title: Dendritic cells treated with miR142-3p 4

city: Chicago

first: Afsar

middle: Raza

last: Naqvi

state: Illinois

address: 801 S Pauline

department: Periodontics

institute: University of Illinois

scan_protocol: After hybridization, each image was analyzed for the following quality metrics: average signal present, signal intensity of species-specific housekeeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.

data_processing:
Data was processed using Genomics Suite 6.6 Statistical Package. The following parameters were applied for hybridization signal processing: Algorithm: RMA; Background Correction: RMA Background Correction; Normalization: Quantile Normalization; Log Probes using Base: 2; Probeset Summarization: Median Polish.
ANOVA test was used to calculate significance of the differential expression in each comparison (miR-142-3p vs control). Differentially expressed transcripts were annotated according to Affymetrix ‘NetAffx Analysis Center’. The significance cut-off was at 0.05.

source_name: Monocytes-derived dendritic cells

label_protocol: 100 ng of total RNA was used as input for transcriptome profiling, we used Affymetrix HTA-2_0 arrays. RNA samples were labeled and hybridized according to standard WT (whole transcript) plus target labeling protocol recommended by the manufacturer.

growth_protocol: Freshly prepared buffy coats were collected from healthy donors and CD14+ monocytes were separated by density gradient centrifugation and magnetic bead isolation. For DCs, monocytes were cultured in RPMI-1640 supplemented with rhGM-CSF (1000U/ml) and rhIL-4 (500U/ml).

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) following manufacturer’s protocol. The RNA was quantitated using the NanoDrop (Thermo Scientific) and integrity assessed using the 2100 Bioanalyzer

treatment_protocol: Transient miRNA overexpression was performed by transfecting miR-142-3p and control negative mimic using Lipofectamine 2000  according to the manufacturer’s instructions. Day 7-differentiated DC were transfected at a final concentration of 50 nM. Red siGLO oligos were used to determine transfection efficiency.

value: Peripheral blood mononuclear cells


title: Dendritic cells treated with control negative mimic 3

status: Public on Dec 07 2020

type: RNA

country: USA

hyb_protocol: RNA samples were labeled and hybridized according to standard WT (whole transcript) plus target labeling protocol recommended by the manufacturer.

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: control negative mimic

tag: tissue


title: AS-153955-LR-22998

type: SRA

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

country: Germany

institute: Charité Universitätsmedizin Berlin

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with NF-kappa-B Inhibitor Zeta (NFKBIZ) in MSCV-GFP

library_source: transcriptomic

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads  (Illumina) were aligned to reference genome mm10 and gtf.-transcriptome annotation release M7 (GENCODE) using STAR two-pass mode ( star 2.4.2a).
GENCODE M7 gtf.-file was used for quantification, performed by STAR (star 2.4.2a) , followed by normalisation, transformation and differential gene expression analysis in DEseq2 -1.12.4.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

organism: Mus musculus

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with  NFKBIZ in MSCV-GFP

extract_protocol:
RNA extraction was performed using Qiagen RNeasy+ kit (Qiagen)  according manufacturer instructions.
Library was generated using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) followed by Nextera XT Kit (Illumina).

value: Myc upregulated lymphoma

tag: overexpression

value: overexpression of NFKBIZ

tag: transduced with

value: NFKBIZ


title: 0284_C40

city: TOULOUSE

first: gilles

last: FOUCRAS

state: State/Province/Region

address: 23 Chemin des Capelles

country: France

institute: ENVT INRA

data_processing:
Read quality was assessed with FastQC software. Reads were aligned in comparison to the bovine reference genome (UMD3.1.87) with STAR software
Count table was generated with Cufflinks/RSEM
Identification of differentially expressed genes (DEGs) was performed with DESeq2 package within the R environment
Genome_build: Bos_taurus.UMD3.1.87
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Blood

extract_protocol:
Whole blood samples were lysed using the buffer provided in the kit and stored at -80°C. Total RNA was extracted on silica columns with Nucleospin RNA blood kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Holstein

value: Blood

tag: age

value: 15 month

tag: immunization protocol

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

tag: time

value: 40 hours post infection

tag: immunization routes

value: Intramuscular / Intramammary


title: 4797-003

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression from single bronchial epithelial cells from subject in imaging cluster 3.

data_processing:
FASTQ files were aligned to the human genome (GRCh37.75) using STAR v2.5.2b in a two-pass manner.
Quality control was performed using FastQC v0.11.3 and RSeQC v2.6.4 and summarized using MultiQC v0.9.
Posterior mean counts were generated using RSEM v1.3.0.
BAM files were processed using Picard v2.8.0 to add read group information.
Genome_build: GRCh37.75

source_name: Bronchial epithelial cells

extract_protocol:
Total RNA was isolated using the QIAGEN miRNeasy Mini kit following the manufacturer's instructions.
Sequencing libraries were prepared from total RNA samples using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold following the manufacturer's instructions.

tag: Sex

value: Male

tag: pack years

tag: imaging cluster


title: AS-153961-LR-23134

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with  MYD88-L265P in MSCV-GFP

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with  MYD88-L265P in MSCV-GFP

value: overexpression of mutated MYD88


title: 4797-006

value: Female


title: 0283_I7

value: 7 days after first immunization


title: Dendritic cells treated with miR142-3p 3


title: 4796-072

description: Gene expression from single bronchial epithelial cells from subject in imaging cluster 1.


title: AS-153954-LR-22998


title: 0283_C4

value: 0 hours post infection


title: AS-153960-LR-22999


title: Dendritic cells treated with control negative mimic 2


title: 0283_C40


title: Dendritic cells treated with miR142-3p 2


title: AS-153953-LR-22998


title: 0282_C12

value: Adjuvant

value: 12 hours post infection

value: Intramuscular (x2)


title: 4796-071


title: AS-153952-LR-22668

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with empty vector MSCV-GFP

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with empty vector MSCV-GFP

value: Myc upregulated lymphoma

value: control (empty vector MSCV-GFP)


title: 0279_C4

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine


title: Dendritic cells treated with control negative mimic 1

value: control negative mimic

value: Peripheral blood mononuclear cells


title: AS-153951-LR-22668


title: AS-153957-LR-22999

value: overexpression of NFKBIZ

value: NFKBIZ


title: 4796-066

description: Gene expression from single bronchial epithelial cells from subject in imaging cluster 2.


title: AS-153956-LR-22998


title: 0275_I0

value: Holstein

value: Blood

value: 15 month

value: 0 days after first immunization


title: Dendritic cells treated with miR142-3p 1


title: 0274_R7

value: 7 days after boost


title: AS-153948-LR-22667


title: 4796-064

value: Male


title: AS-153949-LR-22668


title: AS-153947-LR-22667


title: 4796-055


title: 3735_C4

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: 0 hours post infection

value: Intramuscular / Intramammary


title: 3735_I0


title: AS-153945-LR-22667


title: 4796-053


title: 4796-067


title: 3735_C12

value: 12 hours post infection


title: AS-336708-LR-42261

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-scrambled (MSCV-GFP)

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads  (Illumina) were aligned to reference genome mm10 and gtf.-transcriptome annotation release M7 (GENCODE) using STAR two-pass mode ( star 2.4.2a).
GENCODE M7 gtf.-file was used for quantification, performed by STAR (star 2.4.2a) , followed by normalisation, transformation and differential gene expression analysis in DEseq2 -1.12.4.
Genome_build: mm10
Supplementary_files_format_and_content: txt files include raw counts; normalized counts are available in files on series record.

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-scrambled (MSCV-GFP)

value: Myc upregulated lymphoma

tag: tranduced with myd88-l265p in mscv-gfp

tag: knockdown

value: sh-scrambled control


title: 4796-051

value: Female


title: 4796-065


title: 3734_C40

value: 40 hours post infection


title: 4796-050


title: 3734_C12


title: Healthy_skin_sample_#3 (mRNA)

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix  Human Transcriptome Array 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: The data were analyzed withTranscriptome Analysis Console (TAC) 4.0.1 using  default analysis settings. Row data were log2-transformed and normalized by Robust multichip average (RMA) algorithm normalization.

source_name: skin

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen, Venlo, Netherlands)

treatment_protocol: 3 total skin samples from patients with psoriasis and 3 samples from healthy controls were analysed

tag: disease state

value: control

value: skin


title: Healthy_skin_sample_#2 (mRNA)


title: AS-336707-LR-42260


title: Healthy_skin_sample_#1 (mRNA)


title: Psoriasis_skin_sample_#3 (mRNA)

value: Psoriasis


title: Single nuclei from the area postrema replicate 2

first: Judith

last: Kaye

state: Massachusetts

address: 240 Longwood Ave, LHRRB 6th floor

department: Cell Biology

institute: Harvard University

description: mRNA

data_processing:
FASTQs were made using bcl2fastq (parameters:-p 4 --use-bases-mask Y61,Y8,I8,Y14 --mask-short-adapter-reads 8 --minimum-trimmed-read-length 8 --sample-sheet SampleSheet_FC003510_1234_PF_mm1.csv --create-fastq-for-index-reads --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls).
Alignment, filtering, barcode counting, and UMI counting were performed using zUMIs 2.8.0. Reads were aligned to a mm10 (Ensembl 91) reference transcriptome. The 3' ends of the Glp1r, Ghsr, Prhlr, and Prokr2 loci were extended by 2-6kb to include the complete UTRs.
Genome_build: mm10 (Ensembl 91) (GRCm38)
Supplementary_files_format_and_content: Differential gene expression counts are provided as rds files and can be opened by R using the command readRDS(). These files contain sparseMatrix of UMIs and reads as quantified by zUMIs. Each file contains matrices for introns, exons, and introns + exons.

source_name: area postrema

extract_protocol:
Brains were acutely harvested from 30 adult male C57BL/6J mice (two technical replicates). Coronal brain slices (250 mm, Leica VT1000S vibratome) containing the area postrema (AP) were placed in artificial cerebral spinal fluid (ACSF, 4 C) solution [ACSF solution: (in mM) 126 NaCl, 3 KCl, 20 NaHCO3, 1.25 NaH2PO4, 2 MgCl2, 20 D-glucose, 2 CaCl2, 0.0001 tetrodotoxin, 0.02 6,7-dinitroquinoxaline-2,3-dione, 0.05 DL-2-amino-5-phosphonovaleric acid continually bubbled with carbogen gas (95%O2 / 5%CO2)]. The area postrema was visualized by microscopy and harvested based on anatomical landmarks. Harvested tissue was homogenized (4 C) in buffer containing 0.3% IGEPAL CA-630 and protease inhibitor cocktail (Biotool B14011), and (in mM) 250 sucrose, 25 KCl, 20 NaHCO3, 1.25 NaH2PO4, 5 MgCl2, 20 Tricine-KOH, 0.15 spermine, 0.5 spermidine, and 1 dithiothreitol. Samples were filtered (40 uM strainers), diluted with iodixanol (25% final concentration) and layered on an iodixanol gradient (30% and 40% iodixanol containing 0.04% BSA and RNasin (Promega N2611, 64 units/ml). Samples were centrifuged (18 min, 10,000 g, 4 C) and nuclei collected at the 30-40% iodixanol interface.
Nuclei were individually encapsulated (~3,000 in each of 2 replicates) in small droplets using an inDrop platform with v3 chemistry hydrogels, and cDNA was prepared from individual nuclei (Zilionis et al., 2017).

tag: strain

value: Adult

value: Area postrema (brain)


title: 0274_I0

value: Holstein

value: Blood

value: 15 month

value: Adjuvant

value: Intramuscular (x2)


title: 3725_C40

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route


title: AS-336709-LR-42261

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-PDL1 (MSCV-GFP)

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-PDL1 (MSCV-GFP)

value: knockdown of PD-L1


title: AS-336707-LR-42261


title: AS-336704-LR-42261


title: 3725_C12

value: 12 hours post infection

value: Intramuscular / Intramammary


title: 4796-046

value: Male


title: AS-153946-LR-22667

value: Myc upregulated lymphoma

value: control (empty vector MSCV-GFP)


title: Spleen from tumor-bearing humanized mice 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
Human-mouse chimera
Spleen1

data_processing:
The clonotype calls were generated using the IMSEQ software46 through QIAGEN web-server (https://qiagen.com).
Counts of UMIs supported by at least 3 reads were used as a measurement of relative TCR receptor sequences.
Relative frequencies of unique V-J clonotypes were used to calculate diversity using Shannon-Wiener index and plotted as heatmaps.
Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH) algorithm was used to reveal TCR-antigen specificities.
TCR clusters are represented as circles and reactivity to known melanoma antigens are represented as color coded circles. Known melanoma antigen TCR sequences were derived from vdjdb database (https://vdjdb.cdr3.net/).
Supplementary_files_format_and_content: TCR diversity is represented as bar graphs, Percent VJ clonotypes are represented as heat maps. For execution of GLIPH and visualization of the results, the software R v3.4.1 was used.

source_name: Spleen

growth_protocol: Tumor cells and spleen grown in humanized mice were obtained at the end of the study.

extract_protocol:
RNA was isolated from spleen and tumor tissues and cDNA synthesis was performed using QIAseq Immune Repertoire RNA Library prep kit (QIAGEN).
Enrichment of complete TCR variable region by gene-specific primers targeting constant regions and molecular indexing (UMIs) for accurate and sensitive TCR clonotype and repertoire diversity assessment.
Final libraries were sequenced on Illumina’s NextSeq500 using the 300 cycles mid output sequencing kit.

treatment_protocol: Tumor challenged humanized mice were used for obtaining TCR sequences from tumor-infiltrating T cells and spleen T cells.

tag: cell type

value: Spleen with human lymphocytes


title: AS-336706-LR-42260


title: Psoriasis_skin_sample_#1 (mRNA)

value: skin


title: 4796-052


title: HeLa_RocA rep2

city: Salt Lake City

first: Donald

middle: E

last: Ayer

state: UT

address: 2000 Circle of Hope

institute: University of Utah

data_processing:
STAR 2.6 was used to align the reads to GRCh38/hg38
featureCounts was used to obtain read counts for each gene
FastQC and MultiQC were used to assess sequencing and alignment quality
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: HeLa

growth_protocol: Cells were grown in standard 6-well dishes in DMEM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from cells using a Zymo Research Quick-RNA MiniPrep kit (cat #11-330T) according to the manufacturer's guidelines.
1 µg total RNA was used to generate libraries using a Kapa Stranded mRNA-Seq kit with mRNA capture beads (cat # KK8421) according to the manufacturer's guidelines.

treatment_protocol: Cells were treated with DMSO or 100nM RocA for four hours prior to harvesting.

tag: cell line

value: HeLa

tag: genotype

value: WT

tag: treatment

value: RocA


title: 4796-045

value: Female


title: 4796-044


title: 0292_R7

value: Holstein

tag: tissue

value: Blood

value: 7 days after boost


title: Melanoma tumor from humanized mice 1

source_name: Melanoma tumor

value: Metastatic melanoma


title: 3729_I7

tag: breed

value: 15 month

value: Adjuvant

value: 7 days after first immunization

value: Intramuscular (x2)


title: Psoriasis_skin_sample_#2 (mRNA)

value: Psoriasis


title: 4796-043

tag: age

value: Male


title: 0297_I7

tag: immunization protocol


title: AS-336704-LR-42260

value: Myc upregulated lymphoma

value: sh-scrambled control


title: Spleen from tumor-bearing humanized mice 2

description:
Human-mouse chimera
Spleen2

value: Spleen with human lymphocytes


title: 4796-039


title: Melanoma tumor from humanized mice 2


title: 0292_I7

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

tag: time

value: Intramuscular / Intramammary


title: 4796-047


title: Single nuclei from the area postrema replicate 1

description: mRNA

value: Adult

value: Area postrema (brain)


title: AS-336706-LR-42261

value: knockdown of PD-L1


title: 0286_C12

value: Holstein

value: Blood

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 12 hours post infection

tag: immunization routes


title: AS-336705-LR-42261


title: Type2 sampleID 9-4

first: Marco

last: Martina

state: IL

address: 300 E Superior

department: Physiology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw read counts per gene

source_name: NTS (mouse brainstem)

extract_protocol:
Acute brainstem slices (285-micron thick) were incubated in artificial cerebrospinal fluid for 50 min before extraction. Single neurons were visualized with an infrared digital camer attached to a upright microsope with 40x immersed optic lens. Cellular cytoplasm and nuclei were extracted using a borosilicate glass pipette with a tip diameter of 1.5 microns (3-4MOhm resistance) with gentle negative pressure. After extraction, cytoplasmic material was ejected into a RNAse free PCR tube (containing RNAse inhibitor and lysis buffer) with gentle positive pressure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain (Nucleus of the Solitary Tract)

tag: rna population

value: cytoplasmic RNA and nuclear RNA

tag: cell classification

value: type2 firing property


title: 4796-035

tag: Sex

tag: pack years

tag: imaging cluster


title: Type2 sampleID 9-2


title: Type2 sampleID 10-3


title: 0284_R7

value: 15 month

value: 7 days after boost


title: 0284_C4

value: 0 hours post infection


title: 4796-033

value: Male


title: AS-336705-LR-42260

value: Myc upregulated lymphoma

tag: tranduced with myd88-l265p in mscv-gfp

tag: knockdown


title: Type2 sampleID 10-1

tag: strain


title: AS-336709-LR-42260


title: AS-336708-LR-42260

value: sh-scrambled control


title: 4796-036


title: 4796-032


title: 0283_R7

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: Intramuscular / Intramammary


title: 4796-031


title: 0283_I0

value: 0 days after first immunization


title: 0281_I7

value: 7 days after first immunization

value: Intramuscular (x2)


title: 4796-030


title: Type2 sampleID 6-2


title: Type1 sampleID 9-1

value: type1 firing property


title: Type1 sampleID 8-2


title: 3R4F-2

city: Nagasaki

first: Naoko

last: Hattori

address: Sakamoto 1-12-4

country: Japan

institute: Nagasaki university

data_processing:
Basecalls performed using Illumina MiSeq
RNA-seq reads were aligned to the human hg38 genome assembly using Illumina MiSeq
RPKM were calculated using Partek Genomic suite version 6.6
Genome_build: human hg38
Supplementary_files_format_and_content: RPKM

source_name: Human Caucasian lung carcinoma

growth_protocol: A549 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10 µg/ml gentamicin and 10% fetal bovine serum (Thermo Fisher Scinetific).

extract_protocol:
Total RNA was isolated using ISOGEN II reagent (NIPPON GENE), according to the manufacturer’s protocol.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina)

treatment_protocol: Each samples were treated with 2percent DMSO control, 3R4F, PloomTECH,and Ploom TECH plus for 4hours.

tag: cell line

tag: cell type

value: Human Caucasian lung carcinoma cell line


title: 0279_C40

value: Holstein

value: Blood

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 40 hours post infection


title: Type1 sampleID 4-3

value: Brain (Nucleus of the Solitary Tract)

value: cytoplasmic RNA and nuclear RNA


title: 3R4F-1

tag: treatment


title: 4796-025


title: PloomTECHplus-2

value: PloomTECHplus


title: 4796-023

value: Male


title: 0279_C12

tag: tissue

value: 15 month

value: 12 hours post infection


title: 0275_C4

tag: breed

value: Adjuvant

value: 0 hours post infection


title: PloomTECHplus-1


title: 4796-015

tag: age

value: Female


title: Tumor_KO_Treg_2

city: Gainesville

first: Ryan

last: Kolb

state: FL

address: 1275 Center Drive, M656

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

description: rRNA depleted

data_processing:
samples were sequenced using a NextSeq 500 system at 75 base pairs single-end reads
Sequences were aligned using the Kallisto pseudoalignment protocol and the mm10 mouse genome to geneate estimated counts
Counts were further processed and aggregated based on gene symbol using the Sleuth R package (v0.30.0). Count were transformed in to log2(X+1) values
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with log2(X + 1) counts for all samples

source_name: Tumor

extract_protocol:
Tumors were removed and ezymatically and mechanically dissociated using the mouse tumor dissociation kit from Miltenyi. Spleens were collected and mechanically dissociated by mashing them through a 40μm cell strainer. Mononuclear cells were isolated by density gradient centrifugation. Cells were stained with anti-mouse antibodies and regulatory T cells were isolated by fluorescence activated cell sortring. RNA was extracted using RNeasy plus micro kit (Qiagen) and ribosomal RNA was depleted using NEBnext ultra II rRNA depletion kit.
Libraries were generated using NEBnext Ultra II RNA Library Prep Kit

tag: genotype

value: Tumor

tag: cell line implanted


title: PloomTECH-2

value: PloomTECH


title: 4796-009


title: Tumor_KO_Treg_1

description: rRNA depleted


title: 3735_C40

tag: immunization protocol

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

tag: time

tag: immunization routes

value: Intramuscular / Intramammary


title: PloomTECH-1

value: Human Caucasian lung carcinoma cell line


title: 4796-029

tag: Sex


title: DMSO-2

value: DMSO control


title: 3734_C4

value: Holstein

value: Blood


title: 3732_C4

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: Intramuscular (x2)


title: Spleen_KO_Treg_3

description: rRNA depleted

value: spleen


title: DMSO-1


title: Type1 sampleID 1-2

value: Brain (Nucleus of the Solitary Tract)

tag: rna population

value: cytoplasmic RNA and nuclear RNA

tag: cell classification

value: type1 firing property


title: Spleen_KO_Treg_2

description: rRNA depleted


title: 4796-001

value: Male

tag: pack years

tag: imaging cluster


title: 3732_C12

value: 15 month

value: 12 hours post infection


title: 4795-096


title: 4795-095


title: Spleen_KO_Treg_1

description: rRNA depleted


title: Type1 sampleID 1-1

tag: strain


title: 3729_C4

value: Adjuvant

value: 0 hours post infection


title: 4795-094


title: Tumor_WT_Treg_3

description: rRNA depleted

value: Tumor


title: mouse_embryo_e7.5_facssortedcells_9

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

description: library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Mouse embryo

growth_protocol: Mice were kept in the animal facility of Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany

extract_protocol:
Embryos were dissected in pre-warmed dissection medium (10% fetal calf serum (FCS) in DMEM/F12 containing Glutamax) and washed in pre-warmed PBS.  For the E6.75 time point the extraembryonic part was cut off and a picture of each embryo was taken and single embryos was transferred into the wells of a pre-warmed non-adhesive 96-well plate containing 40 μl of TrypLE Express (Gibco 12604013). The wells were coated with FCS before adding the TrypLE. Embryos were incubated at 37°C for 10 minutes with pipetting up and down once in between and at the end to make a single cell solution. Dissociation was stopped with 120 μl of dissection medium and cells were centrifuged for 2 min at 1000 rpm in the 96-well plate. The supernatant was removed and cells from one embryo were resuspended in 200 μl cold PBS. For hand-picking, the drop containing the cells was placed in a plastic petri dish. Cells were picked under a Leica M165 FC binocular using ES-blastocyst injection pipettes (BioMedical Instruments, blunt, bent ID 15 μm, BA=35°) and placed into 1.2 μl lysis buffer containing polyT primer with unique cell barcode.  Embryos from the E7.5 time point were cut under to chorion to include the extraembryonic mesoderm in the analysis. The embryos were imaged and the embryos of one or two litters were pooled and processed in a FCS coated eppendorf tube in the same way as the E6.75 embryos. After centrifugation the cells were resuspended in 200 μl PBS and kept on ice until flow sorting.
As described in CEL-Seq2 and mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: C57BL/6 WT

value: Whole embryo

value: Embryonic day 7.5


title: 0274_C40

value: Holstein

value: 40 hours post infection


title: 3729_C40

value: Blood


title: Tumor_WT_Treg_2

description: rRNA depleted


title: 61_MC_NOR

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: rRNA depleted, RNase R treated, total RNA

data_processing:
High-throughput sequencing was performed using Illumina NextSeq
Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files
The FASTQ files were mapped aganist the human refrence genome (hg19) using STAR spliced alignment algorith (versions 2.7.0)
Aligned with parameters and –chimericSegmentMin 20, --quantMode GeneCounts
The resulting STAR produced chemiric junction file for each sample processed by CIRCexplorer2 (version 2.3.3) to estimate circRNA abundance
Genome_build: hg19
Supplementary_files_format_and_content: circRNA abundance

source_name: Healthy brain tissue

growth_protocol: Tumour and healthy brain were harvested by neurosurgeon during excision of tumour from consenting patient

extract_protocol:
RNA was extracted using TriZOL and Direct-zol RNA extration columns (Zymo Research). RNA (ug) was digested with Rnase R (2U/ug RNA; Epicentre) for 30mins at 37oC, then purified by Rneasy MinElute Cleanup kit (Qiagen).
Libraries were constructed with RNase R-treated RNA using the TruSeq Stranded Total RNA library preparation kit (with Ribo-zero rRNA depletion module).

value: brain

tag: disease state

value: healthy


title: mouse_embryo_e7.5_facssortedcells_7

description: library of 96 cells


title: 4795-092


title: 3727_I0

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 0 days after first immunization

value: Intramuscular (x2)


title: 4796-008

value: Male


title: 4795-091

value: Female


title: mouse_embryo_e7.5_facssortedcells_5

description: library of 96 cells


title: Spleen_WT_Treg_3

description: rRNA depleted

value: spleen


title: Spleen_WT_Treg_2

description: rRNA depleted


title: 0297_R7

value: 15 month

value: Adjuvant

value: 7 days after boost


title: Spleen_WT_Treg_1

description: rRNA depleted


title: 3727_C4

value: 0 hours post infection


title: 4795-086


title: 0292_I0

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: Intramuscular / Intramammary


title: 4795-081


title: mouse_embryo_e7.5_facssortedcells_8

description: library of 96 cells

value: C57BL/6 WT

value: Whole embryo

value: Embryonic day 7.5


title: 0286_I7

value: Holstein

value: Blood

value: 7 days after first immunization


title: 4795-087


title: wt_3

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

library_source: genomic

data_processing:
Library strategy: CUT&Tag
Reads were aligned using Bowtie2 (v2.3.4.3)
replicates were concatenated
Genome_build: mm9

molecule: genomic DNA

source_name: murine ESC

growth_protocol: cells grown in 6 well dishes

extract_protocol:
Cells were processed according to Kaya-Okur et al., 2019, using Antibody to RNA Polymerase II - Ser5P (Cell Signaling Technologies #13523)
Libraries were made according to Kaya-Okur et al., 2019

tag: genotype/variation

value: wildtype

tag: antibody

value: RNA Polymerase II Ser5P CUT&Tag


title: 4795-074

value: Male


title: mouse_embryo_e7.5_facssortedcells_2

description: library of 96 cells

tag: tissue


title: mouse_embryo_e7.5_facssortedcells_1

description: library of 96 cells


title: mouse_embryo_e7.5_facssortedcells_4

description: library of 96 cells


title: ATAC-Seq 0copy_3

description: ATAC-Seq

data_processing:
Reads were aligned using Bowtie2 (v2.3.4.3)
Genome_build: mm9

extract_protocol:
Cells were processed according to Volk et al., 2018, ESCs were transposed for 30mins
Libraries were made according to Volk et al, 2018

tag: cell type

value: -5 deleted with mNanogV5


title: Tumor_WT_Treg_1

description: rRNA depleted

value: Tumor


title: 4795-072

tag: age


title: ATAC-Seq 0copy_2

description: ATAC-Seq


title: mouse_embryo_e7.5_facssortedcells_12

description: library of 96 cells


title: 4795-071


title: 0284_C12

source_name: Blood

tag: breed

value: 15 month

value: 12 hours post infection


title: mouse_embryo_e7.5_facssortedcells_6

description: library of 96 cells


title: 0284_I0

value: 0 days after first immunization


title: mouse_embryo_e7.5_facssortedcells_11

description: library of 96 cells


title: ATAC-Seq 0copy_1

description: ATAC-Seq


title: 4795-070

source_name: Bronchial epithelial cells


title: mouse_embryo_e7.5_facssortedcells_3

description: library of 96 cells


title: ATAC-Seq wt_3

description: ATAC-Seq


title: 0283_C12


title: mouse_embryo_e7.5_facssortedcells_10

description: library of 96 cells


title: 4795-069


title: 0284_I7


title: 0282_I7

value: Adjuvant

value: Intramuscular (x2)


title: mouse_embryo_e6.75_handpickedcells_2_14

description: library of 96 cells

value: Embryonic day 6.75


title: ATAC-Seq wt_1

description: ATAC-Seq


title: mouse_embryo_e6.75_handpickedcells_2_9

description: library of 96 cells

value: C57BL/6 WT


title: 4795-065

value: Female


title: 0282_I0


title: 0282_C40

value: 40 hours post infection


title: 4795-058


title: mouse_embryo_e6.75_handpickedcells_2_13

description: library of 96 cells

value: Whole embryo


title: 0281_I0

value: Holstein

value: Blood

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine


title: 4795-062


title: 0copy_2

value: RNA Polymerase II Ser5P CUT&Tag


title: 0copy_3


title: mouse_embryo_e6.75_handpickedcells_2_12

description: library of 96 cells


title: 0279_I7

value: 7 days after first immunization


title: 0copy_1

value: -5 deleted with mNanogV5


title: mouse_embryo_e6.75_handpickedcells_1_11

description: library of 96 cells


title: 4795-054

value: Male


title: 4795-056


title: 0274_I7

value: 15 month


title: mouse_embryo_e6.75_handpickedcells_1_10

description: library of 96 cells


title: wt_2

value: wildtype


title: 4795-051


title: ATAC-Seq wt_2

description: ATAC-Seq


title: wt_1


title: 13oht3

data_processing:
Reads were aligned using STAR to mm9
Aligned reads were analyzed using DESeq
Genome_build: mm9

molecule: polyA RNA

growth_protocol: 200K cells were plated in 6 well plates

extract_protocol:
RNA was extracted using Trizol, processed through the Qiagen RNAeasy Mini Plus Kit
RNA-seq libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: 6 days of ethanol (vehicle) or tamoxifen (4OHT)

value: -5 floxed, exogenous mNanogV5

tag: treatment


title: 4795-046


title: H_shTUT3

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

country: China

institute: Jiangsu Jiangyin People's Hospital

data_processing:
After library preparation and pooling of different samples, the samples were subjected for Illumina  sequencing. Commonly, the lncRNA-seq use PE150 (paired-end 150nt) sequencing for 12G raw data.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this  step, clean data (clean reads) were obtained by removing following reads: (1) reads with 5’ adapter;  (2) reads without 3’ adapter or insert sequence; (3) reads with more than 10% N; (4) reads with more  than 50% nucleotides with Qphred<=20; (5) reads with ploy A/T/G/C. Adapter trimming for the removal  of adapter sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and  GC content of the clean data were calculated. All the downstream analyses were based on the clean  data with high quality.
Clean reads for each sample were first mapped to a reference genome with the software HISAT2.  Reads alignment results were transferred to the program StringTie for transcript assembly.
All the transcripts were merged using Cuffmerge softwareQuantification of the transcripts and genes was performed using StringTie software and Reads Per  Kilobase of transcript per Million mapped reads (RPKM) was obtained.
Target gene prediction of lncRNAs was carried out in two ways: the cis-acting target gene prediction,  and trans-acting target gene prediction. The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation  of gene and gene product attributes across all species.
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
* anno_genes.FPKM.xls = abundance measurements  and annotation of known genes
*anno_transcripts.FPKM.xls = abundance measurements and annotation of known transcripts
*lnc_transcripts.FPKM.xls = abundance measurements of known  lncRNA transcripts
*mRNA_gene.FPKM.xls = abundance measurements of known mRNA
*Novel_lncRNA_information.xls = abundance measurements of novel lncRNA
*Novel_mRNA_information.xls = abundance measurements of novel mRNA
*mRNA_transcripts.FPKM.xls = abundance measurements of known mRNA transcripts

source_name: human cervical cancer

extract_protocol:
RNA  was isolated using TRIZOL.RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA).RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0  Flurometer.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human  esophageal carcinoma and cervical cancer cells were treated with  low expression of HUR

value: human cervical cancer

tag: cell line

value: HeLa

tag: condition

value: TUT4 gene interference treatment 3


title: H_shTUT2

value: TUT4 gene interference treatment 2


title: 4795-045


title: 13oht2


title: IMM-inoculated

source_name: CD45+ CD4+ T cells

extract_protocol:
Mononuclear cells were isolated from 2 g of mammary tissue after collagenase type IV and DNAse digestion. Cells were recovered through Percoll gradient centrifugation and stained with PE-labeled CD45 (CC1, BIO-RAD) and FITC-labeled CD4 (CC8, BIO-RAD) mAbs, before cell sorting using a MoFlo Astrios EQ (Beckman Coulter). Total RNA was extracted from samples with Nucleospin XS RNA kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD45+ CD4+ T cells

value: immunized intramuscularly using heat-killed E. coli P4 emulsified in adjuvant plus a mammary boost with 50 µg of protein concentrate prepared from a E. coli P4 supernate

tag: inoculation

value: challenged with E. coli P4


title: IMM-control

value: Holstein

value: non-infected control


title: 4795-041

tag: Sex


title: CONT-Inoculated

value: control (adjuvant only)


title: H_shNC3

value: Interference control 3


title: 4795-042

value: Female


title: H_shTUT1

value: TUT4 gene interference treatment 1


title: CONT-control


title: 4795-040

value: Male


title: H_shNC2

value: Interference control 2


title: 13oht1


title: 13etoh3

value: Vehicle


title: H_shNC1

value: Interference control 1


title: GFP7_D7_3

city: Edinburgh

first: Karl

middle: Emanuel

last: Busch

address: Hugh Robson Building, George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

description: biological replicate 3

data_processing:
Reads were trimmed using Cutadapt (version cutadapt-1.9.dev2) (Martin, 2011)
The reference used for mapping was the Caenorhabditis elegans (build WBcel235) genome from Ensembl. Reads were aligned to the reference genome using STAR (version 2.5.2b) (Dobin et al., 2013) specifying paired-end reads and the option --outSAMtype BAM Unsorted.
Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene_id in the reference genome using featureCounts (version 1.5.1) (Liao et al., 2014)
Genes with biotype rRNA were removed prior to counting.
featureCounts assigns counts on a ‘fragment’ basis as opposed to individual reads such that a fragment is counted where one or both of its reads are aligned and associated with the specified features. Strandedness was set to ‘unstranded’ and a minimum alignment quality of 10 was specified
The raw counts were filtered to remove genes consisting predominantly of near-zero counts, filtering on counts per million (CPM) to avoid artefacts due to library depth.
Genome_build: WBcel235
Supplementary_files_format_and_content: csv file with raw gene counts for all genes and all samples

organism: Caenorhabditis elegans

source_name: sensory neurons

growth_protocol: Animals were cultured at OP50 seeded NGM plates from hatching to L3 stage, and L3 stage animals were transferred to mex-3 RNAi plates until either cell collection at day 1 of adulthood, or day 4 of adulthood for further culturing. 4-day-old adults were then transferred to OP50 seeded NGM plates until day 7 of adulthood.

extract_protocol:
Neurons were isolated by enzymic dissociation followed by FACS sorting, and RNA was extracted using PicoPure RNA isolation kit
cDNA was generated using the Ovation RNA-seq system V2. Libraries were generated using the TruSeq DNA Nano gel free library preparation kit.

treatment_protocol: Animals were either cultured at 21% O2 or 7% O2 environment, with the same temperature and humidity conditions

tag: genotype

value: day 7

tag: developmental stage

value: adult

value: hermaphrodite

value: O2-sensing neurons

tag: culture condition o2 level


title: 4795-039

tag: pack years

tag: imaging cluster


title: GFP7_D7_4

description: biological replicate 4

tag: strain


title: 13etoh1

tag: genotype/variation

value: -5 floxed, exogenous mNanogV5


title: 4795-036


title: GFP7_D7_2

description: biological replicate 2


title: T_shTUT3

source_name: human  esophageal carcinoma

value: human  esophageal carcinoma

value: TUT4 gene interference treatment 3


title: GFP7_D7_1

description: biological replicate 1


title: tomo-seq X. laevis replicate2

first: Jan Philipp

last: Junker

address: Hannoversche Str. 28

department: BIMSB

institute: MDC

description: 3' biased spatially barcoded sub-single cell transcriptome. R1 contains biological information, R2 contains 6 nt UMI and 8 nt section barcode.

data_processing:
zebrafish tomo-seq
demultiplexing with bcl2fastq v2.18.0.12
mapping with STAR v2.5.3a
split counts by section barcode
Genome_build: GRCz10 - release 90
Supplementary_files_format_and_content: csv file containing gene counts per section
xenopus tomo-seq
demultiplexing with bcl2fastq v2.18.0.12
mapping with STAR v2.5.3a
split counts by section barcode and translate gene identifier to gene names
Genome_build: X. tropicalis v9.1 genome assembly, X.laevis v9.2 genome assembly
Supplementary_files_format_and_content: csv file containing gene counts per section
scSLAM-seq zebrafish
demultiplexing using cellranger mkfastq v3.0.2
mapping and whitelisting of cells with cellranger v3.0.2
splitting labeled reads (>1 T-C mutation) from unlabeled into separate fastq files (submitted to this GEO entry)
mapping with STARsolo v2.7.0f_0328
single cell analysis in seurat v3.1.2
Genome_build: GRCz11
Supplementary_files_format_and_content: _barcodes.tsv list of barcodes, _genes.tsv list of genes, and _matrix.tsv count matrix

organism: Xenopus laevis

source_name: mature oocyte

extract_protocol: none provided by the submitter

value: untreated

tag: extraction protocol

value: Fresh frozen, cryo-sectioned oocyte.


title: T_shTUT2

tag: tissue

value: TUT4 gene interference treatment 2


title: GFP21_D7_4

description: biological replicate 4


title: 4795-035

data_processing:
FASTQ files were aligned to the human genome (GRCh37.75) using STAR v2.5.2b in a two-pass manner.
Quality control was performed using FastQC v0.11.3 and RSeQC v2.6.4 and summarized using MultiQC v0.9.
Posterior mean counts were generated using RSEM v1.3.0.
BAM files were processed using Picard v2.8.0 to add read group information.
Genome_build: GRCh37.75

extract_protocol:
Total RNA was isolated using the QIAGEN miRNeasy Mini kit following the manufacturer's instructions.
Sequencing libraries were prepared from total RNA samples using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold following the manufacturer's instructions.


title: T_shTUT1


title: 4795-031


title: tomo-seq X. laevis replicate1


title: GFP21_D7_3

description: biological replicate 3


title: scDesLO D17

city: Pittsburgh

first: Mo

last: Ebrahimkhani

address: A809B Scaife Hall, 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh

data_processing:
Libraries were sent to Novogene for sequencing by an Illumina HiSeq X for an intended read depth of 100,000 reads per cell with 150 bp paired end reads.
The downstream analysis from the sequencing data estimates the actual number of cells sequenced was between 5000 and 7000 which would yield >80k reads per cell. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts (Zheng et al., 2017).
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Two .tsv files and one .mtx files used to generate the gene expression matrix in Seurat 3 for each sample (FeLO and DesLO)

source_name: Designer liver organoid

growth_protocol: Cells were maintained on mTeSR 1 medium until differentiation with regular passaging. For differentiation cells were induced with doxycycline for 5 days with daily medium changes. Cells were then released into single cell suspension with accutase and transduced with lentivirus for further engineering or reseeded as control without transduction and harvested at indicated time points.

extract_protocol: Samples were prepared as described by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Day 17 DesLO were acquired in single cell suspension by incubation with trypsin for 10 minutes at 37°C , followed by gentle pipetting using a serological pipette to dislodge and dissociate aggregates. Two washes in PBS -/- + 0.04% BSA were performed with the cells re-suspended at a final concentration of 1000 cells/μL in PBS -/- + 0.04% BSA. A live cell count was performed with a hemocytometer using Trypan Blue to identify dead cells. Following counting, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 6000 single cells for analysis, accounting for predicted cell loss and doublets as laid out in the user guide for the Chromium Single-Cell 3’ Reagent Kit (10x Genomics).  After generation of GEMs, the cDNA library was prepared by ASU Genomics Core staff following the appropriate steps determined by the 10x Genomics user guide.

treatment_protocol: No additional treatments aside from lentiviral transduction were performed (if indicated)

value: Designer liver organoid

value: GATA6 induced, ATF5, PROX1, CYP3A4 gRNA and dCas9 transduced

tag: day

value: Day 17

tag: sequenced molecule

value: single cell RNA


title: 13etoh2


title: scFeLO D17

source_name: Fetal liver organoid

value: Fetal liver organoid


title: T_shNC2

value: Interference control 2


title: GFP21_D7_1

description: biological replicate 1

tag: age


title: LSC_ATAC_rep2

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

data_processing:
Reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software (version 0.7.17).
Duplicated reads were removed by Picard Markduplicates (version 2.18.16) and only uniquely mapping reads were retained for further analysis.
MACS2 (version 2.1.1) was used to call peak. For sharp peaks, we used the following parameters: -f BAMPE -B --SPMR -q 0.001 --call-summits --fix-bimodal --seed 11521 --extsize 200. For broad peaks (H3K27me3 and H3K4me1), the following parameters were used: -f BAMPE -B --SPMR --fix-bimodal --extsize 500 --broad --broad-cutoff 0.1 --seed 11521.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files with enriched genomic site and quantitative value.

source_name: limbal stem cells

growth_protocol: LSCs and SESCs were grown in 1:1 DMEM/F-12 medium containing  1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.

extract_protocol: Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS).  For ATAC-seq library,  the transposed DNA fragments were amplified and collected using the TruePrep DNA Library Prep Kit (Vazyme Biotech).

treatment_protocol: For ChIP-seq, chromatin was fixed with 1% formaldehyde for 10 min and sheared in a sonification buffer. Fragmented DNA was incubated with primary antibodies overnight at 4℃ and then with Protein A/G Dynabeads  for 1 h. The beads were collected and washed sequentially with the following solutions: high-salt buffer, low-salt wash buffer, and TE buffer.  Elution of the immunoprecipitated protein/DNA complexes was performed using elution buffer at 65℃ for 4 h. Next, the protein/DNA complexes were incubated with proteinase K (Invitrogen) and RNase A (Invitrogen) for 1 h. De-crosslinked DNA was purified using the PCR Purification Kit (Qiagen). For ATAC-seq, In total, 50,000 cells were digested, collected, and lysed in ice-cold lysis buffer for 5 min. Then, Tn5 transposase reactions (Vazyme Biotech, TD501) were performed using the TruePrep DNA Library Prep Kit (Vazyme Biotech).

tag: cell type

value: limbal stem cells

tag: treatment


title: 4795-030

value: Female


title: T_shNC1

tag: cell line

tag: condition

value: Interference control 1


title: GFP21_D7_2

description: biological replicate 2

value: day 7

value: adult

tag: Sex

value: hermaphrodite


title: LSC_ATAC_rep1


title: 4795-019

value: Male


title: GFP7_D1_3

description: biological replicate 3

tag: genotype

value: day 1

value: O2-sensing neurons


title: GFP7_D1_4

description: biological replicate 4

tag: developmental stage


title: 4795-021


title: LSC_SMAD3_rep2

value: untreated


title: 4795-017


title: GFP7_D1_2

description: biological replicate 2

tag: culture condition o2 level


title: VA1_I_72h_S5

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). 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: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text files include log2(TPM) if TPM > 1 else TPM - 1 values for each Sample.

source_name: Ileum

growth_protocol: Stem cells were isolated from human ileum biopsies and cultured in a Matrigel button to form 3D organoids.

extract_protocol:
The organoids were broken down enzymatically and mechanically into single cells and seeded onto transwell inserts. The  ileum monolayers were uninfected and infected by SARS-CoV2 for 48h and 72h timepoints. All monolayers were lysed using TRI-Reagent and RNA was isolated using Zymo Research: Direct-zol RNA MiniPrep Kit.
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: Ileum organoid were infected with SARS-CoV-2 using a BSL-3 facility.

value: Organoid

tag: infection

value: 72h Infection


title: VA1_I_48h_S4

value: 48h Infection


title: LSC_SMAD3_rep1


title: VA1_I_UN_S2

value: Uninfected


title: 4795-014

first: Adam

address: 72 East Concord Street, E632

institute: Boston University School of Medicine

tag: pack years

tag: imaging cluster


title: GFP7_D1_1

description: biological replicate 1

tag: strain


title: LSC_PAX6_rep2


title: 4795-024


title: 4795-013


title: GFP21_D1_4

description: biological replicate 4


title: 4795-012


title: LSC_PAX6_rep1


title: T_shNC3

value: human  esophageal carcinoma

value: Interference control 3


title: GFP21_D1_2

description: biological replicate 2


title: 4795-010


title: LSC_RUNX1_rep1


title: 4795-011


title: LSC_RUNX1_rep2


title: GFP21_D1_1

description: biological replicate 1


title: LSC_scr_H3K27me3_rep2

value: scramble treated


title: 4795-004


title: WW7_D7_4

description: biological replicate 4

source_name: Whole-worm

value: whole worm


title: LSC_shRUNX1_H3K27me3_rep2

value: limbal stem cells

value: shRUNX1 treated


title: WW7_D7_2

description: biological replicate 2

value: day 7


title: GFP21_D1_3

description: biological replicate 3

value: adult


title: 4795-005

value: Female


title: LSC_scr_H3K27me3_rep1


title: LSC_shRUNX1_H3K27me3_rep1


title: 4795-002

value: Male


title: WW7_D7_3

description: biological replicate 3

value: hermaphrodite


title: 4793-011


title: 4795-008


title: LSC_shRUNX1_H3K4me3_rep2


title: WW7_D7_1

description: biological replicate 1


title: WW21_D7_4

description: biological replicate 4


title: 4793-007


title: LSC_shRUNX1_H3K4me3_rep1


title: LSC_scr_H3K4me3_rep2


title: WW21_D7_3

description: biological replicate 3


title: LSC_scr_H3K4me3_rep1


title: WW21_D7_2

description: biological replicate 2


title: 4792-010


title: 4792-009


title: WW21_D7_1

description: biological replicate 1


title: LSC_shRUNX1_H3K4me1_rep2


title: 4792-005


title: WW7_D1_4

description: biological replicate 4

value: day 1


title: WW7_D1_3

description: biological replicate 3


title: LSC_scr_H3K4me1_rep1


title: LSC_shRUNX1_H3K4me1_rep1


title: LSC_scr_H3K4me1_rep2


title: LSC_shRUNX1_H3K27AC_rep2


title: 4791-003


title: 4791-002


title: 4790-041


title: 4790-053


title: WW21_D1_3

description: biological replicate 3


title: WW21_D1_4

description: biological replicate 4


title: 4790-040


title: WW7_D1_2

description: biological replicate 2


title: WW7_D1_1

description: biological replicate 1


title: LSC_shRUNX1_H3K27AC_rep1


title: 4793-005


title: LSC_scr_H3K27AC_rep2


title: WW21_D1_2

description: biological replicate 2


title: 4790-039


title: LSC_scr_H3K27AC_rep1


title: WW21_D1_1

description: biological replicate 1


title: LSC_H3K27me3_rep2

value: untreated


title: LSC_H3K27me3_rep1


title: L-IGF2

city: Shanghai

first: Xuefeng

last: Wang

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

data_processing:
Read pairs were cleared by the NGSQC toolkit to output fastq files
Data were executed by the bismark tool and a modified Mus musculus reference (GRCm38.p6) to output discriminates between cytosine
Discriminates between cytosine in the CpG, CHG and CHH context were revealed in bedgraph files
Genome_build: Mus musculus reference (GRCm38.p6)
Supplementary_files_format_and_content: fastq files were cleared by the NGSQC toolkit
Supplementary_files_format_and_content: bam files were outputed by bismark tool
Supplementary_files_format_and_content: bedgraph files were outputed by bedtools

source_name: Peritoneal macrophages

extract_protocol:
Total DNA was isolated using the QIAamp DNA Mini Kit (Qiagen).
A bisulfite library was prepared according to the Illumina protocol essentially as described (Rademacher et al., 2014). The 667 million read pairs were cleared by the NGSQC toolkit (Dai et al., 2010), excluding reads with a mapping quality lower than 30 (probability to map at a correct position = 0.999) and ignoring bases with base quality lower than 20 (probability that the sequencing process produced the correct base = 0.99). Finally, above 90 gigabytes data of each sample were executed by the bismark tool and a modified Mus musculus reference (GRCm38.p6) to output discriminates between cytosine in the CpG, CHG and CHH context (Krueger and Andrews, 2011).

treatment_protocol: Peritonitis was induced by i.p. injection of 2 ml of 4% (weight/volume) thioglycollate broth media (Ftg, BD). After 24 h and 48 h, mice were injected with IGF2 (R&D Systems) at either low doses (5 ng per mouse; L-IGF2) or a high dose (1,000 ng per mouse, H-IGF2). Peritoneal cells were harvested on day 3.

value: 5 ng IGF2  treated twice


title: 4790-032

last: Gower


title: PBS

value: PBS treated twice


title: 4790-031


title: LSC_H3K4me3_rep1


title: LSC_H3K4me1_rep2


title: 4790-023


title: LSC_H3K27AC_rep1


title: 4790-026


title: LSC_H3K27AC_rep2


title: 4790-025


title: LSC_H3K4me1_rep1


title: 4790-035


title: SESC_rep2

data_processing:
trimmed reads were aligned to human hg19 reference genome with STAR software (version 2.6.1a) to acquire read counts within per gene.
TPM (Transcripts per million reads) values that represent gene expression were generated using RSEM tools (version v1.3.0).
Significantly differentially expressed genes with fold change ≥ 2 and FDR < 0.05 were determined by DESeq2 (version 1.20.0).
Genome_build: hg19
Supplementary_files_format_and_content: excel files include TPM value for each sample and list of the differentially expressed genes.

source_name: skin epithelial stem cells

extract_protocol:
Total RNA were extracted by RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using  NEBNext RNA first and second Strand Synthesis Module (NEB, USA) and KAPA Library Preparation Kit (KAPA Biosystem)

treatment_protocol: Limbus was isolated from postmortem human eyeballs and cut into small pieces, followed by digestion with 0.2% collagenase IV (Gibco) at 37℃ for 2h and further digestion by 0.25% trypsin-EDTA (Gibco) at 37℃ for 15 min. Then, cells were seeded and cultured on polystyrene plates (Corning) coated with 2% Matrigel (BD Biosciences).

value: primary skin epithelial stem cells


title: H-IGF2

value: 1,000 ng IGF2  treated twice


title: 4790-034


title: 4790-022


title: 4790-021


title: SESC_rep1


title: LSC_rep2

value: primary limbal stem cells


title: proliferating_keratinocyte_#3 (miRNA)

first: Markus

last: Jeitler

address: Lazarettgasse 14

institute: Medical University Vienna

hyb_protocol: Affymetrix  Human miRNA 4.0 arrays were hybridized, washed, stained and scanned according to the protocol described in FlashTag Biotin HSR RNA Labeling Kit (P/N 703095 Rev.2) User Manual

data_processing: The data were analyzed withTranscriptome Analysis Console (TAC) 4.0.1 using  default analysis settings. Row data were log2-transformed and normalized by Robust multichip average (RMA) algorithm normalization.

source_name: keratinocytes

label_protocol: 200ng of total RNA were labeled using the FlashTag Biotin HSR RNA Labeling Kit Kit (Catalog Number 901910, Affymetrix, Santa Clara, CA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: from each conditation (pKC, dKC, SE) one samples from an individual healy participan was analysed

tag: disease state

value: healthy

value: proliferating keratinocyte


title: 4790-016


title: LSC_H3K4me3_rep2


title: LSC_rep1


title: skin_equivalent_#3 (miRNA)

value: skin equivalent keratinocyte


title: skin_equivalent_#1 (miRNA)


title: LSC_shSMAD3_rep2


title: 4790-015


title: proliferating_keratinocyte_#2 (miRNA)


title: 4790-011


title: LSC_scramble_S_rep2

value: scramble treated


title: 4790-009


title: differentiated_keratinocyte_#3 (miRNA)

value: differentiated keratinocyte


title: LSC_scramble_S_rep1


title: 4790-008


title: 4790-006


title: LSC_shRUNX1_rep1


title: 4790-005


title: 4790-012


title: skin_equivalent_#2 (miRNA)


title: differentiated_keratinocyte_#1 (miRNA)


title: proliferating_keratinocyte_#1 (miRNA)


title: 4790-027


title: LSC_shSMAD3_rep1


title: 4790-002


title: Healthy_skin_sample_#2 (miRNA)

source_name: skin

treatment_protocol: 3 total skin samples from patients with psoriasis and 3 samples from healthy controls were analyzed (miRNA)

value: control

tag: tissue

value: skin


title: LSC_scramble_R_rep1


title: Healthy_skin_sample_#3 (miRNA)


title: Healthy_skin_sample_#1 (miRNA)


title: Psoriasis_skin_sample_#3 (miRNA)

value: Psoriasis


title: 4790-001

value: Male


title: LSC_shRUNX1_rep2


title: A-sh-Input

first: Lifang

last: Ma

state: China

address: No.241 West Huaihai Road, Xuhui District, Shanghai, P.R. China

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University

data_processing:
Library strategy: MeRIP-seq
Illumina Bcl2FastQ  software used for basecalling
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222)/exomePeak was employed to perform m6A peak calling.Then using Hommer(version:4.8)to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus m6A motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich(version:2.0.7)/MetDiff/exomePeak.
Genome_build: hg19

source_name: human LUAD H1975 cell line

growth_protocol: H1975 cells were in DMEM media with high glucose.

extract_protocol: Not provided

treatment_protocol: Lentivirus-mediated gene interference of METTL3 was performed for 48 hours.

value: lung adenocarcinoma (LUAD)


title: Psoriasis_skin_sample_#2 (miRNA)


title: HH8 NP negative rep1

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Base calling was performed using CASAVA 1.8
RNA-sequencing reads were trimmed using Cutadapt (Martin, 2011) to remove adaptor sequences. Reads were then aligned to the chicken reference genome Galgal5 using HiSat2 (Kim et al., 2019). Reads counts were obtained using feature Counts (Liao et al., 2014).
Differential gene expression analysis for mRNAs between neural plate and neural crest cells was performed using DESeq2 (Love, et al., 2014)
Genome_build: galGal5
Supplementary_files_format_and_content: (1) .csv file containing processed read counts for all samples (2) .csv file containing DESeq2 differential gene expression analysis results between neural plate and neural crest samples

organism: Gallus gallus

source_name: Chicken whole embryo

extract_protocol:
HH4 embryos were transfected with neural plate specific enhancers (listed above) and developed to HH8. Embryo heads were dissected and dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. Dissociated cells were FACs sorted directly into 100ul of lysis buffer form the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific. Am1931) (5,000 cells per smaple). Total RNA was isolated according to manufacturer's protocol.
RNA was poly(A) selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490). TruSeq-barcoded RNA-seq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760) and sequences on an Illumina NextSeq 500 instrument with 150bp paried end reads.

tag: Stage

tag: enhancer utilized for cell sorting

value: Sox2 N2:eGFP and NNE/NC:mCherry (Uchikawa et al., 2003)


title: A-con-MeRIP

value: control sh


title: Healthy_skin_sample_#4 (miRNA)


title: 4438-035

source_name: Bronchial epithelial cells

tag: age


title: 4714-001


title: A-con-Input


title: HH8 NP positive rep2

source_name: Chicken neural plate


title: LSC_scramble_R_rep2

tag: cell type


title: 4790-003


title: 4438-031

value: Female


title: A-sh-MeRIP

tag: treatment


title: tomo-seq zebrafish replicate3

city: Berlin

description: 3' biased spatially barcoded sub-single cell transcriptome. R2 contains biological information, R1 contains 4 nt UMI and 8 nt section barcode.

organism: Danio rerio

source_name: one-cell stage embryo

value: AB wildtype

value: untreated

tag: extraction protocol

value: Fresh frozen, cryo-sectioned embryo.


title: HH8 NP positive rep1


title: Psoriasis_skin_sample_#4 (miRNA)


title: HH8 NP rep2

data_processing:
Base calling was performed using CASAVA 1.8
Small RNA-sequencing reads were processed and quantified using the miRDeep2 modules mapper and quantifier (Friedlander et al., 2012). Briefly, reads were trimmed to remove the 3’ adaptor sequences and were aligned to the chicken reference genome Galgal5 using bowtie with no mismatches allowed. Reads consisting of 18–35 nucleotides were kept for further analysis. Next, mature and star miRNA sequences are mapped against annotated chicken precursor miRNAs obtained from miRbase (Kozomara et al., 2014). Mapped small RNA-sequencing reads were then intersected with the mature miRNA mappings to obtain a read count table. miRDeep 2 parameters: mapper (-h -e -k AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -1 18 -m -i -p) quantifier (-p precursors_miRBase_galGal5.fa -m miRBase_galGal5.fa -r -t Chicken -d -e 0 -W -g 0)
Differential gene expression analysis for mature miRNA reads between neural plate and neural crest cells was performed using DESeq2 (Love, et al., 2014)
Genome_build: galGal5
Supplementary_files_format_and_content: (1) .csv file containing processed read counts for all samples from miRDeep2 (2) .csv file containing DESeq2 differential gene expression analysis results between neural plate and neural crest samples

extract_protocol:
HH4 embryos were transfected with neural plate or neural crest specific enhancers (listed above) and developed to HH8. Embryo heads were dissected and dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. Dissociated cells were FACs sorted (GFP+) directly into 1ml of Trizol (Thermo Fisher Scientific, 15596026)  for total RNA isolation (10,000 cells/experiment). RNA was isolated according to manufacturer's protocol.
Small RNA-sequencing libraries were generated using NEB Next Small RNA Library Prep Set for Illumina (NEB, E7330S), according to manufacturer’s instructions (total RNA input of 100ng/ul for each library). Libraries were size selected on a Pippin Prep instrument for fragments between 105bp and 155bp according to manufacturer’s suggestions. The tru-seq barcoded libraries were sequenced on an Illumina NextSeq 500 instrument with paired-end 37 bp reads.

value: neural plate


title: 4438-029

city: Boston


title: HH8 NP rep3


title: tomo-seq zebrafish replicate1


title: tomo-seq zebrafish replicate2


title: HH8 NP rep1


title: Psoriasis_skin_sample_#1 (miRNA)

city: Vienna


title: 4438-027


title: HH8 NP negative rep2


title: HH8 NC rep3

source_name: Chicken neural crest

value: Tfap2aE1:GFP (Rothstein et al., 2019)

value: neural crest


title: 4438-024


title: 4438-026


title: HH8 NC rep2


title: HH8 NC rep1


title: 4438-022


title: tomo-seq X. tropicalis replicate2

organism: Xenopus tropicalis

value: Fresh frozen, cryo-sectioned oocyte.


title: eIF4A1_RocA3uM_ADP

city: Wakoshi

first: Mingming

last: Chen

state: Saitama

address: Hirisawa 2-2

department: CPR

institute: RIKEN

description: Bind-n-Seq

data_processing:
Library strategy: Bind-n-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Supplementary_files_format_and_content: csv files contain the following values: 1) value: the number of tetramer motifs; 2) probability: the ratio of tetramer motifs to total of sample; 3) probability input: the ratio of tetramer motifs to total of input; 4) Rvalue: probability/probability input

organism: synthetic construct

extract_protocol:
A hundred pmol of SBP-tagged recombinant proteins (DDX3 helicase core or eIF4A1) was incubated with 60 ul of Dynabeads M-270 Streptavidin (Thermo Fisher Scientific), which were pre-equilibrated with equilibration buffer containing 1% Triton X-100, at 4  C for 30 min. Protein-tethered beads were treated with 2 U/ ul Micrococcal Nuclease (Takara) in 0.5   equilibration buffer, and 0.5% Triton X-100 in 30   l at 25  C for 30 min. After the incubation, the beads were washed 5 times with 60   l of equilibration buffer containing 1% Triton X-100, 1 M NaCl, and 5 mM EGTA pH 7.4, and rinsed twice with the same volume of equilibration buffer containing 0.1% Triton X-100. The rinsed beads were then incubated with 50   M oligonucleotide of 5c-*CTCTTTCCCTACACGACGCTCTTCCGATCT*-N30- *ATCGTAGATCGGAAGAGCACACGTCTGAA*-3T (letters in all capitals represent DNA sequence and N represents random RNA sequence) in 30   l of equilibration buffer containing 0.1% Triton X-100, 0.33 U/  l SUPERase   In RNase Inhibitor (Thermo Fisher Scientific), 2 mM ADP and 2 mM Na2HPO4 with 3   M RocA (or 1% DMSO). Following reaction at 37  C for 30 min, the beads were washed 5 times with an equilibration buffer containing 0.1% Triton X-100, 2 mM ADP and 2 mM Na2 HPO4 with 3   M RocA (or 1% DMSO). Beads-tethered protein-RNA complex was eluted using 30   ul of equilibration buffer containing 0.1% Triton X-100, 5 mM D-biotin (Invitrogen), 2 mM ADP and 2 mM Na2HPO4 with 3   M RocA (or 1% DMSO) at 4  C for 30 min. Eluted RNAs were purified using Oligo Clean & Concentrator kit (Zymo Research) and transcribed into DNA library as described in ribosome profiling. RNA Bind-n-Seq with the condition of 2 mM AMP-PNP was performed as described above for the condition of 2 mM ADP and 2 mM Na2HPO4, but incubation with 1   M oligonucleotide.
Bind-n-Seq reference: PMID 24837674

treatment_protocol: DMSO or RocA for 30min

tag: recombinant protein

value: SBP-tagged eIF4A1

tag: binding constructs

value: RocA 3 microM


title: 4438-019

tag: Sex


title: Input

description: Bind-n-Seq

source_name: Input


title: DDX3_RocA3uM_ATP

description: Bind-n-Seq

value: SBP-tagged DDX3


title: DDX3_input_ATP

description: Bind-n-Seq

value: DMSO


title: DDX3_RocA3uM_ADP

description: Bind-n-Seq


title: tomo-seq X. tropicalis replicate1

source_name: mature oocyte


title: 4438-030


title: DDX3_DMSO2_ATP

description:
Bind-n-Seq
Processed data file for this sample is available on GSM4523757.


title: 4438-018


title: 4438-028


title: DDX3_DMSO1_ATP

description:
Bind-n-Seq
Processed data file available at the foot of this record represents both DDX3_DMSO1_ATP and DDX3_DMSO2_ATP.


title: Mouse microglia 312

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Raw BCL files from the Illumina NovaSeq 6000 were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10), and transcript counts quantified for each annotated gene within every cell.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 binary data format

source_name: Mouse microglia 312

extract_protocol:
Microglia extracted from mouse lumbar spinal cord after collagenase IV treatment and mechanical dissociation, followed by Percoll gradient and subsequent FACS sorting (CD45lo,CD11b+,CX3CR1+)
10X Chromium Single Cell 3'

tag: surgery

value: Sham

tag: time point

value: 5 months


title: MCF7_shWWOX_24VC

city: Lodz

first: Andrzej

middle: K.

last: Bednarek

address: Zeligowskiego St. 7/9

department: Department of Molecular Carcinogenesis

country: Poland

institute: Medical University in Lodz

data_processing:
Processing and analysis of sequenced nAnT-iCAGE data was done basing on the workflow proposed by the Data Analysis Center of the Cell Innovation Program (https://cell-innovation.nig.ac.jp/maser/Applications/CAGE-seq_en.html), employing Galaxy – an open source, web-based platform.
FASTQ sequenced data files were first assessed for proper quality by FastQC tool  and splitted by a barcode sequence by means of Barcode Splitter tool.
AfterQC tool was used for filtering, barcode trimming, error removal and quality check of fastq files.
Burrows-Wheeler Alignment tool (BWA) was used for reads alignment and mapping to the human reference genome (GRCh38). The data were recorded in SAM (Sequence Alignment/Map) format, transformed to BAM (Binary Sequence Alignment Map) files and alignments sorted by means of SAMtools package.
Identification of transcription start sites was performed with CAGEr (Haberle, et al., PMID:25653163). Briefly, tag counts were normalized to one million tags using simple TPM and transcription start sites (TSS) were clustered using paraclu. Finally, all genome mapped TSS were cross-identified using FANTOM5 human hg38 true-TSS library (http://fantom.gsc.riken.jp/5/datafiles/reprocessed/). All above done using CAGEr.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Spreadsheet file of hg38 genome coordinates of identified TSS including TPM normalized signals of all samples and cross-identified according to FANTOM5 project: TSScoordinates_TPMexpression_all_samples_F5mapped.txt;  Gene expression was counted as a summary of all TSS of a single gene. Spreadsheet file of gene expression of all samples: TPMexpression_all_genes_all_samples merged.txt

growth_protocol: T47D and MCF7 breast cancer cell lines were obtained from the American Type Culture Collection (ATCC), and grown according to the manufacturer’s protocol in RPMI-1640 Medium (Gibco) with 2 mM L-glutamine (Gibco), 10 mM HEPES, 1 mM sodium pyruvate, 4500 mg/L glucose, 1500 mg/L sodium bicarbonate supplemented with 10% heat inactivated fetal bovine serum (Gibco), antibiotics (Gibco, 0.05 mg/ml penicillin; 0.05 mg/ml streptomycin; 0.1 mg/ml neomycin) and human insulin (ITS insulin/transferrin/selenous acid Premix, BD Biosciences), in a humidified atmosphere containing 5% CO2 at 37°C. BT20 breast carcinoma cell line was obtained from CLS (Cell Lines Service GmbH, Eppelheim, Germany) and grown according to the manufacturer’s protocol in DMEM: Ham’s F12 medium (1:1 mixture) supplemented with 2 mM L-glutamine (Gibco), 10% heat inactivated fetal bovine serum (Gibco) and antibiotics (Gibco, 0.05 mg/ml penicillin; 0.05 mg/ml streptomycin; 0.1 mg/ml neomycin) in a humidified atmosphere containing 5% CO2 at 37°C. Mammary gland adenocarcinoma cell line MDA-MB-231 was obtained from the American Type Culture Collection (ATCC) and was cultured in Advanced DMEM (Dulbecco’s modified Eagle’s medium) with 10% heat-inactivated fetal bovine serum, 4500 mg/L glucose, 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES buffer and antibiotics (penicillin, 50 U/ml; streptomycin, 50 µg/ml; and neomycin, 100 µg/ml), in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted with TRIzol reagent.
The libraries for sequencing were prepared according to Piero Carnici’s protocol [Takahashi, et al., PMID:22362160]. Briefly, polyadenylated and non-poliadenylated RNA was reverse transcribed into cDNA with usage of random prime containing EcoP15I sequence. Next step was biotinylation of the cap site and the 3’ends of hybridized RNAs. Non-hybridized ssRNAs were digested and 5’ complete cDNAs hybridized to biotin-tagged, cap-containing RNAs were separated on streptavidin coated magnetic beads. cDNA was released from RNA and a double stranded 5’ linker with a barcode and EcoP15I sequences was ligated. Subsequently, using the biotinylated 2nd SOL primer, a second strand cDNA was synthetized. The digestion with EcoP15I allowed to cleave 27 bp fragments inside the 5’ end of the cDNA. In the 3’ end of cDNA a 3’ linker with 3’ Ilumina primer sequence was ligated. Next, constructed CAGE tags were amplified and purified. The prepared libraries were sequenced on Illumina HiSeq System.

treatment_protocol: Lentiviral transduction with shRNA gene silencing system. Retroviral transfection for WWOX cDNA inserion.

tag: ectopic wwox expression

value: shWWOX

tag: time of stimulation

value: breast cancer cell line MCF7


title: Mouse microglia 307B

source_name: Mouse microglia 307B

value: SNI


title: 4438-017

value: Male

tag: pack years

tag: imaging cluster


title: 4438-015


title: Mouse microglia 307A

source_name: Mouse microglia 307A

value: Female


title: MCF7_shWWOX_24E2


title: MCF7_shWWOX_3VC


title: 4438-014


title: Mouse microglia 304

source_name: Mouse microglia 304


title: Mouse microglia 306

source_name: Mouse microglia 306


title: 4438-013


title: MCF7_shWWOX_0

value: untreated


title: differentiated_keratinocyte_#2 (miRNA)

tag: disease state

value: healthy

value: differentiated keratinocyte


title: 4438-012


title: MCF7_shControl_24VC

value: shControl

tag: tissue


title: MCF7_shWWOX_3E2


title: Mouse microglia 302

source_name: Mouse microglia 302


title: MCF7_shControl_24E2


title: Mouse microglia 303

source_name: Mouse microglia 303


title: 4438-005


title: 4438-003


title: Mouse microglia 310-R

source_name: Mouse microglia 310-R


title: 4438-016


title: Mouse microglia 210

source_name: Mouse microglia 210

value: 14 days


title: MCF7_shControl_3VC


title: Whole transcriptome at 3 h after S-SBP1 infection of WH7803

city: Guangzhou

first: Sijun

last: Huang

state: Guangdong

address: 164 Xingangxi St

description:
T3h
S-SBP1.rpkm.xls
WH7803.rpkm.xls
WH7803.Differential Expression.xls

data_processing:
Cutadapt (version 1.9.1) was used to remove adapters, primers and reads with base quality lower than 20 based on fastq files. Clean data were aligned to the S-SBP1 genome and the WH7803 genome via software Bowtie2 (v2.1.0). HTSeq (v0.6.1p1) was used to estimate gene expression levels from the pair-end clean data. Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were set < 0.05 to detect differential expressed ones. Samtools v0.1.19 and Bcftools v0.1.19+ were used to carry out SNV calling.
In order to cluster the phage genes based on their expression dynamics, the RPKM  normalization of gene transcript level was used. The package EdgeR implemented in Bioconductor was used to analyze the differential expression of the host genes. Host genes with log2FC ≥ 2 as well as P < 0.05 were considered to be upregulated.
Genome_build: GenBank: NC_009481 for Synechococcus WH7803 and MT424636 For Cyanopodovirus S-SBP1
Supplementary_files_format_and_content: Excel files include RPKM values for each sample
Supplementary_files_format_and_content: Excel files include differential expression of Synechococcus WH7803, comparing the no phage-addition control sample to other phage treated samples

organism:
Synechococcus sp. WH 7803
Synechococcus phage S-SBP1

source_name: Synechococcus sp. strain WH7803 infected by S-SBP1

growth_protocol: Synechococcus sp. WH7803, was growing at 22℃ in the A+ artificial seawater medium under continuous cool white light with an intensity of 10 μmol photon m-2s-1.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®)

treatment_protocol: Exponentially growing host culture (4.7×10^7 cells per ml) was inoculated with phage S-SBP1 at a multiplicity of infection (MOI) of two. To monitor phage growth, two aliquots of 1 ml culture were collected every 0.5-1 h during the first 16 h after adding the phage. One aliquot of the culture was centrifuged at 13000 rpm for 3 min to collect the supernatant (used to measure the extracellular phage abundance) and another aliquot was not treated (used to measure the total phage abundance). The samples were flash frozen in liquid nitrogen and stored at -80 ℃. At the time points 15 min, 1 h, 3 h, 5 h and 7 h after phage lysate addition, 100 ml of culture was sampled and centrifuged at 8000 rpm for 10 min to collect the cells for transcriptomic analysis. A parallel of control group without phage addition was also sampled at the time point of 30 min and 8 h.

tag: host

tag: infection

value: phage S-SBP1

tag: time

value: 3 h


title: Whole transcriptome at 5 h after S-SBP1 infection of WH7803

description:
T5h
S-SBP1.rpkm.xls
WH7803.rpkm.xls
WH7803.Differential Expression.xls

value: 5 h


title: Whole transcriptome at 7 h after S-SBP1 infection of WH7803

description:
T7h
S-SBP1.rpkm.xls
WH7803.rpkm.xls
WH7803.Differential Expression.xls

value: 7 h


title: Whole transcriptome at 1 h after S-SBP1 infection of WH7803

description:
T1h
S-SBP1.rpkm.xls
WH7803.rpkm.xls
WH7803.Differential Expression.xls

value: 1 h


title: 4238-030

tag: age


title: 4238-019


title: MCF7_shControl_3E2


title: MCF7_shControl_0


title: 4238-018


title: Whole transcriptome at 15 min after S-SBP1 infection of WH7803

description:
T15m
S-SBP1.rpkm.xls
WH7803.rpkm.xls
WH7803.Differential Expression.xls

value: 15 min


title: Mouse microglia 212

source_name: Mouse microglia 212

value: Sham


title: Mouse microglia 207-R

source_name: Mouse microglia 207-R


title: 4238-004

description: Gene expression from single bronchial epithelial cells from subject in imaging cluster 3.

source_name: Bronchial epithelial cells


title: Mouse microglia 205

source_name: Mouse microglia 205


title: Mouse microglia 206

source_name: Mouse microglia 206


title: BT20_shWWOX_3VC

value: shWWOX

value: breast cancer cell line BT20


title: 4-6_ham_S96_L004

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: Infected


title: 4238-002


title: Mouse microglia 203

source_name: Mouse microglia 203

value: SNI


title: BT20_shWWOX_3E2


title: 4-5_ham_S95_L004


title: 4-2_ham_S94_L004


title: 4202-025

value: Female


title: Mouse microglia 202

source_name: Mouse microglia 202

value: Male


title: BT20_shWWOX_0

value: untreated


title: 3-6_ham_S93_L004


title: Mouse microglia 209

source_name: Mouse microglia 209


title: Mouse microglia 106

source_name: Mouse microglia 106

value: 3 days


title: BT20_shControl_24VC

value: shControl


title: BT20_shControl_24E2


title: Mouse microglia 106-Redo

source_name: Mouse microglia 106-Redo


title: 4202-017


title: Mouse microglia 105

source_name: Mouse microglia 105


title: 4238-017


title: BT20_shWWOX_24E2


title: BT20_shControl_3VC


title: BT20_shWWOX_24VC


title: 3-2_ham_S91_L004


title: 4202-012


title: Mouse microglia 104

source_name: Mouse microglia 104


title: 4202-006


title: Mouse microglia 103

source_name: Mouse microglia 103


title: Mouse microglia 103-Redo

source_name: Mouse microglia 103-Redo


title: 4202-004


title: 4202-019


title: BT20_shControl_3E2


title: BT20_shControl_0


title: MDA-MB-231_WWOX_24VC

value: WWOX

value: breast cancer cell line MDA-MB-231


title: 4202-003


title: Mouse microglia 102

source_name: Mouse microglia 102


title: MDA-MB-231_WWOX_24E2


title: 3-4_ham_S92_L004


title: MDA-MB-231_WWOX_3VC


title: Mouse microglia 101-R

source_name: Mouse microglia 101-R


title: 4202-015


title: Mouse microglia 004

source_name: Mouse microglia 004

value: Naive


title: MDA-MB-231_WWOX_3E2


title: Mouse microglia 003

source_name: Mouse microglia 003


title: MDA-MB-231_WWOX_0


title: Mouse microglia 002

source_name: Mouse microglia 002


title: MDA-MB-231_vector_24VC

value: vector


title: Mouse microglia 001-R

source_name: Mouse microglia 001-R


title: MDA-MB-231_vector_24E2


title: Blood

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description: Blood

data_processing:
Cellranger 3.0.0 was used for basecalling, demultiplexing and initial analyses to create the single cell count matrix.
In spedific, cellranger mkfastq and cellranger count were used for this purpose with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

source_name: Blood

extract_protocol: CD45+ cells were isolated from the brain, subcutaneous galea, bone flap, and blood at day 7 post-infection by FACS, whereupon single cell RNA sequencing was performed using a 10X Genomics platform

tag: cell type

value: CD45+ cells

tag: days post infection

tag: agent

value: Staphylococcus aureus


title: Bone flap

description: Bone flap

source_name: Bone flap


title: MDA-MB-231_vector_3VC


title: MDA-MB-231_vector_3E2


title: Galea

description: Galea

source_name: Galea


title: Whole transcriptome at 8 h of WH7803 as uninfected control

description:
CT8h
WH7803.rpkm.xls

organism: Synechococcus sp. WH 7803

source_name: Synechococcus sp. strain WH7803

value: uninfected control

value: 8 h


title: RatPyV2 Parotid

first: Bizunesh

last: Abere

state: PENNSYLVANIA

address: 5117 Centre Ave, Research Pav. Suite 1.8

department: Cancer Virology Program

institute: Hillman Cancer Center

data_processing:
Raw FastQ files were trimmed with Trim Galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ using the following parameters -q 25, -e 0.1, and - length 50, and the quality control was performed with FastQC.
Backspliced splice junctions were identified and mapped using CIRI2 prediction algorithm
Genome_build: MCV (JF813003) and RatPyV2 (KX574453)
Supplementary_files_format_and_content: backsplice junctions identified exported as txt
CVG-1vsMCVoutfile.txt (no circRNA detected)
MS-1vsMCVoutfile.txt (no circRNA detected)
HEK-293-MCV-HFvs MCVoutfile.txt
RatParotidvsRatPyV2outfile.txt

organism: Rattus norvegicus

source_name: Tissue

extract_protocol:
Trizol reagent (Invitrogen) was used to extract total RNA, according to the manufacturer’s instructions and treated with DnaseI (Ambion) to remove geomic DNA.
For RNA qulity control and circRNA library preparation, a total amount of 6 μg RNA per sample was used as input material. Ribosomal RNA was removed by rRNA probe andlinear RNA was removed by Rnase R (Lucigen). The CircRNA was interrupted randomly in adding fragmentation buffer.
Using the fragmented CircRNA as a template, the first strand was synthesized with a random hexamers of six bases, followed by the addition of buffer, dNTPs, RNase H and DNA polymerase I to synthesize the second strand of the cDNA, then the CircRNA was purified by AMPure XP beads. The cohesive ends of the DNA were repaired to blunt ends using T4 DNA polymerase and Klenow DNA polymerase, 3'-end plus A-tail and ligated to the sequencing adapter followed by selection of the size of the fragment with AMPure XP beads, afterwards, the second strand of cDNA containing U was degraded with USER enzyme. CircRNA library was amplified by PCR.

treatment_protocol: Samples 3, HEK-293 cells were transfected with a recircularized MCV-HF genome for 5 days and harvested for RNA extraction.

value: Parotid gland

tag: infection status

value: RatPyV2 infected

tag: treatment

value: RnaseR+, ribodepleted RNA


title: Whole transcriptome at 30 min of WH7803 as uninfected control

description:
CT30m
WH7803.rpkm.xls
WH7803.Differential Expression.xls

value: 30 min


title: MDA-MB-231_vector_0


title: HC rep3

first: Weihua

last: Pan

address: 415 Fengyang Road

department: Department of Dermatology

institute: Shanghai Changzheng Hospital

description: circRNAs expression in peripherial blood mononuclear cells  from healthy individuals.

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: peripherial blood mononuclear cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: healthy individuals

value: peripherial blood mononuclear cells


title: Brain

description: Brain

source_name: Brain


title: CM rep2

description: circRNAs expression in peripherial blood mononuclear cells  from cryptococcal meningitis patients.

value: cryptococcal meningitis patients


title: HEK293t Knock-in (KI)_long DNA reads

status: Public on Dec 06 2020

city: West Haven

first: Sarah

middle: A

last: Slavoff

state: Connecticut

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University- West Campus

data_processing:
Library strategy: DNA-seq
Generated raw data (FAST5) was subjected to basecalling using Guppy v.3.4.5.
Raw reads were corrected using the necat.pl script from the package NECAT 0.0.1. Corrected reads were further split at chimeric positions using the SACRA pipeline (https://github.com/hattori-lab/SACRA) according to standard parameters. Finally, non-chimeric reads were mapped to GRCh38 chromosome 19 with ngmlr 0.2.7 and variants were called using sniffles 1.0.12 using parameters specific to ONT sequencing data.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: structural variants called with sniffles are listed in vcf format.

source_name: HEK 293T cell line with a 3xGFP11-FLAG tag appended to the 3' end of alt-RPL36

growth_protocol: The cells were grown at 37 C/5% CO2 in DMEM supplemented with 10% FBS/1% Pen-strep

extract_protocol:
Genomic DNA was extracted with the Qiagen mini kit
DNA was partitioned in droplets by Xdrop™ and subjected to PCR using the enrichment PCR assays. The droplet productions were then sorted by fluorescence activated cell sorting (FACS).The isolated droplets were broken, and DNA was again partitioned in droplets by Xdrop™ and amplified by droplet Multiple Displacement Amplification (dMDA) reactions.
The Minion Oxford Nanopore Sequencing platform was used to generate long-read sequencing data.

tag: cell line

tag: genotype/variation


title: HC rep2


title: HEK293t KO_long DNA reads

source_name: HEK293T cells with CRISPR knockout of alt-RPL36

value: with CRISPR knockout of alt-RPL36


title: CM rep3


title: CM rep1


title: Non-targeting_gRNA_RNASeq

city: Torino

first: Pier Paolo

last: Pandolfi

state: TO

address: 8 Via Verdi

institute: University of Torino

data_processing:
For screening studies, DNA-Seq reads were trimmed, counted and analyzed with MAGeCK v0.5.8
For RNA-Seq, reads were aligned and quantified with Salmon v0.13.1 then normalized with DESeq2 v1.26.0
Genome_build: hg38
Supplementary_files_format_and_content: text files contain normalized read count data for each set of sequencing experiments

source_name: hepatocellular carcinomas

extract_protocol:
For gRNA/shRNA screening screening experiments, genomic DNA was extracted from screened cells using Qiagen Blood and Tissue Kit. For RNA-Seq, RNA was extract with Trizol
For gRNA/shRNA screening libraries, custom primers compatible with Illumina sequencing primers were used to amplified gRNA/shRNA sequences from the genome. For RNA-Seq, RNA libraries were prepared according to Illumina's protocol, conducted by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute

value: hepatocellular carcinomas


title: HC rep1


title: Non-targeting_shRNA_RNASeq


title: circGFP-targeting_shRNA_RNASeq_rep2


title: 0411 D2 PPRA

city: kyoto

first: partha sarathi

last: chowdhury

address: Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan

institute: kyoto university

description: RMA expression value derived from Expression Console software; exon-level analysis

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 17 hr at 45C on Clariom S Array, Mouse. Clariom S Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Clariom S Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST) algorithms prior to Robust Multiarray Average (RMA) using Expresson Console Software (ThermoFisher Scientific) according to the default analysis settings (Gene Level-SST-RMA).

source_name: 0411 day 2 PPARa treated

label_protocol: Biotinylated ssDNA were prepared using GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) according to the standard manufacturer's protocol from 100 ng total RNA.

extract_protocol: total RNA extraction

value: CD8 T cell

tag: gender

value: female


title: 0411 D2 PPRB

source_name: 0411 day 2 PPARb treated


title: circGFP-targeting_gRNA_RNASeq_rep2


title: circGFP-targeting_shRNA_RNASeq_rep1


title: 0411 D2 PPRG

source_name: 0411 day 2 PPARg treated


title: 0411 D2 DMS

source_name: 0411 day 2 DMSO treated


title: circGFP-targeting_gRNA_RNASeq_rep1


title: 0419 D2 PPRG

source_name: 0419 day 2 PPARg treated


title: 0419 D2 DMS

description: RMA expression value derived from Expression Console software; gene-level analysis

source_name: 0419 day 2 DMSO treated


title: 0419 D2 PPRB

source_name: 0419 day 2 PPARb treated


title: 0419 D2 PPRA

source_name: 0419 day 2 PPARa treated