title: Artificial CSF sample 8

description:
raw.counts.mean.samples.csv
aCSF_R8

value: Control

value: Artificial CSF

tag: tissue

tag: cell compartment


title: Young CSF sample 6

status: Public on May 11 2022

type: SRA

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

description:
raw.counts.mean.samples.csv
YM-CSF_R6

library_source: transcriptomic

data_processing:
Each experimental setup was processed as described below:
1. Raw sequencing files were demultiplexed with bcl2fastq, reads were aligned using STAR, and counts of technical replicates were summed up using DESeq2 before performing normalization and differential expression analysis with standard settings.
2. Sequencing quality control was performed using FastQC v0.11.8 and summary reports were generated with MultiQC v1.7. FASTQ files were then analyzed using the SLAM-DUNK pipeline v0.3.4 and the related alleyoop toolchain. The pipeline comprises 1) read mapping, 2) alignment filtering, 3) SNP calling and correction, and 4) 3'-UTR sequence counting. Using NextGenMap reads were aligned against the genome of Rattus norvegicus (release 6.0), which was downloaded in FASTA format from Ensembl release v97. For mapping the following parameters were set; '-5 12, -a 4, -n 1, -ss' leaving rest at default. Resulting Binary sequence Alignment/Map (BAM) format files were filtered to remove low-quality alignments using the parameters '-mq 2, -mi 0.95, -nm -1’ and rest at default. Next, SNPs in alignments, in particular the T to C (T>C) conversions, were called with parameters '-c 10, -f 0.8' and others remaining at default. Statistical independence of distributions of true SNP-callings identified by VarScan2 in relation to the number of T>C reads was assessed with a Mann-Whitney-U test for each sample as initially described in the alleyoop snpeval toolchain module. For the reference set of 3'-UTRs, a genome feature file (GFF3) for the Rattus norvegicus genome (release 6.0) was downloaded from Ensembl release v97, filtered to retain only three_prime_utr features and converted to Browser Extensible Data (BED) format using bedops v2.4.36. The BED file was used in combination with parameters '-c 1, -q 27' for the SLAMDUNK count command, leaving other parameters at default. Resulting 3'-UTR T>C and total read counts were added up on gene-level along all transcripts and alternative 3'-UTRs available per transcript. Entire down-stream analysis was performed using R v3.6.1, data.table v1.12.2, and common tidyverse packages (tidyr, dplyr, purrr, stringr, ggplot2). Differential gene expression analysis was carried out using DESeq2 v1.26.0 on the T>C count and total count matrices separately with standard settings with alpha level set to 0.05. In total, six DESeq2 experiments were performed, two with pooled timepoints (1hr + 6hr) per read-type (design variables Treatment and Time) and four with separate timepoint per read-type (design variable Treatment only). Effect size was calculated using the implementation of cohen’s d from the effsize v0.7.6 package. Gene set enrichment and over-representation analyses were performed using GeneTrail 3.0 65. Category source databases were adjusted independently, and P-values were corrected using the false discovery rate controlling procedure by Benjamini-Hochberg and considered significant if smaller than 0.05.
3. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
4. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
5. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
Genome_build: GRCm38, Rnor_6.0.97
Supplementary_files_format_and_content: For each sample raw gene counts are provided. For SLAM-seq samples also the raw T-to-C counts are provided.

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Frozen dissected hippocampi were thawed on ice and homogenized in 350ml RLT buffer by 20 strokes using a manual homogenizer and total RNA was isolated with the RNeasy Plus Micro kit (Qiagen, 74034). RNA quantity and quality were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies). All samples passed a quality-control threshold (RIN ≥ 9) to proceed to library preparation and RNA-seq on .
Done by Novogene: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
Done by Novogene: Hiseq 4000 (Illumina) using paired-end 100-bp reads. Libraries were sequenced to a depth of >20 million reads per sample

tag: experiment batch

tag: experiment type

value: RNA-seq

tag: age

value: Aged

tag: Sex

value: Male

tag: experimental group

value: Treatment

tag: timepoint

tag: specimen

value: Young mouse CSF

value: Hippocampus

tag: cell type

value: Whole cell


title: Young CSF sample 5

description:
raw.counts.mean.samples.csv
YM-CSF_R5


title: GSK2879552 + ruxolitinib replicate 2

city: Portland

first: Sarah

middle: Ann

last: Carratt

state: Oregon

address: 3181 S.W. Sam Jackson Park Road, Mail Code KR-HEM

country: USA

institute: OHSU

description: RNAseq

data_processing:
Sequencing from Bulk RNA seq was aligned using STAR
Differential Expression was determined using Deseq2
Genome_build: hg38 or mm10

molecule: total RNA

source_name: CSF3RT618I+SETBP1D868N cell line

extract_protocol: Libraries were prepared by BGI

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

tag: treatment

value: 100 nM GSK2879552 + 100 nM ruxolitinib

tag: time point

value: 24 hours

tag: antibody


title: Artificial CSF sample 6

description:
raw.counts.mean.samples.csv
aCSF_R6


title: lung single cell 189

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
lung single cell 189
898s_H6

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

source_name: Lung

extract_protocol:
A 12 week-old female Prox1-GFP mouse was perfused with PBS to clear the blood. Subsequently, the lung was filled with 10 mg mL-1 dispase II in PBS via the trachea and incubated for 10 min at RT. Next, 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I was injected into the lung lobes and lung tissue was minced with scissors in 1.5 mL of 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I. Tissue dissociation was performed for 15 min at 37°C and 750 rpm. Digests were quenched by the addition of 2 mM EDTA f.c., filtered through a 40 µm nylon filter, washed with FACS buffer (PBS, 0.5% FBS, and 2 mM EDTA) for 5 min at 300 g, RT and processed for FACS sorting. Briefly,  Fc-receptor binding was blocked with rat anti-mouse CD16/CD32 for 10 min on ice. Thereafter, samples were incubated with fluorophore-conjugated anti-CD31 (clone 390, 1.0 µg mL-1), anti-CD45 (clone 30-F11, 4 µg mL-1), anti-CD11b (clone M1/70, 4 µg mL-1) and anti-TER-119 (clone TER-119, 4 µg mL-1) antibodies for 20 min on ice. Prior to sorting of CD31+ Prox1-GFP+ CD45- CD11b- Ter119- lymphatic and CD31+ Prox1-GFP- CD45- CD11b- Ter119- blood endothelial cells on a BD FACS Aria III samples were again filtered through a 40 µm filter and supplemented with 1 µM SytoxBlue to label dead cells.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

value: lung

value: adult mice

tag: genotype


title: GSK2879552 replicate 3

description: RNAseq


title: Artificial CSF sample 5

description:
raw.counts.mean.samples.csv
aCSF_R5


title: GSK2879552 replicate 2

description: RNAseq


title: Young CSF sample 4

description:
raw.counts.mean.samples.csv
YM-CSF_R4


title: GSK2879552 replicate 1

description: RNAseq


title: GSK2879552 + ruxolitinib replicate 1

description: RNAseq


title: GSK2879552 replicate 4

description: RNAseq


title: lung single cell 190

description:
lung single cell 190
898s_H7


title: DMSO replicate 4

description: RNAseq

value: DMSO


title: Artificial CSF sample 1

description:
raw.counts.mean.samples.csv
aCSF_R1


title: Artificial CSF sample 7

description:
raw.counts.mean.samples.csv
aCSF_R7


title: Young CSF sample 1

description:
raw.counts.mean.samples.csv
YM-CSF_R1


title: lung single cell 186

description:
lung single cell 186
898s_H3


title: WT_aCD40-IL4_Sµ_1

city: Toulouse

first: Chloé

last: Oudinet

address: 205 route de Narbonne

department: Oncology

country: France

institute: IPBS

library_source: genomic

data_processing:
Library strategy: CSR-HTGTS-Seq
Standard basecalling formats for Nextseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_AJ851868ins reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9_AJ851868ins
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

molecule: genomic DNA

source_name: Splenic mature B cells

extract_protocol:
DNA was extracted overnight at 56 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using CSR-HTGTS-Seq (Dong et al., 2015)

treatment_protocol: Primary splenic B cells were cultured in RPMI medium and stimulated with anti-CD40+IL4 or anti-CD40+TGFb for 96 hrs.

value: WT

tag: activation

tag: treatment protocol

value: cytokine stimulation

tag: target locus

tag: growth conditions

value: RPMI1640; 15percent FBS


title: WT_aCD40-IL4_Sµ_2


title: lung single cell 188

description:
lung single cell 188
898s_H5

tag: tissue


title: Artificial CSF sample 4

description:
raw.counts.mean.samples.csv
aCSF_R4

tag: experiment batch

tag: experiment type

value: Control

value: Artificial CSF

tag: cell compartment


title: lung single cell 187

description:
lung single cell 187
898s_H4

tag: age


title: RNA-seq_E11.5_XX_ECKO_Rep_2

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2.  CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.

source_name: Primordial germ cells

growth_protocol: Control and ECKO male and female embryos were obtained from crosses between OG; Eedfl/fl (Lengner et al., 2007; Yu et al., 2009) homozygous females and BC; Eedf/l+ heterozygous males (Ohinata et al., 2005) at E10.5, E11.5 and E13.5. Embryos were staged by the detection of a vaginal plug on the morning after time-mating pairs were established E0.5.

extract_protocol:
Male and female E11.5 and male E13.5 gonads were extracted and digested in 0.05% trypsin. GFP positive mPGCs were sorted into 300 µL RLT buffer and RNA extracted using the Rneasy Micro Kit (Qiagen)
Following cleanup, the samples were converted to cDNA following the Ovation RNA-seq System V2 protocol (Nugen). cDNA was indexed using the Ovation Rapid DR Multiplex System (Nugen).

value: Primordial germ cells

tag: developmental stage

value: Eed -/-

tag: gender

value: Female


title: RNA-seq_E11.5_XX_Control_Rep_2

tag: cell type

value: wild type


title: RNA-seq_E11.5_XX_ECKO_Rep_1


title: Young CSF sample 2

description:
raw.counts.mean.samples.csv
YM-CSF_R2

value: RNA-seq

value: Aged

tag: Sex

value: Male

tag: experimental group

value: Treatment

tag: timepoint

tag: specimen

value: Young mouse CSF

value: Hippocampus


title: lung single cell 183

description:
lung single cell 183
898s_H23

tag: strain

value: lung

value: adult mice

tag: genotype


title: 48DOXpos replicate 3

description: RNAseq

source_name: CSF3RT618I+SETBP1D868N-dox cell line

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

tag: treatment

value: doxycycline present, SETBP1 expressed

tag: time point

value: 48 hours

tag: antibody


title: RNA-seq_E11.5_XX_Control_Rep_1


title: Artificial CSF sample 2

description:
raw.counts.mean.samples.csv
aCSF_R2

value: Control

tag: tissue

value: Whole cell


title: lung single cell 182

description:
lung single cell 182
898s_H22


title: RNA-seq_E11.5_XX_ECKO_Rep_4

value: Primordial germ cells


title: DMSO replicate 3

description: RNAseq

value: DMSO

value: 24 hours


title: Exercise

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

source_name: pancreas

growth_protocol: Female Wildtype C57BJ 9 week old Mice were orthotopically injected with 1x10^5 FC1242 KPC (KrasG12D; p53) pancreatic cancer cells in survival surgery. Tumors were allowed to grow for 21 days post-surgical implantation, at which points tumors were harvested and mice were euthanized.

extract_protocol:
At Day 21 post-surgery, mice were euthanized and tumors were isolated and weighed. Tumors were digested in digestion buffer (Collagenase IV, DNAse I, Tyrpsin Inhibitor,) to a single cell suspension and filtered through 70um filters. 3 mice from each treament group were pooled together. The remaining cell pellet was stained with CD45 (Apc-cy7, Biolegend) and with PI (proprium iodide) and FACS sorted to isolate 100,000 CD45+ Live (PI negative) cells and submitted to the Genome Technology Core for analysis.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

treatment_protocol: Mice randomized into the "Exercise" group were subject to forced treadmill running on the following regimen: 5 days/week, 30 mins/day at a speed of 15 cm/sec. Mice randomized into the No exercise group remained sedentary for 21 days.

value: pancreas

tag: group

value: exercise

value: immune cell (CD45+ PI neg)

tag: disease state

value: pancreatic cancer


title: lung single cell 184

description:
lung single cell 184
898s_H24


title: WT2

city: Chicoago

first: Serdar

middle: E

last: Bulun

state: IL

address: 303 E Superior Street

department: Obstetrics & Gynecology

institute: Northwestern Feinberg School of Medicine

data_processing:
Aligned to ref genome and barcode counting using Cell Ranger v3.0.2
Genome_build: mm10-3.0.0 with the human aromatase gene CYP19A1
Supplementary_files_format_and_content: csv file, RNA count matrix

source_name: Lower Abdominla Muscle Tissue Homogenates_WT

extract_protocol:
Each tissue was placed in cold wash media (Hyclone Ham’s F-10 nutrient mixture with 1 mM L-glutamate [GE Life Sciences], 10% horse serum [Life Technologies], and penicillin-streptomycin [Omega Scientific]) until completion of tissue harvesting, and then manually minced for ~5 minutes into a slurry. The tissue slurry was incubated in muscle dissociation buffer (wash media + 1000 U/ml collagenase II [Worthington Biochemical]) at 37°C with 70 rpm agitation for 1 hour. The cells were then washed with wash media and centrifuged at 500g for 5 min at 4 °C. The supernatant was discarded with 4 ml of wash media remaining, and 500 µl of stock collagenase II (stock at 1000 U/ml) and 500 µl of stock Dispase II solution (stock at 11 U/ml) were added and incubated at 37°C with 70 rpm agitation for an additional 30 minutes. Cells were then passed through a 20 gauge syringe to further dissociate single cells, washed with wash media, and passed through a 40 µm filter to eliminate multinucleated cells. The cell suspension was then centrifuged at 500g for 5 min at 4 °C, the supernatant was discarded, and red blood cell lysis buffer (BioLegend) was added per the manufacturer’s instructions. Cells were then counted with a hemocytometer and resuspended with an appropriate volume of 1x PBS with 1% bovine serum albumin to achieve 1,000-1,500 cells/µl. The cells were finally passed through a 40-µm FLOWMI TIP cell strainer 2 times to remove any remaining cell debris and large clumps. The final cell suspension was kept on ice in DNA LoBind Tubes (Eppendorf) and submitted for scRNA-seq.
Samples for scRNA-seq were examined first for cell viability, density, singularity, and prep quality, ensuring no clumps and cell debris. Samples passing the quality control process were loaded onto 10x Genomics Chromium to partition and encapsulate single cells into nanoliter-sized GEMs (Gel beads-in-EMulsion). A total of six samples were analyzed, with each targeting 10,000 cells. In the 10x Chromium, each encapsulated cell was lysed within its GEM. The total RNA released was reverse transcribed to cDNA with primers attached to the gel bead, each of which carries a unique 10x barcode for downstream cell separation. Subsequently, the GEMs were broken, and all uniquely barcoded cDNAs were pooled and then amplified by PCR to generate enough material for Illumina sequencing. This library construction process for sequencing was carried out using the 10x Genomics Single-Cell 3’ Reagent Kit Protocol. Sequencing of the 10x libraries is performed on the Illumina HiSeq 4000, at a depth of ~30,000 reads per cell in the Northwestern University NUseq Core.

value: FVB/N

tag: disease

value: 9-10 weeks

value: lower abdominal muscle


title: DMSO replicate 1

description: RNAseq


title: Artificial CSF sample 3

description:
raw.counts.mean.samples.csv
aCSF_R3

tag: experiment batch

tag: experiment type

value: RNA-seq

tag: age

value: Aged

value: Male

value: Artificial CSF

value: Hippocampus

tag: cell compartment


title: RNA-seq_E11.5_XX_ECKO_Rep_3

tag: cell type

tag: developmental stage

value: Eed -/-

tag: gender

value: Female


title: DMSO replicate 2

description: RNAseq

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1


title: lung single cell 185

description:
lung single cell 185
898s_H2

value: lung

value: adult mice


title: WT3

value: Control


title: 48DOXneg replicate 3

description: RNAseq

value: doxycycline withdrawn, SETBP1 silenced

value: 48 hours


title: lung single cell 181

description:
lung single cell 181
898s_H21


title: No Exercise

value: pancreas

value: no exercise

value: immune cell (CD45+ PI neg)

value: pancreatic cancer


title: 48DOXpos replicate 2

description: RNAseq

value: doxycycline present, SETBP1 expressed


title: lung single cell 180

description:
lung single cell 180
898s_H20


title: WT1

value: FVB/N

value: 9-10 weeks

value: lower abdominal muscle


title: RNA-seq_E11.5_XX_Control_Rep_3

value: Primordial germ cells

value: wild type


title: 48DOXpos replicate 1

description: RNAseq


title: 48DOXneg replicate 2

description: RNAseq


title: 48DOXneg replicate 1

description: RNAseq


title: Arom2

source_name: Lower Abdominla Muscle Tissue Homogenates_Arom

value: Scrotal Hernia


title: lung single cell 178

description:
lung single cell 178
898s_H19


title: Arom1


title: BMDMs infected with L. biflexa at the 24-hour time-point [P24_1]

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

institute: Chang Gung Memorial Hospital, Linkou

data_processing:
Primary sequenceing data was produced by Illumina Hiseq 4000 (Flowcell ID: HLYL3BBXX, HVLKJBBXX and HWV2TBBXX).
Fastq files are quality checked with FastQC, v0.11.5 (BabrahamBioinformatics, Cambridge, UK).
Sequenced reads were trimmed using the CLC Genomics Workbench V10.1 on the basis of the per base sequence quality score (Q) >= 20
After this trimming step, sequenced reads were mapped to Mus_musculus GRCM38 using the CLC Genomics Workbench V10.1.
RPKM, Reads Per Kilobase of exon model per Million mapped reads, values for estimating transcript expression levels were done using the CLC Genomics Workbench V10.1.
Genome_build: Mus_musculus GRCM38
Supplementary_files_format_and_content: Tab-delimited text files contain gene name, ID, reads and RPKM values

growth_protocol: Macrophage colony-stimulating factor (M-CSF)-Induced macrophage differentiation from freshly isolated bone marrow cells of C57BL/6 mice aged 7-8 weeks was used for this study. Bone marrow suspensions were cultivated in medium (Dulbecco’s modified Eagle medium/Nutrient Mixture F-12, GlutaMAXTM medium supplemented with 10% fetal bovine serum) containing M-CSF 7 days.Bone marrow cells were cultured for 7 days at a density of 1x10^6 cells per 10 ml of macrophage complete medium in the presence of recombinant M-CSF.

extract_protocol:
Total RNA was extracted from BMDMs using the TRIzol reagent
Total RNA samples were converted to cDNA using the Ovation RNA-seq System V2 (NuGEN). Library construction was performed using the Ovation Ultralow Library System V2 1-96 (NuGEN).

treatment_protocol: BMDMs were incubated with either L. interrogans serovar Copenhageni Fiocruz L1-130 (ATCC number BAA-1198) or L. biflexa serovar Patoc (ATCC number 23582) for 24 hr at 37 °C in 5 % CO2. The multiplicity of infection was 100 bacteria per cell.

tag: strain background

value: Murine bone marrow-derived macrophages (BMDMs)

value: non-pathogenic L. biflexa serovar Patoc (ATCC number 23582)

value: 24hrs after infection


title: 24DOXpos replicate 3

description: RNAseq

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

value: 24 hours


title: lung single cell 176

description:
lung single cell 176
898s_H17

tag: strain

value: lung

value: adult mice


title: BMDMs infected with L. biflexa at the 24-hour time-point [P24_2]


title: lung single cell 177

description:
lung single cell 177
898s_H18

tag: genotype


title: BMDMs infected with L. biflexa at the 24-hour time-point [P24_3]

tag: treatment


title: lung single cell 175

description:
lung single cell 175
898s_H16


title: lung single cell 179

description:
lung single cell 179
898s_H1


title: BMDMs infected with L. interrogans at the 24-hour time-point [C24_1]

value: pathogenic L. interrogans serovar Copenhageni Fiocruz L1-130(ATCC number BAA-1198) isolate recovered from kidneys of hamsters

tag: time point


title: BMDMs infected with L. interrogans at the 24-hour time-point [C24_2]


title: BMDMs infected with L. interrogans at the 24-hour time-point [C24_3]


title: non-infected BMDMs at the 24-hour time-points [E24_1]

value: sterilized Ellinghausen-McCullough-Johnson-Harris (EMJH) medium

value: 24h time-point


title: 24DOXneg replicate 3

description: RNAseq

value: doxycycline withdrawn, SETBP1 silenced

tag: antibody


title: BMDMs infected with L. biflexa at the 2-hour time-point [TP2_3]

value: 2hrs after infection


title: non-infected BMDMs at the 24-hour time-points [E24_3]


title: BMDMs infected with L. biflexa at the 2-hour time-point [TP2_2]


title: lung single cell 173

description:
lung single cell 173
898s_H14

tag: tissue


title: non-infected BMDMs at the 24-hour time-points [E24_2]


title: 24DOXpos replicate 2

description: RNAseq

value: doxycycline present, SETBP1 expressed


title: 24DOXpos replicate 1

description: RNAseq


title: Arom3

value: FVB/N

value: 9-10 weeks

value: lower abdominal muscle


title: lung single cell 174

description:
lung single cell 174
898s_H15


title: 24DOXneg replicate 2

description: RNAseq


title: lung single cell 170

description:
lung single cell 170
898s_H11


title: non-infected BMDMs at the 2-hour time-point [TE2_2]

value: 2hrs time-point


title: BMDMs infected with L. biflexa at the 2-hour time-point [TP2_1]

value: Murine bone marrow-derived macrophages (BMDMs)


title: lung single cell 172

description:
lung single cell 172
898s_H13


title: BMDMs infected with L. interrogans at the 2-hour time-point [TC2_4]


title: BMDMs infected with L. interrogans at the 2-hour time-point [TC2_3]


title: BMDMs infected with L. interrogans at the 2-hour time-point [TC2_2]


title: lung single cell 169

description:
lung single cell 169
898s_H10


title: RIS2

city: tianjin

first: Fu

last: yun

address: 22 Qixiangtai Road, Heping District

country: China

institute: tianjin medical university

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
GCF_000001635.26_GRCm38.p6
Genome_build: tab-delimited text files include FPKM values for each Sample

source_name: 3T3-L1 murine adipocytes

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard  protocols

value: embryo tissue

value: 3T3-L1 murine adipocytes

value: risperidone

value: NIH SWISS


title: S154_Rep3_0Gy_0h

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Rsubreads raw counts per HGNC symbol in text files

organism: Homo sapiens

source_name: UPCI:SCC154 cell line

extract_protocol:
Total RNA was extracted using Nucleospn RNA extraction kit from Macherey & Nagel
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicate

tag: time

tag: treatment irradiation

value: head and neck squamous cell carinoma (HNSCC)

tag: hpv-status

value: HPV-positive


title: SOK6_Rep3_0Gy_0h

source_name: OKF6 cell line

value: oral ketratinocytes

value: HPV-negative


title: S99_Rep3_0Gy_0h

source_name: UPCI:SCC099 cell line


title: RIS1


title: lung single cell 171

description:
lung single cell 171
898s_H12

value: lung

value: adult mice


title: 24DOXneg replicate 1

description: RNAseq

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

value: doxycycline withdrawn, SETBP1 silenced

value: 24 hours


title: Cnot8 KO 24h rep1 rep2 subreads

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: bam file format (two replications in one file)

data_processing:
Circular consensus sequence (CCS) reads were extracted from raw subreads and corrected the sequence errors by ccs (version 4.2.0) with default parameters.
The extracted CCS reads were split into different samples by barcodes and further trimmed to remove the adapters. Processed CCS reads were transformed as standard FASTQ files and mapped to mouse genome (mm10) by minimap2 (version 2.17) with parameters: -ax splice -uf -- secondary = no -- MD -- cs. Repetitive reads were removed. The aligned bam files from mnimap2 were parsed and the soft-clip nucleotide were extracted as the primary 3’poly(A) tail sequence candidates.For high-quality poly(A) tails, we filtered out sequences with less than 4 As at the first 8 bp. To focus on poly(A) tail deadenylation, we discarded transcripts without poly(A) tails (3’ soft clip = 0). We extended upstream continuous ‘A’-tracts in alignments if is necessary for the purpose of misalignment.
We assigned transcripts with defined poly(A) tail to genes with FeatureCounts (version 2.0.1). The ultimate trimmed sequence of the CCS reads was regarded as poly(A) tails. The poly(A) tail length of a given transcript was calculated as the length of the trimmed sequence.
Genome_build: mm10
Supplementary_files_format_and_content: poly A tail result table, which were called by customized pipeline (https://github.com/niehu2018/GV_oocyte_PAIsoSeqAnalysis)

source_name: ESC differentiation at 24h

growth_protocol: EpiLCs were grown in the medium containing N2B27, 20 ng/ml activin A, 12 ng/ml bFGF, and 1% KSR.

extract_protocol:
Total RNA was extracted from cells using RNAzol Reagent. To avoid genomic DNA contamination, total RNA was treated with RQ1 RNase-Free DNase for 30 min at 37 °C, and subsequently purified using the phenol-chloroform extraction and ethanol precipitation.
About 500 ng total RNA was subjected to barcoded end extension, template switching, full-length cDNA amplification, and circular adapter ligation. PAIso-seq was performed to precisely decipher the length and base composition of RNA poly(A) tails using the resultant circular full-length cDNA libraries on the PacBio third-generation sequencing platform.
PAIso-seq

treatment_protocol: EpiLCs were cultured on each well of 12-well plate precoated with a 1:100 mix of Matrigel and DMEM/F12 at 37 °C under 5% CO2,during which, the culture medium was replaced every day.

value: ICR

tag: differentiation hour

value: ESC EpiLC at 24h

value: Cnot8 KO


title: non-infected BMDMs at the 2-hour time-point [TE2_4]

value: Murine bone marrow-derived macrophages (BMDMs)

value: sterilized Ellinghausen-McCullough-Johnson-Harris (EMJH) medium

value: 2hrs time-point


title: RNC2

value: embryo tissue

value: 3T3-L1 murine adipocytes

value: untreat


title: WT 24h rep1 rep2 subreads

description: bam file format (two replications in  one file)

value: Wild type


title: S33_Rep3_0Gy_0h

source_name: Cal33 cell line

value: head and neck squamous cell carinoma (HNSCC)


title: non-infected BMDMs at the 2-hour time-point [TE2_1]


title: lung single cell 165

description:
lung single cell 165
898s_G6

tag: age


title: SOK6_Rep2e_0Gy_0h

value: oral ketratinocytes

value: HPV-negative


title: lung single cell 168

description:
lung single cell 168
898s_G9

value: lung

value: adult mice


title: S131_Rep3_0Gy_0h

source_name: UPCI:SCC131 cell line


title: S40_Rep3_0Gy_0h

source_name: UPCI:SCC040 cell line


title: S33_Rep2e_0Gy_0h


title: S40_Rep2e_0Gy_0h


title: S2_Rep3e_0Gy_0h

source_name: UD-SCC2 cell line

value: HPV-positive


title: S27_Rep3_0Gy_0h

source_name: Cal27 cell line


title: ATAC-Seq E5 6hPR+FGF2 1

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Reads were trimmed using cut adapt and trim galore with the trimming parameters --clip_R1 16 --clip_R2 18 --three_prime_clip_R1 6 --three_prime_clip_R2 4.
Alignment of raw reads to chicken genome GRCg6a was performed with Bowtie2 (Langmead and Salzberg, 2012) using the parameters --very-sensitive -k 5 -p 40.
Aligned reads were deduplicated using Picard tools (Broad Institute, Picard Toolkit).
Peaks were called for samples individually with HMMRATAC (Tarbell and Liu, 2019). HMMRATAC defined open regions were unified across all samples into a consensus peak file using BEDtools merge -d 10 -I (Quinlan and Hall, 2010).
Peaks aligning to the mitochondrial chromosome were discarded, and peak counts were determined using featureCounts with parameters -F SAF -s 0 -T 10 (Liao et al., 2014).
Differential expression testing of peak regions and peak summits was performed with DESeq2.
Genome_build: GRCg6a
Supplementary_files_format_and_content: Normalized peak count matrix from DESeq2.

organism: Gallus gallus

source_name: Retinal pigment epithelium

growth_protocol: White Leghorn chicken eggs obtained from Michigan State University were used. Eggs were incubated in a humidified, rotating incubator at 38 °C before performing experiments at Hamburger Hamilton stage 24 (E4) or 26 (E5).

extract_protocol:
RPE was isolated in cold PBS and two isolated sheets of RPE were collected per biological sample and placed on ice. RPE cells were lysed in cold ATAC-Seq Kit lysis buffer (Active Motif cat. 53150) and nuclei were counted with a hemocytometer.
Approximately 100,000 RPE nuclei from 2 embryos were aliquoted for Tn5 tagmentation per sample and ATAC-seq library preparation was performed using ATAC-Seq Kit (Active Motif cat. 53150) per manufacturer’s instructions.

treatment_protocol: For treated conditions, surgical retinectomy was performed and FGF2-containing heparain beads were delivered to the eye cup at the time of injury.

value: 6hPR + FGF2

tag: Stage


title: ATAC-Seq E4 6hPR+FGF2 1


title: lung single cell 162

description:
lung single cell 162
898s_G3

source_name: Lung


title: S154_Rep2e_0Gy_0h


title: lung single cell 164

description:
lung single cell 164
898s_G5


title: lung single cell 161

description:
lung single cell 161
898s_G2


title: lung single cell 166

description:
lung single cell 166
898s_G7


title: RNA-Seq E5 6hPR+FGF2 3

data_processing:
Low-quality bases and adapters were trimmed using Cutadapt and Trim Galore with the parameters --stringency 3 --length 36
Two-pass alignment with STAR was employed and the parameters --quantMode GeneCounts TranscriptomeSAM --readFilesCommand zcat --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate were used.
Gene counts were generated using Stringtie and Ensembl chicken gene annotation release 101
Differential expression testing was performed with DESeq2 with an expression filter of minimum raw counts 10 across all samples
Genome_build: GRCg6a
Supplementary_files_format_and_content: Normalized gene count matrix from DESeq2.

extract_protocol:
Biological samples were collected directly into 1X DNA/RNA Shield (Zymo, cat. R1200) on ice. RNA was isolated using the Quick-RNA Miniprep Kit (Zymo, cat. R1054) per manufacturer’s instructions, including 15 minutes of in-column DNase I treatment.
RNA libraries were constructed at the DNA Link, Inc. sequencing core (Los Angeles, CA, USA) using the TruSeq Stranded mRNA Library Prep kit (Illumina, cat. 20020594) with 580ng – 1ug of total RNA per sample.

treatment_protocol: For treated conditions, surgical retinectomy was performed. For FGF-treated samples, FGF2-containing heparain beads were delivered to the eye cup at the time of retinectomy.


title: RNC1

tag: cell type

value: NIH SWISS


title: S2_Rep3l_0Gy_0h


title: S2_Rep2e_0Gy_0h


title: S154_Rep2l_0Gy_0h


title: S131_Rep2l_0Gy_0h


title: lung single cell 167

description:
lung single cell 167
898s_G8


title: lung single cell 160

description:
lung single cell 160
898s_G24


title: S131_Rep2e_0Gy_0h


title: S99_Rep2e_0Gy_0h


title: ATAC-Seq E4 6hPR+FGF2 2


title: S99_Rep2l_0Gy_0h


title: S40_Rep2l_0Gy_0h


title: lung single cell 159

description:
lung single cell 159
898s_G23


title: lung single cell 158

description:
lung single cell 158
898s_G22


title: S27_Rep2_0Gy_0h


title: S2_Rep2l_0Gy_0h


title: S154_Rep1e_0Gy_0h


title: S40_Rep1e_0Gy_0h


title: RNA-Seq E5 6hPR+FGF2 2


title: lung single cell 156

description:
lung single cell 156
898s_G20


title: lung single cell 163

description:
lung single cell 163
898s_G4


title: lung single cell 155

description:
lung single cell 155
898s_G1


title: S33_Rep1e_0Gy_0h


title: lung single cell 157

description:
lung single cell 157
898s_G21


title: RNA-Seq E5 6hPR 3


title: S27_Rep1e_0Gy_0h


title: RNA-Seq E5 6hPR+FGF2 1


title: SOK6_Rep2l_0Gy_0h


title: ATAC-Seq E5 6hPR+FGF2 2


title: SOK6_Rep1e_0Gy_0h


title: S131_Rep1e_0Gy_0h


title: S154_Rep1l_0Gy_0h


title: lung single cell 153

description:
lung single cell 153
898s_G18


title: S99_Rep1e_0Gy_0h


title: RNA-Seq E5 6hPR 1


title: RNA-Seq E5 RPE 3

value: Development


title: RNA-Seq E5 6hPR 2


title: S131_Rep1l_0Gy_0h


title: S99_Rep1l_0Gy_0h


title: RNA-Seq E4 6hPR+FGF2 3


title: RNA-Seq E4 6hPR+FGF2 2


title: lung single cell 154

description:
lung single cell 154
898s_G19


title: lung single cell 151

description:
lung single cell 151
898s_G16


title: S2_Rep1e_0Gy_0h


title: lung single cell 152

description:
lung single cell 152
898s_G17


title: S33_Rep2l_0Gy_0h


title: lung single cell 150

description:
lung single cell 150
898s_G15


title: RNA-Seq E4 6hPR+FGF2 1


title: S2_Rep1l_0Gy_0h


title: SOK6_Rep1l_0Gy_0h


title: S40_Rep1l_0Gy_0h


title: S27_Rep1l_0Gy_0h


title: S154_Rep3_8Gy_4h_X

value: 8 Gy X-ray


title: RNA-Seq E4 6hPR 3


title: S131_Rep3_8Gy_4h_X


title: RNA-Seq E4 6hPR 2


title: S99_Rep3_8Gy_4h_X


title: RNA-Seq E5 RPE 1


title: SOK6_Rep3_8Gy_4h_X


title: RNA-Seq E5 RPE 2


title: lung single cell 148

description:
lung single cell 148
898s_G13


title: lung single cell 146

description:
lung single cell 146
898s_G11


title: lung single cell 147

description:
lung single cell 147
898s_G12


title: S40_Rep3_8Gy_4h_X


title: S33_Rep1l_0Gy_0h


title: RNA-Seq E4 6hPR 1


title: RNA-Seq E4 RPE 2


title: lung single cell 149

description:
lung single cell 149
898s_G14


title: RNA-Seq E4 RPE 1


title: S33_Rep3_4Gy_4h_X

value: 4 Gy X-ray


title: RNA-Seq E4 RPE 3


title: S2_Rep3e_8Gy_4h_X


title: S2_Rep3e_4Gy_4h_X


title: S33_Rep3_8Gy_4h_X


title: SOK6_Rep3_4Gy_4h_12C

value: 4 Gy carbon-ion


title: lung single cell 145

description:
lung single cell 145
898s_G10


title: S131_Rep3_4Gy_4h


title: S99_Rep3_4Gy_4h_X


title: lung single cell 144

description:
lung single cell 144
898s_F9


title: S40_Rep3_4Gy_4h_X


title: S131_Rep3_4Gy_4h_12C


title: lung single cell 143

description:
lung single cell 143
898s_F8


title: S99_Rep3_4Gy_4h_12C


title: lung single cell 139

description:
lung single cell 139
898s_F4


title: S27_Rep3_4Gy_4h_X


title: lung single cell 142

description:
lung single cell 142
898s_F7


title: S154_Rep3_4Gy_4h_X


title: SOK6_Rep3_4Gy_4h_X


title: S40_Rep3_4Gy_4h_12C


title: lung single cell 140

description:
lung single cell 140
898s_F5


title: S154_Rep3_4Gy_4h_12C


title: S33_Rep3_4Gy_4h_12C


title: S27_Rep3_4Gy_4h_12C


title: lung single cell 138

description:
lung single cell 138
898s_F3


title: RGD_03

type: RNA

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

hyb_protocol: In order to study the expression of immune-related genes in the tumor microenvironment, 100 ng of total RNA extracted from tumors 15 days after treatment was hybridized to the nCounter PanCancer immune profiling panel

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter instrument.

data_processing: Data was normalized based on the internal positive controls and housekeeping genes using the NACHO R package and default parameters. Differential expresion analysis with limma R package was based on the log2 normalized signal.

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

source_name: DIPG tumor

label_protocol: Followed NanoString nCounter XT gene expression assay protocol.

extract_protocol: Total RNA from tumor pieces was extracted using DirectZol™ RNA MiniPrep Kit (ZymoResearch).

treatment_protocol: We intratumorally injected Delta-24-ACT, Delta-24-RGD or PBS (mock group) 3 days after NP53 cell implantation (0D).

value: DIPG tumor


title: RGD_02


title: lung single cell 137

description:
lung single cell 137
898s_F2


title: RGD_01


title: S154_Rep3_0Gy_4h


title: RGD_04


title: lung single cell 141

description:
lung single cell 141
898s_F6


title: PBS_11

value: PBS


title: S2_Rep3e_4Gy_4h_12C


title: S27_Rep3_8Gy_4h_X


title: S40_Rep3_0Gy_4h


title: PBS_12


title: PBS_10


title: lung single cell 136

description:
lung single cell 136
898s_F24


title: S99_Rep3_0Gy_4h


title: S27_Rep3_0Gy_4h


title: S33_Rep3_0Gy_4h


title: lung single cell 134

description:
lung single cell 134
898s_F22


title: SOK6_Rep3_0Gy_4h


title: ACT_08


title: lung single cell 133

description:
lung single cell 133
898s_F21


title: S154_Rep3_8Gy_72h_X


title: Cnot7-7-KO-ESC-rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw paired-end reads with low quality and adaptors were trimmed by Cutadapt (version 0.3.8), and clean reads were mapped to the mouse genome (mm9) using TopHat2 (version 2.1.1) with default parameters.
The expression level of each gene was determined with gene annotation from UCSC RefSeq database using FeatureCounts (version 2.0.1) and presented as transcripts per million (TPM).
Differentially expressed genes (DEGs) were identified (log2TPM >1, fold change [FC] > 1.5) by comparing expression levels of genes in KO cells with those in normal controls.
Genome_build: mm9
Supplementary_files_format_and_content: text table file for gene expression matrix of all samples

source_name: mouse ESC cell line

growth_protocol: ESCs were grown in 2i/LIF medium. Briefly, 500 ml of N2B27 medium was produced through containing 240 ml DMEM/F12, 240 ml Neurobasal Medium, 2.5 ml N2 supplement, 5 ml B27 supplement, 1% GlutaMAX, 1% MEM non-essential amino acids (NEAA), 1% penicillin-streptomycin, 1% sodium pyruvate, 5 mg/ml bovine serum albumin (BSA), and 0.1 mM b-mercaptoethanol. The 2i/LIF medium for ESCs was generated by supplying 1,000 U/ml recombinant human LIF, 1 mM PD0325901, and 3 mM CHIR99021 in N2B27 medium. EpiLCs were grown in the medium containing N2B27, 20 ng/ml activin A, 12 ng/ml bFGF, and 1% KSR.

extract_protocol:
Total RNA was extracted from cells using RNAzol Reagent. To avoid genomic DNA contamination, total RNA was treated with RQ1 RNase-Free DNase for 30 min at 37 °C, and subsequently purified using the phenol-chloroform extraction and ethanol precipitation.
The mRNA enriched by Oligo(dT) was reversely transcribed, amplified by PCR, and utilized for the construction of Illumina sequencing library. RNA sequencing was performed using the Illumina Hiseq ×-Ten platform with 150 bp pair-end mode.

treatment_protocol: ESCs were cultured on feeder-free petri dishes or plates coated with 0.2% gelatin at 37 °C under 5% CO2. EpiLCs were cultured on each well of 12-well plate precoated with a 1:100 mix of Matrigel and DMEM/F12 at 37 °C under 5% CO2,during which, the culture medium was replaced every day.

value: ICR

value: ESC (0h)

value: Cnot7 KO


title: ACT_06


title: S99_Rep3_8Gy_72h_X

value: head and neck squamous cell carinoma (HNSCC)


title: S131_Rep3_8Gy_72h_X


title: S131_Rep3_0Gy_4h


title: Cnot7-4-KO-ESC-rep1


title: S40_Rep3_8Gy_72h_X


title: S33_Rep3_8Gy_72h_X


title: Cnot7-9-WT-ESC-rep2

value: wild type


title: lung single cell 135

description:
lung single cell 135
898s_F23


title: Cnot7-6-WT-ESC-rep1


title: lung single cell 130

description:
lung single cell 130
898s_F19


title: S2_Rep3l_8Gy_72h_X


title: ACT_07


title: SOK6_Rep3_8Gy_48h_X

value: oral ketratinocytes

value: HPV-negative


title: lung single cell 129

description:
lung single cell 129
898s_F18

value: lung

value: adult mice


title: lung single cell 131

description:
lung single cell 131
898s_F1


title: S154_Rep3_8Gy_48h_X

value: HPV-positive


title: SOK6_Rep3_8Gy_72h_X


title: S2_Rep3e_0Gy_4h


title: S131_Rep3_8Gy_48h_X


title: S99_Rep3_8Gy_48h_X


title: lung single cell 128

description:
lung single cell 128
898s_F17


title: lung single cell 132

description:
lung single cell 132
898s_F20


title: S40_Rep3_8Gy_48h_X


title: Cnot8-5-KO-48h_rep1

value: EpiLC 48h

value: Cnot8 KO


title: lung single cell 127

description:
lung single cell 127
898s_F16


title: Cnot8-2-WT-48h_rep1


title: S27_Rep3_8Gy_72h_X

value: 8 Gy X-ray


title: S27_Rep3_8Gy_48h_X


title: lung single cell 126

description:
lung single cell 126
898s_F15


title: lung single cell 125

description:
lung single cell 125
898s_F14


title: S2_Rep3l_8Gy_48h_X


title: SOK6_Rep3_4Gy_72h_X

value: 4 Gy X-ray


title: Cnot8-8-KO-48h_rep2


title: Cnot8-8-KO-24h_rep2

value: EpiLC 24h


title: lung single cell 124

description:
lung single cell 124
898s_F13


title: S154_Rep3_4Gy_72h_X


title: S131_Rep3_4Gy_72h_X


title: S33_Rep3_4Gy_72h_X


title: S99_Rep3_4Gy_72h_X


title: S2_Rep3l_4Gy_72h_X


title: Cnot8-5-KO-24h_rep1


title: lung single cell 122

description:
lung single cell 122
898s_F11


title: S40_Rep3_4Gy_72h_X


title: S27_Rep3_4Gy_72h_X


title: Cnot8-4-WT-24h_rep2


title: Cnot8-2-WT-24h_rep1


title: SOK6_Rep3_4Gy_48h_X


title: Cnot8-4-WT-48h_rep2


title: lung single cell 123

description:
lung single cell 123
898s_F12


title: S33_Rep3_8Gy_48h_X


title: lung single cell 121

description:
lung single cell 121
898s_F10


title: lung single cell 120

description:
lung single cell 120
898s_E9


title: S99_Rep3_4Gy_48h_X


title: S40_Rep3_4Gy_48h_X


title: Cnot8-5-KO-12h_rep1

value: EpiLC 12h


title: S33_Rep3_4Gy_48h_X


title: Cnot8-4-WT-12h_rep2


title: Cnot8-8-KO-12h_rep2


title: S131_Rep3_4Gy_48h_X


title: S27_Rep3_4Gy_48h_X


title: lung single cell 117

description:
lung single cell 117
898s_E6


title: lung single cell 116

description:
lung single cell 116
898s_E5


title: S154_Rep3_4Gy_48h_X


title: S99_Rep3_4Gy_72h_12C

value: 4 Gy carbon-ion


title: lung single cell 119

description:
lung single cell 119
898s_E8


title: lung single cell 118

description:
lung single cell 118
898s_E7


title: Cnot8-2-WT-12h_rep1

value: ICR


title: Cnot8-5-KO-6h_rep1

value: EpiLC 6h


title: S2_Rep3l_4Gy_48h_X


title: S27_Rep3_4Gy_72h_12C


title: lung single cell 114

description:
lung single cell 114
898s_E3


title: Cnot8-8-KO-6h_rep2


title: S154_Rep3_4Gy_48h_12C


title: S40_Rep3_4Gy_72h_12C


title: S131_Rep3_4Gy_48h_12C


title: Cnot8-8-KO-ESC_rep2

value: ESC (0h)


title: lung single cell 112

description:
lung single cell 112
898s_E24


title: S154_Rep3_4Gy_72h_12C

value: head and neck squamous cell carinoma (HNSCC)


title: S33_Rep3_4Gy_72h_12C


title: Cnot8-5-KO-ESC_rep1


title: S40_Rep3_4Gy_48h_12C


title: S131_Rep3_4Gy_72h_12C


title: S99_Rep3_4Gy_48h_12C


title: S27_Rep3_4Gy_48h_12C


title: lung single cell 113

description:
lung single cell 113
898s_E2


title: lung single cell 111

description:
lung single cell 111
898s_E23


title: lung single cell 115

description:
lung single cell 115
898s_E4


title: S2_Rep3l_4Gy_48h_12C


title: Cnot8-4-WT-6h_rep2

value: wild type


title: SOK6_Rep3_4Gy_72h_12C

value: oral ketratinocytes


title: SOK6_Rep3_4Gy_48h_12C

value: HPV-negative


title: S2_Rep3l_4Gy_72h_12C


title: Cnot8-2-WT-6h_rep1


title: S33_Rep3_4Gy_48h_12C


title: lung single cell 109

description:
lung single cell 109
898s_E21

value: lung


title: Cnot8-2-WT-ESC_rep1


title: lung single cell 110

description:
lung single cell 110
898s_E22

value: adult mice


title: SOK6_Rep3_0Gy_72h


title: Hoxa9 Off 96hrs

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

description:
raw_counts_table.csv
barcode-1-2-1 = Hoxa9 Off 96hrs

data_processing:
The Cell Ranger pipeline v3.0.1 was used with default parameters to map reads
Scanpy v1.4.6 and Seurat v3.0.1 were used to load Cell Ranger .cloupe files and to perform all analysis
Low quality cells (<200 expressed genes; >10% mitochondrial reads) were removed; both normalized read counts (counts per 1,000 reads) and log-normalized read counts were use for analysis and visualizations
Genome_build: mm10 (Ensembl 84)
Supplementary_files_format_and_content: Raw gene count matrix (genes by cells)

source_name: Lys-GFP-ER-HoxA9 cells

growth_protocol: Granulocyte-macrophage progenitor cells containing Hoxa9::ER were cultured in RPMI-1640 supplemented with 10% FBS, 100U ml-1 penicillin, 100 µg ml−1 streptomycin, 2mM L-alanyl-L-glutamine dipeptide and stem cell factor (SCF). The source of SCF was conditioned media generated from a Chinese hamster ovary (CHO) cell line that stably secretes SCF. Conditioned medium was added at a final concentration of 1 - 2 % depending on the batch. β-Estradiol (abbreviated E2) was added to a final concentration of 150 ng/ml from a 3 mg/ml stock dissolved in 100% ethanol.

extract_protocol: 10x Chromium Single Cell 3’ Reagent Kits v2 Protocol

treatment_protocol: For CAF-1 suppression, IPTG was added at a concentration of 500 µM to express IPTG-inducible Chaf1b shRNA. For Hoxa9 inactivation, cells were washed with PBS twice and then cultured in media without Estradiol.

value: Lys-GFP-ER-HoxA9 cells

value: Culture out of beta-estradiol for 96 hours for HOXA9 inactivation


title: S40_Rep3_0Gy_72h


title: Hoxa9 Off 48hrs

description:
raw_counts_table.csv
barcode-1-1-1 = Hoxa9 Off 48hrs

value: Culture out of beta-estradiol for 48 hours for HOXA9 inactivation


title: Hoxa9 Off 0hr

description:
raw_counts_table.csv
barcode-1-0-1 = Hoxa9 Off 0hr

value: Culture with beta-estradiol to serve as a 0hrs control


title: S131_Rep3_0Gy_72h


title: Cnot8-4-WT-ESC_rep2


title: Caf-1 Off 96hrs

description:
raw_counts_table.csv
barcode-1-2-0 = Caf-1 Off 96hrs

value: Culture with IPTG for 96 hours for CAF-1 suppression


title: S154_Rep3_0Gy_72h

value: HPV-positive


title: lung single cell 107

description:
lung single cell 107
898s_E1


title: lung single cell 106

description:
lung single cell 106
898s_E19


title: Caf-1 Off 48hrs

description:
raw_counts_table.csv
barcode-1-1-0 = Caf-1 Off 48hrs

value: Culture with IPTG for 48 hours for CAF-1 suppression


title: Caf-1 Off 0hr

description:
raw_counts_table.csv
barcode-1-0-0 = Caf-1 Off 0hr


title: lung single cell 105

description:
lung single cell 105
898s_E18


title: lung single cell 108

description:
lung single cell 108
898s_E20


title: S99_Rep3_0Gy_72h


title: S33_Rep3_0Gy_72h


title: S27_Rep3_0Gy_72h


title: S131_Rep3_0Gy_48h


title: S2_Rep3l_0Gy_72h


title: lung single cell 102

description:
lung single cell 102
898s_E15


title: S27_Rep3_0Gy_48h


title: W-sucrose6

city: Calgary

first: Savraj

last: Grewal

state: Alberta

address: 3330 Hospital Drive

country: Canada

institute: University of Calgary

data_processing:
1.Using Fast QC for reads quality control. The reads number per sample is around 20 million, and average reads length is 51 bp. All samples passed reads quality control.
2. Map the reads to Drosophila_melanogaster reference version: GCF_000001215.4_Release_6_plus_ISO1_MT_rna
3. QC for reads mapping quality:  at least 90% of reads pseudo aligned to reference.
4. PCA plot for experiments QC, didn’t see obvious experimental problem, for example, uneven rRNA depletion.
5. Apply Wald-test from software sleuth do differential expression analysis, both on transcript level and gene level.
Assembly: Drosophila_melanogaster reference version: GCF_000001215.4_Release_6_plus_ISO1_MT_rna

organism: Drosophila melanogaster

source_name: whole-body RNA, adult female

extract_protocol:
Adult flies were snap frozen on dry ice in groups of 5. Total RNA was then isolated using Trizol according to the manufacturer’s instructions (Invitrogen; 15596-018). Extracted RNA was then DNase treated (Ambion; 2238G) to be used for subsequent qPCR or mRNA sequencing.
RNA libraries were prepared for sequencing using the Ultra II Directional RNA library kit (New England BioLabs) according the manufacturer's instructions

treatment_protocol: Mated adult female flies (~7 days old) were either mock infected (sucrose-fed) or infected with P.e. (feeding with with a sucrose/P.e. solution) for 24 hours.Briefly, Pseudomonas entomophila (P.e) from overnight cultures were pelleted and resuspended in 5% sucrose solution (in sterile water) such that the final concentration of bacteria was OD600= 200. Bacterial pellets were then dissolved in filter sterilized 5% sucrose/water. Chromatography paper (Fisher, Pittsburgh, PA) discs were dipped in the bacterial solution and were carefully placed on standard fly food vials such that they covered the entire food surface. Adult females were first subjected to a 2-hr starvation period in empty vials at 29C. Then 10-12 flies were transferred to each infection vial and then placed in a 29C incubator for the duration of the 24-hour infection period. Mock-infected control flies were placed in similarly prepared vials that contained paper discs soaked in 5% sucrose/water alone.

tag: developmental stage

value: adult

value: whole body

tag: Sex

value: female

tag: treatment condition

value: sucrose-fed (mock infected) control group 6


title: S154_Rep3_0Gy_48h

value: head and neck squamous cell carinoma (HNSCC)


title: W-sucrose5

value: sucrose-fed (mock infected) control group 5


title: lung single cell 104

description:
lung single cell 104
898s_E17

tag: strain


title: S99_Rep3_0Gy_48h


title: S40_Rep3_0Gy_48h


title: lung single cell 101

description:
lung single cell 101
898s_E14

tag: genotype


title: S2_Rep3l_0Gy_48h


title: W-sucrose4

value: sucrose-fed (mock infected) control group 4


title: SOK6_Rep2e_8Gy_4h

value: 8 Gy X-ray

value: oral ketratinocytes

value: HPV-negative


title: S33_Rep3_0Gy_48h


title: lung single cell 103

description:
lung single cell 103
898s_E16

value: lung

value: adult mice


title: lung single cell 99

description:
lung single cell 99
898s_E12


title: S154_Rep2e_8Gy_4h_X


title: SOK6_Rep3_0Gy_48h


title: S33_Rep2e_8Gy_4h


title: S27_Rep2_8Gy_4h_X


title: S131_Rep2e_8Gy_4h_X


title: S40_Rep2e_8Gy_4h_X


title: lung single cell 98

description:
lung single cell 98
898s_E11


title: lung single cell 97

description:
lung single cell 97
898s_E10


title: W-sucrose1

value: sucrose-fed (mock infected) control group 1


title: W-Pe6

value: P.e.-fed, infected group 6


title: S99_Rep2e_8Gy_4h_X


title: lung single cell 100

description:
lung single cell 100
898s_E13


title: SOK6_Rep2e_4Gy_4h_X

value: 4 Gy X-ray


title: S99_Rep2e_4Gy_4h_X


title: S154_Rep2e_4Gy_4h_X

value: HPV-positive


title: S40_Rep2e_4Gy_4h_X


title: lung single cell 95

description:
lung single cell 95
898s_D8


title: W-sucrose2

value: sucrose-fed (mock infected) control group 2


title: S2_Rep2e_8Gy_4h_X


title: S27_Rep2_4Gy_4h_X


title: S131_Rep2e_4Gy_4h_X


title: lung single cell 94

description:
lung single cell 94
898s_D7


title: W-sucrose3

value: adult

value: sucrose-fed (mock infected) control group 3


title: W-Pe4

value: whole body

value: female

value: P.e.-fed, infected group 4


title: W-Pe5

value: P.e.-fed, infected group 5


title: SOK6_Rep2e_4Gy_4h_12C

value: 4 Gy carbon-ion


title: lung single cell 93

description:
lung single cell 93
898s_D6


title: W-Pe3

value: P.e.-fed, infected group 3


title: S2_Rep2e_4Gy_4h_X

value: head and neck squamous cell carinoma (HNSCC)


title: S154_Rep2e_4Gy_4h_12C


title: lung single cell 96

description:
lung single cell 96
898s_D9


title: EM+E2_8_rep3 [M+E_8_3]

city: Wuhan

first: Zhen-Xia

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
We used FastqC (v0.11.8) and MultiQC (v0.9) to evaluate the raw read quality statistics.
eads were mapped to the zebrafish genome (Ensembl v93) by Hisat2 (v2.0.5) with parameters “--dta -x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format (Ensembl v93).
The output of Hisat2 were converted to BAM format and sorted by Samtools (v1.5). The tool Picard MarkDuplicates (v2.18.15) was used to remove duplicates.
Genome_build: GRCz11
Supplementary_files_format_and_content: HTSeq (0.9.1) was used to count reads mapped to each gene with parameters “-t exon –i gene_id -r pos -s reverse”.

organism: Danio rerio

source_name: EM+E2 8d_whole body

growth_protocol: Zebrafish were obtained from Institute of Hydrobiology, Chinese Academy of Sciences (Wuhan). Embryos were incubated in petri dishes after 0 dpf. Each petri dish contained 50 embryos, which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr, and fed twice daily in tank (paramecium at 6-10 dpf, paramecium and fairy shrimp at 11-15 dpf, and fairy shrimp at 16-32 dpf).

extract_protocol:
We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL, measured its purity with NanoPhotometer spectrophotometer (IMPLEN, CA, USA), quantified its concentration with Qubit 3.0 Flurometer (Life Technologies, CA, USA), and checked its integrity by Agilent 2100 bioanalyzer (Agilent Technologies, CA, USA).
Stranded PolyA+ RNA libraries were prepared at Anoroad (Beijing, China) with in-house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System (Illumina Inc., San Diego, CA).

treatment_protocol: Zebrafish were treated with EM and/or E2 continuously before sampling for RNA-seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM (10μg/L) and E2 (100ng/L) either together or alone, as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM, E2 and DMSO to ensure the effectiveness of drugs.

value: AB

tag: treatment

tag: library type

value: fr-firststrand (dUTP)


title: W-Pe2

value: P.e.-fed, infected group 2


title: lung single cell 92

description:
lung single cell 92
898s_D5

value: lung

value: adult mice


title: W-Pe1

value: P.e.-fed, infected group 1


title: lung single cell 91

description:
lung single cell 91
898s_D4


title: 10x, sample male

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: transcriptomic single cell

data_processing:
The quality of the raw sequencing data was checked by FastQC software. The raw sequencing data were processed by cellranger count pipeline to generate the single cell matrix for each sample. The single cell matrix was analyzed by the Seurat package and Harmony was used for batch correction.
The Malpighian tubules and nephrocytes samples were processed and clustered separately, and then were merged by filtering out unrelated cell clusters.
Assembly: Drosophila, FlyBase release r6.31
Supplementary files format and content: gene2cell matrix

source_name: nephrocytes

growth_protocol: Fly strain of the genotype w1118; Dot-Gal4, UAS-GFP.nls  was routinely kept at 18 °C on standard lab food composed of 15g yeast, 8.6g soy flour, 63g corn flour, 5g agar, 5g malt, 74 ml corn syrup per liter.

extract_protocol:
Nephrocytes were dissected under a fluorescence microscope from 5-7 day old Dot-Gal4>GFP.nls male and female adult flies. Ten flies at a time were dissected and samples immediately transferred into 1.5 ml EP tube with Schneider’s medium on ice to avoid exposing the tissues to room temperature for a long period of time. Once 50 flies were dissected, EP tubes were sealed with parafilm and put on dry ice. Next steps involved spraying 100% ethanol to the dry ice near the tube to quickly freeze the sample and storing samples at -80oC for long-term.
Libraries were generated according to 10X genomics v2 protocol.

tag: technology

value: 10x genomics

value: nephrocytes

value: male

value: 5-7 days

value: w1118; Dot-Gal4, UAS-GFP.nls


title: EM+E2_8_rep2 [M+E_8_2]

tag: tissue

value: whole body


title: EM+E2_64_rep1 [M+E_64_2]

source_name: EM+E2 64d_whole body


title: S99_Rep2e_4Gy_4h_12C

tag: replicate

value: HPV-negative


title: S131_Rep2e_4Gy_4h_12C

tag: time


title: EM+E2_8_rep1 [M+E_8_1]


title: 10x, sample female

value: female

value: adult


title: S33_Rep2e_4Gy_4h_X

tag: treatment irradiation

value: 4 Gy X-ray


title: EM+E2_32_rep3 [M+E_32_3]

source_name: EM+E2 32d_whole body


title: ACE2-KO rep2

city: Bydgoszcz

first: Katarzyna

last: Bilińska

address: M.Skłodowskiej-Curie 9

country: Poland

institute: Nicolaus Copernicus University

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 the RNA-Seq reads are aligned to the reference genome (mm10) using Bowtie vs 2.3.3.1 generating genome alignments.
Operating on the RNA-Seq alignments and Cuffinks processing, Cuffidfff tracks the mapped reads and determines the fragment per kilobase per million mapped reads (FPKM) for each transcript in all the samples.
Assembly: mm10
Supplementary files format and content: For each pair of samples (control vs. case), the differential expression values such as fold change and p-value are computed at gene level.

source_name: olfactory epithelium

extract_protocol:
Olfactory mucosa were dissected from nasal cavity under binocular microscope and immediately frozen on dry ice. RNA was extracted using QIAGEN RNeasy Plus Mini kit with gDNA Eliminator columns, the concentration of which was measured using NanoDrop
The library preparation protocol was self-established and validated on the basis of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: olfactory epithelium

value: post natal day 60


title: lung single cell 90

description:
lung single cell 90
898s_D3

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

extract_protocol:
A 12 week-old female Prox1-GFP mouse was perfused with PBS to clear the blood. Subsequently, the lung was filled with 10 mg mL-1 dispase II in PBS via the trachea and incubated for 10 min at RT. Next, 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I was injected into the lung lobes and lung tissue was minced with scissors in 1.5 mL of 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I. Tissue dissociation was performed for 15 min at 37°C and 750 rpm. Digests were quenched by the addition of 2 mM EDTA f.c., filtered through a 40 µm nylon filter, washed with FACS buffer (PBS, 0.5% FBS, and 2 mM EDTA) for 5 min at 300 g, RT and processed for FACS sorting. Briefly,  Fc-receptor binding was blocked with rat anti-mouse CD16/CD32 for 10 min on ice. Thereafter, samples were incubated with fluorophore-conjugated anti-CD31 (clone 390, 1.0 µg mL-1), anti-CD45 (clone 30-F11, 4 µg mL-1), anti-CD11b (clone M1/70, 4 µg mL-1) and anti-TER-119 (clone TER-119, 4 µg mL-1) antibodies for 20 min on ice. Prior to sorting of CD31+ Prox1-GFP+ CD45- CD11b- Ter119- lymphatic and CD31+ Prox1-GFP- CD45- CD11b- Ter119- blood endothelial cells on a BD FACS Aria III samples were again filtered through a 40 µm filter and supplemented with 1 µM SytoxBlue to label dead cells.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology


title: S33_Rep2e_4Gy_4h_12C

value: 4 Gy carbon-ion

value: head and neck squamous cell carinoma (HNSCC)

tag: hpv-status


title: ACE2-KO rep1


title: lung single cell 89

description:
lung single cell 89
898s_D2

value: lung


title: ACE2-KO rep3


title: lung single cell 86

description:
lung single cell 86
898s_D22

value: adult mice


title: S2_Rep2e_4Gy_4h_12C

value: HPV-positive


title: lung single cell 88

description:
lung single cell 88
898s_D24


title: EM+E2_64_rep2 [M+E_64_1]

value: AB

value: fr-firststrand (dUTP)


title: WT rep 3

value: wild type


title: EM+E2_32_rep1 [M+E_32_1]


title: S40_Rep2e_4Gy_4h_12C


title: S27_Rep2_4Gy_4h_12C


title: S154_Rep2e_0Gy_4h

source_name: UPCI:SCC154 cell line


title: WT rep2


title: lung single cell 85

description:
lung single cell 85
898s_D21


title: S131_Rep2e_0Gy_4h


title: EM+E2_32_rep2 [M+E_32_2]


title: SOK6_Rep2e_0Gy_4h

source_name: OKF6 cell line

value: oral ketratinocytes


title: WT rep1


title: lung single cell 84

description:
lung single cell 84
898s_D20


title: lung single cell 87

description:
lung single cell 87
898s_D23


title: lung single cell 82

description:
lung single cell 82
898s_D19


title: EM+E2_2_rep2 [M+E_2_2]

source_name: EM+E2 2d_whole body


title: LC-48h (WT + KO)

description: Use tdTomato gene expression for WT/KO annotation

data_processing:
Illumina Casava1.7 software used for basecalling.
Cellranger v3.0.2
Raw data files from two mixed samples based on 10×Genomics were processed   by Cell Ranger software suite (version 3.0.2) with default parameters, using the   mm10 reference genome (Cell ranger reference version 2020). The standard   reference genome was modified to incorporate with the coding sequence (CDS)   of tdTomato gene. The Seurat package (version 4) was used to analyze the data. Typically, the principal component analysis (PCA) was performed for dimension reduction and t-distributed stochastic neighbor embedding (t-SNE) was further used to project the cells into two dimensions.
Genome_build: mm10 (with tdTomato CDS incorpration)
Supplementary_files_format_and_content: gzipped text file of gene expression matrix and cell barcodes

growth_protocol: ESCs were grown in serum/LIF medium.  EpiLCs were grown in the medium containing N2B27, 20 ng/ml activin A, 12 ng/ml bFGF, and 1% KSR.

extract_protocol:
WT (ROSAmT/mG) and Cnot8 KO ESCs (S/LIF) and 48h-EpiLCs were dissociated into single cells with TrypLE Express (Gibco, 12605010) for 1 min at 37 °C, and equal volume of FBS was used for inactivation of TrypLE Express. Cells were centrifuged at 1,000g for 3 min, washed twice with DPBS, and passed through a 40 um strainer. Then the cells were counted and resuspended in 0.04% BSA in DPBS. Equal cell numbers of WT (ROSAmT/mG) or Cnot8 KO ESCs (S/LIF) were mixed, which was similar to that in 48h-EpiLCs, totally producing 2 samples. The cells were used for construction of scRNA-seq libraries.
The 10X Genomics-based single-cell RNA sequencing (scRNA-seq) libraries were constructed using the Chromium™ Single Cell 3’ Reagent Kits v2 Protocol (CG00052).
10 X Genomics-based scRNA-seq

treatment_protocol: Serum/LIF ESCs were cultured on feeder-coated petri dishes or plates at 37 °C under 5% CO2. EpiLCs were cultured on each well of 12-well plate precoated with a 1:100 mix of Matrigel and DMEM/F12 at 37 °C under 5% CO2,during which, the culture medium was replaced every day.

value: ICR

tag: differentiation hour

value: LC 48h


title: S/LIF ESCs (WT + KO )

value: ESC (0h)


title: lung single cell 83

description:
lung single cell 83
898s_D1

tag: age


title: S33_Rep2e_0Gy_4h

source_name: Cal33 cell line

value: HPV-negative


title: lung single cell 81

description:
lung single cell 81
898s_D18


title: EM+E2_16_rep1 [M+E_16_1]

source_name: EM+E2 16d_whole body

value: whole body


title: S99_Rep2e_0Gy_4h

source_name: UPCI:SCC099 cell line


title: S40_Rep2e_0Gy_4h

source_name: UPCI:SCC040 cell line


title: EM+E2_16_rep3 [M+E_16_3]


title: WGBS_E11.5_XX_Control_Rep_1

data_processing:
The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2.  CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.

source_name: Primordial germ cells

extract_protocol:
Female E10.5 and E11.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Cells were sorted into lysis buffer from Zymo MethylDirect Kit and bisulfite converted, and then constructed libraries with Zymo Pico Methylation Kit.

value: Primordial germ cells

tag: gender

value: Female


title: EM+E2_2_rep1 [M+E_2_1]


title: WGBS_E11.5_XX_ECKO_Rep_2

tag: cell type

value: Eed -/-


title: EM+E2_16_rep2 [M+E_16_2]


title: lung single cell 78

description:
lung single cell 78
898s_D15

source_name: Lung


title: S27_Rep2_0Gy_4h

source_name: Cal27 cell line


title: lung single cell 76

description:
lung single cell 76
898s_D13


title: S131_Rep2l_8Gy_72h_X

source_name: UPCI:SCC131 cell line

value: 8 Gy X-ray


title: lung single cell 79

description:
lung single cell 79
898s_D16


title: lung single cell 80

description:
lung single cell 80
898s_D17


title: WGBS_E11.5_XX_ECKO_Rep_1

tag: developmental stage


title: SOK6_Rep2l_8Gy_72h_X


title: S40_Rep2l_8Gy_72h_X

value: head and neck squamous cell carinoma (HNSCC)


title: lung single cell 75

description:
lung single cell 75
898s_D12

value: lung


title: lung single cell 77

description:
lung single cell 77
898s_D14

value: adult mice


title: S99_Rep2l_8Gy_72h_X


title: 3T3 cells overexpressing PARG Rep2

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina FQ sequencing files were imported into CLC Genomics Workbench version 12.0.
The reads were trimmed to remove adapters then the trimmed reads were mapped to the Mouse genome using CLC’s default parameters (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distances, maximum number of hits per read = 10).
All samples have a minimum of 50 million reads with 92% or greater mapping in pairs to the genome.  At least 97% of the mapped reads mapped to genes.
N=3 for both treatment groups.  Differential expression for RNA-seq analyses was performed in CLC Genomics Workbench 12.0 on the gene-level expression tracks using whole transcriptome RNA-seq with TMM normalization.
Differential expression due to treatment (hPARG+ or control) was tested with the comparison against the control group.
Supplementary_files_format_and_content: csv, Gene RPKM and expression changes

source_name: 3T3 cells overexpressing PARG

growth_protocol: 3T3_pLVX_TetOne-Puro cells were cultured in RPMI-1640 (Bio-Whittaker, Walkersville, MD) supplemented with 10% FBs (Hyclone, Logan, UT), pen/strap (1x), non-essential amino acids (0.1mM)

extract_protocol:
RNeasy kit (Qiagen), mRNA was enriched via Poly(A) selection.
Novogene libraries were prepared using NEB’s Ultra II RNA library kit

treatment_protocol: 3T3 cells were transduced with lentivirus construct encoding PARG cDNA with cleavable mClover3 under TetOne Doxycycline inducible promoter. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml Doxycycline and RNA isolated. 3 wells for untreated control group, 3 wells for treated inducible experimental group.

tag: cell line

tag: type

value: malignant

value: PARG overexpression


title: S27_Rep2_8Gy_72h_X


title: S2_Rep2l_8Gy_72h_X

source_name: UD-SCC2 cell line

value: HPV-positive


title: 3T3 cells not induced Rep3

source_name: 3T3 cells not induced

value: control


title: HFKO1

city: Shenzhen

first: Hengjun

last: Huang

address: 1088 Xueyuan Avenue

department: Department of Biology

institute: Southern University of Science and Technology

data_processing:
Base calling was conducted by Bcl2fastq (v2.17.1.14)
Quality control was performed by FastQC(v0.10.1) and Cutadapt (V1.9.1) was used to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20
Clean reads were mapped to GRCm38 genome using Hisat2(V2.0.1) with the default parameter
Gene expression was calculated using Htseq software (V 0.6.1), which used FPKM (Fragments Per Kilo bases Per Million reads) (Mortazavi, 2008) to calculate gene expression
Differential alternative splicing was analyzed using rMATS(4.1.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: all_fpkm.txt: Text file include gene counts and FPKM values
Supplementary_files_format_and_content: as.txt: Differential alternative splicing

source_name: Spleen

extract_protocol:
FACS sorted follicular B cells (B220+CD93-CD23highCD21low)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: follicular B cells

value: 7 week

value: hnRNPF knockout (HFKO)


title: lung single cell 72

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description:
lung single cell 72
898s_C9

tag: genotype


title: lung single cell 73

description:
lung single cell 73
898s_D10


title: HFWT2

value: WT


title: HFWT1


title: SOK6_Rep2l_8Gy_48h_X

value: oral ketratinocytes

value: HPV-negative


title: S33_Rep2l_8Gy_72h_X


title: lung single cell 69

description:
lung single cell 69
898s_C6


title: lung single cell 71

description:
lung single cell 71
898s_C8


title: 3T3 cells not induced Rep2


title: 3T3 cells not induced Rep1


title: 3T3 cells overexpressing PARG Rep3


title: 3T3 cells overexpressing PARG Rep1


title: HFKO2


title: S154_Rep2l_8Gy_72h_X


title: S131_Rep2l_8Gy_48h_X


title: lung single cell 70

description:
lung single cell 70
898s_C7


title: lung single cell 74

description:
lung single cell 74
898s_D11


title: lung single cell 68

description:
lung single cell 68
898s_C5


title: lung single cell 67

description:
lung single cell 67
898s_C4


title: Learned_Motor Learning_Fgfr2_KO Rep2

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Raw sequencing reads were examined by quality metrics and analyzed using the Cell Ranger pipeline (10X Genomics).
Given that the single-nuclei RNA-seq assay captures unspliced pre-mRNA with introns as well as mature mRNA, a custom reference is not appropriate for alignment that only counts reads aligned to exons. Therefore, we created a new "pre-mRNA" GTF with listing each gene transcript locus as an exon and then run cellranger mkref command to generate a genome reference. Next, the cellranger count command was used to generate raw feature-barcode matrices aligned to the newly generated reference (mm10) above.
To ensure PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level.
To minimize batch effects in combining the different samples, we used cellranger aggr pipeline to equalize the read depth between samples and recomputes the matrices. In this way, the combined cell x UMI count matrix was generated for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: A H5 file of combined cell x UMI count matrix for all samples

source_name: Single nuclei

extract_protocol:
Whole cerebellum or anterior lobules (anterior dorsal cerebellar vermis, ADCV) microdissected from mice upon different training conditions (Activation rotarod (baseline, activation), accelerating motor learning (Baseline, learning, learned), and associated motor learning (Baseline, learning and learned) were rapidly transferred to a chilled dounce homogenizer and dounced in 1.5 ml homogenization buffer containing 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitor to release nuclei. Each sample were mixed with 1.5 ml 50% iodixanol (Sigma) and layered onto 29% iodixanol. The gradient was centrifuged at 10,000 g for 30 mins at 4°C. Nuclei were diluted in 10% BSA with Dyecycle Ruby for FACS. Dyecycle Ruby was used for singlet and GFP for positive was sorted for Purkinje nuclei. After counting and analyzing nuclei integrity, all samples were subjected to library construction by using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics).
Single nuclei libraries were prepared for sequencing using standard protocols
Single nuclei RNA seq

value: Cerebellum

tag: genotype/variation

value: Fgfr2 KO


title: S154_Rep2l_8Gy_48h_X

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Rsubreads raw counts per HGNC symbol in text files

extract_protocol:
Total RNA was extracted using Nucleospn RNA extraction kit from Macherey & Nagel
RNA libraries were prepared for sequencing using standard Illumina protocols


title: lung single cell 65

description:
lung single cell 65
898s_C2


title: ATAC-seq_p53-KO

first: Jia

last: Yuan

address: Yueyang road 320, Xuhui, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Reads were aligned to the (GRCm38/mm10) reference mouse genome.
Use Markduplicates to examine aligned records in BAM datasets to locate duplicate molecules
Use MACS2 callpeak to call peaks from alignment results
Use Wig/BedGraph-to-bigWig to convert  Bed files produced from the previous step to bigWig.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig files

source_name: primary macrophage

growth_protocol: bone marrow cells were isolated from femurs and tibias of adult mice and cultured for 5 days in a DMEM medium supplemented with M-CSF conditional medium

extract_protocol:
Fragmentation and PCR amplification were performed according to Vazyme ATAC-seq kit.
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: Fifty thousand viable primary macrophages were lysed in 10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40 to obtain the nuclear pellet.

value: p53 knock out

value: primary macrophage


title: E2_8_rep3 [E_8_3]

last: Chen

source_name: E2 8d_whole body

value: AB

tag: treatment

value: whole body

tag: library type

value: fr-firststrand (dUTP)


title: ATAC-seq_WT

value: wild type


title: S99_Rep2l_8Gy_48h_X

value: 8 Gy X-ray

tag: tissue

value: head and neck squamous cell carinoma (HNSCC)


title: lung single cell 64

description:
lung single cell 64
898s_C24

value: lung

value: adult mice


title: E2_8_rep2 [E_8_2]


title: Baseline_Motor Learning_Fgfr2_KO Rep2


title: E2_8_rep1 [E_8_1]


title: CHIP-seq_p53-KO input

data_processing:
Reads were aligned to the (GRCm38/mm10) reference mouse genome.
Use Markduplicates to examine aligned records in BAM datasets to locate duplicate molecules
Use MACS2 callpeak to call peaks from alignment results
Use bamCoverage generates a coverage bigWig file from a given BAM or CRAM file.
Use computeMmatrix prepares data for plotting a heatmap or a profile of given regions.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bedGraph files

extract_protocol:
Lysates were clarified from sonicated nuclei and nucleus proteins-DNA complexes were isolated with indicated antibodies. And then the immunoprecipitated DNA were purified and subjected to high-throughput sequencing
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: non-treated (NT) or treated with nigericin after LPS priming (Nig)

value: none; untreated


title: lung single cell 66

description:
lung single cell 66
898s_C3


title: CHIP-seq_p53-KO SIRT1

tag: chip antibody

value: Sirt1 (CST, 8469S)


title: S40_Rep2l_8Gy_48h

tag: replicate

tag: time


title: SOK6_Rep2l_4Gy_72h_X

source_name: OKF6 cell line

tag: treatment irradiation

value: 4 Gy X-ray

tag: hpv-status


title: E2_64_rep2 [E_64_2]

source_name: E2 64d_whole body

tag: age


title: ATAC-seq_Ezh2-KO

value: Ezh2 knock out


title: S27_Rep2_8Gy_48h_X

value: HPV-negative


title: lung single cell 62

description:
lung single cell 62
898s_C22


title: S33_Rep2l_8Gy_48h_X

source_name: Cal33 cell line


title: S2_Rep2l_8Gy_48h_X

value: HPV-positive


title: S154_Rep2l_4Gy_72h_X

source_name: UPCI:SCC154 cell line


title: lung single cell 60

description:
lung single cell 60
898s_C20


title: E2_64_rep1 [E_64_1]


title: lung single cell 61

description:
lung single cell 61
898s_C21


title: E2_32_rep2 [E_32_2]

source_name: E2 32d_whole body


title: S99_Rep2l_4Gy_72h_X

source_name: UPCI:SCC099 cell line


title: E2_32_rep3 [E_32_3]


title: CHIP-seq_Ezh2-KO input


title: lung single cell 58

description:
lung single cell 58
898s_C19


title: lung single cell 59

description:
lung single cell 59
898s_C1


title: E2_32_rep1 [E_32_1]


title: CHIP-seq_p53-WT input


title: S40_Rep2l_4Gy_72h_X

source_name: UPCI:SCC040 cell line


title: CHIP-seq_Ezh2-KO SIRT1


title: lung single cell 63

description:
lung single cell 63
898s_C23

source_name: Lung


title: lung single cell 57

description:
lung single cell 57
898s_C18


title: E2_2_rep3 [E_2_3]

source_name: E2 2d_whole body


title: lung single cell 56

description:
lung single cell 56
898s_C17


title: CHIP-seq_Ezh2-WT input


title: CHIP-seq_Ezh2-WT SIRT1


title: CHIP-seq_p53-WT SIRT1


title: S131_Rep2l_4Gy_72h_X

source_name: UPCI:SCC131 cell line


title: lung single cell 54

description:
lung single cell 54
898s_C15


title: CHIP-seq_macrophage input


title: S27_Rep2_4Gy_72h_X

source_name: Cal27 cell line


title: lung single cell 55

description:
lung single cell 55
898s_C16


title: E2_2_rep1 [E_2_1]


title: SOK6_Rep2l_4Gy_48h_X

value: oral ketratinocytes


title: S2_Rep2l_4Gy_72h_X

source_name: UD-SCC2 cell line


title: S33_Rep2l_4Gy_72h_X


title: S154_Rep2l_4Gy_48h_X


title: S131_Rep2l_4Gy_48h_X


title: EM+E2_2_rep3 [M+E_2_3]

source_name: EM+E2 2d_whole body


title: E2_16_rep3 [E_16_3]

source_name: E2 16d_whole body


title: E2_16_rep1 [E_16_1]


title: CHIP-seq_macrophage-NT p53


title: E2_16_rep2 [E_16_2]


title: CHIP-seq_macrophage H3k27ac

value: H3K27ac (Abcam, ab4729)


title: CHIP-seq_macrophage-NT input

value: primary macrophage


title: E2_2_rep2 [E_2_2]

value: AB


title: lung single cell 51

description:
lung single cell 51
898s_C12


title: lung single cell 50

description:
lung single cell 50
898s_C11


title: CHIP-seq_macrophage-NT EZH2


title: lung single cell 49

description:
lung single cell 49
898s_C10


title: DMSO_64_rep3 [D_64_3]

source_name: DMSO 64d_whole body

value: DMSO (100μl/L)

value: whole body


title: CHIP-seq_macrophage H3k27me3

source_name: primary macrophage

value: wild type


title: S33_Rep2l_4Gy_48h_X


title: S99_Rep2l_4Gy_48h_X


title: lung single cell 53

description:
lung single cell 53
898s_C14


title: CHIP-seq_macrophage-Nig input

value: treated with nigericin after LPS priming


title: lung single cell 48

description:
lung single cell 48
898s_B9


title: lung single cell 52

description:
lung single cell 52
898s_C13


title: S27_Rep2_4Gy_48h_X

value: head and neck squamous cell carinoma (HNSCC)


title: CHIP-seq_macrophage-Nig EZH2


title: lung single cell 47

description:
lung single cell 47
898s_B8

value: lung


title: SOK6_Rep2l_4Gy_72h_12C

value: 4 Gy carbon-ion


title: S2_Rep2l_4Gy_48h_X


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_4

city: Taipei

first: Pao-Yang

address: 128 Sec. 2, Academia Rd, Nankang,

institute: Academia Sinica

source_name: Primordial germ cells

extract_protocol:
Female E12.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Single Cell RNA sequencing libraries were prepared according to the Smart Seq 2 single cell sequencing protocol (Picelli et al., 2014). The RNA was converted to cDNA in each well using Superscript II (Invitrogen). The cDNA was amplified in each well using a KAPA HiFI HotStart polymerase (KAPA Biosystems) in a PCR run for 18 cycles. cDNA was tagged via the Nextera Tagmentation kit (Illumina) using libraries A and C (Illumina). Indexed cDNA was pooled and run on a 2% agarose gel and the smear between 200-500 bp was extracted. Gel extract was cleaned with the Qiagen Gel Extraction Kit (Qiagen) and sent for sequencing.

value: Primordial germ cells

tag: gender

value: Male


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_2

tag: cell type


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_1

tag: developmental stage


title: lung single cell 45

description:
lung single cell 45
898s_B6

value: adult mice


title: lung single cell 46

description:
lung single cell 46
898s_B7


title: S154_Rep2l_4Gy_72h_12C


title: lung single cell 44

description:
lung single cell 44
898s_B5


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_5


title: S40_Rep2l_4Gy_48h_X

value: 4 Gy X-ray


title: lung single cell 43

description:
lung single cell 43
898s_B4


title: S2_Rep2e_0Gy_4h


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_3


title: S40_Rep2l_4Gy_72h_12C

value: HPV-negative


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_7


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_6


title: S131_Rep2l_4Gy_72h_12C


title: lung single cell 40

description:
lung single cell 40
898s_B24


title: lung single cell 41

description:
lung single cell 41
898s_B2


title: S27_Rep2_4Gy_72h_12C


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_8


title: lung single cell 42

description:
lung single cell 42
898s_B3


title: lung single cell 39

description:
lung single cell 39
898s_B23


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_17

value: Eed -/-


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_20


title: S2_Rep2l_4Gy_72h_12C

value: HPV-positive


title: lung single cell 38

description:
lung single cell 38
898s_B22


title: SOK6_Rep2l_4Gy_48h_12C

source_name: OKF6 cell line

value: oral ketratinocytes


title: S33_Rep2l_4Gy_72h_12C


title: S154_Rep2l_4Gy_48h_12C


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_18


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_21


title: Carcino-2

city: Guangzhou

first: li

middle: hao

last: yuan

address: International Biotech Island

institute: Forevergen Biosciences Co.,Ltd

data_processing:
fastqc do QC
Sequenced reads were filter by SOAPnuke1.4.1(-f AGATCGGAAGAGC -r AGATCGGAAGAGC -A 0.62 -l 5 -q 0.25 -Q 2)
fastqc do cleandata QC
bwa-0.7.12 Compare to the reference genome ;CIRI_v2.0.5 get circ sequence
Transcripts Per Kilobase of exon model per Million mapped reads(TPM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM  values for each Sample

source_name: tongue carcinoma tissues

extract_protocol:
Total RNA samples were isolated from obtained tongue tissues using the TRIzolTM reagent. Then, size distribution and integrity of RNA samples from tongue tissues were assessed using Agilent 2100 Bioanalyzer and agarose gel electrophoresis, followed with the removal of rRNA constitutes using the TruSeq RNA Sample Preparation Kit.
RNA library was established from similar volumes of RNA samples in each group using the NEBNext® RNA Library Prep Kit for Illumina, after which they were subjected to deep sequencing on a HiseqTM 2000 system.

tag: Sex

value: tongue carcinoma tissues


title: S99_Rep2l_4Gy_72h_12C


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_19


title: Carcino-1


title: lung single cell 37

description:
lung single cell 37
898s_B21


title: lung single cell 35

description:
lung single cell 35
898s_B1


title: lung single cell 36

description:
lung single cell 36
898s_B20


title: S99_Rep2l_4Gy_48h_12C


title: lung single cell 34

description:
lung single cell 34
898s_B19


title: lung single cell 33

description:
lung single cell 33
898s_B18


title: S40_Rep2l_4Gy_48h_12C


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_22


title: Nor-2

source_name: non-cancerous tongue tissue

value: non-cancerous tongue tissue


title: Nor-3


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_23


title: lung single cell 32

description:
lung single cell 32
898s_B17


title: S33_Rep2l_4Gy_48h_12C

source_name: Cal33 cell line


title: Nor-1


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_24


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_2

value: Female


title: Carcino-3


title: S2_Rep2l_4Gy_48h_12C


title: lung single cell 31

description:
lung single cell 31
898s_B16


title: lung single cell 30

description:
lung single cell 30
898s_B15


title: lung single cell 29

description:
lung single cell 29
898s_B14


title: S131_Rep2l_4Gy_48h_12C


title: lung single cell 28

description:
lung single cell 28
898s_B13


title: S131_Rep2l_0Gy_72h


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_1


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_4


title: refed-BAT31

city: Graz

first: Ingeborg

last: Klymiuk

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical Univ Graz

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip® fluidics station 450: protocol FS450_0002 (7) for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 3.2.)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

source_name: brown adipose tissue

label_protocol: Affymetrix WT PLUS Reagent Kit P/N 703147 Rev3, (Cat No. 902280); Lot: 4248402

extract_protocol: Qiagen microRNAEasy

tag: tag

tag: groupt

value: refed


title: lung single cell 27

description:
lung single cell 27
898s_B12

tag: strain

tag: genotype


title: S27_Rep2_4Gy_48h_12C

first: Kristian

address: Marchioninistr. 15

institute: LMU University Hospital


title: S99_Rep2l_0Gy_72h

source_name: UPCI:SCC099 cell line


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_5

value: wild type


title: lung single cell 26

description:
lung single cell 26
898s_B11


title: S40_Rep2l_0Gy_72h

source_name: UPCI:SCC040 cell line


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_7


title: S154_Rep2l_0Gy_72h

source_name: UPCI:SCC154 cell line


title: lung single cell 25

description:
lung single cell 25
898s_B10

source_name: Lung


title: lung single cell 24

description:
lung single cell 24
898s_A9


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_6


title: refed-BAT7


title: SOK6_Rep2l_0Gy_72h


title: S33_Rep2l_0Gy_72h


title: S27_Rep2_0Gy_72h


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_8


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_3


title: lung single cell 23

description:
lung single cell 23
898s_A8