title: SVF, KO, H3K9bhb, ChIP_1

description: Library name: p21iWAT_SVF_KO_H3K9bhb_1_ChIPseq


title: SVF, 1,3BD, input_2

status: Public on Jul 22 2025

type: SRA

city: Taipei

first: Chung-Lin

last: Jiang

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

library_source: genomic

data_processing:
All ChIP-seq FASTQ reads were trimmed for the adapter and low-quality bases using Trim-galore tools (v0.6.7), then followed by alignment to mouse GRCm38/mm10 genome using Bowtie2 aligner (v2.4.2) with the default setting. BAM files were sorted and deduplicated by SAMTools (v1.13). Significant H3K9ac, H3K14ac, and H3K9bhb peaks were generated using MACS2 (v2.2.9.1) peak caller with a cutoff value: -p-value < 0.05. MACS2-identified peaks were subjected to BEDtools (v2.3.0) to determine overlapping regions of two interested data and Annotation analysis provided by HomerTools (v4.1) to evaluate ChIP enrichment on genomic features. Bigwig files were generated by DeepTools (v3.3.1) bamcoverage, and these were visualized in Integrative Genomics Viewer (IGV, v2.17). The differential coverages were normalized to input coverage by subtraction, and the comparison between treatment and control coverage was conducted by log2 foldchange using DeepTools bamCompare with the following parameters: –operation subtract, –centerReads, –normalizeUsing CPM, –scaleFactorsMethod None. Both ChIP-seq and differential coverages were subjected to DeepTools computeMatrix and plotHeatmap for generating heatmap.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: inguinal white adipose tissue

extract_protocol:
Cross-linked with 1% formaldehyde for 5 min at 37°C, and quenched with 125 mM glycine for 5 min at 37°C. After cell lysis, chromatin was sonicated using a Bioruptor (1.5 mL tube).
Sequencing libraries were constructed using a NEBNext Ultra II DNA Library Prep kit (New England Biolabs, MA, USA).

tag: tissue

value: inguinal white adipose tissue

tag: cell type

value: stromal vascular fraction

tag: genotype

value: wild type

tag: treatment

tag: chip antibody


title: 6264496006_R06C01 whole blood

type: genomic

city: Boston

first: Benjamin

middle: A

last: Raby

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

description: Sample collected in EDTA tube, DNA for methylation was extracted

hyb_protocol: Using standard Illumina Infinium Human Methylation 450K BeadChip array hyb protocol.

scan_protocol: Using standard Illumina Infinium Human Methylation 450K BeadChip array scan protocol.

data_processing: Normalization was performed using the within-array combination of Noob (Triche et al. 2013) in R package “minfi” and BMIQ (Teschendorff et al. 2013) in R package “wateRmelon”. The minfi package was used to identify and remove 25,165 probes with SNPs. Sex was imputed by DNA methylation and 23 samples were removed due to mismatch between reported and genetic imputed sex. ComBat (Johnson, 2017) from the sva R package (Leek, 2023) was used for batch effect correction, transforming to m-values, then back transforming to beta-values.

label: Cy3, Cy5

organism: Homo sapiens

source_name: WhiteBloodCells from Purple Top EDTA tubes

label_protocol: Cy3, Cy5

extract_protocol: PureGene Blood Kit (Qiagen, Germantown, Maryland), AllPrep DNA Mini Kit (Qiagen)

tag: sample id

tag: subject id

tag: Sex

value: F

tag: age

tag: asthma

value: Y


title: D13_Untransduced_DN4

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

library_source: transcriptomic

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p13 (Gencode release 35) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Assembly: GRCh38.p13 (Gencode release 35)
Supplementary files format and content: tab-delimited text files with DESeq2 VST log2 values for each Sample

molecule: total RNA

source_name: Peripheral blood

extract_protocol:
Cells were counted and lysed with 800 µl to 1 ml TRIzol (15596026, ambion) reagent, incubated for 10 minutes at RT and stored at -80 °C. Chloroform (C2432-26ML, Honeywell) was added at 160 µl or 200 µl respectively, to defrosted samples followed by vigorous shake for 15 seconds and 3 minutes at RT incubation. A centrifugation step at 11,000 rpm for 15 minutes at 4 °C was followed by collection of the aqueous phase. 400 µl isopropanol and 10 µl glycogen (AM9510, Invitrogen) were added and the mixture was incubated for 10 minutes at RT. Samples were centrifuged at 11,000 rpm for 10 minutes at 4 °C and the pellet was washed three times with 75% ethanol followed by a centrifugation step at 9,000 rpm for 5 minutes at 4 °C. RNA pellets were air dried for 10 minutes and dissolved in 30 µl RNase free water. RNA was incubated at 55 °C for 10 minutes, treated with DNases for genomic DNA removal (AM1906, Invitrogen) and stored at -20 °C.
Sequencing libraries and sequencing were carried out by Novogene.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Lymphoprep density gradient, 2000 rpm centrifugation for 20 minutes at room temperature (RT). PBMCs were washed with phosphate saline buffer (PBS), counted, and labelled appropriately, based on a human memory B cells isolation kit (130-093-546, Miltenyi Biotec), with B cell biotin antibody cocktail for 20 minutes at 4 °C. Magnetic isolation of total B cells was performed upon incubation for 20 minutes at 4 °C with anti-biotin beads. Following the previously established in vitro plasma cell differentiation method, memory B cells were isolated following magnetic labeling with anti-CD23 beads (130-094-510, Miltenyi Biotec) and co-cultured in a 24 well-plate format at 2x10^5 cells/ml with 2x10^4 cells/ml CD40L-L stromal cells in IMDM CM containing IL-2 (40 U/ml), IL-21 (100 ng/ml) and F(ab’)2 fragments goat anti-human IgG, IgM and IgA (20 µg/ml) (109-006-064, Jackson Immunoresearch). At day 3 of B cell differentiation in vitro, activated B cells were seeded without CD40L-L stromal cells in a new 24 well-plate at 0.33x10^5 cells/ml for the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 conditions and at 1x10^5 cells/ml for the rest of the conditions, in IMDM CM containing IL-2 (20 U/ml), IL-21 (50 ng/ml) and supplements (lipid mixture 1; chemically defined (200X) and MEM amino acids solution (50X)). At day 6, the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 cells were re-seeded at 0.66x10^5 cells/ml, and the rest of the conditions at 2x10^6 cells/ml in IMDM CM containing APRIL (100 ng/ml), IL-21 (10 ng/ml), IL-6 (10 ng/ml) and supplements at 1 ml final volume per well. At day 9, the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 cells were splitted following a 1:2 ratio, and appropriate volume of the day 6 complete medium was added to all the conditions aiming at a final volume of 2 ml per well. At day 13 onwards, the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 cells were re-seeded at 0.33x10^5 cells/ml, and the rest of the conditions at 1x10^6 cells/ml in IMDM CM containing APRIL (100 ng/ml), IL-6 (10 ng/ml) and supplements at 2 ml final volume per well.

value: Peripheral blood

value: plasma-cell

tag: time point


title: serum exosomes, PH034, week 0, 0hr

city: Dayton

first: Madhavi

last: Kadakia

state: OH

address: 3640 Colonel Glenn Hwy

department: Biochemistry and Molecular Biology

institute: Wright State University

description:
PH034w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

library_source: other

data_processing:
Data processing performed in Partek Flow v10.0.21.0706
Reads were trimmed to a fixed length based on an average PHRED quality score greater than 20.
Trimmed reads were alighed to miRbase v21/hg38 using Bowtie aligner (seed mismatch =1, seed length = 10) and quantitated using miRBase v21.
Reads were normalized using the Trimmed Mean of M values (TMM) normalization method with an offset of 1.0.
Assembly: miRBase v21 of the hg38 (GRCh38) assembly.
Supplementary files format and content: tab-delimited text files listing raw read counts for each sample
Supplementary files format and content: tab-delimited text files listing TMM-normalized read counts for each sample

molecule: other

source_name: serum exosomes

extract_protocol:
Muscle: Total RNA isolated using mirVana Paris Kit (Fisher); Serum exosomes: Exosomes isolated using Total Exosome Isolation from Serum Kit (Life Tech) and exosomal RNA purified using the Total Exosome RNA and Protein Isolation Kit (Life Tech).  XX RNA was used for construction of sequencing libraries.
cDNA was barcoded with IonExpress RNA-Seq Barcode 1-16 kit (Life Tech). 7.5picomoles each of 8-10 barcoded libraries were pooled and clonally amplified onto IonSphere Particles and enriched using the OneTouch2 (Life Tech).

treatment_protocol: All participants completed 12 weeks of either TRAD or HITT exercise followed by a 4 week detraining period.

value: serum exosomes

tag: participant id

value: HITT

tag: week

value: week 0

tag: time

value: Female


title: SVF, 1,3BD, input_1


title: D13_Untransduced_DN3


title: 6264496006_R05C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: SVF, 1,3BD, H3K9bhb, ChIP_2


title: SVF, KO, Input, ChIP_1

description: Library name: p21iWAT_SVF_KO_input_1_ChIPseq

extract_protocol:
Cross-linked with 1% formaldehyde for 5 min at 37°C, and quenched with 125 mM glycine for 5 min at 37°C.  After cell lysis, chromatin was sonicated using a Bioruptor (1.5 mL tube)
Sequencing libraries were constructed using a NEBNext Ultra II DNA Library Prep kit (New England Biolabs, MA, USA).


title: serum exosomes, PH031, week 16, rest

description:
PH031w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 16

value: rest

value: Male


title: 6264496006_R05C01 whole blood


title: D13_Untransduced_DN1


title: 6264496006_R04C02 whole blood


title: serum exosomes, PH031, week 12, 3hr

description:
PH031w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: SVF, 1,3BD, H3K14ac, ChIP_2

value: inguinal white adipose tissue

value: stromal vascular fraction

value: H3k14ac (abcam, #abab52946)


title: 6264496006_R04C01 whole blood

value: F

value: Y


title: D13_T58I-t2A-BCL2_DN4

value: Peripheral blood

value: plasma-cell


title: serum exosomes, PH031, week 12, 24hr

description:
PH031w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: D13_T58I-t2A-BCL2_DN3


title: SVF, 1,3BD, H3K9bhb, ChIP_1

value: wild type


title: SVF, 1,3BD, H3K14ac, ChIP_1


title: 6264496006_R03C02 whole blood


title: serum exosomes, PH031, week 12, 0hr

description:
PH031w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D13_T58I-t2A-BCL2_DN1


title: 6264496006_R03C01 whole blood

value: N


title: SVF, 1,3BD, H3K9ac, ChIP_2

value: H3k9ac (abcam, #ab4441)


title: serum exosomes, PH031, week 0, pre

description:
PH031w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: pre


title: serum exosomes, PH031, week 0, 3hr

description:
PH031w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: 6264496006_R01C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: D13_MSCV-backbone_DN4


title: serum exosomes, PH031, week 12, pre

description:
PH031w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: Male


title: SVF, Water, input_2

value: inguinal white adipose tissue

value: stromal vascular fraction

value: Water


title: 6264496006_R01C01 whole blood

value: F

value: Y


title: SVF, Water, input_1


title: serum exosomes, PH031, week 0, 24hr

description:
PH031w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH031, week 0, 0hr

description:
PH031w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D6_Untransduced_DN4

value: Peripheral blood

value: plasmablast


title: 6264488133_R06C01 whole blood


title: D13_T58I-t2A-BCL2_DN2

value: plasma-cell


title: SVF, Water, H3K9bhb, ChIP_2

value: wild type


title: D13_MYC.delMB0-BCL2_DN3


title: 6264488133_R05C02 whole blood

value: N


title: serum exosomes, PH025, week 16, rest

description:
PH025w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 16

value: rest

value: Female


title: D6_Untransduced_DN1


title: D6_T58I-t2A-BCL2_DN4


title: SVF, Water, H3K9bhb, ChIP_1


title: 6264488133_R05C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: SVF, 1,3BD, H3K9ac, ChIP_1

value: H3k9ac (abcam, #ab4441)


title: serum exosomes, PH025, week 12, pre

description:
PH025w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 12

value: pre


title: SVF, Water, H3K14ac, ChIP_2

value: inguinal white adipose tissue

value: stromal vascular fraction

value: Water

value: H3k14ac (abcam, #abab52946)


title: D6_T58I-t2A-BCL2_DN2

value: Peripheral blood

value: plasmablast


title: 6264488133_R04C02 whole blood

value: F

value: N


title: D6_T58I-t2A-BCL2_DN1


title: serum exosomes, PH025, week 12, 3hr

description:
PH025w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: SVF, Water, H3K14ac, ChIP_1

value: wild type


title: serum exosomes, PH025, week 12, 24hr

description:
PH025w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: SVF, Water, H3K9ac, ChIP_2


title: D13_MSCV-backbone_DN1

value: plasma-cell


title: D6_MSCV-backbone_DN4


title: 6264488133_R03C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: SVF, Water, H3K9ac, ChIP_1

value: H3k9ac (abcam, #ab4441)


title: serum exosomes, PH025, week 12, 0hr

description:
PH025w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 12


title: D6_MSCV-backbone_DN3


title: 6264488133_R03C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: Y


title: serum exosomes, PH025, week 0, pre

description:
PH025w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: pre


title: D6_MSCV-backbone_DN1


title: 6264488133_R02C02 whole blood


title: 10x HD72 NSC

city: Novato

first: Carlos

last: Galicia Aguirre

address: 8001 Redwood Blvd

institute: Buck Institute

library_source: transcriptomic single cell

data_processing:
Cell ranger was utilized to data processing (cellranger-7.1.0)
Assembly: GRCh38
Supplementary files format and content: csv, raw counts

source_name: iPSC derived Neuronal Stem Cells

extract_protocol:
NSCs and MSNs were cultured in six well plates coated with 50 µg/mL of Matrigel (Corning) overnight. Cells were treated with Accutase (Thermo Fisher, A1110501) for 5 minutes, and the cells were centrifuged and resuspended in DPBS.
Cells were encapsulated, barcoded and transformed into libraries utilizing a Chromium Next GEM Single Cell 3ʹ Kit v3.1.

value: iPSC derived Neuronal Stem Cells


title: 10x C116 NSC


title: D3_Untransduced_DN4

value: Peripheral blood


title: serum exosomes, PH025, week 0, 3hr

description:
PH025w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264488133_R02C01 whole blood


title: D3_Untransduced_DN3

value: plasmablast


title: 10x C116 MSN

source_name: iPSC derived Medium Spiny Neurons

value: iPSC derived Medium Spiny Neurons


title: 6264488133_R01C02 whole blood


title: serum exosomes, PH025, week 0, 0hr

description:
PH025w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264488133_R01C01 whole blood

value: N


title: serum exosomes, PH023, week 16, rest

description:
PH023w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 16

value: rest


title: 6264488133_R04C01 whole blood


title: Bulk HD72 MSN treated with Cerulenin Bio rep 3

data_processing:
Reads were aligned to the GRCh38 primary assembly genome reference utilizing STAR 2.7.10a. Features were counted with the summarizeoverlaps function part of the GenomicAlignments R package
Assembly: GRCh38
Supplementary files format and content: csv, raw counts

extract_protocol: RNA was extracted from MSNs utilizing an RNA extraction kit (Bioline, BIO-52073) for Bulk RNA sequencing.

value: 250nM Cerulenin in DMSO


title: 6264488090_R06C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: serum exosomes, PH023, week 12, pre

description:
PH023w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: Bulk HD72 MSN treated with Cerulenin Bio rep 2


title: D3_T58I-t2A-BCL2_DN3


title: 6264488090_R06C01 whole blood


title: serum exosomes, PH023, week 12, 3hr

description:
PH023w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: Bulk HD72 MSN treated with Cerulenin Bio rep 1


title: D3_T58I-t2A-BCL2_DN1


title: 6264488090_R05C02 whole blood

value: M


title: serum exosomes, PH025, week 0, 24hr

description:
PH025w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH023, week 12, 24hr

description:
PH023w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: Bulk HD72 MSN treated with Cerulenin Vehicle (DMSO) Bio rep 3

value: DMSO


title: 6264488090_R05C01 whole blood


title: 10x HD72 MSN


title: D3_Untransduced_DN1


title: D3_T58I-t2A-BCL2_DN4


title: serum exosomes, PH023, week 0, pre

description:
PH023w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: pre


title: Bulk HD72 MSN treated with Cerulenin Vehicle (DMSO) Bio rep 1


title: serum exosomes, PH023, week 12, 0hr

description:
PH023w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D3_MSCV-backbone_DN1

value: Peripheral blood


title: 6264488090_R04C02 whole blood


title: D3_MSCV-backbone_DN3

value: plasmablast


title: serum exosomes, PH023, week 0, 3hr

description:
PH023w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496019_R04C01 whole blood

value: Y


title: Bulk C116 MSN Bio rep 3

data_processing:
Reads were aligned to the GRCh38 primary assembly genome reference utilizing STAR 2.7.10a. Features were counted with the summarizeoverlaps function part of the GenomicAlignments R package.
Assembly: GRCh38
Supplementary files format and content: csv, raw counts

value: iPSC derived Medium Spiny Neurons


title: Bulk HD72 MSN treated with Cerulenin Vehicle (DMSO) Bio rep 2


title: 6264488090_R03C02 whole blood


title: serum exosomes, PH023, week 0, 24hr

description:
PH023w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: D0_None_DN2

value: B-cell


title: D0_None_DN1


title: serum exosomes, PH023, week 0, 0hr

description:
PH023w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264488090_R03C01 whole blood


title: Bulk C116 MSN Bio rep 1


title: serum exosomes, PH021, week 16, rest

description:
PH021w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: A375_OPN9652_3

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

data_processing:
De-multiplexing and data aggregation was performed using the Braod Picard Pipeline
RNA sequencing fastq files were aligned to the GRCh38 human reference genome using Star aligner (gencode v39)
RSEM was used to quantify gene and transcript level expression
normalized counts data were calculated using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with normalized counts

extract_protocol:
Qiagen RNeasy mini kit
TruSeq RNA Library Prep Kit v2

treatment_protocol: 48 hour treatment of OPN-9652 or OPN-9643

tag: cell line

value: metastatic melanoma

value: Parental


title: 6264488090_R02C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F

value: N


title: D3_MSCV-backbone_DN4


title: A375_OPN9652_2


title: Bulk HD72 MSN Bio rep 3


title: serum exosomes, PH021, week 12, pre

description:
PH021w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 12

value: Female


title: 6264488090_R04C01 whole blood

value: M


title: Bulk HD72 MSN Bio rep 2


title: A375_OPN9652_1


title: 6264488090_R02C01 whole blood


title: serum exosomes, PH021, week 12, 3hr

description:
PH021w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264488090_R01C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: 6264488090_R01C01 whole blood


title: Bulk C116 MSN Bio rep 2


title: serum exosomes, PH021, week 12, 24hr

description:
PH021w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: A375_OPN8643_2


title: serum exosomes, PH021, week 12, 0hr

description:
PH021w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: A375_OPN8643_3


title: Bulk HD72 MSN Bio rep 1


title: A375_OPN8643_1


title: serum exosomes, PH021, week 0, pre

description:
PH021w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: pre


title: A375_DMSO_3

value: DMSO


title: serum exosomes, PH021, week 0, 3hr

description:
PH021w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841150_R06C01 whole blood

value: Y


title: 6057841150_R04C02 whole blood


title: PEO1 rep2

city: Heidelberg

first: Bryce

last: Lim

address: In Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
Library strategy: HiC-Seq
HiCUP v0.7.2 (truncating, mapping, filtering, deduplication)
Translocations called using SeqMonk
Copy number called using HiCnv
Genome_build: hg19
Supplementary_files_format_and_content: translocation events

growth_protocol: RPMI 1640 + 10% FBS + 1% sodium pyruvate

extract_protocol: Dovetail Hi-C library kit

tag: organ

value: Ovary

tag: disease type

value: HGSOC


title: PEO4 rep2


title: PEO23 rep2


title: A375_DMSO_2


title: 6057841150_R03C01 whole blood

tag: tissue


title: A375_DMSO_1

tag: cell type


title: PEO23 rep1


title: 6057841150_R02C02 whole blood


title: 6057841150_R01C02 whole blood


title: 6057841150_R06C02 whole blood


title: PEO14 rep1


title: serum exosomes, PH020, week 16, rest

description:
PH020w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: HITT

value: week 16


title: PEO4 rep1


title: PEO14 rep2


title: 421_OPN9652_3

value: metastatic melanoma

tag: genotype


title: 6057841136_R06C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: serum exosomes, PH020, week 12, 3hr

description:
PH020w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

tag: treatment


title: serum exosomes, PH020, week 12, pre

description:
PH020w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: PEO1 rep1


title: 421_OPN9652_2


title: serum exosomes, PH021, week 0, 0hr

description:
PH021w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 421_OPN9652_1


title: 421_OPN8643_3


title: serum exosomes, PH021, week 0, 24hr

description:
PH021w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH020, week 12, 24hr

description:
PH020w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH020, week 12, 0hr

description:
PH020w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 421_OPN8643_2


title: 6057841136_R05C02 whole blood


title: 421_OPN8643_1


title: serum exosomes, PH020, week 0, pre

description:
PH020w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841136_R05C01 whole blood

value: F


title: 6057841136_R04C02 whole blood


title: 6057841136_R04C01 whole blood


title: serum exosomes, PH020, week 0, 3hr

description:
PH020w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH020, week 0, 24hr

description:
PH020w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 421_DMSO_3


title: 421_DMSO_2


title: 6057841136_R03C02 whole blood


title: 421_DMSO_1


title: serum exosomes, PH020, week 0, 0hr

description:
PH020w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841136_R06C01 whole blood

value: N


title: 6057841136_R03C01 whole blood


title: 218_OPN9652_3


title: strain YJ-09, high SAM level, 36h, rep3

city: Tianjin

first: Xinchen

last: Zhang

address: No. 92 Weijin Street

country: China

institute: Tianjin University

description:
Library name: YJ-09_3
Column name in raw2_fpkm.txt: YJ-06_3

data_processing:
Clean reads were obtained by removing reads which contain adapter, poly-N and low quality reads using fastp software. Meanwhile, the GC content of Q20 and Q30 were calculated.
The obtained clean reads were used for downstream analysis. Reference genome and gene annotation files  (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000146045.2/) were download from the website of National Center for Biotechnology Information. The index of reference genome was built using HISAT v2.0.5 and paired-end clean reads were aligned to this.
FeatureCounts (1.5.0-p3) was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Assembly: Saccharomyces cerevisiae S288C R64
Supplementary files format and content: raw_fpkm.txt include FPKM values for samples YJ-04_1, YJ-04_2, YJ-04_3, YJ-06_1, YJ-06_2, YJ-06_3.
Supplementary files format and content: raw2_fpkm.txt include FPKM values for samples YJ-08_1, YJ-08_2, YJ-08_3, YJ-09_1, YJ-09_2, YJ-09_3.

organism: Saccharomyces cerevisiae

source_name: strain

extract_protocol:
Frozen samples were cryogenically grinded into powder, and total RNA was extracted using the RNAprep Pure Plant Plus Kit (TIANGEN, China). Agilent 2100 bioanalyzer (Agilent Technologies, CA, USA) was used to detect RNA integrity and total amount accurately.
Fast RNA-seq Lib Prep Kit V2 (Cat.No.RK20306) was used to prepare library for transcriptome sequencing. After the library construction, Qubit 2.0 Fluorometer was used for preliminary quantification. The insert size was detected using Agilent 2100 bioanalyzer. Then the effective concentration of the library was quantified using qRT-PCR. The effective concentration of the library need higher than 1.5 nM.

value: strain

value: introduce plasmid pRS416


title: 6057841136_R02C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: strain YJ-09, high SAM level, 36h, rep2

description:
Library name: YJ-09_2
Column name in raw2_fpkm.txt: YJ-06_2


title: serum exosomes, PH017, week 16, rest

description:
PH017w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: rest

value: Female


title: 218_OPN9652_2


title: 6057841136_R02C01 whole blood


title: serum exosomes, PH017, week 12, pre

description:
PH017w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: pre


title: 218_OPN9652_1


title: strain YJ-08, low SAM level, 36h, rep3

description:
Library name: YJ-08_3
Column name in raw2_fpkm.txt: YJ-05_3


title: serum exosomes, PH017, week 12, 3hr

description:
PH017w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: strain YJ-09, high SAM level, 36h, rep1

description:
Library name: YJ-09_1
Column name in raw2_fpkm.txt: YJ-06_1


title: 218_OPN8643_3


title: serum exosomes, PH017, week 12, 24hr

description:
PH017w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841136_R01C02 whole blood


title: 6057841136_R01C01 whole blood

value: Y


title: 218_OPN8643_2


title: strain YJ-08, low SAM level, 36h, rep1

description:
Library name: YJ-08_1
Column name in raw2_fpkm.txt: YJ-05_1


title: 218_OPN8643_1


title: 6057841133_R06C01 whole blood

value: M


title: strain YJ-08, low SAM level, 36h, rep2

description:
Library name: YJ-08_2
Column name in raw2_fpkm.txt: YJ-05_2


title: 6057841133_R05C02 whole blood


title: serum exosomes, PH017, week 12, 0hr

description:
PH017w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH017, week 0, pre

description:
PH017w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: 218_DMSO_3

value: DMSO


title: 218_DMSO_2


title: serum exosomes, PH017, week 0, 3hr

description:
PH017w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: serum exosomes, PH017, week 0, 24hr

description:
PH017w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: HK2_siCLOCK_rep1

type: RNA

first: Yen-Sung

last: Huang

address: Academia Sinica, No.128, Sec2,

department: Institute of Biomedical Sciences

description: Gene expression in CLOCK-depleted cells

hyb_protocol: Total Cy3 labeled cDNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 028004_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HK2, siRNA, 48 h, replicate1

label_protocol: Using Maxima H Minus First Strand cDNA Synthesis Kit System (Thermo Scientific), we labeled 10ug total RNA with Cy3 and purified by purification module in the kit. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000.

growth_protocol: HK2 human proximal tubular cells (ATCC, Manassas, VA, USA) were grown in medium supplied in a Keratinocyte SFM Kit (17005042, Thermo Scientific) supplemented with 10% fetal bovine serum (Thermo Scientific). Cells were cultured in a humidified incubator (37°C with 5% CO2) and were detached with trypsin-EDTA solution (Thermo Scientific).

extract_protocol: Total RNA was extracted by commercial kit (NucleoSpin, Macherey-Nagel®). The concentration of RNA was quantified by Nanodrop 2000 spectrophotometer (Thermo Scientific) and the quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HK2 cells were transfected with 10 nmol/L specific siRNA oligonucleotides against BMAL1 or CLOCK using RNAiMAX  Total RNA was extracted from siCtrl-, siBMAL1-, siCLOCK-cells after 2 days of transfection.  For melatonin treatemtn, HK2 cells were treated with ethanol (EtOH, 10 nM) or melatonin (10 nM) for 18 h then RNA extraction .

tag: genotype/variation

value: CLOCK-depleted


title: HK2_EtOH_rep1

description: Gene expression in EtOH-treated cells

source_name: HK2, EtOH, 18 h, replicate1

value: EtOH-treated


title: 6057841133_R05C01 whole blood

tag: sample id

value: WhiteBloodCells from Purple Top EDTA tubes


title: strain YJ-06, high SAM level, 36h, rep2

description:
Library name: YJ-06_2
Column name in raw_fpkm.txt: YJ-03_2

value: introduce bikaverin biosynthesis module


title: HK2-melatonin_rep1

description: Gene expression in melatonin-treated cells

source_name: HK2, melatonin, 18 h, replicate1

value: melatonin-treated


title: HK2_siCtrl_rep2

description: Gene expression in control cells

source_name: HK2, siRNA, 48 h, replicate2

value: control


title: 6057841133_R04C02 whole blood

tag: subject id


title: serum exosomes, PH017, week 0, 0hr

description:
PH017w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

tag: Sex


title: strain YJ-04, low SAM level, 36h, rep3

description:
Library name: YJ-04_3
Column name in raw_fpkm.txt: YJ-02_3

value: strain


title: 218_DMSO_1

value: metastatic melanoma


title: strain YJ-06, high SAM level, 36h, rep1

description:
Library name: YJ-06_1
Column name in raw_fpkm.txt: YJ-03_1


title: 6057841133_R04C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

tag: age


title: 421_siYAP2_3

treatment_protocol: 72 hour treatment following depletion of YAP1 or TAZ

value: siYAP


title: 6057841133_R03C01 whole blood

tag: asthma


title: strain YJ-04, low SAM level, 36h, rep2

description:
Library name: YJ-04_2
Column name in raw_fpkm.txt: YJ-02_2


title: HK2_siCtrl_rep1

description: Gene expression in control cells


title: HK2_siBMAL1_rep1

description: Gene expression in BMAL1-depleted cells


title: serum exosomes, PH015, week 12, pre

description:
PH015w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: Male


title: serum exosomes, PH015, week 16, rest

description:
PH015w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: 6057841133_R02C02 whole blood

value: M

value: Y


title: strain YJ-04, low SAM level, 36h, rep1

description:
Library name: YJ-04_1
Column name in raw_fpkm.txt: YJ-02_1


title: strain YJ-06, high SAM level, 36h, rep3

description:
Library name: YJ-06_3
Column name in raw_fpkm.txt: YJ-03_3


title: 6057841133_R02C01 whole blood


title: 421_siYAP2_1


title: serum exosomes, PH015, week 12, 24hr

description:
PH015w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 6057841133_R01C02 whole blood

value: F

value: N


title: 421_siYAP1_3


title: 421_siYAP1_2


title: 6057841120_R05C02 whole blood


title: 6057841133_R01C01 whole blood


title: serum exosomes, PH015, week 0, pre

description:
PH015w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 0

value: pre


title: 421_siYAP1_1


title: Yeast, wildtype, 5h40m, rep3

city: Chennai

first: Himanshu

last: Sinha

email: hsinha@gmail.com, sinha@iitm.ac.in

address: Dept of Biotechnology

country: India

institute: IIT Madras

data_processing:
The raw Fastq files were given as input to a customised Snakemake pipeline, which performs quality checks using FASTQC and MutiQC, removes rRNA contamination, performs alignment using STAR, and finally gives the feature counts as output. The feature count file was then provided as input to the IDEP 2.0 software for initial quality checks. The low counts were filtered such that three counts per million (edge R) were in at least three samples
Assembly: S288c reference genome
Supplementary files format and content: Feature count matrix for all samples

extract_protocol:
RNA was extracted from yeast cells using Qiagen RNeasy mini kit (Cat No.74106). The cell pellet was resuspended in buffer RLT and incubated at room temperature for 5 min to achieve complete lysis. The lysate mixed with half volume of absolute alcohol was loaded into RNeasy spin column placed in 2 ml collection tube. The tubes were centrifuge at 8,000 rpm for 1 min, and flow through discarded. On column DNase I (Cat No.79254) treatment and subsequent column washes was performed according to manufacturer’s protocol. RNA was eluted from the column using Nuclease free water.The concentration and purity of RNA quantified using Nanodrop Spectrophotometer (Thermo Scientific; 2000). The integrity of RNA in the samples assessed on Tapestation (Agilent). RNA concentration quantified using Qubit RNA HS assay kit (Q32855).
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® Ultra™ II Directional RNA Library Prep Kit following manufacturer's protocol

treatment_protocol: The SS (wildtype) and MMTT (allele replacement )  strains were first grown in YPD (yeast extract (1%), Peptone(2%) and Dextrose (2%) )and then in YPA  (yeast extract (1%), Peptone(2%) and Acetate (1%) ) and transferred to the sporulation medium (1% potassium acetate and amino acid supplements). The samples were taken at 0h, 30min, 45min, 1h10min, 1h40min, 2h30min, 3h50min, 5h40min, and 8h30min and were snap frozen and stored at -80 degree

tag: strain

value: Sporulation


title: Yeast, wildtype, 8h30m, rep3


title: Yeast, wildtype, 45m, rep3


title: 421_siYAP2_2


title: 421_siTAZ2_3

value: siTAZ


title: serum exosomes, PH015, week 12, 3hr

description:
PH015w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

tag: participant id


title: Yeast, wildtype, 3h50m, rep3


title: 6057841120_R05C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: serum exosomes, PH015, week 0, 3hr

description:
PH015w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

tag: week


title: Yeast, wildtype, 30m, rep3

tag: time


title: 421_siTAZ2_2

tag: cell line

value: metastatic melanoma


title: Yeast, wildtype, 2h30m, rep3


title: serum exosomes, PH015, week 0, 24hr

description:
PH015w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841120_R04C02 whole blood


title: serum exosomes, PH015, week 0, 0hr

description:
PH015w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841120_R04C01 whole blood


title: serum exosomes, PH008, week 16, rest

description:
PH008w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: Female


title: serum exosomes, PH015, week 12, 0hr

description:
PH015w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: Male


title: 421_siTAZ1_3


title: Yeast, wildtype, 1h10m, rep3


title: 6057841120_R03C02 whole blood


title: serum exosomes, PH008, week 12, pre

description:
PH008w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841120_R02C02 whole blood


title: serum exosomes, PH008, week 12, 3hr

description:
PH008w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841120_R02C01 whole blood


title: 421_siTAZ1_1


title: 421_siCTRL_3

value: siCTRL


title: 6057841120_R01C02 whole blood

value: M


title: serum exosomes, PH008, week 12, 24hr

description:
PH008w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Yeast, wildtype, 5h40m, rep2


title: 421_siCTRL_2


title: serum exosomes, PH008, week 12, 0hr

description:
PH008w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 421_siTAZ2_1


title: serum exosomes, PH008, week 0, pre

description:
PH008w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841118_R06C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: Y


title: serum exosomes, PH008, week 0, 3hr

description:
PH008w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841120_R01C01 whole blood


title: 421_nosiRNA_3

value: nosiRNA


title: 421_siCTRL_1


title: Yeast, wildtype, 1h40m, rep3


title: Yeast, wildtype, 3h50m, rep2


title: 6057841118_R06C01 whole blood


title: 421_nosiRNA_2


title: Yeast, wildtype, 0h, rep3


title: Yeast, wildtype, 2h30m, rep2


title: serum exosomes, PH008, week 0, 24hr

description:
PH008w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Yeast, wildtype, 30m, rep2


title: 6057841118_R05C02 whole blood

value: F


title: 421_nosiRNA_1


title: serum exosomes, PH008, week 0, 0hr

description:
PH008w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841118_R05C01 whole blood

value: N


title: 421_siTAZ1_2


title: 218_siYAP2_3

value: siYAP


title: Yeast, wildtype, 8h30m, rep2


title: Yeast, wildtype, 45m, rep2


title: serum exosomes, PH006, week 16, rest

description:
PH006w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 16

value: rest


title: 6057841118_R04C02 whole blood


title: 218_siYAP2_2


title: Yeast, wildtype, 0h, rep2

value: Sporulation


title: serum exosomes, PH006, week 12, 3hr

description:
PH006w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 218_siYAP2_1

value: metastatic melanoma


title: serum exosomes, PH006, week 12, pre

description:
PH006w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: pre


title: 6057841118_R03C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: 218_siYAP1_3


title: Yeast, wildtype, 5h40m, rep1


title: 6057841118_R03C01 whole blood


title: 6057841118_R02C02 whole blood


title: serum exosomes, PH006, week 12, 0hr

description:
PH006w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: serum exosomes, PH006, week 12, 24hr

description:
PH006w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Yeast, wildtype, 45m, rep1


title: Yeast, wildtype, 3h50m, rep1


title: 218_siYAP1_2


title: 6057841118_R02C01 whole blood


title: 218_siTAZ2_3

value: siTAZ


title: Yeast, wildtype, 1h10m, rep2


title: 218_siYAP1_1


title: serum exosomes, PH006, week 0, pre

description:
PH006w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: Yeast, wildtype, 1h40m, rep2


title: 6057841109_R06C02 whole blood

value: M

value: Y


title: 6057841118_R01C02 whole blood


title: Yeast, wildtype, 30m, rep1


title: serum exosomes, PH006, week 0, 24hr

description:
PH006w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841109_R06C01 whole blood


title: 218_siTAZ1_3


title: 218_siTAZ2_2


title: 6057841109_R04C01 whole blood


title: serum exosomes, PH004, week 16, rest

description:
PH004w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: Female


title: Yeast, wildtype, 2h30m, rep1


title: serum exosomes, PH006, week 0, 0hr

description:
PH006w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 218_siTAZ2_1


title: 6057841109_R04C02 whole blood


title: serum exosomes, PH004, week 12, pre

description:
PH004w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Yeast, wildtype, 1h40m, rep1


title: Yeast, wildtype, 8h30m, rep1


title: serum exosomes, PH006, week 0, 3hr

description:
PH006w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 218_siTAZ1_2


title: 218_siTAZ1_1


title: Yeast, wildtype, 0h, rep1


title: 6057841109_R03C01 whole blood


title: Yeast, allele replacement, 8h30m, rep3


title: serum exosomes, PH004, week 12, 3hr

description:
PH004w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841109_R03C02 whole blood


title: Yeast, wildtype, 1h10m, rep1


title: 6057841109_R02C02 whole blood


title: serum exosomes, PH004, week 12, 24hr

description:
PH004w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 218_siCTRL_3

value: siCTRL


title: 218_siCTRL_1


title: serum exosomes, PH004, week 0, 3hr

description:
PH004w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: Yeast, allele replacement, 5h40m, rep3


title: 218_siCTRL_2


title: serum exosomes, PH004, week 12, 0hr

description:
PH004w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Yeast, allele replacement, 3h50m, rep3


title: 6057841109_R01C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: 6057841109_R01C02 whole blood

value: F


title: serum exosomes, PH004, week 0, 24hr

description:
PH004w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841107_R05C02 whole blood

value: N


title: Yeast, allele replacement, 30m, rep3

value: Sporulation


title: 218_nosiRNA_1

value: nosiRNA


title: Yeast, allele replacement, 2h30m, rep3


title: A375_siYAP2_3

value: metastatic melanoma

value: Parental

value: siYAP


title: serum exosomes, PH004, week 0, 0hr

description:
PH004w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH001, week 16, rest

description:
PH001w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: 218_nosiRNA_3


title: 6057841107_R03C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: Yeast, allele replacement, 1h10m, rep3


title: 6057841104_R06C02 whole blood


title: Yeast, allele replacement, 1h40m, rep3


title: 6057841109_R02C01 whole blood


title: Yeast, allele replacement, 45m, rep3


title: A375_siYAP2_2


title: serum exosomes, PH001, week 12, pre

description:
PH001w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: pre


title: serum exosomes, PH004, week 0, pre

description:
PH004w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: Yeast, allele replacement, 0h, rep3


title: A375_siYAP2_1


title: serum exosomes, PH001, week 12, 3hr

description:
PH001w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: 6057841104_R05C02 whole blood


title: Yeast, allele replacement, 8h30m, rep2


title: Yeast, allele replacement, 5h40m, rep2


title: A375_siYAP1_2


title: 218_nosiRNA_2


title: 6057841104_R04C02 whole blood

value: Y


title: A375_siYAP1_3


title: serum exosomes, PH001, week 12, 0hr

description:
PH001w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: serum exosomes, PH001, week 12, 24hr

description:
PH001w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: 6057841104_R04C01 whole blood

value: F


title: Yeast, allele replacement, 45m, rep2


title: A375_siYAP1_1


title: 6057841104_R03C02 whole blood

value: M


title: Yeast, allele replacement, 3h50m, rep2

value: Sporulation


title: A375_siTAZ2_3

value: siTAZ


title: serum exosomes, PH001, week 0, 3hr

description:
PH001w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841104_R03C01 whole blood


title: Yeast, allele replacement, 30m, rep2


title: 6057841104_R02C01 whole blood

value: N


title: Yeast, allele replacement, 2h30m, rep2


title: serum exosomes, PH001, week 0, 24hr

description:
PH001w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH001, week 0, 0hr

description:
PH001w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6057841104_R05C01 whole blood


title: A375_siTAZ2_2

value: metastatic melanoma

value: Parental


title: 6057841104_R01C02 whole blood


title: Yeast, allele replacement, 1h40m, rep2


title: A375_siTAZ1_3


title: A375_siTAZ2_1


title: Yeast, allele replacement, 1h10m, rep2


title: 6057841104_R01C01 whole blood


title: 6026818168_R06C02 whole blood


title: HSALR, GSK3 inhibitor tideglusib 2

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were aligned to the Mus musculus genome build mm10 using STAR3. Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library5.
DEseq2 was also used to calculate fold changes and p_x0002_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 library7. Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER8.
Assembly: mm10
Supplementary files format and content: tab-delimited file with gene symbol and transcripts per million

source_name: Gastric mucle from 3-month old HSA mouse treated with GSK3 inhibitor tideglusib

extract_protocol: Total RNA was extracted from gastrocnemius of mice using Trizol. RNA integrity was examined by agarose gel electrophoresis.Extracted RNA was usedfor RNAseq analysis in Omega Bio services (Norcross, GA, USA).RNA samples were re-purified usinga Qiagen RNeasy cleanup kit.The quality of the isolated RNA was verified by calculation of RNA integrity number using Agilent Technologies.Ribosomal RNAs were depleted from the RNA samples prior to libraries preparation. Libraries were sequenced with at least 60M reads per sample

treatment_protocol: Three-month old homozygous DMSXL mice of both genders were treated with tideglusib (Sigma) dissolved in labrosol at the dose 0.1 mg/g of body weight, 2 times a week for 2 weeks. Following drug withdrawal for 11 days, the treatment was continued for additional 3 weeks in a female group of mice and for 6 weeks in a male group of mice.

value: skeletal muscle (gastric)

value: HSALR

value: GSK3 inhibitor tideglusib

value: 3 months


title: HSALR, GSK3 inhibitor tideglusib 3


title: A375_siTAZ1_2


title: serum exosomes, PH001, week 0, pre

description:
PH001w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: Yeast, allele replacement, 0h, rep2


title: A375_siTAZ1_1


title: HSALR, GSK3 inhibitor tideglusib 1


title: Yeast, allele replacement, 8h30m, rep1


title: A375_siCTRL_3

value: siCTRL


title: 6026818168_R06C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: HSALR, vehicle 3

source_name: Gastric mucle from 3-month old HSA mouse treated with vehicle

value: Vehicle


title: 6026818168_R05C02 whole blood


title: HSALR, vehicle 2


title: Yeast, allele replacement, 5h40m, rep1


title: A375_siCTRL_2


title: Yeast, allele replacement, 45m, rep1


title: A375_siCTRL_1


title: HSALR, vehicle 1


title: A375_nosiRNA_3

value: nosiRNA


title: WT, no treatment 3

source_name: Gastric muscle from 3-month old WT mouse

value: WT


title: 6026818168_R03C02 whole blood

value: F

value: Y


title: 6026818168_R03C01 whole blood


title: WT, no treatment 2


title: Yeast, allele replacement, 30m, rep1

value: Sporulation


title: A375_nosiRNA_1


title: Yeast, allele replacement, 2h30m, rep1


title: 6026818168_R02C02 whole blood


title: Yeast, allele replacement, 1h40m, rep1


title: WT, no treatment 1


title: Exp5.IP

city: Guangzhou

first: Huiying

last: Song

address: Tianhejinsuilu

institute: Zhongshan Ophthalmic Center of Sun Yat-sen University

description:
Methylated_RNA_sites.mRNA
Methylated_RNA_sites.LncRNA
Methylated_RNA_sites.circRNA

data_processing:
3’ adaptor-trimming and low-quality reads were removed using the cutadapt software (v1.9.3)
The high-quality clean reads were aligned to the reference genome (UCSC hg19) using the Hisat2 software (v2.0.4)
The gene-level FPKM was got as the expression profiles of RNA using the cuffdiff software (part of cufflinks) ,on which the fold change and p-value were calculated based.
Model-based Analysis of ChIP-Seq (MACS) software (v1.4.2) was used to identify mathylated genes in each sample.
DiffeReps software was used for identification of differential methylated genes.
Gene ontology (GO) database and the latest Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to perform GO analysis and pathway enrichment analysis on differentially methylated RNA genes.
MEME software was used for motif analysis
Assembly: hg19
Supplementary files format and content: excel format

source_name: Vitreous fluid

extract_protocol:
RNA was extracted using trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA)

value: Vitreous fluid

tag: group

value: pathological myopia

tag: antibody


title: 6026818168_R01C02 whole blood

tag: tissue

value: M


title: 6026818168_R02C01 whole blood


title: 6026818168_R01C01 whole blood


title: Exp5.Input


title: 6026818168_R04C02 whole blood

value: N


title: 6026818168_R04C01 whole blood


title: Yeast, allele replacement, 3h50m, rep1


title: Yeast, allele replacement, 0h, rep1


title: Exp3.IP


title: 6026818165_R06C02 whole blood


title: A375_nosiRNA_2

tag: cell type

value: metastatic melanoma

value: Parental


title: Yeast, allele replacement, 1h10m, rep1

tag: genotype


title: 6026818165_R06C01 whole blood


title: Exp3.Input


title: 6026818165_R05C02 whole blood


title: Exp2.IP


title: 6026818165_R05C01 whole blood


title: Exp4.Input


title: Exp4.IP


title: Exp2.Input


title: STING and LTbR agonist, Cd45 positive cells, scRNAseq

first: Fumiaki

last: Kanamori

state: FL

address: 600 5th Street S

department: Department of Orthopaedic Surgery

institute: Johns Hopkins All Children’s Hospital.

description: 10X genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger Count v.7.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
KPC tumors were surgically resected. Tumors were excised and mechanically dissociated into smaller fragments. These fragments underwent enzymatic digestion with LiberaseTM (300 μg/mL) and mechanical dissociation using the GentleMACS Octo dissociator (protocol: hard tumor dissociation, TDK-3, 1 hour at 37°C). Following dissociation, the cell suspension was filtered using a 70 μm strainer and then washed twice with RPMI medium at 400 rcf for 5 minutes. After dead/live cell staining and blocking non-specific binding using anti-FcRII/III (Biolegends) for 10 minutes, cells were stained with anti-CD45 antibody for 1 hour at 4C. Live CD45+ leukocytes were sorted by CytoFLEX SRT (Beckman).
Library generation was performed according to the manufacturer’s instruction (Chromium GEM-X Single Cell 5’ Reagent Kits v2, 10X Genomics). Briefly, Cd45 positive cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).   Poly-adenylated mRNA contained in each single GEM was reverse transcripted to cDNA that includes an Ilumina R1 primer, Unique Molecular Identifier (UMI), and 10X barcode.  The barcoded cDNA was cleaned up with Dynabeads MyOne SILANE, amplified by PCR, and appropriate size fragments were selected with SPRI select.  For gene expression library construction, Ilumina R2 primer, paired-end constructs with P5 and P7, and sample index were added.

value: tumor

value: KPC

value: Cd45 positive cells

tag: treatment

value: STING and LTbR agonist

tag: sample barcode_tsv


title: 6026818165_R04C02 whole blood

tag: sample id

value: WhiteBloodCells from Purple Top EDTA tubes


title: 6026818165_R04C01 whole blood

tag: subject id


title: Replicate 2, iPSC-derived kidney organoids at day 16 of differentiation protocol, donor 2

city: Ramat Gan

first: Benjamine

last: Dekel

address: Tel Hashomer

country: Israel

institute: heba Medical Center: Tel Hashomer, Tel Aviv, IL

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI
Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Normalization and differential expression was performed using DESeq2
Assembly: hg38
Supplementary files format and content: Excel file includes the normalized counts

source_name: Human iPSC-derived kidney organoids

extract_protocol:
Sample were processed with Trizol and Total RNA was prepared using a Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's instructions.
Bulk MARS-Seq protocol

value: Human iPSC-derived kidney organoids

value: iPSC-derived kidney organoids


title: Replicate 1, iPSC-derived kidney organoids at day 16 of differentiation protocol, donor 2

value: WT


title: Exp1.IP


title: Exp1.Input


title: Control5.IP

value: control


title: Replicate 2, iPSC-derived kidney organoids at day 16 of differentiation protocol, donor 1


title: 6026818165_R02C02 whole blood

tag: Sex


title: 6026818165_R03C01 whole blood

value: F

tag: age


title: Control5.Input


title: 6026818165_R01C02 whole blood

tag: asthma

value: Y


title: STING agonist, Cd45 positive cells, scRNAseq

description: 10X genomics

value: STING agonist


title: Replicate 1, iPSC-derived kidney organoids at day 16 of differentiation protocol, donor 1


title: Control4.IP

value: Vitreous fluid


title: Untreated, Cd45 positive cells, scRNAseq

description: 10X genomics

value: Untreated


title: Replicate 3, Adult kidney tissue after nephrectomy

source_name: Human Adult Kidney

value: Human Adult Kidney

value: primary sample

value: adult kidney tisssue


title: 6026818165_R01C01 whole blood

source_name: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: Replicate 2, Adult kidney tissue after nephrectomy


title: 6026818164_R06C01 whole blood


title: LTbR agonist, Cd45 positive cells, scRNAseq

description: 10X genomics

value: tumor

value: KPC

value: LTbR agonist


title: Control4.Input


title: Replicate 1, Adult kidney tissue after nephrectomy


title: Control3.IP


title: 6026818164_R05C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: 3rd internode, Fe deprivation, biol rep 2

city: Upton

first: Meng

last: Xie

state: NY

address: 50 Bell Ave

institute: Brookhaven National Laboratory

description:
P30_IN3
Normalized_counts_Fedeprivation_IN3_3rep.tabular

data_processing:
After removing adapters and low-quality sequences, clean reads were aligned to the Populus trichocarpa genome v3.1 (Phytozome) using HISAT2 (v2.2.1).
Transcripts were then assembled using StringTie (v2.2.1).
DEGs were identified using DESeq2 (v2.11.40.7) with the criteria of fold change > 2 and P < 0.05.
Assembly: Populus trichocarpa v3.1
Supplementary files format and content: tabular files include normalized counts for each sample

organism: Populus trichocarpa

source_name: 3rd internode

extract_protocol:
Total RNAs for Fe deprivation samples were isolated using the Spectrum Plant Total RNA Kit with on-column Dnase treatment (Sigma); Total RNAs of PtrbHLH011 OE samples were isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with on-column DNase (Qiagen) to remove genomic DNA contamination.
Illumina RNASeq w/PolyA Selection for Ctrl and Fe deprivation samples; DNBSEQ Eukaryotic Strand-specific mRNA library for Empty vector and PtrbHLH011 OE samples

value: 3rd internode

value: Fe deprivation


title: Control3.Input


title: Replicate 3, adult kidney organoids after 2 passages

value: adult kidney organoid

value: WT


title: 6026818164_R05C01 whole blood

value: F


title: Control2.Input

value: control


title: 3rd internode, Fe deprivation, biol rep 1

description:
P22_IN3
Normalized_counts_Fedeprivation_IN3_3rep.tabular


title: Control2.IP


title: Replicate 2, adult kidney organoids after 2 passages


title: Replicate 1, adult kidney organoids after 2 passages


title: 6026818164_R04C01 whole blood

value: Y


title: 3rd internode, control treatment, biol rep 2

description:
P13_IN3
Normalized_counts_Fedeprivation_IN3_3rep.tabular

value: Ctrl


title: Control1.IP

value: Vitreous fluid


title: hNEC-sorted_CD66c-High_TubLow_donor2

city: Prague

first: Martin

last: Zmuda

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Microbiology of the Czech Academy of Sciences

description:
Library name: Non_infected_Tub_low
salmon.merged.gene_tpm_batch2.tsv
salmon.merged.gene_counts_batch2.tsv

data_processing:
Sequencing was performed on the Illumina NextSeq 500 platform with 75 bp single-end reads. A total of 60 million reads and 30 million reads per sample were obtained for donor 1 and 2, respectively.
Raw sequencing reads were preprocessed with the nf-core/RNAseq pipeline (version 3.10.1) using the default settings for STAR + Salmon. Reads were mapped to the ENSEMBL reference genome and transcriptome (Homo_sapiens GRCh38.dna_sm.primary assembly genome and GRCh38.110 transcriptome).
Assembly: GRCh38
Supplementary files format and content: tab-delimited salmon.merged.gene_tpm_batch1.tsv and salmon.merged.gene_tpm_batch2.tsv file contains tpm for each sample
Supplementary files format and content: tab-delimited salmon.merged.gene_counts_batch1.tsv and salmon.merged.gene_counts_batch2.tsv contains raw gene counts for each sample

source_name: primary nasal epithelial cells, air-liquid interface culture, day 30

growth_protocol: Air-liquid interface cultures of primary human nasal epithelial cells (hNECs) were prepared as described in current manuscript Zmuda M., Malcova I., Pravdova B., Cerny O., Vondrova D., Kamanova J. 2025. Limited response of primary nasal epithelial cells to Bordetella pertussis infection. DOI 10.1128/spectrum.01267-25

extract_protocol:
Total RNA was extracted according to the instructions of the RNeasy plus micro kit (Qiagen, Cat# 74134). RNA concentration and quality were assessed using the DS-11 spectrophotometer DeNovix. In addition, RNA integrity was analyzed using an Agilent Bioanalyzer 2100 (Agilent Technologies, USA).
Only samples with a minimum RNA integrity number (RIN) of 7 were included for library preparation. The libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio, Cat# 634411), using 2 ng of RNA as input per sample. Preparation of library was performed by following standard manufacturer's protocol.

treatment_protocol: hNECs cultured on Transwell membranes were stained with 2x concentrated Tubulin Tracker Green (Invitrogen, Cat. #T34078), applied apically in 200 µl of HBSS. The cells were incubated for 1 hour at 37°C in a 5% CO₂ atmosphere. After incubation, the solution was discarded, and the hNECs were washed twice apically with 200 µl of HBSS. To detach the hNECs from the Transwell membranes, the cells were incubated for 30 minutes in Accutase solution (Invitrogen, Cat. #00-4555-56) supplemented with Collagenase D (1 mg/ml, Roche, Cat. #11088858001) and DNase I (200 µg/ml, Roche, Cat. #10104159001). For this process, 600 µl of the solution was added to the bottom compartment, and 200 µl was applied apically. Following the incubation, the released cells were collected, centrifuged at 350 g for 5 minutes, washed once with flow cytometry buffer (5 % fetal calf serum and 2 mM EDTA in PBS) and resuspended in flow cytometry buffer containing anti-CD66c (clone B6.2, Exbio, Cat. #. 1P-863-T100) and anti-CD271 (clone NGFR5, Exbio, Cat. #. T7-642-T100). Antibody staining was performed on ice for 1 hour.  Following staining, the cells were sorted directly into the RLT lysis buffer using BD Influx cell sorter, with at least 2 x 10^4 cells collected per population.

value: primary cells - secretory club cells

tag: batch


title: hNEC-sorted_CD271-High_TubLow_donor2

description:
Library name: Non_infected_CD271
salmon.merged.gene_tpm_batch2.tsv
salmon.merged.gene_counts_batch2.tsv

value: primary nasal epithelial cells, air-liquid interface culture, day 30

value: primary cells - basal cells


title: hNEC-sorted_CD66c-High_TubLow_donor1

description:
Library name: Tub_low
salmon.merged.gene_tpm_batch1.tsv
salmon.merged.gene_counts_batch1.tsv


title: hNEC-sorted_CD271-High_TubLow_donor1

description:
Library name: CD271
salmon.merged.gene_tpm_batch1.tsv
salmon.merged.gene_counts_batch1.tsv


title: hNEC-sorted_CD66c-Low_TubHigh_donor2

description:
Library name: Non_infected_Tub_high
salmon.merged.gene_tpm_batch2.tsv
salmon.merged.gene_counts_batch2.tsv

value: primary cells - ciliated cells


title: hNEC-sorted_CD66c-High_TubMid_donor2

description:
Library name: Non_infected_Tub_mid
salmon.merged.gene_tpm_batch2.tsv
salmon.merged.gene_counts_batch2.tsv

value: primary cells - secretory goblet cells


title: hNEC-sorted_CD66c-High_TubMid_donor1

description:
Library name: Tub_mid
salmon.merged.gene_tpm_batch1.tsv
salmon.merged.gene_counts_batch1.tsv


title: hNEC-sorted_CD66c-Low_TubHigh_donor1

description:
Library name: Tub_high
salmon.merged.gene_tpm_batch1.tsv
salmon.merged.gene_counts_batch1.tsv


title: 6026818164_R03C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

data_processing: Normalization was performed using the within-array combination of Noob (Triche et al. 2013) in R package “minfi” and BMIQ (Teschendorff et al. 2013) in R package “wateRmelon”. The minfi package was used to identify and remove 25,165 probes with SNPs. Sex was imputed by DNA methylation and 23 samples were removed due to mismatch between reported and genetic imputed sex. ComBat (Johnson, 2017) from the sva R package (Leek, 2023) was used for batch effect correction, transforming to m-values, then back transforming to beta-values.

extract_protocol: PureGene Blood Kit (Qiagen, Germantown, Maryland), AllPrep DNA Mini Kit (Qiagen)

value: M


title: Replicate 3, First passage of adult kidney organoids

value: Human Adult Kidney

value: primary sample


title: 6026818164_R03C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: leaf tissue, Fe deprivation, biol rep 3

description:
P30_YL
Normalized_counts_Fe deprivation_YL.tabular
Name in processed data file: StringTie on data 57 and data 224: Gene counts

source_name: leaf

value: leaf

value: Fe deprivation


title: Control1.Input


title: 6026818164_R02C02 whole blood


title: 3rd internode, control treatment, biol rep 1

description:
P11_IN3
Normalized_counts_Fedeprivation_IN3_3rep.tabular

value: 3rd internode


title: Replicate 2, First passage of adult kidney organoids

value: adult kidney organoid

value: WT


title: leaf tissue, Fe deprivation, biol rep 2

description:
P22_YL
Normalized_counts_Fe deprivation_YL.tabular
Name in processed data file: StringTie on data 57 and data 223: Gene counts


title: Replicate 1, First passage of adult kidney organoids


title: 6026818164_R02C01 whole blood

value: F

value: Y


title: Midgut, 48h, Low Virus, rep8

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences at least 25 nucleotides (nt) in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment against the reference genome.
Genes were counted using featureCounts version 1.5.0-p3 from the Subreads package (parameters: -t gene -g ID -s 1 -R).
Assembly: Aedes aegypti (assembly AaegL5.0) from NCBI
Supplementary files format and content: Count files generated using featureCounts: they contain one row per gene or de novo transcript.
Supplementary files format and content: Excel files contain the results of the RNA-Seq differential analysis performed using R version 4.4.3 and the edgeR package version 4.4.2. Lowly expressed genes were filtered out using the filterByExpr() function (from the edgeR package) with min.count=10.
Supplementary files format and content: gff3 file contains new Aedes aegypti transcripts found in the RNA-Seq data using Blast2go.

molecule: polyA RNA

organism: Aedes aegypti

source_name: Midgut

growth_protocol: Mosqouito rearing is described in the associated publication.

extract_protocol:
Midguts were dissected in 1X phosphate-buffered saline (PBS). Individual midguts were immediately homogenized for 30 sec at 6,000 rpm in tubes containing ~20 1-mm glass beads (BioSpec) in 500 μL of TRIzol (Life Technologies) and stored at -80°C. 100 μL of chloroform (Sigma-Aldrich) were added samples homogeneized by manual shaking for 30 sec. After a 5-min incubation at 4°C, samples were centrifuged at 4°C for 15 min at 14,000 rpm. The upper aqueous phase was harvested and transferred to a cold tube containing 400 μL of 2-propanol (Sigma-Aldrich). Samples were incubated at -20°C overnight and centrifuged at 4°C for 15 min at 14,000 rpm to pellet RNA. The pellet was washed twice with 1mL of 70% ice-cold ethanol (Sigma-Aldrich) at 4°C for 10 min at 14,000 rpm, and allowed to dry for 10 min at room temperature. Total RNA was resuspended in 7 μL RNase-free water.
Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input Mammalian following manufacturer’s instructions (Clontech, 635005). The quality of all libraries was assessed with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen). Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: Mosquito virus infection are detailled in the associated publication.

value: Midgut

value: Primary midgut cells

tag: infection level

value: Low

tag: virus

value: Dengue 1

value: Midgut cells

value: Bakoumba wild-type strain

value: DENV-1 infection


title: leaf tissue, Fe deprivation, biol rep 1

description:
P7_YL
Normalized_counts_Fe deprivation_YL.tabular
Name in processed data file: StringTie on data 57 and data 222: Gene counts


title: Midgut, 48h, Low Virus, rep7

tag: time


title: 6026818164_R01C01 whole blood

value: M


title: 6026818164_R01C02 whole blood

value: N


title: Replicate 3, Week 18 human fetal kidney tissue

source_name: Human Fetal Kidney

value: Human Fetal Kidney

tag: cell line

value: primary sample

value: fetal kideny tissue


title: leaf tissue, control treatment, biol rep 3

description:
P17_YL
Normalized_counts_Fe deprivation_YL.tabular
Name in processed data file: StringTie on data 57 and data 221: Gene counts

value: leaf

value: Ctrl


title: Replicate 2, Week 18 human fetal kidney tissue

value: WT


title: Midgut, 48h, Low Virus, rep6


title: Midgut, 48h, Low Virus, rep5


title: leaf tissue, control treatment, biol rep 2

description:
P13_YL
Normalized_counts_Fe deprivation_YL.tabular
Name in processed data file: StringTie on data 57 and data 220: Gene counts


title: 6026818161_R06C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: Replicate 1, Week 18 human fetal kidney tissue


title: leaf tissue, control treatment, biol rep 1

description:
P11_YL
Normalized_counts_Fe deprivation_YL.tabular
Name in processed data file: StringTie on data 57 and data 219: Gene counts


title: Midgut, 48h, Low Virus, rep4

value: Midgut


title: Replicate 2, Human Fetal kidney organoids passaged twice and cultured for 8 weeks

value: fetal kideny organoid


title: DNBS, day 3, replicate 4

city: Suwon-si, Gyeonggi-do

first: kim

last: jungtak

state: suwon

address: Yeongtong-gu, 206, World cup-ro, songjaegwan 711

country: South Korea

institute: Microbiology part/ajou University

description:
Library name: 12_12
Record-seq

data_processing:
Raw FASTQ files were processed using a Snakemake script provided in the ETH Zurich protocol (https://doi.org/10.3929/ethz-b-000396475) in a Linux operating system. In brief, the workflow includes quality control of the raw files using fastqc, trimming by trimmomatic, fastq to fasta conversion using FASTX-toolkit, extraction of spacer sequences using a provided python script, read alignment to reference genomes by bowtie2, and generation of count matices by Subread FeatureCounts.
Assembly: BL21(de3), pFS_0453 (plasmid)
Supplementary files format and content: E.coli processed genome counts, xlsx

organism: Escherichia coli BL21(DE3)

source_name: Mouse gut microbiota

extract_protocol:
Reporter E. coli was orally administered to mouse models 11 hours prior to each observation time point. For the observation, 100mg of feces were collected per mouse, diluted in PBS containing 10mM Tris-EDTA and centrifuged for 1 minute at 200xg. Retrieved bacterial pellet was purified using QIAprep spin Miniprep kit for spacer acquisition analysis.
Library was constructed according to ETH Zurich protocol "Recording transcriptional histories using record-seq" (https://doi.org/10.3929/ethz-b-000396475).

value: Mouse gut microbiota


title: Midgut, 48h, Low Virus, rep3

value: Primary midgut cells

value: Low

value: Dengue 1


title: 6026818161_R05C01 whole blood

first: Benjamin

last: Raby

address: 300 Longwood Ave

value: Y


title: DNBS, day 3, replicate 3

description:
Library name: 12_10
Record-seq


title: Midgut, 48h, Low Virus, rep2

value: Midgut cells

value: Bakoumba wild-type strain

value: DENV-1 infection


title: Replicate 1, Human Fetal kidney organoids passaged twice and cultured for 8 weeks

value: Human Fetal Kidney

value: primary sample


title: 6026818161_R04C02 whole blood

value: N


title: 3rd internode, control treatment, biol rep 3

description:
Library name: Ctrl_internode_R3
P17_IN3
Normalized_counts_Fedeprivation_IN3_3rep.tabular

value: 3rd internode

value: Ctrl


title: DNBS, day 3, replicate 2

description:
Library name: 12_7
Record-seq


title: 3rd internode, Fe deprivation, biol rep 3

description:
Library name: Fe deprivation_internode_R3
P7_IN3
Normalized_counts_Fedeprivation_IN3_3rep.tabular

value: Fe deprivation


title: Midgut, 48h, High Virus, rep8

value: High


title: 6026818161_R03C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: DNBS, day 3, replicate 1

description:
Library name: 12_3
Record-seq

value: Mouse gut microbiota


title: Replicate 3, Human Fetal kidney organoids cultured for 3 weeks

value: fetal kideny organoid

value: WT


title: Replicate 2, Human Fetal kidney organoids cultured for 3 weeks


title: Midgut, 48h, Low Virus, rep1

value: Midgut

value: Primary midgut cells

value: Low

value: Dengue 1


title: 6026818161_R04C01 whole blood

value: Y


title: VehC, day 3, replicate 5

description:
Library name: 11_12
Record-seq


title: Replicate 3, Human Fetal kidney organoids passaged twice and cultured for 8 weeks

value: Human Fetal Kidney


title: Midgut, 48h, High Virus, rep7

value: Midgut cells

value: Bakoumba wild-type strain

value: DENV-1 infection


title: Replicate 1, Human Fetal kidney organoids cultured for 3 weeks

value: primary sample


title: 6026818161_R03C01 whole blood


title: 6026818161_R06C01 whole blood

value: F


title: 6026818161_R02C02 whole blood


title: Midgut, 48h, High Virus, rep6

value: High


title: VehC, day 3, replicate 4

description:
Library name: 11_9
Record-seq


title: p63beta_Epidermis_R4

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier 1

department: Dept. of Exper. Medicine

country: Italy

institute: University of Rome "Tor Vergata"

data_processing:
The paired-end 42 bp sequencing reads (PE42) [Keratinocytes] or 150 bp (PE150) [Epidermis] generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the STAR algorithm with default settings.
Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands were discarded. The gene annotations were obtained from Subread package (originally from NCBI RefSeq database). Genes with the same Entrez gene identifiers were also merged into one gene.
Pairwise comparisons were performed with the DESeq2 software packagea. For comparisons with replicates a Wald test was used to determine significance, and any gene with an adjusted p-value of less than 0.1 was considered differently expressed..
Assembly: mm10
Supplementary files format and content: tab delimited text file containing counts produced by featureCounts or Salmon
Supplementary files format and content: tab delimited text file containing  FKPM/TPM values produced by featureCounts or Salmon
Supplementary files format and content: Excel file containing DEseq2 results (p63_C_terminus_XXXX_DESeq2_results_allgenes.xlsx)

source_name: Skin

extract_protocol:
RNeasy mini kit QIAGEN following manufacture's instruction
Illumina’s TruSeq Stranded mRNA Library kit following manufacture's instruction

value: Skin

value: Epidermal cells

value: KRT14-Cre; Trp63-Ex13fl/fl (p63beta)

tag: culture conditions

value: Epidermises were isolated from newborn mouse. Newborn mouse pups were sacrificed and the epidermises were separated from dermis by overnight incubation in trypsin.


title: Midgut, 48h, High Virus, rep5


title: 6026818161_R02C01 whole blood

institute: Boston Children's Hospital

value: WhiteBloodCells from Purple Top EDTA tubes


title: p63beta_Epidermis_R2


title: Midgut, 48h, High Virus, rep4

value: Midgut


title: 6026818161_R01C01 whole blood


title: DSS_D24, DSS, day 24, replicate 3

description:
Library name: 10_7
Record-seq

value: Mouse gut microbiota


title: Midgut, 48h, High Virus, rep3

value: Primary midgut cells


title: 6026818161_R01C02 whole blood

value: M


title: VehC, day 3, replicate 1

description:
Library name: 11_1
Record-seq


title: 6026818160_R06C02 whole blood

value: Y


title: DSS_D24, DSS, day 24, replicate 2

description:
Library name: 10_4
Record-seq


title: p63beta_Epidermis_R1


title: 6026818160_R06C01 whole blood


title: Midgut, 48h, High Virus, rep1

value: Dengue 1


title: p63alpha_Epidermis_R3

value: Trp63-Ex13fl/fl (p63alpha)


title: 6026818160_R05C02 whole blood


title: p63beta_Epidermis_R3


title: DSS_D24, DSS, day 24, replicate 1

description:
Library name: 10_2
Record-seq


title: Midgut, 24h, Low Virus, rep8

value: Low

value: Midgut cells

value: Bakoumba wild-type strain


title: HC_D24, water, day 24, replicate 3

description:
Library name: 9_7
Record-seq


title: VehC, day 3, replicate 2

description:
Library name: 11_2
Record-seq


title: Midgut, 48h, High Virus, rep2

value: DENV-1 infection


title: Midgut, 24h, Low Virus, rep7


title: p63alpha_Epidermis_R4


title: p63alpha_Epidermis_R1


title: 6026818160_R04C02 whole blood

value: F


title: Midgut, 24h, Low Virus, rep5


title: 6026818160_R04C01 whole blood


title: CD34 low fibroblasts - pubertal mammary gland 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
RNA-Seq reads were aligned against to the Mouse (GRCm38/mm10) reference genome and the reads were counted using Rsubread (version 2.6.2) and Rsubread's built-in mm10 annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: Comma-separated file containing raw sequence read counts for all samples together with Entrez GeneID, chromosome (Chr), start and end genomic positions, strand and genomic length.

source_name: mammary gland

extract_protocol:
FACS sorted cells were resuspended in QIAzol for RNA-extraction following the manufacturer’s protocol for the miRNeasy micro kit (Qiagen #217084), including the on-column DNase digestion (Qiagen #79256).
A minimum of 10 ng of total RNA was used for sequencing libraries following Illumina’s TruSeq RNA v2 protocol (Illumina #RS-122-2001). Libraries were sequenced on an Illumina NextSeq 500.

tag: strain

value: FVB/N

value: mammary gland

value: CD34 low fibroblasts

tag: mouse pool


title: 6026818160_R05C01 whole blood

city: Boston

tag: tissue


title: HC_D24, water, day 24, replicate 2

description:
Library name: 9_5
Record-seq


title: Midgut, 24h, Low Virus, rep6

tag: cell type

tag: genotype


title: CD34 high fibroblasts - pubertal mammary gland 3

value: CD34 high fibroblasts


title: HC_D24, water, day 24, replicate 1

description:
Library name: 9_1
Record-seq


title: DSS_D15, DSS, day 15, replicate 3

description:
Library name: 8_12
Record-seq


title: p63alpha_Epidermis_R2

value: Skin

value: Epidermal cells

value: Epidermises were isolated from newborn mouse. Newborn mouse pups were sacrificed and the epidermises were separated from dermis by overnight incubation in trypsin.


title: Midgut, 24h, Low Virus, rep4

value: Midgut

value: Primary midgut cells

tag: treatment


title: VehC, day 3, replicate 3

description:
Library name: 11_3
Record-seq

value: Mouse gut microbiota


title: DSS_D15, DSS, day 15, replicate 2

description:
Library name: 8_4
Record-seq


title: CD34 low fibroblasts - pubertal mammary gland 2


title: 6026818160_R03C01 whole blood

tag: sample id

value: WhiteBloodCells from Purple Top EDTA tubes

value: Y


title: CD34 high fibroblasts - pubertal mammary gland 2


title: 6026818160_R03C02 whole blood

tag: subject id


title: DSS_D15, DSS, day 15, replicate 1

description:
Library name: 8_1
Record-seq


title: Midgut, 24h, Low Virus, rep3

value: Low

value: Dengue 1


title: Midgut, 24h, Low Virus, rep2

value: Midgut cells

value: Bakoumba wild-type strain


title: CD34 high fibroblasts - pubertal mammary gland 1


title: 6026818160_R02C01 whole blood

tag: Sex

value: M


title: Midgut, 24h, Low Virus, rep1

value: DENV-1 infection


title: HC_D15, water, day 15, replicate 2

description:
Library name: 7_5
Record-seq


title: HC_D15, water, day 15, replicate 3

description:
Library name: 7_12
Record-seq


title: CD34 positive - Tumor 1

data_processing:
RNA-Seq reads were aligned against to the Mouse (GRCm38/mm10) reference genome using Rsubread's align function (Rsubread version 2.2.6). Reads were counted using Rsubread featureCounts and Rsubread's inbuilt mm10 annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: Comma-separated file containing raw sequence read counts for all samples together with Entrez gene ID, chromosome,  gene length, gene description and gene type.

source_name: mammary tumor

value: mammary tumor

tag: tumor

value: CD34 positive fibroblasts


title: 6026818160_R01C02 whole blood

tag: age

tag: asthma


title: 6026818160_R01C01 whole blood

value: F


title: HC_D15, water, day 15, replicate 1

description:
Library name: 7_4
Record-seq


title: Midgut, 24h, High Virus, rep7

tag: infection level

value: High


title: CD34 low fibroblasts - pubertal mammary gland 1

value: FVB/N

value: mammary gland

value: CD34 low fibroblasts


title: 6026818155_R06C02 whole blood

value: N


title: CD34 negative - Tumor 1

value: CD34 negative fibroblasts


title: DSS_D9, DSS, day 9, replicate 3

description:
Library name: 6_8
Record-seq

value: Mouse gut microbiota


title: CD34 positive - Tumor 2


title: Midgut, 24h, High Virus, rep6

value: Midgut

value: Primary midgut cells

tag: virus


title: 6026818155_R06C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: Y


title: Midgut, 24h, High Virus, rep5

value: Dengue 1

tag: time

value: Midgut cells

value: Bakoumba wild-type strain


title: 6026818155_R05C02 whole blood


title: CD34 negative - Tumor 2

value: mammary tumor


title: DSS_D9, DSS, day 9, replicate 2

description:
Library name: 6_3
Record-seq


title: Midgut, 24h, High Virus, rep8

tag: cell line

value: DENV-1 infection


title: DSS_D9, DSS, day 9, replicate 1

description:
Library name: 6_1
Record-seq


title: 6026818155_R05C01 whole blood

value: F


title: CD34 positive - Tumor 3

value: CD34 positive fibroblasts


title: Midgut, 24h, High Virus, rep4

value: High


title: 6026818155_R04C02 whole blood


title: HC_D9, water, day 9, replicate 2

description:
Library name: 5_5
Record-seq


title: CD34 negative - Tumor 3


title: 6026818155_R03C02 whole blood


title: Midgut, 24h, High Virus, rep3


title: Midgut, 24h, High Virus, rep2


title: HC_D9, water, day 9, replicate 1

description:
Library name: 5_3
Record-seq


title: Midgut, 24h, High Virus, rep1


title: p63beta_Ker_RNA_R2

description:
p63_C_terminus_Keratinocytes_gene_matrix_FPKM.txt
p63_C_terminus_Keratinocytes_featureCounts.txt
p63_C_terminus_Keratinocytes_DESeq2_results_allgenes.xlsx

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the STAR algorithm with default settings.
Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands were discarded. The gene annotations  were obtained from Subread package (originally from NCBI RefSeq database). Genes with the same Entrez gene identifiers were also merged into one gene.
Pairwise comparisons were performed with the DESeq2 software packagea. For comparisons with replicates a Wald test was used to determine significance, and any gene with an adjusted p-value of less than 0.1 was considered differently expressed. For comparisons without replicates, differentially expressed genes had a shrunken log fold change greater than 0.3.
Assembly: mm10
Supplementary files format and content: tab delimited text file containing counts produced by featureCounts (p63_C_terminus_XXXX_featureCounts.txt)
Supplementary files format and content: tab delimited text file containing FKPM values (p63_C_terminus_XXXX_gene_matrix_FPKM.txt)
Supplementary files format and content: Excel file containing DEseq2 results (p63_C_terminus_XXXX_DESeq2_results_allgenes.xlsx)

value: Skin

value: Cultured keratinocytes

value: KRT14-Cre; Trp63-Ex13fl/fl (p63beta)

tag: culture conditions

value: Primary mouse keratinocytes were isolated from newborn mouse. Newborn mouse pups were sacrificed and the epidermises were separated from dermis by overnight incubation in trypsin.  Epidermises were minced with scissors and triturated by pipetting several times. Single cells were filtered through a 100-μm cell strainer (Corning), centrifuged at 200 g for 5 min and plated in low calcium medium EMEM (Lonza, containing 8% chelate FBS, antibiotic/antimycotic solution (Sigma) and 0.05mM CaCl2) on dishes pre-coated with rat tail collagen type I (Corning). Twenty-four hours later, adherent cells were washed three times in PBS and collected.


title: p63beta_Ker_RNA_R1


title: DSS_D5, DSS, day 5, replicate 3

description:
Library name: 2_5
Record-seq

value: Mouse gut microbiota


title: 6026818155_R02C01 whole blood


title: p63alpha_Ker_RNA_R3

value: Trp63-Ex13fl/fl (p63alpha)


title: 6026818155_R02C02 whole blood

value: M


title: K89_FPKM

city: Taipei

institute: Academia Sinica

data_processing:
The sequence was determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA).
Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: renal tissue

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. MACHEREY-NAGEL NuceloSpin RNA Kit (Cat#740955.50) was used with 1 ug of total RNA for the construction of sequencing libraries.
Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

tag: strain

value: BALB/c

value: post natal week 8

tag: gender

value: male

tag: time point


title: DSS_D5, DSS, day 5, replicate 1

description:
Library name: 2_2
Record-seq

tag: tissue


title: K87_FPKM


title: DSS_D5, DSS, day 5, replicate 2

description:
Library name: 2_3
Record-seq


title: HC_D9, water, day 9, replicate 3

description:
Library name: 5_7
Record-seq


title: 6026818155_R01C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: N


title: p63alpha_Ker_RNA_R2

tag: cell type

tag: genotype


title: p63beta_Ker_RNA_R3


title: HC_D5, water, day 5, replicate 3

description:
Library name: 1_8
Record-seq


title: 6026818155_R01C01 whole blood

tag: sample id

value: Y


title: 6026818155_R03C01 whole blood

tag: subject id


title: p63alpha_Ker_RNA_R1


title: K83_FPKM


title: K81_FPKM


title: HC_D5, water, day 5, replicate 2

description:
Library name: 1_5
Record-seq


title: K91_FPKM


title: p63beta_ChIP_seq_H3K27ac

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing were mapped to the genome using the BWA algorithm (“bwa aln/samse” with default settings). Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. Duplicate reads (“PCR duplicates”) were removed.
Peaks were called using either the MACSa or SICERb algorithms. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Super-Enhancers were predicted using Active Motif’s proprietary algorithm.
Assembly: mm10
Supplementary files format and content: Enrichment regions in bed format and read pileup in bigwig format

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min at roome temperature and quenched by adding 0.125 M glycine for 10 min. The cells were washed with PBS, collected and shipped to Active Motif, where the ChIP with indicated antibodies was performed.
CUT&Tag-IT™ Assay Kit (Active Motif)

value: Cultered pirmary mouse keratinocytes

value: KRT14-Cre;Trp63-Ex13fl/fl (p63alpha)

value: Primary mouse keratinocytes were isolated from newborn mouse. Newborn mouse pups were sacrificed and the epidermises were separated from dermis by overnight incubation in trypsin. Epidermises were minced with scissors and triturated by pipetting several times. Single cells were filtered through a 100-μm cell strainer (Corning), centrifuged at 200 g for 5 min and plated in low calcium medium EMEM (Lonza, containing 8% chelate FBS, antibiotic/antimycotic solution (Sigma) and 0.05mM CaCl2) on dishes pre-coated with rat tail collagen type I (Corning). Twenty-four hours later, adherent cells were washed three times in PBS and collected.

tag: antibody

value: ChIP anti-H3K27ac antibody (Active Motif, #39133, lot 31521015), ab volume 4 ul, chromatin amount 4.25 ug)


title: 6026818149_R06C02 whole blood

tag: Sex

value: F


title: HC_D5, water, day 5, replicate 1

description:
Library name: 1_3
Record-seq


title: K79_FPKM

tag: age


title: 6026818149_R06C01 whole blood

tag: asthma


title: p63alpha_ChIP_seq_H3K27ac

value: Skin


title: stem tissue, PtrbHLH011 overexpression, biol rep 2

description:
DT6-1-SX3_1
Normalized_counts_PtrbHLH011 OE_stem.tabular

organism: Populus tremula x Populus alba

source_name: stem

value: stem

value: PtrbHLH011 OE


title: p63beta_ChIP_seq_p63

value: ChIP anti-p63 antibody (CST, #39692, lot 3), ab volume 25 ul, chromatin amount 12 ug)


title: stem tissue, PtrbHLH011 overexpression, biol rep 1

description:
DT6-1-SX1_1
Normalized_counts_PtrbHLH011 OE_stem.tabular


title: DSLc, DSS+Lc, day 5, replicate 1

description:
Library name: 34_5_1
Record-seq

value: Mouse gut microbiota


title: 6026818149_R04C02 whole blood


title: p63alpha_ChIP_seq_p63

value: Trp63-Ex13fl/fl (p63alpha)


title: stem tissue, empty vector control, biol rep 2

description:
Ctrl2-SX2_1
Normalized_counts_PtrbHLH011 OE_stem.tabular

value: Empty vector


title: Lc, day 5, replicate 2

description:
Library name: 33_4_1
Record-seq


title: stem tissue, empty vector control, biol rep 1

description:
Ctrl2-SX1_1
Normalized_counts_PtrbHLH011 OE_stem.tabular


title: T287A-Sham_3

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

data_processing:
The FastQC tool (version 0.11.8) was used for quality control to determine low quality and adaptor portion of the reads for trimming.
Trimmomatic (version 0.39) was used for read-trimming.
Trimmed reads were aligned to the mouse reference genome (mm10) using HiSAT2 (version 2.1.0, default settings).
Count matrix for each sample was produced by counting aligned reads using featureCounts (version 1.6.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Heart

extract_protocol:
RNeasy Micro Kit (Qiagen) was used to isolate RNA from whole hearts, according to manufacturer’s recommendations.
KAPA mRNA HyperPrep kit (Kapa Biosystems) was used according to the manufacturer's instructions to prepare the RNA sequencing libraries.

value: Heart

value: CaMKII{delta} T287A

value: Male

value: 12 weeks

tag: treatment

value: sham surgery at 10 weeks of age


title: leaf tissue, PtrbHLH011 overexpression, biol rep 3

description:
DT6-1-L3_1
Normalized_counts_PtrbHLH011 OE_leaf.tabular

value: leaf


title: T287A-Sham_2


title: 6026818149_R02C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: Y


title: DSLc, DSS+Lc, day 5, replicate 2

description:
Library name: 34_12_1
Record-seq


title: 6026818149_R05C02 whole blood

value: M


title: DSS, day 5, replicate 3

description:
Library name: 32_5_1
Record-seq


title: leaf tissue, PtrbHLH011 overexpression, biol rep 2

description:
DT6-1-L2_1
Normalized_counts_PtrbHLH011 OE_leaf.tabular


title: 6026818149_R01C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: N


title: Lc, day 5, replicate 3

description:
Library name: 33_5_1
Record-seq


title: T287A-Sham_1


title: 6026818149_R01C01 whole blood


title: leaf tissue, PtrbHLH011 overexpression, biol rep 1

description:
DT6-1-L1_1
Normalized_counts_PtrbHLH011 OE_leaf.tabular


title: p63_ChIP_seq_input

value: Skin

value: Cultered pirmary mouse keratinocytes

value: Primary mouse keratinocytes were isolated from newborn mouse. Newborn mouse pups were sacrificed and the epidermises were separated from dermis by overnight incubation in trypsin. Epidermises were minced with scissors and triturated by pipetting several times. Single cells were filtered through a 100-μm cell strainer (Corning), centrifuged at 200 g for 5 min and plated in low calcium medium EMEM (Lonza, containing 8% chelate FBS, antibiotic/antimycotic solution (Sigma) and 0.05mM CaCl2) on dishes pre-coated with rat tail collagen type I (Corning). Twenty-four hours later, adherent cells were washed three times in PBS and collected.

value: Input


title: T287A-sTAC_3

value: sTAC surgery at 10 weeks of age


title: DSS, day 5, replicate 1

description:
Library name: 32_2_1
Record-seq

value: Mouse gut microbiota


title: 6026818149_R04C01 whole blood

value: F


title: 6026818149_R03C02 whole blood


title: leaf tissue, empty vector control, biol rep 3

description:
Ctrl2-L3_1
Normalized_counts_PtrbHLH011 OE_leaf.tabular

value: Empty vector


title: T287A-sTAC_2

value: Heart

value: CaMKII{delta} T287A


title: Lc, day 5, replicate 1

description:
Library name: 33_3_1
Record-seq


title: 6026818062_R06C02 whole blood


title: Con, day 5, replicate 3

description:
Library name: 31_8_1
Record-seq


title: leaf tissue, empty vector control, biol rep 2

description:
Ctrl2-L2_1
Normalized_counts_PtrbHLH011 OE_leaf.tabular


title: 6026818062_R06C01 whole blood


title: T287A-sTAC_1

value: Male

value: 12 weeks


title: Con, day 5, replicate 2

description:
Library name: 31_5_1
Record-seq


title: leaf tissue, empty vector control, biol rep 1

description:
Ctrl2-L1_1
Normalized_counts_PtrbHLH011 OE_leaf.tabular

value: leaf


title: 6026818062_R05C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: DSS, day 5, replicate 2

description:
Library name: 32_3_1
Record-seq


title: WT-Sham_3

value: WT, C57Bl6

value: sham surgery at 10 weeks of age


title: Con, day 5, replicate 1

description:
Library name: 31_3_1
Record-seq


title: 6026818062_R04C02 whole blood

value: Y


title: protoplast, PtrbHLH011, Input, biol rep 3

data_processing:
Clean reads were obtained by filtering raw reads to remove adapter sequences and low-quality reads.
clean reads were mapped to the reference genome of Populus tremula and Populus alba (www.aspendb.org), respectively, using the BWA-MEM package (v0.7.17.2)
Mapped data from ChIP samples and Input samples from three biological replicates were then pooled for peak calling using MACS2 (v2.2.7.1).
The ChIPseeker package (v1.18.0) was then used to annotate narrow peaks identified by MACS2.
Assembly: sPta717alba and sPta717tremula (www.aspendb.org)
Supplementary files format and content: Excel files for annotated narrowpeaks

source_name: Mesophyll protoplast

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 mins. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonicator (Diagenode)
ChIP-seq libraries were prepared using the ThruPLEX DNA-Seq Kit and DNA Unique Dual Index Kit (Takara) according to the manufacturer’s manual

value: Mesophyll protoplast

value: PtrbHLH011-10xMyc was transiently expressed

tag: chip antibody


title: 6026818062_R04C01 whole blood

value: M

value: N


title: WT-Sham_1


title: WT-Sham_2


title: 6026818062_R03C02 whole blood


title: WT-sTAC_3

value: sTAC surgery at 10 weeks of age


title: protoplast, PtrbHLH011, Input, biol rep 1


title: WT-sTAC_2


title: protoplast, PtrbHLH011, Input, biol rep 2


title: 6026818062_R03C01 whole blood


title: protoplast, PtrbHLH011, ChIP, biol rep 3

value: anti-Myc


title: WT-sTAC_1


title: 6026818062_R02C01 whole blood


title: protoplast, PtrbHLH011, ChIP, biol rep 2


title: 6026818062_R01C01 whole blood

value: F


title: protoplast, PtrbHLH011, ChIP, biol rep 1