title: 3′-tag RNA-seq PSAPKO neuron

description:
3′-tag RNA-seq
WT_vs_PSAPKO.csv

value: PSAP KO


title: KO_4h_rep3

status: Public on Jun 23 2020

type: SRA

city: Planegg-Martinsried

first: Vigo

last: Heissmeyer

state: Bayern

address: Großhaderner Str. 9

department: Institute for Immunology

country: Germany

institute: Ludwig-Maximilians-Universität

library_source: transcriptomic

data_processing:
The reads were mapped with STAR1 (version 2.3.1z4) against the mouse genome (GRCm38)
Read counts for genes were derived in two ways: 1. counting read pairs fully contained within annotated genes and 2. counting only read pairs fully consistent with at least one annotated transcript using the ENSEMBL2 annotation GRCm38.75.
Differential analysis: Based on these two count types we   performed a robust differential analysis: we derived three down-sampled count variants: (i) raw read  counts (ii) unique fragment counts (i.e. read pairs mapped exactly to the same genomic positions are only counted once) and (iii) down-sampled counts as proposed in Erhard and Zimmer3. We performed then on all resulting 6 count tables differential analysis using four methods: DESeq4, edgeR5, limma6 and empiRe7. The resulting 6x4=24 outcomes with estimated log2(FC) (FC = fold change) values and multiple-testing corrected p-values were then in turn used to derive a conservative combined differential analysis table: for every gene in a given condition pair we selected the least significant (maximum) p-value (columns with suffix worst_fdr) from these 24 combinations and the weakest log2(FC) (i.e. the one with minimum abs(log2(FC))) (columns log2fc). If the direction of the log2(FC) estimates  was inconsistent (i.e. some where > 0 and some <0) we set the corresponding log2(FC) to zero.
Genome_build: GRCm38
Supplementary_files_format_and_content: roquin_regnase_tcell_knockout_timecourses_with_readinfos.csv (For each gene normed counts per sample (replicate data in columns with suffix counts, robust log2fc-s and fdr-s (see data processing steps above))

molecule: total RNA

organism: Mus musculus

source_name: CD4 T cells

growth_protocol: CD4 T cells were isolated from spleens of Cd4-Cre-ERt2 (WT), Rc3h1/2 fl/fl; Cd4-Cre-ERt2 (iDKO), Zc3h12a fl/fl; Cd4-Cre-ERt2 (iKO) or Rc3h1/2 fl/fl; Zc3h12a fl/f; Cd4-Cre-ERt2 (iTKO) mice and the KO of respective genes induced via 4´-OH-tamoxifen treatment.  Afterwards, the T cells were activated in vitro with anti-CD3/28 under Th1 conditions for 40h, cultivated for further 2 days in IL-2 containing media, and with or without restimulation with anti-CD3/28 subjected for RNA isolation and RNA Seq.

extract_protocol:
T cells were pelleted, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Universal RNA-Seq Library Preparation Kit (NuGEN)

treatment_protocol: T cells were either left untreated (0h) or restimulated for 1h, 2h or 4 with anti-CD3/28.

tag: strain

tag: tissue

value: spleen

tag: cell type

value: Splenic CD4 T cells

tag: genotype

value: Zc3h12a fl/fl; Cd4-Cre-ERt2 (KO)

tag: treatment

value: Restimulation with anti-CD3/28 for 4h


title: IP IgG

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description:
IP of IgG
Paired-end 50bp
processed data file: DAP3_eCLIP-seq_peaks.xlsx

data_processing:
Library strategy: eCLIP-seq
Raw data starting from fastq files are processed and analyzed by using CSI NGS Portal: https://csibioinfo.nus.edu.sg/csingsportal
eCLIP pipeline developed by Gene Yeo's lab was used to identify the peaks. The full protocol is available here: https://github.com/YeoLab/eclip
The peaks were annotated by ANNOVAR for the genes and the genomic regions. For the annotation, the mid-point (i.e. the base at the center) of the peaks are used rather than the entire region for simplicity.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DAP3_eCLIP-seq_peaks.xlsx: The processed data file contains the peaks identified by eCLIP-Seq pipeline and the gene annotations added by ANNOVAR.

organism: Homo sapiens

source_name: human esophageal squamous carcinoma cells

growth_protocol: RPMI medium 10% FBS.

extract_protocol:
Cell lysate was harvested according to eCLIP protocol.
Library was prepared according to eCLIP protocol.

tag: cell line

value: esophageal squamous carcinoma cell line

tag: antibody

value: IgG


title: Untreated AT3 tumor Rep 1

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2016_1 were also provide

molecule: polyA RNA

source_name: mammary gland tumor

growth_protocol:
M/D: Fifty mg slow-release (90 days) medroxyprogesterone acetate (MPA) pellets (Innovative Research of America) were implanted subcutaneously by surgery into 6-9 week-old female (day 0). Mice were administered 200 µL of a 5 mg mL-1 7,12-dimethylbenz[a]anthracene (DMBA; from Sigma-Aldrich) solution in corn oil (Sigma-Aldrich), by oral gavage once a week on weeks 1, 2, 3, 5, 6 and 7 after implantation of the MPA pellet. When tumors reached 0.25cm2 the animals were randomized to the different treatment groups.
AT3: For tumorigenicity assays, 1.0 x 10^6 AT3 cells were injected subcutaneously. When tumors reached 0.25cm2 the animals were randomized to the different treatment groups.

extract_protocol:
Tumors were removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.
mRNA libraries were prepared using the Truseq mRNA library prep kit (Illumina) and sequenced in paired end mode (2X75)

treatment_protocol: 0.5 % NAM was added to the drinking water for 10 days. Drinking water was changed once a week

tag: agent


title: BloodSample132Chemo: 0Radiation: 1

type: genomic

city: Los Angeles

first: Mary

middle: Elizabeth

last: Sehl

state: CA

address: 100 UCLA Medical Plaza, Suite 550

department: Medicine / Hematology-Oncology

country: USA

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Noob normalization using preprocessNoob in the minfi R package

label: Cy3, Cy5

molecule: genomic DNA

source_name: BloodSample132Chemo: 0Radiation: 1

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

extract_protocol: Genomic DNA of whole blood samples

tag: time point

tag: age

tag: chemotherapy any

tag: radiationtherapy any

tag: female

tag: batch number


title: KO_4h_rep2


title: NAM_treated M/D tumor Rep 3

value: NAM


title: TKO_0h_rep3

value: Rc3h1/2 fl/fl; Zc3h12a fl/fl; Cd4-Cre-ERt2 (TKO)

value: untreated


title: NAM_treated M/D tumor Rep 4


title: BloodSample131Chemo: 0Radiation: 1

source_name: BloodSample131Chemo: 0Radiation: 1


title: Input IgG

description:
Size-matched input of IgG
Paired-end 50bp
processed data file: DAP3_eCLIP-seq_peaks.xlsx


title: BloodSample130Chemo: 1Radiation: 1

source_name: BloodSample130Chemo: 1Radiation: 1


title: NAM_treated M/D tumor Rep 2


title: KO_4h_rep1


title: NAM_treated M/D tumor Rep 1


title: KO_2h_rep4

value: Restimulation with anti-CD3/28 for 2h


title: BloodSample129Chemo: 1Radiation: 1

source_name: BloodSample129Chemo: 1Radiation: 1


title: BloodSample128Chemo: 0Radiation: 1

source_name: BloodSample128Chemo: 0Radiation: 1


title: TC32_Wnt_TGFBi_2

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Basecalling was performed by Casava v1.8.2
Reads were trimmed using Trimmomatic v0.36 using options: ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:25 SLIDINGWINDOW:4:15 .
Trimmed reads were aligned to the hg38 reference genome and annotated transcripts (gencode release 26) using RSEM v1.2.31 and the STAR aligner (v2.5.2a) with and default options.
Gene-level counts and expression values in TPM and FPKM were generated by RSEM v1.2.31.
Genome_build: hg38
Supplementary_files_format_and_content: Each gene expression text file is a tab-delimited table derived from RSEM output and has the following columns (header included): 1) ensembl_gene: Ensembl gene ID, 2) gene_name: HGNC gene symbol, 3) length, 4) effective_length, 5) expected_count: un-normalized read count, 6) TPM: transcripts per million normalized counts, and 7) FPKM: fragments per million normalized counts.  See RSEM documentation for full description of columns.

growth_protocol: Cells were cultured in RPMI 1640 media supplemented with 10% fetal bovine serum.

extract_protocol:
RNA extraction was performed using the Zymo Quick RNA kit - R1050
Libraries were prepapred using the Illumina TruSeq stranded kit.

treatment_protocol: Cells were treated with vehicle (PBS) or Wnt3a for 4 h, followed by vehicle (DMSO) or TGFBi (SB-505124) for 24 h prior to RNA extraction.

value: Ewing sarcoma-derived cells


title: Untreated M/D tumor Rep 4


title: Input XL1

description:
Size-matched input of DAP3 replicate 1
Paired-end 50bp
processed data file: DAP3_eCLIP-seq_peaks.xlsx


title: BloodSample127Chemo: 0Radiation: 1

source_name: BloodSample127Chemo: 0Radiation: 1


title: KO_2h_rep3


title: KO_2h_rep2


title: Mouse_proB_Mettl14KO_Input.rep1

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
Library strategy: MeRIP-seq
MeRIP-seq
Base-calling was performed using CASAVA.
MeRIP-seq and Input sequencing data were sent to trim-galore to remove low quality reads and adaptor sequence contaminants under default parameters except for “–length 50,”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
m6A peaks and Mett14 dependent  m6A  peaks were identified using exomePeak R/Bioconductor package with default parameters.
Profiles of m6A tag density in Ctrl and Mett14KO proB cells on m6A peaks are generated by plotProfile tool in deeptools 2.0 tool suite.
Genome_build: mm9
Supplementary_files_format_and_content: bed
RIP-Seq
Base-calling was performed using CASAVA.
RIP-seq and Input sequencing reads were aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Fpkm value of samples were generated by cufflinks
Reads count of samples were called by featureCounts function in Rsubread package
Genome_build: mm9
Supplementary_files_format_and_content: csv

source_name: proB cell

growth_protocol: B220+ cells were enriched and cultured in the presence of IL-7 for 5 days.  WT and Mettl14 KO CD19+CD2-Igκ/λ- cells were sorted and subject to m6A-seq analysis (n=2 for WT group and n=1, pooled from 3 mice, for Mettl14 KO group).

extract_protocol:
Total RNA was extracted with Trizol, polyA RNA was enriched with the Dynabeads mRNA Purification Kit (cat# 61006), RNA was fragmented to ~200nt with sonication, and m6A IP was performed with the EpiMark N6-Methyladenosine Enrichment Kit (cat# E1610S)
Library constructed with the SMARTer Stranded Total RNA-Seq Kit v.2 (cat# 634412)

value: Mettl14 Knockout


title: TC32_Wnt_TGFBi_1


title: TC32_Wnt_3


title: KO_2h_rep1


title: BloodSample125Chemo: 1Radiation: 1

source_name: BloodSample125Chemo: 1Radiation: 1


title: BloodSample126Chemo: 1Radiation: 1

source_name: BloodSample126Chemo: 1Radiation: 1


title: Untreated M/D tumor Rep 2


title: BloodSample124Chemo: 0Radiation: 1

source_name: BloodSample124Chemo: 0Radiation: 1


title: TC32_Wnt_TGFBi_3


title: TC32_Wnt_1


title: KO_1h_rep4

value: Restimulation with anti-CD3/28 for 1h


title: TC32_Wnt_2


title: BloodSample123Chemo: 0Radiation: 1

source_name: BloodSample123Chemo: 0Radiation: 1


title: KO_1h_rep2


title: NAM_1d S Rep 5

source_name: Spleen

extract_protocol:
Lymph nodes and spleens were removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.
mRNA libraries were prepared using the Truseq mRNA library prep kit (Illumina) and sequenced in paired end mode (2X75)

treatment_protocol: 0.5% NAM was added to the drinking water of treated animals. NAM was replaced every 7 days.


title: KO_1h_rep3


title: NAM_1d S Rep 4


title: TC32_Veh_3


title: BloodSample122Chemo: 0Radiation: 1

source_name: BloodSample122Chemo: 0Radiation: 1


title: TC32_Veh_2


title: KO_1h_rep1


title: Untreated M/D tumor Rep 3


title: BloodSample121Chemo: 0Radiation: 1

source_name: BloodSample121Chemo: 0Radiation: 1


title: NAM_1d S Rep 3


title: NAM_1d S Rep 2


title: KYSE180_shDAP3 #2

description:
DAP3 knockdown
Strand-specific RNA-Seq
processed data file: dap3_kd_specific_editing_sites_in_escc.xlsx

data_processing:
Reads with adapters, unknown bases more than 10% and low quality bases (<=5) more than 50% were removed using SAOPnuke software.
Clean reads were then mapped to reference genome (hg19) using bwa (v0.7.15-r1140). PCR duplicates were removed with samtools (v1.4.1). The reads with mapping quality score less than 20 were discarded.
Variants were called with an in-house variant caller (Perl script) from the samtools mpileup data.
Candidate editing sites were filtered as the following: SNPs from different databases (1000 Genomes Project, NHLBI GO Exome Sequencing Project (http://evs.gs.washington.edu/EVS/), dbSNP v138) were removed, sites within the first 6 bases of the reads were excluded. For sites not located in Alu elements, the candidates within the 4 bases of a splice junction on the intronic side, and those residing in the homopolymeric regions and in the simple repeats were all removed. Candidate variants located in the reads that map to the non-unique regions of the genome by using BLAT were also excluded. Only A-to-G editing sites based on the strand information were retained.
To obtain high confidence editing events, the candidate sites were required to be supported by at least 20 reads of which at least 2 are edited and both shDAP3 knockdown treatments to result in at least 10% change in the editing level in the same direction.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: dap3_kd_specific_editing_sites_in_escc.xlsx: Excel sheet includes DAP3 knockdown specific high confidence editing events in 2 different ESCC cell lines.

extract_protocol:
Total RNA samples were extracted using Qiagen RNeasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Human ESCC cells were treated with specific shRNAs for silencing DAP3.

tag: shRNA

value: shDAP3 #2


title: BloodSample120Chemo: 1Radiation: 1

source_name: BloodSample120Chemo: 1Radiation: 1


title: Untreated M/D tumor Rep 1


title: NAM_1d S Rep 1


title: KYSE180_shDAP3 #1

source_name: human esophageal squamous carcinoma cells

value: shDAP3 #1


title: BloodSample119Chemo: 1Radiation: 1

source_name: BloodSample119Chemo: 1Radiation: 1


title: KO_0h_rep3

source_name: CD4 T cells


title: KO_0h_rep2


title: BloodSample117Chemo: 0Radiation: 1

source_name: BloodSample117Chemo: 0Radiation: 1


title: BloodSample118Chemo: 1Radiation: 1

source_name: BloodSample118Chemo: 1Radiation: 1


title: KYSE180_shScr

description:
Scramble shRNA treated
Strand-specific RNA-Seq
processed data file: dap3_kd_specific_editing_sites_in_escc.xlsx

value: shScr


title: KO_0h_rep1


title: NAM_3d S Rep 5


title: NAM_3d S Rep 4


title: EC109_shDAP3 #2


title: NAM_3d S Rep 3


title: BloodSample116Chemo: 1Radiation: 1

source_name: BloodSample116Chemo: 1Radiation: 1


title: EC109_shDAP3 #1


title: DKO_4h_rep3

value: Rc3h1/2 fl/fl; Cd4-Cre-ERt2 (DKO)


title: NAM_3d S Rep 2


title: DKO_4h_rep4

value: spleen


title: TC32_Veh_1


title: BloodSample115Chemo: 0Radiation: 1

source_name: BloodSample115Chemo: 0Radiation: 1


title: EC109_shScr


title: BloodSample114Chemo: 0Radiation: 1

source_name: BloodSample114Chemo: 0Radiation: 1


title: DKO_4h_rep2

value: Splenic CD4 T cells


title: NAM_3d S Rep 1


title: KO_0h_rep4

value: Zc3h12a fl/fl; Cd4-Cre-ERt2 (KO)


title: BloodSample113Chemo: 1Radiation: 1

source_name: BloodSample113Chemo: 1Radiation: 1


title: DKO_4h_rep1

value: Restimulation with anti-CD3/28 for 4h


title: NAM_14d S Rep 4


title: NAM_14d S Rep 5


title: NAM_14d S Rep 3


title: BloodSample112Chemo: 0Radiation: 1

source_name: BloodSample112Chemo: 0Radiation: 1


title: NAM_14d S Rep 2


title: NAM_14d S Rep 1


title: BloodSample110Chemo: 0Radiation: 1

source_name: BloodSample110Chemo: 0Radiation: 1


title: DKO_2h_rep3


title: BloodSample111Chemo: 0Radiation: 1

source_name: BloodSample111Chemo: 0Radiation: 1


title: DKO_2h_rep1


title: BloodSample109Chemo: 1Radiation: 1

source_name: BloodSample109Chemo: 1Radiation: 1


title: Untreated S Rep 5

source_name: Spleen


title: DKO_1h_rep4


title: BloodSample108Chemo: 0Radiation: 1

source_name: BloodSample108Chemo: 0Radiation: 1


title: BloodSample107Chemo: 0Radiation: 1

source_name: BloodSample107Chemo: 0Radiation: 1


title: DKO_1h_rep3


title: DKO_2h_rep4


title: Untreated S Rep 3


title: BloodSample106Chemo: 0Radiation: 1

source_name: BloodSample106Chemo: 0Radiation: 1


title: DKO_1h_rep2


title: Untreated S Rep 2


title: DKO_1h_rep1


title: DKO_2h_rep2


type: RNA

city: Indianapolis

first: Rebecca

last: Davidson

state: IN

address: 5042 Melrose Ave

department: Biochemistry and Molecular Biology

institute: IUSM

description: Gene expression data from RANKL stimulation, Stat3 siRNA; biological rep 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: All microarray analyses were performed using the R environment for statistical computing (version 2.15.1).

label: biotin

source_name: RAW 264.7 cells transfected with siStat3 at 24 hours and RANKL 24 hours later

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RAW264.7 cells were seeded at 10^5 cells on 6cm dishes with 5mL MEM-alpha 10% FCS antibiotic-free medium.

extract_protocol: RNA extraction was performed using Qiagen RNeasy Mini Kit per manufacturer's instructions.

treatment_protocol: Cells were grown for 24 hours and treated with 25nM siRNA (either NC control or siRNA for Stat3). After 24 hours, media was changed to MEM-alpha with 10% FCS 1% antibiotic and either 0.1% BSA or 50ng/mL RANKL.


description: Gene expression data from RANKL stimulation, Stat3 siRNA; biological rep 1


title: BloodSample105Chemo: 1Radiation: 1

source_name: BloodSample105Chemo: 1Radiation: 1


description: Gene expression data from RANKL stimulation, Stat3 siRNA; biological rep 2


description: Gene expression data from RANKL stimulation, scramble siRNA; biological rep 2

source_name: RAW 264.7 cells transfected with siScramble at 24 hours and RANKL 24 hours later


title: Untreated S Rep 1


description: Gene expression data from RANKL stimulation, scramble siRNA; biological rep 3


description: Gene expression data from RANKL stimulation, scramble siRNA; biological rep 1


description: Gene expression data from DMSO control, Stat3 siRNA; biological rep 2

source_name: RAW 264.7 cells transfected with siStat3 at 24 hours and DMSO 24 hours later


title: NAM_1d LN Rep 2

source_name: lymph node


description: Gene expression data from DMSO control, Stat3 siRNA; biological rep 3


description: Gene expression data from DMSO control, Stat3 siRNA; biological rep 1


title: Untreated S Rep 4


title: DKO_0h_rep3

source_name: CD4 T cells


title: DKO_0h_rep4


title: BloodSample103Chemo: 1Radiation: 1

source_name: BloodSample103Chemo: 1Radiation: 1


title: NAM_1d LN Rep 1


title: Control_021_ND7

city: Cincinnati

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

description: Inferior Turbinate Brushing

data_processing:
STAR Alignment to GRCh38
Count File Compilation

extract_protocol:
RNEasy
NEBNext Single Cell/Low Input

value: nasal brushings

tag: endotype

tag: disease state

value: Control

tag: time


title: DKO_0h_rep2

tag: strain

tag: tissue


title: BloodSample102Chemo: 1Radiation: 1

source_name: BloodSample102Chemo: 1Radiation: 1


title: NAM_3d LN Rep 4


description: Gene expression data from DMSO control, scramble siRNA; biological rep 3

source_name: RAW 264.7 cells transfected with siScramble at 24 hours and DMSO 24 hours later


title: DKO_0h_rep1

tag: cell type

tag: genotype


title: BloodSample101Chemo: 0Radiation: 1

source_name: BloodSample101Chemo: 0Radiation: 1


description: Gene expression data from DMSO control, scramble siRNA; biological rep 2

tag: cell line


title: NAM_3d LN Rep 3


title: Control_021_ND1

description: Inferior Turbinate Brushing


title: Control_021_ND3

description: Inferior Turbinate Brushing


description: Gene expression data from DMSO control, scramble siRNA; biological rep 1


title: Ino80E13cKO_atac

first: Kenneth

middle: Y

last: Kwan

address: 109 Zina Pitcher Pl

department: MBNI & Human Genetics

library_source: genomic

data_processing:
Sample barcodes separated with Illumina bcl2fastq v2.17.
UMI extracted into read name with UMI-tools v0.5.3. Command invocation: umi_tools extract --stdin {input} --stdout {output} --extract-method=string --bc-pattern=NNNNNNNN --log {log}
Adapter reads removed with Cutadapt v1.13. Command invocation: cutadapt -a {NEX_ONE_PRIMER} -A {NEX_TWO_PRIMER} --minimum-length 30 -o {output[0]} -p {output[1]} {input}
Reads aligned to reference genome with bwa v0.7.15. Command invocation:  bwa mem -M {BWA_INDEX_PREFIX} {input.reads} 2> {log} | samtools sort -o {output}
Duplicate reads marked by Picard. Command invocation:  PicardCommandLine MarkDuplicates  I={input}  O={output} M={log.stats}  ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT TMP_DIR=$(mktemp -d)
Mitochondrial and duplicate reads removed with samtools. Command invocation: samtools idxstats {input[0]} | cut -f 1 | grep -v {MT_LABEL} | xargs samtools view -u -F 1804 -f 2 -q 10 {input}> {output}
Bam files were converted to bedGraphs using bedtools genomecov with scaling to library size
BedGraphs were converted to bigwigs using bedClip and bedGraphToBigWig
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig files for each sample contain the deduplicated and scaled ATACseq reads.

source_name: Cerebral cortex

extract_protocol:
Nuclei were isolated from freshly micro-dissected embryonic 13.5 cortices and homoginezed with a Dounce morter and pestle. 50,000 nuclei per sample where then subjected to the standard ATACseq protocol (Buenrostro et al. 2015)
Nuclei were isolated from freshly micro-dissected embryonic 13.5 cortices and 50,000 nuclei per sample were subjected to the standard ATACseq protocol (Buenrostro et al. 2015)

tag: condition

value: cKO

tag: batch

value: cerebral cortex

tag: Sex

value: male


title: BloodSample104Chemo: 1Radiation: 1

source_name: BloodSample104Chemo: 1Radiation: 1

tag: time point

tag: age


title: BloodSample100Chemo: 1Radiation: 1

source_name: BloodSample100Chemo: 1Radiation: 1

tag: chemotherapy any

tag: radiationtherapy any


title: Ino80E13control_atac

value: control


title: BloodSample98Chemo: 0Radiation: 1

source_name: BloodSample98Chemo: 0Radiation: 1

tag: female

tag: batch number


title: NAM_14d LN Rep 4


title: BloodSample99Chemo: 0Radiation: 1

source_name: BloodSample99Chemo: 0Radiation: 1


title: Control_020_ND14

description: Inferior Turbinate Brushing

tag: endotype


title: Control_020_ND1

description: Inferior Turbinate Brushing

tag: disease state


title: NAM_3d LN Rep 1


title: BloodSample97Chemo: 1Radiation: 1

source_name: BloodSample97Chemo: 1Radiation: 1


title: BloodSample96Chemo: 0Radiation: 1

source_name: BloodSample96Chemo: 0Radiation: 1


title: NAM_14d LN Rep 3


title: NAM_14d LN Rep 2


title: BloodSample95Chemo: 0Radiation: 1

source_name: BloodSample95Chemo: 0Radiation: 1


title: Control_019_ND3

description: Inferior Turbinate Brushing

tag: time


title: NAM_14d LN Rep 1

tag: strain


title: Control_019_ND7

description: Inferior Turbinate Brushing

tag: tissue


title: BloodSample94Chemo: 0Radiation: 1

source_name: BloodSample94Chemo: 0Radiation: 1


title: Control_019_ND1

description: Inferior Turbinate Brushing

value: A


title: Control_018_ND7

description: Inferior Turbinate Brushing


title: Untreated LN Rep 3


title: Control_018_ND3

description: Inferior Turbinate Brushing


title: Control_018_ND1

description: Inferior Turbinate Brushing


title: BloodSample91Chemo: 0Radiation: 1

source_name: BloodSample91Chemo: 0Radiation: 1


title: Untreated LN Rep 1


title: BloodSample93Chemo: 0Radiation: 1

source_name: BloodSample93Chemo: 0Radiation: 1


title: NAM_3d LN Rep 2

source_name: lymph node


title: Control_020_ND7

description: Inferior Turbinate Brushing


title: BloodSample90Chemo: 0Radiation: 1

source_name: BloodSample90Chemo: 0Radiation: 1


title: BloodSample89Chemo: 0Radiation: 1

source_name: BloodSample89Chemo: 0Radiation: 1


title: BloodSample88Chemo: 0Radiation: 1

source_name: BloodSample88Chemo: 0Radiation: 1


title: Control_017_ND1

description: Inferior Turbinate Brushing


title: Doc5_pos_rep1 (RNA-seq)

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Subread-1.6.4; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in 2 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.10 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

extract_protocol:
RNA extraction from sorted P14 T cells was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

value: Male

tag: cell type

value: ID3GFP+ P14 T cells

tag: infection

value: LCMV Docile


title: Doc5_pos_rep2 (RNA-seq)


title: Doc5_neg_rep2 (RNA-seq)

value: ID3GFP- P14 T cells


title: Doc5_neg_rep1 (RNA-seq)


title: Control_015_ND7

description: Inferior Turbinate Brushing


title: Control_017_ND3

description: Inferior Turbinate Brushing


title: BloodSample87Chemo: 0Radiation: 1

source_name: BloodSample87Chemo: 0Radiation: 1


title: Control_013_ND1

description: Inferior Turbinate Brushing


title: BloodSample86Chemo: 0Radiation: 1

source_name: BloodSample86Chemo: 0Radiation: 1


title: Control_012_ND1

description: Inferior Turbinate Brushing


title: Untreated LN Rep 2


title: BloodSample85Chemo: 1Radiation: 1

source_name: BloodSample85Chemo: 1Radiation: 1


title: BloodSample92Chemo: 0Radiation: 1

source_name: BloodSample92Chemo: 0Radiation: 1


title: BloodSample84Chemo: 0Radiation: 1

source_name: BloodSample84Chemo: 0Radiation: 1


title: Control_017_ND7

description: Inferior Turbinate Brushing


title: Doc21_neg_rep2 (RNA-seq)


title: Control_003_ND1

description: Inferior Turbinate Brushing


title: BloodSample83Chemo: 0Radiation: 1

source_name: BloodSample83Chemo: 0Radiation: 1


title: BloodSample82Chemo: 0Radiation: 1

source_name: BloodSample82Chemo: 0Radiation: 1


title: ARDS_019_ND1

description: Inferior Turbinate Brushing

value: C

value: PARDS


title: Doc12_pos_rep2 (RNA-seq)

value: spleen


title: Doc12_pos_rep1 (RNA-seq)


title: ARDS_018_ND3

description: Inferior Turbinate Brushing


title: ARDS_018_ND1

description: Inferior Turbinate Brushing


title: Doc12_neg_rep2 (RNA-seq)


title: BloodSample80Chemo: 0Radiation: 1

source_name: BloodSample80Chemo: 0Radiation: 1


title: BloodSample79Chemo: 0Radiation: 1

source_name: BloodSample79Chemo: 0Radiation: 1


title: ARDS_017_ND14

description: Inferior Turbinate Brushing


title: Arm5_pos_rep2 (RNA-seq)

value: LCMV Armstrong


title: Doc12_neg_rep1 (RNA-seq)


title: Doc21_pos_rep1 (RNA-seq)


title: ARDS_017_ND7

description: Inferior Turbinate Brushing


title: BloodSample78Chemo: 0Radiation: 1

source_name: BloodSample78Chemo: 0Radiation: 1


title: Doc21_pos_rep2 (RNA-seq)


title: BloodSample77Chemo: 0Radiation: 1

source_name: BloodSample77Chemo: 0Radiation: 1


title: Arm5_pos_rep1 (RNA-seq)


title: Arm5_neg_rep2 (RNA-seq)


title: BloodSample76Chemo: 0Radiation: 1

source_name: BloodSample76Chemo: 0Radiation: 1


title: ARDS_017_ND1

description: Inferior Turbinate Brushing

value: B


title: Doc21_neg_rep1 (RNA-seq)


title: Control_002_ND1_NEB

description: Inferior Turbinate Brushing


title: ARDS_016_ND14

description: Inferior Turbinate Brushing


title: Arm5_neg_rep1 (RNA-seq)


title: Arm21_pos_rep2 (RNA-seq)


title: BloodSample75Chemo: 0Radiation: 1

source_name: BloodSample75Chemo: 0Radiation: 1


title: BloodSample74Chemo: 0Radiation: 1

source_name: BloodSample74Chemo: 0Radiation: 1


title: ARDS_016_ND7

description: Inferior Turbinate Brushing


title: SCC1_AID_Neuron_Ctrl_rep1

city: Beijing

first: Ke

last: Zhang

state: Beijing

address: Haidian District

department: School of Life Sciences

country: China

institute: Tsinghua university

data_processing:
Basecalls performed using CASAVA version 1.8
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples.

extract_protocol:
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously with minor modification (Picelli et al., 2014). Cells were lysed in hypotonic lysis buffer (Amresco, M334), and the polyadenylated mRNAs were captured by the PolyT primers. After ~3–10 min lysis at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were sheared by Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.

treatment_protocol: SCC1-AID-GFP mESCs were cultured in non-adhesive bacterial dishes using ES culture medium  minus LIF for 4 days. Retinoic acid (RA) was then added to medium to a final  concentration of 2µg/mL. Medium was changed every day. On the 5th day of adding RA, embryonic bodies were dissociated by 0.25% Trypsin-EDTA and plated to poly-L-ornithine and Laminin pre-coated dish. Cells were cultured in DMEM/F-12 with B27 and were incubated for two days. The medium was switched to BME with B27 for another two days and then treated without/with Auxin (500 μM) for 1day. The differentiated cells were dissociated into single cells. Sorting was then conducted using FACS Jazz to remove all the dead cells. Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO (SCC1 -) groups, while the differentiated cells without the auxin treatment were collected as SCC1 WT (SCC1 +) groups.

value: neuron

tag: auxin treatment

value: no

tag: genotype

value: SCC1 WT


title: Arm21_pos_rep1 (RNA-seq)


title: SCC1_AID_Neuron_Auxin_rep1

value: yes

value: SCC1 KO


title: BloodSample73Chemo: 1Radiation: 1

source_name: BloodSample73Chemo: 1Radiation: 1


title: ARDS_016_ND3

description: Inferior Turbinate Brushing

value: nasal brushings


title: ARDS_017_ND3

description: Inferior Turbinate Brushing


title: BloodSample72Chemo: 0Radiation: 1

source_name: BloodSample72Chemo: 0Radiation: 1


title: Arm21_neg_rep2 (RNA-seq)


title: ARDS_016_ND1

description: Inferior Turbinate Brushing


title: BloodSample70Chemo: 0Radiation: 1

source_name: BloodSample70Chemo: 0Radiation: 1


title: Mouse_lung_nuclei2

city: Saint Louis

first: Jeffrey

last: Koenitzer

state: MO

address: 660 Euclid Ave.

institute: Washington University in St. Louis

description: single cell RNA-seq

data_processing:
sNuc-10X Chromium:We used the  zUMIs pipeline (Parekh et al., 2018), to process the single cell and nucleus sequencing data from mouse lung. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to a mouse reference genome (mm10) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: UMI count table

source_name: Lung

extract_protocol:
Lung single cell suspension protocol: Lungs were obtained freshly from wild type C57Bl/6J mice and cells isolated using a combination of enzymatic (collagenase, DNAse for 30 min at 37 C) and mechanical (GentleMacs, lung1 and lung2 programs) digestion. Dead cells and degraded nucleotides were removed with an Optiprep gradient, prior to microfluidic coencapsulation with barcoded beads according to the 10x Chromium protocol.
Lung nucleus isolation protocol: Lung tissue from wild type adult C57Bl/6J mice was isolated at the time of sacrifice and snap frozen in liquid nitrogen. Later, tissue was cut to ~7mm pieces, injected with 1 mL ice-cold Nuclei EZ Lysis buffer (NUC-101, Sigma-Aldrich) supplemented with protease and Rnase inhibitors, and minced in additional lysis buffer followed by mechanical dissociation using GentleMacs lung1 and 2 programs. Suspended nuclei were filtered through 40 micron mesh, washed with cold PBS with Rnase inhibitor, and passed through a 5 micron filter, pelleted at 600 x g, and resuspended in PBS+BSA with dilution to 10,000 nuclei/ul for 10x Chromium analysis
RNA libraries were prepared for sequencing using standard 10X Chromium procedure

tag: transcriptome

value: Single nuclei

tag: platform

value: 10x Chromium


title: Arm21_neg_rep1 (RNA-seq)

tag: Sex

value: Male


title: Mouse_lung_cells

description: single cell RNA-seq

value: Single cells


title: Mouse_lung_nuclei1

description: single cell RNA-seq


title: ARDS_015_ND3

description: Inferior Turbinate Brushing


title: BloodSample69Chemo: 0Radiation: 1

source_name: BloodSample69Chemo: 0Radiation: 1

tag: time point

tag: age


title: ARDS_015_ND1

description: Inferior Turbinate Brushing


title: Hi-C_SCC1_diff_auxin_rep1

description: EB_SCC1_auxin_rep12_allValidPairs.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size and 300Kb bin size wereused and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples. While the validpair txt file indicates the paired interaction reads for each sample.

source_name: SCC1-AID-mESC cell line

extract_protocol:
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq

treatment_protocol: SCC1-AID-mESC cell line was generously provided by Dr. Robert Klose. mESCs were cultured in DMEM supplemented with 10 % Fetal Bovine Serum (FBS), MEM Non-Essential Amino Acids Solution (Gibco, Cat#. 111040050), GlutaMAX™ Supplement (Gibco, Cat # 35050061), 2-mercaptoethanol (Specialty media, Cat # ES-007-E), EmbryoMax 100X nucleosides (Millipore, Cat # ES-008-D), LIf (1000 U/ml, Millipore, Cat # ESG1107. For differentiation, ESCs were cultured in medium without LIF for 3 days. and treated without/with auxin (500 μM)(Nora et al., 2017) (Sigma, Cat # 6505-45-9) for 1 day. SCC1-AID differentiated cells were dissociated into single cells. Sorting was then conducted using FACS Jazz (BD Biosciences). Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO groups, while the differentiated cells retaining relatively high GFP fluorescence signals without the auxin treatment were collected as SCC1 positive groups.


title: ARDS_014_ND14

description: Inferior Turbinate Brushing


title: Doc5_neg_rep3 (ATAC-seq)

data_processing:
The paired-end libraries were mapped to the GRCm38/mm10 reference genome by using Subread-1.6.2. Only uniquely mapped read-pairs were allowed in mapping. Peaks were then called from the mapping results by using Homer (v4.9) at an FDR cutoff of 1E-5.
The peaks from all the samples were merged by taking the union of the peaks; the merged peaks were then assigned to the nearest genes in the NCBI RefSeq gene annotation for mm10 (build 38.1). The mapped read-pairs were assigned to the merged peak regions by using featureCounts.
Merged peaks were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.7 in at least 2 libraries. Counts were converted to log2 CPM values, library normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each merged peak, and empirical Bayes moderated t-statistics were used to assess differences of accessibility of the chromatin. Merged peaks were called differential if they achieved a false discovery rate of 0.2 or less, and have a fold change greater than 2 between the two compared cell types.
Genome_build: mm10
Supplementary_files_format_and_content: Supp_Raw_Counts.txt
tab-delimited files consisting of log2 CPM (counts per million mapped reads) values of peaks and their corresponding genes

growth_protocol: P14 T cells were transferred into naïve mice and challenged with LCMV Docile or Armstrong; cells were isolated based on ID3GFP and TIM3 expression

extract_protocol:
DNA was extracted using cell lysis buffer as described previously (Buenrostro, et al 2013)
Libraries were generated following the protocol as described previously (Buenrostro, et al 2013)

value: LCMV Docile


title: Doc5_pos_rep1 (ATAC-seq)

value: ID3GFP+ P14 T cells


title: Doc5_neg_rep1 (ATAC-seq)

value: ID3GFP- P14 T cells


title: Doc5_pos_rep3 (ATAC-seq)


title: ARDS_014_ND1

description: Inferior Turbinate Brushing

value: PARDS


title: Hi-C_SCC1_diff_con_rep1


title: BloodSample67Chemo: 0Radiation: 1

source_name: BloodSample67Chemo: 0Radiation: 1

tag: chemotherapy any

tag: radiationtherapy any


title: Zf_30h_trunk

city: Tampa

first: Saulius

last: Sumanas

state: Florida

address: 560 Channelside Dr

institute: University of South Florida

description: Single-cell RNAseq

data_processing:
All processing was performed in 10X Genomics CellRanger v3.0.2 using default parameters
Raw basecall files were assembled into fastq files using 'mkfastq' function
The 'count' function was used to align Fastq files to zebrafish genome v.11  and to obtain the gene expression matrices
Genome_build: GRCz11
Supplementary_files_format_and_content: mtx matrix files

organism: Danio rerio

source_name: Zebrafish Trunks

extract_protocol:
Whole wildtype zebrafish trunks at 30 hpf were dissociated into a single cell suspension using a cold protease treatment.Single-cell suspensions were processed through the Chromium platform (10X Genomics) to generate single-cell cDNA libraries
cDNA was amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: 30 hpf

value: trunk

value: wildtype


title: ARDS_013_ND7

description: Inferior Turbinate Brushing


title: BloodSample71Chemo: 0Radiation: 1

source_name: BloodSample71Chemo: 0Radiation: 1

tag: female

tag: batch number


title: ARDS_013_ND3

description: Inferior Turbinate Brushing

tag: endotype

tag: disease state


title: BloodSample66Chemo: 0Radiation: 1

source_name: BloodSample66Chemo: 0Radiation: 1


title: Doc21_pos_rep3 (ATAC-seq)

value: spleen

tag: time


title: Doc21_pos_rep1 (ATAC-seq)

tag: tissue


title: ARDS_013_ND1

description: Inferior Turbinate Brushing


title: BloodSample64Chemo: 1Radiation: 1

source_name: BloodSample64Chemo: 1Radiation: 1


title: ARDS_012_ND7

description: Inferior Turbinate Brushing


title: Doc21_neg_rep3 (ATAC-seq)

tag: cell type


title: Doc21_neg_rep1 (ATAC-seq)

tag: infection


title: BloodSample65Chemo: 1Radiation: 1

source_name: BloodSample65Chemo: 1Radiation: 1


title: BloodSample68Chemo: 0Radiation: 1

source_name: BloodSample68Chemo: 0Radiation: 1


title: Arm5_pos_rep3 (ATAC-seq)

value: LCMV Armstrong


title: BloodSample62Chemo: 1Radiation: 1

source_name: BloodSample62Chemo: 1Radiation: 1


title: ARDS_012_ND1

description: Inferior Turbinate Brushing


title: ARDS_011_ND14

description: Inferior Turbinate Brushing


title: ARDS_011_ND7

description: Inferior Turbinate Brushing


title: Arm5_neg_rep3 (ATAC-seq)


title: ARDS_012_ND3

description: Inferior Turbinate Brushing


title: Arm5_pos_rep1 (ATAC-seq)


title: BloodSample60Chemo: 0Radiation: 1

source_name: BloodSample60Chemo: 0Radiation: 1


title: BloodSample61Chemo: 0Radiation: 1

source_name: BloodSample61Chemo: 0Radiation: 1


title: BloodSample59Chemo: 1Radiation: 1

source_name: BloodSample59Chemo: 1Radiation: 1


title: Arm5_neg_rep1 (ATAC-seq)


title: ARDS_011_ND3

description: Inferior Turbinate Brushing

value: B


title: Arm21_pos_rep3 (ATAC-seq)


title: BloodSample63Chemo: 1Radiation: 1

source_name: BloodSample63Chemo: 1Radiation: 1


title: CD163- d6, donor 3

city: Montreal

first: Marika

last: Sarfati

state: Qc

address: 900 Rue St Denis

country: Canada

institute: CRCHUM

hyb_protocol: 5 µg DNA target was hybridized on GeneChip® Clariom™ D human (Thermo Fisher Scientific) and incubated at 45°C in the GeneChip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (ThermoFisher) using GeneChip Hybridization Wash and Stain kit according to the manufacturer’s instructions (ThermoFisher).

scan_protocol: The microarrays were scanned on a GeneChip® scanner 3000 (ThermoFisher).

data_processing: The preprocessing of the microarray data was done in R and its derived library for genomic data analysis, Bioconductor. We used the Bioconductor package oligo to load the CEL files in R environment and the rma function implemented in oligo for background subtraction, normalization and log2 transformation.

source_name: In vitro, GM-CSF+IFNg+IL23, day 6

label_protocol: Sense-strand cDNA was synthesized from 9 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the GeneChip® WT PicoTerminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific).

extract_protocol: Total RNA was extracted using the Machery-Nagel Nucleospin kit as per manufacturer's protocol.

tag: cytokine cocktail

tag: cd163 expression

tag: timepoint

value: day 6

value: Inflammatory monocyte-like cells

tag: donor

tag: donor diagnosis

value: Healthy


title: Arm21_pos_rep1 (ATAC-seq)

tag: Sex


title: CD163+ d12, donor 3

source_name: In vitro, TGFβ+IL10, day 12

value: day 12

value: Macrophages


title: CD163- d12, donor 3


title: ARDS_010_ND14

description: Inferior Turbinate Brushing

value: nasal brushings


title: CD163+ d12, donor 2


title: CD163- d12, donor 2


title: CD163+ d12, donor 1


title: CD163- d6, donor 2


title: 2yr_3 pectoral muscle

city: Chengdu

first: Xun

last: Wang

state: China

address: Huimin road 211#, Wenjiang district

institute: Sichuan agricultural university

description:
micRNAs from pectoral muscle in 2-year pigeon
identified miRNA reads count.txt

data_processing:
the initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences were then mapped to the pigeon reference genome (Columba livia, ColLiv2, GenBank assembly accession: GCA_001887795.1) (https://www. ncbi.nlm.nih.gov/assembly/GCA _001887795.1) with stringent criteria (0 mismatch for full length) using Bowtie software.
Next, mappable reads were extended in the reference genome as predicted miRNA precursors. Only candidate precursors that perfectly matched to known pigeon (Columba livia) mature miRNAs annotated by miRBase (Release 22.0) were identified as known pigeon miRNAs.
Subsequently, to identify the conserved miRNAs, we performed alignments between remaining candidate precursors and seed sequences of mature miRNAs from chicken (Gallus gallus), zebra finch (Taeniopygia guttata) and other mammals, allowing no mismatch.
Novel miRNAs were further predicted using the miRDeep2 core algorithm
Genome_build: Genome database:pigeon genome (assembly GCA_001887795.1); miRbase version: V22.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads

organism: Columba livia

source_name: pectoral muscle

extract_protocol:
Total RNA was respectively extracted from frozen pectoral muscle samples with TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
The quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer with Agilent RNA 6000 nano Reagents Part 1 kit (Agilent Technologies, USA). Each development stage has three replicates that came from the three pigeons. Total RNA of each replicate was individually used for library construction. For each library, small RNA ranging from 10-45 nt in length was purified by polyacrylamide gel electrophoresis and ligated using proprietary adaptors. The modified small RNA was then reverse-transcribed to cDNA and amplified by PCR. Finally, libraries were sequenced by an Illumina Hiseq 2500 platform and generate 50 bp single-end reads.

treatment_protocol: 12 parent white king pigeons (6 male and 6 female at 2- year-old) and 24 squabs (mixed sex) were grouped into 3 stages (12 replicates for each stage): the age of 1 day (1d),  28 day (28d) and 2 years old (2yr). After weighing the body weight, pigeons were anaesthetized with ether and subsequently euthanized. Next,the pectoral muscle tissues from the same anatomical location were collected from pigeons. Subsequently, the samples for small RNA sequencing were stored frozen in liquid nitrogen and stored at −80◦C until RNA extraction,

value: pectoral muscle

tag: developmental stage


title: 2yr_1 pectoral muscle


title: Arm21_neg_rep1 (ATAC-seq)

value: Male


title: ARDS_011_ND1

description: Inferior Turbinate Brushing


title: BloodSample58Chemo: 1Radiation: 1

source_name: BloodSample58Chemo: 1Radiation: 1

tag: time point

tag: age

tag: chemotherapy any


title: BloodSample57Chemo: 1Radiation: 1

source_name: BloodSample57Chemo: 1Radiation: 1

tag: radiationtherapy any

tag: female

tag: batch number


title: BloodSample54Chemo: 1Radiation: 1

source_name: BloodSample54Chemo: 1Radiation: 1


title: BloodSample55Chemo: 0Radiation: 1

source_name: BloodSample55Chemo: 0Radiation: 1


title: BloodSample56Chemo: 0Radiation: 1

source_name: BloodSample56Chemo: 0Radiation: 1


title: 2yr_2 pectoral muscle


title: CD163- d6, donor 1


title: ARDS_010_ND1

description: Inferior Turbinate Brushing

tag: endotype

tag: disease state

tag: time


title: 28d_3 pectoral muscle

description:
micRNAs from pectoral muscle in 28-day pigeon
identified miRNA reads count.txt

tag: tissue


title: ARDS_010_ND3

description: Inferior Turbinate Brushing


title: Arm21_neg_rep3 (ATAC-seq)

tag: cell type

tag: infection


title: Ino80E13dKOG

data_processing:
Sample barcodes separated with Illumina bcl2fastq v2.17.
UMI extracted into read name with UMI-tools v0.5.3. Command invocation: umi_tools extract --stdin {input} --stdout {output} --extract-method=string --bc-pattern=NNNNNNNN --log {log}
Adapter reads removed with Cutadapt v1.13. Command invocation: cutadapt -o {TRIM_DIR}/{sample}.fastq.gz -b {FULL_PRIMER} --cut 2 --discard-trimmed {input}
Reads aligned to reference genome with STAR v2.5.2a. Command invocation: STAR --genomeDir {input.genome} --readFilesIn {input.reads} --readFilesCommand zcat --outFileNamePrefix {MAP_DIR}/{wildcards.sample} --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --runThreadN {NUM_THREADS}
Reads deduplicated by UMI and position with UMI-tools v0.5.3. Command invocation: umi_tools dedup -I {sorted_bam} -S {dedup_bam}
Gene counts quantified by HTSeq v0.6.1p1. Command invocation: htseq-count --format bam --mode intersection-nonempty --type gene {input} {GTF} > {output}
Gene counts normalized with edgeR v3.20.9.
Genome_build: mm10
Supplementary_files_format_and_content: The tsv files for each sample contain the deduplicated gene counts as Tab-Separated Values (TSV).

source_name: dKO_cerebral cortex

extract_protocol:
Total RNA was isolated from freshly micro-dissected embryonic 13.5 cortices using Trizol and RNA Clean & Concentrator Kit. 600ng of total RNA was used for library generation.
The ClickSeq procedure used was previously described (Routh et al. 2017). Briefly, total RNA was extracted using Trizol (Invitrogen) according to manufacturer’s protocol. The RNA was then treated with DNaseI, cleaned and concentrated using RNA Clean and Concentrator Kit (Zymo Research). Ribosomal RNA was removed using NEBNext rRNA Depletion Kit (NEB). Reverse transcription was carried out with SuperScript II (Invitrogen) following manufacturer’s procedures using 1:30 5mM AzdNTP:dNTP and 3’Genomic Adapter-6N RT primer (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN). The reaction was then treated with RNaseH to remove RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The azido-terminated cDNA was diluted with DMSO and click adaptor (/5Hexynyl/NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT). The click reaction was initiated by adding Cu2+ (Lumiprobe) in presence of vitamin C.  The resulting click ligation was purified using DNA Clean and Concentrator Kit (Zymo). The final amplification step was carried out using 2x One Taq Hot Start Mastermix (NEB), using Illumina universal primer (AATGATACGGCGACCACCGAG) and Illumina indexing primer (CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT).  The PCR reaction was cleaned using Ampure XP magnetic beads (Beckman) at 1.25x ratio, which size-selects for product size above 200bp. The resulting library was analyzed using TapeStation (Agilent) to check for proper size distribution and quality of DNA.

tag: strain background

value: mixed C57BL/6 and 129

tag: litter

value: male

tag: genotype/variation

value: dKO; Emx1-Cre Ino80/Trp53 conditional double mutant

value: cerebral cortex

tag: batch


title: CD163- d12, donor 1

tag: cytokine cocktail

tag: cd163 expression

tag: timepoint

tag: donor

tag: donor diagnosis


title: Ino80E13dKOF

tag: developmental stage

tag: Sex


title: BloodSample53Chemo: 1Radiation: 1

source_name: BloodSample53Chemo: 1Radiation: 1

extract_protocol: Genomic DNA of whole blood samples

tag: time point

tag: age

tag: chemotherapy any

tag: radiationtherapy any

tag: female

tag: batch number


title: ARDS_009_ND7

description: Inferior Turbinate Brushing

tag: tissue

tag: endotype

tag: disease state

value: PARDS

tag: time


title: 28d_1 pectoral muscle


title: ARDS_009_ND14

description: Inferior Turbinate Brushing


title: 1d_3 pectoral muscle

description:
micRNAs from pectoral muscle  in 1-day pigeon
identified miRNA reads count.txt


title: BloodSample52Chemo: 0Radiation: 1

source_name: BloodSample52Chemo: 0Radiation: 1


title: ARDS_009_ND3

description: Inferior Turbinate Brushing


title: 28d_2 pectoral muscle


title: 1d_2 pectoral muscle

description:
micRNAs from pectoral muscle in 1-day pigeon
identified miRNA reads count.txt


title: Ino80E13dKOE

tag: strain background

tag: litter

tag: genotype/variation

tag: batch


title: ARDS_009_ND1

description: Inferior Turbinate Brushing

value: C


title: Ino80E13cKOE

source_name: cKO_cerebral cortex

value: female

value: cKO; Emx1-Cre Ino80 conditional mutant


title: BloodSample50Chemo: 1Radiation: 1

source_name: BloodSample50Chemo: 1Radiation: 1


title: Ino80E13dKOD


title: 1d_1 pectoral muscle


title: ARDS_008_ND7

description: Inferior Turbinate Brushing


title: BloodSample49Chemo: 1Radiation: 1

source_name: BloodSample49Chemo: 1Radiation: 1


title: BloodSample48Chemo: 1Radiation: 1

source_name: BloodSample48Chemo: 1Radiation: 1


title: Ino80E13cKOC


title: Ino80E13cKOD


title: ARDS_008_ND3

description: Inferior Turbinate Brushing


title: Ino80E13ctrlI

source_name: control_cerebral cortex

value: control


title: ARDS_008_ND1

description: Inferior Turbinate Brushing

value: B


title: BloodSample47Chemo: 1Radiation: 1

source_name: BloodSample47Chemo: 1Radiation: 1


title: BloodSample51Chemo: 0Radiation: 1

source_name: BloodSample51Chemo: 0Radiation: 1


title: BloodSample46Chemo: 1Radiation: 1

source_name: BloodSample46Chemo: 1Radiation: 1


title: ARDS_007_ND14

description: Inferior Turbinate Brushing


title: Ino80E13ctrlF


title: 30vs42.5_2nd

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

hyb_protocol: Labeled cDNA (4.5 μg each) are mixed with 1 × hybridization buffer (6 × SSC, 0.2% SDS, 5 × Denhardt’s solution, 0.1 mg/ml denatured salmon sperm DNA) in a total volume of 340 μl, and denatured at 95˚C for 2 min. The hybridization mixture was hybridized to a microarray in an Agilent Technologies Microarray chamber at 60˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 5 minutes with wash buffer 1 (2x SSC, 0.2% SDS) at room temperature , 5 minutes with wash buffer 2 (0.2x SSC, 0.2% SDS) at 60˚C, and 5 minutes with wash buffer 3 (0.2x SSC) at room temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm. PMT is set to 100% for Cy3 and Cy5 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE2-NonAT_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 13.0 software from Agilent. After taking the average of two replicate features on each array, normalization of the data was done in GeneSpring GX using the Lowess normalization algorithm without baseline transformation.

organism: Corynebacterium glutamicum ATCC 13032

source_name: Anaerobic 30 C

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) or cyanine 5 (Cy5) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

growth_protocol: Strains were aerobically cultivated at 30.0ºC for 16 h in 500 mL of a nutrient rich medium (A medium containing 2 g yeast extract, 7 g casamino acids, 2 g urea, 7 g ammonium sulfate, 0.5 g KH2PO4, 0.5 g K2HPO4, 0.5 g MgSO4･7H2O, 6 mg FeSO4･7H2O, 6 mg MnSO4･5H2O, 1 mg ZnSO4･7H2O, 0.2 mg CuSO4･5H2O, 0.2 mg NiCl2･6H2O, 0.2 mg biotin, 0.2 mg thiamin per liter supplemented with 2% [w/v] glucose) in a 2 L flask.

extract_protocol: Total RNA was extracted from C. glutamicum cells using NucleoSpin RNA II kit (Macherey-Nagel, Germany) according to the manufacture's manual.

treatment_protocol: Cultures were harvested by centrifugation (8,000 rpm, 4°C, 10 min) and washed once with minimum medium (BT medium) without urea (7 g ammonium sulfate, 0.5 g KH2PO4, 0.5 g K2HPO4, 0.5 g MgSO4･7H2O, 6 mg FeSO4･7H2O, 6 mg MnSO4･5H2O, 1 mg ZnSO4･7H2O, 0.2 mg CuSO4･5H2O, 0.2 mg NiCl2･6H2O, 0.2 mg biotin, 0.2 mg thiamin per liter). Samples of 3.6 g of washed cells were resuspended in 54 mL of BT medium without urea, resulting in suspensions of cells at 6% wet weight/volume in 60 mL reaction solution in a lidded 100 mL medium bottle. At the beginning of reactions, 4.32 g of glucose (400 mM) and 1.01 g NaHCO3 (200 mM) were added in reaction solution. Cell suspensions were incubated at 30 or 42.5°C for 2 h.

tag: temperature

source_name: Anaerobic 42.5 C


title: 30vs42.5_3rd


title: BloodSample45Chemo: 1Radiation: 1

data_processing: Noob normalization using preprocessNoob in the minfi R package

source_name: BloodSample45Chemo: 1Radiation: 1


title: 30vs42.5_1st


title: ARDS_007_ND7

description: Inferior Turbinate Brushing


title: Ino80E13dKOC

tag: developmental stage


title: ARDS_003_ND7

description: Inferior Turbinate Brushing


title: ARDS_010_ND7

description: Inferior Turbinate Brushing


title: ChIP-seq input replicate 1

city: Bonn

first: Stefan

middle: Andreas

last: Juranek

state: NRW

address: Venusber-Campus 1

department: Medizinische Klinik III

institute: UK Bonn

description: W303 Zuo1myc tag strain

data_processing:
HiSeq Control Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie2 (Langmead et al. Genome Biology 2009)
Peaks were called using MACS2 (Zhang et al. Genome biology 2008) using default parameters for narrow peaks
Genome_build: sacCer3
Supplementary_files_format_and_content: Called peaks are provided in a tsv file

organism: Saccharomyces cerevisiae W303

growth_protocol: Cells were growth at 30°C for 5 hours, and crosslinked with 1% formaldehyde at OD = 0.6

extract_protocol:
Cells were lysate by FastPrep, sonicate for DNA shearing, immunoprecipitate with myc antibody
Library preparation was performed with NEBNext Ultra II DNA library kit for Ilumina as described in manufacturer’s instructions.

tag: strain

value: Myc tag


title: BloodSample44Chemo: 1Radiation: 1

source_name: BloodSample44Chemo: 1Radiation: 1

tag: time point


title: Ino80E13dKOB

tag: Sex


title: ARDS_002_ND1_NEB

description: Inferior Turbinate Brushing


title: Ino80E13dKOA


title: ChIP-seq Myc IP replicate 2

description: W303 Zuo1myc tag strain


title: BloodSample42Chemo: 1Radiation: 1

source_name: BloodSample42Chemo: 1Radiation: 1

tag: age

tag: chemotherapy any


title: ChIP-seq Myc IP replicate 1

description: W303 Zuo1myc tag strain


title: ARDS_001_ND1

description: Inferior Turbinate Brushing

extract_protocol:
RNEasy
Nextera-XT

value: A

value: ARDS


title: ARDS_001_ND3

description: Inferior Turbinate Brushing


title: Ino80E13cKOB


title: BloodSample41Chemo: 1Radiation: 1

source_name: BloodSample41Chemo: 1Radiation: 1

tag: radiationtherapy any

tag: female


title: Ino80E13ctrlH

tag: tissue


title: Ino80E13cKOA


title: ChIP-seq input replicate 2

description: W303 Zuo1myc tag strain


title: BloodSample40Chemo: 0Radiation: 1

source_name: BloodSample40Chemo: 0Radiation: 1

tag: batch number


title: ARDS_001_ND7

description: Inferior Turbinate Brushing

tag: endotype

tag: disease state


title: ARDS_002_ND1

description: Inferior Turbinate Brushing

tag: time


title: Ino80E13ctrlC

tag: strain background

tag: litter


title: BloodSample39Chemo: 0Radiation: 1

source_name: BloodSample39Chemo: 0Radiation: 1


title: Ino80E13ctrlD

tag: genotype/variation

tag: batch


title: ARDS_002_ND3

description: Inferior Turbinate Brushing


title: ARDS_002_ND7

description: Inferior Turbinate Brushing


title: BloodSample37Chemo: 0Radiation: 1

source_name: BloodSample37Chemo: 0Radiation: 1


title: BloodSample36Chemo: 0Radiation: 1

source_name: BloodSample36Chemo: 0Radiation: 1


title: BloodSample38Chemo: 0Radiation: 1

source_name: BloodSample38Chemo: 0Radiation: 1


title: ARDS_004_ND1

description: Inferior Turbinate Brushing


title: BloodSample43Chemo: 1Radiation: 1

source_name: BloodSample43Chemo: 1Radiation: 1


title: Ino80E13ctrlB

tag: developmental stage


title: Ino80E13ctrlA


title: mouse_hippocampus_18mo_FAsupplemented_Replicate1

city: Lynchburg

first: Abigail

last: Lawton

state: Virginai

address: 1971 University Blvd

department: Biology and Chemistry

institute: Liberty University

description: Gene expression after 18 months of folic acid supplementation

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering between the two groups of samples. Hierarchical Clustering was performed using the R software (version 2.15). GO analysis and Pathway analysis were performed in the standard enrichment computation method

source_name: mouse hippocampus, 18 months folic acid normal levels (control)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: mice were kept on a 12 hr light/dark cycle in a temperature controlled room for the duration of the study.

extract_protocol: hippocampi were soaked in RNALater for 24 hr at 4 Celcius before being stored at -80 Celcius until ready for extraction. RNA was extracted using Trizol (Invitrogen) with the standard protocol provided by the manufacturer

treatment_protocol: FA mice were give AIN93G normal folic acid (2 mg/ml), and DEF mice were deprived of all folate beginning post-weaning

tag: strain

value: 18 months

tag: gender

value: hippocampus

tag: sample type

value: folic acid supplementation


title: mouse_hippocampus_18mo_FAsupplemented_Replicate2

scan_protocol: Agilent DNA Microarray Scanner (part number G2505C).

tag: age


title: mouse_hippocampus_18mo_FAsupplemented_Replicate3


title: ARDS_005_ND14

description: Inferior Turbinate Brushing

value: nasal brushings


title: BloodSample35Chemo: 0Radiation: 1

source_name: BloodSample35Chemo: 0Radiation: 1

tag: time point

tag: chemotherapy any


title: BloodSample34Chemo: 1Radiation: 1

source_name: BloodSample34Chemo: 1Radiation: 1

tag: radiationtherapy any

tag: female


title: Control_010_ND3

description: Inferior Turbinate Brushing

tag: tissue

value: Control


title: BloodSample33Chemo: 1Radiation: 1

source_name: BloodSample33Chemo: 1Radiation: 1

tag: batch number


title: Control_002_ND1

description: Inferior Turbinate Brushing

tag: endotype

tag: disease state


title: BloodSample32Chemo: 0Radiation: 1

source_name: BloodSample32Chemo: 0Radiation: 1


title: Control_002_ND3

description: Inferior Turbinate Brushing

tag: time


title: BloodSample31Chemo: 0Radiation: 1

source_name: BloodSample31Chemo: 0Radiation: 1


title: BloodSample30Chemo: 1Radiation: 1

source_name: BloodSample30Chemo: 1Radiation: 1


title: mouse_hippocampus_18mo_FAdeficient_Replicate2

description: Gene expression after 18 months of folic acid deficiency

source_name: mouse hippocampus, 18 months folic acid deficiency

value: folic acid deficiency


title: mz_240707_mz_R1R2_18d_2

city: Zurich

first: LUIGI

last: MADDALUNO

address: Otto Stern Weg 7

country: Switzerland

institute: ETH

description: K5-R1/R2 mouse epidermis P18

hyb_protocol: Biotin-labeled cRNA samples (15μg) were hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) using standard procedures.

scan_protocol: Raw data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix).

data_processing:
Algorithm: ExpressionStat 5.0
Probability scores and fold changes were calculated using the Rosetta Resolver software (Rosetta Biosoftware, Seattle, WA).

source_name: Untreated Mouse

label_protocol: Total RNA samples (2μg) were reverse-transcribed and in vitro transcribed in the presence of biotin-labeled nucleotides using an IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA). cRNAs were purified, quantified, and the quality was determined using a Bioanalyzer 2100.

growth_protocol: We isolated RNA from mouse epidermis separated by dispase treatment according to the isolation protocol of Chomczynski P (1987)

extract_protocol: The RNA was  purified using the RNeasy MinElute kit (Qiagen, Basel, Switzerland), and the quality was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany).

treatment_protocol: ccc

value: epidermis


title: mouse_hippocampus_18mo_FAdeficient_Replicate3


title: BloodSample29Chemo: 1Radiation: 1

source_name: BloodSample29Chemo: 1Radiation: 1


title: Control_009_ND14

description: Inferior Turbinate Brushing


title: mouse_hippocampus_18mo_FAdeficient_Replicate1


title: mz_240707_mz_R1R2_18d_3

description: K5-R1/R2 mouse epidermis P18


title: mouse_hippocampus_4mo_FAsupplemented_Replicate2

description: Gene expression after 4 months of folic acid supplementation

source_name: mouse hippocampus, 4 months folic acid normal levels (control)

value: 4 months


title: mouse_hippocampus_4mo_FAsupplemented_Replicate3


title: mouse_hippocampus_4mo_FAdeficient_Replicate3

description: Gene expression after 4 months of folic acid deficiency

source_name: mouse hippocampus, 4 months folic acid deficiency


title: mz_240707_mz_WT_18d_3

description: Wild Type mouse epidermis P18

value: Wild Type


title: mz_240707_mz_R1R2_18d_1

description: K5-R1/R2 mouse epidermis P18


title: BloodSample28Chemo: 0Radiation: 1

source_name: BloodSample28Chemo: 0Radiation: 1


title: mz_240707_mz_WT_18d_1

description: Wild Type mouse epidermis P18


title: mouse_hippocampus_4mo_FAdeficient_Replicate1


title: mouse_hippocampus_4mo_FAsupplemented_Replicate1


title: BloodSample26Chemo: 1Radiation: 1

source_name: BloodSample26Chemo: 1Radiation: 1


title: mouse_hippocampus_4mo_FAdeficient_Replicate2


title: Control_001_ND1

description: Inferior Turbinate Brushing

value: C


title: BloodSample27Chemo: 0Radiation: 1

source_name: BloodSample27Chemo: 0Radiation: 1


title: mz_240707_mz_WT_18d_2

description: Wild Type mouse epidermis P18


title: BloodSample25Chemo: 1Radiation: 1

source_name: BloodSample25Chemo: 1Radiation: 1


title: BV_Ctrl_18 (circRNA)

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

organism: Rattus norvegicus

source_name: blood vessel, Ctrl

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.) Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: Wistar

value: blood vessel

value: male

value: 7 week

tag: treatment

value: Ctrl


title: BloodSample81Chemo: 1Radiation: 1

last: Sehl

address: 100 UCLA Medical Plaza, Suite 550

source_name: BloodSample81Chemo: 1Radiation: 1


title: BloodSample24Chemo: 0Radiation: 1

source_name: BloodSample24Chemo: 0Radiation: 1


title: BV_Ctrl_17 (circRNA)


title: BV_Ctrl_20 (circRNA)


title: BV_Ctrl_18 (mRNA)

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner .Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.


title: BV_Ctrl_20 (mRNA)


title: plasma_20s_8

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

description: SAMPLE 35

hyb_protocol: 0.6 µg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 8x60K custom  design (OaksLab)mouse Microarrays (Design-ID 062646) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 6x8K array slides (Scan resolution 10 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse skin, 20 s/mm², replicate 8

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Bio&Sell, Feucht, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: After 24 h, the animals were euthanized by cervical dislocation and the tissue from the skin areas were removed. The tissue samples for RNA and proteins were transferred directly into liquid nitrogen after sampling and stored at - 80 °C until homogenization. fresh tissues from ears were removed, snap-frozen in liquid nitrogen, and stored at -80°C. Homogenization was performed in RNA lysis buffer (Bio&Sell, Feucht, Germany) for gene expression analysis, or in RIPA buffer containing protease and phosphatase inhibitors (cOmplete Mini, phosSTOP, PMSF, Sigma-Aldrich, Traunstein, Germany) for protein validation experiments using a FastPrep-24 5G homogenizator (MP biomedicals, Heidelberg, Germany). The skin samples for histology were placed in 4% paraformaldehyde for further processing.  Paraffin blocks were cut into 5 µm-sections using a microtome to retrieve tissue sections that were stained with hematoxylin and eosin (H&E; Carl-Roth, Karlsruhe, Germany).

treatment_protocol: An atmospheric pressure argon plasma jet (kINPenMed; neoplas tools, Greifswald, Germany) was used, which ionized a flow (5 standard liters per minute) of argon gas (purity 99.9999; Air Liquide, Krefeld, Germany) at 1 MHz. Plasma treatment of wounds was performed using the tip of the plasma effluent at a constant distance of 8 mm using a autoclavable spacer. Mice were exposed to 3 s/mm² or 20 s/mm² of plasma or were left untreated (0s/mm²) and compared to controls (n=9).

value: skin tissue

value: female

value: after 20 s of plasma treatment in skin tissue


title: BV_Ctrl_17 (mRNA)


title: plasma_20s_9

description: SAMPLE 36

source_name: mouse skin, 20 s/mm², replicate 9


title: plasma_20s_7

description: SAMPLE 34

source_name: mouse skin, 20 s/mm², replicate 7


title: BloodSample23Chemo: 0Radiation: 1

first: Mary

institute: UCLA

source_name: BloodSample23Chemo: 0Radiation: 1


title: BloodSample22Chemo: 0Radiation: 1

source_name: BloodSample22Chemo: 0Radiation: 1


title: BV_Ctrl_15 (circRNA)


title: BV_Ctrl_15 (mRNA)


title: plasma_20s_5

description: SAMPLE 32

source_name: mouse skin, 20 s/mm², replicate 5


title: BV_Ctrl_16 (circRNA)


title: plasma_20s_6

description: SAMPLE 33

source_name: mouse skin, 20 s/mm², replicate 6


title: BV_LPS_7 (circRNA)

source_name: blood vessel, LPS

value: LPS


title: BV_LPS_6 (mRNA)


title: BloodSample21Chemo: 0Radiation: 1

source_name: BloodSample21Chemo: 0Radiation: 1


title: BV_Ctrl_16 (mRNA)


title: BV_LPS_7 (mRNA)


title: BV_LPS_6 (circRNA)


title: plasma_20s_4

description: SAMPLE 31

source_name: mouse skin, 20 s/mm², replicate 4


title: BloodSample20Chemo: 0Radiation: 1

source_name: BloodSample20Chemo: 0Radiation: 1


title: plasma_20s_2

description: SAMPLE 29

source_name: mouse skin, 20 s/mm², replicate 2


title: BV_LPS_5 (circRNA)


title: BV_LPS_5 (mRNA)


title: BloodSample19Chemo: 0Radiation: 1

source_name: BloodSample19Chemo: 0Radiation: 1


title: plasma_20s_3

description: SAMPLE 30

source_name: mouse skin, 20 s/mm², replicate 3


title: BloodSample18Chemo: 1Radiation: 1

source_name: BloodSample18Chemo: 1Radiation: 1


title: BloodSample17Chemo: 1Radiation: 1

source_name: BloodSample17Chemo: 1Radiation: 1


title: BloodSample16Chemo: 1Radiation: 1

source_name: BloodSample16Chemo: 1Radiation: 1


title: BV_LPS_3 (mRNA)


title: plasma_20s_1

description: SAMPLE 28

source_name: mouse skin, 20 s/mm², replicate 1


title: BV_LPS_3 (circRNA)


title: plasma_3s_9

description: SAMPLE 27

source_name: mouse skin, 3 s/mm², replicate 9

value: after 3 s of plasma treatment in skin tissue


title: BV_LPS_1 (circRNA)


title: BloodSample15Chemo: 1Radiation: 1

source_name: BloodSample15Chemo: 1Radiation: 1


title: BV_LPS_1 (mRNA)


title: plasma_3s_7

description: SAMPLE 25

source_name: mouse skin, 3 s/mm², replicate 7


title: plasma_3s_8

description: SAMPLE 26

source_name: mouse skin, 3 s/mm², replicate 8


title: BloodSample14Chemo: 1Radiation: 1

source_name: BloodSample14Chemo: 1Radiation: 1


title: BloodSample13Chemo: 1Radiation: 1

source_name: BloodSample13Chemo: 1Radiation: 1


title: BloodSample12Chemo: 0Radiation: 1

source_name: BloodSample12Chemo: 0Radiation: 1


title: E: 20-3-14 A 1% UNSTIM

city: Cambridge

first: Benjamin

middle: James

last: Stewart

address: Wellcome Genome Campus

department: Cellular Genetics

country: United Kingdom

institute: Wellcome Sanger Institute

description: Gene expression data from bone marrow B cells after 3 days of culture in 1% O2; hypoxic conditions

hyb_protocol: not provided

scan_protocol: Raw image data was acquired using Koadarray v2.4 software

data_processing: Background subtracted intensity signal values were imported into R and processed using the oligo package

source_name: Bone marrow B cells after 3 days of culture in 1% O2; hypoxic conditions

label_protocol: not provided

growth_protocol: RBC-lysed single-cell bone marrow suspensions were cultured in RPMI-1640 supplemented with 15% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin, 1 mM sodium pyruvate, 50 uM 2-mercaptoethanol. 4X10^6 cells were cultured in humidified Whitley H35 hypoxystation (Don Whitley Scientific) at 1% O2 or normoxic condition, 37°C, 5% CO2 for 3 days

extract_protocol: not provided

treatment_protocol: Cells were exposed to 1% oxygen tension or normoxic (21%) conditions.

value: Bone marrow B cells


title: plasma_3s_6

description: SAMPLE 24

source_name: mouse skin, 3 s/mm², replicate 6


title: G: 20-3-14 B 1% UNSTIM


title: C: 20-3-14 B NOR UNSTIM

description: Gene expression data from bone marrow B cells after 3 days of culture in normoxic conditions

source_name: Bone marrow B cells after 3 days of culture in normoxic conditions


title: Dppa_WT_58

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

description:
Sampe 129
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

data_processing:
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Amplicon-bisulfite-seq: As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam".Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.5 www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3, parameters: --paired).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

source_name: Dppa2/4 WT clone 58

growth_protocol: E14 mouse ESCs were grown using standard serum/LIF culture conditions (DMEM, 4,500 mg/L glucose, 4 mM L-glutamine, 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/mL penicillin, 1 mg/mL streptomycin, 0.1 mM nonessential amino acids, 50 mM b-mercaptoethanol, 103 U/mL LIF) at 37 degrees Celsius in normal oxygen, feeder-free on gelatin coated plates.

extract_protocol:
RNAseq: Total RNA was isolated using TriReagent (Sigma) or RNA-DNA allprep columns (Qiagen) 0.5-1mg DNAse treated (Thermo Fisher EN0525).
ChIPseq: Ten million cells were fixed in 1% formaldehyde (Fisher Scientific 28906) in DMEM (Invitrogen 41966-052) for 10 minutes, quenched in 0.125M glycine, and scraped off cell culture dishes using cell scrapers. Cells were lysed with buffers LB1 (50mM Hepes-KOH (pH 7.5), 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal CA-630, 0.25% Triton-X 100), LB2 (10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 (10mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x Protease Inhibitors (Roche)) consecutively, before fragmenting chromatin by sonicating for 30 cycles of 30s ON high /30s OFF (Diagenode Bioruptor). For each ChIP, 5µg antibody (anti-Ash2l Bethyl Labs A300-489, anti-Ezh2 CST D2C9, anti-H2A.Z Abcam ab4174, anti-H3K4me3 Abcam ab8580, anti-H3K27me3 Active Motif AM39155, anti-IgG Abcam ab125938, anti-Ring1b CST D22F2) was pre-bound to protein G dynabeads (Invitrogen) and blocked with 0.5% BSA in PBS. Sonicated DNA was added to antibody-bound beads with 10% Triton-X 100 and incubated overnight at 4°C on a rotator. Beads and DNA were washed 6 times with RIPA buffer (50mM HEPES-KOH (pH 7.6), 1mM EDTA, 0.7% Na-Deoxycholate, 1% Igepal CA-630, 0.5M LiCl), followed by one wash in 1x TBS and overnight incubation at 65°C with elution buffer (50 mM Tris- HCl, pH 8; 10 mM EDTA; 1% SDS). For precipitation of chromatin, samples were treated with RNase A and Proteinase K. DNA was purified using MinElute PCR purification columns (Qiagen 28006) and eluted in 30µL of TE. DNA was quantified using HS DNA Qubit (ThermoFisher) or PicoGreen (ThermoFisher) assays.
ATACseq: 10,000 cells were trypsinised and immediately processed for ATACseq.
NOMEseq: Cells were fixed on 15cm plates wih Fixation solution (Active-Motif) for 10minutes at room temperature then processed according to Active Motif NOME-seq kit protocol.
amplicon bisulfite: Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) or the AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions and eluted into TE buffer or H2O.
RNAseq: Opposite strand-specific polyA RNA libraries were made using 1 µg of DNase- treated RNA at the Sanger Institute Illumina bespoke pipeline and sequenced using the Illumina HiSeq2 platform.
ChIPseq: libraries generated using MicroPlex Library Preparation Kit (Diagenode) following the manufacturer’s instructions. Libraries were quality controlled using bioanalyser HS DNA chips (Agilent) and single-end 50bp reads sequenced using the Illumina HiSeq2 sequencing platform.
ATACseq: ATAC-seq libraries were performed as previously described (Buenrostro, Wu, Chang, & Greenleaf, 2015) with the following modification to use on 10,000 cells: initial transposition reaction was performed with 10,000 cells, 10ml 2x TD buffer, 0.5ml Tn5 enzyme and 9.5ml H2O for 30minutes at 37 degrees Celsius. A total of 15 cycles of amplification were used. Two technical replicates were performed per clone, with 3 WT and 3 Dppa2/4 DKO clones used (total of 12 samples).
NOMEseq: Whole genome bisulfite libraries were generated using NOME-seq kit from Active Motif (103946) according to manufacturer’s instructions with 6 cycles of amplification for 2 WT clones (clones 57 and 58) and 1 Dppa2/4 DKO clone (clone 43).
amplicon bisulfite: 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with either magnetic bead or column clean-up and eluted/resuspended in elution buffer. Amplicons of interest were amplified using 2x KAPA HiFi Uracil+ ReadyMix using primers containing UMI for deduplication and PCR adapters for a second round of PCR to adapt sample-specific barcodes and adapters for Illumina Sequencing. Libraries were sequenced using the Illumina MiSeq platform with a 10% PhIX spike-in and paired-end 250bp reads.
: RNA-seq or ChIP-seq or NOME-seq or amplicon bisulfite-seq

treatment_protocol: Stable overexpression cell lines were generated using Lipofectamine 2000 on preplated cells and resistant cells selected with appropriate antibiotics for at least 1 week before sorting single cells into 96 well plates by flow cytometry using a BD Aria III or BD Influx high-speed cell sorter, and clonal expansion. CRISPR double knockout ESC line (clone 43) was described previously (M. Eckersley-Maslin et al., 2019), and additional CRISPR double knockout ESC lines (clone 37 and clone 53) generated as previously described (M. Eckersley-Maslin et al., 2019). For embryoid bodies, 2x106 mESCs were cultured on 10cm low-attachment dishes in standard ESC medium containing all described components except LIF.

tag: cell type

value: embryonic stem cell

tag: culture conditions

value: serum/LIF

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter

tag: chip antibody


title: BloodSample11Chemo: 0Radiation: 1

city: Los Angeles

source_name: BloodSample11Chemo: 0Radiation: 1


title: A: 20-3-14 A NOR UNSTIM


title: shRNA_Dppa2_recovery_B

description:
Sampe 128
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: inducible shRNA cells treated with dox for 7 days then dox washout for 14 days

tag: strain

value: E14 ESCs containing inducible shRNA hairpin against Dppa2


title: plasma_3s_5

description: SAMPLE 23

source_name: mouse skin, 3 s/mm², replicate 5

tag: gender


title: BloodSample9Chemo: 1Radiation: 1

source_name: BloodSample9Chemo: 1Radiation: 1


title: shRNA_Dppa4_noDox_B

description:
Sampe 126
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: inducible shRNA cells untreated

value: E14 ESCs containing inducible shRNA hairpin against Dppa4


title: Dppa_DKO_53

description:
Sampe 127
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: Dppa2/4 DKO clone 53


title: BloodSample8Chemo: 1Radiation: 1

source_name: BloodSample8Chemo: 1Radiation: 1


title: 13: 15-4-14 A 1% UNSTIM


title: BloodSample7Chemo: 1Radiation: 1

source_name: BloodSample7Chemo: 1Radiation: 1


title: Dppa_WT_57

description:
Sampe 125
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: Dppa2/4 WT clone 57


title: plasma_3s_4

description: SAMPLE 22

source_name: mouse skin, 3 s/mm², replicate 4


title: Dppa_WT_MC3

description:
Sampe 124
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: Dppa2/4 WT parental line (no CRISPR)

value: E14 ESCs, contains MERVL::tdTomato reporter


title: BloodSample5Chemo: 1Radiation: 1

source_name: BloodSample5Chemo: 1Radiation: 1


title: Dppa_DKO_43

description:
Sampe 123
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: Dppa2/4 DKO clone 43


title: plasma_3s_3

description: SAMPLE 21

source_name: mouse skin, 3 s/mm², replicate 3


title: 11: 15-4-14 B NOR UNSTIM


title: shRNA_Dppa4_noDox_C

description:
Sampe 122
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx


title: plasma_3s_2

description: SAMPLE 20

source_name: mouse skin, 3 s/mm², replicate 2


title: 15: 15-4-14 B 1% UNSTIM

source_name: Bone marrow B cells after 3 days of culture in 1% O2; hypoxic conditions


title: plasma_0s_9

description: SAMPLE 18

source_name: mouse skin, 0 s, replicate 9

value: after 0 s of plasma treatment in skin tissue


title: plasma_0s_8

description: SAMPLE 17

source_name: mouse skin, 0 s, replicate 8


title: plasma_0s_7

description: SAMPLE 16

source_name: mouse skin, 0 s, replicate 7


title: Dppa_DKO_36

description:
Sampe 121
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: Dppa2/4 DKO clone 36


title: plasma_0s_5

description: SAMPLE 14

source_name: mouse skin, 0 s, replicate 5


title: plasma_0s_4

description: SAMPLE 13

source_name: mouse skin, 0 s, replicate 4


title: plasma_3s_1

description: SAMPLE 19

source_name: mouse skin, 3 s/mm², replicate 1


title: plasma_0s_6

description: SAMPLE 15

source_name: mouse skin, 0 s, replicate 6


title: plasma_0s_2

description: SAMPLE 11

source_name: mouse skin, 0 s, replicate 2


title: BloodSample3Chemo: 1Radiation: 1

source_name: BloodSample3Chemo: 1Radiation: 1


title: BloodSample2Chemo: 1Radiation: 1

source_name: BloodSample2Chemo: 1Radiation: 1


title: 9: 15-4-14 A NOR UNSTIM

source_name: Bone marrow B cells after 3 days of culture in normoxic conditions


title: BloodSample1Chemo: 1Radiation: 1

source_name: BloodSample1Chemo: 1Radiation: 1


title: shRNA_Dppa2_recovery_C

description:
Sampe 118
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: inducible shRNA cells treated with dox for 7 days then dox washout for 14 days


title: plasma_0s_1

description: SAMPLE 10

source_name: mouse skin, 0 s, replicate 1


title: BloodSample4Chemo: 1Radiation: 1

source_name: BloodSample4Chemo: 1Radiation: 1


title: CROP-seq_CRISPRa_10x_lane_1

city: San Francisco

first: Ruilin

last: Tian

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

description: CROP-seq

data_processing:
For CROP-seq, Cellranger (version 3.1.0,10X Genomics) with default parameters was used to align reads and generate digital expression matrices from single-cell sequencing data. For 3'-tag RNA-seq, Salmon v0.14.1 was used to obtain transcript abundance counts
For CROP-seq, the Scanpy package (version 1.4.6) (Wolf et al., 2018) implemented in Python was used for downstream analysis of the digital expression matrices with mapped sgRNA identities. For 3'-tag RNA-seq, Gene-level count estimates were obtained using tximport v1.8.0
Differential gene expression analysis using DESeq2 v1.20.0
Genome_build: GRCh38
Supplementary_files_format_and_content: For the 3'-tag RNA seq data, files containing gene Enzemble ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj and Gene symbol are provided in Comma-separated values (.csv) format. For the CROP-seq data, expression matrices output by cellranger are provided in .h5 format.

source_name: Human iPSC-derived neuron

growth_protocol: Regular Neuronal Medium

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument.
Libraries were prepared according to the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) from 10X Genomics.

value: human neuron

tag: genotype

value: WT


title: CROP-seq_CRISPRa_10x_lane_2

description: CROP-seq


title: shRNA_Dppa2_plusDox_B

description:
Sampe 116
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: inducible shRNA cells treated with dox for 7 days


title: 2-3: Arabidopsis nid1 ko-Low nitrate treatment

city: seoul

first: Wonje

last: Lee

address: anam

country: South Korea

institute: biosystems

data_processing:
bcl2fastq2 (Version 2.20) software used for basecalling.
Using bowtie to align RNA-seq data to reference genome(Arabidopsis thaliana GCF_000001735.4) and get histogram for insert size
Using Tophat v2.0.13 to mapping the read to reference(Arabidopsis thaliana GCF_000001735.4) and generate bam files.
Fragments Per Kilobase of transcript per Million(FPKM) was calculated from mapped reads using cuffdiff v2.2.1
Genome_build: Arabidopsis thaliana GCF_000001735.4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: The seedlings were grown in a growth chamber at 23 °C and 60% relative humidity under long-day conditions (light 16h, dark 8h)

extract_protocol:
Total RNA was extracted by using Trizol reagent. Stranded 101bp paired-end library prepared with TruSeq Stranded mRNA Library Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Growth plants uner 20 Mm nitrate 1/2 MS medium then transffered to nitrate-deficient condition before treatment 6hours of 0.05 Mm nitrate

value: Whole plant

tag: age

value: 9-day-old seedlings

value: nid1 knockout mutant

value: Nitrate 0.05 mM, 6 hours


title: 2-2: Arabidopsis nid1 ko-Low nitrate treatment


title: control_7

description: SAMPLE 7

source_name: mouse skin, control, replicate 7

value: skin tissue

value: female

value: non-treated mouse


title: shRNA_Dppa4_plusDox_C

description:
Sampe 120
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx


title: shRNA_Dppa2_noDox_C

description:
Sampe 115
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

source_name: inducible shRNA cells untreated


title: CROP-seq_CRISPRi_10x_lane_3

description: CROP-seq


title: plasma_0s_3

description: SAMPLE 12

source_name: mouse skin, 0 s, replicate 3

value: male


title: control_8

description: SAMPLE 8

source_name: mouse skin, control, replicate 8


title: CROP-seq_CRISPRi_10x_lane_4

description: CROP-seq


title: shRNA_Dppa4_recovery_B

description:
Sampe 119
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

value: embryonic stem cell


title: control_6

description: SAMPLE 6

source_name: mouse skin, control, replicate 6


title: CROP-seq_CRISPRi_10x_lane_2

description: CROP-seq


title: control_9

description: SAMPLE 9

source_name: mouse skin, control, replicate 9


title: control_5

description: SAMPLE 5

source_name: mouse skin, control, replicate 5


title: shRNA_Dppa2_plusDox_C

description:
Sampe 113
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

value: serum/LIF


title: 1-3: Arabidopsis Col-0-Low nitrate treatment

value: Wild-type


title: shRNA_Dppa4_recovery_C

description:
Sampe 117
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx


title: 1-2: Arabidopsis Col-0-Low nitrate treatment


title: shRNA_Dppa2_noDox_B

description:
Sampe 114
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

value: E14 ESCs containing inducible shRNA hairpin against Dppa2


title: 2-1: Arabidopsis nid1 ko-Low nitrate treatment


title: 1-1: Arabidopsis Col-0-Low nitrate treatment


title: control_4

description: SAMPLE 4

source_name: mouse skin, control, replicate 4


title: shRNA_Dppa4_plusDox_B

description:
Sampe 112
amplicon bisulfite seq
Processed_data_Samples_112-129.xlsx

value: E14 ESCs containing inducible shRNA hairpin against Dppa4


title: CROP-seq_CRISPRi_10x_lane_1

description: CROP-seq


title: control_2

description: SAMPLE 2

source_name: mouse skin, control, replicate 2