title: LS-15932_S62_E1-50

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq 2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: GRCh38.p2

value: Non-Neuronal

value: Oligo


title: MO8

status: Public on Sep 21 2021

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.3.1093 based on the statistical language R version 3.5.1

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: type

value: Mucosal melanoma

tag: exact anatomic site

value: Mouth


title: Cell_0239_E11.5_FACS-EHT_het

type: SRA

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

library_source: transcriptomic

data_processing:
Basecall files generated from NextSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq. Alignment was performed by STAR 2.4.2a to ensemble reference genome (GRCm38 release 87) with default parameters. Read counts from BAM files were extracted using htseq (version 0.6.1p1) with the following setting --format=bam --stranded=no --type=exon --idattr=gene_id. Count table was loaded into the R environment (R version 3.6.2).
Genome_build: Mus musculus.GRCm38 release 87

molecule: polyA RNA

organism: Mus musculus

source_name: Aorta gonad mesonephros

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)

tag: developmental stage

tag: strain

value: ICR

tag: genotype

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: GE5

value: Genital


title: LS-15932_S61_E1-50

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

description:
human_LGN_2021_exon-matrix.csv
human_LGN_2021_intron-matrix.csv

source_name: Human - dLGN - PC

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia. The brain tissues of two adult M. nemestrina (southern pig-tailed macaque) and one M. fascicularis  (crab-eating macaque) were obtained through the Tissue Distribution Program of the Washington  National Primate Research Center and conformed to the guidelines provided by the US National  Institutes of Health. All procedures were approved by the Institutional Animal Care and Use Commit-  tee of the University of Washington under protocol number 4277-01.

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

tag: Sex

value: M

tag: age

value: PC

tag: facs gating

value: NeuN-pos

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster

value: MP


title: V6-stalk

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

data_processing:
Library strategy: degradome-seq
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences.
CleaveLand4.pl was used to processed the data
Supplementary_files_format_and_content: txt file, the result of CleaveLand4, degradome density file

molecule: total RNA

organism: Zea mays

source_name: RNA from Stalk

growth_protocol: Maize (Zea mays ssp. mays) ‘B73’ plants were cultivated in a phytotron at 25°C with 65% relative humidity under a 14-h/10-h light/dark cycle.

extract_protocol:
Total RNA was extracted from the maize tissues using TRIzol reagent (Molecular Research Center) according to the manufacturer’s instructions. Agilent Bioanalyzer 2100 system was used to check the quality of the extracted RNA, and only RNA of high integrity was used for the analysis.
The degradome-seq library was constructed based on a previously described method (Zhai et al., 2014). Degradome-seq was performed on the Illumina HiSeq 2500 platform (Berry Genomics) to produce 50-bp single- end reads.

tag: tissue

tag: cultivar


title: Cell_0238_E11.5_FACS-EHT_het


title: NAMPT LKO fast 24-5

city: St. Louis

first: Brian

last: DeBosch

state: Missouri

address: 660 South Euclid Avenue

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Liver

growth_protocol: Littermate WT and NAMPT LKO mice were grown to adulthood ~12wks of age

extract_protocol:
Trizol reagent was used to isolate total RNA, performed exactly per manufacturer protocol on 50-100mg liver tissue homogenate
oligo-dT

treatment_protocol: Mice were fasted on aspen bedding 24h or 22h + 2hr refeeding period prior to sacrifice

value: Liver


title: LS-15932_S59_E1-50

value: GABA


title: WT Fast 24-2


title: LS-15932_S60_E1-50


title: LS-15932_S58_E1-50


title: Cell_0237_E11.5_FACS-EHT_het


title: PS6

value: Sinus


title: WT fast-refeed


title: Cell_0235_E11.5_FACS-HE_Gfi1_het


title: Cell_0236_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S57_E1-50


title: NAMPT LKO fast 24-4


title: LS-15932_S48_E1-50

source_name: Human - dLGN - MC

value: MC

value: NeuN-neg


title: AN8

value: Anorectal


title: metastasis (rep1)

type: RNA

city: Ramat Gan,

first: Maya

middle: Ramot

last: Goshen

address: Derech Sheba 2,

department: Clinical Microbiology and Immunology

country: Israel

institute: Tel Aviv University

description:
test
WM266

data_processing: CEL files were processed using Affymetrix Expression Console Software into log2 RMA values using Affymetrix default analysis settings. When combining the 3 replicates together, in order to remove batch effect the first component in the principal component analysis was subtracted. The normalized data for all 3 replicates together can be found in the file "normalized_data_with_gene_name.txt" on the series record.

label: biotin

source_name: skin melanoma

label_protocol: Biotinylated cRNA were prepared  using WT expression kit according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

growth_protocol: cell lines WM115 and WM266-4 were obtained from the ATCC and were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1%NaP, 1%L-glu, 1%pen/strep and 1%non-essential amino acids all purchased from Biological-Industries, Israel

extract_protocol: For the first repeat, the total RNA was extracted using the miRNeasy micro kit (Qiagen) and RNA was loaded on Affymetrix Human Gene 1.0 ST Array Strip. In the following 2 biological repeats, total RNA was extracted using GeneAll Hybrid-R miRNA kit and RNA was loaded on Affymetrix Human Gene 2.1 ST Array Strip.

tag: cell line

tag: tumor stage

value: skin metastasis


title: Cell_0233_E11.5_FACS-HE_Gfi1_het


title: HPC-3

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat 2.0.6.
Fragments Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using cufflink 2.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: bone marrow

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/NJ

value: bone marrow

tag: cell type

value: Bone Marrow Hematopoietic Progenitor Cells (HPC)

value: post natal day 42

value: wild type


title: LS-15932_S41_E1-50

value: M


title: Cell_0232_E11.5_FACS-HE_Gfi1_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: WT Fast 24-3


title: NAMPT LKO fast 24-2


title: NAMPT LKO fast 24-3


title: HPC-2


title: primary (rep1)

description:
control
WM115

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: skin primary tumor


title: Cell_0231_E11.5_FACS-HE_Gfi1_het


title: WT Fast - refeed


title: HPC-1


title: Cell_0230_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S33_E1-50

value: NeuN-pos

value: Glut

value: MP


title: BM-M-3

value: Leukemic Progenitors (LP)

value: median phase

value: PML-RAR


title: MO6

tag: type

value: Mucosal melanoma

value: Mouth


title: NAMPT LKO fast 24-1

value: Liver


title: LS-15932_S32_E1-50

value: PC

value: NeuN-neg

value: Non-Neuronal

value: Oligo


title: Cell_0229_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S35_E1-50

value: M

value: MC


title: GE13

tag: exact anatomic site

value: Genital


title: LS-15932_S31_E1-50

value: GABA


title: BM-M-2

value: FVB/NJ

value: bone marrow


title: WT Fast 24-1


title: NC7

value: Nasal


title: Cell_0228_E11.5_FACS-HE_Gfi1_het

tag: developmental stage

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Western diet-fed SIRT1 LKO x AAV8-NAMPT5

growth_protocol: Littermate WT and SIRT LKO mice were grown to adulthood ~8wks of age

treatment_protocol: Mice were injected with AAV8 encoding empty vector or SIRT1

tag: strain


title: Cell_0234_E11.5_FACS-HE_Gfi1_het

tag: genotype


title: GE14


title: BM-E-3

value: Leukemic Progenitors (LP)

value: early phase

value: PML-RAR


title: Western diet-fed SIRT1 LKO x AAV8-NAMPT4

value: Liver


title: Cell_0227_E11.5_FACS-HE_Gfi1_het


title: BM-E-2


title: LS-15932_S29_E1-50

tag: donor

value: PC

value: NeuN-pos


title: LS-15932_S26_E1-50

tag: Sex

value: Non-Neuronal


title: Cell_0226_E11.5_FACS-HE_Gfi1_het


title: Cell_0225_E11.5_FACS-HE_Gfi1_het


title: Western diet-fed SIRT1 LKO x AAV8-NAMPT2

tag: age


title: BM-M-1

value: median phase


title: AN2

value: Mucosal melanoma

value: Anorectal


title: GE4

value: Genital


title: LS-15932_S24_E1-50

value: M

tag: facs gating

value: NeuN-neg

value: Oligo


title: Western diet-fed SIRT1 LKO x AAV8-NAMPT1


title: Cell_0224_E11.5_FACS-HE_Gfi1_het


title: AN1


title: AN10


title: db/db AdNAMPT4

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.4.0b
Gene counts quantitated with Subread:featureCount 1.4.5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: diabetic mice

growth_protocol: Littermate db/db mice were grown to 5wk of age and randomized

extract_protocol:
Trizol reagent was used to isolate total RNA, performed exactly per manufacturer protocol on 50-100mg liver tissue homogenate
Ribo-Zero

treatment_protocol: Mice were injected with adenovirus encoding GFP or NAMPT via tail vein

value: NAMPT overexpression


title: PS8

value: Sinus


title: LS-15932_S23_E1-50

tag: sequencing batch

value: Astro


title: NC8

value: Nasal


title: Western diet-fed WT x AAV8-NAMPT6


title: Cell_0223_E11.5_FACS-HE_Gfi1_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: NC10


title: LS-15932_S22_E1-50

tag: cell class

value: GABA


title: Western diet-fed WT x AAV8-NAMPT5

value: Liver


title: Cell_0222_E11.5_FACS-HE_Gfi1_het


title: db/db AdNAMPT2


title: LS-15932_S21_E1-50

value: PC

value: NeuN-pos

tag: cell cluster


title: Western diet-fed WT x AAV8-NAMPT4

tag: tissue


title: db/db AdNAMPT1


title: AN11


title: LS-15932_S19_E1-50

value: Non-Neuronal


title: Western diet-fed SIRT1 LKO x AAV8-NAMPT3


title: GE11

value: Mucosal melanoma


title: LS-15932_S16_E1-50

source_name: Human - dLGN - KC

value: KC


title: Cell_0219_E11.5_FACS-HE_Gfi1_het


title: Cell_0220_E11.5_FACS-HE_Gfi1_het


title: Western diet-fed WT x AAV8-NAMPT3


title: Western diet-fed WT x AAV8-NAMPT2


title: LS-15932_S15_E1-50

value: Glut

value: MP


title: db/db AdGFP3

value: control


title: db/db AdGFP4


title: Cell_0218_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S27_E1-50

value: M


title: db/db AdGFP2


title: LS-15932_S14_E1-50


title: NC13


title: GE3

value: Genital


title: Cell_0217_E11.5_FACS-HE_Gfi1_het


title: Western diet-fed WT x AAV8-NAMPT1


title: LS-15932_S13_E1-50


title: db/db AdGFP1


title: Western diet-fed WT x AAV8-EV7


title: Cell_0216_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S12_E1-50


title: PTSD179-D2

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

library_source: genomic

data_processing:
BISMARK version 0.22.1 was used to perform DNA methylation calls
The human genome, hg38, was indexed using bismark_genome_preparation module.
Alignment was performed in a paired-end mode using BISMARK.
Deduplication of reads was performed using duplicate_bismark module. Bismark_methylation_extractor module was used to extract methylated sites.
RnBeads version 2.8.0 was used to perform differential methylation analysis with R version 4.0.
Genome_build: hg38
Supplementary_files_format_and_content: Bed file format compressed with gzip and methylation interval

source_name: Peripheral blood mononuclear cells

extract_protocol: Accel-NGS Methyl-Seq DNA Library kit

tag: phenotype

value: MDD

value: Peripheral blood mononuclear cells

tag: subject

tag: timepoint


title: Western diet-fed WT x AAV8-EV8


title: Western diet-fed SIRT1 LKO x AAV8-EV5


title: PTSD179-D1


title: Cell_0215_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S11_E1-50

value: Oligo


title: LS-15932_S03_E1-50


title: AN3

value: Anorectal


title: Cell_0214_E11.5_FACS-HE_Gfi1_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Western diet-fed SIRT1 LKO x AAV8-EV4

value: Liver


title: PTSD172-D2

value: Control


title: Western diet-fed SIRT1 LKO x AAV8-EV3


title: Cell_0212_E11.5_FACS-HE_Gfi1_het


title: PTSD172-D1


title: PTSD165-D2

value: PTSD and MDD


title: Cell_0213_E11.5_FACS-HE_Gfi1_het


title: Western diet-fed WT x AAV8-EV6


title: Cell_0221_E11.5_FACS-HE_Gfi1_het


title: LS-15932_S02_E1-50

value: NeuN-pos


title: Cell_0211_E11.5_FACS-HE_Gfi1_het


title: Western diet-fed WT x AAV8-EV4


title: LS-15931_S95_E1-50

value: Non-Neuronal


title: PTSD165-D1


title: Western diet-fed WT x AAV8-EV2


title: Cell_0210_E11.5_FACS-HE_Gfi1_het


title: BM-E-1

value: FVB/NJ

value: bone marrow

tag: cell type

value: Leukemic Progenitors (LP)

value: early phase

value: PML-RAR


title: PTSD153-D2


title: LS-15932_S09_E1-50

value: M

value: KC

value: Glut

value: MP


title: Western diet-fed WT x AAV8-EV1


title: LS-15931_S94_E1-50


title: Western diet-fed SIRT1 LKO x AAV8-EV2


title: Cell_0209_E11.5_FACS-HE_Gfi1_het


title: LS-15931_S92_E1-50


title: PTSD153-D1

value: Peripheral blood mononuclear cells


title: Cell_0208_E11.5_FACS-HE_Gfi1_het

value: ICR


title: Western diet-fed SIRT1 LKO x AAV8-EV1


title: LS-15931_S91_E1-50


title: PTSD138-D2

value: MDD


title: Cell_0207_E11.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Chow-fed WT x AAV8-EV3

value: Liver


title: Cell_0206_E11.5_FACS-HE_Gfi1_het


title: Cell_0205_E11.5_FACS-HE_Gfi1_het


title: PTSD138-D1


title: Chow-fed WT x AAV8-EV2


title: LS-15931_S87_E1-50


title: PTSD127-D2

value: PTSD and MDD


title: Cell_0204_E11.5_FACS-HE_Gfi1_het


title: Cell_0203_E11.5_FACS-HE_Gfi1_het


title: LS-15931_S84_E1-50

value: NeuN-pos


title: PTSD136-D2


title: PTSD127-D1


title: Cell_0202_E11.5_FACS-HE_Gfi1_het


title: Cell_0201_E11.5_FACS-HE_Gfi1_het


title: PTSD124-D2

value: Control


title: LS-15931_S83_E1-50


title: LS-15931_S89_E1-50


title: LS-15931_S90_E1-50


title: Cutts-mm_AD7-2Lung24h

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome mm10 by using STAR_2.5.3 software with default parameters
Reads from the alignment were sorted and indexed according to chromosomes
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1 with “--nonunique all” option
Raw read counts were normalized and a differential expression analysis was performed with DESeq2 by applying an adjusted p-value <0.05 and an absolute log2-ratio larger than 1
Genome_build: mm10

source_name: Lung

extract_protocol:
RNA from the whole lungs and spleen was extract by the Tripure/Chloroform method
Libraries were prepared using Ovation® SoLo RNA-Seq system (NuGEN Technologies) and underwent paired-end sequencing (25×106 paired-end reads/sample, Novaseq 6000 platform)

value: lung

value: wild type

tag: treatment

value: intranasally infected with Brucella melitensis


title: PTSD124-D1


title: Cell_0200_E11.5_FACS-HE_Gfi1_het


title: PTSD116-D2


title: PTSD136-D1


title: Cutts-mm_AD5-2LungN

value: naive mice


title: Cell_0199_E11.5_FACS-HE_Gfi1_het


title: Cutts-mm_AD3-1Lung24h


title: Chow-fed WT x AAV8-EV1


title: Cutts-mm_AD1-NaiveLung


title: LS-15931_S79_E1-50

value: PC

value: GABA


title: LS-15931_S85_E1-50

value: M

value: KC


title: db/db AdNAMPT3

value: NAMPT overexpression


title: Cell_0198_E11.5_FACS-HE_Gfi1_het


title: PTSD114-D2

value: Peripheral blood mononuclear cells


title: Cutts-mm_AD1-1LungN


title: LS-15931_S78_E1-50

value: Non-Neuronal

value: Oligo


title: Cell_0197_E11.5_FACS-HE_Gfi1_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: LS-15931_S77_E1-50


title: PTSD114-D1

value: PTSD and MDD


title: RNA of Pleural tumor cells from mice with LNP-CDN+PD-L1 treatment_Sample 3

city: Winston Salem

first: Dawen

last: Zhao

state: NC

address: Medical Center Blvd

department: Biomedical Engineering

institute: Wake Forest School of Medicine

description:
fpkm_genename.xls
N_P_3_T

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. 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.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.   Kyoto Encyclopedia of Genes and Genomes (KEGG) was analyzed by R package clusterProfiler to test the statistical enrichment of differential expression genes in KEGG pathways. KEGG terms with adjusted P value less than 0.05 were considered significant enrichment.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_genename.xls (Tab-delimited xls file)

source_name: Pleural tumor cells

extract_protocol:
he mice were sacrificed on day 13 and pleural fluid was gently aspirated using a 1-ml syringe through the diaphragm, and its volume was measured with a 1 mL pipette. The pleural fluids were centrifuged at 500 g for 10 min and cell pellet was further treated with 2 mL ACK Lysing Buffer (Thermo Fisher) to delete red blood cells for 10 min at 4 °C in 15-mL conical centrifuge tube. 10 mL cold PBS was added to stop the lysis, and the cells were centrifuged at 500 g for 5 min. The total RNA from MPE cell pellets were extracted by TRIzol Reagent. For r pleural tumors, tissues were cut into small pieces in PBS on ice and further processed in 1 x tumor digestion buffer (1 mg/mL Collagenase IV, 0.1 mg/mL Hyaluronidase, and 20 U/mL DNAse) at 37 °C for 1 h under rotation. The cell suspension was gathered by filtering through cell strainer. After centrifuge at 500 g for 5 min, the cell pellet was washed once by 5 mL PBS followed by centrifuge at 500 g for 5 min. The pellet was treated with ACK lysing buffer to remove red blood cells. The total RNA from pleural tumor cell pellets were extracted by TRIzol Reagent as well.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated  cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  Clustering and sequencing

treatment_protocol: The LLC MPE mice (n = 3/treatment) were treated with intrapleural PBS, LNP-cGAMP (1 µg), anti-PD-L1 Ab (10F.9G2; 30 µg; BioXCell) or LNP-cGAMP plus anti-PD-L1 Ab on day 11.

value: Pleural Tumor


title: LS-15931_S82_E1-50

value: NeuN-pos

value: Glut

value: MP


title: LS-15931_S76_E1-50


title: LS-15931_S81_E1-50


title: PTSD112-D2

value: MDD


title: PTSD112-D1


title: LS-15931_S75_E1-50


title: RNA of Pleural tumor cells from mice with LNP-CDN+PD-L1 treatment_Sample 2

description:
fpkm_genename.xls
N_P_2_T


title: Cell_0196_E11.5_FACS-HE_Gfi1_het


title: PTSD116-D1


title: LS-15931_S74_E1-50


title: RNA of Pleural tumor cells from mice with LNP-CDN+PD-L1 treatment_Sample 1

description:
fpkm_genename.xls
N_P_1_T


title: Cell_0195_E11.5_FACS-HE_Gfi1_het


title: Cell_0194_E11.5_FACS-Endo_Gfi1_het


title: RNA of Pleural tumor cells from mice with PD-L1 treatment_Sample 3

description:
fpkm_genename.xls
P_3_T


title: Cell_0193_E11.5_FACS-Endo_Gfi1_het


title: LS-15931_S73_E1-50


title: PTSD111-D2


title: PTSD108-D2


title: PTSD111-D1


title: Cell_0192_E11.5_FACS-Endo_Gfi1_het


title: RNA of Pleural tumor cells from mice with PD-L1 treatment_Sample 2

description:
fpkm_genename.xls
P_2_T


title: RNA of Pleural tumor cells from mice with PD-L1 treatment_Sample 1

description:
fpkm_genename.xls
P_1_T


title: PTSD108-D1


title: LS-15931_S71_E1-50


title: LS-15931_S72_E1-50

value: NeuN-neg

value: Astro


title: Cell_0191_E11.5_FACS-Endo_Gfi1_het


title: Cell_0190_E11.5_FACS-Endo_Gfi1_het


title: PTSD102-D2


title: RNA of Pleural tumor cells from mice with LNP-CDN treatment_Sample 3

description:
fpkm_genename.xls
N_3_T

value: LNP-CDN


title: LS-15931_S70_E1-50

value: M

value: PC

value: OPC


title: RNA of Pleural tumor cells from mice with LNP-CDN treatment_Sample 2

description:
fpkm_genename.xls
N_2_T


title: PTSD102-D1

value: Peripheral blood mononuclear cells


title: Cell_0189_E11.5_FACS-Endo_Gfi1_het


title: RNA of Pleural tumor cells from mice with PBS treatment_Sample 3

description:
fpkm_genename.xls
CTR_3_T

value: PBS


title: PTSD100-D2


title: RNA of Pleural tumor cells from mice with LNP-CDN treatment_Sample 1

description:
fpkm_genename.xls
N_1_T


title: RNA of Pleural tumor cells from mice with PBS treatment_Sample 2

description:
fpkm_genename.xls
CTR_2_T


title: PTSD100-D1


title: LS-15931_S66_E1-50


title: Cell_0187_E11.5_FACS-Endo_Gfi1_het


title: LS-15931_S69_E1-50

value: GABA


title: LS-15931_S68_E1-50


title: LS-15931_S65_E1-50


title: PTSD079-D2

value: Control


title: PTSD079-D1


title: Cell_0186_E11.5_FACS-Endo_Gfi1_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: RNA of MPE cells from mice with LNP-CDN+PD-L1 treatment_Sample 3

description:
fpkm_genename.xls
N_P_3_M

source_name: MPE cells

value: Pleural Fluid


title: Cell_0185_E11.5_FACS-Endo_Gfi1_het


title: Cell_0184_E11.5_FACS-Endo_Gfi1_het


title: LS-15931_S60_E1-50

value: MC

value: NeuN-pos

value: Non-Neuronal


title: LS-15931_S62_E1-50

value: Oligo


title: RNA of Pleural tumor cells from mice with PBS treatment_Sample 1

description:
fpkm_genename.xls
CTR_1_T

value: Pleural Tumor


title: PTSD071-D2

value: MDD


title: PTSD071-D1


title: Cell_0182_E11.5_FACS-Endo_Gfi1_het


title: PTSD063-D2


title: Cell_0183_E11.5_FACS-Endo_Gfi1_het


title: Cell_0188_E11.5_FACS-Endo_Gfi1_het


title: RNA of MPE cells from mice with LNP-CDN+PD-L1 treatment_Sample 2

description:
fpkm_genename.xls
N_P_2_M


title: LS-15931_S55_E1-50


title: RNA of MPE cells from mice with LNP-CDN+PD-L1 treatment_Sample 1

description:
fpkm_genename.xls
N_P_1_M


title: PTSD063-D1


title: LS-15931_S52_E1-50

value: Glut

value: MP


title: Cell_0180_E11.5_FACS-Endo_Gfi1_het


title: LS-15931_S54_E1-50

value: M


title: Cell_0181_E11.5_FACS-Endo_Gfi1_het


title: PTSD059-D2


title: PTSD059-D1


title: LS-15931_S30_E1-50

value: PC


title: Cell_0179_E11.5_FACS-Endo_Gfi1_het


title: PTSD057-D2

value: Peripheral blood mononuclear cells


title: Cell_0177_E11.5_FACS-Endo_Gfi1_het


title: RNA of MPE cells from mice with LNP-CDN treatment_Sample 2

description:
fpkm_genename.xls
N_2_M

value: LNP-CDN


title: LS-15931_S25_E1-50


title: RNA of MPE cells from mice with PD-L1 treatment_Sample 1

description:
fpkm_genename.xls
P_1_M


title: RNA of MPE cells from mice with PD-L1 treatment_Sample 3

description:
fpkm_genename.xls
P_3_M


title: RNA of MPE cells from mice with LNP-CDN treatment_Sample 1

description:
fpkm_genename.xls
N_1_M


title: LS-15931_S19_E1-50


title: LS-15931_S22_E1-50

value: Astro


title: RNA of MPE cells from mice with PD-L1 treatment_Sample 2

description:
fpkm_genename.xls
P_2_M


title: RNA of MPE cells from mice with PBS treatment_Sample 2

description:
fpkm_genename.xls
CTR_2_M

value: PBS


title: LS-15931_S20_E1-50


title: Cell_0175_E11.5_FACS-Endo_Gfi1_het

value: ICR


title: PTSD054-D1

value: PTSD and MDD


title: RNA of MPE cells from mice with PBS treatment_Sample 3

description:
fpkm_genename.xls
CTR_3_M

value: Pleural Fluid


title: PTSD057-D1

value: Control


title: PTSD054-D2


title: RNA of MPE cells from mice with PBS treatment_Sample 1

description:
fpkm_genename.xls
CTR_1_M


title: LS-15931_S18_E1-50

value: NeuN-pos


title: Cell_0178_E11.5_FACS-Endo_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: LS-15931_S27_E1-50

value: GABA


title: RNA of MPE cells from mice with LNP-CDN treatment_Sample 3

description:
fpkm_genename.xls
N_3_M


title: Cell_0173_E11.5_FACS-Endo_Gfi1_het


title: PTSD053-D1


title: PTSD053-D2


title: PTSD047-D2


title: Cell_0176_E11.5_FACS-Endo_Gfi1_het


title: Cell_0171_E11.5_FACS-Endo_Gfi1_het


title: LS-15931_S13_E1-50

value: KC


title: LS-15931_S17_E1-50


title: Cell_0168_FACS-ACE_SinglePos

data_processing:
Basecall files generated from NovaSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq. Alignment was performed by STAR 2.4.2a to ensemble reference genome (GRCm38 release 87) with default parameters. Read counts from BAM files were extracted using htseq (version 0.6.1p1) with the following setting --format=bam --stranded=no --type=exon --idattr=gene_id. Count table was loaded into the R environment (R version 3.6.2).
Genome_build: Mus musculus.GRCm38 release 87
Supplementary_files_format_and_content: count

value: Aorta gonad mesonephros

tag: cell type/fraction


title: PTSD047-D1


title: LS-15931_S12_E1-50

value: Non-Neuronal


title: Cell_0172_E11.5_FACS-Endo_Gfi1_het

tag: developmental stage


title: Cell_0169_FACS-ACE_SinglePos

tag: strain


title: Cell_0166_FACS-ACE_SinglePos

tag: genotype


title: Cell_0167_FACS-ACE_SinglePos


title: PTSD038-D1


title: LS-15931_S11_E1-50

tag: donor

value: Glut

value: MP


title: Cell_0169_E11.5_FACS-Endo_Gfi1_het


title: PTSD038-D2


title: LS-15931_S10_E1-50

tag: Sex

value: M

value: Oligo


title: PTSD029-D2

value: Peripheral blood mononuclear cells


title: PTSD029-D1


title: Cell_0174_E11.5_FACS-Endo_Gfi1_het


title: Cell_0162_FACS-ACE_SinglePos


title: Cell_0167_E11.5_FACS-Endo_Gfi1_het


title: Cell_0165_FACS-ACE_SinglePos


title: PTSD028-D1

value: MDD


title: LS-15931_S06_E1-50

tag: age

value: Astro


title: Cell_0164_E11.5_FACS-Endo_Gfi1_het

value: ICR


title: Cell_0160_FACS-HE_DoublePos


title: Cell_0159_FACS-ACE_SinglePos


title: Cell_0165_E11.5_FACS-Endo_Gfi1_het


title: Cell_0161_FACS-ACE_SinglePos


title: LS-15931_S03_E1-50

tag: facs gating


title: LS-15931_S01_E1-50

tag: sequencing batch


title: Cell_0161_E11.5_FACS-Endo_Gfi1_het


title: Cell_0163_FACS-ACE_SinglePos


title: Cell_0168_E11.5_FACS-Endo_Gfi1_het


title: Cell_0164_FACS-ACE_SinglePos


title: LS-15931_S04_E1-50

tag: cell class


title: PTSD024-D1


title: LS-15931_S09_E1-50

tag: cell cluster


title: Cell_0170_E11.5_FACS-Endo_Gfi1_het


title: PTSD026-D1

tag: tissue


title: PTSD021-D2

tag: phenotype


title: Cell_0160_E11.5_FACS-Endo_Gfi1_het


title: Cell_0157_FACS-ACE_SinglePos


title: LS-15930_S92_E1-50


title: LS-15930_S94_E1-50


title: PTSD024-D2

tag: subject


title: Cell_0166_E11.5_FACS-Endo_Gfi1_het


title: Cell_0159_E11.5_FACS-Endo_Gfi1_het


title: LS-15930_S89_E1-50


title: PTSD021-D1

tag: timepoint


title: PTSD026-D2


title: PTSD028-D2


title: LS-15930_S91_E1-50


title: LS-15930_S90_E1-50


title: Cell_0156_FACS-ACE_SinglePos


title: PTSD019-D1


title: Cell_0153_FACS-ACE_SinglePos


title: PTSD018-D2

value: PTSD and MDD


title: Cell_0162_E11.5_FACS-Endo_Gfi1_het


title: Cell_0158_FACS-ACE_SinglePos


title: PTSD018-D1


title: Cell_0154_FACS-ACE_SinglePos


title: Cell_0163_E11.5_FACS-Endo_Gfi1_het


title: PTSD019-D2


title: PTSD009-D2


title: LS-15930_S88_E1-50

value: NeuN-neg


title: Cell_0150_FACS-ACE_SinglePos


title: LS-15930_S87_E1-50


title: Cell_0158_E11.5_FACS-Endo_Gfi1_het


title: Cell_0149_FACS-ACE_SinglePos


title: Cell_0156_E11.5_FACS-Endo_Gfi1_het


title: Cell_0152_FACS-ACE_SinglePos


title: Cell_0148_FACS-ACE_SinglePos


title: LS-15930_S82_E1-50


title: Cell_0151_FACS-ACE_SinglePos


title: LS-15930_S83_E1-50


title: Cell_0157_E11.5_FACS-Endo_Gfi1_het


title: Cell_0154_E11.5_FACS-Endo_Gfi1_het


title: Cell_0155_FACS-ACE_SinglePos


title: Cell_0153_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S80_E1-50

value: PC


title: LS-15930_S84_E1-50

value: NeuN-pos


title: Cell_0151_E10.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: LS-15930_S86_E1-50


title: Cell_0155_E11.5_FACS-Endo_Gfi1_het


title: Cell_0152_E10.5_FACS-HE_Gfi1_het


title: PTSD008-D2

value: Control


title: Cell_0150_E10.5_FACS-HE_Gfi1_het


title: PTSD009-D1


title: LS-15930_S81_E1-50

value: KC


title: PTSD008-D1


title: LS-15930_S79_E1-50


title: Cell_0149_E10.5_FACS-HE_Gfi1_het


title: Cell_0146_FACS-ACE_SinglePos

value: Aorta gonad mesonephros


title: Cell_0147_FACS-ACE_SinglePos


title: 162_GS1493_C_DHF_pos_200

city: La Jolla

first: Alba

last: Grifoni

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: PBMCs

growth_protocol: PBMC were isolated from human blood samples from patients at the time of diagnosis/admission and at discharge from hispital or after recovery

extract_protocol:
Cells were lysed in 8 μL of lysis buffer composed by 0.2% Triton X-100, 2 U/ul of recombinant RNase inhibitor (Clontech/Takara), 5 mM dNTP mix (Life Technologies) in 0.2 ml PCR tube (Maxymum recovery, Axygen). RNA extraction, reverse transcription, cDNA amplification, fragmentation, additional PCR amplification, final library purification, and quality control were performed as described (methodology section).
Sequencing was performed according to a paired-end strategy using the HiSeq2500 sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.
Smart-seq2

treatment_protocol: Following isolation, to stimulate DNV specific CD8+ T cells, 268 DENV-specific CD8 epitopes that account for 90% of the IFNgamma response were synthesized (A&A, San Diego, CA), resuspended in DMSO, pooled, lyophilized, and resuspended at 1mg/ml

tag: disease group

value: DHF

tag: geographic location

value: Sri Lanka

tag: cell subset

tag: days from fever onset (if empty, it is ifn negative or less than 4 days)


title: 161_GS1493_A_DHF_pos_400


title: LS-15930_S78_E1-50

value: GABA


title: Cell_0145_FACS-ACE_SinglePos

tag: strain

tag: developmental stage

tag: cell type/fraction


title: Cell_0148_E10.5_FACS-HE_Gfi1_het

tag: genotype


title: 160_GS1493_C_DHF_neg_400


title: Cell_0144_FACS-ACE_SinglePos


title: 159_GS1493_A_DHF_neg_400


title: Cell_0146_E10.5_FACS-HE_Gfi1_het


title: Cell_0147_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S76_E1-50

tag: donor

tag: Sex

value: M

tag: age

value: Glut

value: MP


title: Cell_0143_FACS-ACE_SinglePos


title: 158_GS1793_C_DHF_pos_400


title: LS-15930_S75_E1-50

tag: facs gating

tag: sequencing batch

tag: cell class


title: Cell_0142_FACS-ACE_SinglePos

tag: tissue


title: Cell_0141_FACS-ACE_SinglePos


title: Cell_0144_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S74_E1-50

tag: cell cluster


title: 156_GS1468_C_DF_pos_259

value: DF


title: 157_GS1793_A_DHF_pos_116


title: Cell_0140_FACS-ACE_SinglePos


title: Cell_0143_E10.5_FACS-HE_Gfi1_het


title: Cell_0139_FACS-ACE_SinglePos


title: LS-15930_S77_E1-50


title: Cell_0142_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S72_E1-50


title: Cell_0138_FACS-ACE_SinglePos


title: 153_GS1793_A_DHF_neg_200


title: Cell_0141_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S71_E1-50


title: LS-15930_S68_E1-50


title: LS-15930_S73_E1-50


title: 151_GS1468_A_DF_neg_200


title: Cell_0137_FACS-ACE_SinglePos


title: Cell_0140_E10.5_FACS-HE_Gfi1_het


title: Cell_0145_E10.5_FACS-HE_Gfi1_het


title: 150_GS1613_C_DHF_pos_400


title: LS-15930_S66_E1-50


title: Cell_0136_FACS-ACE_SinglePos


title: Cell_0139_E10.5_FACS-HE_Gfi1_het


title: 152_GS1468_C_DF_neg_400


title: LS-15930_S65_E1-50


title: Cell_0138_E10.5_FACS-HE_Gfi1_het


title: Cell_0135_FACS-HE_DoublePos


title: 149_GS1613_A_DHF_pos_400


title: 148_GS0990_C_DF_pos_400


title: Cell_0134_FACS-ACE_SinglePos


title: LS-15930_S63_E1-50

value: MC

value: Non-Neuronal

value: Micro


title: Cell_0133_FACS-ACE_SinglePos

value: ICR


title: LS-15930_S61_E1-50


title: 147_GS0990_A_DF_pos_200


title: Cell_0132_FACS-ACE_SinglePos


title: Cell_0135_E10.5_FACS-HE_Gfi1_het


title: Cell_0134_E10.5_FACS-HE_Gfi1_het


title: 146_GS1613_C_DHF_neg_400


title: LS-15930_S58_E1-50

value: Oligo


title: LS-15930_S59_E1-50

value: NeuN-pos


title: Cell_0136_E10.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: 145_GS1613_A_DHF_neg_400


title: Cell_0130_FACS-ACE_SinglePos


title: Cell_0131_FACS-ACE_SinglePos


title: Cell_0129_FACS-ACE_SinglePos


title: 142_GS1585_C_DHF_pos_400


title: LS-15930_S55_E1-50


title: Cell_0132_E10.5_FACS-HE_Gfi1_het


title: Cell_0137_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S57_E1-50


title: LS-15930_S56_E1-50

value: NeuN-neg


title: Cell_0133_E10.5_FACS-HE_Gfi1_het


title: 143_GS0990_A_DF_neg_400


title: 141_GS1585_A_DHF_pos_400


title: LS-15930_S54_E1-50


title: 144_GS0990_C_DF_neg_400


title: Cell_0131_E10.5_FACS-HE_Gfi1_het


title: 140_GS1434_C_DF_pos_400


title: Cell_0128_FACS-ACE_SinglePos


title: Cell_0130_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S52_E1-50


title: Cell_0129_E10.5_FACS-HE_Gfi1_het


title: Cell_0128_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S47_E1-50

value: PC


title: Cell_0127_E10.5_FACS-HE_Gfi1_het


title: Cell_0124_FACS-ACE_SinglePos

value: Aorta gonad mesonephros


title: Cell_0125_FACS-ACE_SinglePos


title: Cell_0127_FACS-ACE_SinglePos


title: 138_GS1585_C_DHF_neg_400

value: DHF


title: Cell_0126_FACS-HE_DoublePos


title: LS-15930_S45_E1-50

value: Astro


title: Cell_0123_FACS-ACE_SinglePos


title: LS-15930_S46_E1-50

value: OPC


title: 137_GS1585_A_DHF_neg_400

value: Sri Lanka


title: Cell_0125_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S44_E1-50

value: M


title: Cell_0121_FACS-ACE_SinglePos


title: 136_GS1434_C_DF_neg_400


title: LS-15930_S41_E1-50

value: Glut

value: MP


title: Cell_0123_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S32_E1-50


title: Cell_0122_FACS-ACE_SinglePos


title: Cell_0124_E10.5_FACS-HE_Gfi1_het


title: 139_GS1434_A_DF_pos_400

value: DF


title: 133_GS1513_A_DHF_pos_200


title: 132_GS1243_C_DF_pos_200


title: LS-15930_S30_E1-50

value: Non-Neuronal


title: 135_GS1434_A_DF_neg_400


title: Cell_0121_E10.5_FACS-HE_Gfi1_het


title: Cell_0119_FACS-ACE_SinglePos


title: 131_GS1243_A_DF_pos_400


title: Cell_0117_FACS-ACE_SinglePos


title: 134_GS1513_C_DHF_pos_400


title: Cell_0116_FACS-ACE_SinglePos


title: LS-15930_S50_E1-50

value: MC


title: Cell_0118_FACS-ACE_SinglePos

value: ICR


title: Cell_0122_E10.5_FACS-HE_Gfi1_het


title: Cell_0120_FACS-ACE_SinglePos


title: Cell_0126_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S29_E1-50


title: Cell_0119_E10.5_FACS-HE_Gfi1_het


title: Cell_0115_FACS-ACE_SinglePos


title: LS-15930_S27_E1-50

value: GABA


title: Cell_0120_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S26_E1-50

value: NeuN-pos


title: Cell_0114_FACS-ACE_SinglePos


title: LS-15930_S25_E1-50


title: Cell_0117_E10.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: 127_GS1243_A_DF_neg_400


title: 128_GS1243_C_DF_neg_400


title: 129_GS1513_A_DHF_neg_200


title: 125_GS1294_A_DHF_neg_200


title: Cell_0112_FACS-ACE_SinglePos


title: 130_GS1513_C_DHF_neg_400


title: Cell_0113_FACS-ACE_SinglePos


title: LS-15930_S31_E1-50

value: Oligo


title: Cell_0116_E10.5_FACS-HE_Gfi1_het


title: Cell_0115_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S23_E1-50

value: PC


title: 123_GS1279_A_DF_neg_400


title: LS-15930_S22_E1-50


title: Cell_0114_E10.5_FACS-HE_Gfi1_het


title: Cell_0113_E10.5_FACS-HE_Gfi1_het


title: 122_GS1294_C_DHF_pos_400


title: Cell_0110_FACS-ACE_SinglePos

value: Aorta gonad mesonephros


title: 121_GS1294_A_DHF_pos_158

value: DHF


title: Cell_0111_FACS-ACE_SinglePos


title: LS-15930_S16_E1-50

value: KC

value: NeuN-neg


title: Cell_0112_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S12_E1-50


title: 119_GS1279_A_DF_pos_400

value: Sri Lanka


title: 120_GS1279_C_DF_pos_400


title: Cell_0111_E10.5_FACS-Endo_Gfi1_het


title: Cell_0108_FACS-ACE_SinglePos


title: Cell_0118_E10.5_FACS-HE_Gfi1_het


title: LS-15930_S11_E1-50

value: M


title: Cell_0107_FACS-ACE_SinglePos


title: Cell_0109_E10.5_FACS-Endo_Gfi1_het


title: Cell_0106_FACS-ACE_SinglePos


title: LS-15930_S10_E1-50


title: 117_GS1093_A_DHF_neg_400


title: 118_GS1093_C_DHF_neg_400


title: Cell_0105_FACS-ACE_SinglePos


title: LS-15930_S08_E1-50

value: Astro


title: LS-15930_S21_E1-50

value: Micro


title: 116_GS0986_C_DF_neg_400

value: DF


title: Cell_0108_E10.5_FACS-Endo_Gfi1_het


title: Cell_0109_FACS-ACE_SinglePos


title: LS-15930_S04_E1-50

value: Non-Neuronal

value: OPC


title: 115_GS0986_A_DF_neg_400


title: Cell_0103_FACS-ACE_SinglePos

value: ICR


title: Cell_0107_E10.5_FACS-Endo_Gfi1_het


title: Cell_0106_E10.5_FACS-Endo_Gfi1_het


title: Cell_0104_FACS-ACE_SinglePos


title: LS-15930_S06_E1-50

value: Glut

value: MP


title: Cell_0105_E10.5_FACS-Endo_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: LS-15930_S03_E1-50

value: NeuN-pos


title: 114_GS1093_C_DHF_pos_400


title: Cell_0102_FACS-ACE_SinglePos


title: LS-15930_S02_E1-50


title: Cell_0104_E10.5_FACS-Endo_Gfi1_het


title: Cell_0110_E10.5_FACS-Endo_Gfi1_het


title: Cell_0101_FACS-ACE_SinglePos


title: 113_GS1093_A_DHF_pos_400


title: 112_GS0986_C_DF_pos_400


title: LS-15930_S01_E1-50


title: LS-15909_S06_E1-50

value: PC


title: Cell_0099_FACS-ACE_SinglePos

value: Aorta gonad mesonephros


title: LS-15909_S14_E1-50


title: Cell_0098_FACS-ACE_SinglePos


title: 108_GS1030_C_DF_neg_400


title: LS-15909_S04_E1-50


title: Cell_0103_E10.5_FACS-Endo_Gfi1_het


title: Cell_0096_FACS-ACE_SinglePos


title: Cell_0099_E10.5_FACS-Endo_Gfi1_het


title: Cell_0097_FACS-ACE_SinglePos


title: Cell_0102_E10.5_FACS-Endo_Gfi1_het


title: Cell_0100_E10.5_FACS-Endo_Gfi1_het


title: 107_GS1030_A_DF_neg_400


title: LS-15909_S03_E1-50


title: LS-15909_S01_E1-50


title: Cell_0098_E10.5_FACS-Endo_Gfi1_het


title: Cell_0095_FACS-ACE_SinglePos


title: 109_GS1282_A_DHF_neg_400

value: DHF


title: 105_GS1282_A_DHF_pos_400


title: Cell_0097_E10.5_FACS-Endo_Gfi1_het


title: Cell_0100_FACS-ACE_SinglePos


title: LS-15908_S07_E1-50


title: 104_GS1030_C_DF_pos_400


title: 111_GS0986_A_DF_pos_400


title: Cell_0096_E10.5_FACS-Endo_Gfi1_het


title: Cell_0093_FACS-ACE_SinglePos


title: LS-15908_S06_E1-50


title: 106_GS1282_C_DHF_pos_219


title: Cell_0095_E10.5_FACS-Endo_Gfi1_het


title: 103_GS1030_A_DF_pos_400


title: Cell_0092_FACS-ACE_SinglePos


title: 102_GS0979_C_DHF_neg_400


title: Cell_0091_FACS-ACE_SinglePos


title: Cell_0093_E10.5_FACS-Endo_Gfi1_het


title: LS-15908_S04_E1-50

value: GABA


title: LS-15908_S02_E1-50


title: Cell_0088_FACS-ACE_SinglePos


title: 99_GS1598_A_DF_neg_400


title: 98_GS0979_C_DHF_pos_400


title: LS-15907_S06_E1-50


title: LS-15908_S03_E1-50


title: Cell_0101_E10.5_FACS-Endo_Gfi1_het


title: Cell_0090_FACS-ACE_SinglePos


title: 101_GS0979_A_DHF_neg_400


title: Cell_0091_E10.5_FACS-Endo_Gfi1_het


title: Cell_0094_E10.5_FACS-Endo_Gfi1_het


title: 95_GS1598_A_DF_pos_400


title: 97_GS0979_A_DHF_pos_400


title: Cell_0090_E10.5_FACS-Endo_Gfi1_het


title: LS-15907_S05_E1-50


title: Cell_0092_E10.5_FACS-Endo_Gfi1_het


title: Cell_0087_FACS-ACE_SinglePos


title: Cell_0086_FACS-ACE_SinglePos


title: Cell_0089_E10.5_FACS-Endo_Gfi1_het


title: 92_GS1616_C_DF_neg_400


title: Cell_0089_FACS-ACE_SinglePos


title: 91_GS1616_A_DF_neg_400


title: Cell_0085_FACS-ACE_SinglePos


title: 90_GS1616_C_DF_pos_400


title: Cell_0084_FACS-ACE_SinglePos


title: LS-15908_S08_E1-50

value: NeuN-neg


title: LS-15907_S04_E1-50


title: Cell_0087_E10.5_FACS-Endo_Gfi1_het


title: LS-15907_S01_E1-50


title: 87_GS1221_A_DHF_pos_400

value: Sri Lanka


title: Cell_0082_FACS-ACE_SinglePos


title: 86_GS1089_C_DF_pos_400


title: LS-15906_S07_E1-50

value: M


title: Cell_0086_E10.5_FACS-Endo_Gfi1_het


title: Cell_0081_FACS-ACE_SinglePos


title: Cell_0080_FACS-ACE_SinglePos


title: LS-15906_S03_E1-50


title: 85_GS1089_A_DF_pos_104


title: Cell_0083_E10.5_FACS-Endo_Gfi1_het


title: LS-15906_S01_E1-50


title: Cell_0079_FACS-ACE_SinglePos


title: Cell_0088_E10.5_FACS-Endo_Gfi1_het


title: rrhs_ts3

city: Lausanne

first: Franziska

last: Gruhl

address: University of Lausanne, Quartier Sorge

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

data_processing:
Read quality assessment and mapping: Basecalling was performed with the Illumina Casava software (v 1.9) and read quality assessed with FastQC (v 0.10.1). The ensembl annotations for opossum (monDom5), mouse (mm10), rat (rn5), rhesus macaque (rheMac2) and human (hg38) were used to build transcriptome indexes for mapping with TopHat2 (v 2.0.11). TopHat2 was run with default settings and the --mate-inner-dist and --mate-std-dev options set to 50 and 200 respectively. The mate-inner-distance parameter was estimated based on the fragment analyzer report.
CircRNA annotation: We developed a custom pipeline to detect circRNAs, which performs the following steps: Unmapped reads with a phred quality value of at least 25 are used to generate 20 bp anchor pairs from the terminal 3' and 5'-ends of the read. Anchors are remapped with bowtie2 (v 2.1.0) on the reference genome. Mapped anchor pairs are filtered for 1) being on the same chromosome, 2) being on the same strand and 3) for having a genomic mapping distance to each other of a maximum of 100 kb. Next, anchors are extended upstream and downstream of their mapping locus. They are kept if pairs are extendable to the full read length. During this procedure a maximum of two mismatches is allowed. Next, all unpaired reads are selected from the accepted_hits.bam file generated by TopHat2 (singletons) and assessed for whether the mate read (second read of a paired-end sequencing read) of the anchor pair mapped between the backsplice coordinates. All anchor pairs for which 1) the mate did not map between the genomic backsplice coordinates, 2) the mate mapped to another backsplice junction or 3) the extension procedure could not reveal a clear breakpoint are removed. Based on the remaining candidates, a backsplice index is built with bowtie2 and all reads are remapped on this index to increase the read coverage by detecting reads that cover the BSJ with less than 20 bp, but at least 8 bp. Candidate reads that were used to build the backsplice index and now mapped to another backsplice junction are removed. Upon this procedure, the pipeline provides a first list of backsplice junctions. The set of scripts, which performs the identification of putative BSJs, as well as a short description of how to run the pipeline are reposited on GitHub (https://github.com/Frenzchen/ncSplice_circRNAdetection).
CircRNA expression levels: CPM (counts per million) values for backsplice junctions were calculated for each tissue as follows: counts = mean(counts_rep1, counts_rep2, counts_rep3); totalMappedReads =mean(mappedReads_rep1, mappedReads_rep2, mappedReads_rep3); CPM= counts*10^6/totalMappedReads  To distinguish putative backsplice junctions from the technical and biological noise background, the enrichment of the previously defined junctions in RNase R treated samples was calculated. The enrichment was defined as CPM increase in RNase R treated versus untreated samples: enrichment = CPM_RNase R/CPM_untreated  Candidates with a log2-enrichment of smaller 1.5 were removed. Expression levels for all circRNAs can be found in the files mdCircRNA_cpms.txt (opossum), mmCircRNA_cpms.txt (mouse), rnCircRNA_cpms.txt (rat), rmCircRNA_cpms.txt (rhesus macaque) and hsCircRNA_cpms.txt (human).
CircRNA transcript reconstruction: To reconstruct the exon structure of circRNA transcripts in each tissue, we made use of the junction enrichment in RNase R treated samples. To normalize junction reads across libraries, the size factors ( size factor = median(x/geometric mean) ) based on the geometric mean ( geometric mean = product(x)^(1/length(x)) ) of common junctions in untreated and treated samples was calculat, with x being a vector containing the number of reads per junction. We then compared read coverage for junctions outside and inside the BSJ for each gene and used the log2-change of junctions outside the backsplice junction to construct the expected background distribution of change in junction coverage upon RNase R treatment. The observed coverage change of junctions inside the backsplice was then compared to the expected change in the background distribution and junctions with a log2-change outside the 90% confidence interval were assigned as circRNA junction. A loose cut-off was chosen here, because involved junctions can show a decrease in coverage if their linear isoform was present at high levels before (degradation levels of linear isoforms do not correlate with the enrichment levels of circRNAs). Next, we reconstructed a splicing graph for each circRNA candidate, in which network nodes are exons connected by splice junctions (edges). Connections between nodes are weighted by the coverage in the RNase R treated samples. The resulting network graph is directed (because of the known circRNA start and stop coordinates), acyclic (because splicing always proceeds in one direction), weighted and relatively small. We used a simple breadth-first-search algorithm to traverse the graph and to define the strength for each possible isoform by its mean coverage. For further analyses, only the strongest isoform was considered.  A gtf-file with the circRNA annotation for each species has been deposited (mdCircRNAs.gtf, mmCircRNA.gtf, rnCircRNAs.gtf, rmCircRNAs.gtf, hsCircRNAs.gtf).
Genome_build: opossum: monDom5 (ensembl release 75, feb 2014); mouse: mm10 (ensembl release 75, feb 2014); rat: rn5 (ensembl release 75, feb 2014); rhesus macaque: rheMac2 (ensembl release 77, oct 2014); human: hg38 (ensembl release 77, oct 2014)
Supplementary_files_format_and_content: tab-delimited text files include CPM values for all circRNAs.
Supplementary_files_format_and_content: gtf-files contain the circRNA annotation (genes, transcripts and exons) for each species.

source_name: Testis

extract_protocol:
Tissue was dissected at indicated ages (see section ”Samples” in GEO metadata). RNA for mouse, rat, rhesus and human was extracted using the RNeasy protocol from QIAGEN; for opossum, a TRIzol/chloroform-based protocol was used. Tissues were stored at -80 C until library preparation.
We used 5µg of RNA per tissue as starting material for library preparation, which were treated with RNase R for 1 h at 37 ̊C to degrade linear RNAs, followed by RNA purification with RNA Clean & Concentrator-5 kit (Zymo Research) according to the manufacturer’s protocol. Libraries were prepared from the purified RNA with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold according to the protocol with the following modifications to select larger fragments: 1). Instead of the recommended 8 min at 68 ̊C for fragmentation, we incubated samples for only 4 min at 68 ̊C to increase the fragment size; 2). In the final PCR clean-up after enrichment of the DNA fragments, we changed the 1:1 ratio of DNA to AMPure XP Beads to a 0.7:1 ratio to select for binding of larger fragments. Libraries were analyzed on the fragment analyzer for their quality and sequenced with the Illumina HiSeq 2500 platform.

value: Testis

value: wild type

value: 22 years

tag: treatment

value: RNase R-treated


title: LS-15906_S06_E1-50


title: Cell_0083_FACS-ACE_SinglePos


title: Cell_0094_FACS-ACE_SinglePos


title: 83_GS1221_A_DHF_neg_400

tag: disease group


title: rrhs_ts2

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: 41 years


title: Cell_0085_E10.5_FACS-Endo_Gfi1_het

value: ICR


title: Cell_0078_FACS-ACE_SinglePos


title: Cell_0081_E10.5_FACS-Endo_Gfi1_het


title: 82_GS1089_C_DF_neg_400

value: DF

tag: geographic location


title: Cell_0080_E10.5_FACS-Endo_Gfi1_het


title: rrhs_ts1

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: 21 years


title: 81_GS1089_A_DF_neg_200

tag: cell subset


title: cohs_ts3

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: untreated


title: 80_GS1080_C_DHF_pos_400

tag: days from fever onset (if empty, it is ifn negative or less than 4 days)


title: cohs_ts2

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt


title: Cell_0075_FACS-ACE_SinglePos

tag: strain


title: Cell_0076_FACS-ACE_SinglePos

tag: developmental stage


title: Cell_0078_E10.5_FACS-Endo_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0074_FACS-ACE_SinglePos

tag: cell type/fraction


title: Cell_0077_E10.5_FACS-Endo_Gfi1_het

tag: genotype


title: 78_GS1137_C_DF_pos_400


title: rrhs_ce3

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

source_name: Cerebellum

value: Cerebellum

value: 25 years


title: Cell_0076_E10.5_FACS-Endo_Gfi1_het


title: Cell_0073_FACS-ACE_SinglePos

value: Aorta gonad mesonephros


title: rrhs_ce2

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt


title: 77_GS1137_A_DF_pos_200


title: Cell_0075_E10.5_FACS-Endo_Gfi1_het


title: LS-15906_S04_E1-50

tag: donor

value: PC

value: NeuN-pos

value: Glut

value: MP


title: 76_GS1080_C_DHF_neg_400

value: DHF

value: Sri Lanka


title: Cell_0077_FACS-ACE_SinglePos


title: Cell_0071_FACS-ACE_SinglePos


title: rrhs_ce1

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: wild type

value: 29 years


title: Cell_0079_E10.5_FACS-Endo_Gfi1_het


title: Cell_0074_E10.5_FACS-Endo_Gfi1_het


title: 75_GS1080_A_DHF_neg_400


title: cohs_ce3

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt


title: Cell_0069_FACS-ACE_SinglePos


title: 79_GS1080_A_DHF_pos_400


title: 74_GS1137_C_DF_neg_400


title: Cell_0072_E10.5_FACS-Endo_Gfi1_het


title: Cell_0070_FACS-ACE_SinglePos


title: Cell_0073_E10.5_FACS-Endo_Gfi1_het


title: cohs_ts1

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: Testis


title: 73_GS1137_A_DF_neg_400


title: cohs_ce1

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt


title: Cell_0068_FACS-ACE_SinglePos

value: ICR


title: Cell_0072_FACS-ACE_SinglePos


title: Cell_0067_FACS-ACE_SinglePos


title: rrhs_lv3

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: Liver

value: 64 years

value: RNase R-treated


title: Cell_0070_E11.5_FACS-IAHC_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: 72_GS1031_C_DHF_pos_400


title: Cell_0071_E10.5_FACS-Endo_Gfi1_het


title: cohs_lv1

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: untreated


title: 70_GS1459_C_DF_pos_400

value: DF


title: 71_GS1031_A_DHF_pos_400


title: 69_GS1459_A_DF_pos_400


title: cohs_ce2

description:
hsCircRNAs.gtf
hsCircRNA_cpms.txt

value: Cerebellum

value: 41 years


title: Cell_0065_FACS-ACE_SinglePos

value: Aorta gonad mesonephros


title: Cell_0068_E11.5_FACS-IAHC_het


title: Cell_0069_E11.5_FACS-IAHC_het


title: HCT116 DKO1 Repli-Seq R2 G2

city: Darlinghurst

first: Qian

last: Du

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Repli-Seq reads were aligned to hg19 using bowtie v1.1.0 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
To avoid bias from duplications or repeats, read densities were calculated in 150 bp intervals and intervals were excluded from further analysis if they contained greater than 20 reads per 150 bp window. Read densities were calculated in 50 kb sliding windows at 1 kb intervals across the remaining genomic regions, excluding chrY and chrM. Read densities were normalised to reads/counts per million and 50kb windows with low coverage (5 reads/counts per million) were removed.
To account for variation in sequencing coverage, mapability and cell-type specific copy-number variations, the remaining 50 kb window reads/counts per million values in all 6 fractions of a given sample were converted to a percentage of total signal at each 1kb locus called Percent-normalised Density Values (PNDV).
PNDV values were then converted into a single replication timing weighted average score per 1kb loci using the following formula: Weighted Average = (0.917*G1)+(0.750*S1)+(0.583*S2)+(0.417*S3)+(0.250*S4)+(0*G2). The formula for this transformation was obtained from the ENCODE method for “Replication Timing by Repli-Seq”.
Replicate WA values per cell line were averaged and used for downstream analysis.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig

source_name: colorectal cancer cell line

growth_protocol: Cell lines were cultured in McCoy’s 5A modified medium (Gibco, #16600-082) supplemented with heat inactivated foetal bovine serum (10%, Gibco, 16000-044).

extract_protocol:
Cells were labeled with BrdU (50uM, Sigma, #B5002) for two hours. Labeled cells were sorted into 6 fractions across the cell cycle (G1b, S1, S2, S3, S4, G2M) on the FACSAria III based on DNA content labeling using propidium iodide. DNA extraction and BrdU-labeled DNA immunoprecipitation were performed with anti-BrdU antibody (40uL of 25ug/mL, BD Pharmingen, #555627). Validation of BrdU immunoprecipitation was carried out using qPCR on known Early (BMP1) and Late (DPPA2) loci (primers from Ryba et. al. (2011)).
10 ng of ssDNA was used as input for the Epicenter EpiGnome™ Methyl-Seq Kit (Illumina, EGMK81312, later called the TruSeq® DNA Methylation kit) and processed according to manufacturer’s instructions. The ssDNA was not bisulphite converted prior to library preparation. Libraries were sequenced on the HiSeq 2500 as 50bp single-end reads.
Repli-Seq

tag: cell line


title: 68_GS1031_C_DHF_neg_400


title: Cell_0063_FACS-ACE_SinglePos

source_name: Aorta gonad mesonephros


title: Cell_0067_E11.5_FACS-IAHC_het


title: Cell_0064_FACS-ACE_SinglePos


title: HCT116 DKO1 Repli-Seq R2 S4


title: HCT116 DKO1 Repli-Seq R2 S3


title: Cell_0062_FACS-ACE_SinglePos


title: 67_GS1031_A_DHF_neg_400


title: HCT116 DKO1 Repli-Seq R2 S2


title: Cell_0065_E11.5_FACS-IAHC_het


title: 66_GS1459_C_DF_neg_400


title: Cell_0063_E11.5_FACS-IAHC_het


title: 64_GS1301_C_DHF_pos_400


title: Cell_0066_FACS-ACE_SinglePos


title: HCT116 DKO1 Repli-Seq R2 G1


title: Cell_0060_FACS-ACE_SinglePos


title: 63_GS1301_A_DHF_pos_400


title: 60_GS1301_C_DHF_neg_400


title: HCT116 DKO1 Repli-Seq R2 S1


title: 59_GS1301_A_DHF_neg_400


title: Cell_0057_FACS-HE_DoublePos


title: Cell_0061_FACS-ACE_SinglePos


title: HCT116 DKO1 Repli-Seq R1 S3


title: 89_GS1616_A_DF_pos_400


title: Cell_0064_E11.5_FACS-IAHC_het


title: Cell_0059_FACS-ACE_SinglePos


title: HCT116 DKO1 Repli-Seq R1 G2


title: HCT116 DKO1 Repli-Seq R1 S4


title: Cell_0056_FACS-ACE_SinglePos


title: Cell_0062_E11.5_FACS-IAHC_het


title: 53_GS1511_A_DF_pos_400


title: Cell_0066_E11.5_FACS-IAHC_het


title: HCT116 DKO1 Repli-Seq R1 S2


title: Cell_0059_E11.5_FACS-IAHC_het


title: Cell_0058_FACS-ACE_SinglePos


title: Cell_0060_E11.5_FACS-IAHC_het


title: Cell_0058_E11.5_FACS-IAHC_het


title: Cell_0054_FACS-ACE_SinglePos


title: HCT116 DKO1 Repli-Seq R1 S1


title: 56_GS1298_C_DHF_pos_400


title: Cell_0061_E11.5_FACS-IAHC_het


title: Cell_0057_E11.5_FACS-IAHC_het


title: 52_GS1298_C_DHF_neg_400


title: HCT116 WT Repli-Seq R2 G2


title: 47_GS1207_A_DHF_neg_400


title: Cell_0055_FACS-ACE_SinglePos


title: Cell_0056_E11.5_FACS-IAHC_het


title: Cell_0052_FACS-ACE_SinglePos


title: Cell_0051_FACS-ACE_SinglePos


title: Cell_0054_E11.5_FACS-IAHC_het


title: HCT116 DKO1 Repli-Seq R1 G1


title: HCT116 WT Repli-Seq R2 S4


title: Cell_0053_FACS-ACE_SinglePos


title: Cell_0053_E11.5_FACS-IAHC_het


title: 46_GS1497_C_DF_neg_400


title: Cell_0055_E11.5_FACS-IAHC_het


title: Cell_0050_FACS-ACE_SinglePos


title: HCT116 WT Repli-Seq R2 G1


title: 45_GS1497_A_DF_neg_400


title: Cell_0051_E11.5_FACS-IAHC_het


title: HCT116 WT Repli-Seq R2 S2


title: 44_GS1207_C_DHF_pos_400


title: Cell_0048_FACS-HE_DoublePos


title: Cell_0052_E11.5_FACS-IAHC_het


title: HCT116 WT Repli-Seq R2 S1


title: HCT116 WT Repli-Seq R2 S3


title: 40_GS1105_C_DHF_neg_400


title: Cell_0047_FACS-HE_DoublePos


title: Cell_0049_E11.5_FACS-IAHC_het


title: 41_GS1497_A_DF_pos_200


title: HCT116 WT Repli-Seq R1 S3


title: 43_GS1207_A_DHF_pos_400


title: Cell_0048_E11.5_FACS-Endo_Gfi1_het


title: Cell_0084_E10.5_FACS-Endo_Gfi1_het


title: 39_GS1105_A_DHF_neg_400


title: Cell_0049_FACS-HE_DoublePos


title: HCT116 WT Repli-Seq R1 G2


title: 42_GS1497_C_DF_pos_400


title: Cell_0050_E11.5_FACS-IAHC_het


title: 36_GS1105_C_DHF_pos_200


title: HCT116 WT Repli-Seq R1 S2


title: 37_GS1126_A_DF_neg_400


title: Cell_0047_E11.5_FACS-Endo_Gfi1_het


title: 35_GS1105_A_DHF_pos_400


title: HCT116 WT Repli-Seq R1 S4


title: Cell_0082_E10.5_FACS-Endo_Gfi1_het


title: Cell_0045_FACS-HE_DoublePos


title: Cell_0046_FACS-HE_DoublePos


title: Cell_0042_FACS-HE_DoublePos


title: HCT116 WT Repli-Seq R1 S1


title: Cell_0044_E11.5_FACS-Endo_Gfi1_het


title: Cell_0043_FACS-HE_DoublePos


title: Cell_0044_FACS-HE_DoublePos


title: 33_GS1126_A_DF_pos_200


title: KLF5_R1-D567_ChIP-seq rep1

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

description:
D567KLF5-1
processed data file: D567_ETH_KLF5.bigwig
processed data file: D567KLF5merged.narrowPeak

data_processing:
Fastqs were mapped using bwa (v. 0.7.17) against the human (hg19) reference genome.
Mapped data were filtered to keep only reads with a mapq = 1. Bam files were filtered using bedtools (v. 2.27.1) to remove any ENCODE blacklisted regions (ENCFF001TDO.bed).
MACS2 (v. 2.1.1) was used for peak calling using paired treatment and control bam files.
We used the bedtools ‘intersect’ and ‘subtract’ functions to obtain final peak sets. For the peak sets derived from KLF5 ChIP-Seq, we reduced the number of peaks by finding the intersect across all replicates.
Data from treatment replicates were merged to create bam files and bigwigs for visualization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: narrowPeak

source_name: R1-D567 prostate cancer cells

growth_protocol: R1-AD1 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco) with 10% fetal bovine serum (FBS) and antibiotics (penicillin and streptomycin). R1-D567 were cultured in RPMI1640 medium with 10% charcoal stripped FBS (CSS).

extract_protocol:
Nuclear extracts were subjected to sonication on dry ice for eight cycles at 40% amplitude using a 450 Sonifer (Branson). Each cycle consisted of 10 s pulse / 10 s rests for 1 min, with 5 min rests between cycles to achieve DNA fragmentation of 200-500 bp. Lysates were pre-cleared by 1h incubation with Protein A/G Plus agarose beads (GE) pre-blocked with tRNA (Sigma). Lysates were immunoprecipitated overnight with 5 ug KLF5 antibody and tRNA-blocked Protein A/G Plus agarose beads. DNA was purified using a PCR purification kit (Qiagen).
Rubicon ChIP Sample Preparation Kit (Illumina).

treatment_protocol: R1-AD1 and R1-D567 cells were seeded at 5 x 10^6 cells/plate on 100 mm dishes in RPMI 1640 supplemented with 10% charcoal-stripped, steroid depleted FBS (CSS), allowed to adhere for 72 h, then re-fed for another 4 h with RPMI 1640 containing 5% CSS with ethanol (0.1% v/v) or 1 nM DHT prior to fixation.

tag: cell type

value: Prostate cancer

tag: hormone treatment

tag: passages

tag: chip antibody


title: Cell_0039_FACS-HE_DoublePos

tag: tissue


title: 30_GS1073_C_DF_neg_400


title: Cell_0042_E11.5_FACS-Endo_Gfi1_het


title: 31_GS1094_A_DHF_neg_400


title: Cell_0045_E11.5_FACS-Endo_Gfi1_het


title: Cell_0040_FACS-HE_DoublePos


title: Cell_0046_E11.5_FACS-Endo_Gfi1_het


title: Cell_0038_FACS-HE_DoublePos


title: KLF5_R1-D567_ChIP-seq rep2

description:
D567KLF5-2
processed data file: D567_ETH_KLF5.bigwig
processed data file: D567KLF5merged.narrowPeak


title: 32_GS1094_C_DHF_neg_400


title: input DNA_R1-D567 rep 2

description:
D567INPUT-2
Control file for normalization.


title: Cell_0037_FACS-HE_DoublePos


title: HCT116 WT Repli-Seq R1 G1


title: Cell_0041_E11.5_FACS-Endo_Gfi1_het


title: KLF5_R1-AD1_ETH_ChIP-seq rep2

description:
AD1KLF5ETH-2
processed data file: AD1_ETH_KLF5.bigwig
processed data file: AD1KLF5ETHmerged.narrowPeak

source_name: R1-AD1 prostate cancer cells

value: 0.1% ethanol (vehicle control), 24h


title: KLF5_R1-AD1_ETH_ChIP-seq rep1

description:
AD1KLF5ETH-1
processed data file: AD1_ETH_KLF5.bigwig
processed data file: AD1KLF5ETHmerged.narrowPeak


title: Cell_0041_FACS-HE_DoublePos


title: Cell_0036_FACS-HE_DoublePos


title: Cell_0040_E11.5_FACS-Endo_Gfi1_het


title: 27_GS1094_A_DHF_pos_400

value: DHF


title: KLF5_R1-AD1_DHT_ChIP-seq rep2

description:
AD1KLF5DHT-2
processed data file: AD1_DHT_KLF5.bigwig
processed data file: AD1KLF5DHTmerged.narrowPeak

value: 1 nM DHT, 24h


title: 28_GS1094_C_DHF_pos_200

value: Sri Lanka


title: Cell_0039_E11.5_FACS-Endo_Gfi1_het


title: Cell_0043_E11.5_FACS-Endo_Gfi1_het


title: Cell_0038_E11.5_FACS-Endo_Gfi1_het


title: KLF5_R1-AD1_DHT_ChIP-seq rep1

description:
AD1KLF5DHT-1
processed data file: AD1_DHT_KLF5.bigwig
processed data file: AD1KLF5DHTmerged.narrowPeak


title: input DNA_R1-D567 rep 1

description:
D567INPUT-1
Control file for normalization.


title: Cell_0033_FACS-HE_DoublePos


title: Cell_0034_FACS-HE_DoublePos


title: Cell_0037_E11.5_FACS-Endo_Gfi1_het


title: input DNA_R1-AD1 rep 2

description:
AD1INPUT-2
Control file for normalization.


title: Cell_0035_FACS-HE_DoublePos


title: 26_GS1073_C_DF_pos_400


title: 29_GS1073_A_DF_neg_200


title: 25_GS1073_A_DF_pos_196


title: Cell_0030_FACS-HE_DoublePos


title: 23_GS1283_A_DHF_neg_200


title: Cell_0032_FACS-HE_DoublePos


title: Cell_0036_E11.5_FACS-Endo_Gfi1_het


title: Cell_0034_E11.5_FACS-Endo_Gfi1_het


title: input DNA_R1-AD1 rep 1

description:
AD1INPUT-1
Control file for normalization.


title: 21_GS1134_A_DF_neg_200


title: Cell_0032_E11.5_FACS-HE_Gfi1_het


title: Cell_0033_E11.5_FACS-Endo_Gfi1_het


title: Cell_0035_E11.5_FACS-Endo_Gfi1_het


title: 22_GS1134_C_DF_neg_400


title: rrrm_ts2

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

organism: Macaca mulatta

value: wild type

tag: age

value: 9 years


title: rrrm_ts1

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

value: Testis

value: 8 years

tag: treatment


title: 24_GS1283_C_DHF_neg_200

tag: disease group


title: Cell_0031_FACS-HE_DoublePos

value: ICR


title: rrrm_ts3

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

value: RNase R-treated


title: corm_ts3

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: Cell_0031_E11.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0028_FACS-HE_DoublePos


title: 19_GS1283_A_DHF_pos_128

tag: geographic location


title: 20_GS1283_C_DHF_pos_200

tag: cell subset


title: Cell_0029_FACS-HE_DoublePos


title: Cell_0030_E11.5_FACS-HE_Gfi1_het


title: corm_ts1

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

value: untreated


title: Cell_0026_FACS-HE_DoublePos


title: Cell_0029_E11.5_FACS-HE_Gfi1_het


title: 16_GS0956_C_DHF_neg_200


title: 18_GS1134_C_DF_pos_400

value: DF

tag: days from fever onset (if empty, it is ifn negative or less than 4 days)


title: rrrm_ce3

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

value: Cerebellum


title: 15_GS0956_A_DHF_neg_400


title: Cell_0023_FACS-HE_DoublePos

tag: strain


title: Cell_0028_E11.5_FACS-HE_Gfi1_het

tag: developmental stage


title: Cell_0025_FACS-HE_DoublePos

tag: cell type/fraction


title: Cell_0026_E11.5_FACS-HE_Gfi1_het

tag: genotype


title: Cell_0024_FACS-HE_DoublePos


title: Cell_0022_FACS-HE_DoublePos


title: corm_ce3

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: 14_GS0629_C_DF_neg_400


title: rrrm_lv3

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

source_name: Liver

value: Liver


title: Cell_0027_FACS-HE_DoublePos

value: Aorta gonad mesonephros


title: rrrm_ce1

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: 13_GS0629_A_DF_neg_400


title: Cell_0025_E11.5_FACS-HE_Gfi1_het


title: corm_ce1

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: 12_GS0956_C_DHF_pos_200


title: corm_ts2

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: 11_GS0956_A_DHF_pos_400


title: rrrm_lv2

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: Cell_0024_E11.5_FACS-HE_Gfi1_het


title: Cell_0020_FACS-HE_DoublePos


title: Cell_0023_E11.5_FACS-HE_Gfi1_het


title: 9_GS0629_A_DF_pos_200


title: rrrm_lv1

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: Cell_0027_E11.5_FACS-HE_Gfi1_het


title: Cell_0022_E11.5_FACS-HE_Gfi1_het


title: Cell_0019_FACS-HE_DoublePos


title: 8_GS0851_C_DHF_neg_400


title: corm_lv3

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: Cell_0018_FACS-HE_DoublePos


title: Cell_0021_FACS-HE_DoublePos


title: corm_lv2

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt


title: 7_GS0851_A_DHF_neg_400


title: Cell_0021_E11.5_FACS-HE_Gfi1_het


title: Cell_0020_E11.5_FACS-HE_Gfi1_het


title: Cell_0017_FACS-HE_DoublePos


title: 6_GS0613_C_DF_neg_400


title: Cell_0018_E11.5_FACS-HE_Gfi1_het


title: Cell_0015_FACS-HE_DoublePos


title: 2_GS0613_C_DF_pos_400


title: HNRNPL.CHIPseq_input

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

description: HNRNPL.CHIPseq

data_processing:
Raw ChIP-seq reads were aligned using Bowtie v2.3.
MACS2 (version 2.2.4) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped among all replicates were obtained using bedtools.
hg19

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
10 million cells were crosslinked with 2mM DSG and 1% formaldehyde in the experiment. The ChIP experiment was done using the Lab ChIP-seq protocol, DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: HNRNPLi siRNA knockdown and induced to differentiation by 1.2mM calcium

value: undifferentiated keratinocytes


title: Cell_0019_E11.5_FACS-HE_Gfi1_het


title: HNRNPL.CHIPseq_rep3

description: HNRNPL.CHIPseq


title: Cell_0017_E11.5_FACS-HE_Gfi1_het


title: Cell_0016_FACS-HE_DoublePos


title: 5_GS0613_A_DF_neg_400


title: Cell_0014_FACS-ENDO

value: ENDO


title: Cell_0013_FACS-ENDO


title: HNRNPL.CHIPseq_rep2

description: HNRNPL.CHIPseq


title: 1_GS0613_A_DF_pos_400


title: Cell_0016_E11.5_FACS-HE_Gfi1_het


title: HNRNPLi.RNAseq.rep2

description: HNRNPLi.RNAseq

data_processing:
NOVASEQ pair-end reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 85 2018-05-02). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
hg19

growth_protocol: Primary keratinocytes were grown on culture dishes  in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with NEBNext Ultra II RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: HNRNPL siRNA knockdown and continued culturing in growth medium for four days

tag: timepoints

value: 4 days

value: undifferentiated keratinocytes transfected with HNRNPL siRNA


title: Cell_0015_E11.5_FACS-HE_Gfi1_het


title: HNRNPL.CHIPseq_rep1

description: HNRNPL.CHIPseq


title: Cell_0012_FACS-ENDO


title: HNRNPLi.RNAseq.rep1

description: HNRNPLi.RNAseq


title: P2CHIP_pooled_input

value: undifferentiated keratinocytes transfected with control and HNRNPL siRNA


title: corm_lv1

description:
rmCircRNAs.gtf
rmCircRNA_cpms.txt

value: wild type


title: Cell_0014_E11.5_FACS-HE_Gfi1_het


title: Cell_0011_FACS-ENDO


title: CTLi.RNAseq.rep2

description: HNRNPLi.RNAseq

value: undifferentiated keratinocytes transfected with control siRNA


title: HNRNPLi.P2CHIP_rep2


title: Cell_0013_E11.5_FACS-HE_Gfi1_het


title: CTLi.P2CHIP_rep2


title: CTLi.RNAseq.rep1

description: HNRNPLi.RNAseq


title: Cell_0008_FACS-ENDO


title: in vitro ligation-Rep1 indepth

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

description: Nanobody library generated by in vitro ligation strategy.

data_processing:
PE reads were assigned to samples based on barcodes.
Reads were filtered by QIIME quality filters.
Clean reads were merged by FLASH software.
Genome_build: NA
Supplementary_files_format_and_content: fasta files, containing nucleotide sequence of the nanobody library, were generated for each sample.

growth_protocol: HEK293T cells were maintained in DMEM (CORNING) supplemented with 10% FBS (CORNING) and 1% penicillin-streptomycin solution (CORNING) at 37℃ with 5% CO2.

extract_protocol:
Forty-eight hours after transfection, total RNAs were extracted by RNAiso Plus reagent (TaKaRa) and reverse transcripted into cDNAs by PrimeScriptTM RT reagent Kit with gDNA Eraser (TaKaRa). KOD DNA polymerase was used to amplify nanobody sequences.
PCR products were subjected to sequencing library construction by using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina).

treatment_protocol: HEK293T cells were plated into 6-well plates the day before transfection (~70% confluency). For LBAG-HR strategy, a total of 1000ng/well of ldsDNAs, containing upstream and downstream ldsDNAs, were cotransfected into HEK293T cells by Lipofectamine 2000 (Thermo Fisher). To guarantee equal molar of upstream and downstream ldsDNAs were cotransfected, the amount ratio between the two ldsDNAs was determine by the length of ldsDNAs. For in vitro ligation strategy, 1000ng/well ligation DNA was directly transfected into 6-well plated HEK293T cells.

tag: cell line

tag: strategy

value: in vitro ligation

tag: barcode 1

value: CTTGTA

tag: barcode 2

value: CCAACA


title: Cell_0007_FACS-ENDO

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)

value: ICR


title: HNRNPLi.P2CHIP_rep1


title: in vitro ligation-Rep3

value: GGCTAC

value: CTCAGA


title: Cell_0010_E11.5_FACS-HE_Gfi1_het

data_processing:
Basecall files generated from NextSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq. Alignment was performed by STAR 2.4.2a to ensemble reference genome (GRCm38 release 87) with default parameters. Read counts from BAM files were extracted using htseq (version 0.6.1p1) with the following setting --format=bam --stranded=no --type=exon --idattr=gene_id. Count table was loaded into the R environment (R version 3.6.2).
Genome_build: Mus musculus.GRCm38 release 87

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0012_E11.5_FACS-HE_Gfi1_het


title: Cell_0011_E11.5_FACS-HE_Gfi1_het


title: Cell_0009_FACS-ENDO


title: CTLi.P2CHIP_rep1


title: in vitro ligation-Rep2

value: CTATAC


title: Cell_0006_FACS-ENDO


title: Nuc-seq

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
The 10x Genomics 3' v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger (v5.0.1) pipeline.
Genome_build: GRCz10.88
Supplementary_files_format_and_content: For 10x Genomics 3' GEX v3 data: output of CellRanger pipeline including gene expression matrix, features and barcodes.

organism: Danio rerio

source_name: Zebrafish melanomas (BRAF-V600E)

extract_protocol:
Adult tumor-bearing fish were dissected to obtain only the tumor and surrounding tissues (i.e head and tail were removed). The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer (Sigma-Aldrich #NUC101). The nuclear suspension was then spun down at 4°C (500g, 5 min). After resuspending the pellet in 1 mL wash buffer (250 mM sucrose, 50 mM citric acid, 1% BSA, 20 mM DTT, 0.2U/µL RNAse inhibitor), the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei, using a BD FACSAria III cell sorter (BD Biosciences). Approximately equal numbers of GFP+ (tumor) and GFP- (microenvironment) nuclei were collected.
Equal numbers of sorted GFP+ (tumor) and GFP- (microenvironment) nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet-based snRNA-seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) and Chromium Single Cell 3’ Chip G (10X Genomics). Approximately 12,000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.

tag: sample type

value: Single nucleus suspension


title: M5_3

city: Xi'an

first: Hai

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart_seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases.
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Genome_build: Anas_platyrhynchos.BGI_duck_1.0.90
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/anas_platyrhynchos/dna/Anas_platyrhynchos.BGI_duck_1.0.dna.toplevel.fa.gz
Genome_build: ftp://ftp.ensembl.org/pub/release-90/gtf/anas_platyrhynchos/Anas_platyrhynchos.BGI_duck_1.0.90.gtf.gz
Supplementary_files_format_and_content: The BAM (Binary Alignment/Map) file format is a generic and highly compressed format for storing alignments.txt file could use as BAMs in Cuffquant to quantifies gene and transcript expression levels. ]

organism: Anas platyrhynchos

source_name: HDC

growth_protocol: Seperated cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L_glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols

treatment_protocol: Peripheral blood samples from 45-week-old male specific pathogen-free (SPF) ducks and removed erythrocytes from blood samples using erythrocyte lysis solution. Then, cells were first separated by density gradient centrifugation using a duck lymphocyte isolation kit.The peripheral blood mononuclear cells (PBMCs), which were located in the middle layer, were further separated by differential adhesion in culture dishes preloaded with sterilized glass coverslips according to the different adherent properties of PBMCs.

tag: Sex

value: male

tag: cell type

value: Duck peripheral white blood cells

tag: subgroup

value: HDC


title: Cell_0010_FACS-ENDO

city: manchester

first: Muhammmad

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

tag: tissue

value: Aorta gonad mesonephros

value: ENDO


title: LBAG-HR-Rep1 indepth

description: Nanobody library generated by ldsDNA-based AND-gate, homologous recombination (LBAG-HR) strategy.

value: LBAG-HR


title: Cell_0005_FACS-ENDO


title: Cell_0006_E11.5_FACS-HE_Gfi1_het


title: Cell_0007_E11.5_FACS-HE_Gfi1_het


title: LBAG-HR-Rep3

value: CTAGCT


title: Cell_0004_FACS-ENDO


title: Cell_0003_FACS-ENDO


title: M5_1

tag: age


title: M2_3

source_name: SPP

value: SPP


title: Cell_0002_FACS-ENDO


title: Cell_0009_E11.5_FACS-HE_Gfi1_het


title: in vitro ligation-Rep1

value: in vitro ligation


title: Cell_0004_E11.5_FACS-HE_Gfi1_het


title: LBAG-HR-Rep1


title: M2_2


title: M2_1


title: M1_3

source_name: ADC

value: ADC


title: Cell_0001_FACS-ENDO


title: Cell_0008_E11.5_FACS-HE_Gfi1_het


title: HCT116 DKO1 scRepli-Seq S

data_processing:
Data was mapped and processed using the 10X Genomics Cell Ranger DNA (v1.1.0) software with default parameters. Bam files generated by Cell Ranger DNA was split into individual cells/barcodes using SAMtools (Li et al. 2009) (v1.10) and filtered to remove duplicates and MAPQ < 10 reads with SAMtools, and reads overlapping hg19 blacklist (DAC) regions with BEDtools (Quinlan et al. 2010) (v2.26.0). Cells/barcodes with less than 1M reads were discarded.
Single S-phase cell reads were counted in non-overlapping 80kb bins using the 'binReads' command from scCNV R package AneuFinder (Bakker et al. 2016) (v1.14.0). 80kb binned counts were normalised against the merged G1 cell control using the 'correctMappability' command from AneuFinder (v1.5.0). Mappability-corrected 80kb bin data was binarised using the 'findCNVs' command in AneuFinder (v.1.14.0) using the following parameters: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state=("1-somy" or "2-somy"). In each HMM model, state '1' indicates un-replciated, state '2' indicates replicated and state '0' indicates no data. We generated two HMM models per cell, specifying either "1-somy" or "2-somy" as the most frequent state. For most cells, there was little difference between the two HMM models. We determined that a cell had ‘evenHMM’ if the absolute differences in bin numbers between 1-somy state ‘1’ and 2-somy state ‘1’ is less than 1,500 bins, and the same for state ‘2’. A cell was ‘unevenHMM’ if the absolute differences were greater than 1,500 bins for both states. ‘unevenHMM’ cells were then assigned as Early or Late through visual comparison of the HMM bed file against the earliest and latest ‘evenHMM’ cells. For final HMM calls, we used the 2-somy calls for ‘evenHMM’ cells, the 1-somy calls for ‘unevenHMM’ cells that were assigned as Early and the 2-somy calls for ‘unevenHMM’ cells that were assigned as Late.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Table of binarised HMM calls in 80kb bins across the genome (rows) for HCT116 and DKO1 S-phase cells (columns).

extract_protocol:
Cells were stained with live cell double stranded DNA dye, Vybrant DyeCycle Violet Ready Flow (Invitrogen, #R37172) and sorted on the FACS Aria III into 4 fractions: G1, Early, Mid and Late.
Single Cell Repli-Seq libraries were constructed using the Chromium 10X Single Cell CNV Solution according to manufacturer's instructions. Equal numbers of Early, Mid and Late cells were pooled prior to use in the Single Cell CNV system to meet the minimum recommended cell recovery number (250 cells). For S-phase cells, we used a ~500 cells/uL stock concentration. For G1 cells, we used a 60 cells/uL stock concentration. Libraries were sequenced on an Illumina NovaSeq 6000 S4 flowcell (200 cycles).


title: HCT116 DKO1 scRepli-Seq G1


title: LNP-cGAMP+PD-L1: MPE cells from mice with LNP-cGAMP+PD-L1 treatment

data_processing:
Quality Control, Barcod processing, alignment, feature counting and sample aggratation by CellRanger Single Cell Software Suite (v.3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene-by-cell matrix of gene expression, including barcodes, and feature genes

source_name: MPE live cells

extract_protocol:
The mice were sacrificed on day 13 and pleural fluid was gently aspirated using a 1-ml syringe through the diaphragm, and its volume was measured with a 1 mL pipette. The pleural fluids were centrifuged at 500 g for 10 min and cell pellet was further treated with 2 mL ACK Lysing Buffer (Thermo Fisher) to delete red blood cells for 10 min at 4 °C in 15-mL conical centrifuge tube. 10 mL cold PBS was added to stop the lysis, and the cells were centrifuged at 500 g for 5 min. The cell pellets were then re-pooled with same ratio from three mice.
Droplets and libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 according to manufacturer's protocol (10X genomics). Generated libraries were sequenced on Illumina NOVASEQ 6000

value: Pleural Fluid

value: Malignant pleural effusion (MPE)


title: M1_2


title: Cell_0001_E11.5_FACS-HE_Gfi1_het

value: ICR


title: M1_1


title: LBAG-HR-Rep2

value: GGCTAC

value: CGGAAT


title: HCT116 WT scRepli-Seq S


title: Cell_0003_E11.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: genomic DNA from peripheral blood SARS-COV-2- 196

status: Public on Sep 20 2021

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

description:
SARS-COV-2- peripheral blood sample
204658390048_R07C01

hyb_protocol: The bisulfite converted amplified DNA products were denatured into single strands and hybridized to the customized Infinium 850K BeadChip (EPIC+; Illumina Inc., San Diego, CA) via allele-specific annealing to either the methylation specific probe or the non-methylation probe. Hybridization to the chip was followed by single base extension with labeled di-deoxynucleotides according to Illumina’s Infinium protocol

scan_protocol: The hybridized BeadChips were stained, washed, and scanned to show the intensities of the un-methylated and methylated bead types using Illumina’s iScan System.

data_processing:
IDAT files were processed, filtered, and normalized using the SeSAMe R package65. Type I probe channel was empirically determined from signal intensities. Probe detection p-values (representing the ability to differentiate true signal from background fluorescence) were calculated for each color channel using pOOBAH, which leverages the fluorescence of out-of-band (OOB) probes. Normalization was performed using noob, which uses OOB probes to perform a normal-exponential deconvolution of fluorescent intensities. Finally, a common dye bias that results in greater intensities in the Red color channel was corrected to ensure that the distribution of intensities in the two color channels were equal. Probes with detection p-values > 0.05 were removed, as well as probes overlapping SNPs with global MAF >1% in dbSNP, probes with poor mapping, and probes containing non-unique sequence according to Wanding Zhou et al Nucleic Acids Research 2018.
seSAMe-normalized (Type I probe channels inferred from data, pOOBAH for detection p-value calculations, noob normalization, Type I probe dye bias linear correction) Average Beta

source_name: SARS-COV-2- 196

label_protocol: Bisulfite converted DNA was labelled with Cy3 and Cy5 dyes per manufacturer's instructions

extract_protocol: Genomic DNA was extracted from COVID-19+ peripheral blood on the bead-based, automated extraction Maxwell(R) RSC System (Promega) in a biological safety cabinet in compliance with CDC safety guidelines and procedures for handling COVID-19 biospecimens (biospecimens from COVID-19+  cases), and from controls on the Autogen FlexSTAR+ using Autogen’s FlexiGene Blood extraction kit (Holliston, MA).

value: negative

value: Female

tag: race

value: White

tag: ethnicity

value: Not Hispanic or Latino

value: No Panel

tag: hemoglobin

tag: hematocrit

value: No

value: Floor Admission

value: Home

tag: severity score


title: CTR: MPE cells from mice with PBS treatment

tag: strain


title: genomic DNA from peripheral blood SARS-COV-2+ 94

description:
SARS-COV-2+ peripheral blood sample
204658390048_R06C01

source_name: SARS-COV-2+ 94

value: positive

value: Male

value: BlackorAA

value: Nursing home or skilled rehab


title: genomic DNA from peripheral blood SARS-COV-2- 101

description:
SARS-COV-2- peripheral blood sample
204658390048_R08C01

source_name: SARS-COV-2- 101

value: Other

value: Hispanic or Latino


title: genomic DNA from peripheral blood OtherInfection 60

description:
OtherInfection+ peripheral blood sample
204658390048_R05C01

value: other infection

value: Yes

value: ICU


title: LNP-cGAMP: MPE cells from mice with LNP-cGAMP treatment

value: Pleural Fluid

value: Malignant pleural effusion (MPE)


title: genomic DNA from peripheral blood OtherInfection 45

description:
OtherInfection+ peripheral blood sample
204658390048_R01C01

value: White


title: Cell_0005_E11.5_FACS-HE_Gfi1_het

last: Fadlullah Wilmot

tag: developmental stage

value: ICR

tag: genotype

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: PD-L1: MPE cells from mice with PD-L1 treatment


title: Cell_0002_E11.5_FACS-HE_Gfi1_het


title: genomic DNA from peripheral blood OtherInfection 36

description:
OtherInfection+ peripheral blood sample
204658390048_R03C01

value: Not Hispanic or Latino

value: No


title: genomic DNA from peripheral blood SARS-COV-2- 225

description:
SARS-COV-2- peripheral blood sample
204658390044_R04C01

source_name: SARS-COV-2- 225

value: negative

value: Asian


title: genomic DNA from peripheral blood OtherInfection 7

description:
OtherInfection+ peripheral blood sample
204658390044_R03C01

value: Female

value: Death


title: genomic DNA from peripheral blood SARS-COV-2- 192

description:
SARS-COV-2- peripheral blood sample
204658390044_R05C01

source_name: SARS-COV-2- 192

value: No Panel

value: Home


title: genomic DNA from peripheral blood SARS-COV-2- 214

description:
SARS-COV-2- peripheral blood sample
204658390044_R01C01

source_name: SARS-COV-2- 214

value: Male

value: Other

value: Hispanic or Latino

value: Nursing home or skilled rehab


title: genomic DNA from peripheral blood OtherInfection 19

description:
OtherInfection+ peripheral blood sample
204658390044_R02C01

value: other infection

value: Floor Admission


title: HCT116 WT scRepli-Seq G1

source_name: colorectal cancer cell line

tag: cell line


title: M5_2

value: male

value: Duck peripheral white blood cells

value: HDC


title: genomic DNA from peripheral blood SARS-COV-2- 112

description:
SARS-COV-2- peripheral blood sample
204658390043_R07C01

source_name: SARS-COV-2- 112

value: BlackorAA

value: Not Hispanic or Latino

value: Yes

value: ICU


title: genomic DNA from peripheral blood SARS-COV-2- 272

description:
SARS-COV-2- peripheral blood sample
204658390043_R04C01

source_name: SARS-COV-2- 272

value: negative

value: White


title: genomic DNA from peripheral blood OtherInfection 25

description:
OtherInfection+ peripheral blood sample
204658390043_R08C01

value: No