title: CleftProband_422

data_processing:
532.tif and 635.tif files were analyzed using DEVA software to generate a data_summary.txt file and segMNT.txt file. Data_summary.txt files were analyzed using Nexus 7 Software to generate NexusData.bed files and then compared to the segMNT.txt file using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. NimbleGen's DEVA segMNT algorithm, which minimizes squared error relative to the segment means, was used as a second algorithm for all copy number calls after data extraction, LOESS spatial correction and background correction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.

extract_protocol: DNA was extracted from whole blood samples using the Quickgene610L.

value: cleft palate only

value: not applicable


title: HeLa cells, BLTF enriched nuclear RNA

status: Public on Dec 01 2022

type: SRA

city: Beijing

first: Haofan

last: Sun

address: Grindtorpsvägen 11 7tr Lgh 1803, Grindtorpsvägen 11, 183 32 Täby

country: China

institute: National Center for Protein Sciences, Beijing

library_source: transcriptomic

data_processing:
To estimate the content of RNA biotypes in libraries, reads were aligned to the hg38 assembly using STAR.
Counting was performed with HTSeq-count using the gene set annotated by GENCODE Release 21 (GRCh38) and using the GTF feature ‘gene’ for counting.
Assembly: hg38
Supplementary files format and content: Tab-separated values files

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: Hela

extract_protocol:
RNAs were purified by TRIzol following the manufacturer’s instructions
The RNA samples were prepared with the TruSeq RNA Library Prep Kit v2.

tag: cell line

value: Hela

tag: cell type

value: Human cervix carcinoma

tag: treatment

value: BLTF enrichment


title: CleftProband_420

type: genomic

city: Iowa City

first: J.

middle: Robert

last: Manak

state: Iowa

address: 455 Biology Building, 129 East Jefferson Street

department: Biology and Pediatrics

country: USA

institute: The University of Iowa

hyb_protocol: 34 ug of each labeled DNA was co-hybridized to a Roche NimbleGen human whole genome tiling microarray (Human CGH 2.1M Whole-Genome Tiling v2.0D Array)

scan_protocol: Arrays were scanned on a Roche NimbleGen microarray scanner.

molecule: genomic DNA

source_name: genomic DNA from whole blood

label_protocol: 1 ug of case DNA was labeled with Cy3-coupled nonamers and 1 ug of control DNA (from an unaffected male from the Philippines) was labeled with Cy5-coupled nonamers.

tag: Sex

value: female

tag: syndromic versus non-syndromic

value: non-syndromic

tag: cleft type

value: cleft lip only

tag: cleft laterality

value: right

source_name: DNA from an unaffected male from the Philippines

value: male

value: unaffected


title: HeLa cells, cytoplasmic RNA

molecule: nuclear RNA

value: density gradient centrifugation


title: Balb-C female mouse liver_S8_L003_Nafion BP2-3.0 [GRC362-19_S8]

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

data_processing:
Sequencing and base calling were completed using the Illumina NextSeq 500 according to standard methods. The sequenced mRNA reads were mapped to the mouse genome in a Partek Flow suite. Pre and post  alignment QC checks were done on each sample to relate all data for the single sample to the corresponding sequenced reads. The processed data matrix is derived from the Partek output file.
genome build: GRCm38.p5; GCF_000001635.25
Supplementary_files_format_and_content: The processed data matrix contains a single data point per sample that represents the summary of results from the four (4) fastq files produced per sample. Therefore, the sample names (20 total) in the matrix file are the ‘root name’ of the four (4) related metadata sample names (80 total), e.g., data matrix sample GRC362-01_S14 is a summary of data from samples GRC362-01_S14_L001, GRC362-01_S14_L002, GRC362-01_S14_L003 and GRC362-01_S14_L004.

molecule: total RNA

organism: Mus musculus

source_name: Balb-C female mouse liver_Nafion BP2-3.0

extract_protocol: The livers tissues (~50-100 mg) were preserved in RNAlater (Qiagen, Valencia, CA) and stored at -80°C until RNA extraction. Total RNA was extracted from tissue samples 2-6 months later with Trizol by polytron homogenization. The resultant RNA was further purified using the RNeasy Mini Kit (Qiagen), and RNA integrity was checked with Bioanalyzer RNAnanochip. Samples were submitted to EPA core facility for processing and analysis using the Illumina mouse whole genome platform and NexSeq 500 system.

treatment_protocol: Balb-C female mice at 10-12 weeks of age were dosed by gavage for 7 consecutive days using 20-gauge stainless steel feeding needles. Doses of 0, 0.03, 0.3, 3.0, and 6.0 mg/kg-day were administered once daily in the afternoon. Control animals were administered an equal volume of deionized water. Four biological replicates consisting of individual animals were included in each dose group.

tag: strain

value: Balb-C

tag: age

value: 10-12 weeks

value: Nafion BP2

tag: dose

value: 3.0 mg/kg

tag: tissue

value: liver


title: 2M, ovoid cells

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M.smegmatis MC2 155 genome using bowtie2 with parameters -p 4 (and --local --dovetail in case paired-end sample)
Reads counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of reads (or fragments) overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped reads were used in a subsequent analysis. The files "Counts_XX.txt" represent these counts (File "Counts_all.txt" contains values for all samples).
Assembly: NC_008596.1

organism: Mycolicibacterium smegmatis MC2 155

source_name: bacterial culture

growth_protocol: Cells were first grown in Nutrient broth (“Himedia”, India) in the presence of 0.05 % Tween-80 at 37 °C and 200 rpm for 24 h. The resulting culture was added at a concentration of 105–106 cells/ml to 250 ml of Sauton (pH 7.0, for “active” cultures) or modified Sauton (pH 6.0-6.2, for “dormant” cultures) medium. The modified Sauton medium contained (per litre): 0.5 g KH2PO4; 1.4 g MgSO4·7H2O; 4 g L-asparagine; 60 ml glycerol; 0.05 g ferric ammonium citrate; 2 g sodium citrate, and 0.1 ml 1% ZnSO4·7H2O, supplemented with 0.05% Tween-80. The modification included a decrease of the initial pH to 6.0–6.2 (no titration with NaOH) (Kudykina et al., 2011). Cultures were incubated at 37°C under constant shaking for 10–20 days, and pH values were periodically measured. Active control cultures were harvested at late exponential/pre-stationary phase. Dormant cells were harvested when cultures entered the post-stationary phase, changing the color and reaching pH 6.0–6.2 (after 13–15 days of cultivation). Cultures were transferred to plastic-capped tubes (50 ml) and maintained under static conditions without agitation at room temperature for up to 30 days post inoculation.

extract_protocol:
Active and dormant (ovoid) cultures were harvested by centrifugation at 7000 rpm for 15 min and washed 3 times with an ice-cold PBSm buffer containing (per liter) 8 g NaCl, 0.2 g MgCl2, and 0.24 g Na2HPO4 (pH 7.0). The bacterial pellet was re-suspended in the same buffer containing phenylmethanesulfonyl fluoride (PMSF) then lysed by using zirconium beads on a bead beater homogenizer (MP Biomedicals FastPrep-24) for 30 sec, three times. The bacterial lysate was centrifuged at 13000 rpm for 10 min at 4 °C. The supernatant was separated into membrane and cytosolic fractions using ultracentrifugation at 105000g and 4 °C for 2 h. The membrane fraction was washed with PBSm using ultracentrifugation. For RNA isolation the pellet was re-suspended in ice-cold 100 mM HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) buffer (pH 8.0) containing 5 mM EDTA and the zwitterionic detergent CHAPS (3-(3-cholamidopropyl) dimethylammonio-1-propanesulfonate hydrate (2%) (w/v)).
Total RNA waw isolated by phenol-chloroform extraction as described previously [Rustad TR, Roberts DM, Liao RP, Sherman DR. Isolation of mycobacterial RNA. Methods Mol Biol. 2009;465:13–21.]
After isolation RNA was treated with Turbo DNase (Life Technologies, USA) to remove traces of genomic DNA. Amounts and purity of RNA were determined spectrophotometrically; integrity of RNA was assessed in 1% agarose gel. Sequencing libraries were generated using the resulting RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, USA) according to the manufacturers' protocol.

value: bacterial culture

tag: state

value: dormant (ovoid)


title: Balb-C female mouse liver_S8_L002_Nafion BP2-3.0 [GRC362-19_S8]


title: 7M, active cells

value: active


title: CleftProband_419

value: cleft lip and cleft palate

value: bilateral


title: HeLa cells, nuclear RNA

value: Hela

value: Human cervix carcinoma


title: 1M, active cells


title: CleftProband_418

value: female

value: syndromic

value: cleft lip only

value: Midline


title: ahtet_Rad21PK_2

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

library_source: genomic

data_processing:
ChIP-seq samples were sequenced on either Hiseq2500 with single-end method (50-bp reads) or Novaseq6000 with pair-end method (150-bp reads). S.pombe Hi-C samples were sequenced on Hiseq4000 with pair-end method (100-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (V3.04.04, Novocraft technologies) with default parameters. Aligned reads were converted into BAM and replicates were merged using samtools (v1.10). Significantly enriched peaks were identified using MACS2 (v.2.1.4) and mapped reads were quantified using Deeptools (v3.1.3) and bwtool (v1.0).
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner. Strand-specific signal tracks of RNA-seq were generated by using bam2wig.py from RseQC (v3.0.1).
Hi-C data were aligned to the S.pombe genome (ASM294v2) using bowtie2 and normalized using HiC-Pro (v2.11.0-beta). The raw and ICE-normalized matrix was generated at 1-kb and 2.5-kb bin resolution using valid interaction pairs.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: ChIP-seq: Yeast ChIP-seq bigwig files were created using deeptools bamCoverage (RPM normalization). In case of calibrated bigWigs for set4 experiments, samtools flagstat was used to count reads that were mapped to s.pombe and s.cerevisiae respectively. The occupancy ratio (OR) was calculated according to the previous publication (Hu, B. et al 2015). Then the calibrated s.pombe ChP (Rad21-5FLAGand notag) bigwigs were created using bamCoverage –scaleFactor option; Hi-C: ICE normalized HiC matrix text files and abs files (in HiC-Pro format); RNA-seq: bigwig files and normalized forward/reverser RPKM test files. The number of mapped reads was further analyzed using HOMER and DESeq.

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: S. pombe: 1) For Hi-C experiments, yeast cells were grown to mid-log phases at 32 degrees, unless indicated otherwise. 2) For ChIP-seq in tetracycline-regulated system, cells were grown to mid-log phase at 30 degress in YES medium supplied with 2.5 ug/ml of anhydrotetracycline (ahTet). Depletion of rrp6+ was achieved by culturing cells in YES medium that lacks ahTet at indicated times (8, 12hr). Recovery of rrp6+ was achieved by culturing cells at fresh YES medium containing 2.5ug/ml of ahTet. 3) for ChIP-seq experiments, yeast cells were grown to mid-log phases at 30 degrees, unless indicated otherwise.

extract_protocol:
S. pombe (ChIP) : Fixed cells were sonicated twelve times (15 sec on, 180 sec off) using a Fisher Scientific sonic Dismembrator Model 500 sonicator at 30% output. The immunoprecipitated DNA was eluted using SigmaPrep™ spin column and then subjected to protease treatment and cross-linking reversal. Subsequently, the DNA was purified using Qiaquick PCR purification kit (Qiagen).
S. pombe (RNA isolation): DNase-treated mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.
S.pombe (in situ Hi-C): formaldehyde-fixed cells (1.6 x 10^7 cells) were digested with zymolyase. Restriction enzyme digestion (MboI – 4 cutter), filling-in, ligation, crosslink reversal, DNA shearing and library construction were done according to previous publications (Rao, SSP et al 2014) with minor modifications.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT). mRNA-seq libraries were made using NEXTflex™ Rapid Directional mRNA-Seq kit (5138-10, BIOO) from purified mRNA.

tag: genotype

tag: chip antibody

value: Mouse anti V5-Tag (MCA1360, Biorad)

value: treated with anhydrotetracycline (ahTet)


title: Parental cell lines, BRMS1 WT, replicate 1

city: New York

first: Yuan

last: Liu

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Assembly: GRC37/hg19
Supplementary files format and content: tab-delimited file containing raw counts

growth_protocol: RPMI + 10% FBS

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (74104, Qiagen), in accordance with the manufacturer’s protocol
library preparation and RNA sequencing were performed by the Integrated Genomics Operation at MSK using Illumina HiSeq with 50 paired-end reads, and approximately 30 million reads were generated for each sample

value: epithelial cells

value: BRMS1 WT


title: Balb-C female mouse liver_S15_L004_Nafion BP2-3.0 [GRC362-18_S15]

value: Balb-C

value: 10-12 weeks

value: Nafion BP2

value: 3.0 mg/kg


title: WT_RNAseq_HEK293FT_rep2

city: boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

description: mRNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were mapped to the human genome (GRCh37/hg19) with Kallisto (version 1.15.0).
Transcript abundances were normalized with Transcripts Per Million (TPM) mapped reads.
Differentially expressed genes were identified by DESeq2 ((v1.18.1)) with fold change>2 and Benjamini–Hochberg false discovery rate adjusted P < 0.05.
deeptool (v/3.0.2) was used to generate bigwig files for visualization in IGV tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file normalized to RPGC for each Sample

molecule: polyA RNA

extract_protocol:
For mRNA-seq, total RNA was isolated from human cells with an RNA purification kit (Qiagen, 74134) and genomic DNA was removed by genomic DNA binding columns in the kit.
For RNA-seq, two μg of total RNA was used to start RNA-seq library construction. Poly(A)-containing mRNA was isolated by poly-A selection beads and further reverse transcribed to cDNA. The resulting cDNA was ligated with adapters, amplified by PCR, and further cleaned to obtain the final library. Libraries were sequenced on an Illumina Hiseq machine (Novogene) to obtain 150 bp paired-end reads.

tag: sirna

value: no

tag: knockout

tag: medium

value: DMEM

tag: antibody


title: WT_RNAseq_HEK293FT_rep1

description: mRNA-seq

tag: cell line


title: Balb-C female mouse liver_S15_L003_Nafion BP2-3.0 [GRC362-18_S15]

tag: treatment

value: liver


title: CleftProband_417

tag: Sex

value: male

value: non-syndromic

value: cleft lip and cleft palate

value: bilateral

value: unaffected


title: Balb-C female mouse liver_S8_L001_Nafion BP2-3.0 [GRC362-19_S8]

value: female


title: RING1B_Q1371Q138A_RNAseq_HEK293FT_rep2

description: mRNA-seq

value: RING1B Q137A/Q138A mutation


title: CleftProband_416

tag: syndromic versus non-syndromic

value: syndromic

value: left


title: CleftProband_421

tag: cleft type

value: right


title: CleftProband_415

tag: cleft laterality


title: Balb-C female mouse liver_S15_L002_Nafion BP2-3.0 [GRC362-18_S15]

tag: strain

value: Balb-C


title: ahtet_plus30min_Rad21PK_2

value: Mouse anti V5-Tag (MCA1360, Biorad)

value: treated with anhydrotetracycline (ahTet) for 30min


title: RING1B_Q1371Q138A_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: CleftProband_414

value: cleft palate only

value: not applicable


title: Balb-C female mouse liver_S15_L001_Nafion BP2-3.0 [GRC362-18_S15]

tag: age

value: 10-12 weeks

value: Nafion BP2

value: 3.0 mg/kg


title: RING1AB_KO_no_siRNA_RNAseq_HEK293FT_rep2

description: mRNA-seq

value: no

value: RING1A and RING1B double knockout

value: DMEM


title: ahtet_plus30min_Rad21PK_1


title: ahtet_plus30min_PK_notag_2


title: CleftProband_413

value: non-syndromic

value: cleft lip only

value: male

value: unaffected


title: ahtet_Rad21PK_1

value: treated with anhydrotetracycline (ahTet)


title: CleftProband_412


title: ahtet_plus30min_PK_notag_1


title: ahtet_plus4hr_Rad21PK_2

value: treated with anhydrotetracycline (ahTet) for 4hr


title: RING1AB_KO_no_siRNA_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: Balb-C female mouse liver_S5_L002_Nafion BP2-3.0 [GRC362-17_S5]

value: Balb-C

value: female

tag: dose

value: liver


title: Sample_R116019T

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

description:
Read_Counts_Matrix_Gene_Level.txt.gz
TPM_Matrix_Gene_Level.txt.gz

data_processing:
Real Time Analysis (RTA) and CASAVA v1.8 for base-calling
Salmon for quantification and counting reads
Genome_build: hg38
Supplementary_files_format_and_content: Both TPM and read counts are tab-limited text files

source_name: tumor

extract_protocol:
Samples were treated with 1mL TRIzol reagent according to manufacturer's instructions. Nanodrop ND-1000 was used for RNA density/purity detection. Agilent BioAnalyzer 2100 was used for RNA quality control. rRNA depletion was conducted before RNA-seq library preparation using TruSeq Stranded Total RNA Library Prep Kit.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

tag: individual

tag: disease state

value: HCC

tag: tissue

value: tumor


title: Sample_R116019N

source_name: Adjacent tissue

value: Adjacent normal


title: CleftProband_411

value: cleft lip and cleft palate

value: left


title: ahtet_plus4hr_Rad21PK_1

tag: genotype

tag: chip antibody

value: Mouse anti V5-Tag (MCA1360, Biorad)


title: Sample_R079779T


title: Balb-C female mouse liver_S5_L001_Nafion BP2-3.0 [GRC362-17_S5]

value: 10-12 weeks

value: Nafion BP2

value: 3.0 mg/kg


title: Balb-C female mouse liver_S18_L004_Nafion BP2-0.3 [GRC362-16_S18]

source_name: Balb-C female mouse liver_Nafion BP2-0.3

value: 0.3 mg/kg


title: CleftProband_410

value: syndromic

value: cleft lip only

value: Microform

value: male


title: CleftProband_409

value: non-syndromic

value: bilateral

value: unaffected


title: Sample_R079779N

value: HCC


title: Balb-C female mouse liver_S5_L004_Nafion BP2-3.0 [GRC362-17_S5]

value: Balb-C

value: female

value: liver


title: CleftProband_408

value: cleft palate only

value: not applicable


title: Balb-C female mouse liver_S18_L003_Nafion BP2-0.3 [GRC362-16_S18]

value: 10-12 weeks


title: Sample_R079741T

value: tumor


title: ahtet_plus4hr_PK_notag_2

value: Mouse anti V5-Tag (MCA1360, Biorad)

value: treated with anhydrotetracycline (ahTet) for 4hr


title: Sample_R079741N

value: Adjacent normal


title: ahtet_PK_notag_2

value: treated with anhydrotetracycline (ahTet)


title: ahtet_plus4hr_PK_notag_1


title: Balb-C female mouse liver_S5_L003_Nafion BP2-3.0 [GRC362-17_S5]

value: Nafion BP2

value: 3.0 mg/kg


title: CleftProband_407

value: non-syndromic

value: cleft lip only

value: right

value: male


title: Balb-C female mouse liver_S18_L002_Nafion BP2-0.3 [GRC362-16_S18]

value: Balb-C

value: 0.3 mg/kg


title: CleftProband_406

value: female

value: cleft lip and cleft palate

value: bilateral

value: unaffected


title: Balb-C female mouse liver_S18_L001_Nafion BP2-0.3 [GRC362-16_S18]

value: 10-12 weeks

value: liver


title: ahtet_PK_notag_1

value: Mouse anti V5-Tag (MCA1360, Biorad)


title: Sample_P116019T

value: HCC

value: tumor


title: ahtet_minus12hr_Rad21PK_2

value: anhydrotetracycline (ahTet) withdrawal for 12hr


title: Balb-C female mouse liver_S11_L004_Nafion BP2-0.3 [GRC362-15_S11]

value: Nafion BP2


title: Sample_P116019N

value: Adjacent normal


title: ahtet_minus12hr_Rad21PK_1


title: Balb-C female mouse liver_S11_L003_Nafion BP2-0.3 [GRC362-15_S11]


title: CleftProband_404

value: non-syndromic

value: left


title: Sample_P079779T


title: ahtet_minus12hr_PK_notag_2


title: Balb-C female mouse liver_S11_L002_Nafion BP2-0.3 [GRC362-15_S11]


title: CleftProband_403

value: syndromic

value: right

value: male


title: Sample_P079779N


title: ahtet_minus12hr_PK_notag_1


title: Sample_P079741T


title: CleftProband_401

value: female


title: CleftProband_402

value: cleft lip only


title: Balb-C female mouse liver_S19_L004_Nafion BP2-0.3 [GRC362-14_S19]

value: Balb-C

value: 0.3 mg/kg


title: Balb-C female mouse liver_S19_L003_Nafion BP2-0.3 [GRC362-14_S19]

value: 10-12 weeks


title: Sample_P079741N


title: CleftProband_400

value: cleft lip and cleft palate

value: bilateral

value: unaffected


title: Sample_P070913T

value: HCC

value: tumor


title: Balb-C female mouse liver_S19_L002_Nafion BP2-0.3 [GRC362-14_S19]

value: Nafion BP2

value: liver


title: Sample_P070913N

value: Adjacent normal


title: CleftProband_399

value: left


title: CleftProband_398

value: non-syndromic


title: Balb-C female mouse liver_S19_L001_Nafion BP2-0.3 [GRC362-14_S19]


title: ahtet_minus8hr_PK_notag_1

value: Mouse anti V5-Tag (MCA1360, Biorad)

value: anhydrotetracycline (ahTet) withdrawal for 8hr


title: CleftProband_405

value: female

value: right

value: male


title: Sample_075199T


title: Balb-C female mouse liver_S16_L004_Nafion BP2-0.3 [GRC362-13_S16]

value: Balb-C

value: 0.3 mg/kg


title: CleftProband_397

value: cleft palate only

value: not applicable


title: Sample_075199N


title: Balb-C female mouse liver_S11_L001_Nafion BP2-0.3 [GRC362-15_S11]

value: 10-12 weeks


title: ahtet_minus8hr_Rad21PK_2


title: ahtet_minus8hr_Rad21PK_1


title: Balb-C female mouse liver_S16_L003_Nafion BP2-0.3 [GRC362-13_S16]


title: Sample_074848T

value: HCC


title: CleftProband_396

value: cleft lip and cleft palate

value: bilateral

value: unaffected


title: Balb-C female mouse liver_S16_L001_Nafion BP2-0.3 [GRC362-13_S16]

value: Nafion BP2

value: liver


title: ahtet_minus8hr_PK_notag_2


title: Balb-C female mouse liver_S16_L002_Nafion BP2-0.3 [GRC362-13_S16]


title: Sample_074720T

value: tumor


title: CleftProband_394

value: non-syndromic

value: left


title: CleftProband_395

value: cleft lip only


title: Sample_074848N

value: Adjacent normal


title: CleftProband_393

value: male


title: Sample_074720N


title: CleftProband_392

value: female


title: Balb-C female mouse liver_S17_L003_Nafion BP2-0.03 [GRC362-12_S17]

source_name: Balb-C female mouse liver_Nafion BP2-0.03

value: Balb-C


title: Balb-C female mouse liver_S17_L004_Nafion BP2-0.03 [GRC362-12_S17]


title: Sample_074607T


title: Balb-C female mouse liver_S17_L002_Nafion BP2-0.03 [GRC362-12_S17]


title: Sample_074607N


title: Balb-C female mouse liver_S17_L001_Nafion BP2-0.03 [GRC362-12_S17]


title: Sample_070880T


title: CleftProband_390

value: right


title: CleftProband_389


title: Sample_070880N


title: Balb-C female mouse liver_S3_L003_Nafion BP2-0.03 [GRC362-11_S3]


title: CleftProband_388


title: Balb-C female mouse liver_S3_L002_Nafion BP2-0.03 [GRC362-11_S3]


title: Balb-C female mouse liver_S3_L004_Nafion BP2-0.03 [GRC362-11_S3]


title: CleftProband_386


title: Neuroblastoma cell line SK-N-AS, nontransfected, 6Gy, replicate 3

type: RNA

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

hyb_protocol: Samples were hybridized with Clariom D Human Arrays (Affymetrix) and scanned at the Northwestern University NUSeq Core Facililty.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data analysis was performed using the Affymetrix software, Transcriptome Analysis Console (TAC) version 4.0.  Expression values have been normalized by Robust Multi-chip Analysis (RMA).

label: biotin

source_name: Neuroblastoma cell line SK-N-AS

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were maintained in high-glucose Dulbecco’s modified Eagle medium with 10% fetal bovine serum in presence of 1x antibiotic antimycotic solution and 1x Essential amnio acids solution in 5% CO2 at 37°C.  Plates intended for SK-N-DZ cells wells coated with Geltrex

extract_protocol: RNA was isolated with the mirVanaTM kit. cDNA for gene expression analysis was generated from 1 μg of DNAse-treated total RNA using SuperScript® III First-Strand Synthesis SuperMix. The GeneChip WT PLUS Reagent Kit was used for RNA sample preparation for array hybridization

treatment_protocol: For transfection experiments, 6 x 10E5 cells per well were seeded in 6 well plate one day prior transfection. Transfections with control and miR-1228 and miR34a pre-miRs were done with Lipofectamine RNAiMax. Twenty to twenty four hours after transfection cells were irradiated with 6 or 4 Gy of 160 kpV X-rays; 1h later RNA was harvested.

tag: transfection

value: nontransfected

tag: radiation dose

value: Female


title: Neuroblastoma cell line SK-N-DZ, nontransfected, 4Gy, replicate 3

source_name: Neuroblastoma cell line SK-N-DZ


title: Neuroblastoma cell line SK-N-DZ, nontransfected, 4Gy, replicate 1


title: Balb-C female mouse liver_S3_L001_Nafion BP2-0.03 [GRC362-11_S3]

value: 10-12 weeks


title: CleftProband_391


title: Neuroblastoma cell line SK-N-DZ, nontransfected, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-AS, nontransfected, 0Gy, replicate 2


title: Neuroblastoma cell line SK-N-AS, nontransfected, 6Gy, replicate 1


title: Neuroblastoma cell line SK-N-AS, nontransfected, 6Gy, replicate 2


title: Sample_070103N

value: HCC


title: CleftProband_385

value: cleft lip and cleft palate

value: bilateral


title: Balb-C female mouse liver_S6_L003_Nafion BP2-0.03 [GRC362-10_S6]

value: Nafion BP2


title: Sample_070785T


title: Sample_070785N


title: CleftProband_387

value: unaffected


title: Neuroblastoma cell line SK-N-DZ, nontransfected, 0Gy, replicate 2


title: Neuroblastoma cell line SK-N-AS, nontransfected, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-DZ, nontransfected, 4Gy, replicate 2


title: Sample_067754T

value: tumor


title: CleftProband_383

value: non-syndromic


title: Sample_070103T


title: Neuroblastoma cell line SK-N-AS, nontransfected, 0Gy, replicate 1


title: Neuroblastoma cell line SK-N-DZ, nontransfected, 0Gy, replicate 1


title: Balb-C female mouse liver_S6_L004_Nafion BP2-0.03 [GRC362-10_S6]

value: liver


title: Sample_067754N


title: CleftProband_384

value: left


title: Balb-C female mouse liver_S6_L002_Nafion BP2-0.03 [GRC362-10_S6]


title: CF, sorted lung trAMs, after 6 weeks of recovery from chronic LPS, rep2

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

institute: Yale University

data_processing:
After quality control (FastQC), reads generated from each sample were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package in Bioconductor (https://bioconductor.org). Differentially expressed genes were identified with the glmQLFTest function using a double threshold on gene expression changes and associated statistical significance (absolute log2 fold change > 0.75, p-value < 0.05). To identify, within each cellular population, genes differentially regulated in CF between T1 and T2, the following contrast, based on 2 factors, was used: (CFT2 - WTT2) - (CFT1 - WTT1). Functional annotation and enrichment analysis were performed with the enrichR package (https://maayanlab.cloud/Enrichr).
Assembly: GRCm38.p5
Supplementary files format and content: gene_counts_table.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned RNA-seq reads.

source_name: RNA-seq from CF sorted lung trAMs after 6 weeks of recovery from chronic LPS, biological replicate 2

extract_protocol:
Lungs of treated WT and CF mice were perfused to remove circulating blood cells and single cell suspension from lung tissues were isolated using a lung dissociation kit (Miltenyi). Cells were stained and FACS-sorted, and RNA was extracted using miRNEasy Micro kit (Qiagen, MD). Markers used to sort monocytes/macrophages are: cMons: CD45+CD11b+MHC-II-Ly6C+; IMs: CD45+CD11b+MHC-II+; moAMs: CD45+CD11c+SiglecFdim; trAMs: CD45+CD11c+SiglecF+
The RNA integrity (RIN) and quantity was determined on the Agilent 2100 Bioanalyzer (Agilent, CA) with Agilent RNA 6000 Pico Kit (Agilent, CA). Only samples with RIN ≥8.0 were used for library preparation. Reverse transcription and cDNA preamplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, MI), and sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina, CA, USA), according to manufacturers’ instructions. Libraries were pooled and sequenced on Illumina HiSeq4000 (Illumina, CA, USA) using paired-end sequencing for 100 cycles.

treatment_protocol: For chronic LPS time point (T1), WT and CF mice were nebulized with 12.5 mg of LPS of Pseudomonas aeruginosa (L9413 Millipore Sigma) dissolved in PBS three times per week for five weeks (15 doses total, 15 minutes of nebulization with 5ml each) and sacrificed 24 h after the last neblization.  For the recovery time point (T2), WT and CF mice were left to recover for six weeks following LPS nebulizations.

tag: cell type

value: primary lung tissue resident alveolar macrophage

value: 6 weeks of recovery after 15 doses of LPS over 5 weeks


title: Balb-C female mouse liver_S6_L001_Nafion BP2-0.03 [GRC362-10_S6]

value: female


title: Balb-C female mouse liver_S20_L004_Nafion BP2-0.03 [GRC362-09_S20]

value: Balb-C


title: CF, sorted lung trAMs, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from CF sorted lung trAMs after 6 weeks of recovery from chronic LPS, biological replicate 1


title: CleftProband_381

value: male


title: Neuroblastoma cell line SK-N-DZ, control miR overexpression, 4Gy, replicate 3

value: control miR overexpression


title: CleftProband_382

value: cleft lip only


title: Neuroblastoma cell line SK-N-AS, control miR overexpression, 6Gy, replicate 3

value: Female


title: Balb-C female mouse liver_S20_L003_Nafion BP2-0.03 [GRC362-09_S20]

value: 10-12 weeks


title: CleftProband_380


title: CF, sorted lung moAMs, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from CF sorted lung moAMs after 6 weeks of recovery from chronic LPS, biological replicate 2

value: primary lung monocyte derived alveolar macrophage


title: Neuroblastoma cell line SK-N-AS, control miR overexpression, 6Gy, replicate 1


title: Balb-C female mouse liver_S20_L002_Nafion BP2-0.03 [GRC362-09_S20]


title: CF, sorted lung moAMs, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from CF sorted lung moAMs after 6 weeks of recovery from chronic LPS, biological replicate 1


title: CleftProband_379

value: right


title: CleftProband_378

value: cleft lip and cleft palate

value: bilateral


title: Neuroblastoma cell line SK-N-DZ, control miR overexpression, 4Gy, replicate 2


title: Balb-C female mouse liver_S20_L001_Nafion BP2-0.03 [GRC362-09_S20]

value: Nafion BP2


title: CF, sorted lung IMs, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from CF sorted lung IMs after 6 weeks of recovery from chronic LPS, biological replicate 2

value: primary lung interstitial macrophage


title: CF, sorted lung IMs, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from CF sorted lung IMs after 6 weeks of recovery from chronic LPS, biological replicate 1


title: Balb-C female mouse liver_S12_L003_DMSO-0 [GRC362-04_S12]

source_name: Balb-C female mouse liver_DMSO-0

value: Control

value: 0 mg/kg

value: liver


title: CleftProband_377

source_name: genomic DNA from whole blood

value: non-syndromic

source_name: DNA from an unaffected male from the Philippines

value: unaffected


title: CF, sorted lung cMons, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from CF sorted lung cMons after 6 weeks of recovery from chronic LPS, biological replicate 2

value: primary lung classical monocyte

value: 6 weeks of recovery after 15 doses of LPS over 5 weeks


title: Neuroblastoma cell line SK-N-AS, control miR overexpression, 6Gy, replicate 2

value: control miR overexpression


title: CleftProband_376

value: male

value: left


title: Neuroblastoma cell line SK-N-DZ, control miR overexpression, 4Gy, replicate 1

value: Female


title: Balb-C female mouse liver_S12_L002_DMSO-0 [GRC362-04_S12]

value: Balb-C

value: 10-12 weeks

value: female


title: CleftProband_375

value: cleft lip only

value: right


title: CF, sorted lung cMons, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from CF sorted lung cMons after 6 weeks of recovery from chronic LPS, biological replicate 1


title: Balb-C female mouse liver_S12_L001_DMSO-0 [GRC362-04_S12]


title: WT, sorted lung trAMs, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from WT sorted lung trAMs after 6 weeks of recovery from chronic LPS, biological replicate 2

value: primary lung tissue resident alveolar macrophage


title: Balb-C female mouse liver_S13_L004_DMSO-0 [GRC362-03_S13]

value: Control


title: Neuroblastoma cell line SK-N-AS, control miR overexpression, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-DZ, control miR overexpression, 0Gy, replicate 3


title: CleftProband_373

value: cleft lip and cleft palate


title: WT, sorted lung trAMs, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from WT sorted lung trAMs after 6 weeks of recovery from chronic LPS, biological replicate 1


title: Neuroblastoma cell line SK-N-AS, control miR overexpression, 0Gy, replicate 2


title: WT, sorted lung moAMs, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from WT sorted lung moAMs after 6 weeks of recovery from chronic LPS, biological replicate 2

value: primary lung monocyte derived alveolar macrophage


title: CleftProband_372

value: non-syndromic


title: Balb-C female mouse liver_S13_L003_DMSO-0 [GRC362-03_S13]

value: 0 mg/kg

value: liver


title: Neuroblastoma cell line SK-N-DZ, control miR overexpression, 0Gy, replicate 2


title: Balb-C female mouse liver_S13_L002_DMSO-0 [GRC362-03_S13]


title: CleftProband_371

value: unaffected


title: WT, sorted lung moAMs, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from WT sorted lung moAMs after 6 weeks of recovery from chronic LPS, biological replicate 1

value: 6 weeks of recovery after 15 doses of LPS over 5 weeks


title: CleftProband_370

value: male


title: Balb-C female mouse liver_S9_L004_DMSO-0 [GRC362-02_S9]


title: WT, sorted lung IMs, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from WT sorted lung IMs after 6 weeks of recovery from chronic LPS, biological replicate 1

value: primary lung interstitial macrophage


title: CleftProband_369


title: WT, sorted lung IMs, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from WT sorted lung IMs after 6 weeks of recovery from chronic LPS, biological replicate 2


title: Neuroblastoma cell line SK-N-DZ, control miR overexpression, 0Gy, replicate 1

source_name: Neuroblastoma cell line SK-N-DZ

value: control miR overexpression

value: Female


title: Balb-C female mouse liver_S12_L004_DMSO-0 [GRC362-04_S12]

value: Balb-C

value: 10-12 weeks


title: Balb-C female mouse liver_S13_L001_DMSO-0 [GRC362-03_S13]

value: female


title: CleftProband_368

value: cleft lip only

value: right


title: WT, sorted lung cMons, after 6 weeks of recovery from chronic LPS, rep2

source_name: RNA-seq from WT sorted lung cMons after 6 weeks of recovery from chronic LPS, biological replicate 2

value: primary lung classical monocyte


title: CleftProband_367

value: cleft palate only

value: not applicable


title: WT, sorted lung cMons, after 6 weeks of recovery from chronic LPS, rep1

source_name: RNA-seq from WT sorted lung cMons after 6 weeks of recovery from chronic LPS, biological replicate 1


title: CleftProband_366

value: syndromic

value: cleft lip and cleft palate

value: left


title: CleftProband_365

value: non-syndromic

value: unaffected


title: CF, sorted lung trAMs, after chronic LPS, rep2

source_name: RNA-seq from CF sorted lung trAMs after chronic LPS, biological replicate 2

value: primary lung tissue resident alveolar macrophage

value: 15 doses of LPS over 5 weeks


title: Neuroblastoma cell line SK-N-AS, miR-34a overexpression, 6Gy, replicate 3

source_name: Neuroblastoma cell line SK-N-AS

value: miR-34a overexpression


title: CleftProband_364

value: unknown

value: male


title: CF, sorted lung trAMs, after chronic LPS, rep1

source_name: RNA-seq from CF sorted lung trAMs after chronic LPS, biological replicate 1


title: Balb-C female mouse liver_S9_L003_DMSO-0 [GRC362-02_S9]

source_name: Balb-C female mouse liver_DMSO-0

value: Balb-C

value: 10-12 weeks

value: Control

value: 0 mg/kg

value: liver


title: Balb-C female mouse liver_S9_L002_DMSO-0 [GRC362-02_S9]

value: female


title: Balb-C female mouse liver_S14_L004_DMSO-0 [GRC362-01_S14]


title: CF, sorted lung moAMs, after chronic LPS, rep2

source_name: RNA-seq from CF sorted lung moAMs after chronic LPS, biological replicate 2

value: primary lung monocyte derived alveolar macrophage


title: Balb-C female mouse liver_S14_L002_DMSO-0 [GRC362-01_S14]


title: CleftProband_363

source_name: genomic DNA from whole blood

source_name: DNA from an unaffected male from the Philippines


title: CF, sorted lung moAMs, after chronic LPS, rep1

source_name: RNA-seq from CF sorted lung moAMs after chronic LPS, biological replicate 1


title: Neuroblastoma cell line SK-N-AS, control miR overexpression, 0Gy, replicate 1

value: control miR overexpression

value: Female


title: CleftProband_362

value: syndromic

value: cleft lip and cleft palate

value: bilateral


title: CF, sorted lung IMs, after chronic LPS, rep2

source_name: RNA-seq from CF sorted lung IMs after chronic LPS, biological replicate 2

value: primary lung interstitial macrophage


title: Balb-C female mouse liver_S14_L003_DMSO-0 [GRC362-01_S14]


title: Balb-C female mouse liver_S14_L001_DMSO-0 [GRC362-01_S14]


title: Balb-C female mouse liver_S9_L001_DMSO-0 [GRC362-02_S9]


title: CF, sorted lung IMs, after chronic LPS, rep1

source_name: RNA-seq from CF sorted lung IMs after chronic LPS, biological replicate 1

value: 15 doses of LPS over 5 weeks


title: CleftProband_361

value: non-syndromic

value: unaffected


title: CleftProband_360

value: male

value: cleft palate only

value: not applicable


title: CF, sorted lung cMons, after chronic LPS, rep2

source_name: RNA-seq from CF sorted lung cMons after chronic LPS, biological replicate 2

value: primary lung classical monocyte


title: S-5LP-1WTInput20191223

city: Tianjin

first: Zhiqiang

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

data_processing:
Basecalls performed using HiSeqX
ChIP-seq reads were aligned to the hg38 genome assembly using BWA version 0.7.13 with the following configurations -q 5 -l 32 -k 2
Data were filtered using Picard-tools version 1.126
peaks were called using macs2 version 2.1.0 with the following setting: -pvalue 0.01 --keep-dup all --extsize -1 --shift 0
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using macs2; Scores represent an average read coverage
Supplementary files format and content: narrowpeak files

source_name: The LP-1 cell derived from the peripheral blood of a patient with IgG-lambda myeloma in leukemic transformation

growth_protocol: LP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For HP1g ChIP,  cells were cross-linked with 1% formaldehyde. The crosslink was stopped by adding  2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with HP1g (17-646). After elution and reversal cross-linking, DNA was purified and sequenced on HiSeq X ten.
Construction of ChIP-seq library was performed using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3  (Vazyme).

tag: cell line

value: myeloma


title: S-7LP-1WTHP1chip20191223


title: Neuroblastoma cell line SK-N-DZ, miR-34a overexpression, 4Gy, replicate 3

value: miR-34a overexpression


title: CleftProband_359

value: female


title: PBMC in cubated with the inactive peptide segment of PFOR

city: Jinan

first: Ming

last: Li

state: Shandong

address: Wenhuaxi Road #107

institute: Shandong University, Qilu Hospital

library_source: transcriptomic single cell

data_processing:
The comparison software cellranger (v5.0.0) was used to align the reads to the human reference genome (GRCh38).
Supplementary files format and content: "barcodes.tsv","features.tsv","matrix.mtx" produced by cellranger programme

source_name: peripheral blood cells

growth_protocol: RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 mg/mL)

extract_protocol:
fresh cell collected
scRNA-seq of 10xGenomics based on droplet capture technology
Bulk PCR amplification
Perform 30 end sequencing

treatment_protocol: incubated with PFOR or peptide control

value: peripheral blood cells

value: PBMC

value: WT

tag: treatment


title: CleftProband_358

tag: Sex

value: left


title: PBMC in cubated with intact PFOR protein

value: cubated with intact PFOR protein


title: WT, sorted lung trAMs, after chronic LPS, rep2

source_name: RNA-seq from WT sorted lung trAMs after chronic LPS, biological replicate 2

value: primary lung tissue resident alveolar macrophage


title: WT, sorted lung trAMs, after chronic LPS, rep1

source_name: RNA-seq from WT sorted lung trAMs after chronic LPS, biological replicate 1


title: OCI-LY19R rep3

city: Singapore

first: chenchen

last: peng

address: 60 Nanyang Dr, Singapore 637551

department: SBS

country: Singapore

institute: NTU

description:
LY19_R_R3_L3
fpkm_acquireResistance.txt

data_processing:
Trimmomatic was used to remove adapters and the bases of poor quality from raw reads. Trimmed reads were aligned to reference genome hg38 by STAR. featureCount was used to gererate raw counts of each sample from trimmed reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

growth_protocol: OCI-LY3, HT, OCI-LY19, SUDHL5  were obtained from American Type Culture Collection (Manassas, VA, USA) and authenticated by STR profiling. OCI-LY3, HT were maintained in RPMI Medium (Hyclone). supplemented with 20% heat inactivated FBS (Sigma); OCI-LY19, SUDHL5 were maintained in RPMI Medium supplemented with 15% heat inactivated FBS;

extract_protocol: The trizol-isolated total RNA samples were first quantitated by Qubit RNA BR Assay (Thermo Scientific) and assessed for their quality by Agilent bioanalyzer run using RNA 6000 Nano Kit to determine the RIN scores for the samples. The RNA samples were then treated with the RNase-free, Turbo DNase I (Thermo Scientific), followed by poly (A) mRNA enrichment using NEBNext® Poly(A) mRNA Magnetic Isolation Module according to manufacturer’s instructions. Subsequently, the RNA library is prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit according to manufacturer’s recommendation. All libraries underwent 8 cycles of PCR with the recommended conditions. NEBNext oligos from NEB were ligated to allow for multiplexing of samples. After library preparation, the samples were quantitated and run on the Bioanalyzer using DNA High Sensitivity DNA Analysis kit to determine library molarities. Libraries were pooled which was then diluted to a final concentration of 5 nM. Pooled and diluted library was sent for next-generation RNA-seq by NovogeneAIT Genomics (Singapore). Library was loaded onto the Nextseq 500 and sequencing was performed using a 75-cycle high output v2 kit. The gene expression level is calculated by the reads per kilobase/million mapped reads method. Each sample was prepared as three biological triplicates to ensure the reliability of RNA-seq data.

treatment_protocol:
OCI-LY3, HT, OCI-LY19, SUDHL5 cells were treated with or without 0.2uM doxorubicin. At 24 hours post treatment , after which total RNA were harvested.
The parental doxorubicin-sensitive cells (OCI-LY19S) were maintained in a drug-free medium, and acquired doxorubicin-resistant cells (OCI-LY19R) were routinely maintained in the presence of low dose (20 nM) of doxorubicin, which was removed one week before being used for the experimental studies

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: maintained in 20 nM doxorubicin, which was removed one week before being used for the experiment


title: CleftProband_356

tag: syndromic versus non-syndromic

value: non-syndromic


title: WT, sorted lung moAMs, after chronic LPS, rep2

source_name: RNA-seq from WT sorted lung moAMs after chronic LPS, biological replicate 2

value: primary lung monocyte derived alveolar macrophage

value: 15 doses of LPS over 5 weeks


title: OCI-LY19R rep2

description:
LY19_R_R2_L3
fpkm_acquireResistance.txt


title: CF, sorted lung cMons, after chronic LPS, rep1

source_name: RNA-seq from CF sorted lung cMons after chronic LPS, biological replicate 1


title: OCI-LY19R rep1

description:
LY19_R_R1_L3
fpkm_acquireResistance.txt


title: CleftProband_355

tag: cleft type

value: cleft palate only

value: male

value: unaffected


title: WT, sorted lung moAMs, after chronic LPS, rep1

source_name: RNA-seq from WT sorted lung moAMs after chronic LPS, biological replicate 1


title: CleftProband_357

value: cleft lip and cleft palate

tag: cleft laterality

value: bilateral


title: OCI-LY19S rep3

description:
LY19_S_R3_L3
fpkm_acquireResistance.txt

value: untreated


title: CleftProband_354

value: right


title: CleftProband_374

value: female

value: not applicable


title: WT, sorted lung IMs, after chronic LPS, rep2

source_name: RNA-seq from WT sorted lung IMs after chronic LPS, biological replicate 2

value: primary lung interstitial macrophage


title: WT, sorted lung IMs, after chronic LPS, rep1

source_name: RNA-seq from WT sorted lung IMs after chronic LPS, biological replicate 1


title: CleftProband_353


title: WT, sorted lung cMons, after chronic LPS, rep2

source_name: RNA-seq from WT sorted lung cMons after chronic LPS, biological replicate 2

value: primary lung classical monocyte


title: CleftProband_352

value: left


title: OCI-LY19S rep2

description:
LY19_S_R2_L3
fpkm_acquireResistance.txt

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: WT


title: OCI-LY19S rep1

description:
LY19_S_R1_L3
fpkm_acquireResistance.txt


title: CleftProband_351

value: non-syndromic


title: SUDHL5 DOXO 24h ctrl rep3

description:
SuDHL5_24H_R3_L3
fpkm_4cells0h24h.txt

value: 0.2 µM doxorubicin

tag: time


title: WT, sorted lung cMons, after chronic LPS, rep1

source_name: RNA-seq from WT sorted lung cMons after chronic LPS, biological replicate 1

value: 15 doses of LPS over 5 weeks


title: Heart, PTX3 100, 3

city: Hang Zhou

first: Zhifei

last: Xu

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited xls files include RPKM values for each sample.

source_name: heart

extract_protocol:
RNA from Vehicle and PTX3 100 heart were extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: heart

value: PTX3 100ng-treated

value: 2 weeks after treatment


title: 300 nM CEP treated KAS_2h

city: Richmond

first: Liang

last: Zhou

state: Virginia

address: 401 college street

department: Internal Medicine

institute: Virginia Commonwealth University

description:
Test Group-CEP
Study #3: KAS CEP-2 hr

data_processing:
For the normalization it uses the average of a housekeeping gene: GAPDH. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change file reports treatment/control (i.e., PF/UT) ratios.

label: SYBR Green

label_protocol: Holding Stage: 50 0C 2 mins, 95 0C 10 mins; Cycling Stage: 95 0C 15 secs, 60.0 0C 1 mins, 40 Cycles.

growth_protocol: U266 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum and penicillin-streptomycin. KAS/6-1 cells were maintained in RPMI-1640 supplemented with 2 ng/ml IL-6, 10% fetal bovine serum and penicillin-streptomycin.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: U266 or KAS/6-1 cells (3.5 × 105/ml × 10 ml) were seeded in 100 mm dishes at DAY 1. On DAY 2, cells were treated with indicated doses of  Chk1 inhibitors and then collected for next step.

value: Multiple myeloma cell line


title: SUDHL5 DOXO 24h ctrl rep1

description:
SuDHL5_24H_R1_L3
fpkm_4cells0h24h.txt


title: SUDHL5 DOXO 24h ctrl rep2

description:
SuDHL5_24H_R2_L3
fpkm_4cells0h24h.txt


title: Heart, PTX3 100, 2


title: Neuroblastoma cell line SK-N-DZ, miR-34a overexpression, 4Gy, replicate 1

source_name: Neuroblastoma cell line SK-N-DZ

value: miR-34a overexpression

value: Female


title: Neuroblastoma cell line SK-N-DZ, miR-34a overexpression, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-DZ, miR-34a overexpression, 0Gy, replicate 2


title: SUDHL5 0h ctrl rep3

description:
SuDHL5_0H_R3_L3
fpkm_4cells0h24h.txt

value: untreated


title: 50 nM PF treated KAS_2h

description:
Test Group-PF
Study #3: KAS PF-2 hr


title: Neuroblastoma cell line SK-N-AS, miR-34a overexpression, 6Gy, replicate 2

source_name: Neuroblastoma cell line SK-N-AS


title: Neuroblastoma cell line SK-N-DZ, miR-34a overexpression, 0Gy, replicate 1


title: SUDHL5 0h ctrl rep2

description:
SuDHL5_0H_R2_L3
fpkm_4cells0h24h.txt


title: Neuroblastoma cell line SK-N-AS, miR-34a overexpression, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-AS, miR-34a overexpression, 0Gy, replicate 2


title: Neuroblastoma cell line SK-N-AS, miR-1228 overexpression, 0Gy, replicate 1

value: miR-1228 overexpression


title: Heart, PTX3 100, 1


title: SUDHL5 0h ctrl rep1

description:
SuDHL5_0H_R1_L3
fpkm_4cells0h24h.txt


title: Neuroblastoma cell line SK-N-DZ, miR-1228 overexpression, 4Gy, replicate 3


title: Neuroblastoma cell line SK-N-DZ, miR-1228 overexpression, 4Gy, replicate 2


title: Neuroblastoma cell line SK-N-AS, miR-34a overexpression, 6Gy, replicate 1


title: Heart, Vehicle, 3

value: Vehicle


title: Neuroblastoma cell line SK-N-AS, miR-1228 overexpression, 6Gy, replicate 3


title: Heart, Vehicle, 2


title: Neuroblastoma cell line SK-N-DZ, miR-1228 overexpression, 0Gy, replicate 1


title: Neuroblastoma cell line SK-N-AS, miR-1228 overexpression, 6Gy, replicate 2


title: Neuroblastoma cell line SK-N-DZ, miR-1228 overexpression, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-AS, miR-1228 overexpression, 0Gy, replicate 3


title: Neuroblastoma cell line SK-N-AS, miR-1228 overexpression, 0Gy, replicate 2


title: 100 nM PF treated U266_4h

description:
Test Group-PF
Study #1: U266 PF-4 hr


title: OCI-LY19 DOXO 24h ctrl rep3

description:
A188_LY19_24H_r3_L6
fpkm_4cells0h24h.txt


title: Heart, Vehicle, 1


title: WT_P0

first: Yalu

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

data_processing:
Cell Ranger (v4.0.0) was used for demultiplexing and counting
data were processed with the Seurat R package
Assembly: refdata-gex-mm10-2020
Supplementary files format and content: mtx

source_name: Kidney

extract_protocol:
Kidneys were minced with a sterile razor blade. Approximately 65 mg tissue was digested in liberase TM (0.3 mg/mL, Sigma, TM5401119001), hyaluronidase (10 μg/mL, Sigma, H4272), DNaseI (20 μg/mL, Roche, 0471672800) at 37°C for 40 min, followed by incubation with 0.25% trypsin EDTA at 37°C for 30 min. Trypsin was inactivated using 10% fetal bovine serum in PBS. Cells were then resuspended in PBS supplemented with 0.04% bovine serum albumin. After filtration through a 40 μm strainer, cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method.
The cDNA and library were generated using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Single Index Kit T Set A (10X Genomics, PN-1000213) according to the manufacturer’s manual.

tag: strain

value: wild type

tag: age


title: OCI-LY19 DOXO 24h ctrl rep1

description:
A181_LY19_24H_r1_L6
fpkm_4cells0h24h.txt


title: LSK cells – aged+CASIN 3

city: Hospitalet de Llobregat

first: Maria Carolina

last: Florian

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: Regenerative Medicine

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

data_processing:
Raw data (FASTQ files) were mapped to the reference genome, filtered and counted using the «cellranger count» command in the CellRanger software v3.1.0 (10x Genomics) with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered count matrices in MEX format obtained from CellRanger. The files «*_barcodes.tsv.gz» contains the information on the cell barcodes (columns of the matrix); the files «*_features.tsv.gz» contains the information on the features (rows of the matrix); and the files «*_matrix.mtx.gz» containes the expression counts in sparse matrix format.

source_name: Lin- cKit+ Sca1+ sorted cells from bone marrow

growth_protocol: no cell culture

extract_protocol:
Lin- Sca1+ cKit+ cells have been harvested and processed from BM from young, aged and CASIN-treated aged mice as described in Grigoryan et al., 2018.
Viably frozen cells were thawn, counted and subjected to single-cell RNA sequencing according to the manufactures recommendations. The chemistry version used for all samples was 3' v3. Cite-seq libraries were generated from the small RNA fraction.
10X Genomics scRNA-seq plus cite-seq version A (poly-A based oligo)

treatment_protocol: Aged+CASIN mice have been treated with CASIN by performing i.p. injections for 4 days, one injection every 24 hours at a dose of 25mg/kg in cyclodextrin. Young and aged control mice were injected with equivalent amount of cyclodextrin.

value: Bone marrow

value: >80 weeks old

value: CASIN (1 i.p. injection/24h for 4 days)

tag: sequencing batch


title: OCI-LY19 DOXO 24h ctrl rep2

description:
A187_LY19_24h_L5
fpkm_4cells0h24h.txt

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: WT


title: Untreated KAS_2h

description:
Control Group-UT
Study #3: KAS UT-2 hr


title: Untreated U266_16h

description:
Control Group-UT
Study #2: U266 UT-16 hr


title: Adult, sample3, SVZ+caudate

first: Nadejda

last: Tsankova

state: New York

address: 1245 Madison Avenue

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

description: nuclear RNA

data_processing:
Gene expression count matrices were generated with CellRnager(v3.1.5)
Seurat metadata was generated using Seurat(v4.0.4), Filtering step: i) Doublets were removed using DoubletFinder(v2.0.3) ii)Low quality nuclei removal (< 400 unique genes, < 1,000 UMI counts, or > 15% mitochondrial genes)
UMAP embeddings: "Dimensionality reduction was applied on the scaled expression of top 2,000 variable genes by Principal component analysis (PCA) (Seurat::RunPCA). To mitigate inter-sample technical variation when analyzing multiple samples, we normalized and integrated the data using the SCTransform workflow in Seurat, which finds mutual nearest neighbors (or anchors) to integrate different samples. PCA was re-computed using the top 3,000 variable features followed by nearest-neighbor graph construction (Seurat::FindNeighbors), unbiased Louvain clustering (Seurat::FindClusters), and Uniform Manifold Approximation and Projection (UMAP) (Seurat::RunUMAP) for visualization of the data in two dimensions."
Combined_log-normalized_AveExp_snRNAseq_Human.xlsx: Processed, log-normalized average gene expression data calculated for each of the following integrated objects: all prenatal germinal matrix samples, subclustered glia and progenitors from all prenatal germinal matrix samples, all prenatal cortical plate samples, subclustered glia and progenitors from 24-41gw samples, all adult SVZ+caudate samples, all adult neocortex samples. All clusters are also annotated by cell type / state. UMAPS of each object are included along with cell type abbreviations.
Assembly: GRCh38 human genome pre-mRNA transcriptome sequences
Supplementary files format and content: "barcodes.tsv.gz" contains barcodes sequences, "features.tsv.gz" contains feature ID and names, "matrix.mtx.gz" contains matrices with gene ID, cell ID and UMI information
Supplementary files format and content: "Seuratmetadata" files: comma separated file with Seurat metadata including barcode information, sample ID, nCounts_RNA, nFeatures_RNA, nCounts_SCT, nFeatures_SCT, percent.mt, and cell type annotations for each cluster of each sample
Supplementary files format and content: "UMAPembedding": comma separated file with UMAP cordinates
Supplementary files format and content: "Combined_log-normalized_AveExp_snRNAseq_Human.xlsx"; Excel sheet.

source_name: Brain, svz+caudate

extract_protocol:
Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3’ gene expression (3’ GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers.
P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus.

value: Brain, svz+caudate

tag: developmental stage

value: 53 years

value: female

value: postmortem, non-pathological


title: 100 nM PF treated U266_16h

description:
Test Group-PF
Study #2: U266 PF-16 hr


title: Untreated U266_4h

description:
Control Group-UT
Study #1: U266 UT-4 hr


title: Neuroblastoma cell line SK-N-DZ, miR-34a overexpression, 4Gy, replicate 2


title: OCI-LY19 0h ctrl rep3

description:
A188_LY19_0H_r3_L4
fpkm_4cells0h24h.txt


title: Neuroblastoma cell line SK-N-DZ, miR-1228 overexpression, 4Gy, replicate 1


title: Neuroblastoma cell line SK-N-AS, miR-1228 overexpression, 6Gy, replicate 1


title: Meso78

city: Dallas

first: Olga

last: Gupta

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

hyb_protocol: The Affymetrix GeneChip Hybridization, Wash, and Stain kit was used for array processing. Arrays were incubated for 17 h in GeneChip hybridization oven 645 at 45°C with rotation at 60 rpm.

scan_protocol: The chips were subsequently scanned with GeneChip scanner 3000.

data_processing:
Raw data were analyzed using Affymetrix expression console 1.4. Expression array analysis for individual genes was performed filtering for P <.05 and a fold change of ≥2.0. This method was used to rank the genes expressed differentially between the high-IR and low-IR participants.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Mesothelial cells from research participant 78

label_protocol: Isolated total RNA was amplified, labeled, and hybridized using the Clariom D platform following the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). Briefly, the Affymetrix GeneChip WT Pico Kit was used for cDNA preparation and biotin labeling. cRNA was purified using an Affymetrix magnetic bead protocol.

growth_protocol: Omental adipose tissue from both cohorts was minimally digested with 0.125% trypsin for 20 minutes at 37 degrees C on a rotating stand.  The undigested adipose tissue was removed and the remaining trypsin and cells were centrifuged at 600 g for 5 minutes at 4 degrees C.  The upper layer was discarded and the pellet was resuspended in Media 199 supplemented with 5% FBS, 0.5% ITS, Hydrocortisone (0.4ug/ml), 1% Pen/Strep and 0.1% Gentamicin, plated on a 12-well collagen coated plate and grown to confluency.  When the mesothelial cells reached confluency they were uniformly cobblestone in appearance.

extract_protocol: RNA was prepared from the mesothelial cells by lysing the cells in TRIzol (Invitrogen, Carlsbad, CA) and isolated RNA was processed using standard protocols using QIAGEN’s RNeasy Micro and RNeasy Lipid Tissue Kits

tag: subject id

value: research participant 78

tag: diabetes type

tag: insulin resistance

value: T2DM or high insulin resistance

tag: subject status

value: experiment

value: adipose mesothelial cells


title: LSK cells – aged+CASIN 2

tag: tissue


title: Adult, sample3, neocortex

description: nuclear RNA

source_name: Brain, neocortex

value: Brain, neocortex


title: OCI-LY19 0h ctrl rep2

description:
A180_LY19_0h_L5
fpkm_4cells0h24h.txt

tag: cell type

tag: genotype

value: untreated


title: LSK cells – aged+CASIN 1

tag: treatment


title: Adult, sample2, SVZ+caudate

description: nuclear RNA

value: 45 years

tag: Sex


title: OCI-LY19 0h ctrl rep1

description:
A181_LY19_0H_r1_L6
fpkm_4cells0h24h.txt

tag: cell line


title: Neuroblastoma cell line SK-N-AS, miR-34a overexpression, 0Gy, replicate 1

tag: transfection

value: miR-34a overexpression

tag: radiation dose

value: Female


title: Meso67

source_name: Mesothelial cells from research participant 67

value: research participant 67


title: Adult, sample2, neocortex

description: nuclear RNA


title: HT DOXO 24h ctrl rep3

description:
A188_HT_24H_r3_L6
fpkm_4cells0h24h.txt

source_name: HT

value: HT

value: 0.2 µM doxorubicin

tag: time


title: LSK cells – aged control 3

tag: strain

value: Bone marrow

value: >80 weeks old

value: Control


title: LSK cells – aged control 2

tag: age


title: Adult, sample1, SVZ+caudate

description: nuclear RNA

value: Brain, svz+caudate

value: 28 years

value: male


title: Adult, sample1, neocortex

description: nuclear RNA

value: postmortem, non-pathological


title: LSK cells – aged control 1

tag: sequencing batch


title: HT DOXO 24h ctrl rep1

description:
A181_HT_24H_r1_L6
fpkm_4cells0h24h.txt

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: WT


title: HT DOXO 24h ctrl rep2

description:
A187_HT_24H_r2_L6
fpkm_4cells0h24h.txt


title: LSK cells – young control 3

value: 10-12 weeks old


title: Neuroblastoma cell line SK-N-DZ, miR-1228 overexpression, 0Gy, replicate 2

value: miR-1228 overexpression


title: LSK cells – young control 2


title: Meso40

source_name: Mesothelial cells from research participant 40

value: research participant 40

value: Low insulin resistance

value: control

value: adipose mesothelial cells


title: Prenatal, sample15, cortical plate

description: nuclear RNA

source_name: Brain, cortical plate

value: Brain, cortical plate

tag: developmental stage

value: 38.3 weeks gestation

value: female


title: HT 0h ctrl rep2

description:
A187_HT_0H_r2_L6
fpkm_4cells0h24h.txt

value: HT

value: untreated


title: Meso61

source_name: Mesothelial cells from research participant 61

tag: subject id

value: research participant 61

value: T2DM or high insulin resistance

value: experiment


title: HT 0h ctrl rep3

description:
A188_HT_0H_r3_L6
fpkm_4cells0h24h.txt


title: Prenatal, sample14, germinal matrix

description: nuclear RNA

source_name: Brain, germinal matrix

value: Brain, germinal matrix

value: 33.2 weeks gestation

value: male

value: postmortem, non-pathological


title: HT 0h ctrl rep1

description:
A181_HT_0H_r1_L6
fpkm_4cells0h24h.txt

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: WT


title: LSK cells – young control 1

value: Bone marrow

value: 10-12 weeks old

value: Control


title: Meso56

source_name: Mesothelial cells from research participant 56

value: research participant 56

tag: diabetes type

value: Low insulin resistance

value: control

value: adipose mesothelial cells


title: Meso58

source_name: Mesothelial cells from research participant 58

value: research participant 58

tag: insulin resistance


title: Meso46

source_name: Mesothelial cells from research participant 46

value: research participant 46

tag: subject status


title: Prenatal, sample14, cortical plate

description: nuclear RNA

tag: tissue

value: Brain, cortical plate


title: Meso59

source_name: Mesothelial cells from research participant 59

value: research participant 59

tag: cell type


title: Prenatal, sample15, germinal matrix

description: nuclear RNA

value: Brain, germinal matrix

value: 38.3 weeks gestation

value: female


title: Meso66

source_name: Mesothelial cells from research participant 66

value: research participant 66

value: T2DM or high insulin resistance

value: experiment


title: OCI-LY3 DOXO 24h ctrl rep3

description:
A188_LY3_24h_L5
fpkm_4cells0h24h.txt

value: Diffuse large B-cell lymphoma (DLBCL) cell line

tag: genotype

value: WT

value: 0.2 µM doxorubicin


title: 4OHT-treated jejunal organoids, rep4 [X4OHT_Jour4_N4]

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

data_processing:
The mapping is performed with “Star 2.4.0f1”.
The basecalling is performed directly with the HiSeq instrument and run with the tool “Illumina RTA”
The “Illumina bcl2fastq 1.8.4” tool is used to generate the FASTQ prior to the alignment
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file

source_name: 4OHT-treated jejunal organoids

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
Libraries were generated from 250 ng of total RNA as follows: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs, Whitby, Canada). cDNA synthesis was achieved using NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England BioLabs). The remaining steps of library preparation were performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: To induce deletion of Hnf4a, 4OHT-inducible jejunal organoids (VilCreERT2/Hnf4αfx/fx ) were treated with 0.5 µM hydroxytamoxifen for 24 h and then split. Jejunal organoids were harvested on day 4 after the last passage, and total RNA was isolated.

tag: strain background

value: Villin-CreERT2; Hnf4aflox/flox

tag: tissue/cell type

value: Epithelial organoids culture derived from mouse jejunum

tag: treatment

value: 4OHT (hydroxytamoxifen for Hnf4a deletion)

tag: time point


title: 4OHT-treated jejunal organoids, rep3 [X4OHT_Jour4_N3]


title: Meso64

source_name: Mesothelial cells from research participant 64

value: research participant 64

value: adipose mesothelial cells


title: Meso35

source_name: Mesothelial cells from research participant 35

value: research participant 35

value: Low insulin resistance

value: control


title: Meso38

source_name: Mesothelial cells from research participant 38

value: research participant 38


title: Prenatal, sample13, germinal matrix

description: nuclear RNA

value: Brain, germinal matrix

value: 32.8 weeks gestation

tag: Sex

value: postmortem, non-pathological


title: Meso29

source_name: Mesothelial cells from research participant 29

value: research participant 29


title: Meso26

source_name: Mesothelial cells from research participant 26

value: research participant 26

value: T2DM or high insulin resistance

value: experiment


title: OCI-LY3 DOXO 24h ctrl rep2

description:
A187_LY3_24H_r2_L4
fpkm_4cells0h24h.txt

tag: cell line

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: WT

value: 0.2 µM doxorubicin

tag: time


title: Prenatal, sample13, cortical plate

description: nuclear RNA

value: Brain, cortical plate

value: female


title: 4OHT-treated jejunal organoids, rep2 [X4OHT_Jour4_N2]

value: Villin-CreERT2; Hnf4aflox/flox

value: Epithelial organoids culture derived from mouse jejunum

value: 4OHT (hydroxytamoxifen for Hnf4a deletion)


title: Meso24

source_name: Mesothelial cells from research participant 24

value: research participant 24

tag: age

value: adipose mesothelial cells


title: Meso22

source_name: Mesothelial cells from research participant 22

value: research participant 22

value: Low insulin resistance

value: control


title: OCI-LY3 DOXO 24h ctrl rep1

description:
A181_LY3_24H_r1_L4
fpkm_4cells0h24h.txt


title: Meso21

source_name: Mesothelial cells from research participant 21

value: research participant 21


title: Prenatal, sample12, germinal matrix

description: nuclear RNA

value: Brain, germinal matrix

value: 26 weeks gestation

value: postmortem, non-pathological


title: OCI-LY3 0h ctrl rep3

description:
A188_LY3_0H_r3_L4
fpkm_4cells0h24h.txt

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: untreated


title: Prenatal, sample11, germinal matrix

description: nuclear RNA

value: 25.8 weeks gestation


title: Prenatal, sample12, cortical plate

description: nuclear RNA

source_name: Brain, cortical plate

value: Brain, cortical plate


title: Prenatal, sample11, cortical plate

description: nuclear RNA

value: female


title: HBV in-vivo 993 WGS

city: Beijing

first: Zhiyi

last: Jing

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS

data_processing:
The HBV-host chimeric DNA were predicted by SurVirus
Genome_build: GRCh37 (hg19) human reference genome, GRCm38 (mm10) mouse reference genome, HBV genotype D (u95551.1) reference genome reference genome.
Supplementary_files_format_and_content: abundance of integration sites

source_name: humanized liver samples

extract_protocol:
PHH cells were obtained from FRG humanized liver mice with two-step perfusion as previously describe with slight modification(Yan et al., 2012 Walter E et al.,1996).
following the instruction of NEXTflex Rapid DNA-seq Kit (BIOO SCIENTIFIC)

value: humanized liver samples

value: Primary human hepatocytes (PHH)

tag: mouse strain


title: DMSO-treated jejunal organoids, rep4 [DMSO_Jour4_N4]

source_name: DMSO-treated jejunal organoids

value: Villin-CreERT2; Hnf4aflox/flox

value: Epithelial organoids culture derived from mouse jejunum

value: DMSO (vehicule)


title: DMSO-treated jejunal organoids, rep3 [DMSO_Jour4_N3]


title: 4OHT-treated jejunal organoids, rep1 [X4OHT_Jour4_N1]

value: 4OHT (hydroxytamoxifen for Hnf4a deletion)


title: OCI-LY3 0h ctrl rep1

description:
A181_LY3_0h_L5
fpkm_4cells0h24h.txt

value: WT


title: OCI-LY3 0h ctrl rep2

description:
A187_LY3_0H_r2_L4
fpkm_4cells0h24h.txt


title: DMSO-treated jejunal organoids, rep2 [DMSO_Jour4_N2]


title: DMSO-treated jejunal organoids, rep1 [DMSO_Jour4_N1]


title: 4OHT-treated jejunal organoids, rep4 [X4OHT_Jour2_N4]


title: Prenatal, sample10, germinal matrix

description: nuclear RNA

source_name: Brain, germinal matrix

tag: developmental stage

value: 24.7 weeks gestation

value: male


title: Prenatal, sample10, cortical plate

description: nuclear RNA


title: Cal62_output_mismatch2

city: wuhan

first: wei

last: yang

address: No.299 Bayi Road

institute: wuhan university

data_processing:
Library strategy: AMfU-seq
The 150 bp pair-end reads from Illumina sequencing were first sent for adaptor and quality trimming using trim_galore, and reads shorter than 20 nt after trimming were excluded.
Processed reads were then mapped to the human genome (hg38) by Bowtie2 with parameter “-L 20 -N 1”. To quantify the fU sites, only the proper pair alignments was persisted for the downstream pipelines.
Peak calling was performed using MACS 2.2.6 with default settings and the input library as control.
Sam2tsv was used to determine the T-to-C substitutions in peaks region (https://github.com/lindenb/jvarkit). Substitutions with a base Phred quality score of >27 were retained. Background substitutions in input library were excluded for substitution identification. In order to minimize errors from potentially misaligned reads, we only considered positions with coverage more than 10 reads. The cytosine ratio was set range from 20% to 50%. The high confidence fU modified sites were extracted by intersecting replicate 1 and replicate 2.
Genome_build: hg38
Supplementary_files_format_and_content: fU_sites_informations.xlsx

growth_protocol: The human thyroid carcinoma cells (CAL-62 cell line) was used in this study. The human thyroid carcinoma cells were collected from The First Affiliated Hospital, Sun Yat-sen University. CAL-62 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin. The DMEM was removed from the 10×10 cm dish while the cells filled in the bottom of the dish. The cells were maintained at 37 ℃ under a humidified atmosphere containing 5% CO2.

extract_protocol: The samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina following its manufacturer's instruction in parallel for Illumina sequencing.

treatment_protocol: After that the cells were washed twice with 1×PBS buffer, subsequently digested with trypsin-EDTA solution containing 0.25% trypsin and 0.02% EDTA dissolved in 1×PBS buffer. Next, the cells were collected by centrifugation at 1,000 g for 3 min. Then the genomic DNA was extracted from cells using a DNeasy® Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions. Finally, the concentration of genomic DNA was measured by a Nanodrop 2000, and the genomic DNA was stored at -20 °C for the following experiments. The 50 μg/ml of tetrahydrouridine (THU) was used in this step to prevent the deamination of 5-formylcytosine.

value: pull-down using azi-BIAN; during library preparation,  pH 8.8 was used to make the 5-formyluracil sites read as cytosine


title: Bone marrow-derived macrophages from C57BL/6J (WT) mice #3

city: Madrid

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

institute: CIB (CSIC)

data_processing:
BGISEQ-500 platform
Low quality reads were removed. Clean reads were mapped to reference genome GRCm38 using Bowtie with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were calculated with  RSEM
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Bone marrow-derived macrophages were obtained by flushing the femurs of 6- to 10-wk-old C57BL/6 and Cd28 KO mice, and culturing cells during 7 days in DMEM supplemented with 10% FCS and 50 mM 2-ME, containing human M-CSF (25 ng/ml), with cytokine addition every 2 days.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

value: Bone marrow-derived mouse macrophages

value: C57BL/6J (WT)


title: 4OHT-treated jejunal organoids, rep3 [X4OHT_Jour2_N3]


title: Prenatal, sample9, germinal matrix

description: nuclear RNA

value: Brain, germinal matrix

value: 23.7 weeks gestation

value: postmortem, non-pathological


title: Bone marrow-derived macrophages from C57BL/6J (WT) mice #2


title: 4OHT-treated jejunal organoids, rep2 [X4OHT_Jour2_N2]


title: Cal62_output_mismatch1

source_name: thyroid carcinoma cells (CAL-62 cell line)


title: Bone marrow-derived macrophages from C57BL/6J (WT) mice #1


title: Meso11

source_name: Mesothelial cells from research participant 11

tag: subject id

value: research participant 11

value: Low insulin resistance

value: control

value: adipose mesothelial cells


title: Prenatal, sample9, cortical plate

description: nuclear RNA

value: Brain, cortical plate


title: Meso10

source_name: Mesothelial cells from research participant 10

value: research participant 10

tag: diabetes type


title: Meso07

source_name: Mesothelial cells from research participant 07

value: research participant 07

tag: insulin resistance

value: T2DM or high insulin resistance

value: experiment


title: Meso08

source_name: Mesothelial cells from research participant 08

value: research participant 08

tag: subject status


title: Meso04

source_name: Mesothelial cells from research participant 04

value: research participant 04


title: Meso03

source_name: Mesothelial cells from research participant 03

value: research participant 03


title: Prenatal, sample8, germinal matrix

description: nuclear RNA

tag: tissue

value: 23.3 weeks gestation

value: male


title: Meso02

source_name: Mesothelial cells from research participant 02

value: research participant 02

tag: cell type


title: Cal62_input2

value: without treatment


title: Bone marrow-derived macrophages from Cd28 KO mice #3

value: Bone marrow-derived mouse macrophages

tag: genotype

value: Cd28 KO


title: Prenatal, sample8, cortical plate

description: nuclear RNA

value: postmortem, non-pathological


title: DMSO-treated jejunal organoids, rep4 [DMSO_Jour2_N4]

tag: strain background

value: Villin-CreERT2; Hnf4aflox/flox

value: Epithelial organoids culture derived from mouse jejunum

value: DMSO (vehicule)


title: Prenatal, sample7, germinal matrix

description: nuclear RNA

value: Brain, germinal matrix

value: 22 weeks gestation


title: Cal62_output_nonmismatch1

value: pull-down using azi-BIAN; during library preparation,  pH 7.2 was used to make the 5-formyluracil sites read as thymine


title: HBV in-vivo 18 WGS

value: humanized liver samples

value: Primary human hepatocytes (PHH)


title: Cal62_output_nonmismatch2


title: Bone marrow-derived macrophages from Cd28 KO mice #1


title: Cal62_input1


title: 4OHT-treated jejunal organoids, rep1 [X4OHT_Jour2_N1]

source_name: 4OHT-treated jejunal organoids

tag: tissue/cell type

value: 4OHT (hydroxytamoxifen for Hnf4a deletion)


title: Prenatal, sample7, cortical plate

description: nuclear RNA

value: Brain, cortical plate

tag: treatment


title: DMSO-treated jejunal organoids, rep3 [DMSO_Jour2_N3]

tag: time point


title: DMSO-treated jejunal organoids, rep2 [DMSO_Jour2_N2]


title: Prenatal, sample6, germinal matrix

description: nuclear RNA

value: 21.3 weeks gestation

tag: Sex


title: DMSO-treated jejunal organoids, rep1 [DMSO_Jour2_N1]


title: HBVΔx in-vitro 01

data_processing:
The de-multiplexed reads were processed using the 10X CellRanger pipeline and aligned to the GRCh37 (hg19) human reference genome, GRCm38 (mm10) mouse reference genome, HBV genotype D (u95551.1) reference genome, HBV genotype A reference genome, HBV genotype C reference genome, and HDV genotype I reference genome.
Genome_build: GRCh37 (hg19) human reference genome, GRCm38 (mm10) mouse reference genome, HBV genotype D (u95551.1) reference genome, HBV genotype A reference genome, HBV genotype C reference genome, and HDV genotype I reference genome.
Supplementary_files_format_and_content: Each element of the MTX file is the number of UMIs associated with a feature/gene (row) and a barcode (column). The TSV files are features/genes and barcode sequences corresponding to row and column indices, respectively.

source_name: primary human hepatocyte

growth_protocol: PHH cells were grown in primary hepatocytes maintenance medium containing Williams E medium supplemented with 5 μg/ml transferrin, 10 ng/ml EGF, 3 μg/ml insulin, 2 mM L-glutamine, 18 μg/ml hydrocortisone, 40 ng/ml dexamethasone, 5 ng/ml sodium selenite, 2% DMSO, 100 U/ml penicillin, and 100 μg/ml streptomycin hydrocortisone (100 mg/ml), insulin (2.5 mg/ml), transferrin (2.5 mg/ml), and selenium (2.5 mg/ml); all other cells were grown in 50:50 M199:MCDB106 medium supplemented with 15% FBS, 10 ng/mL EGF, 0.4 µg/mL hydrocortisone, 50 units/mL penicillin and 100 µg/mL streptomycin.)

extract_protocol:
Collect the cells with trypsin digestion
Follow the 10x Genomic ChrominusTM Single Cell 5' Library& Gel Bead Kit  pipeline

value: primary human hepatocyte

tag: host mouse strain

tag: days treated with hbv


title: Bone marrow-derived macrophages from Cd28 KO mice #2


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P8, Salinity S30, replicate a

city: Fort Pierce

first: David

last: Bradshaw

state: FL

department: Aquaculture & Stock Enhancement

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP8a

data_processing:
Sequenced reads from 57 RNA Seq libraries were imported into CLC Genomics Workbench (Qiagen, Hilden, Germany) where they were quality checked and trimmed to remove low quality and adapter sequences.
The resulting filtered, paired-end reads were then mapped to the S. dumerili reference genome (NCBI Genome: 12614) with > 74% mapping success. Gene expression values were calculated as transcripts per million (TPM).
Differentially expressed genes (DEGs) were calculated in the CLC Genomics Workbench and were defined as biologically significant with an absolute fold change ≥ 2 and statistically significant with an FDR p-value ≤ 0.05 when compared to expression under control conditions (30 ppt) within the same DPH.
Transcript-level counts, lengths, and TPM abundances were imported into R and converted to a gene-level set of tables using the library tximport/tximportData (1.18.0).
Genome_build: S. dumerili reference genome (NCBI Genome: 12614)
Supplementary_files_format_and_content: Raw transcript counts matrix from CLC Genomics
Supplementary_files_format_and_content: Raw gene counts matrix from CLC Genomics
Supplementary_files_format_and_content: DESeq2 variance stabilizing transformed transcript counts matrix
Supplementary_files_format_and_content: DESeq2 variance stabilizing transformed gene counts matrix
Supplementary_files_format_and_content: Transcript name to Entrez Gene ID matrix table

organism: Trachinotus carolinus

source_name: whole body

growth_protocol: After hatching in a salinity of ~ 30 ppt, Florida pompano larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning.

extract_protocol:
 Total RNA was extracted a set of homogenized larval samples using the Qiagen RNeasy Mini Kit and kept at -20°C. All extracts were checked for concentration (ng/µL) using a Qubit Fluorometer 3 (ThermoFisher Scientific, Waltham, MA, USA) and quality (A260/A280) using a ThermoFisher NanoDrop Spectrophotometer 2000.
Purified RNA samples were sent to GeneWiz (South Plainfield, NJ, USA) for high-throughput sequencing. Samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on one flowcell lane. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Whole fish (numbers varied with days post hatch) were placed into tubes containing RNAlater (Invitrogen, Waltham, MA, USA) stored at 4°C for 24 hours, and finally stored at -20°C until processed for nucleic acid extractions.

tag: days post hatch

tag: tank number

tag: salinity

tag: replicate

value: a

tag: feeding

value: MF


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP9a


title: HBV in-vivo 18

extract_protocol:
PHH cells were obtained from FRG humanized liver mice with two-step perfusion as previously describe with slight modification(Yan et al., 2012 Walter E et al.,1996).
Follow the 10x Genomic ChrominusTM Single Cell 5' Library& Gel Bead Kit  pipeline


title: 4OHT-treated jejunal organoids + Wnt3A, rep2

source_name: Jejunum

treatment_protocol: To induce deletion of Hnf4a, 4OHT-inducible jejunal organoids (VilCreERT2/Hnf4αfx/fx ) were treated with 0.5 µM hydroxytamoxifen for 24 h and then split. 200 ng/mL of recombinant mouse Wnt3A protein was added to the culture medium. Jejunal organoids were harvested on day 2 after the last passage, and total RNA was isolated.

tag: strain

value: 4OHT (hydroxytamoxifen for Hnf4a deletion) + Wnt3A


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP7a


title: 4OHT-treated jejunal organoids + Wnt3A, rep3


title: Prenatal, sample5, germinal matrix

city: New York

description: nuclear RNA

tag: developmental stage

value: 20.3 weeks gestation

value: female


title: HBV in-vivo 492


title: HBV in-vivo 907


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP6a


title: DMSO-treated jejunal organoids + Wnt3A, rep3

value: Villin-CreERT2; Hnf4aflox/flox

value: DMSO (vehicule) + Wnt3A


title: 4OHT-treated jejunal organoids + Wnt3A, rep1

value: Epithelial organoids culture derived from mouse jejunum


title: DMSO-treated jejunal organoids + Wnt3A, rep2


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P1, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP1a


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP4a


title: HBV in-vivo 02


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D24, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST24DP5a


title: tDPC_P3_3

city: Guangzhou

first: Yuxin

address: Nanfang Dadao Street, Baiyun district

institute: Nanfang Hospital of Southern Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq X Ten platform and single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase. Randfold tools soft was used for novel miRNA secondary structure prediction.
Genome_build: hg18
Supplementary_files_format_and_content: tab-deimited text files include FPKM values for each Sample.

source_name: hair follicles from human scalp

extract_protocol:
DPCs were isolated from human dermal papilla and cultured.Total RNAs of DPC-fresh, DPC-P0 and DPC-P3 were extracted and used for mRNA sequencing.
RNA quality was verified using an Agilent 2100 Bio-analyzer (Agilent Technologies, Santa Clara, CA). Libraries for mRNA sequencing were generated using the NEBNext Multiplex RNA Library Prep Kit for Illumina (NEB,USA) according to the manufacturer’s instructions.

tag: tissue

value: cultured P3 dermal papilla cells


title: tDPC_P3_2


title: DMSO-treated jejunal organoids + Wnt3A, rep1

tag: cell type


title: tDPC_P3_1


title: Prenatal, sample5, cortical plate

description: nuclear RNA

source_name: Brain, cortical plate

value: postmortem, non-pathological


title: Prenatal, sample6, cortical plate

description: nuclear RNA

value: male


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP9a

value: Eart + MF


title: Prenatal, sample3, germinal matrix

description: nuclear RNA

value: Brain, germinal matrix

value: 19 weeks gestation


title: Prenatal, sample4, cortical plate

description: nuclear RNA

value: Brain, cortical plate

value: 19.7 weeks gestation


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P8, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP8a


title: tDPC_P0_3

value: cultured P0 dermal papilla cells


title: HCT116, SP2509, rep2

first: Raghuvaran

last: Shanmugam

state: Singapore

address: 61 Biopolis Dr, Proteos,

institute: Institute of Molecular and Cell Biology

data_processing:
Base quality assessment of raw sequence was performed using FastQC v0.11.8 and Trimmomatic v0.32 was used to filter low quality bases and adapter sequences.
Spliced alignment was performed using HISAT2 with reference to Homo sapiens (GRCh38) genome index.
Gene-level expression counts were quantified (strand-specific read counting) using featureCounts (subread-v1.6.2 package).
Differential genes expression analysis was performed by using edgeR v3.26.4 package.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts of every gene for all samples.

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS (Gibco), penicillin and streptomycin (Gibco).

extract_protocol: NEBNext ultra II RNA directional library preparation

treatment_protocol: DMSO or SP2509 (3 uM) for 48 hours

tag: cell line

tag: disease state

value: colon cancer

tag: genotype

value: Wildtype


title: tDPC_P0_2


title: HCT116, siPIR, rep2

tag: treatment

value: PIRIN Knockdown


title: Prenatal, sample2, germinal matrix

description: nuclear RNA

value: 18 weeks gestation


title: Prenatal, sample4, germinal matrix

description: nuclear RNA

value: female


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP6a

value: a


title: Prenatal, sample2, cortical plate

description: nuclear RNA


title: Prenatal, sample1, germinal matrix

description: nuclear RNA

value: 17 weeks gestation


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP5a


title: tDPC_P0_1


title: fDPC_P0_3

value: freshly isolated dermal papilla cells


title: Prenatal, sample1, cortical plate

description: nuclear RNA


title: HCT116, CTRL, UT, rep2

value: untreated


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP4a