title: chOS-108: Osteosarcoma_Chemosensitivity_poor

city: Nitona, Chuo-ku

first: Yasutoshi

last: Tatsumi

state: Chiba

department: Research Institute

country: Japan

institute: Chiba Cancer Center

hyb_protocol: Oligo aCGH/ChiP-on-chip Hybridization kit were used for hybridization. After hybridization, slides were washed with Oligo aCGH/ChiP-on-chip Wash Buffer kit.

scan_protocol: Scanned on Agilent G2505B or G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1, 10.7.3.1, 11.0.1.1).

data_processing: Agilent Feature Extraction Software (version 9.5.3.1, 10.7.3.1, 11.0.1.1) was used for background subtraction and LOWESS normalization.

source_name: Osteosarcoma pre-therapeutic biopsy samples

label_protocol: 0.5 µg of genomic DNA were laveled with Genomic DNA Enzymatic Labeling Kit.

extract_protocol: Genomic DNA was extracted by the standard proteinase K digestion method or using an AllPrep DNA/RNA Mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Preoperative chemotherapy containing MAP regimen (methotrexate, adriamycin, cis-platinum) was administered to all patients. If radiological evaluation with CT or MRI during preoperative chemotherapy demonstrated enlargement of the primary tumor, ifosfamide was added to MAP regimen. Definitive tumor resection was performed after preoperative chemotherapy, and chemotherapy response was evaluated histologically with resected tumor according to the area of necrosis; good response means that the necrotic area in the tumor was 90% or over, and poor response means under 90%.

tag: tissue

value: Osteosarcoma pre-therapeutic biopsy

source_name: normal placenta tissue

value: normal placenta


title: chOS-104: Osteosarcoma_Chemosensitivity_good

status: Public on Jun 01 2021

type: genomic

molecule: genomic DNA

organism: Homo sapiens


title: chOS-99: Osteosarcoma_Chemosensitivity_good


title: F_P7_hyperoxia_CD45_1_DC28_M14

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: total RNA

organism: Mus musculus

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: ZFP-1_ChIP_rep2

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: ZFP-1_N2_L3_AA539-AA604_yapc_IDR_peaks.bed

library_source: genomic

data_processing:
ChIPseq reads were mapped to ce10 using BWA aln with default parameters. For each factor, peaks were called for each replicate separately using yapc as in Janes et al 2018, except for BLMP-1, which were called using macs2. Replicate peaks were combined using IDR.
Genome_build: ce10
Supplementary_files_format_and_content: Each bigWig file contains input and GC content corrected linear coverage.
Supplementary_files_format_and_content: Each bed file contains peaks combined from replicates using IDR with p values <=0.01.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Strains were grown in liquid culture at 20°C using standard S-basal medium with HB101 bacteria. Animals were first grown to the adult stage, bleached to obtain embryos, and the embryos hatched without food in M9 buffer for 24 hrs at 20°C to obtain synchronized starved L1 larvae. L1 larvae were grown in a further liquid culture at 20°C then harvested at the L3 stage. Worms were collected, washed in M9 buffer, floated on sucrose, washed again in M9, then frozen into small pellets by dripping worm slurry into liquid nitrogen, which was stored at -80°C until use.

extract_protocol:
Extract preparation and chromatin immunoprecipitation were performed as in Kolasinska-Zwierz et al. (2009) with the following modifications: tissue was fixed for 10 min in 1.5 mM EGS (Pierce 21565) then formaldehyde added to 1% for a further 10 min before quenching with 0.125M glycine and washing 2X with PBS plus protease inhibitors. Pellets were washed once in FA buffer, then resuspended in 1 ml FA buffer per 1 mL of ground worm powder and the extract sonicated to an average size of 250 base pairs with a Diagenode Bioruptor or Bioruptor Pico for 28 pulses of 30 s followed by 30 s pause.
Following ChIP and DNA purification, libraries were prepared using the Illumina TruSeq kit. Fragments in the 250–300 base pair range were selected using Agencourt AMPure XP beads. Two biological replicate ChIPs were conducted for each factor.

tag: strain

tag: developmental stage

tag: chip antibody

value: ZFP-1 (JA lab; Q2059)


title: chOS-106: Osteosarcoma_Chemosensitivity_good


title: ZFP-1_ChIP_rep1


title: chOS-97: Osteosarcoma_Chemosensitivity_good


title: F_P7_hyperoxia_CD45_1_DC28_O2

value: mast cell


title: chOS-95: Osteosarcoma_Chemosensitivity_poor


title: TOP-2_ChIP_rep1

description: TOP-2_N2_L3_AA727-AA165_yapc_IDR_peaks.bed

value: TOP-2 (JA lab; Q5515)


title: La_EC10_1

city: Vandoeuvre-les-Nancy

first: Damien

last: Blaudez

address: Faculté des Sciences et Technologies Bld des Aiguillettes, BP 70239

country: France

institute: LIEC UMR 7360 CNRS-Université de Lorraine

data_processing:
Illumina HiSeq 2500 with chemistry v4 applying the high-output run mode, using a 2x100 bp paired-end sequencing
Sequenced reads were trimmed for adaptor sequence Trimmomativ v0.36.1 and FastQC v0.67 used for quality check. Reads passing the quality check were mapped on the reference genome (S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/) of S. cerevisiae using TopHat v2.1.1. Reads that were mapped on the reference genome were quantified using HTSeq-count v0.6.1p1. Finally, differential gene expression analysis between treatments was carried out using DESeq2 v1.14.1. Differentially expressed genes between conditions were obtained and expressed as log2-fold change with adjusted p-values calculated via a Benjamini-Hochberg test. A cut-off adjusted p-value of < 0.01 was applied.
Genome_build: S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/
Supplementary_files_format_and_content: tab-delimited text file include normalized gene count for each sample.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: The wild-type strain was grown in YNB-β-glycerophosphate liquid medium

extract_protocol:
Cells were harvested by centrifugation at 4000 rpm for 1 min at room temperature and snap frozen. After cell disruption by bead-beating, total RNAs were column purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions, and gDNA was removed using DNAse I (Sigma Aldrich). RNA integrity was further assessed using a Bioanalyzer 2100 (Agilent, CA, USA).
Strand-specific cDNA libraries were prepared using the TruSeq-3 library kit

treatment_protocol: Cultures were inoculated at an OD600nm of 0.05 and once the cultures reached an OD600nm of 0.6, cells were exposed for 1 h to 50 or 160 µM lanthanum, or to 6 or 8 µM of ytterbium, corresponding to their EC10 and EC50, respectively

tag: agent

value: lanthanum

tag: concentration

value: La EC10 (50 microM)

tag: time point

value: 1 hour


title: F_P7_hyperoxia_CD45_1_DC28_I1

tag: sequencing run

value: DC I


title: chOS-91: Osteosarcoma_Chemosensitivity_poor

tag: tissue


title: WSU-DLCL2 72h KDM5i 4 [WSU_K4_input]

city: London

first: James

last: Heward

state: England

address: Haemato Oncology, Barts Cancer Institute, Charterhouse Square

institute: Barts Cancer Institute

description:
WSU_K4_input
Chromatin

data_processing:
For ChIP-seq analysis - Input FASTQ files were mapped to hg19 using Bowtie, whilst H3K4me1/H3K4me3 FASTQ files were mapped to hg19 and dm3. The number of reads mapping to the dm3 genome were used to calculate a scaling factor and sequencing reads were randomly removed from samples requiring normalization using SAMtools (samtools view -b -s <scaling.factor> <filename.bam> > <scaled.bam>). Peaks were identified using the broad source option in MACS2 (macs2 callpeak -t <filename.bam> -c <input.bam> --broad -n <filename> -g hs --broad-cutoff 0.1 -q 0.05) and regions known to result in poor quality sequencing (https://www.encodeproject.org/annotations/ENCSR636HFF/) removed using BEDtools.
For KDM5i RNA-seq analysis - mRNA isolation and strand-specific cDNA libraries were prepared using the Illumina TruSeq stranded mRNA Prep kit according to the manufacturer's instructions. WSU-DLCL2/WSU#22 cells were sequenced using 2x40bp reads generated on the NextSeq 500. Only genes that achieved at least one read per million reads (CPM) in at least 3 samples were kept. Aligned reads numbers were further normalised using the ‘cqn’ method, accounting for gene length and GC content. Differential expression (DE) analysis was then performed using the edgeR R package, employing the generalised linear model (GLM) approach, for the treated versus control pairwise matched comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files of ChIP-seq data.
Supplementary_files_format_and_content: RNA_analysis.xlsx: Data matrix of log CPM and DE values for RNA-seq analysis.

source_name: WSU-DLCL2 cells

growth_protocol: Cells were cultured in RPMI-1640 media at 37°C 5% CO2.

extract_protocol:
mRNA was extracted using QIAGEN RNeasy kits. ChIP was performed using a modified version of the Active Motif ChIP-IT High Sensitivity Kit protocol.
RNA-seq libraries were prepared using the TruSeq stranded mRNA Prep kit and ChIP-seq libraries prepared using the NEBNext Ultra II kit.

treatment_protocol: Cells were treated with DMSO or 1μM KDM5-inh1 for 72 hours.

tag: cell line

tag: genotype/variation

value: Parental

tag: sample type

value: ChIP input


title: WSU-DLCL2 72h KDM5i 5 [WSU_K5_input]

description:
WSU_K5_input
Chromatin

tag: treatment


title: SIN-3_ChIP_rep1

description: SIN-3_N2_L3_AA766-XM002_yapc_IDR_peaks.bed

value: SIN-3 (JA lab; Q6013)


title: F_P7_hyperoxia_CD45_1_DC28_J16

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: DC III


title: chOS-90: Osteosarcoma_Chemosensitivity_poor

value: Osteosarcoma pre-therapeutic biopsy


title: WSU-DLCL2 72h DMSO 6 [WSU_D6_input]

description:
WSU_D6_input
Chromatin

value: DMSO


title: WSU#22 72h DMSO 4 [WSU22_D4_input]

description:
WSU22_D4_input
Chromatin

source_name: WSU#22 KMT2D -/+ mutant cells

value: KMT2D -/+ mutant


title: chOS-85: Osteosarcoma_Chemosensitivity_poor

value: normal placenta


title: chOS-84: Osteosarcoma_Chemosensitivity_poor


title: chOS-92: Osteosarcoma_Chemosensitivity_poor


title: BLMP-1_ChIP_rep2

description: BLMP-1_N2_L3_AA722-AA940_macs2_IDR_peaks.bed

tag: strain

value: BLMP-1 (JA lab; Q2919)


title: F_P7_hyperoxia_CD45_1_DC28_A13

value: F

value: hyperoxia

value: immune

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_B12

value: neutrophil


title: WSU-DLCL2 72h DMSO 5 [WSU_D5_input]

description:
WSU_D5_input
Chromatin

tag: chip antibody


title: BLMP-1_ChIP_rep1

tag: developmental stage


title: met2set25_ARC_pooled

data_processing:
Library strategy: ARC-C
Pair-end ARC-C reads were trimmed for adpator sequence by cutadapt, then mapped independently for each end to ce10 using BWA mem with default parameters. Read pairs with both ends mapped uniquely and confidently (MQ>=30 and NM<=2) to the nuclear genome and outside modENCODE black-listed regions were kept and PCR duplicates were removed by sambamba markdup. The remaining read pairs were regarded as valid read pairs. Valid read pairs mapping to different chromosomes or greater than 600bp apart on the same chromosome were regarded as trans- or cis-informative read pairs, respectively. Only cis-informative read pairs were analysed.
Contact maps were made from cis-informative read pairs by binning the genome into fixed-with non-overlapping bins and counting the number of read pairs between each pair of bins. The contact maps were normalised by matrix balancing using the Knight-Ruiz algorithm.
Genome_build: ce10
Supplementary_files_format_and_content: mtx files were generated using python package scipy, each containing cis-contact maps in matrix market format.

extract_protocol:
Frozen worm pellets were ground into a fine powder in which worms were broken into ~10 fragments. 1 ml of worm powder was then fixed in 10 ml of 1% formaldehyde in PBS at room temperature (RT) for 10 min with gentle shaking then quenched for 5 min with a final concentration of 125mM glycine. Fixed worm fragments were then washed with Buffer A (340mM sucrose, 15mM Tris-HCl pH7.5, 2mM MgCl2, 0.5mM spermidine, 0.15 mM spermine, 1mM DTT, protease inhibitors), resuspended in 7 ml Buffer A, then the material dounced 20 strokes in a 7 ml stainless steel tissue grinder (VWR-#432-5005). The material was spun at 100g for 5 minutes and the supernatant containing nuclei was transferred to a new tube and kept. The pellet was resuspended in Buffer A and again dounced with 20 strokes. After spinning, the two supernatants containing nuclei were pooled.
Three aliquots of 10 million fixed nuclei were spun down at 1,000g and resuspended in 200ul of 1x DNase buffer (Roche) and chromatin was digested with 25, 50, or 100U/ml DNase I at 25C for 10min. The reactions were then quenched with a final concentration of 25mM EDTA and 5mM Tris pH 7.5. Nuclei were washed twice with 1ml of ice-cold Nuclear Washing Buffer (340mM sucrose, 15mM Tris-HCl pH7.5, 25mM EDTA, 0.5mM spermidine, 0.15mM spermine, 1mM DTT, protease inhibitors). Nuclei were then resuspended in 100ul of end repair master-mix (10ul 10x NEB End Repair Buffer, 5ul NEB End Repair Enzyme Mix, 85ul H2O) and incubated at 20C for 30min with rotation. Thereafter, 400ul of ligation master-mix was added (40ul 10x ligation buffer, 5ul T4 DNA ligase [400,000 units/ml], 355ul H2O) and the mixture was incubated at 4C overnight with rotation. Nuclei were pelleted, resuspended in 50ul of tagmentation master-mix (22.5ul H2O, 25ul 2x Nextera TD buffer, 2.5ul Nextera Tn5 transposase) and incubated at 37C for 30 min. 5ul of 1% SDS and 2ul of NEB Proteinase K [800U/ml] was added and left at 65C for 15 min before DNA from the mixture was purified using Qiagen MinElute columns. Large fragments (>500bp) were removed from the purified DNA using two rounds of 0.6vol AMPure XP beads. Prior to PCR amplification, a test qPCR amplification using 1/20th of the input DNA was performed and the cycle number for PCR was determined by the midpoint of the exponential phase of the amplification curve. The resultant DNA was amplified with NEBNext Ultra II Q5 Master-mix under the following PCR conditions: 72 °C for 5 min, 98 °C for 30 s, and cycling at 98°C for 10s, 63°C for 30s and 72°C for 1min using the determined cycle number. The library was size-selected with AMPure XP beads to a final range of 200-700bp (insert size: ~70-570bp). Libraries made from nuclei digested with different concentrations of DNase I were quality tested by qPCR at the gap-3 promoter. DNAse I over- or under-digestion led to poor enrichment of regulatory elements. Good libraries generally had gap-3 promoter enrichment values of >4-fold.

tag: genotype

value: met-2 set-25


title: F_P7_hyperoxia_CD45_1_DC28_H21

tag: sequencing run

value: Mac III


title: chOS-82: Osteosarcoma_Chemosensitivity_good

tag: tissue


title: WSU#22 72h KDM5i 3 [WSU22_K3]

description:
WSU22_K3
processed data file: RNA_analysis.xlsx

tag: cell line

tag: genotype/variation


title: chOS-83: Osteosarcoma_Chemosensitivity_poor


title: F_P7_hyperoxia_CD45_1_DC28_G18

tag: gender

tag: treatment


title: blmp1_ARC_pooled


title: WSU-DLCL2 72h KDM5i 6 [WSU_K6_input]

description:
WSU_K6_input
Chromatin

tag: sample type


title: WSU-DLCL2 72h DMSO 4 [WSU_D4_input]

description:
WSU_D4_input
Chromatin


title: chOS-81: Osteosarcoma_Chemosensitivity_good


title: N2_ARC_pooled


title: WSU#22 72h KDM5i 1 [WSU22_K1]

description:
WSU22_K1
processed data file: RNA_analysis.xlsx


title: chOS-79: Osteosarcoma_Chemosensitivity_good


title: F_P7_hyperoxia_CD45_1_DC28_M6

tag: plate

tag: well

tag: timepoint

value: mast cell


title: F_P7_hyperoxia_CD45_1_DC28_D4

tag: cell type

tag: cell subtype

value: mast cell II


title: WSU#22 72h DMSO 3 [WSU22_D3]

description:
WSU22_D3
processed data file: RNA_analysis.xlsx


title: WSU#22 72h DMSO 2 [WSU22_D2]

description:
WSU22_D2
processed data file: RNA_analysis.xlsx


title: F_P7_hyperoxia_CD45_1_DC28_B7

tag: mousename

tag: coverage


title: F_P7_hyperoxia_CD45_1_DC28_J13

tag: number of genes


title: WSU#22 72h DMSO 1 [WSU22_D1]

description:
WSU22_D1
processed data file: RNA_analysis.xlsx


title: WSU#22 72h KDM5i 2 [WSU22_K2]

description:
WSU22_K2
processed data file: RNA_analysis.xlsx


title: F_P7_hyperoxia_CD45_1_DC28_K6


title: WSU-DLCL2 72h KDM5i 2 [WSU_K2]

description:
WSU_K2
processed data file: RNA_analysis.xlsx

value: Parental


title: chOS-76: Osteosarcoma_Chemosensitivity_good


title: TOP-2_ChIP_rep2

tag: strain

tag: developmental stage

tag: chip antibody

value: TOP-2 (JA lab; Q5515)


title: chOS-80: Osteosarcoma_Chemosensitivity_good

tag: tissue


title: WSU-DLCL2 72h KDM5i 1 [WSU_K1]

description:
WSU_K1
processed data file: RNA_analysis.xlsx

tag: cell line


title: chOS-63: Osteosarcoma_Chemosensitivity_good


title: chOS-62: Osteosarcoma_Chemosensitivity_good


title: F_P7_hyperoxia_CD45_1_DC28_O12

tag: sequencing run

value: Mac IV


title: SIN-3_ChIP_rep2

value: SIN-3 (JA lab; Q6013)


title: chOS-55: Osteosarcoma_Chemosensitivity_good

value: Osteosarcoma pre-therapeutic biopsy


title: chOS-56: Osteosarcoma_Chemosensitivity_good


title: chOS-58: Osteosarcoma_Chemosensitivity_good


title: control, replicate 2

type: RNA

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

hyb_protocol: Fragmented and biotin-labeled single-strand cDNA (5.5 μg each) hybridized on GeneChip® MTA 1.0 for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Expression Console version 1.4.1 (Affymetrix) using default settings for backgroud correction, normalization and summarization.

label: biotin

source_name: control, whole brain

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

growth_protocol: Mice were housed in plastic cages containing wood chips and covered with a wire lid. The cages were kept at 24±1 °C under a 12 h light/dark cycle (lights on at 8:00). The diet were standard laboratory food and water ad libitum.

extract_protocol: Total RNA was extracted from each source using RNeasy Lipid Tissue Mini Kit (QIAGEN) according to the manufacturer's protocol. 100 ng of total RNA was subsequently carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (Affymetrix).

treatment_protocol: At 10-week of age, mice were intraperitoneally injected on five sequential days with 50 mg/kg/day of Tamoxifen (10 mg/ml) dissolved in sunflower seed oil to induce the Cre recombinase. All mice were sacrified at the 10th day after tamoxifen injection, and the brain were used for analysis.

value: whole brain

tag: Sex

value: male

tag: age

tag: genotype/variation

value: plp-Syn; Cre+/-


title: chOS-52: Osteosarcoma_Chemosensitivity_good

value: normal placenta


title: MSA, replicate 2

source_name: MSA, whole brain

value: MSA


title: MSA, replicate 1


title: SCC-1_ChIP_rep2

description: SCC-1_N2_L3_AA204-AA246_yapc_IDR_peaks.bed


title: chOS-54: Osteosarcoma_Chemosensitivity_poor


title: WSU-DLCL2 72h DMSO 3 [WSU_D3]

description:
WSU_D3
processed data file: RNA_analysis.xlsx

tag: treatment

value: DMSO


title: control, replicate 3


title: F_P7_hyperoxia_CD45_1_DC28_O20

tag: gender

value: F

tag: plate

tag: well

value: hyperoxia

value: immune


title: control, replicate 1


title: F_P7_hyperoxia_CD45_1_DC28_P19

tag: timepoint

tag: cell type

tag: cell subtype

value: DC III


title: WSU-DLCL2 72h DMSO 2 [WSU_D2]

description:
WSU_D2
processed data file: RNA_analysis.xlsx


title: WSU-DLCL2 72h KDM5i 3 [WSU_K3]

description:
WSU_K3
processed data file: RNA_analysis.xlsx


title: SCC-1_ChIP_rep1


title: WSU-DLCL2 72h DMSO 1 [WSU_D1]

description:
WSU_D1
processed data file: RNA_analysis.xlsx


title: F_P7_hyperoxia_CD45_1_DC28_J9

tag: mousename

tag: coverage

tag: number of genes


title: chOS-51: Osteosarcoma_Chemosensitivity_good


title: chOS-50: Osteosarcoma_Chemosensitivity_poor


title: F_P7_hyperoxia_CD45_1_DC28_C4

value: B cell


title: Day 31 ABCA3:GFP- Replicate 3

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

country: USA

institute: Center for Regenerative Medicine at Boston University

data_processing:
Sequence reads were aligned to a combination of the human genome reference (GRCh38) and GFP reporter sequence, using STAR v.2.5.2b
Counts per gene were summarized using the featureCounts function from the subread package v.1.6.2.
The edgeR package v.3.25.10 was used to import, organize, filter and normalize the data. Genes that were not expressed in at least one of the experimental groups were filtered out (keeping only genes that had at least 0.5 counts per million of mapped reads in at least 3 libraries)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix of fragments per kilobase per million reads mapped

molecule: polyA RNA

source_name: BU3AG23CR6 human iPSC

growth_protocol: To derive distal lung epithelial cells, PSCs were first dissociated into single cells suspension and 1.8-2X106 cells were plated per well (triplicate wells, n=3) of a 6-well tissue culture plate coated with Matrigel for 24 hours in mTeSR media containing ROCK inhibitor (RI) prior to differentiation into definitive endoderm differentiation using the Definitive Endoderm Kit (Stem Cell Technologies, 05110) for 3 days (day 0-3). To drive anteriorization of definitive endoderm, day 3 cells were then passed 1:3-1:6 to a new plate in complete serum free differentiation medium (cSFDM) described in Gouon-Evans et al. (2006) supplemented with 2mM of dorsomorphin (DS, Stemgent, 040024) and 10mM SB431543 (SB, Biotechne, 1614) (together constituting DS/SB media) for 3 days (day 3-6) plus 10mM RI for the first 24 hrs. On day 6, cells were re-fed with cSFDM media supplemented with 3mM CHIR (Biotechne, 4423) 100nM retinoic acid (Sigma-Aldrich, R2625), and 10ng/mL rhBMP4 (BioTechne, 314BP) for specification of lung lineage. On day 15, cells were single-cell dissociated by trypsin for fluorescence activated cell sorting using CD47hi/CD26lo staining strategy detailed in Hawkins et al (2017) to enrich for NKX2-1+ lung primordial progenitors, re-plated in 3D Matrigel (Corning, 356231) in the concentration of 400 cells/ml and fed with cSFDM media supplemented with CHIR, KGF, dexamethasone, cyclic AMP and IBMX, constituting the "CK+DCI distal lung differentiation media" described in Jacob et al. (2019, 2020) containing RI for the first 72 hours then subsequently re-fed with CK+DCI medium every other day onward. On day 31, live, ABCA3:GFP reporter positive cells and reporter negative cells were sorted for total RNA extraction followed by global transcriptomic analysis (biological triplicate samples, n=3).

extract_protocol:
Following cell sorting for desired cell population, biological triplicate (n=3) samples of purified RNA was harvested using Qiazol and RNA Sample Preparation Kit v2 (QIAGEN).
Total mRNA was isolated using magnetic beads-based poly(A) selection, fragmented, and randomly fragmented for reverse transcription, followed by synthesis of cDNA fragments. cDNA fragments were then end-paired, and ligated to Illumina Paired-End sequencing adapters. The products were end-paired and PCR-amplified to create the final cDNA library.
Sequencing of pooled libraries were done using NextSeq 500 (Illumina). The quality of the raw data was assessed using FastQC v.0.11.7. Sequence reads were aligned to a combination of the human genome reference (GRCh39) and GFP reporter sequence, using STAR v.2.6.0c. Counts per gene were summarized using the featureCounts function from the subread package v.1.6.2.

tag: developmental stage

value: day 31 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: enriched for epithelial cells by ABCA3:GFP negative reporter sorting


title: MSA, replicate 3

tag: strain

tag: tissue


title: chOS-49: Osteosarcoma_Chemosensitivity_good


title: F_P7_hyperoxia_CD45_1_DC28_F12

tag: sequencing run

value: Mac III


title: Day 31 ABCA3:GFP- Replicate 1


title: F_P7_hyperoxia_CD45_1_DC28_C21

value: neutrophil


title: Dox_24_5

city: Charlottesville

first: Jason

last: Papin

state: VA

address: 415 Lane Rd

department: Biomedical Engineering

institute: University of Virginia

description:
raw_gene_counts.csv
differential_expression.xlsx

data_processing:
Kallisto v 0.46.0 was used to pseudo-align raw fastq files under default settings to the Rattus norvegicus Ensembl v96 transcriptome.
Transcript abundances were aggregated to the Entrez gene level using the tximport package in R.
Genes with low counts (<10) across all samples within a treatment group were removed.
Differentially expressed genes (DEGs) were determined using DESeq2 with a significance threshold of FDR < 0.1.
Genome_build: Ensembl v96 transcriptome
Supplementary_files_format_and_content: raw counts and differential expression for all genes

organism: Rattus norvegicus

source_name: Primary neonatal cardiomyocytes

growth_protocol: Primary neonatal rat cardiomyocytes were isolated and cultured according to the protocol published in Ryall et al, 2014. Cell were manintained for ~36 hours in plating media before being serum starved overnight before treatment exposure.

extract_protocol:
Cells were lysed with Trizol, mized with chloroform and spun in phase-lock gel tubes inside a cold room. The upper phase was decanted into new tubes and isopropanol and glycogen were added to the mixture which was incubated at -20C overnight. DNA was removed using the TURBO DNA-free kit (Invitrogen, #!M1907).
RNA was sent to GeneWiz (https://www.genewiz.com/en) for PolyA selection, library construction, and sequencing

treatment_protocol: Cells were treated for either 6 or 24 hours with the specified drugs or control.

value: Dox


title: F_P7_hyperoxia_CD45_1_DC28_G8


title: chOS-46: Osteosarcoma_Chemosensitivity_poor

value: Osteosarcoma pre-therapeutic biopsy


title: H47_RB_CaptureSeq

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute

data_processing:
Deduplication using UMI_tools (umi_tools 1.0.0)
Trimmed for quality reads using TrimGalore (TrimGalore 0.4.1)
Aligned to human transcriptome and HIV-1 genome using bowtie2 (bowtie2 2.3.4.1)
Counts summed by custom Python script
Genome_build: Primary transcriptome GRCh38.p12 release 28, HIV-1 alignments made to consensus sequences derived from the study participant
Supplementary_files_format_and_content: umi_tools and trimgalore return a .fastq. Bowtie2 aligns to a .sam file. Normalized and unnormalized counts in .txt

source_name: Non-naïve, resting CD4+ T cells

growth_protocol: Isolated from blood

extract_protocol:
Cells were pelleted and resuspended in 1 mL Trizol, RNA was extracted by chloroform extraction and isopropanol precipitation.
mRNA was enriched using oligo d(t) Dynabeads. 3'Phosphorylation with rSAP, linker ligation with T4 RNA ligase truncated KQ, excess linker degraded with RecJ and 5'Deadenylase. RT was performed with SuperScriptt III. cDNAs were isolated by gelextraction on a 10% TBE-Urea gel and extracted by isopropanol precipitation. cDNAs were circularized with circLigase and amplified by PCR with phusion polymerase. PCR products were purified by gel extraction from an 8% TBE gel and isopropanol precipitation. Samples were quantified by Bioanalyzer. CaptureSeq was perfomed on cDNA after circularization using Arbor Biosciences MyBaits custom probe kit.

treatment_protocol: 24 hour stimulation in RPMI media supplemented with 10% FBS and Penn/Strep

tag: stimulation

value: 20 nM Romidpesin and 1 nM Bryostatin-1

tag: library type

value: CaptureSeq

tag: hiv alignment

value: Full length genome


title: F_P7_hyperoxia_CD45_1_DC28_K19

tag: gender

tag: plate

tag: treatment

value: Mac V


title: Day 31 ABCA3:GFP+ Replicate 1

value: enriched for epithelial cells by ABCA3:GFP positive reporter sorting


title: F_P7_hyperoxia_CD45_1_DC28_L7

value: F

tag: well

tag: timepoint

tag: cell type


title: F_P7_hyperoxia_CD45_1_DC28_E18

value: hyperoxia

tag: cell subtype

value: DC I

tag: mousename

tag: coverage


title: Dox_24_7


title: JMJD-2_ChIP_rep2

description: JMJD-2_N2_L3_PK021-MH004_yapc_IDR_peaks.bed

tag: developmental stage

tag: chip antibody

value: JMJD-2 (JA lab; Q3951)


title: F_P7_hyperoxia_CD45_1_DC28_I8

value: immune

tag: number of genes


title: Day 31 ABCA3:GFP- Replicate 2

value: day 31 distal lung directed differentiation

tag: culture media

tag: isolation method


title: Day 31 ABCA3:GFP+ Replicate 3

value: CK+DCI


title: chOS-40: Osteosarcoma_Chemosensitivity_good

tag: tissue

value: normal placenta


title: Dox_24_6


title: Dox_24_4


title: Day 31 ABCA3:GFP+ Replicate 2


title: F_P7_hyperoxia_CD45_1_DC28_I7

tag: sequencing run

value: Mac III


title: chOS-45: Osteosarcoma_Chemosensitivity_poor


title: chOS-41: Osteosarcoma_Chemosensitivity_good


title: JMJD-2_ChIP_rep1

tag: strain


title: chOS-48: Osteosarcoma_Chemosensitivity_poor


title: chOS-42: Osteosarcoma_Chemosensitivity_poor


title: Dox_24_3


title: F_P7_hyperoxia_CD45_1_DC28_E13

tag: gender

value: neutrophil


title: Dox_24_2

value: Dox


title: Dox_24_1


title: F_P7_hyperoxia_CD45_1_DC28_P21

tag: plate


title: H47_IL15_CaptureSeq

tag: stimulation

tag: library type

tag: hiv alignment


title: chOS-39: Osteosarcoma_Chemosensitivity_good

value: Osteosarcoma pre-therapeutic biopsy


title: H47_RMD_CaptureSeq

value: 20 nM Romidpesin


title: H47_Bryo_CaptureSeq

value: 10 nM Bryostatin-1

value: CaptureSeq


title: chOS-34: Osteosarcoma_Chemosensitivity_poor


title: F_P7_hyperoxia_CD45_1_DC28_N19

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: Mac V


title: F_P7_hyperoxia_CD45_1_DC28_H4

tag: cell subtype

tag: mousename

tag: coverage


title: F_P7_hyperoxia_CD45_1_DC28_K23

value: B cell

tag: number of genes


title: Dox_6_7


title: chOS-36: Osteosarcoma_Chemosensitivity_poor


title: H47_Unstimulated_CaptureSeq

value: Unstimulated

value: Full length genome


title: chOS-32: Osteosarcoma_Chemosensitivity_good


title: H47_PMA-iono_CaptureSeq

value: 50 ng/mL PMA and 1 uM Ionomycin


title: F_P7_hyperoxia_CD45_1_DC28_J18

value: F

value: hyperoxia

value: mast cell


title: F_P7_hyperoxia_CD45_1_DC28_I18

value: immune

value: Mac II


title: H24_IL15_CaptureSeq


title: chOS-38: Osteosarcoma_Chemosensitivity_poor

value: normal placenta


title: chOS-33: Osteosarcoma_Chemosensitivity_poor


title: Dox_6_4


title: Dox_6_5


title: Dox_6_3


title: H24_RB_CaptureSeq

value: 20 nM Romidpesin and 1 nM Bryostatin-1


title: Dox_6_6

value: Dox


title: F_P7_hyperoxia_CD45_1_DC28_M12

value: Mac III


title: Dox_6_1


title: F_P7_hyperoxia_CD45_1_DC28_E19

value: Mac IV


title: DMSO2_24_7


title: chOS-26: Osteosarcoma_Chemosensitivity_good

value: Osteosarcoma pre-therapeutic biopsy


title: chOS-27: Osteosarcoma_Chemosensitivity_good


title: F_P7_hyperoxia_CD45_1_DC28_K11


title: chOS-31: Osteosarcoma_Chemosensitivity_good


title: H24_PMA-iono_CaptureSeq

value: CaptureSeq


title: H24_Unstimulated_CaptureSeq


title: H24_RMD_CaptureSeq

value: 20 nM Romidpesin


title: F_P7_hyperoxia_CD45_1_DC28_L16


title: DMSO2_24_6


title: DMSO2_24_5


title: Dox_6_2


title: F_P7_hyperoxia_CD45_1_DC28_F17

value: DC I


title: DMSO2_24_4


title: H20_IL15_CaptureSeq


title: F_P7_hyperoxia_CD45_1_DC28_H12


title: chOS-25: Osteosarcoma_Chemosensitivity_good


title: H24_Bryo_CaptureSeq

value: 10 nM Bryostatin-1


title: chOS-21: Osteosarcoma_Chemosensitivity_poor


title: F_P7_hyperoxia_CD45_1_DC28_K7


title: DMSO2_24_3


title: H20_Bryo_CaptureSeq

value: Full length genome


title: DMSO2_24_2


title: F_P7_hyperoxia_CD45_1_DC28_I6

value: Mac V


title: H20_RMD_CaptureSeq


title: H20_PMA-iono_CaptureSeq

value: 50 ng/mL PMA and 1 uM Ionomycin


title: H20_RB_CaptureSeq


title: F_P7_hyperoxia_CD45_1_DC28_M7

value: F

value: hyperoxia


title: chOS-23: Osteosarcoma_Chemosensitivity_good


title: DMSO2_24_1


title: chOS-13: Osteosarcoma_Chemosensitivity_poor


title: F_P7_hyperoxia_CD45_1_DC28_A14

value: immune


title: H20_Unstimulated_CaptureSeq

value: Unstimulated


title: DMSO2_6_7


title: chOS-18: Osteosarcoma_Chemosensitivity_good

value: normal placenta


title: F_P7_hyperoxia_CD45_1_DC28_L12


title: chOS-17: Osteosarcoma_Chemosensitivity_poor


title: H47_RB_RNAseq

value: 20 nM Romidpesin and 1 nM Bryostatin-1

value: RNAseq


title: chOS-5: Osteosarcoma_Chemosensitivity_good


title: DMSO2_6_6


title: DMSO2_6_5


title: H47_IL15_RNAseq


title: F_P7_hyperoxia_CD45_1_DC28_F5


title: F_P7_hyperoxia_CD45_1_DC28_E2


title: DMSO2_6_3


title: H47_RMD_RNAseq


title: DMSO2_6_2


title: F_P7_hyperoxia_CD45_1_DC28_K22

value: Mac III


title: F_P7_hyperoxia_CD45_1_DC28_A4


title: WTC11 RBM20 8-bp deletion Homo Ribo- replicate 2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: GCaMP6 is expressed from AAVS1

data_processing:
To identify, quantify and annotate circular RNAs from back-splice junctions we first aligned the RNASeq results using TopHat2 on the RiboMinus depleted paired-end RNA-Seq FASTQ files, via the CIRCexplorer2 pipeline, on each individual sample (default options). This workflow identified far greater putative circRNAs than using the same pipeline with STAR 2.4.0. For differential circRNA analysis we ran RUVSEQ from the CSBB pipeline (https://github.com/csbbcompbio/CSBB-v3.0) on the back-splice junction counts for each sample for all relevant comparison groups. This workflow applies the software EdgeR to perform a differential expression analysis using a generalized linear model approach using the upper quartile normalization. All together, we identified circRNAs for 448 genes, with evidence of at least two reads per circRNA. circRNAs with a non-adjusted EdgeR p<0.1 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited-text
Supplementary_files_format_and_content: CIRCexplorer2 back-splice junction read counts

source_name: iPS cell-derived cardiomyocytes

growth_protocol: The iPS cell lines were differentiated into iPS-CMs using the method that controls WNT signaling by small molecules 16. Briefly, iPS cells were seeded at 1.25–2.5x104 cells/cm2 onto 12-well plates coated with 80 μg/μl growth factor-reduced Matrigel (BD Biosciences) in mTeSR1 supplemented with 10 μM Y-27632 (Selleckchem) for 24 h (day –3). mTeSR1 medium was changed daily for the next 2 days. On day 0, iPS cells were treated with 12 μM CHIR99021 (CHIR) (Tocris) in RPMI supplemented with B-27 (RPMI/B27) without insulin (Life Technologies) for exactly 24 h. On day 1, the culture medium was replaced with fresh RPMI/B27 without insulin and maintained for 48 h. On day 3, cells were treated with 5 μM IWP2 (Tocris) in RPMI/B27 without insulin and maintained for 48 h. On day 5, fresh RPMI/B27 without insulin was added to the cells, and on day 7, the medium was switched to RPMI/B27 with insulin. Afterward, fresh RPMI/B27 with insulin was added to the cells every 3 days. We used a metabolic selection protocol with glucose-free DMEM containing lactate to purify iPS-CMs. Cells were replated on day 15–18 of differentiation, and then on day 20–22 media were replaced with DMEM (without glucose, with sodium pyruvate, Thermo Fisher Scientific) supplemented with Glutamax, non-essential amino acids, and buffered lactate (4 mM). Stock-buffered lactate solution was prepared by dissolving sodium L-lactate powder (Sigma-Aldrich) at 1 M concentration in 1 M HEPES solution. Lactate media were exchanged 2–3 times, with a total exposure of 48 hours for each treatment. After the final lactate treatment (day 24–28), media were changed to RPMI/B27. The purified iPS-CMs at day 30 were harvested for RNA-Seq or cryopreserved for further analyses.

extract_protocol: Total RNA was purified from iPS-CMs by using TRIzol and PureLink RNA Mini Kit (Thermo Fisher Scientific) according manufactures’ instructions. The RNAseq libraries were prepared from the purified RNA by using RiboMinus RNA Library Prep Kit. Paired-end 75 bp RNAseq was performed with HiSeq (Illumina).

tag: cell line

value: WTC11 from a healthy male patient

tag: differentiation

value: WNT modulation method day 26

tag: genotype

value: RBM20 8-bp deletion Homo

tag: purification

value: Lactate method (PMID:23168164)


title: H47_PMA-iono_RNAseq


title: F_P7_hyperoxia_CD45_1_DC28_K21

tag: sequencing run

tag: gender

value: NK cell


title: WTC11 RBM20 8-bp deletion Homo Ribo- replicate 1

description: GCaMP6 is expressed from AAVS1


title: DMSO2_6_1


title: DMSO1_24_6


title: H34_RB_RNAseq

tag: stimulation

value: Splice region


title: H47_Unstimulated_RNAseq

tag: library type

value: Full length genome


title: F_P7_hyperoxia_CD45_1_DC28_O18

tag: plate

value: Mac IV


title: H47_Bryo_RNAseq

value: 10 nM Bryostatin-1

tag: hiv alignment


title: F_P7_hyperoxia_CD45_1_DC28_K16

value: F

tag: well

tag: timepoint


title: H34_IL15_RNAseq


title: DMSO1_24_4

tag: treatment


title: WTC11 RBM20 R636S Homo Ribo- replicate 1

description: GCaMP6 is expressed from AAVS1

value: RBM20 R636S Homo


title: 24h_wt_SHOX

city: Heidelberg

first: Sandra

last: Hoffmann

address: Im Neuneheimer Feld 366

department: Human Molecular Genetics

country: Germany

institute: University of Heidelberg

hyb_protocol: Hybridization was performed at 58° C in GEX-HCB buffer (Illumina) at a concentration of 100 ng cRNA/µl for 20 h

scan_protocol: The arrays were scanned using a Beadstation array scanner

data_processing: Data extraction was done for all beads individually, and outliers were removed if > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal and standard deviation for each probe. For each analyzed time point, we compared signals of normalized gene expression of SHOX-WT transfected samples to SHOX-HM transfected controls

source_name: Normal Human Dermal Fibroblast

label_protocol: For array hybridization, we prepared biotin-labeled cRNA from 250 µg total RNA according to Illumina’s recommended sample labeling procedure using the MessageAmp™ II aRNA Amplification Kit (Thermo Fisher Scientific)

growth_protocol: Normal human dermal fibroblasts (NHDF cells; PromoCell: C12300) were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Thermo Fisher Scientific), supplemented with 10% fetal bovine serum, penicillin (100 U/mL), and streptomycin (100 μg/mL) in a 5% CO2-humidified incubator at 37° C

extract_protocol: Total RNA from NHDF cells was isolated using Illustra RNAspin Isolation Kit (Cytiva) according to the manufacturer’s instructions

treatment_protocol: 1x106 NHDF cells were transfected with 3.5 µg pcDNA4/TO-SHOX-WT using the Amaxa® Human Dermal Fibroblasts Nucleofector® Kit (Lonza) according to the manufacturer’s instructions. In control experiments, NHDF were transfected with 3.5 µg pcDNA4/TO-SHOX-HM, which encodes a homeodomain-mutant of SHOX leading to the amino acid exchange Y141D

tag: time point

value: 24 hours after transfection


title: 24h_HM_SHOX


title: chOS-3: Osteosarcoma_Chemosensitivity_good

tag: tissue

value: Osteosarcoma pre-therapeutic biopsy


title: 6h_HM_SHOX

value: 6 hours after transfection


title: 12h_HM_SHOX

value: 12 hours after transfection


title: 6h_wt_SHOX


title: DMSO1_24_3


title: 12h_wt_SHOX


title: WTC11 RBM20 R636S Het Ribo- replicate 3

description: GCaMP6 is expressed from AAVS1

value: RBM20 R636S Het


title: H34_Bryo_RNAseq

value: RNAseq


title: F_P7_hyperoxia_CD45_1_DC28_M5

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage


title: DMSO1_24_2


title: H34_RMD_RNAseq

value: 20 nM Romidpesin


title: DMSO1_24_5


title: WTC11 RBM20 R636S Het Ribo- replicate 1

description: GCaMP6 is expressed from AAVS1

tag: cell line

value: WTC11 from a healthy male patient

tag: differentiation

value: WNT modulation method day 26

tag: genotype

value: Lactate method (PMID:23168164)


title: WTC11 RBM20 R636S Het Ribo- replicate 2

description: GCaMP6 is expressed from AAVS1

tag: purification


title: F_P7_hyperoxia_CD45_1_DC28_G11

tag: sequencing run

tag: gender

value: Mac IV

tag: number of genes


title: DMSO1_24_1


title: F_P7_hyperoxia_CD45_1_DC28_E12

tag: plate

value: Mac V


title: F_P7_hyperoxia_CD45_1_DC28_M11

value: F

tag: well


title: WTC11 Wild-Type Ribo- replicate 1

description: GCaMP6 is expressed from AAVS1

value: Wild-Type


title: DMSO1_6_6

tag: timepoint


title: H34_Unstimuated_RNAseq

tag: stimulation

value: Unstimulated

tag: library type

tag: hiv alignment

value: Splice region


title: Airway epithelial cells (basal cells) - RNAseq [8f70_40b0-2A]

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description:
gene.counts.txt
gene.counts.normalized.txt

data_processing:
RNAseq reads were mapped to the human reference genome (hg19) using STAR
Gene counts were generated from STAR (--quantMode GeneCounts)
removed X, Y, and mitochondrial genes
Gene counts were voom transformed (TMM normalized)
Genome_build: hg19
Supplementary_files_format_and_content: gene count files were processed using R; files contain gene counts (or normalized gene counts) for each sample; rows are gene Ensembl IDs and the columns are sample names
Supplementary_files_format_and_content: .txt; gene counts for each sample
Supplementary_files_format_and_content: .txt; normalized gene counts (TMM normalized) for each sample

source_name: Cultured airway epithelial cells (basal cells)

growth_protocol: Nasal airway epithelial cells (basal cells) were cultured in collagen-coated (PureCol, INAMED BioMaterials, catalog number 5,409, 3 mg/mL, 1:15 dilution) tissue culture plates (6 wells of 2x 12 well plates) using BEGM overnight at 37°C and 5% CO2.

extract_protocol:
QIAGEN AllPrep DNA/RNA Kit
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: In preparation for rhinovirus (HRV-16; RV) infection/stimulation, plates at 50-60% confluency were incubated overnight in BEGM without hydrocortisone (HC) followed by a two-hour RV infection at a multiplicity of infection (MOI) of 2 and vehicle treatment (Bronchial epithelial cell basal medium (BEBM) + Gentamicin/Amphotericin) at 33°C (low speed rocking, ~15 RPM). RV- and vehicle-treated cells were washed and then were cultured at 33°C for 46 hours (48 hours total) in BEGM without HC. Cell viability was determined based on trypan blue staining or a LDH assay

tag: treatment

value: vehicle

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: CRS

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: WTC11 Wild-Type Ribo- replicate 2

description: GCaMP6 is expressed from AAVS1

tag: cell line

tag: differentiation

tag: genotype

tag: purification


title: F_P7_hyperoxia_CD45_1_DC28_P11

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: H24_RB_RNAseq

tag: stimulation

value: 20 nM Romidpesin and 1 nM Bryostatin-1

tag: library type

value: RNAseq

tag: hiv alignment

value: Full length genome


title: H24_IL15_RNAseq


title: F_P7_hyperoxia_CD45_1_DC28_M15

tag: treatment

value: basophil


title: Airway epithelial cells (basal cells) - RNAseq [8f70_40b0-1A]

value: RV

tag: atopy

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: DMSO1_6_5

tag: timepoint


title: H24_Bryo_RNAseq

value: 10 nM Bryostatin-1


title: F_P7_hyperoxia_CD45_1_DC28_B3

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: cell type

tag: cell subtype

value: DC I

tag: mousename


title: DMSO1_6_4

tag: treatment


title: H24_RMD_RNAseq

tag: stimulation

value: 20 nM Romidpesin

tag: library type

tag: hiv alignment


title: DMSO1_6_3


title: Airway epithelial cells (basal cells) - RNAseq [6f90_420d-2A]

value: vehicle

value: Female

tag: atopy

tag: asthma

tag: steroids

value: Oral

value: yes

tag: smoking

tag: crs


title: Airway epithelial cells (basal cells) - RNAseq [6f90_420d-1A]

value: Yes

value: Never

value: CRS

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: H34_PMA-iono_RNAseq

value: 50 ng/mL PMA and 1 uM Ionomycin

value: Splice region


title: F_P7_hyperoxia_CD45_1_DC28_K14

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_G17

tag: treatment

tag: cell type

tag: cell subtype

value: neutrophil

tag: mousename


title: DMSO1_6_2


title: H24_PMA-iono_RNAseq

tag: stimulation

tag: library type

value: RNAseq

tag: hiv alignment

value: Full length genome


title: Airway epithelial cells (basal cells) - RNAseq [1413_4602-2A]

value: Male

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: tech

tag: rin


title: F_P7_hyperoxia_CD45_1_DC28_K8

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

value: basophil


title: Airway epithelial cells (basal cells) - RNAseq [0ebb_471b-2A]

tag: treatment

value: vehicle

value: Prior

value: CB

tag: age

tag: surgeon


title: Ace_24_7

value: Ace


title: H24_Unstimulated_RNAseq

tag: stimulation

value: Unstimulated

tag: library type


title: F_P7_hyperoxia_CD45_1_DC28_F8

tag: cell type

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: H20_RB_RNAseq

value: 20 nM Romidpesin and 1 nM Bryostatin-1

tag: hiv alignment


title: Ace_24_6


title: F_P7_hyperoxia_CD45_1_DC28_G23

value: Mac III


title: H20_IL15_RNAseq


title: Airway epithelial cells (basal cells) - RNAseq [0ebb_471b-1A]

value: RV

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: CRS

tag: tech

tag: rin


title: Ace_24_5

tag: treatment

tag: timepoint


title: H20_Bryo_RNAseq

tag: stimulation

value: 10 nM Bryostatin-1

value: RNAseq


title: Airway epithelial cells (basal cells) - RNAseq [c9d1_4237-2A]

tag: gender

value: Female

value: Never

value: Control

value: RN

tag: age

tag: surgeon


title: Ace_24_3


title: Ace_24_4


title: Airway epithelial cells (basal cells) - RNAseq [c9d1_4237-1A]

value: No


title: F_P7_hyperoxia_CD45_1_DC28_M2

tag: sequencing run

value: F

tag: plate

tag: well

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

tag: mousename


title: H20_RMD_RNAseq

value: 20 nM Romidpesin

tag: library type

tag: hiv alignment

value: Full length genome


title: F_P7_hyperoxia_CD45_1_DC28_M22

value: Mac IV

tag: coverage

tag: number of genes


title: H20_Unstimulated_RNAseq

value: Unstimulated


title: H20_PMA-iono_RNAseq

value: 50 ng/mL PMA and 1 uM Ionomycin


title: Ace_24_1

value: Ace


title: Ace_6_6


title: Airway epithelial cells (basal cells) - RNAseq [16ac_4246-1A]

value: RV

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: Nasal

value: yes

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

tag: rin


title: F_P7_hyperoxia_CD45_1_DC28_P18

tag: sequencing run

tag: gender

tag: timepoint

tag: treatment

value: Mac III


title: Airway epithelial cells (basal cells) - RNAseq [16ac_4246-2A]

value: vehicle

value: No

value: RN

tag: age

tag: surgeon


title: Ace_24_2


title: F_P7_hyperoxia_CD45_1_DC28_B8

value: F

tag: plate

tag: well

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: T cell

tag: mousename


title: F_P7_hyperoxia_CD45_1_DC28_F20

value: Mac IV

tag: coverage

tag: number of genes


title: DMSO1_6_1


title: rCMT3 methylC-seq bent cotyledon (Line #3; biorep #1)

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description:
Sample 9
Single-end 100 base read methylC-seq data from first biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #3).
allC_rCMT3_L3_BentCotyledon.tsv

data_processing:
MethylC-seq (samples 1 to 26): Adapters and the first six bases corresponding to random hexamers used during the pre-amplification step were trimmed from MethylC-seq reads using Trim Galore. Bisulfite-converted reads were aligned against the TAIR10 genome (Lamesch et al., 2012) using Bismark (bismark --non_directional -q --score-min L,0,-0.4) (Krueger and Andrews, 2011). Methylpy software was used to extract weighted methylation rate at each available cytosine from BAM files containing only deduplicated and uniquely mapped reads (Schultz et al., 2015).
mRNA-seq (samples 27 to 35): Raw FASTQ files were quality filtered and trimmed for adapter sequences with Trim Galore using default parameters. Trimmed reads were aligned using STAR (Dobin et al., 2013) against a genome index generated using the TAIR10 genome fasta file and all transcripts in the GTF of Ensembl build TAIR10 annotation set (release version 44). Aligned transcriptome bam files were used to quantify read counts per gene and transcript abundance using RSEM (Li and Dewey, 2011).
Genome_build: TAIR10
Supplementary_files_format_and_content: MethylC-seq (samples 1-26): TSV files for methylC-seq processed data files (allC_GENOTYPE_TISSUE.tsv.gz) were output from MethylPy (Schultz et al., 2015) and have following seven columns: 1) chromosome, 2) coordinate position, 3) strand, 4) trinucleotide context, 5) number of reads supporting methylation, 6) number of total reads, 7) whether (1) or not (0) binomial test was performed.
Supplementary_files_format_and_content: mRNA-seq (samples 27-35): TSV files for mRNA-seq processed data files (GENOTYPE_TISSUE_BIOREP.genes.results) were output from RSEM (Li and Dewey, 2011) and have following seven columns: 1) gene_id, 2) transcript(s), 3) transcript length, 4) effective_length, 5) expected_count, 6) TPM, 7) FPKM.

organism: Arabidopsis thaliana

source_name: Bent cotyledon embryos (8 days after pollination)

growth_protocol: Arabidopsis thaliana accession Columbia-0 (Col-0) were grown in controlled growth chambers at 20-22˚C under a 16-h light/8-h dark cycle with incandescent lights (130 to 150 µmol/m2/s).

extract_protocol:
Samples 1 to 26 : Genomic DNA was extracted with Quick-DNATM Micro prep Kit (Zymo D3020). MethylC-seq libraries were generated as previously described (Papareddy et al. 2020).
Samples 27 to 35: Total RNA was isolated with TRIzol reagent (Thermo Fisher Scientific). Smart-seq2 mRNA libraries were generated from 1 µl of the 7 µl bent cotyledon embryo total RNA as previously described (Picelli 2013; Hoffman 2019).

tag: accession

value: rCMT3 (cmt3-11)

tag: genotype

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #3)

tag: tissue

value: Bent cotyledon embryos


title: F_P7_hyperoxia_CD45_1_DC28_I2

value: mast cell II


title: Airway epithelial cells (basal cells) - RNAseq [1413_4602-1A]

value: RV

value: Male

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

tag: tech

tag: rin


title: rCMT3 methylC-seq bent cotyledon (Line #3; biorep #2)

description:
Sample 10
Single-end 100 base read methylC-seq data from second biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #3).
allC_rCMT3_L3_BentCotyledon.tsv


title: rCMT3 methylC-seq bent cotyledon (Line #1; biorep #2)

description:
Sample 8
Single-end 100 base read methylC-seq data from second biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #1).
allC_rCMT3_L1_BentCotyledon.tsv

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #1)


title: Airway epithelial cells (basal cells) - RNAseq [e109_4585-2A]

tag: treatment

tag: gender

value: Current

value: Control

tag: age

tag: surgeon


title: Ace_6_5

value: Ace

tag: timepoint


title: Airway epithelial cells (basal cells) - RNAseq [5399_4680-2A]

value: vehicle

value: Yes

value: No

value: Nasal

value: yes

value: CB


title: F_P7_hyperoxia_CD45_1_DC28_G6

tag: sequencing run

value: F

tag: plate

tag: well

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage


title: Ace_6_4


title: F_P7_hyperoxia_CD45_1_DC28_A6

value: Mac IV

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [e109_4585-1A]

value: RV

value: Male

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: RN


title: Ace_6_3

tag: treatment


title: rCMT3 methylC-seq bent cotyledon (Line #1; biorep #1)

description:
Sample 7
Single-end 100 base read methylC-seq data from first biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #1).
allC_rCMT3_L1_BentCotyledon.tsv

tag: accession

value: rCMT3 (cmt3-11)

tag: genotype

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #1)

tag: tissue

value: Bent cotyledon embryos


title: AD_3

city: Dunedin

first: Joanna

last: Williams

address: Great King St

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Torrent Suite Software 4.2 used for basecalling
Reads were trimmed for adapter sequences using AdapterRemoval, trimmed for quality using Trimmomatic, then mapped to hg38 genome using STAR v2.5.4b
MiRNA were analysed separately, and mapped to human miRNA sequences obtained from mirBase using MirDeep2.
Differential expression analysis was performed using edgeR in R version 4.0.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of raw read counts for each sample

source_name: Middle temporal gyrus

extract_protocol:
Tissues were received from the Victorian Brain Bank. Total RNA was extracted using mirVana PARIS RNA isolation kit (Invitrogen) according to manufacturer's instructions.
Up to 500ng total RNA was used for library preparation using modifications to the Ion Total RNA-Seq kit v2 (Life Technologies) protocol. The major modifications were as follows: ligation of Ion adapters was performed at 16C for 16 hours; rRNA depletion was achieved by the use of QIASeq FastSelect rRNA removal kit (QIAGen). Samples were pooled into two mixed pools and sequenced on the Ion Proton platform on ion PI v3 chips.

value: brain

tag: diagnosis

value: Alzheimer's disease


title: F_P7_hyperoxia_CD45_1_DC28_O14

tag: sequencing run

tag: gender

tag: timepoint


title: Airway epithelial cells (basal cells) - RNAseq [21f6_4a02-2A]

value: vehicle

value: Female

value: No

value: Inhaled

value: Prior

tag: crs

value: Control

tag: tech

tag: rin

tag: age

tag: surgeon


title: Ace_6_2

value: Ace


title: Airway epithelial cells (basal cells) - RNAseq [5399_4680-1A]

tag: atopy

value: Yes

value: Nasal

value: yes

value: Never

value: CB


title: CT_4


title: F_P7_hyperoxia_CD45_1_DC28_A23

value: F

tag: plate

tag: well

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Ace_6_1

tag: treatment


title: AD_2

tag: tissue

value: brain

tag: diagnosis

value: Alzheimer's disease


title: Airway epithelial cells (basal cells) - RNAseq [c47b_49c5-2A]

value: vehicle

tag: gender

value: Male

tag: asthma

tag: steroids

tag: smoking


title: F_P7_hyperoxia_CD45_1_DC28_E5

tag: sequencing run

tag: timepoint

value: Mac IV


title: F_P7_hyperoxia_CD45_1_DC28_L14


title: CT_3


title: Airway epithelial cells (basal cells) - RNAseq [21f6_4a02-1A]

value: RV

value: Female

tag: atopy

value: No

value: Inhaled

value: Prior

tag: crs

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: CT_2


title: F_P7_hyperoxia_CD45_1_DC28_N23

tag: plate

tag: well

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage


title: 5FU_24_5

tag: treatment


title: Airway epithelial cells (basal cells) - RNAseq [d2ad_4e13-2A]

tag: gender

tag: asthma

tag: steroids

value: Nasal

value: yes

value: Never

value: Control


title: CT_1

tag: tissue

tag: diagnosis


title: F_P7_hyperoxia_CD45_1_DC28_E17

tag: sequencing run

value: F

tag: timepoint

value: hyperoxia

value: immune

value: basophil

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [c47b_49c5-1A]

tag: atopy

tag: smoking

tag: crs

tag: tech

value: CB

tag: rin

tag: age


title: Airway epithelial cells (basal cells) - RNAseq [d2ad_4e13-1A]

tag: surgeon


title: 5FU_24_3


title: AD_1

value: brain

value: Alzheimer's disease


title: F_P7_hyperoxia_CD45_1_DC28_P9

tag: plate

tag: well

tag: cell type

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage


title: Airway epithelial cells (basal cells) - RNAseq [fcd5_4862-2A]

tag: treatment

value: vehicle

tag: gender

value: Female

tag: asthma

tag: steroids


title: 5FU_24_2

tag: timepoint


title: F_P7_hyperoxia_CD45_1_DC28_C10

tag: sequencing run

tag: number of genes


title: Rabbit IgG Input control in sgMga

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm10 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1
Supplementary_files_format_and_content: bigwig

source_name: sgMga Kras G12D Trp53 -/- lung cancer cells

extract_protocol:
Cells were stored in Trizol and RNA extracted using the Zymogenetics directZol miniprep kit. For ChIp Seq, Cells were crosslinked in formaldehyde and ChIP was performed.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 kit. Fixed ChIP samples were processed by micrococcal nuclease treatment, followed by construction of single strand libraries.

treatment_protocol: Cell lines from both groups were cultured in 10% FBS containing DMEM with antibiotics (penicillin/ streptomycin)

value: derived from Kras G12D Trp 53 -/- tumors


title: Airway epithelial cells (basal cells) - RNAseq [fcd5_4862-1A]

value: RV

tag: atopy

value: No

tag: smoking

value: Prior

tag: crs

tag: tech


title: 5FU_24_1


title: 5FU_24_6


title: RNApolII IP in sgMga


title: F_P7_hyperoxia_CD45_1_DC28_N18

tag: plate

value: Mac III


title: 5FU_6_6


title: Airway epithelial cells (basal cells) - RNAseq [bf8a_4f2b-2A]

value: Yes

value: Never

value: CRS

value: RN

tag: rin

tag: age

tag: surgeon


title: 5FU_6_5


title: F_P7_hyperoxia_CD45_1_DC28_F3

value: F

tag: well

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: neutrophil

tag: mousename


title: 5FU_24_4

tag: treatment


title: F_P7_hyperoxia_CD45_1_DC28_B19

tag: gender

tag: coverage


title: Mga IP in sgMga


title: 5FU_6_4

tag: timepoint


title: L3mbtl2 IP in sgMga


title: Airway epithelial cells (basal cells) - RNAseq [16e4_494f-2A]

tag: asthma

tag: steroids

value: yes


title: Airway epithelial cells (basal cells) - RNAseq [16e4_494f-1A]

tag: atopy

tag: smoking


title: DMSO2_6_4


title: Airway epithelial cells (basal cells) - RNAseq [bf8a_4f2b-1A]

tag: crs

tag: tech


title: F_P7_hyperoxia_CD45_1_DC28_D5

tag: sequencing run

tag: plate

tag: number of genes


title: E2f6 IP in sgMga


title: Airway epithelial cells (basal cells) - RNAseq [bcf7_46c2-2A]

value: Control

tag: rin

tag: age

tag: surgeon


title: Rabbit IgG Input control in sgControl

source_name: Control Kras G12D Trp53 -/- lung cancer cells

tag: cell type


title: 5FU_6_3

tag: treatment


title: Airway epithelial cells (basal cells) - RNAseq [bcf7_46c2-1A]

tag: gender


title: RNApolII IP in sgControl


title: Airway epithelial cells (basal cells) - RNAseq [3f1a_423c-2A]

value: vehicle


title: Mouse IgG Input control in sgMga


title: F_P7_hyperoxia_CD45_1_DC28_N7

source_name: distal lung

tag: well

tag: cell subtype

tag: mousename

tag: coverage


title: 974_repro

city: New Orleans

first: Victoria

last: Belancio

state: LA

address: 1430 Tulane Avenue

department: Structural and Cellular Biology

institute: Tulane University School of Medicine

data_processing:
We used Bowtie1 to concordantly map read pairs (-X 600) with a single preferred mapping location (-m 1) with the tryhard switch (-y) that forces it to exhaustively search each read pair against the reference genome. The same alignment parameters were used in this study with either mm10 or rn6 genomes.
The generated bam file was strand separated and then intersected with the same-oriented annotation for full-length L1s. Manual curation of resulting L1 loci with greater than 10 mapped reads was performed using IGV
After aligning the .fastq sequences to the appropriate reference genome (mm10 or rn6), we used a list of LINE-1 element genomic coordinates downloaded from L1 base (http://l1base.charite.de/) to quantify how many reads from the aligned files overlapped with annotated LINE-1 element coordinates. This was performed using 'bedtools coverage'. L1 loci are annotated at 'UID-' and their corresponding number of reads are in the 10th column from the left side of the .txt file.
L1Base - L1Resources<http://l1base.charite.de/>
L1Resources. This web portal is dedicated to putatively active LINE-1 elements. What are LINE-1s? LINE-1 (Long Interspersed Nucleotide Element 1, L1) are the only autonomous retrotransposons in the group of non-LTR retrotransposons.
All scripts and protocols used in this analysis are available in our previous publication RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level (doi: 10.3791/59771).
Genome_build: mm10 or rn6
Supplementary_files_format_and_content: L1 loci are annotated at 'UID-' and their corresponding number of reads are in the 10th column from the left side of the .txt file.

molecule: cytoplasmic RNA

source_name: repro

extract_protocol:
Organ samples of approximately 10 mm3 were bluntly dissected and then homogenized in 0.5-1mL of lysis buffer (150 mM NaCl, 50 mM HEPES pH 7.4, 25 ug/mL digitonin with 1000 U/mL SUPERase-In Rnase inhibitor added just prior to application) to lyse the cytoplasmic membrane. The mixture was lightly homogenized in a dounce homogenizer with an autoclaved B pestle, incubated on ice for 5 minutes and then centrifuged for 2 min at 1000 rpm at 4oC. Supernatant, containing the cytoplasmic fraction, was mixed with pre-chilled 7.5 mL of Trizol and 1.5 mL of chloroform and then centrifuged for 35 min at 4000 rpm at 4oC. The aqueous portion was transferred to 4.5 mL of chilled chloroform, mixed and centrifuged for 10 min at 4000 rpm at 4oC. The resulting aqueous portion was precipitated with 4.5 mL of isopropanol overnight in 80oC, centrifuged for 45 min at 4oC at 4000 rpms, washed with 10 mL of ethanol and re-suspended in RNAse-free water.
Cytoplasmic RNA samples were submitted to BGI Genomics for selection of polyadenylated RNAs, and strand-specific, paired-end library preparation. During this study, we used two methods of RNA sequencing with the same read depth: BGI DNA nanoball sequencing (DNBseq), which produces 150 bp read lengths, and Illumina sequencing, which produces 100 bp read lengths. For samples sequenced using Illumina sequencing, samples were pooled in groups of 5-7 and applied to a single lane of an Illumina HiSeq 2500/4000 instrument.

tag: strain

tag: organ

value: repro

tag: Sex

value: Male


title: Mouse IgG Input control in sgControl

value: derived from Kras G12D Trp 53 -/- tumors


title: F_P7_hyperoxia_CD45_1_DC28_C22

tag: timepoint


title: 5FU_6_2


title: 5FU_6_1


title: 974_lung

source_name: lung

value: lung


title: F_P7_hyperoxia_CD45_1_DC28_O15

tag: sequencing run

value: Mac V


title: Mga IP in sgControl


title: Airway epithelial cells (basal cells) - RNAseq [9145_49d8-2A]

value: Female

tag: atopy

tag: asthma

value: No

tag: steroids

value: Nasal

tag: smoking

tag: crs

tag: tech


title: 974_liver

source_name: liver

value: liver

tag: age


title: F_P7_hyperoxia_CD45_1_DC28_G16

tag: gender

tag: plate

tag: treatment

tag: cell type

value: Mac III

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_J23

value: F

tag: well

tag: cell subtype

value: mast cell

tag: mousename

tag: coverage


title: F_P7_hyperoxia_CD45_1_DC28_K18

tag: sequencing run

tag: timepoint

value: hyperoxia

value: immune


title: 974_brain

source_name: brain

tag: strain

tag: organ

value: brain

tag: Sex


title: 968_repro


title: E2f6 IP in sgControl


title: sgL3mbtl2 + sgPcgf6 3

source_name: mouse lung cancer cell line

value: mouse non small cell lung cancer cell

tag: viral vector used

value: lentiCRISPRv2Puro sgL3mbtl2 + LentiCRISPRv2Puro sgPcgf6


title: Airway epithelial cells (basal cells) - RNAseq [7240_43f5-1A]

value: RV

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Prior

tag: crs

value: Control

tag: tech

value: CB

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [7240_43f5-2A]

tag: treatment

value: vehicle

tag: gender

value: Male

tag: age


title: 968_lung

value: lung


title: F_P7_hyperoxia_CD45_1_DC28_P2

tag: sequencing run

tag: plate

tag: well

tag: cell type

tag: cell subtype

value: T cell

tag: mousename

tag: coverage

tag: number of genes


title: sgL3mbtl2 + sgPcgf6 2

tag: viral vector used


title: Airway epithelial cells (basal cells) - RNAseq [acb0_4eb2-2A]

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Never

value: CRS


title: 968_liver

tag: strain

tag: organ

value: liver

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [3f1a_423c-1A]

tag: treatment

tag: gender

value: Female

value: No

tag: crs

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: sgL3mbtl2 + sgPcgf6 1

tag: cell type

value: mouse non small cell lung cancer cell


title: L3mbtl2 IP in sgControl

value: derived from Kras G12D Trp 53 -/- tumors


title: F_P7_hyperoxia_CD45_1_DC28_P17

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [9145_49d8-1A]

value: RV

tag: atopy

tag: asthma

tag: steroids

value: Nasal

value: yes

tag: smoking

value: Control


title: F_P7_hyperoxia_CD45_1_DC28_D18

tag: gender

tag: treatment

value: DC II


title: 968_brain

tag: strain

tag: organ

value: brain

tag: age

tag: Sex

value: Male


title: Airway epithelial cells (basal cells) - RNAseq [acb0_4eb2-1A]

value: Yes

value: Never

tag: crs

value: CRS

tag: tech

value: CB

tag: rin

tag: surgeon


title: 967_repro

value: repro


title: sgPcgf6 3 [RNA-Seq]

tag: cell type

value: mouse non small cell lung cancer cell

tag: viral vector used

value: lentiCRISPRv2Puro sgPcgf6


title: F_P7_hyperoxia_CD45_1_DC28_H6

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: sgPcgf6 2 [RNA-Seq]


title: F_P7_hyperoxia_CD45_1_DC28_G3

tag: gender

tag: treatment

value: immune

value: Mac III


title: F_P7_hyperoxia_CD45_1_DC28_N8


title: Airway epithelial cells (basal cells) - RNAseq [1b8e_429b-2A]

value: vehicle

tag: atopy

tag: asthma

tag: steroids

tag: smoking

tag: age


title: sgL3mbtl2 3 [RNA-Seq]

tag: cell type

value: lentiCRISPRv2Puro sgL3mbtl2


title: Airway epithelial cells (basal cells) - RNAseq [89cb_44b7-1A]

value: RV

value: No

value: Prior

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: surgeon


title: sgPcgf6 1 [RNA-Seq]

tag: viral vector used


title: F_P7_hyperoxia_CD45_1_DC28_L6

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: basophil


title: F_P7_hyperoxia_CD45_1_DC28_D10

tag: gender

tag: treatment

tag: mousename

tag: coverage

tag: number of genes


title: 967_liver

tag: strain

tag: organ

value: liver

tag: age

tag: Sex

value: Male


title: F_P7_hyperoxia_CD45_1_DC28_E14

tag: cell type


title: Airway epithelial cells (basal cells) - RNAseq [1b8e_429b-1A]

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

tag: tech

value: CB

tag: rin

tag: surgeon


title: 967_brain

value: brain


title: sgL3mbtl2 1 [RNA-Seq]

value: mouse non small cell lung cancer cell

tag: viral vector used


title: F_P7_hyperoxia_CD45_1_DC28_B15

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

tag: cell subtype

value: Mac II

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [fcc4_4f9f-2A]

value: vehicle

tag: atopy

value: CRS

tag: age


title: Airway epithelial cells (basal cells) - RNAseq [89cb_44b7-2A]

value: No

tag: asthma

tag: steroids

value: Prior


title: Airway epithelial cells (basal cells) - RNAseq [fcc4_4f9f-1A]

value: RV

tag: smoking

tag: crs

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_F22

tag: cell type

value: basophil

tag: coverage

tag: number of genes


title: rCMT3 mRNA-seq bent cotyledon (Line #3; biorep #2)

description:
Sample 34
Single-end 50 base read mRNA-seq data from second biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #3) from two NGS lanes (i.e. technical replicates).
rCMT3_L3_Bentcotyledon_BioRep_R2.genes.results

tag: accession

value: rCMT3 (cmt3-11)

tag: genotype

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #3)

tag: tissue

value: Bent cotyledon embryos


title: rCMT3 mRNA-seq bent cotyledon (Line #3; biorep #3)

description:
Sample 35
Single-end 50 base read mRNA-seq data from second biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #3) from two NGS lanes (i.e. technical replicates).
rCMT3_L3_Bentcotyledon_BioRep_R3.genes.results


title: sgMga3 [RNA-Seq]

tag: viral vector used

value: lentiCRISPRv2Puro sgMga


title: rCMT3 mRNA-seq bent cotyledon (Line #3; biorep #1)

description:
Sample 33
Single-end 50 base read mRNA-seq data from first biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #3) from two NGS lanes (i.e. technical replicates).
rCMT3_L3_Bentcotyledon_BioRep_R1.genes.results


title: 967_lung

tag: strain

tag: organ

value: lung

tag: Sex

value: Male


title: Airway epithelial cells (basal cells) - RNAseq [d89d_472e-1A]

tag: treatment

tag: gender

value: Yes

value: yes

value: Current

tag: tech

value: CB

tag: rin

tag: surgeon


title: rCMT3 mRNA-seq bent cotyledon (Line #1; biorep #3)

description:
Sample 32
Single-end 50 base read mRNA-seq data from second biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #1) from two NGS lanes (i.e. technical replicates).
rCMT3_L1_Bentcotyledon_BioRep_R3.genes.results

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #1)


title: sgMga2 [RNA-Seq]

value: mouse non small cell lung cancer cell


title: sgMga1 [RNA-Seq]


title: Airway epithelial cells (basal cells) - RNAseq [9bfe_41f4-2A]

value: vehicle

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

value: CRS

tag: age


title: sgL3mbtl2 2 [RNA-Seq]

tag: cell type

value: lentiCRISPRv2Puro sgL3mbtl2


title: rCMT3 mRNA-seq bent cotyledon (Line #1; biorep #2)

description:
Sample 31
Single-end 50 base read mRNA-seq data from second biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #1) from two NGS lanes (i.e. technical replicates).
rCMT3_L1_Bentcotyledon_BioRep_R2.genes.results

tag: accession

tag: genotype


title: Airway epithelial cells (basal cells) - RNAseq [9bfe_41f4-1A]

value: RV

tag: crs

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_A1

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: mast cell

tag: mousename

tag: coverage

tag: number of genes


title: rCMT3 mRNA-seq bent cotyledon (Line #1; biorep #1)

description:
Sample 30
Single-end 50 base read mRNA-seq data from first biological replicate of bent cotyledon embryos with miR823 non-cleavable version of CMT3 transgene (line #1) from two NGS lanes (i.e. technical replicates).
rCMT3_L1_Bentcotyledon_BioRep_R1.genes.results

value: rCMT3 (cmt3-11)

tag: tissue

value: Bent cotyledon embryos


title: Empty2 [RNA-Seq]

tag: viral vector used

value: lentiCRISPRv2Puro empty


title: F_P7_hyperoxia_CD45_1_DC28_B17

tag: gender

tag: treatment

value: Mac V


title: Col-0 mRNA-seq bent cotyledon (biorep #2)

description:
Sample 28
Single-end 50 base read mRNA-seq data from second biological replicate of bent cotyledon Col-0 embryos from two NGS lanes (i.e. technical replicates).
WT_Bentcotyledon_BioRep_R2.genes.results

value: wild type


title: Airway epithelial cells (basal cells) - RNAseq [d89d_472e-2A]

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: yes

tag: smoking

value: Current

tag: tech

value: CB

tag: rin

tag: age

tag: surgeon


title: Empty1 [RNA-Seq]

tag: cell type

value: mouse non small cell lung cancer cell


title: F_P7_hyperoxia_CD45_1_DC28_L9

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: Mac III


title: F_P7_hyperoxia_CD45_1_DC28_L11

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_A5

tag: gender

tag: treatment

value: neutrophil


title: chrRNA_m6A_IP_Control

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

description:
Chromatin associated RNA
No heat shock
chrRNA_m6A_Conrol.xlsx

data_processing:
The adaptor and low quality bases of all sequencing data were removed by Cutadapt.
For all RNA-seq data, the adaptor CTGTAGGCACCATCAAT was used. The first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428. For m6A-seq, the adaptor was set as AAAAAAAAAA. The trimmed reads were aligned to mouse transcriptome, using STAR with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: For RNA-seq data, the processed data files are tab separated RPKM values. The first column is gene name, and the second column is RPKM value. For m6A-seq data,  the processed data files are predicted m6A sites. The first column is gene name, the second column is the position of m6A, the third column is the estimated m6A peak density, and the fourth column is m6A motif.

source_name: chrRNA m6A IP Control

growth_protocol: Mouse embryonic fibroblast cells were passaged every 2d in medium DMEM plus 10% FBS.

extract_protocol:
MEF cells were fractionated into cytoplasmic and chromatin fractions. Briefly, cells were collected, washed and collected. 200 μL ice cold cytoplasmic lysis buffer (10 mM Tris-HCl pH 7.5, 0.15% NP-40, 150 mM NaCl, 25 mM a-amanitin, 10 U SUPERase. In and protease inhibitor mix) were added to the cell pellet and incubated on ice for 5 min, then gently pipetted up the cell lysate over 2.5 volumes of chilled sucrose buffer (25% sucrose in lysis buffer) and centrifuged at 4 °C with 16,000 g for 10 min. The supernatant was collected as cytoplasmic fraction. Gently added 800 μL ice cold nuclei wash buffer (0.1% Triton X-100, 1 mM EDTA, in PBS, 25 mM a-amanitin, 10 U SUPERase. In and protease inhibitor mix) to the  nuclei pellet and centrifuged at 4 °C with 1,150 g for 2 min. The supernatant was removed completely. The remaining nuclei pellet was resuspended in 200 μL ice cold glycerol buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 50% glycerol,10 U SUPERase. In and protease inhibitor mix) by pipetting up and down, then equal volume of ice cold nuclei lysis buffer (1% NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1M Urea, 0.2 mM EDTA, 1 mM DTT, 25 mM a-amanitin, 10 U SUPERase. In and protease inhibitor mix) was added and mixed by pulse vortexing. After 2 min incubation on ice, the lysis was centrifuged at 4 °C with 18,500 g for 2 min. The supernatant was collected as soluble nuclear fraction/nucleoplasm. Pellet was treated as chromotin-associated fraction. The relavant RNA were extracted by Trizo LS or Trizol.
RNA was dephosphorylation for 1 h at 37 °C in a 15 μL reaction (1 × T4 polynucleotide kinase buffer, 10 U SUPERase In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40–60 nt (were excised. RNA fragments were dissolved by soaking overnight in 400 μL RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U mL−1 SUPERase In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were resuspended in nuclease-free water. Next, 0.15 μg linker (rApp/NNNNCTGTAGGCACCATCAAT/3ddC) was added to the RNA fragments, heated at 70 °C for 90 s and then cooled to room temperature, followed by ligation for 3 h at 22 °C in a 20 μL reaction (T4 RNL2 reaction buffer, 10 U SUPERase In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel. Regions in the gel corresponding to 65-85 nt were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, ethanol purified RNA fragments were re-suspended in nuclease-free water.    For reverse transcription, the following oligos containing barcodes were used (Phos represents phosphorylation, NNN represents random sequence, SpC18 represents Hexa-ethyleneglycol spacer):    (Phos)CTANNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT AGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTT CCGATCTATTGATGGTGCCTACAG    (Phos)AGCNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT AGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTT CCGATCTATTGATGGTGCCTACAG    (Phos)ATTNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT    AGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTT CCGATCTATTGATGGTGCCTACAG    (Phos)CCGNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT AGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTT CCGATCTATTGATGGTGCCTACAG    The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized RT primer (and incubated at 75 °C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris-HCl pH 8.4, 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by using DNA gel elution buffer (300 mM NaCl, 1mM EDTA). First-strand cDNA was circularized in 20 μL of reaction containing 1 × CircLigase buffer, 2.5mM MnCl2, 1 M Betaine and 100 U CircLigase II (Epicenter). Circularization was performed at 60 °C for 1 h, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol.

treatment_protocol: The heat stressed cells (HS) were subject to heat shock (42ºC) for 1 h and recovery at 37ºC for 3 h

value: Mouse embryonic fibroblasts

tag: genotype

tag: strain

tag: antibody

value: m6A (Millipore, ABE572 and Synaptic Systems, 202 003)


title: Airway epithelial cells (basal cells) - RNAseq [71cb_4385-1A]

value: RV

value: Female

tag: atopy

value: No

tag: asthma

tag: steroids

value: Inhaled

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

value: RN

tag: rin


title: Airway epithelial cells (basal cells) - RNAseq [ac28_4568-2A]

value: vehicle

value: Never

value: Control

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [71cb_4385-2A]

value: yes


title: Airway epithelial cells (basal cells) - RNAseq [a7dc_4ab3-1A]

value: Nasal

value: CB


title: F_P7_hyperoxia_CD45_1_DC28_E23

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: mast cell

tag: mousename


title: Empty3 [RNA-Seq]

value: mouse non small cell lung cancer cell

tag: viral vector used

value: lentiCRISPRv2Puro empty


title: Col-0 mRNA-seq bent cotyledon (biorep #1)

description:
Sample 27
Single-end 50 base read mRNA-seq data from first biological replicate of bent cotyledon Col-0 embryos from two NGS lanes (i.e. technical replicates).
WT_Bentcotyledon_BioRep_R1.genes.results

tag: accession

tag: genotype

value: wild type

tag: tissue

value: Bent cotyledon embryos


title: Airway epithelial cells (basal cells) - RNAseq [a7dc_4ab3-2A]

tag: treatment

tag: gender

value: Female

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking


title: F_P7_hyperoxia_CD45_1_DC28_O7

tag: sequencing run

value: DC II

tag: coverage

tag: number of genes


title: chrRNA_Input_PostHS

description:
Chromatin associated RNA
42ºC 1 h,  37ºC 3 h
none

source_name: chrRNA Input PostHS

value: Mouse embryonic fibroblasts

tag: strain

tag: antibody


title: chrRNA_Input_Control

description:
Chromatin associated RNA
No heat shock
none

source_name: chrRNA Input Control

tag: cell type


title: chrRNA_m6A_IP_PostHS

description:
Chromatin associated RNA
42ºC 1 h,  37ºC 3 h
chrRNA_m6A_PostHS.xlsx

source_name: chrRNA m6A IP PostHS

value: m6A (Millipore, ABE572 and Synaptic Systems, 202 003)


title: rCMT3 methylC-seq plants (Line #3; biorep #1)

description:
Sample 25
Single-end 75 base read methylC-seq data from first biological replicate of three-week old plants with miR823 non-cleavable version of CMT3 transgene (line #3).
allC_rCMT3_L3_Seedling.tsv

source_name: Plants three weeks after germination

value: rCMT3 (cmt3-11)

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #3)

value: Seedlings


title: rCMT3 methylC-seq plants (Line #3; biorep #2)

description:
Sample 26
Single-end 75 base read methylC-seq data from second biological replicate of three-week old plants with miR823 non-cleavable version of CMT3 transgene (line #3).
allC_rCMT3_L3_Seedling.tsv


title: Airway epithelial cells (basal cells) - RNAseq [ac28_4568-1A]

description:
gene.counts.txt
gene.counts.normalized.txt

value: RV

value: Yes

value: Never

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_P20

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

tag: cell subtype

value: Mac V

tag: mousename


title: F_P7_hyperoxia_CD45_1_DC28_J12

tag: sequencing run

tag: gender

value: mast cell II


title: rCMT3 methylC-seq plants (Line #1; biorep #4)

description:
Sample 24
Single-end 75 base read methylC-seq data from four biological replicate of three-week old plants with miR823 non-cleavable version of CMT3 transgene (line #1).
allC_rCMT3_L1_Seedling.tsv

tag: accession

tag: genotype

value: cmt3 mutant with miR823 non-cleavable version of CMT3 transgene (line #1)

tag: tissue


title: Col-0 mRNA-seq bent cotyledon (biorep #3)

description:
Sample 29
Single-end 50 base read mRNA-seq data from third biological replicate of bent cotyledon Col-0 embryos from two NGS lanes (i.e. technical replicates).
WT_Bentcotyledon_BioRep_R3.genes.results

value: wild type

value: Bent cotyledon embryos


title: cytRNA_seq_PostHS

description:
Cytoplasmic RNA
42ºC 1 h,  37ºC 3 h
rpkm_cytRNA_seq_PostHS_8427_AAT.txt

source_name: cytRNA seq PostHS

tag: cell type

value: Mouse embryonic fibroblasts

tag: strain

tag: antibody


title: Airway epithelial cells (basal cells) - RNAseq [61eb_4fc3-2A]

source_name: Cultured airway epithelial cells (basal cells)

value: vehicle

value: Male

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: CRS

tag: tech

tag: rin


title: F_P7_hyperoxia_CD45_1_DC28_A2

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

value: Mac III

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_N16

tag: sequencing run

tag: gender

tag: cell type

value: B cell

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [61eb_4fc3-1A]

value: RV

tag: atopy

tag: asthma

value: Never

tag: age

tag: surgeon


title: rCMT3 methylC-seq plants (Line #1; biorep #2)

description:
Sample 22
Single-end 75 base read methylC-seq data from second biological replicate of three-week old plants with miR823 non-cleavable version of CMT3 transgene (line #1).
allC_rCMT3_L1_Seedling.tsv

tag: accession

value: rCMT3 (cmt3-11)

tag: genotype

value: miR823 non-cleavable version of CMT3 transgene in cmt3 mutant background (line #1)

tag: tissue

value: Seedlings


title: Airway epithelial cells (basal cells) - RNAseq [d76f_4712-2A]

value: Yes

tag: steroids

tag: smoking

tag: crs

tag: tech

value: RN

tag: rin


title: rCMT3 methylC-seq plants (Line #1; biorep #1)

description:
Sample 21
Single-end 75 base read methylC-seq data from first biological replicate of three-week old plants with miR823 non-cleavable version of CMT3 transgene (line #1).
allC_rCMT3_L1_Seedling.tsv


title: cCMT3 methylC-seq plants (Line #3; biorep #2)

description:
Sample 20
Single-end 75 base read methylC-seq data from second biological replicate of three-week old plants with miR823 cleavable version of CMT3 transgene (line #3).
allC_gCMT3_L3_Seedling.tsv

value: cCMT3 (cmt3-11)

value: miR823 cleavable version of CMT3 transgene in cmt3 mutant background (line #3)


title: F_P7_hyperoxia_CD45_1_DC28_C8

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

tag: cell subtype

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_H20

tag: sequencing run

tag: gender

tag: cell type

tag: mousename


title: F_P7_hyperoxia_CD45_1_DC28_H2


title: F_P7_hyperoxia_CD45_1_DC28_D14

value: DC III


title: PND16 Small- Rep3

city: Chicago,

first: Francesca

middle: E.

last: Duncan

address: 303 E. Superior Street, Lurie 10-109

department: Department of Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC. Reads were aligned to the Mus musculus genome build mm10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC. DEseq was also used to calculate fold changes and p-values. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library. Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER. Several database sources were referenced for enrichment analysis, including Interpro, NCBI, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment. Additional gene enrichment is available from the following partner institutions: Advaita (http://www.advaitabio.com/ipathwayguide).
Genome_build: mm10
Supplementary_files_format_and_content: Oocytes_normalizedCountsWithAnnotations.txt
Supplementary_files_format_and_content: Oocytes_rawCountsWithAnnotations.txt

source_name: Ovary

extract_protocol:
RNA was isolated using RNeasy Plus mini kit (Qiagen, Germany, 74134)
cDNA synthesis was performed using NEB Next Ultra II directional RNA library prep kit (New England Biolabs, Ipswich, MA, E7760S) after rRNA depletion (NEB Next rRNA depletion kit, E6310S).

tag: age

value: postnatal day; PND 16

tag: strain

tag: cohort

value: PND16 Small


title: cCMT3 methylC-seq plants (Line #1; biorep #2)

description:
Sample 18
Single-end 75 base read methylC-seq data from second biological replicate of three-week old plants with miR823 cleavable version of CMT3 transgene (line #1).
allC_gCMT3_L1_Seedling.tsv

tag: accession

tag: genotype

value: miR823 cleavable version of CMT3 transgene in cmt3 mutant background (line #1)

tag: tissue


title: Airway epithelial cells (basal cells) - RNAseq [7fee_4d30-1A]

value: Male

tag: atopy

tag: asthma

tag: steroids

value: yes

tag: smoking

tag: crs

value: CRS

tag: tech

value: CB

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [7fee_4d30-2A]

tag: treatment

value: vehicle

tag: gender

value: Never


title: chrRNA_seq_Control

description:
Chromatin associated RNA
No heat shock
rpkm_chrRNA_Control_8427_CGG.txt

source_name: chrRNA seq Control

tag: cell type

value: Mouse embryonic fibroblasts

tag: antibody


title: PND16 Small- Rep2

tag: age

tag: strain


title: chrRNA_seq_PostHS

description:
Chromatin associated RNA
42ºC 1 h,  37ºC 3 h
rpkm_chrRNA_PostHS_8427_TAG.txt

source_name: chrRNA seq PostHS


title: cCMT3 methylC-seq plants (Line #3; biorep #1)

description:
Sample 19
Single-end 75 base read methylC-seq data from first biological replicate of three-week old plants with miR823 cleavable version of CMT3 transgene (line #3).
allC_gCMT3_L3_Seedling.tsv

tag: accession

value: Seedlings


title: PND16 Small- Rep1

tag: cohort


title: F_P7_hyperoxia_CD45_1_DC28_H18

first: Fabio

last: Zanini

address: High and Botany St

institute: University of New South Wales

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: cCMT3 methylC-seq plants (Line #1; biorep #1)

description:
Sample 17
Single-end 75 base read methylC-seq data from first biological replicate of three-week old plants with miR823 cleavable version of CMT3 transgene (line #1).
allC_gCMT3_L1_Seedling.tsv

value: cCMT3 (cmt3-11)

tag: genotype

tag: tissue


title: rCMT3 methylC-seq plants (Line #1; biorep #3)

description:
Sample 23
Single-end 75 base read methylC-seq data from third biological replicate of three-week old plants with miR823 non-cleavable version of CMT3 transgene (line #1).
allC_rCMT3_L1_Seedling.tsv

value: rCMT3 (cmt3-11)

value: cmt3 mutant with miR823 non-cleavable version of CMT3 transgene (line #1)


title: Col-0 methylC-seq plants (biorep #2)

description:
Sample 16
Single-end 75 base read methylC-seq data from second biological replicate of Col-0 three-week old plants.
allC_WT_Seedling.tsv

value: wild type


title: PND40- Rep3

value: postnatal day; PND 40


title: Airway epithelial cells (basal cells) - RNAseq [bbd0_41ec-2A]

tag: treatment

tag: gender

tag: atopy

value: No

tag: asthma

tag: steroids

value: Nasal

tag: smoking

tag: crs

tag: tech

value: RN

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [bbd0_41ec-1A]

value: RV

value: Male

tag: age


title: F_P7_hyperoxia_CD45_1_DC28_N5

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype


title: cytRNA_seq_Control

description:
Cytoplasmic RNA
No heat shock
rpkm_cytRNA_seq_Control_8427_GCT.txt

source_name: cytRNA seq Control

tag: genotype

tag: strain

tag: antibody


title: F_P7_hyperoxia_CD45_1_DC28_I11

source_name: distal lung

tag: gender

tag: treatment

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: PND40- Rep2

tag: cohort


title: Airway epithelial cells (basal cells) - RNAseq [4cb0_4702-2A]

value: vehicle

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Prior

tag: crs

value: Control

tag: tech

value: CB

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [d76f_4712-1A]

value: Never

value: CRS

tag: age


title: Col-0 methylC-seq plants (biorep #1)

description:
Sample 15
Single-end 75 base read methylC-seq data from first biological replicate of Col-0 three-week old plants.
allC_WT_Seedling.tsv

tag: accession

tag: genotype

value: wild type

tag: tissue

value: Seedlings


title: PND40- Rep1

value: postnatal day; PND 40

tag: strain


title: F_P7_hyperoxia_CD45_1_DC28_N9

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [4cb0_4702-1A]

value: RV

tag: atopy

tag: asthma

value: No

tag: steroids

tag: smoking

tag: crs

tag: tech


title: PND16 Large- Rep3

tag: age

value: postnatal day; PND 16

tag: cohort

value: PND16 Large


title: mir823-2 methylC-seq bent cotyledon (biorep #1)

description:
Sample 13
Single-end 75 base read methylC-seq data from first biological replicate of bent cotyledon mir823-2 embryos.
allC_miR823_L2_BentCotyledon2020.tsv

source_name: Bent cotyledon embryos (8 days after pollination)

tag: accession

tag: genotype

value: mir823-2 mutant

tag: tissue

value: Bent cotyledon embryos


title: F_P7_hyperoxia_CD45_1_DC28_O16

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

value: hyperoxia

value: immune

value: T cell

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [d2bb_43a4-2B]

description:
gene.counts.txt
gene.counts.normalized.txt

tag: treatment

value: vehicle

value: Female

tag: atopy

value: Nasal

value: yes

value: Prior

value: RN

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [bd64_4344-2A]

value: Male

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: CRS

value: CB


title: F_P7_hyperoxia_CD45_1_DC28_D23

tag: timepoint

tag: cell type

tag: cell subtype

value: DC II

tag: mousename


title: mir823-2 methylC-seq bent cotyledon (biorep #2)

description:
Sample 14
Single-end 75 base read methylC-seq data from second biological replicate of bent cotyledon mir823-2 embryos.
allC_miR823_L2_BentCotyledon2020.tsv

tag: accession

tag: genotype

tag: tissue


title: Airway epithelial cells (basal cells) - RNAseq [d2bb_43a4-1B]

value: RV

tag: gender

value: No

tag: tech

tag: age


title: PND16 Large- Rep2

value: postnatal day; PND 16

tag: strain

tag: cohort

value: PND16 Large


title: mir823-1 methylC-seq bent cotyledon (biorep #2)

description:
Sample 12
Single-end 75 base read methylC-seq data from second biological replicate of bent cotyledon mir823-1 embryos.
allC_miR823_L1_BentCotyledon2020.tsv

value: mir823-1 mutant

value: Bent cotyledon embryos


title: F_P7_hyperoxia_CD45_1_DC28_N10

tag: sequencing run

value: F

tag: plate

tag: well

tag: treatment

value: hyperoxia

value: immune

value: Mac V

tag: coverage

tag: number of genes


title: mir823-1 methylC-seq bent cotyledon (biorep #1)

description:
Sample 11
Single-end 75 base read methylC-seq data from first biological replicate of bent cotyledon mir823-1 embryos.
allC_miR823_L1_BentCotyledon2020.tsv


title: PND13- Rep2

value: postnatal day; PND 13


title: F_P7_hyperoxia_CD45_1_DC28_O3

tag: timepoint

tag: cell type

value: mast cell II


title: Airway epithelial cells (basal cells) - RNAseq [bd64_4344-1A]

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Prior

tag: crs

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [4d6c_4f66-2B]

value: vehicle

tag: gender

value: Female

value: Yes

value: Current

value: Control

tag: tech

value: RN

tag: age


title: PND13- Rep3

tag: strain

tag: cohort


title: F_P7_hyperoxia_CD45_1_DC28_E1

tag: sequencing run

tag: plate

tag: well

tag: treatment

tag: cell subtype

value: Mac III

tag: mousename


title: F_P7_hyperoxia_CD45_1_DC28_B2

tag: timepoint

tag: cell type

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [4d6c_4f66-1B]

value: RV

tag: atopy

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: rin