549/D3 cells; 12 days of culture


title: HEV_12_1


title: uninfected_12_3


title: uninfected_12_2


title: MP05: DLBCL tissue RNA


title: HEV_4_1

source_name: A549/D3 infected with HEV; 4 days of culture


title: HEV_4_3


title: HEV_4_2


title: HEV_12_3


title: MP03: DLBCL tissue RNA


title: Patient_Two_C

value: C


title: uninfected_4_2


title: MP02: DLBCL tissue RNA


title: MP11: DLBCL tissue RNA


title: Ifnar1 WT untreated 0h [rep3_WTxUSx0h]

status: Public on Jan 19 2021

city: Bethesda

first: Iain

last: Fraser

state: MD

address: 9000 Rockville Pike, Bldg. 4, Rm. 109A, MSC-0421

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
Gene-level expression quantification was performed using RSEM v1.3.0
Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
Standard differential expression was performed using the R package limma with voom normalization
Genome_build: mm10
Supplementary_files_format_and_content: raw expression (expected counts) and FPKM text file generated from RSEM

source_name: mouse mone marrow-derived macrophages

extract_protocol:
TriReagent (Zymo) extraction
Sequencing libraries were produced using the TruSeq Stranded mRNA kit

value: Ifnar1 WT

tag: agent


title: MP01: DLBCL tissue RNA


title: Ifnar1 WT exposed to STm for 8h [rep2_WTxSTmx8h]

tag: genotype

value: STm


title: Ifnar1 WT exposed to STm for 6h [rep3_WTxSTmx6h]


title: Ifnar1 WT exposed to STm for 8h [rep3_WTxSTmx8h]


title: Ifnar1 WT exposed to STm for 8h [rep1_WTxSTmx8h]


title: Ifnar1 WT exposed to STm for 6h [rep2_WTxSTmx6h]


title: Ifnar1 WT untreated 0h [rep1_WTxUSx0h]


title: Ifnar1 WT exposed to STm for 2h [rep2_WTxSTmx2h]


title: Ifnar1 WT exposed to LPS for 8h [rep3_WTxLPSx8h]

value: LPS


title: Ifnar1 WT exposed to STm for 4h [rep2_WTxSTmx4h]


title: Ifnar1 WT exposed to STm for 2h [rep3_WTxSTmx2h]


title: Ifnar1 WT exposed to STm for 2h [rep1_WTxSTmx2h]


title: Ifnar1 WT exposed to STm for 6h [rep1_WTxSTmx6h]


title: Ifnar1 WT exposed to STm for 4h [rep1_WTxSTmx4h]


title: Ifnar1 WT exposed to STm for 4h [rep3_WTxSTmx4h]


title: Ifnar1 WT exposed to LPS for 8h [rep2_WTxLPSx8h]


title: Ifnar1 WT exposed to LPS for 8h [rep1_WTxLPSx8h]


title: Ifnar1 WT exposed to LPS for 4h [rep3_WTxLPSx4h]


title: Ifnar1 WT exposed to LPS for 4h [rep2_WTxLPSx4h]


title: Ifnar1 WT exposed to LPS for 2h [rep1_WTxLPSx2h]


title: Ifnar1 WT exposed to LPS for 4h [rep1_WTxLPSx4h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 8h [rep3_WTxBcx8h]

value: Burkholderia thailandensis


title: Ifnar1 WT exposed to LPS for 2h [rep2_WTxLPSx2h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 8h [rep2_WTxBcx8h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 8h [rep1_WTxBcx8h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 4h [rep2_WTxBcx4h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 6h [rep2_WTxBcx6h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 4h [rep1_WTxBcx4h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 4h [rep3_WTxBcx4h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 6h [rep1_WTxBcx6h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 2h [rep3_WTxBcx2h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 6h [rep3_WTxBcx6h]


title: Ifnar1 WT exposed to Burkholderia thailandensis for 2h [rep2_WTxBcx2h]


title: Ifnar1 KO exposed to STm for 8h [rep1_KOxSTmx8h]

value: B6.129S2-Ifnar1tm1Agt/Mmjax (Ifnar1-/-, stock #32045-JAX)

value: Ifnar1 KO


title: Ifnar1 WT exposed to Burkholderia thailandensis for 2h [rep1_WTxBcx2h]


title: Ifnar1 KO exposed to STm for 6h [rep3_KOxSTmx6h]


title: Ifnar1 KO untreated 0h [rep1_KOxUSx0h]


title: Ifnar1 KO untreated 0h [rep3_KOxUSx0h]


title: Ifnar1 KO exposed to STm for 8h [rep2_KOxSTmx8h]


title: Ifnar1 KO exposed to STm for 8h [rep3_KOxSTmx8h]


title: Ifnar1 KO untreated 0h [rep2_KOxUSx0h]


title: Ifnar1 KO exposed to STm for 6h [rep2_KOxSTmx6h]


title: Ifnar1 KO exposed to STm for 4h [rep3_KOxSTmx4h]


title: Ifnar1 KO exposed to STm for 2h [rep3_KOxSTmx2h]


title: Ifnar1 KO exposed to STm for 4h [rep1_KOxSTmx4h]


title: Ifnar1 KO exposed to STm for 4h [rep2_KOxSTmx4h]


title: Ifnar1 KO exposed to STm for 2h [rep2_KOxSTmx2h]


title: Ifnar1 WT exposed to LPS for 2h [rep3_WTxLPSx2h]


title: Ifnar1 KO exposed to STm for 2h [rep1_KOxSTmx2h]


title: Ifnar1 KO exposed to LPS for 8h [rep2_KOxLPSx8h]


title: Ifnar1 KO exposed to LPS for 4h [rep3_KOxLPSx4h]


title: Ifnar1 KO exposed to LPS for 4h [rep2_KOxLPSx4h]


title: Ifnar1 KO exposed to LPS for 4h [rep1_KOxLPSx4h]


title: Ifnar1 WT untreated 0h [rep2_WTxUSx0h]


title: Ifnar1 KO exposed to LPS for 2h [rep2_KOxLPSx2h]


title: Ifnar1 KO exposed to LPS for 2h [rep1_KOxLPSx2h]


title: Ifnar1 KO exposed to LPS for 2h [rep3_KOxLPSx2h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 8h [rep3_KOxBcx8h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 6h [rep3_KOxBcx6h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 8h [rep1_KOxBcx8h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 8h [rep2_KOxBcx8h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 6h [rep2_KOxBcx6h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 6h [rep1_KOxBcx6h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 4h [rep1_KOxBcx4h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 2h [rep2_KOxBcx2h]


title: DMSO0.3_750_t4_S174_R1_001

status: Public on Dec 22 2020

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
controls for dose 100
DMSO_3e-04_750

data_processing:
bcl files were processed into fastq files with bcl2fastq v.2.17.1.14
Fastq files were processed with the manufacturer's script generate_reference.R and pete.star.script_3.0.R where tables of feature counts were generated for each samples.
Genome_build: Human TempO-Seq® Tox+ Surrogate (S1500+) custom probe annotation
Supplementary_files_format_and_content: table of probe counts for each sample, grouped by exposure length

source_name: human liver spheroids Insphero

growth_protocol: 14 day in minimal media

extract_protocol:
not extracted, tempoSeq lysis buffer used to lyse cells, which were then frozen and 2ul used for TempO-Seq library building
Assay Principle
The TempO-Seq assay utilizes a detector oligo (DO) pool specific to the RNA targets to be monitored. BioSpyder offers fixed content and custom DO pools to measure focused sets of transcripts, up to whole transcriptomes. The assay can utilize purified RNA, cell lysates, tissue lysates, or FFPE tissue lysates (FFPE kit available separately). In addition, both positive and negative control samples can be included.
Samples are annealed to a matched pair of detector oligos (DOs), with each pair targeting a single gene. The DO pool targets up to tens of thousands of RNA sequences, depending on the targeted gene content of the assay, but all share the same pair of primer binding sequences (indicated in Fig 1. by the red and yellow sections of each DO). The DOs hybridize to sequences of the targeted RNA molecule such that their respective 3’ and 5’ ends are adjacent. Each UDO has an additional target-specific sequence at their 3’ end that hybridizes to the targeted RNA.
After DO annealing, excess oligos and mis-hybridized or weakly hybridized DOs are removed by nuclease digestion, and the annealed oligos are ligated to form amplifiable templates. The ligated DOs are amplified with one pair of primers (making each PCR reaction single-plex regardless of the number of genes measured), with a different combination of sample index/tag sequences assigned to each sample. The PCR products are pooled together into a sequencing library, which is then purified and run on an Illumina NGS to count the number of ligated detector oligo sequences per sample (ThermoFisher-compatible kit under development). Because TempO-Seq includes an end-point PCR reaction, quantitation of the amplified products before library pooling is not needed. Very low concentration and negative control samples are expected to show low reads in the sequencing data.
BioSyder -TempO-Seq protocol v2.1 sept 6,2017
Human S1500, index E,F,H,G were used for indexing

treatment_protocol: PFAS replenished every 3rd day with media change

tag: chemical

value: DMSO

tag: dose(um)

tag: time point (days)


title: Ifnar1 KO exposed to Burkholderia thailandensis for 4h [rep3_KOxBcx4h]


title: Ifnar1 KO exposed to Burkholderia thailandensis for 2h [rep1_KOxBcx2h]


title: DMSO0.3_749_t4_S173_R1_001

description:
controls for dose 100
DMSO_3e-04_749


title: Ifnar1 KO exposed to LPS for 8h [rep1_KOxLPSx8h]


title: DMSO0.3_746_t4_S170_R1_001

description:
controls for dose 100
DMSO_3e-04_746


title: DMSO0.3_745_t4_S169_R1_001

description:
controls for dose 100
DMSO_3e-04_745


title: Ifnar1 KO exposed to Burkholderia thailandensis for 2h [rep3_KOxBcx2h]


title: DMSO0.3_653_t4_S77_R1_001

description:
controls for dose 100
DMSO_3e-04_653


title: DMSO0.3_650_t4_S74_R1_001

description:
controls for dose 100
DMSO_3e-04_650


title: DMSO0.17_751_t4_S175_R1_001

description:
controls for dose 50
DMSO_0.00017_751


title: DMSO0.3_649_t4_S73_R1_001

description:
controls for dose 100
DMSO_3e-04_649


title: DMSO0.3_654_t4_S78_R1_001

description:
controls for dose 100
DMSO_3e-04_654


title: Ifnar1 KO exposed to LPS for 8h [rep3_KOxLPSx8h]


title: DMSO0.17_747_t4_S171_R1_001

description:
controls for dose 50
DMSO_0.00017_747


title: DMSO0_760_t4_S184_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_760


title: DMSO0_764_t4_S188_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_764


title: DMSO0.17_652_t4_S76_R1_001

description:
controls for dose 50
DMSO_0.00017_652


title: DMSO0.17_656_t4_S80_R1_001

description:
controls for dose 50
DMSO_0.00017_656


title: DMSO0.17_655_t4_S79_R1_001

description:
controls for dose 50
DMSO_0.00017_655


title: Ifnar1 KO exposed to Burkholderia thailandensis for 4h [rep2_KOxBcx4h]


title: DMSO0_757_t4_S181_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_757


title: DMSO0_756_t4_S180_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_756


title: DMSO0_758_t4_S182_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_758


title: DMSO0_754_t4_S178_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_754


title: DMSO0_755_t4_S179_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_755


title: DMSO0_664_t4_S88_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_664


title: DMSO0_662_t4_S86_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_662


title: DMSO0_668_t4_S92_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_668


title: DMSO0_661_t4_S85_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_661


title: DMSO0.3_557_t3_S173_R1_001

description:
controls for dose 100
DMSO_3e-04_557


title: DMSO0.3_558_t3_S174_R1_001

description:
controls for dose 100
DMSO_3e-04_558


title: DMSO0.17_559_t3_S175_R1_001

description:
controls for dose 50
DMSO_0.00017_559


title: DMSO0.3_458_t3_S74_R1_001

description:
controls for dose 100
DMSO_3e-04_458


title: DMSO0.3_457_t3_S73_R1_001

description:
controls for dose 100
DMSO_3e-04_457


title: DMSO0.17_651_t4_S75_R1_001

description:
controls for dose 50
DMSO_0.00017_651


title: DMSO0.3_554_t3_S170_R1_001

description:
controls for dose 100
DMSO_3e-04_554


title: DMSO0.17_555_t3_S171_R1_001

description:
controls for dose 50
DMSO_0.00017_555


title: DMSO0.17_556_t3_S172_R1_001

description:
controls for dose 50
DMSO_0.00017_556


title: DMSO0_759_t4_S183_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_759


title: DMSO0.3_461_t3_S77_R1_001

description:
controls for dose 100
DMSO_3e-04_461


title: DMSO0.17_464_t3_S80_R1_001

description:
controls for dose 50
DMSO_0.00017_464


title: DMSO0.17_460_t3_S76_R1_001

description:
controls for dose 50
DMSO_0.00017_460


title: DMSO0.17_459_t3_S75_R1_001

description:
controls for dose 50
DMSO_0.00017_459


title: DMSO0.3_750_S174_R1_001

description:
controls for dose 100
DMSO_3e-04_750


title: DMSO0.3_749_S173_R1_001

description:
controls for dose 100
DMSO_3e-04_749


title: DMSO0.3_462_t3_S78_R1_001

description:
controls for dose 100
DMSO_3e-04_462


title: DMSO0.17_560_t3_S176_R1_001

description:
controls for dose 50
DMSO_0.00017_560


title: DMSO0.3_746_S170_R1_001

description:
controls for dose 100
DMSO_3e-04_746


title: DMSO0_663_t4_S87_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_663


title: DMSO0.17_463_t3_S79_R1_001

description:
controls for dose 50
DMSO_0.00017_463


title: DMSO0.3_654_S78_R1_001

description:
controls for dose 100
DMSO_3e-04_654


title: DMSO0.17_656_S80_R1_001

description:
controls for dose 50
DMSO_0.00017_656


title: DMSO0.17_652_S76_R1_001

description:
controls for dose 50
DMSO_0.00017_652


title: DMSO0.17_751_S175_R1_001

description:
controls for dose 50
DMSO_0.00017_751


title: DMSO0.17_655_S79_R1_001

description:
controls for dose 50
DMSO_0.00017_655


title: DMSO0.17_651_S75_R1_001

description:
controls for dose 50
DMSO_0.00017_651


title: DMSO0_768_S192_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_768


title: DMSO0_764_S188_R1_001


title: DMSO0_755_S179_R1_001


title: DMSO0_754_S178_R1_001


title: DMSO0_759_S183_R1_001


title: DMSO0_753_S177_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_753


title: DMSO0_757_S181_R1_001


title: DMSO0_758_S182_R1_001


title: DMSO0_668_S92_R1_001


title: DMSO0_672_S96_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_672


title: DMSO0_664_S88_R1_001


title: DMSO0.3_745_S169_R1_001

description:
controls for dose 100
DMSO_3e-04_745


title: DMSO0_662_S86_R1_001


title: sc Healthy control 3

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description:
scHeatlhy 3
single cell RNA sequencing

data_processing:
Cellranger software suite (v3.1.0) was used to process the scRNAseq data
The Seurat package for R v3.1.5  was used for downstream analysis
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38

source_name: Skin

extract_protocol:
4 mm punch biopsies of skin were obtained on separate days from 3 patients with GA and 3 healthy volunteers.. Biopsies were immediately bisected and placed in dispase (10 mg/mL) (Dispase II Sigma Cat# D4693) in RPMI with 2% FBS for 45 minutes at 37°C with shaking at 125 RPM. The tissue was removed from the dispase solution, minced in a sterile plate with a scalpel, and then subsequently incubated with liberase (0.5 mg/mL) (Liberase TH Sigma Cat# 5401135001) in RPMI with 2% FBS for 45 minutes at 37°C with shaking at 125 RPM. The dispase solution was placed on ice. After incubation in the liberase, the dispase solution was combined (to recover any additional cells from the dispase) and the mixture was triturated and filtered through a 100 mM sterile filter. Cells were washed with RPMI + 2% FBS and RBCs were lysed with ACK Lysing Buffer (Lonza Cat# 10-548E) and washed again in RPMI + 2% FBS. Cells were stained with LIVE/DEAD Red viability dye (ThermoFisher Cat# L23102), FC block (Biolegend Cat#422301) and CD45 Alexa Fluor 488 (Biolegend Cat# 304017) in RPMI + 0.1% FBS. Viable cells were isolated using a BD FACS Aria cell sorter and sorted into cold RPMI + 2% FBS. CD45 positivity was recorded but not used as a criterion for sorting. Up to 10,000 cells (depending on yield) were loaded onto a 10X chromium controller for each sample according to the manufacturer’s instructions.
Single cell libraries were created according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA).
Single cell RNA sequencing

tag: tissue

value: Skin

value: Healthy control


title: DMSO0_663_S87_R1_001


title: DMSO0.3_650_S74_R1_001

description:
controls for dose 100
DMSO_3e-04_650


title: Healthy control 1

data_processing:
Reads were aligned using HISTAT2 (version 2.1.0) against the Genome Reference Consortium Human Build 38 (hg38)
Quantification was done using RefSeq Transcripts release 93.
Quantified reads were normalized to log2(FPKM+1
Differentially expressed genes between control, pre-treatment, and during treatment groups, was carried out on Qlucore Omics Explorer (version 3.5, Qlucore AB, Lund, Sweden)
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini kits (Qiagen cat# 74704) according to the manufacturer’s instructions. Homogenization of the tissue was achieved using a rotor-homogenizer (PowerGen 125, ThermoFisher). .
RNA was submitted to the Yale Stem Cell Center and complementary DNA libraries were prepared and 100-base pair paired-end stranded sequencing was performed on an Illumina HiSeq 4000, also at Yale Stem Cell Center

treatment_protocol: Five patients with severe, long-standing GA were enrolled and treated with tofacitinib monotherapy (5 mg twice daily) for 6 months; concomitant use of topical or other medications for GA was not permitted

value: healthy control


title: Healthy control 2


title: sc Healthy control 1

description:
scHealthy 1
single cell RNA sequencing


title: DMSO0.17_752_S176_R1_001

description:
controls for dose 50
DMSO_0.00017_752


title: DMSO0.3_649_S73_R1_001

description:
controls for dose 100
DMSO_3e-04_649


title: sc Healthy control 2

description:
scHealthy 2
single cell RNA sequencing


title: Normal-P06

status: Public on Dec 07 2020

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
FASTQ files were generated from raw sequencing data using Illumina BaseSpace and Illumina Local Run Manager Software.
FASTQ files were analyzed with HTG EdgeSeq parser software to generate raw counts for 2,083 miRs per sample.
Supplementary_files_format_and_content: Raw counts obtained by using HTG EdgeSeq parser software

source_name: Plasma

growth_protocol: Blood samples of healthy donors and cancer patients were collected and processed.

extract_protocol:
Blood samples were allowed to clot at RT for 1-3 hours, centrifuged, processed, filtered for cell contamination, and cryopreserved at -80°C . Aliquots of serum or plasma were thawed only once and mixed, before being analyzed for miR profiling by HTG WTA.
Libraries were prepared according to Illumina instrument sequencing protocols. Probe-captured miR samples were amplified and indexed via polymerase chain reaction (PCR) using master mix (dNTP 10 mM, 5X Hemo Klentaq® Reaction buffer, Hemo Klentaq® DNA polymerase (New England Biolabs Inc., Ipswich, MA), forward, and reverse primers (HTG Molecular Diagnostics Inc., Tucson, AZ).
Following PCR, library cleanup was performed using Ampure® XP beads (Beckman Coulter Inc., Brea, CA). Samples were mixed and incubated with the beads at RT for 5 minutes. The bead-bound libraries were washed twice with 80% ethanol to remove leftover PCR reagents and enzymes. After washing, the samples were dried at RT for 2 minutes to allow residual ethanol to evaporate. The libraries were eluted off the beads with 10 mM Tris-HCl, pH 8.0.

treatment_protocol: Plasma samples were lysed with HTG Biofluids buffer or Plasma Lysis buffer, respectively with Proteinase K.

tag: gender

value: f

value: Normal - Cancer-free

value: Plasma


title: Normal-P05

value: m


title: Normal-P03


title: Normal-P01


title: Mel-06-P2

value: Melanoma

tag: treatment

value: IO treated


title: DMSO0_760_S184_R1_001


title: DMSO0_661_S85_R1_001


title: UN_CT_1_ham_S89_L004

city: La Jolla

first: Debashis

last: Sahoo

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0), Mesocricetus auratus genome (MesAur1.0 ). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. A custom python script was used to organize the data and log reduced using log2(TPM) if TPM > 1 and TPM - 1 if TPM <= 1.
Genome_build: kallisto index on Mesocricetus_auratus.MesAur1.0.ncrna.fa.gz + Mesocricetus_auratus.MesAur1.0.cdna.all.fa.gz.
Supplementary_files_format_and_content: tab-delimited text files include log2(TPM) if TPM > 1 else TPM - 1 values for each Sample.

organism: Mesocricetus auratus

source_name: Lung

growth_protocol: Hamster lung samples were collected from previously published study (PMID:32540903).

extract_protocol:
The lungs were harvested from the hamsters and homogenized in TRI-Reagent. RNA were extracted after infection using the Quick-RNA MicroPrep Kit (Zymo Research, USA) according to the manufacture’s instruction. RNA was converted into cDNA using the qScript™ cDNA SuperMix (Quantabio).
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Hamster were infected with SARS-CoV-2 using a BSL-3 facility.

tag: condition

value: Uninfected

tag: infection


title: KO-IRN234

status: Public on Nov 20 2020

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

institute: Medical University of South Carolina

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the moused genome (mm10).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited .txt files include the DESEQ2 output for the KO-IFT88 vs WT-IFT88. Comparison.  Columns to the right of the Base Mean column represent DEseq2 output.  WT-IR28N-3, WT-IRN272-9, KO-IR28N-6, KO-IR28N-9, KO-IRN234 contain raw count data for the two Wild-Type (NfatC1Cre(+); Ift88f/f ) and three        KO-IFT88 (NfatC1Cre(+), Ift88+/+)    RNAseq libraries. Symbol represent the HUGO Gene symbols for Mus musculus.

source_name: Heart Mitral leaflets

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

value: Mitral Valve tissue

value: Knockout(NfatC1Cre(+), Ift88+/+)


title: KO-IR28N-9


title: WT-IR28N-3

value: Wild-Type(NfatC1Cre(+); Ift88f/f )


title: KO-IR28N-6


title: Dp16/D-KO_F1

status: Public on Oct 01 2020

city: Guangzhou

first: Xiaoling

last: Jiang

state: Guangdong

address: 9 Jinsui Road, Tianhe District

department: Department of Genetics and Endocrinology

institute: Guangzhou Women and Children's Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to obtain clean data
The obtained clean reads were mapped to mouse genome mm10 using HISAT
Differentially expressed genes between groups were identified with DEGseq
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

extract_protocol:
Hippocampi were fast isolated and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent.
mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads.mRNA molecules were fragmented.First-strand cDNA was generated using random hexamer-primed reverse transcription,followed by a second-strand cDNA synthesis.The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments.amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution.The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library.The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by synthesis.

tag: strain background

value: Trisomy with Dyrk1a dosage corrected

tag: age

value: 2-3 months

value: Hippocampus


title: Dp16;D-KO/K-KO_M1

value: Trisomy with Dyrk1a and Kcnj6 dosage corrected


title: Dp16;D-KO/K-KO_M2


title: Dp16/D-KO_M2


title: WT_M2

value: Wild type


title: WT_F1


title: Normal-P02

tag: disease state


title: Mal_Subject 1_VDJ+GEX scRNA-seq

status: Public on Sep 30 2020

city: Atlanta

first: Arun

last: Boddapati

state: GA

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

data_processing:
The sample replicates were split into 8 Hiseq 2500 sequencing anes and library pool contained 1/10 of VDJ and 9/10 of gene expression.S1 flow cell for sequencing.  Count matrix and VDJ contig files were generated using Cell Ranger v3.0 (10X Genomics). Further, the resultant counts matrices were processed using an inhouse single-cell RNA-seq pipeline that uses Seurat v 3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: CSV files are generated from CellrangerV3.0 and Integrated matrix file is generated by integrating VDJ contig file with the gene expression matrix SeuratV3.0

source_name: Peripheral mononuclear blood cells (PBMCs)

growth_protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were isolated with the EasySep  Human B cell isolation kit on a RoboSep platform

extract_protocol:
Cells were encapsulated in droplets using the Chromium Controller (10X Genomics). Reverse transcription and cDNA amplification were performed using the Chromium Single Cell 5’ kit (10X Genomics). All steps were done according to manufacturer’s instructions. 100 ng of cDNA (25% of generated cDNA) was used as input for library preparation.
Libraries were sequenced using the Illumina Hiseq3000 platform 8 lanes of sequencing at 26bp-8bp-98bp according to 10X Genomics sequencing recommendations.

value: Malaria

value: 18 years

tag: Sex

value: Female

value: Blood


title: Dp16_M1

tag: genotype/variation

value: Trisomy


title: RGDS2

status: Public on Sep 21 2020

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the moused genome (mm10).
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited .txt files include the DESEQ2 output for the KO-IFT88 vs WT-IFT88. Comparison.  Columns to the right of the Base Mean column represent DEseq2 output.  WT-IR28N-3, WT-IRN272-9, KO-IR28N-6, KO-IR28N-9, KO-IRN234 contain raw count data for the two Wild-Type (NfatC1Cre(+); Ift88f/f ) and three        KO-IFT88 (NfatC1Cre(+), Ift88+/+)    RNAseq libraries. Symbol represent the HUGO Gene symbols for Mus musculus.

source_name: human umbilical vein endothelial cells (HUVECs)

growth_protocol: HUVECs (p2-p3) were encapsulated into 0.125mmol/g peptide-modified alginate (at alginate concentration = 1% (w/v)) at the density of 2 million cells/mL with EGM for 24 hours

treatment_protocol: No special treatment has been made to each group

tag: sample type

value: Cellularized peptide modified alginate hydrogels


title: Mel-06-P1

value: Melanoma

value: Plasma


title: LDAP3


title: LDAP1


title: RGDS3


title: T230

status: Public on Sep 18 2020

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include normalized median scaling values for each cell.
Supplementary_files_format_and_content: Embryo_annotation.csv is related to F366 and F379.
Supplementary_files_format_and_content: Adrenal_gland_annotation.csv is related to F2, F7, F106, and F107.
Supplementary_files_format_and_content: Tumor_dataset_annotation.csv is related to T10, T19, T27, T34, T40, T44, T69, T71, T75, T92, T162, T174, T188, T200, T214, and T230.

source_name: neuroblastoma tissue

extract_protocol:
Tumor tissues were resected by surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour. The fetal adrenal tissues were collected  and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: male


title: UN_CT_3_ham_S90_L004

value: Uninfected


title: T188


title: T214

value: female


title: Dp16/D-KO_M1


title: T162


title: F379

source_name: fetal adrenal tissue

value: about 4 PCW


title: WT-IRN272-9

value: Mitral Valve tissue

value: Wild-Type(NfatC1Cre(+); Ift88f/f )


title: RGDS4


title: Dp16_M2

value: 2-3 months

value: Hippocampus


title: T200


title: 5-8h male vas-GFP Sxl-GFP sample

status: Public on Sep 10 2020

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

data_processing:
Alignment and generation of feature-barcode matrices was performed with Cell Ranger (unsexed: version 3.0.1, sexed: version 3.1.0)
Data was preprocessed using PCA (number of dimensions=100) with Monocle3
Dimension reduction using the UMAP method (maximum components=2) was performed with Monocle3
Clustering analysis with the leiden algorithm was done with Monocle3
Genome_build: Drosophila BDGP6.28
Supplementary_files_format_and_content: The features, barcode, and matrix files were generated by Cell Ranger
Supplementary_files_format_and_content: exprs_*.csv: Count matrix

organism: Drosophila melanogaster

source_name: germ cells

growth_protocol: Eggs were laid on 0.8% grape juice plates for the designated periods at 25°C or for double the time at 18°C

extract_protocol:
Embryos were dechorinated and homogenized with the loose pestle in a Dounce homogenizer for 6-7 strokes, filtered twice through 70mm mesh and collected at 850 g for 2 min, and FACS sorted for GFP expression.
Unsexed sample: 10X Genomics Chromium Single Cell 3' v2 kit; sexed samples: 10X Genomics Chromium Single Cell 3' v3 kit

value: Sxl-GFP, vas-GFP

tag: developmental stage

value: 5-8h embryos


title: LDAP2


title: T175


title: UR-2 (7days +CAF)_H3K9me2

status: Public on Sep 09 2020

city: Edinburgh

first: Sito

last: Torres-Garcia

address: 6.4 Michael Swann Building. Max Born Crescent

institute: Wellcome Centre for Cell Biology. University of Edinburgh

description: ChIP DNA

data_processing:
ChIP-Seq: Raw reads were de-multiplexed and trimmed using Trimmomatic (v0.35) to remove adapter contamination and regions of poor sequencing quality. Trimmed reads were aligned to the S. pombe reference genome (972h-, ASM294v2.20) using Bowtie2 (v2.3.3). Resulting bam files were processed using Samtools (v1.3.1) and picard-tools (v2.1.0) for sorting, removing duplicates and indexing. Ratios IP/input were calculated using BamCompare (deepTools v2.0) in SES mode for normalisation.
sRNA-Seq: Raw reads were de-multiplexed. Raw reads were trimmed using Cutadapt (v1.17) to remove adapters and filter out reads <19 nt and >25 nt. Filtered fastq files were then processed using SCRAM and coverage files (.csv) at defined locations (cen1L, hba1 locus, ncRNA394 locus) were obtained.
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: ChIP-Seq: bigWig files of ratio IP/input. sRNA-Seq: csv files indicating coverage over specific genomic locations (cen1L / hba1locus / ncRNA394 locus).

source_name: S. pombe cells

growth_protocol: Cells were grown in liquid yeast extract plus supplements (YES) media at 32C to a concentration of 5x10^6-1x10^7 cells/mL

extract_protocol:
Cells were lysed by bead beating and chromatin was sheared by sonication. Lysates were incubated with antibody and Protein-G Dynabeads overnight. Immunoprecipitated genomic DNA was recovered using PCR purification columns.
Libraries were prepared for Illumina sequencing with 1-5 ng of ChIP or 10 ng of input DNA using NEXTflex adaptors and Ampure XP beads. Barcoded libraries were pooled and sequenced following Illumina HiSeq 2000, NextSeq or MiniSeq workflows.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temperature

value: h- ED972 wild-type (wt)

tag: phenotype

value: Unstable 16 mM Caffeine Resistant Isolate

value: no treatment

tag: chip antibody

value: 5.1.1 mouse monoclonal anti-H3K9me2 antibody kindly provided by Takeshi Urano (Nakagawachi et al. 2003. Oncogene)


title: UR-27_H3K9me2

description: ChIP DNA

tag: genotype


title: UR-28_H3K9me2

description: ChIP DNA


title: UR-30_H3K9me2

description: ChIP DNA


title: UR-29_H3K9me2

description: ChIP DNA


title: UR-24_H3K9me2

description: ChIP DNA


title: UR-25_H3K9me2

description: ChIP DNA


title: F366


title: Dp16_F1

value: Trisomy


title: 5-8h female vas-GFP Sxl-GFP sample


title: UR-23_H3K9me2

description: ChIP DNA


title: UR-20_H3K9me2

description: ChIP DNA


title: UR-26_H3K9me2

description: ChIP DNA


title: UR-22_H3K9me2

description: ChIP DNA


title: UR-19_H3K9me2

description: ChIP DNA


title: UR-16_H3K9me2

description: ChIP DNA


title: UR-17_H3K9me2

description: ChIP DNA


title: UR-18_H3K9me2

description: ChIP DNA


title: UR-2 (7days +CAF 14 days -CAF)_H3K9me2

description: ChIP DNA


title: UR-14_H3K9me2

description: ChIP DNA


title: UR-15_H3K9me2

description: ChIP DNA


title: UR-12_H3K9me2

description: ChIP DNA


title: UR-13_H3K9me2

description: ChIP DNA


title: UR-11_H3K9me2

description: ChIP DNA


title: UR-21_H3K9me2

description: ChIP DNA


title: UR-9_H3K9me2

description: ChIP DNA


title: UR-10_H3K9me2

description: ChIP DNA


title: UR-1_sRNA

description: Total Small RNA

extract_protocol:
Cells were collected and processed using the mirVana miRNA Isolation kit (Invitrogen). Resulting sRNA was treated with TURBO DNase (Invitrogen) and used for library construction.
Libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to manufacturer’s instructions. Libraries were pooled and sequenced on an Illumina NextSeq 500/550 platform by 50 bp single-end sequencing.


title: UR-2_sRNA

description: Total Small RNA


title: wt 14mM CAF_H3K9me2

description: ChIP DNA

value: wild-type phenotype

value: treated with 14 mM CAF for 18 hr


title: wt no treatment_H3K9me2

description: ChIP DNA


title: UR-2_H3K9me2

description: ChIP DNA


title: wt_sRNA

description: Total Small RNA


title: SR-1_H3K9me2

description: ChIP DNA

value: h- pap1-N424STOP

value: Stable 16 mM Caffeine Resistant Isolate


title: UR-7_H3K9me2

description: ChIP DNA


title: UR-8_H3K9me2

description: ChIP DNA


title: UR-6_H3K9me2

description: ChIP DNA


title: Control-P70

status: Public on Sep 08 2020

city: Buffalo

first: Jacky

middle: Louis

last: chow

address: Elm and Carlton Streets

department: Immunology

institute: Roswell Park

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Read counts are obtained using featureCounts from Subread v1.6.0 with –fracOverlap 1 option
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts csv file format

source_name: renal cell carcinoma

extract_protocol:
Primary tumors were dissassociated and then frozen in single cell suspension. Thawed cells were immediately lysed in QIAzol, RNA was isolated by chloroform extraction and ethanol extraction. Samples were run through RNeasy Mini spin column with DNAse treatment.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA kit protocols

treatment_protocol: RCC patients wre treated with 15 Gy SBRT at primary lesion followed by nephrectomy at 4 weeks post-radiation

value: primary rcc tumor

value: F

tag: pathologic t stage

value: nephrectomy only


title: Control-P21


title: SBRT-P13

value: 1x 15 Gy SBRT, nephrectmoy at 4 weeks


title: Control-P78

value: M


title: UR-4_H3K9me2

description: ChIP DNA


title: SBRT-P10


title: wt_H3K9me2

description: ChIP DNA


title: UR-3_H3K9me2

description: ChIP DNA


title: UR-5_H3K9me2

description: ChIP DNA


title: Control-P54


title: wt 1mM H2O2_H3K9me2

description: ChIP DNA

value: treated with 1 mM H2O2 for 18 hr


title: Control-P34


title: SBRT-P3


title: Control-P19


title: UR-1_H3K9me2

description: ChIP DNA


title: SBRT-P14


title: SBRT-P15


title: Control-P51


title: Control-P32


title: SARS-CoV-2 Infected Vero cells, DMS-treated, rep 1

status: Public on Sep 01 2020

city: Cambridge

first: Silvi

last: Rouskin

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description:
deep234plus_1_29882_popavg_reacts_nobv.txt
sars30kb_deep234_SARS2MN985325WA_plus_combined.ct
sars30kb_deep234_SARS2MN985325WA_plus_combined.dot

data_processing:
Reads were aligned to the genome of SARS-CoV-2 strain USA-WA1/2020 (GenBank: MN985325.1) using Bowtie2 v2.3.4.1 with the parameters --local --no-unal --no-discordant --no-mixed -L 12 -X 1000.
Mutations with respect to the reference genome were identified using DREEM software.
Average mutational frequencies ber base were computed and normalized (setting the median of the top 5% of frequences to 1, scaling linearly, and winsorizing all values >1 to 1) using DREEM software.
The structure of the entire genome was folded in ten segments using the Fold program from RNAstructure v6.0.1 with the normalized mutational frequencies as folding constraints.
Reads were filtered using DREEM if they had a pair of mutations closer than 4 bases, had a mutation next to a position with no information, or had a number of mutations greater than 3 standard deviations above the median among all reads.
Filtered reads were clustered and the mutation rate per position in each cluster was computed and normalized (setting the median of the top 5% of frequences to 1, scaling linearly, and winsorizing all values >1 to 1) with DREEM.
The structure of the frameshift element was folded using the ShapeKnots program from RNAstructure v6.0.1 with the normalized cluster mutation rates as constraints in folding.
Genome_build: USA-WA1/2020 (GenBank: MN985325.1)

organism:
Chlorocebus aethiops aethiops
Severe acute respiratory syndrome coronavirus 2

source_name: Vero cells

growth_protocol: Vero cells (ATCC CCL-81) were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) plated into 100 mm dishes and infected at a MOI of 0.01 with 2019-nCoV/USA-WA1/2020 (Passage 6). Infected cells  were incubated at 37 °C, 5% CO2 and harvested 2 days post infection. Infected cell pellets were centrifuged at 5000xg for 5 min at 4 °C and resuspended in Trizol (Ambion).

extract_protocol:
The cells were centrifuged at 1,000g for 5 min at 4 °C. The cells were washed twice by resuspending the pellet with 15 ml PBS with 30% β-mercaptoethanol and centrifugation to pellet then just once with 15 ml PBS. After washes, the pellet was resuspended in 1 ml Trizol (ThermoFisher Scientific) and RNA was extracted following the manufacturer’s specifications. Total RNA was purified using RNA Clean and Concentrator -25 kit (Zymo).
rRNA was subtracted from the RNA extracted from Vero cells using rRNA subtraction mix and RNase H (Lucigen). RNA was fragmented at 70 °C for 2.5 min. The ends were dephosphorylated and repaired with Shrimp Alkaline Phosphatase at 37 °C for 1 h. Linker was added with T4 RNA ligase at 22 °C for 18 h. RNA was reverse-transcribed with TGIRT-III (Ingex) at 60 °C for 1.5 h. RT product was gel-purified and size-selected for ~250 nt, circularized with CircLigase (Lucigen), and PCR-amplified with Phusion High-Fidelity DNA Polymease (NEB) for up to 16 cycles. The product was run on a gel to select for fragments ~300 nt and sequenced on an iSeq100 (Illumina).

treatment_protocol: 200 μl DMS (or 2% v/v) was added dropwise to the plated Vero cells 48 h post SARSCoV-2 infection and incubated for 4 min at 37 °C. DMS was neutralized by adding 15 ml PBS (ThermoFisher Scientific) with 30% β-mercaptoethanol.

tag: cell type

value: Kidney epithelial cell

tag: cell line

value: ATCC CCL-81

tag: sars-cov-2 strain

value: SARS-CoV-2 strain USA-WA1/2020 (Passage 6)

tag: dms treatment


title: SBRT-P16

tag: tissue

tag: treatment


title: wt 7mM CAF_H3K9me2

description: ChIP DNA

value: h- ED972 wild-type (wt)

value: treated with 7 mM CAF for 18 hr


title: SBRT-P6


title: SBRT-P1


title: Control_No_Copper_replicate_3

status: Public on Jul 28 2020

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

data_processing:
Paired-end RNA-seq data were aligned to the human genome assembly (build hg38) using STAR (version 2.5a) with quantMode parameter set to ‘TranscriptomeSAM’.
Raw gene counts were calculated using RSEM (version 1.2.31) command rsem-calculate-expression.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table (.csv) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each Sample

source_name: Neuroblastoma cell line

extract_protocol:
RNA was isolated using RNeasy mini kit (Qiagen, cat#74104). Illumina TruSeq stranded mRNA Library prep was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: untreated (4h)


title: Control_replicate_3

value: untreated (24h)


title: SARS-CoV-2 Infected Vero cells, DMS-treated, rep 2


title: Control_No_Copper_replicate_1


title: Control_No_Copper_replicate_2


title: Mel-P24-4

status: Public on Jul 15 2020

description: miRNA

growth_protocol: Blood. tissue, and urine samples of healthy donors and cancer patients were collected and processed.

extract_protocol:
Blood samples were allowed to clot at RT for 1-3 hours, centrifuged, processed as serum, filtered for cell contamination, and cryopreserved at -80°C . Aliquots of serum or plasma were thawed only once and mixed, before being analyzed for miR profiling by HTG WTA. Urine samples from healthy donors (n=8) and advanced stage melanoma patients’ (n=9) were collected and processed for miR NGS detection. Tumor tissues were obtained from elective surgeries performed at SJHC (D.K.). Formalin-fixed and paraffin-embedded (FFPE) tissues were obtained for HTG WTA
Libraries were prepared according to Illumina instrument sequencing protocols. Probe-captured miR samples were amplified and indexed via polymerase chain reaction (PCR) using master mix (dNTP 10 mM, 5X Hemo Klentaq® Reaction buffer, Hemo Klentaq® DNA polymerase (New England Biolabs Inc., Ipswich, MA), forward, and reverse primers (HTG Molecular Diagnostics Inc., Tucson, AZ).
Following PCR, library cleanup was performed using Ampure® XP beads (Beckman Coulter Inc., Brea, CA). Samples were mixed and incubated with the beads at RT for 5 minutes. The bead-bound libraries were washed twice with 80% ethanol to remove leftover PCR reagents and enzymes. After washing, the samples were dried at RT for 2 minutes to allow residual ethanol to evaporate. The libraries were eluted off the beads with 10 mM Tris-HCl, pH 8.0.

value: Melanoma - IO treated


title: Mel-P23-3

description: miRNA


title: Control_replicate_2


title: Mel-P24-3

description: miRNA


title: Mel-P24-2

description: miRNA


title: Mel-P24-1

description: miRNA


title: Mel-P23-2

description: miRNA


title: Mel-P23-4

description: miRNA


title: Mel-P23-1

description: miRNA


title: Mel-P22-3

description: miRNA


title: Mel-P22-1

description: miRNA


title: Mel-P21-1

description: miRNA


title: Mel-P20-4

description: miRNA


title: Mel-P20-3

description: miRNA


title: Mel-P20-1

description: miRNA


title: Control_replicate_1


title: Mel-P20-2

description: miRNA


title: Mel-P21-3

description: miRNA


title: Mel-P19-3

description: miRNA


title: Mel-P19-2

description: miRNA


title: Mel-P19-4

description: miRNA


title: Mel-P18-4

description: miRNA


title: Mel-P19-1

description: miRNA


title: Mel-P18-3

description: miRNA


title: Mel-P18-2

description: miRNA


title: Mel-P15-3

description: miRNA


title: Mel-P15-4

description: miRNA


title: Mel-P15-2

description: miRNA


title: Mel-P18-1

description: miRNA


title: Mel-P12-4

description: miRNA


title: Mel-P15-1

description: miRNA


title: Mel-P21-2

description: miRNA


title: Mel-P12-3

description: miRNA


title: Mel-P12-2

description: miRNA


title: Mel-P12-1

description: miRNA


title: Mel-P10-2

description: miRNA


title: Mel-P10-3

description: miRNA


title: Mel-P09-4

description: miRNA


title: Mel-P21-4

description: miRNA


title: Mel-P10-4

description: miRNA


title: Mel-P10-1

description: miRNA


title: Mel-P09-2

description: miRNA


title: Mel-P22-2

description: miRNA


title: Mel-P09-1

description: miRNA


title: Mel-P08-3

description: miRNA


title: Mel-P08-2

description: miRNA


title: Mel-P09-3

description: miRNA


title: Mel-P08-1

description: miRNA


title: Mel-P06-4

description: miRNA


title: Mel-P07-2

description: miRNA


title: Mel-P07-4

description: miRNA


title: Mel-P07-3

description: miRNA


title: Mel-P07-1

description: miRNA


title: Mel-P06-1

description: miRNA


title: Mel-P06-3

description: miRNA


title: Mel-P02-4

description: miRNA


title: Mel-P05-3

description: miRNA


title: Mel-P05-1

description: miRNA


title: Mel-P05-2

description: miRNA


title: Mel-P02-3

description: miRNA


title: Mel-P02-2

description: miRNA


title: Mel-P06-2

description: miRNA


title: Mel-P02-1

description: miRNA


title: Mel-P08-4

description: miRNA


title: Mel-P01-4

description: miRNA


title: Mel-P01-2

description: miRNA


title: Mel-P05-4

description: miRNA


title: Normal-S2-44

description: miRNA

source_name: Serum

value: Normal - Cancer-free


title: Normal-S2-39

description: miRNA


title: Normal-S2-47

description: miRNA


title: Normal-S2-43

description: miRNA


title: Normal-S2-48

description: miRNA


title: Normal-S2-45

description: miRNA


title: Normal-S2-41

description: miRNA


title: Normal-S2-40

description: miRNA


title: Normal-S2-46

description: miRNA


title: Normal-S2-42

description: miRNA