title: CH077 CEMM7 31dpi

description:
379_8
Counts CH077 in CEMM7.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: sham_aob_decomp_#24_RV_rep1

status: Public on Apr 15 2024

type: SRA

city: Giessen

first: Axel

last: Weber

state: Hesse

address: Schubertstrasse 81

department: Rudolf Buchheim Institute of Pharmakology

country: Germany

institute: Justus-Liebig-University Giessen

description:
col_names:"raw_reads.sham_PAB_decomp_#24_RV", "normalized_reads.sham_PAB_decomp_#24_RV", "fpkm.sham_PAB_decomp_#24_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1039

library_source: transcriptomic

data_processing:
Nexflow nf/core rna_seq v1.5 dev
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore integrated into nf-core/rnaseq (parameter- Quality limit: 20)
Trimmed reads were mapped to rnor6 usinf STAR integrated into nf-core/rnaseq (default parameters)
Readcount extraction was perfomed using FeatureCounts integrated into nf-core/rnaseq
Normalization and differential expression analysis was performed using DEseq2 for Galaxy (using DEseq2's internal median based normalization)
Assembly: rnor6
Supplementary files format and content: bigwig files
Supplementary files format and content: unnormalized read count, DEseq2-normalized read count and FPKM count tables in single CSV file
Supplementary files format and content: DEseq2 Output in two Excel files

molecule: polyA RNA

organism: Rattus norvegicus

source_name: right ventricle

extract_protocol:
RNA was extracted using TRIzol, cleaned using Macherey & Nagel Nucleospin RNA kit
Libraries were prepared using NEBnext Ultra II RNA Library kit with poly-A Enrichment module according to manual;  0.67ng of RNA were used for library preparation

treatment_protocol: 6 month old weanling rats were clipped nonconstrictively at the pulmonary artery or aorta respectively. Compensatory hypertrophy of left or right ventricle developed 7 weeks after banding, after which the samples for tehe compensatory phase were harvested. Heart failure developed 21 (right ventricle) or 25 (left ventricle) weeks, after which decompensatory samples were harvested

tag: strain background

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

tag: tissue

value: whole heart; left ventricle

tag: Sex

value: male

tag: animal id

tag: age

value: 30 weeks

tag: treatment

value: sham

tag: disease progression

value: decompensatory

tag: treatment time

value: 24 weeks


title: R62_AOB-F_m_RV_#108_rep3

description:
col_names:"raw.reads.AOB_decompensatory_male_#108_RV", "normalized.reads.AOB_decompensatory_male_#108_RV", "fpkm.AOB_decompensatory_male_#108_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

data_processing:
Nexflow nf/core rna_seq v3.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore integrated into nf-core/rnaseq (parameter- Quality limit: 20)
Trimmed reads were mapped to rnor6 usinf STAR integrated into nf-core/rnaseq (default parameters)
Readcount extraction was perfomed using FeatureCounts (Rsubreads v2.2.6), disallowing multiple overlap
Normalization and differential expression analysis was performed using DEseq2 1.28.1, using the independed filtering option and beta_prior LFC-shrinkage
Assembly: rnor6
Supplementary files format and content: bigwig files
Supplementary files format and content: unnormalized read count, DEseq2-normalized read count and FPKM count tables in single csv-file
Supplementary files format and content: DEseq2 Output in Excel file

molecule: total RNA

extract_protocol:
After extraction and perfusion for cleanup, fre hearts were digested using collagenase II in a Langendorff aparatus for 25 minutes. Afterwards the ventricles were seperated, cut into small pieces and digested again with collagenase II for 5min. Afterwards the suspension was filtered using a nylon filter (200µm), and cardiac myocytes seperated from other cell types via a series of centrifugation steps.
RNA was extracted  using Macherey & Nagel Nucleospin RNA kit
Libraries were prepared by Novagene using a rRNA depletion strategy

treatment_protocol: 6 month old weanling rats were clipped nonconstrictively at the pulmonary artery or aorta respectively. Compensatory hypertrophy of left or right ventricle developed 7 weeks after banding, after which the samples for the compensatory phase were harvested. Heart failure developed 22 (right ventricle) or 26 (left ventricle) weeks, after which decompensatory samples were harvested

tag: cell type

value: cardiac myocytes

value: right ventricle

value: 31 weeks

value: aortic banding

value: 26 weeks


title: R66_AOB-F_f_RV_#86_rep5

description:
col_names:"raw.reads.AOB_decompensatory_female_#86_RV", "normalized.reads.AOB_decompensatory_female_#86_RV", "fpkm.AOB_decompensatory_female_#86_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: female


title: CH077 CEMM7 20dpi IFN

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

description:
379_7
Counts CH077 in CEMM7.xlsx

library_source: other

data_processing:
SeqPrep to merge paired ends into one file (Using Galaxy)
FastQC for quality control (Using Galaxy)
MAGeCK count using the gRNA_list_by_gene.tab (in supplementary file) to attribute each read to a unique gRNA and a gene (Using Galaxy)
MAGeCK test comparing either one time point to input virus or dNef to WT for the same time point using the normalized counts file from the MAGeCK count (Using Galaxy)
Assembly: gRNA list are indicated in gRNA_list_by_gene.tab (in supplementary file)
Supplementary files format and content: "Counts" file are the output of the MAGeCK count showing normalized counts of the gRNA listed by genes taregtted
Supplementary files format and content: "Test" file are the genes output of the MAGeCK Test showing enrichement of the targetted genes in the condition compared to a refence condition
Supplementary files format and content: "Test sgRNA" file are the sgRNA output of the MAGeCK Test showing enrichement of the targetted genes in the condition compared to a refence condition

molecule: other

organism: Human immunodeficiency virus 1

source_name: Virus-containing supernatant

growth_protocol: Supernatants are collected from HIV-1 infected cell lines at various time points and after passaging of the cells. The virus in the supernantant is concentrated and lysed

extract_protocol:
Total RNA was isolated using the Viral RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
cDNA reactions were performed according to the manufacturer’s instructions of the PrimeScript™ RT Reagent Kit (Takara) using primers specifically targeting the U6 and scaffold region (forward primer 5´-CCGACTCGGTGCCACTTTTT-3´, reverse primer 5´-CGTGACGTAGAAAGTAATAATTT-CTTGGG-3´). cDNA reactions were purified using the Monarch PCR Purification Kit (NEB) and eluted in 10µl elution buffer. The gRNA cassette was amplified using the NEBNext® High-Fidelity 2X PCR Master Mix and primers including Illumina adaptors and 8nt barcodes to allow Next Generation Sequencing (NGS) analysis. PCR reactions were purified using the Monarch PCR Purification Kit (NEB) and eluted in 10µl elution buffer.

treatment_protocol: For samples indicated, cells were treated with 1000U/mL of IFN-β for CEMM7 Cas9 cells and repleanished every 3 days or with 100U/mL of IFN-β for SupT1 CCR5 Cas9 cells

tag: cell line

value: Cell line

value: IFN-β


title: B cells, IL-4+anti-CD40, vehicle, replicate 1, exp1

city: Bunkyo-ku

first: Etsuko

last: Toda

state: Tokyo

country: Japan

institute: Nippon Medical School

description:
IL4CD40_1
gene_count_1
gene_fpkm_1

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using Fastp (remove reads containing N>10% ; remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50% of the read)
Trimmed sequence reads were mapped to mm10 using HISAT2 v2.0.5 (parameter: Default)
Read count extraction and normalization were performed using featureCounts v1.5.0-p3
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Mus musculus

source_name: Spleen

growth_protocol: B cells were isolated and seeded at 4 × 100000 cells/well in 48-well plates and culture for 3 hours in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted from the cell samples using the RNeasy Mini kit (Qiagen) and frozen at -80 °C for next-generation RNA sequencing (Novogene, Beijing, China).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: B cells without stimulation and without inhibitor (NS_DMSO), stimulated with LPS without inhibitor (LPS_DMSO), stimulated with IL-4 + anti-CD40 without inhibitor (IL4CD40_DMSO), stimulated with LPS and treated with 1 uM DSF (LPS_DSF) or ibrutinib (LPS_IBRU), and stimulated with IL-4 + anti-CD40 and treated with 1 uM DSF (IL4CD40_DSF)or ibrutinib (IL4CD40_IBRU).

value: Spleen

tag: strain

value: B cell

tag: genotype

value: WT


title: B cells, LPS, disulfiram, replicate 4 exp1

description:
LPSDSF_4
gene_count_1
gene_fpkm_1

value: LPS+disulfiram


title: B cells, IL-4+anti-CD40, vehicle, replicate 2, exp1

description:
IL4CD40_2
gene_count_1
gene_fpkm_1


title: R60_AOB-F_m_RV_#105_rep2

description:
col_names:"raw.reads.AOB_decompensatory_male_#105_RV", "normalized.reads.AOB_decompensatory_male_#105_RV", "fpkm.AOB_decompensatory_male_#105_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: male


title: sham_aob_decomp_#24_LV_rep1

description:
col_names:"raw_reads.sham_AOB_decomp_#24_LV", "normalized_reads.sham_AOB_decomp_#24_LV", "fpkm.sham_AOB_decomp_#24_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1038

source_name: left ventricle

value: whole heart

value: left ventricle

value: 30 weeks

value: sham


title: CH077 CEMM7 20dpi

description:
379_6
Counts CH077 in CEMM7.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: CH077 CEMM7 11dpi IFN

description:
379_5
Counts CH077 in CEMM7.xlsx


title: B cells, LPS, disulfiram, replicate 3, exp1

description:
LPSDSF_3
gene_count_1
gene_fpkm_1


title: R59_AOB-F_m_LV_#105_rep2

description:
col_names:"raw.reads.AOB_decompensatory_male_#105_LV", "normalized.reads.AOB_decompensatory_male_#105_LV", "fpkm.AOB_decompensatory_male_#105_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: 31 weeks

value: aortic banding

value: decompensatory


title: PAB_decomp_#36_LV_rep3

description:
col_names:"raw_reads.PAB_decomp_#36_LV", "normalized_reads.PAB_decomp_#36_LV", "fpkm.PAB_decomp_#36_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1036

value: 27 weeks

value: pulmonary artery banding

value: 21 weeks


title: PAB_decomp_#36_RV_rep3

description:
col_names:"raw_reads.PAB_decomp_#36_RV", "normalized_reads.PAB_decomp_#36_RV", "fpkm.PAB_decomp_#36_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1037

value: whole heart; left ventricle


title: B cells, LPS, disulfiram, replicate 2, exp1

description:
LPSDSF_2
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT

value: LPS+disulfiram


title: R58_AOB-F_m_RV_#82_rep1

description:
col_names:"raw.reads.AOB_decompensatory_male_#82_RV", "normalized.reads.AOB_decompensatory_male_#82_RV", "fpkm.AOB_decompensatory_male_#82_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: right ventricle

value: male

value: 26 weeks


title: sham_pab_decomp_#31_RV_rep2

description:
col_names:"raw_reads.sham_PAB_decomp_#31_RV", "normalized_reads.sham_PAB_decomp_#31_RV", "fpkm.sham_PAB_decomp_#31_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1035

value: sham


title: B cells, LPS, disulfiram, replicate 1, exp1

description:
LPSDSF_1
gene_count_1
gene_fpkm_1


title: R57_AOB-F_m_LV_#82_rep1

description:
col_names:"raw.reads.AOB_decompensatory_male_#82_LV", "normalized.reads.AOB_decompensatory_male_#82_LV", "fpkm.AOB_decompensatory_male_#82_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: left ventricle


title: sham_pab_decomp_#31_LV_rep2

description:
col_names:"raw_reads.sham_PAB_decomp_#31_LV", "normalized_reads.sham_PAB_decomp_#31_LV", "fpkm.sham_PAB_decomp_#31_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1034

value: whole heart


title: CH077 CEMM7 5dpi IFN

description:
379_3
Counts CH077 in CEMM7.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line

value: IFN-β


title: CH077 CEMM7 5dpi

description:
379_2
Counts CH077 in CEMM7.xlsx


title: R56_Sham-F_f_RV_#114_rep9

description:
col_names:"raw.reads.sham_decompensatory_female_#114_RV", "normalized.reads.sham_decompensatory_female_#114_RV", "fpkm.sham_decompensatory_female_#114_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: female

value: 31 weeks

value: decompensatory


title: PAB_decomp_#32_RV_rep2

description:
col_names:"raw_reads.PAB_decomp_#32_RV", "normalized_reads.PAB_decomp_#32_RV", "fpkm.PAB_decomp_#32_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1033

value: whole heart; left ventricle

value: 27 weeks

value: pulmonary artery banding

value: 21 weeks


title: R61_AOB-F_m_LV_#108_rep3

description:
col_names:"raw.reads.AOB_decompensatory_male_#108_LV", "normalized.reads.AOB_decompensatory_male_#108_LV", "fpkm.AOB_decompensatory_male_#108_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: male

value: aortic banding


title: CH077 CEMM7 Input

description:
379_1
Counts CH077 in CEMM7.xlsx

source_name: Virus stock

value: Virus stock


title: B cells, LPS, vehicle, replicate 3, exp1

description:
LPS_3
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT

value: LPS


title: B cells, LPS, vehicle, replicate 2, exp1

description:
LPS_2
gene_count_1
gene_fpkm_1


title: NL4.3 CEMM7 n=3 20dpi IFN

description:
362_26
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line


title: PAB_decomp_#32_LV_rep2

description:
col_names:"raw_reads.PAB_decomp_#32_LV", "normalized_reads.PAB_decomp_#32_LV", "fpkm.PAB_decomp_#32_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1032

value: whole heart

value: left ventricle


title: R54_Sham-F_f_RV_#113_rep8

description:
col_names:"raw.reads.sham_decompensatory_female_#113_RV", "normalized.reads.sham_decompensatory_female_#113_RV", "fpkm.sham_decompensatory_female_#113_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: female

value: 31 weeks

value: sham

value: decompensatory

value: 26 weeks


title: B cells, LPS, vehicle, replicate 1, exp1

description:
LPS_1
gene_count_1
gene_fpkm_1


title: PAB_decomp_#28_RV_rep1

description:
col_names:"raw_reads.PAB_decomp_#28_RV", "normalized_reads.PAB_decomp_#28_RV", "fpkm.PAB_decomp_#28_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1031

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: male

value: 27 weeks

value: pulmonary artery banding

value: 21 weeks


title: NL4.3 dNef CEMM7 20dpi

description:
410_7
Counts dNef vs WT.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: NL4.3 CEMM7 n=3 15dpi IFN

description:
362_24
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test sgRNA NL4.3 CEMM7 15dpi IFN vs input N=1-3.xlsx

value: Cell line

value: IFN-β


title: NL4.3 CEMM7 n=3 20dpi

description:
362_25
Counts NL4.3 in CEMM7 N=1-3.xlsx


title: PAB_decomp_#28_LV_rep1

description:
col_names:"raw_reads.PAB_decomp_#28_LV", "normalized_reads.PAB_decomp_#28_LV", "fpkm.PAB_decomp_#28_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1030

value: whole heart

value: left ventricle


title: NL4.3 CEMM7 n=3 15dpi

description:
362_23
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test sgRNA NL4.3 CEMM7 15dpi untreated vs input N=1-3.xlsx


title: R52_Sham-F_f_RV_#112_rep7

description:
col_names:"raw.reads.sham_decompensatory_female_#112_RV", "normalized.reads.sham_decompensatory_female_#112_RV", "fpkm.sham_decompensatory_female_#112_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: female


title: CH077 CEMM7 11dpi

description:
379_4
Counts CH077 in CEMM7.xlsx


title: R53_Sham-F_f_LV_#113_rep8

description:
col_names:"raw.reads.sham_decompensatory_female_#113_LV", "normalized.reads.sham_decompensatory_female_#113_LV", "fpkm.sham_decompensatory_female_#113_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: 31 weeks

value: sham

value: decompensatory


title: NL4.3 CEMM7 n=3 10dpi IFN

description:
362_22
Counts NL4.3 in CEMM7 N=1-3.xlsx


title: B cells, unstimulated, replicate 3, exp1

description:
NS_3
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT

value: No stimuli


title: B cells, unstimulated, replicate 2, exp1

description:
NS_2
gene_count_1
gene_fpkm_1


title: AOB_#20_RV_rep4

description:
col_names:"raw_reads.AOB_comp_#20_RV", "normalized_reads.AOB_comp_#20_RV", "fpkm.AOB_comp_#20_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1027

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: male

value: 11 weeks

value: aortic banding

value: compensatory

value: 7 weeks


title: R50_Sham-F_f_RV_#95_rep6

description:
col_names:"raw.reads.sham_decompensatory_female_#95_RV", "normalized.reads.sham_decompensatory_female_#95_RV", "fpkm.sham_decompensatory_female_#95_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: 26 weeks


title: B cells, LPS, vehicle, replicate 4, exp1

description:
LPS_4
gene_count_1
gene_fpkm_1

value: LPS


title: R51_Sham-F_f_LV_#112_rep7

description:
col_names:"raw.reads.sham_decompensatory_female_#112_LV", "normalized.reads.sham_decompensatory_female_#112_LV", "fpkm.sham_decompensatory_female_#112_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: female

value: 31 weeks


title: NL4.3 CEMM7 n=3 10dpi

description:
362_21
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line


title: R55_Sham-F_f_LV_#114_rep9

description:
col_names:"raw.reads.sham_decompensatory_female_#114_LV", "normalized.reads.sham_decompensatory_female_#114_LV", "fpkm.sham_decompensatory_female_#114_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: sham

value: decompensatory


title: B cells, unstimulated, replicate 1, exp1

description:
NS_1
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT

value: No stimuli


title: R49_Sham-F_f_LV_#95_rep6

description:
col_names:"raw.reads.sham_decompensatory_female_#95_LV", "normalized.reads.sham_decompensatory_female_#95_LV", "fpkm.sham_decompensatory_female_#95_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat


title: NL4.3 CEMM7 n=3 5dpi

description:
362_20
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: IFN-β


title: E14.5_Ikba_LT-HSC_2  [Cut&Tag]

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description: Read length: 150bp

library_source: genomic

data_processing:
Followed steps for data preprocessing (i) Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap.
(ii) Trimmed reads were aligned to GRCm38 reference genome with Bowtie2 aligner tool (v2.4.4) (Langmead & Salzberg, 2012). Reference genome was retrieved from Ensembl FTP site (http://ftp.ensembl.org/pub/release-102/).
(iii) Bowtie2 was executed with following parameters: --no-mixed –no-discordant –dovetail –very-sensitive-local. Multi-mapped reads and those reads showing MAPQ < 20 were filtered out.
(iv) [Only applicable for H3K27me3 samples] Peak calling was performed with SEACR (v1.3) in stringent mode without considering IgG control sample (Meers et al., 2019). For this purpose, required input bedgraph files were obtained from deduplicated BAM files using bedtools (v2.30) following SEACR authors guidelines (Quinlan & Hall, 2010). The top 0.5% of peaks were retrieved for downstream analysis.
(v) BigWig files were obtained from BAM files with duplicates using deepTools (v3.5.1)
Assembly: mm10
Supplementary files format and content: BigWig files and detected SEACR peaks in .bed files (only applicable for H3K27me3 experiments)
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: fetal liver

growth_protocol: Primary E14.5 fetal liver LT-HSCs and AGM CD31+ cells were obstained by disecting fetal liver or AGMs from E14.5 or E11.5 embryos folled by FACS sorting.

extract_protocol:
cut and tag experiments were performed on lightly fixed cell suspension and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with unique index primers and NEBNext HiFi 2x PCR Master mix (cat#M0541S) as decribed in bentop cut and tag v3.

tag: developmental time

value: fetal liver

tag: cells

tag: antibody

value: anti IkB-a targeting pIkBa Ser32


title: R48_Sham-F_f_RV_#93_rep5

description:
col_names:"raw.reads.sham_decompensatory_female_#93_RV", "normalized.reads.sham_decompensatory_female_#93_RV", "fpkm.sham_decompensatory_female_#93_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: 26 weeks


title: PAB_#19_RV_rep4

description:
col_names:"raw_reads.PAB_comp_#19_RV", "normalized_reads.PAB_comp_#19_RV", "fpkm.PAB_comp_#19_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1025

value: whole heart; left ventricle

value: male

value: 11 weeks

value: pulmonary artery banding

value: compensatory

value: 7 weeks


title: sham_pab_decomp_#30_RV_rep1

description:
col_names:"raw_reads.sham_PAB_decomp_#30_RV", "normalized_reads.sham_PAB_decomp_#30_RV", "fpkm.sham_PAB_decomp_#30_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1029

value: 27 weeks

value: sham

value: decompensatory

value: 21 weeks


title: B cells, unstimulated, replicate 4, exp1

description:
NS_4
gene_count_1
gene_fpkm_1

value: Spleen

value: B cell

value: WT

value: No stimuli


title: R47_Sham-F_f_LV_#93_rep5

description:
col_names:"raw.reads.sham_decompensatory_female_#93_LV", "normalized.reads.sham_decompensatory_female_#93_LV", "fpkm.sham_decompensatory_female_#93_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: left ventricle

value: female

value: 31 weeks


title: naive mice, biol rep4

city: San Diego

first: Xin

last: Sun

state: CA

address: 9500 Gilman Dr., CMME, Room 1055

department: Department of Pediatrics, Department of Biological Sciences

country: USA

institute: UNIVERSITY OF CALIFORNIA AT SAN DIEGO

description:
Raw data in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object.
Reads alignment files in fastqs-intergrated_Yujuan_nTS_WT.rds

library_source: transcriptomic single cell

data_processing:
Sequencing was carried out on NovaSeq (Illumina) platform at the Institute for Genomic Medicine, UCSD.
Cell Ranger package (version 3.0.2) was used to align the raw reads onto the mouse reference genome (GRCm38) with default parameters and generate the feature-barcode matrix.
CellBender (v0.3.0) was then used to remove technical artifacts and ambient RNA to produce improved estimates of gene expression.
R package Seurat (v4.0) was then used to perform data quality control, normalization, principal components analysis, uniform manifold approximation and projection (UMAP) generation, and differential gene expression testing.
Nuclei with <5% mitochondrial reads and greater than 2,000 unique genes were considered high quality cells and filtered for further analyses, following the filtering criteria commonly used in neuronal snRNA-seq studies including those on brainstem neurons. Additionally, DoubletFinder (v2.0) was used to remove doublets and SCTransform was used to normalize feature expression. Harmony (v1.2.0) was used to integrate individual datasets across three conditions (naive, saline, HDM).
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary files format and content: For data from all conditions(WT, Saline or HDM-treated mice): Raw data-Reads alignment files in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object.

molecule: nuclear RNA

growth_protocol: All Mice used in this experiment are bred in the standard facility of UCSD with approval protocol from IACUC

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics Chromium Controller (10x Genomics, Pleasanton, CA) to generate single cell GEMs. cDNA extraction and amilification were excecuted using Chromium Single Cell 3' Reagent Kits (v3 Chemistry, PN-1000075, 10X Genomics) folloing User Guide provided by 10X Genomics.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v3 (PN-1000075, 10x Genomics) following User Guide provided by 10X Genomics.
scRNA-seq library for 10X Genomics sequencing

treatment_protocol: Saline or house dust mite (HDM) intranasal delivery to the mice

value: tissue-solitary nucleus of the brainstem

value: age and sex:12week, male

value: wild-type

value: no treatment


title: NL4.3 CEMM7 n=2 20dpi

description:
362_17
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 20 dpi untreated.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line


title: sham_pab_decomp_#30_LV_rep1

description:
col_names:"raw_reads.sham_PAB_decomp_#30_LV", "normalized_reads.sham_PAB_decomp_#30_LV", "fpkm.sham_PAB_decomp_#30_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1028

value: whole heart

value: male

value: 27 weeks

value: sham

value: decompensatory

value: 21 weeks


title: sham_#17_RV_rep4

description:
col_names:"raw_reads.sham_comp_#17_RV", "normalized_reads.sham_comp_#17_RV", "fpkm.sham_comp_#17_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1023

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: 11 weeks

value: compensatory

value: 7 weeks


title: NL4.3 CEMM7 n=2 20dpi IFN

description:
362_18
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 20 dpi IFN.xlsx

value: IFN-β


title: Thyroid, Tbx3Δthy-2 [KO3]

city: Tianjin

first: Zhenlei

last: Zhang

address: Qixiangtai Road 22

country: China

institute: Tianjin Medical University

data_processing:
Filter. In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads);
Alignment. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
FPKM. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM for each Sample

source_name: thyroid

extract_protocol:
RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: thyroid

value: Tpo-Cre


title: AOB_#9_RV_rep3

description:
col_names:"raw_reads.AOB_comp_#9_RV", "normalized_reads.AOB_comp_#9_RV", "fpkm.AOB_comp_#9_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1021

value: aortic banding


title: Thyroid, Tbx3Δthy-1 [KO1]


title: NL4.3 CEMM7 n=2 15dpi

description:
362_15
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 15 dpi untreated.xlsx
Test sgRNA NL4.3 CEMM7 15dpi untreated vs input N=1-3.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: PAB_#19_LV_rep4

description:
col_names:"raw_reads.PAB_comp_#19_LV", "normalized_reads.PAB_comp_#19_LV", "fpkm.PAB_comp_#19_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1024

value: whole heart

value: left ventricle

value: pulmonary artery banding


title: R45_Sham-F_m_LV_#109_rep4

description:
col_names:"raw.reads.sham_decompensatory_male_#109_LV", "normalized.reads.sham_decompensatory_male_#109_LV", "fpkm.sham_decompensatory_male_#109_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: male

value: 31 weeks

value: sham

value: 26 weeks


title: R44_Sham-F_m_RV_#96_rep3

description:
col_names:"raw.reads.sham_decompensatory_male_#96_RV", "normalized.reads.sham_decompensatory_male_#96_RV", "fpkm.sham_decompensatory_male_#96_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: right ventricle

value: decompensatory


title: NL4.3 CEMM7 n=2 15dpi IFN

description:
362_16
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 15 dpi IFN.xlsx
Test sgRNA NL4.3 CEMM7 15dpi IFN vs input N=1-3.xlsx

value: Cell line

value: IFN-β


title: AOB_#20_LV_rep4

description:
col_names:"raw_reads.AOB_comp_#20_LV", "normalized_reads.AOB_comp_#20_LV", "fpkm.AOB_comp_#20_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1026

value: 11 weeks

value: compensatory

value: 7 weeks


title: NL4.3 CEMM7 n=2 10dpi IFN

description:
362_14
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 10 dpi IFN.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: R43_Sham-F_m_LV_#96_rep3

description:
col_names:"raw.reads.sham_decompensatory_male_#96_LV", "normalized.reads.sham_decompensatory_male_#96_LV", "fpkm.sham_decompensatory_male_#96_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle


title: Thyroid, Tbx3+/+-1 [WT1]

value: thyroid

value: WT

value: Tpo-Cre


title: AOB_#9_LV_rep3

description:
col_names:"raw_reads.AOB_comp_#9_LV", "normalized_reads.AOB_comp_#9_LV", "fpkm.AOB_comp_#9_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1020

value: whole heart

value: male

value: aortic banding


title: NL4.3 CEMM7 n=3 Input

description:
362_19
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: Virus stock


title: R42_Sham-F_m_RV_#92_rep2

description:
col_names:"raw.reads.sham_decompensatory_male_#92_RV", "normalized.reads.sham_decompensatory_male_#92_RV", "fpkm.sham_decompensatory_male_#92_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: right ventricle

value: 31 weeks

value: sham

value: 26 weeks


title: NL4.3 CEMM7 n=2 10dpi

description:
362_13
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 10 dpi untreated.xlsx

value: Cell line


title: PAB_#6_RV_rep3

description:
col_names:"raw_reads.PAB_comp_#6_RV", "normalized_reads.PAB_comp_#6_RV", "fpkm.PAB_comp_#6_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1019

value: whole heart; left ventricle

value: 11 weeks

value: pulmonary artery banding

value: compensatory

value: 7 weeks


title: R41_Sham-F_m_LV_#92_rep2

description:
col_names:"raw.reads.sham_decompensatory_male_#92_LV", "normalized.reads.sham_decompensatory_male_#92_LV", "fpkm.sham_decompensatory_male_#92_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: decompensatory


title: R46_Sham-F_m_RV_#109_rep4

description:
col_names:"raw.reads.sham_decompensatory_male_#109_RV", "normalized.reads.sham_decompensatory_male_#109_RV", "fpkm.sham_decompensatory_male_#109_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: male


title: PAB_#6_LV_rep3

description:
col_names:"raw_reads.PAB_comp_#6_LV", "normalized_reads.PAB_comp_#6_LV", "fpkm.PAB_comp_#6_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1018

value: whole heart


title: naive mice, biol rep3

description:
Raw data in fastqs format. UMI count matrix files (h5) from cellranger. Seurat object in R object.
Reads alignment files in fastqs-intergrated_Yujuan_nTS_WT.rds

value: tissue-solitary nucleus of the brainstem

value: age and sex:12week, male

value: wild-type

value: no treatment


title: NL4.3 CEMM7 n=2 5dpi

description:
362_12
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 5 dpi untreated.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: IFN-β


title: Liver, 3 hour, nevirapine, rep2

city: Toronto

first: Jack

last: Uetrecht

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

data_processing:
Data processing was performed by The Centre for Applied Genomics Bioinformatics Facility at The Hospital for Sick Children (Toronto, ON). Reads were trimmed using Trim Galore version 0.5.0 (https://github.com/FelixKrueger/TrimGalore) and fastq.gz files were aligned to the GRCm39 mouse reference genome using STAR aligner version 2.6.0c (Dobin et al. 2013) using M27 Gencode gene annotation. Raw read counts were extracted using htseq-count version 0.6.1p2 (Anders et al. 2015).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Liver

extract_protocol:
Animals were euthanized by CO2 exsanguination. Liver tissue was removed and placed in at least 10 volumes of RNAlater solution and stored at 4C for at least 1 week. RNAlater-treated samples (30 mg) were disrupted using a Polytron homogenizer in 500 μL TRIzol reagent. Samples were vortexed with 100 μL chloroform, incubated at room temperature for 5 minutes, and centrifuged at 13,200 rpm for 15 minutes. The aqueous phase was placed in a new tube and diluted with an equal volume of freshly prepared 70% ethanol. RNA extraction was performed using an RNEasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA was quantified using an Ultrospec 2100 pro UV/visible spectrophotometer (Biochrom).
Library preparation was performed by The Centre for Applied Genomics Sequencing Facility at The Hospital for Sick Children (Toronto, ON) using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s protocol for use with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) with 300 ng of total RNA used as input material. Library quality was assessed using a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies), and RNA libraries were quantified by RT-qPCR using the Kapa Library Quantification Kit for Illumina platforms using the ABI Prism Kit protocol (KAPA Biosystems).

treatment_protocol: Nevirapine, as a suspension in 0.5% methylcellulose dissolved in phosphate-buffered saline (PBS), was administered at doses up to 400 mg/kg by oral gavage due to its limited solubility. To maintain consistency across experiments, nevirapine was administered starting at 8 AM on the day of the experiment. Vehicle control-treated animals were administered an equivalent volume of 0.5% methylcellulose in PBS. Animals were given ad libitum access to food and water throughout the study.

value: Male

value: Liver

tag: drug administration_route

value: Oral gavage

value: Nevirapine (400 mg/kg


title: Liver, 3 hour, nevirapine, rep3


title: NL4.3 CEMM7 n=2 Input

description:
362_11
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: Virus stock


title: sham_#4_RV_rep3

description:
col_names:"raw_reads.sham_comp_#4_RV", "normalized_reads.sham_comp_#4_RV", "fpkm.sham_comp_#4_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1017

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: 11 weeks

value: sham

value: compensatory

value: 7 weeks


title: Thyroid, Tbx3+/+-2 [WT3]

value: thyroid

value: WT

value: Tpo-Cre


title: Liver, 3 hour, nevirapine, rep1


title: R40_Sham-F_m_RV_#91_rep1

description:
col_names:"raw.reads.sham_decompensatory_male_#91_RV", "normalized.reads.sham_decompensatory_male_#91_RV", "fpkm.sham_decompensatory_male_#91_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

value: male

value: 31 weeks

value: decompensatory

value: 26 weeks


title: R39_Sham-F_m_LV_#91_rep1

description:
col_names:"raw.reads.sham_decompensatory_male_#91_LV", "normalized.reads.sham_decompensatory_male_#91_LV", "fpkm.sham_decompensatory_male_#91_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle


title: sham_#4_LV_rep3

description:
col_names:"raw_reads.sham_comp_#4_LV", "normalized_reads.sham_comp_#4_LV", "fpkm.sham_comp_#4_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1016

value: whole heart


title: sham_#17_LV_rep4

description:
col_names:"raw_reads.sham_comp_#17_LV", "normalized_reads.sham_comp_#17_LV", "fpkm.sham_comp_#17_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N1022

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat


title: Liver, 3 hour, vehicle, rep3

value: Male

value: Liver

value: Oral gavage

value: Vehicle control (0.5% methylcellulose in phosphate-buffered saline)


title: R38_PAB-H_f_RV_#173_rep6

description:
col_names:"raw.reads.PAB_compensatory_female_#173_RV", "normalized.reads.PAB_compensatory_female_#173_RV", "fpkm.PAB_compensatory_female_#173_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: female

value: 11 weeks

value: pulmonary artery banding

value: compensatory

value: 7 weeks


title: Liver, 3 hour, vehicle, rep2


title: AOB_#16_RV_rep2

description:
col_names:"raw_reads.AOB_comp_#16_RV", "normalized_reads.AOB_comp_#16_RV", "fpkm.AOB_comp_#16_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0907

value: whole heart; left ventricle

value: aortic banding


title: NL4.3 CEMM7 n=1 20dpi IFN

description:
362_10
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 20 dpi IFN.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: Cell line

value: IFN-β


title: R37_PAB-H_f_LV_#173_rep6

description:
col_names:"raw.reads.PAB_compensatory_female_#173_LV", "normalized.reads.PAB_compensatory_female_#173_LV", "fpkm.PAB_compensatory_female_#173_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: left ventricle


title: AOB_#16_LV_rep2

description:
col_names:"raw_reads.AOB_comp_#16_LV", "normalized_reads.AOB_comp_#16_LV", "fpkm.AOB_comp_#16_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0906

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart

value: male


title: NL4.3 CEMM7 n=1 20dpi

description:
362_9
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 20 dpi untreated.xlsx


title: NL4.3 CEMM7 n=1 15dpi IFN

description:
362_8
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 15 dpi IFN.xlsx
Test sgRNA NL4.3 CEMM7 15dpi IFN vs input N=1-3.xlsx


title: AOB_#12_LV_rep1

description:
col_names:"raw_reads.AOB_comp_#12_LV", "normalized_reads.AOB_comp_#12_LV", "fpkm.AOB_comp_#12_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0905


title: R36_PAB-H_f_RV_#168_rep5

description:
col_names:"raw.reads.PAB_compensatory_female_#168_RV", "normalized.reads.PAB_compensatory_female_#168_RV", "fpkm.PAB_compensatory_female_#168_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle


title: NL4.3 CEMM7 n=1 15dpi

description:
362_7
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 15 dpi untreated.xlsx
Test sgRNA NL4.3 CEMM7 15dpi untreated vs input N=1-3.xlsx


title: 21D HX IM, scRNAseq

city: Aurora

first: Sushil

last: Kumar

institute: University of Colorado Anschutz medical campus

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39  v.104
Supplementary files format and content: Tab-separated values files (Combined) unfilterd raw read counts and normalized filterd read counts

source_name: Lung

extract_protocol:
Freshly collected interstitial macrophge from Cx3cr1+/GFP reporter mice used for single cell RNA sequence.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Interstitial Macrophage

value: Lung

value: C57BL/6J Cx3Cr1/-

value: 6-8 weeks old


title: Liver, 3 hour, vehicle, rep1

value: Male

value: Liver

value: Oral gavage

value: Vehicle control (0.5% methylcellulose in phosphate-buffered saline)


title: 7D HX IM, scRNAseq

description: 10x Genomics


title: NL4.3 CEMM7 n=1 10dpi IFN

description:
362_6
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 10 dpi IFN.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9


title: AOB_#12_RV_rep1

description:
col_names:"raw_reads.AOB_comp_#12_RV", "normalized_reads.AOB_comp_#12_RV", "fpkm.AOB_comp_#12_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0904

value: whole heart; left ventricle

value: 11 weeks

value: aortic banding

value: compensatory

value: 7 weeks


title: PAB_#22_RV_rep2

description:
col_names:"raw_reads.PAB_comp_#22_RV", "normalized_reads.PAB_comp_#22_RV", "fpkm.PAB_comp_#22_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0903

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: male

value: pulmonary artery banding


title: R35_PAB-H_f_LV_#168_rep5

description:
col_names:"raw.reads.PAB_compensatory_female_#168_LV", "normalized.reads.PAB_compensatory_female_#168_LV", "fpkm.PAB_compensatory_female_#168_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: left ventricle

value: female


title: NL4.3 CEMM7 n=1 10dpi

description:
362_5
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 10 dpi untreated.xlsx

value: Cell line


title: 3D HX IM, scRNAseq

description: 10x Genomics

value: Interstitial Macrophage

value: Lung

value: C57BL/6J Cx3Cr1/-

value: 6-8 weeks old


title: R34_PAB-H_m_RV_#160_rep4

description:
col_names:"raw.reads.PAB_compensatory_male_#160_RV", "normalized.reads.PAB_compensatory_male_#160_RV", "fpkm.PAB_compensatory_male_#160_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle


title: 1D HX IM, scRNAseq

description: 10x Genomics


title: PAB_#22_LV_rep2

description:
col_names:"raw_reads.PAB_comp_#22_LV", "normalized_reads.PAB_comp_#22_LV", "fpkm.PAB_comp_#22_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0902

value: whole heart


title: NL4.3 CEMM7 n=1 5dpi IFN

description:
362_4
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: Virus-containing supernatant

value: CEM-M7 Cas9

value: IFN-β


title: R32_PAB-H_m_RV_#158_rep3

description:
col_names:"raw.reads.PAB_compensatory_male_#158_RV", "normalized.reads.PAB_compensatory_male_#158_RV", "fpkm.PAB_compensatory_male_#158_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: 11 weeks

value: compensatory

value: 7 weeks


title: PAB_#3_RV_rep1

description:
col_names:"raw_reads.PAB_comp_#3_RV", "normalized_reads.PAB_comp_#3_RV", "fpkm.PAB_comp_#3_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0901

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: whole heart; left ventricle

value: male

value: pulmonary artery banding


title: NL4.3 CEMM7 n=1 Input IFN

description:
362_2
Counts NL4.3 in CEMM7 N=1-3.xlsx

value: Virus stock


title: PAB_#3_LV_rep1

description:
col_names:"raw_reads.PAB_comp_#3_LV", "normalized_reads.PAB_comp_#3_LV", "fpkm.PAB_comp_#3_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0900

value: left ventricle


title: SL IM, replicate 1, scRNAseq

description: 10x Genomics

value: Interstitial Macrophage

value: Lung


title: SL IM, replicate 2, scRNAseq

description: 10x Genomics

value: C57BL/6J Cx3Cr1/-

value: 6-8 weeks old


title: R31_PAB-H_m_LV_#158_rep3

description:
col_names:"raw.reads.PAB_compensatory_male_#158_LV", "normalized.reads.PAB_compensatory_male_#158_LV", "fpkm.PAB_compensatory_male_#158_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes


title: R30_PAB-H_m_RV_#151_rep2

description:
col_names:"raw.reads.PAB_compensatory_male_#151_RV", "normalized.reads.PAB_compensatory_male_#151_RV", "fpkm.PAB_compensatory_male_#151_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle


title: NL4.3 CEMM7 n=1 Input

description:
362_1
Counts NL4.3 in CEMM7 N=1-3.xlsx


title: R29_PAB-H_m_LV_#151_rep2

description:
col_names:"raw.reads.PAB_compensatory_male_#151_LV", "normalized.reads.PAB_compensatory_male_#151_LV", "fpkm.PAB_compensatory_male_#151_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx


title: sham_#14_LV_rep2

description:
col_names:"raw_reads.sham_comp_#14_LV", "normalized_reads.sham_comp_#14_LV", "fpkm.sham_comp_#14_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0898

value: whole heart

value: sham


title: sham_#14_RV_rep2

description:
col_names:"raw_reads.sham_comp_#14_RV", "normalized_reads.sham_comp_#14_RV", "fpkm.sham_comp_#14_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0899

value: 11 weeks


title: hari roots, OX390-Sm-3_S1

city: Villa Elisa-La Plata

first: Maria

middle: Eugenia

last: Zanetti

state: BUENOS AIRES

department: Instituto de Biotecnología y Biología Molecular

country: Argentina

institute: Universidad Nacional de La Plata

data_processing:
RNA-Seq reads were aligned to theM. truncatulagenome version v.5 (Pecrix et al., 2018) using HiSAT2 (Kim et al., 2019)
Transcript assembly was performed using StringTie (Pertea et al., 2015), which is used to assemble and quantify full-length transcripts. Then, the StringTie files for each sample were merged using the StringTie Merge tool.
Tables of "genes counts" were generated using StringTie
DEseq2 tool was used keeping only the genes that had FPKM values ≥ 1 in at least one of the libraries.
Assembly: M. truncatulagenome version v.5 (Pecrix et al., 2018)
Supplementary files format and content: Gene_counts

organism: Medicago truncatula

source_name: hari roots

growth_protocol: Seeds were surface-sterilized and germinated for 24 h at 25°C in the dark on agar plates containing 10% (w/v). Roots were transformed with the EV or the OX390 binary vector  by A. rhizogenes-mediated transformation essentially as described previously (Boisson Dernier et al., 2001). Transformed seedlings were transferred to Petri dishes containing Fahraeus agar media (Fahraeus, 1957) supplemented with 8 mM KNO3 and 12.5 µg/ml kanamycin for 7 days. Seedlings were grown at 25°C on a 16/8-h day/night. Plants that developed hairy roots were transferred to slant boxes containing Fahraeus media free of nitroge,  covered with sterile filter paper and mantained under the growth conditions mentioned above for 7 days.

extract_protocol:
Total RNA extraction was performed using Trizol according to the manufacturer’s instructions (Thermo Fisher). RNA concentration was determined by measuring OD260 using a Nanodrop ND-1000 (Nanodrop Technologies), RNA integrity was analyzed by capillary electrophoresis using a Bioanalyzer 2100 (Agilent Technologies). All samples exceeded the Illumina recommended minimum value of RIN (RNA integrity number).
Libraries were prepared from 1.5 μg of RNA using  the TruSeq RNA Illumina Sample Preparation Kit v2 and sequenced at the Université de Paris Saclay, France using the HisSeq4000 platform with single end reads of 76 nts.

treatment_protocol: Seven days after transplantation to free mitrogen media, roots were inoculated with 10 ml water or with 10 ml of a 1:1000 dilution of S. meliloti 1021 (Meade and Signer, 1977). .

value: hari roots

tag: expressing

value: All root cell types

value: Jemalomng A17

value: 48 hours post-inoculation with S. meliloti (Sm)


title: TPS236_084

city: Chapel Hill

first: Timothy

middle: P

last: Sheahan

state: North Carolina

address: 3113 MHRC 135 Dauer Drive, Campus Box 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

data_processing:
FastQ file quality was assessed using FastQC and MultiQC.
FastQ reads were mapped and quantified using Kallisto (0.46.2) to the reference build GRCm39
Counts per million (CPM) was calculated and normalized using EdgeR, keeping only rows with at least 5 cells indicating a count-per-million (CPM) of at least 1.
Expression data was filtered and normalized using Limma's VOOM.
Differentially expressed genes (DEGs) were identified by linear modeling and Bayesian statistics using the Limma package.
Assembly: GRCm39
Supplementary files format and content: *.tar.gz files contain one of each file listed below per sample which is indicated by the "*" pattern.
Supplementary files format and content: abundance.tsv files contain abundance quantifications per sample.
Supplementary files format and content: run_info.json files contain Kallisto run information per sample.
Supplementary files format and content: abundance.h5 files are hd5f binary files containing run info, abundance estimates, bootstrap estimates, and transcript length information per sample.

source_name: whole lung lobe

extract_protocol:
Mice were euthanized via overdose of isofluorane, and a single lung lobe was homogenized in 1 ml of TRIzol reagent. Total RNA was extracted using Qiagen Rneasy isolation kit as per manufacturer's protocol.
KAPA total RNA with Ribo Erase.

value: whole lung lobe

tag: age and_strain

value: 10 week old BALB/c

value: Female

tag: days post_infection

value: Uninfected

value: PBS


title: sham_#13_RV_rep1

description:
col_names:"raw_reads.sham_comp_#13_RV", "normalized_reads.sham_comp_#13_RV", "fpkm.sham_comp_#13_RV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0897

tag: strain background

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

tag: tissue

value: whole heart; left ventricle

tag: Sex

value: male

value: compensatory

value: 7 weeks


title: hari roots, OX390-Sm-1_S1

tag: treatment


title: TPS236_083


title: R28_PAB-H_m_RV_#145_rep1

description:
col_names:"raw.reads.PAB_compensatory_male_#145_RV", "normalized.reads.PAB_compensatory_male_#145_RV", "fpkm.PAB_compensatory_male_#145_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: right ventricle

tag: animal id

tag: age

value: pulmonary artery banding

tag: disease progression


title: R33_PAB-H_m_LV_#160_rep4

description:
col_names:"raw.reads.PAB_compensatory_male_#160_LV", "normalized.reads.PAB_compensatory_male_#160_LV", "fpkm.PAB_compensatory_male_#160_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

tag: cell type

value: left ventricle

value: 11 weeks

tag: treatment time


title: sham_#13_LV_rep1

description:
col_names:"raw_reads.sham_comp_#13_LV", "normalized_reads.sham_comp_#13_LV", "fpkm.sham_comp_#13_LV"
Whole_Heart_reads.csv
Whole_Heart_DEseq2_Output_p1_F1-F21.xlsx
Whole_Heart_DEseq2_Output_p2_F22-F55.xlsx
N0896

value: sham


title: R26_AOB-H_f_RV_#167_rep6

description:
col_names:"raw.reads.AOB_compensatory_female_#167_RV", "normalized.reads.AOB_compensatory_female_#167_RV", "fpkm.AOB_compensatory_female_#167_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: female

value: aortic banding


title: R27_PAB-H_m_LV_#145_rep1

description:
col_names:"raw.reads.PAB_compensatory_male_#145_LV", "normalized.reads.PAB_compensatory_male_#145_LV", "fpkm.PAB_compensatory_male_#145_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx


title: hari roots, OX390-Mock-3_S1

value: hari roots

value: All root cell types

tag: genotype

value: Jemalomng A17

value: 48 hours post-inoculation with water (mock)


title: TPS236_082

value: whole lung lobe

value: 10 week old BALB/c

value: Female

value: Uninfected

value: PBS


title: hari roots, OX390-Mock-1_S1


title: NL4.3 CEMM7 n=1 5dpi

description:
362_3
Counts NL4.3 in CEMM7 N=1-3.xlsx
Test NL4.3 in CEMM7 N=1-2 5 dpi untreated.xlsx

value: Virus-containing supernatant

tag: cell line

value: CEM-M7 Cas9

value: Cell line


title: R25_AOB-H_f_LV_#167_rep6

description:
col_names:"raw.reads.AOB_compensatory_female_#167_LV", "normalized.reads.AOB_compensatory_female_#167_LV", "fpkm.AOB_compensatory_female_#167_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: left ventricle

value: compensatory

value: 7 weeks


title: TPS236_081


title: Single-cell 5’ RNA-seq of Bactrian camel: C4 PBMC 56 days post-immunization

city: Shanghai

first: Zhen

last: Wang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Sequencing reads were processed by the Cell Ranger pipeline (v6.1.2, 10x Genomics), including demultiplexing, barcoded processing, UMI counting and aggregation.
Single-cell BCR sequences were constructed using TRUST4 (v1.0.6) and annotated with IgBLAST (v1.10.0), taking known IGHV/D/J/C sequences of Bactrian camels as the reference (Ming et al. Mol Ecol Resour 2020, 20:770).
Assembly: BCGSAC_Cfer_1.0 (GCF_009834535.1)
Supplementary files format and content: Filtered single-cell gene expression matrix, cell barcodes and gene features using Cell Ranger
Supplementary files format and content: BCR sequences constructed using TRUST4 and annotated using IgBLAST (AIRR format)
Supplementary files format and content: BCR assignment to cell barcodes (tab-seperated values)

organism: Camelus bactrianus

source_name: blood

extract_protocol:
For each camel, 50 ml peripheral blood was collected from the jugular vein and placed in sodium citrate anticoagulation tubes after disinfection treatment. The collections were made following the guidelines from the Camel Protection Association of Inner Mongolia. PBMCs were isolated from the peripheral blood with density gradient centrifugation using the Ficoll-Paque medium. 3ml PBMCs were transferred into 5ml cryotubes with 2ml cell freezing medium. Cells were stored frozen at -80°C for one day and then transported to sequencing lab on dry ice.
The viability of thawed cells was examined to exceed 80% with trypan blue staining. Single-cell libraries were constructed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics, 5’ Library Kit) according to the manufacturer’s instructions. Specifically, cells, barcoded gel beads and partitioning oil were combined on a microfluidic chip to form Gel Beads-in-Emulsion (GEMs). Within each GEM, a single cell was lysed and the transcripts were identically barcoded through reverse transcription. The cDNA libraries were sequenced on an Illumina NovaSeq platform to generate 2×150-bp paired-end reads.

value: blood

value: PBMC

value: post-immunization


title: R24_AOB-H_f_RV_#166_rep5

description:
col_names:"raw.reads.AOB_compensatory_female_#166_RV", "normalized.reads.AOB_compensatory_female_#166_RV", "fpkm.AOB_compensatory_female_#166_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle

value: female

value: 11 weeks

value: aortic banding


title: TPS236_080

value: whole lung lobe

value: 10 week old BALB/c

value: Female

value: MA10 infected + GS5245 + PF332


title: Single-cell 5’ RNA-seq of Bactrian camel: C4 PBMC 42 days post-immunization


title: hari roots, EV-Sm-3_S1

value: hari roots

value: EV

value: All root cell types

value: Jemalomng A17

value: 48 hours post-inoculation with S. meliloti (Sm)


title: hari roots, EV-Sm-1_S1


title: TPS236_079


title: Single-cell 5’ RNA-seq of Bactrian camel: C3 PBMC 56 days post-immunization


title: TPS236_085

value: Uninfected

value: PBS


title: Single-cell 5’ RNA-seq of Bactrian camel: C3 PBMC 42 days post-immunization

value: blood

value: PBMC


title: TPS236_078


title: R22_AOB-H_f_RV_#164_rep4

description:
col_names:"raw.reads.AOB_compensatory_female_#164_RV", "normalized.reads.AOB_compensatory_female_#164_RV", "fpkm.AOB_compensatory_female_#164_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: right ventricle

value: compensatory

value: 7 weeks


title: hari roots, EV-Mock-3_S1

value: 48 hours post-inoculation with water (mock)


title: Single-cell 5’ RNA-seq of Bactrian camel: C4 PBMC

value: pre-immunization


title: hari roots, EV-Mock-1_S1


title: R21_AOB-H_f_LV_#164_rep4

description:
col_names:"raw.reads.AOB_compensatory_female_#164_LV", "normalized.reads.AOB_compensatory_female_#164_LV", "fpkm.AOB_compensatory_female_#164_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: female

value: 11 weeks

value: aortic banding


title: TPS236_077

value: whole lung lobe

value: 10 week old BALB/c

value: Female

value: MA10 infected + GS5245 + PF332


title: Single-cell 5’ RNA-seq of Bactrian camel: C3 PBMC

value: blood


title: TPS236_076


title: MDM, recombinant_IL27, rep3

city: Medellin

first: Yordi

middle: Sebastián

last: Tamayo Molina

state: Antioquia

country: Colombia

institute: University of Antioquia

data_processing:
Clean reads were obtained by removing low-quality adapter, poly N-containing, and shorter-than-70 bp reads using trimmomatic
The location of the reads on the reference genome was determined quickly and precisely by comparing reads with the reference genome using the HISAT2 software
he new transcripts were then assembled using String Tie software and the feature count tool in Subread software
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts bacth corrected for each sample

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was obtained using Direct-zol™ RNA Miniprep. RNA samples were treated with a DNase I column to remove contaminating genomic DNA. RNA was quantified by spectrophotometry, and 1μg of RNA was used for bulk RNA-Seq.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: Peripheral blood mononuclear cells

value: Primary human cell

value: Macrophages

value: WT


title: R20_AOB-H_f_RV_#147_rep3

description:
col_names:"raw.reads.AOB_compensatory_female_#147_RV", "normalized.reads.AOB_compensatory_female_#147_RV", "fpkm.AOB_compensatory_female_#147_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: right ventricle

value: compensatory


title: MDM, recombinant_IL27, rep2


title: Single-cell 5’ RNA-seq of Bactrian camel: C2 PBMC

value: PBMC

value: pre-immunization


title: TPS236_075


title: R19_AOB-H_f_LV_#147_rep3

description:
col_names:"raw.reads.AOB_compensatory_female_#147_LV", "normalized.reads.AOB_compensatory_female_#147_LV", "fpkm.AOB_compensatory_female_#147_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: female

value: 11 weeks

value: 7 weeks


title: MDM, recombinant_IL27, rep1


title: Single-cell 5’ RNA-seq of Bactrian camel: C1 PBMC


title: R18_AOB-H_m_RV_#172_rep2

description:
col_names:"raw.reads.AOB_compensatory_male_#172_RV", "normalized.reads.AOB_compensatory_male_#172_RV", "fpkm.AOB_compensatory_male_#172_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: male

value: aortic banding


title: TTA-1, GDC-0994, rep3

city: guangzhou

first: Yulu

last: Chen

state: guangdongsheng

address: No. 58 Zhongshan Second Road

department: Precision Medicine Research Institute

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
Clustering and sequen：After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Quality control：The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome：Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Quantification of gene expression level：featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression level
Assembly: GRCh38, NCBI
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: KHM-5M was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and TTA-1 was cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS).All cells were incubated under the condition of 37 °C and 5% CO2.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies,, CA, USA)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Cells were seeded on 6-well plates and treated with GDC-0994 (1μM) or DMSO for 24 hours.

value: Anaplastic thyroid carcinoma

value: BRAF  WT


title: MDM, untreated, rep3

value: Peripheral blood mononuclear cells

value: Primary human cell

value: Mock


title: R17_AOB-H_m_LV_#172_rep2

description:
col_names:"raw.reads.AOB_compensatory_male_#172_LV", "normalized.reads.AOB_compensatory_male_#172_LV", "fpkm.AOB_compensatory_male_#172_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat


title: MDM, untreated, rep2

value: Macrophages

value: WT


title: TTA-1, GDC-0994, rep2


title: R23_AOB-H_f_LV_#166_rep5

description:
col_names:"raw.reads.AOB_compensatory_female_#166_LV", "normalized.reads.AOB_compensatory_female_#166_LV", "fpkm.AOB_compensatory_female_#166_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: compensatory


title: TPS236_074

value: whole lung lobe

value: 10 week old BALB/c

value: Female

value: MA10 infected + GS5245 + PF332


title: TPS236_072


title: R16_AOB-H_m_RV_#171_rep1

description:
col_names:"raw.reads.AOB_compensatory_male_#171_RV", "normalized.reads.AOB_compensatory_male_#171_RV", "fpkm.AOB_compensatory_male_#171_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle

value: 11 weeks

value: 7 weeks


title: TTA-1, GDC-0994, rep1

value: Anaplastic thyroid carcinoma


title: MDM, untreated, rep1


title: TPS236_071


title: TTA-1, DMSO, rep3

value: BRAF  WT

value: DMSO


title: R15_AOB-H_m_LV_#171_rep1

description:
col_names:"raw.reads.AOB_compensatory_male_#171_LV", "normalized.reads.AOB_compensatory_male_#171_LV", "fpkm.AOB_compensatory_male_#171_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: male

value: aortic banding


title: TPS236_059

value: MA10 infected + PF332


title: CD45+ cells

city: Boston

first: Julia

last: Frede

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5'. Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5'. Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Assembly: hg19
Supplementary files format and content: Filtered counts matrix with raw counts for all samples: counts_matrix.csv

source_name: Bone marrow

extract_protocol:
100 cells were directly sorted into 96 well plates containing TCL buffer
Full-length low-input RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.
100 cell pools were directly sorted into 96 well plates containing TCL buffer.
Full-length low-input RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.
Low-input RNA-Seq

value: Bone marrow

value: CD45+ cells


title: TTA-1, DMSO, rep2


title: R14_Sham-H_f_RV_#162_rep7

description:
col_names:"raw.reads.sham_compensatory_female_#162_RV", "normalized.reads.sham_compensatory_female_#162_RV", "fpkm.sham_compensatory_female_#162_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: female

value: sham

value: compensatory


title: R13_Sham-H_f_LV_#162_rep7

description:
col_names:"raw.reads.sham_compensatory_female_#162_LV", "normalized.reads.sham_compensatory_female_#162_LV", "fpkm.sham_compensatory_female_#162_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx


title: TPS236_058

value: whole lung lobe

value: 10 week old BALB/c

value: Female


title: TTA-1, DMSO, rep1

value: Anaplastic thyroid carcinoma


title: TPS236_057


title: ANGiS 1-2 mCherry eGFP

city: Cambridge

first: Jeffrey

last: Davis

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

description:
SC-beta cells  expressinng INS-mCherry and IAPP-eGFP post-sorting from differentiation 1-2
S4_paired

data_processing:
Trimmomatic was run on all samples individually to ensure read quality and lengths were sufficient for alignnment
Reads were then aligned and quantified using Trinity differential expression analysis pipeline using default settings for differential expression analysis
Alignment and transcript counts were generated using rsem 1.2.29 and STAR 2.6.0c builds.
Counts were then assembled into an expression matrix using trinity
Expression matrix was analyzed for diferential expression using edgeR and a cutoff p value of 0.05
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly
Supplementary files format and content: CSV file contains TMM values for all aligned transcripts for each sample.
Supplementary files format and content: matrix.counts.matrix contains all raw counts data after alignment using rsem and STAR

source_name: Differentiated iPS Cells

growth_protocol: ANGis 1016 iPS cells were differentiated to Stage 6 Day 14 of the Pagliuca et al protocol for differentiation of SC-beta cells from pluripotent stem cells.

extract_protocol:
used zymo direct-zol RNA extraction kit to isolate RNA
RNA concentrations were confirmed using Tapestation and samples were submitted for RNA seq at a concentration of 5 ng/uL in 15 uL volumes.
Library was generated usinng Wafergen PrepX DNA library preparation protocol by the Harvard Biopolymers Facility

treatment_protocol: At stage 6 day 14 clusters were dissociated and sorted based on IAPP-eGFP and INS-mCherry expression into INS+ IAPP- and INS+ IAPP+ cells. RNA was collected and sequennced as desccribed below.

value: Differentiated iPS Cells

value: 1016 ANGiS

value: SC-beta

value: INS-mCherry IAPP-eGFP

value: Sorted for INS-mCherry and IAPP-eGFP


title: ANGiS 2-2 mCherry eGFP

description:
SC-beta cells  expressinng INS-mCherry and IAPP-eGFP post-sorting from differentiation 2-2
S7_paired


title: ANGiS 1-1 mCherry eGFP

description:
SC-beta cells  expressinng INS-mCherry and IAPP-eGFP post-sorting from differentiation 1-1
S2_paired


title: KHM-5M, GDC-0994, rep3

value: BRAF V600E


title: TPS236_073

value: MA10 infected + GS5245 + PF332


title: ANGiS 2-2 mCherry

description:
SC-beta cells only expressinng INS-mCherry post-sorting from differentiation 2-2
S6_paired

value: Sorted for INS-mCherry only


title: R11_Sham-H_f_LV_#157_rep6

description:
col_names:"raw.reads.sham_compensatory_female_#157_LV", "normalized.reads.sham_compensatory_female_#157_LV", "fpkm.sham_compensatory_female_#157_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: left ventricle

value: 11 weeks

value: 7 weeks


title: KHM-5M, GDC-0994, rep2


title: TPS236_055

value: MA10 infected + PF332


title: R9_Sham-H_f_LV_#156_rep5

description:
col_names:"raw.reads.sham_compensatory_female_#156_LV", "normalized.reads.sham_compensatory_female_#156_LV", "fpkm.sham_compensatory_female_#156_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: female

value: sham

value: compensatory


title: R10_Sham-H_f_RV_#156_rep5

description:
col_names:"raw.reads.sham_compensatory_female_#156_RV", "normalized.reads.sham_compensatory_female_#156_RV", "fpkm.sham_compensatory_female_#156_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle


title: ANGiS 2-1 mCherry

description:
SC-beta cells only expressinng INS-mCherry post-sorting from differentiation 2-1
S3_paired

value: Differentiated iPS Cells

value: 1016 ANGiS


title: TPS236_054

value: whole lung lobe

value: 10 week old BALB/c

value: Female


title: TPS236_053


title: KHM-5M, DMSO, rep2

value: Anaplastic thyroid carcinoma

value: BRAF V600E

value: DMSO


title: KHM-5M, DMSO, rep3


title: ANGiS 1-1 mCherry

description:
SC-beta cells only expressinng INS-mCherry post-sorting from differentiation 1-1
S1_paired

value: SC-beta

value: INS-mCherry IAPP-eGFP

value: Sorted for INS-mCherry only


title: R8_Sham-H_f_RV_#154_rep4

description:
col_names:"raw.reads.sham_compensatory_female_#154_RV", "normalized.reads.sham_compensatory_female_#154_RV", "fpkm.sham_compensatory_female_#154_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: 11 weeks

value: 7 weeks


title: R12_Sham-H_f_RV_#157_rep6

description:
col_names:"raw.reads.sham_compensatory_female_#157_RV", "normalized.reads.sham_compensatory_female_#157_RV", "fpkm.sham_compensatory_female_#157_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: cardiac myocytes

value: female

value: sham


title: R7_Sham-H_f_LV_#154_rep4

description:
col_names:"raw.reads.sham_compensatory_female_#154_LV", "normalized.reads.sham_compensatory_female_#154_LV", "fpkm.sham_compensatory_female_#154_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: left ventricle

value: compensatory


title: ANGiS 1-2 mCherry

description:
SC-beta cells only expressinng INS-mCherry post-sorting from differentiation 1-2
S5_paired

value: Differentiated iPS Cells

value: 1016 ANGiS


title: KHM-5M, GDC-0994, rep1


title: Replica 3 0615 SCR

city: Beer Sheva

first: Ran

middle: Taube Pathology Rm

last: Taube

state: ISRAEL

address: Biotechnology Building 3, room 324

department: Microbiology

country: Israel

institute: Ben Gurion University

data_processing:
For analysis: Quality Control was conducted by evaluating the quality of the FASTQ files using 'Fastqc' (v0.12.1). Subsequently, the samples underwent quality trimming via the 'Fastp' software (v0.23.3). To identify potential contaminations, 'fastq-screen' software was applied.
Assembly: Read alignment involved aligning the reads to the Human GRCh38 genome (Ensembl release 110) using 'STAR' software (v2.7.10b). Read assignments to coding regions were determined using the 'SubRead' package ('FeatureCounts' v2.0.6).
Supplementary files format and content: Finally, BAM files were sorted using ‘samtools’. Differential expression analysis was conducted in DAVID. PCA was performed to evaluate data dispersion, revealing a batch effect among samples collected on different dates. A correction was implemented in the DESeq2 model to minimize this batch effect. Finally, the indicated groups were compared (without including the control in the model), identifying 90 DEGs. The selected cutoff values were an adjusted p-value <0.05 and a fold-change > 2. For enrichment analysis, the DAVID program was employed to identify enriched pathways and terms associated with the selected genes

source_name: Primary CD4+ T cells

extract_protocol:
For RNA extraction from cells, J-Lat 6.3 cells were stimulated with P/I and sorted based on their GFP expression (n=4). For analysis of transcriptome upon Cytor depletion in primary CD4+ T cells, cells were stimulated with CD3/CD28 beads and then subjected to Cytor KD by transducing cells with lentivirus that drive the expression of shRNA that target Cytor (n=3). RNA from both cell types was purified utilizing the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. The integrity of the isolated RNA was tested using the Agilent High Sensitivity RNA Kit and Tapestation 4200
Libraries construction for  sequencing was performed using the NEBNext Ultra II RNA kit (NEB;E7770L). Quantification of the library was performed using dsDNA HS Assay Kit and Qubit 2.0 (Molecular Probes, Life Technologies), and qualification was done using the Agilent D1000 Tapestation Kit and Tapestation 4200. 150 nM of each library was pooled together and was diluted to 4nM according to NextSeq manufacturer’s instructions. 1.6 pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced on an Illumina NextSeq 500 instrument, 75 cycles of single-read sequencing.

value: Primary CD4+ T cells

value: T cells


title: KHM-5M, DMSO, rep1

value: Anaplastic thyroid carcinoma

value: BRAF V600E


title: R6_Sham-H_m_RV_#170_rep3

description:
col_names:"raw.reads.sham_compensatory_male_#170_RV", "normalized.reads.sham_compensatory_male_#170_RV", "fpkm.sham_compensatory_male_#170_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle

value: male


title: TPS236_056

value: whole lung lobe

value: 10 week old BALB/c

value: Female

value: MA10 infected + PF332


title: TPS236_051


title: Mesenchymal Stem Cells, nonporous, day 14, biol 6

city: Durham

first: Seth

last: Edwards

state: NH

address: 105 Main St

department: Chemical Engineering

institute: University of New Hampshire

data_processing:
Paired reads were trimmed using Trimmomatic.
Trimmed reads were aligned to Human reference genome using STAR.
Htseq-count was used to generate count data for each read.
Assembly: hg38
Supplementary files format and content: Raw count data in tab delimited file.

source_name: adult mesenchymal stem cell

growth_protocol: MSCs were grown on TCPS in growth medium (MEM-α, 10% FBS, 1% Pen/Strep) in incubator at 37 °C and 5% CO_2 until near confluency, then encapsulated in either nonporous or porous hydrogel conditions.

extract_protocol:
Samples were mechanically disrupted, and RNA was extracted using TRIzol (Invitrogen).
Librarys were prepared using a KAPA adapter kit and purified using KAPA Pure Beads. Libraries were quantified using Qubit 2.0, dsDNA Assay Kit, and validated using TapeStation 4200.

treatment_protocol: 48 hours after encapsulation, samples were supplemented with osteogenic differentiation medium. RNA was extracted from samples at 3 and 14 days after induction of differentiation. Samples were given fresh media daily.

value: adult mesenchymal stem cell

value: Osteogenic differentiaion

tag: time point

value: 14 days after introdution of osteogenic differentiation media


title: Replica 2 0606 SCR


title: TPS236_030

value: MA10 infected + GS5245


title: Mesenchymal Stem Cells, nonporous, day 14, biol 5


title: Replica 1 0522 SCR


title: R5_Sham-H_m_LV_#170_rep3

city: Giessen

first: Axel

last: Weber

institute: Justus-Liebig-University Giessen

description:
col_names:"raw.reads.sham_compensatory_male_#170_LV", "normalized.reads.sham_compensatory_male_#170_LV", "fpkm.sham_compensatory_male_#170_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

data_processing:
Nexflow nf/core rna_seq v3.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore integrated into nf-core/rnaseq (parameter- Quality limit: 20)
Trimmed reads were mapped to rnor6 usinf STAR integrated into nf-core/rnaseq (default parameters)
Readcount extraction was perfomed using FeatureCounts (Rsubreads v2.2.6), disallowing multiple overlap
Normalization and differential expression analysis was performed using DEseq2 1.28.1, using the independed filtering option and beta_prior LFC-shrinkage
Assembly: rnor6
Supplementary files format and content: bigwig files
Supplementary files format and content: unnormalized read count, DEseq2-normalized read count and FPKM count tables in single csv-file
Supplementary files format and content: DEseq2 Output in Excel file

extract_protocol:
After extraction and perfusion for cleanup, fre hearts were digested using collagenase II in a Langendorff aparatus for 25 minutes. Afterwards the ventricles were seperated, cut into small pieces and digested again with collagenase II for 5min. Afterwards the suspension was filtered using a nylon filter (200µm), and cardiac myocytes seperated from other cell types via a series of centrifugation steps.
RNA was extracted  using Macherey & Nagel Nucleospin RNA kit
Libraries were prepared by Novagene using a rRNA depletion strategy

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes

value: left ventricle

value: 11 weeks

value: sham

value: compensatory

value: 7 weeks


title: TPS236_029


title: Mesenchymal Stem Cells, nonporous, day 14, biol 4


title: R4_Sham-H_m_RV_#159_rep2

description:
col_names:"raw.reads.sham_compensatory_male_#159_RV", "normalized.reads.sham_compensatory_male_#159_RV", "fpkm.sham_compensatory_male_#159_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

source_name: right ventricle

value: right ventricle


title: Replica 3 0615 OE

value: Primary CD4+ T cells

value: T cells


title: Replica 2 0606 OE


title: R3_Sham-H_m_LV_#159_rep2

description:
col_names:"raw.reads.sham_compensatory_male_#159_LV", "normalized.reads.sham_compensatory_male_#159_LV", "fpkm.sham_compensatory_male_#159_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: male


title: TPS236_027

value: whole lung lobe

value: 10 week old BALB/c

value: Female


title: TPS236_052

value: MA10 infected + PF332


title: Mesenchymal Stem Cells, nonporous, day 14, biol 3

value: adult mesenchymal stem cell

value: Osteogenic differentiaion

value: 14 days after introdution of osteogenic differentiation media


title: Mesenchymal Stem Cells, nonporous, day 14, biol 2


title: Replica 1 0522 OE


title: R1_Sham-H_m_LV_#152_rep1

description:
col_names:"raw.reads.sham_compensatory_male_#152_LV", "normalized.reads.sham_compensatory_male_#152_LV", "fpkm.sham_compensatory_male_#152_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: F1-generation children derived from female Wistar Kyoto x male Lewis rat

value: cardiac myocytes


title: TPS236_026

value: MA10 infected + GS5245


title: Mesenchymal Stem Cells, nonporous, day 14, biol 1


title: Replica 3 0615 SH


title: TPS236_025


title: Mesenchymal Stem Cells, porous, day 14, biol 4


title: PNUTS EC-KO 3

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

data_processing:
fastqc, 0.10.1; bowtie2, 2.2.6; tophat, 2.1.0; samtools, 1.2; picard, v1.139; cufflinks, 2.2.1; cuffmerge, 1.0.0; cuffquant, 2.2.1; featureCounts, v1.4.6-p4; cuffnorm, 2.2.1; cuffdiff, 2.2.1;
Assembly: mm10
Supplementary files format and content: Microsoft Excel Spreadsheet containing FPKM values per strand for each sample

source_name: lungs

extract_protocol:
All samples were prepared using miRNeasy Kit (Qiagen) including DNase treatment.
Illumina TruSeq stranded total RNA sample preparation kit (Illumina) with rRNA depletion

treatment_protocol: Mice received 6 intraperitoneal injections of tamoxifen on day 1, 2, 3, 4, 5 and 8 of the experiment. Mice were terminated at day 12. Entire lungs were excised and homogenized before RNA isolation.

value: lungs

value: Cdh5-CreERT2; PNUTS-fl/fl

value: tamoxifen


title: PNUTS EC-KO 2


title: TPS236_024


title: Replica 2 0606 SH


title: TPS236_023


title: PNUTS WT 3

value: PNUTS-fl/fl


title: Mesenchymal Stem Cells, porous, day 14, biol 2


title: TPS236_028


title: PNUTS WT 2


title: Replica 4 Latent

source_name: Jurkat - 6.3 (Jlat)

value: Jurkat - 6.3 (Jlat)


title: TPS236_021


title: R2_Sham-H_m_RV_#152_rep1

description:
col_names:"raw.reads.sham_compensatory_male_#152_RV", "normalized.reads.sham_compensatory_male_#152_RV", "fpkm.sham_compensatory_male_#152_RV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx

value: right ventricle

value: 11 weeks

value: sham

value: compensatory

value: 7 weeks


title: PNUTS EC-KO 1


title: Mesenchymal Stem Cells, porous, day 14, biol 1


title: TPS236_010

value: whole lung lobe

value: 10 week old BALB/c

value: Female

value: MA10 infected + Vehicle


title: TPS236_022


title: TPS236_008


title: Mesenchymal Stem Cells, nonporous, day 3, biol 4

value: adult mesenchymal stem cell

value: Osteogenic differentiaion

value: 3 days after introdution of osteogenic differentiation media


title: C2C12 cells, lenvatinib-treated-3

city: Chiba

first: Junjie

last: Ao

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, Chiba University

data_processing:
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited xlsx file includes raw counts for all samples
Supplementary files format and content: tab-delimited csv file includes raw counts for all samples

growth_protocol: C2C12 myoblast cells were cultured in DMEM supplemented with 10% fetal calf serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen, Valencia, CA).
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).

treatment_protocol: C2C12 cells were maintained in DMEM medium containing 2% horse serum for differentiation, and treated with or without lenvatinib 1μM.

value: myoblast

value: WT

value: differentiation; lenvatinib 1μM


title: Replica 2 Active

value: T cells


title: PNUTS WT 1

value: lungs

value: PNUTS-fl/fl

value: tamoxifen


title: Mesenchymal Stem Cells, nonporous, day 3, biol 6


title: Mesenchymal Stem Cells, porous, day 14, biol 3

value: 14 days after introdution of osteogenic differentiation media


title: Replica 1 0522 SH

value: Primary CD4+ T cells


title: Mesenchymal Stem Cells, nonporous, day 3, biol 3


title: Replica 3 Active

value: Jurkat - 6.3 (Jlat)


title: Replica 4 Active


title: Replica 2 Latent


title: TPS236_005

value: whole lung lobe


title: TPS236_007

value: 10 week old BALB/c


title: Mesenchymal Stem Cells, nonporous, day 3, biol 2


title: Replica 1 Active


title: C2C12 cells, lenvatinib-untreated-3

value: differentiation


title: Replica 3 Latent


title: TPS236_004

value: Female

value: MA10 infected + Vehicle


title: Mesenchymal Stem Cells, nonporous, day 3, biol 1

value: adult mesenchymal stem cell

value: Osteogenic differentiaion


title: Replica 1 Latent


title: TPS236_003


title: C2C12 cells, lenvatinib-treated-2

value: myoblast


title: Mesenchymal Stem Cells, nonporous, day 3, biol 5

value: 3 days after introdution of osteogenic differentiation media


title: Mesenchymal Stem Cells, porous, day 3, biol rep 4


title: C2C12 cells, lenvatinib-untreated-2

value: WT


title: WRAP53_Rep3_IP

city: Baltimore

first: Taeyoung

last: Hwang

state: MD

address: 855 N. Wolfe St, 3rd floor, Suite 300

institute: Lieber Institute for Brain Development

data_processing:
The sequencing reads were assigned to the designed oligonucleotides by mapping barcode sequences. Barcode sequences can be retrieved from the provided oligo pool fasta file: it is 10 nucleotides long from the end following the removal of the final 17 nucleotides.
Sequencing reads were counted for a given oligonucleotide if they have less than or equal to 2 mismatches between a read and a designed target sequence. The designed target sequences can be retrieved from the provided oligo pool fasta file: it is the remaining sequence following the removal of the first 16 nucleotides and the final 27 nucleotides.
Assembly: Not applicable, using custom sequences
Supplementary files format and content: Tab-delimited files include sequencing read counts for oligonucleotides and samples.
Library strategy: Amplicon-seq

growth_protocol: HEK293T cells cultured in DMEM plus 10% FBS, 1% Penicillin-streptomycin, and 1% GlutaMAX supplement (Gibco) were passaged onto 15-cm dishes.

extract_protocol:
For the reverse cross-linking reaction, lysates were mixed with 33 μL of reverse crosslinking buffer (3X PBS, 6% N-Lauroylsarcosine, 30 mM EDTA, 15 mM DTT), 10 μL of Proteinase K (Ambion), and 1 μL of RNaseOUT (Invitrogen) and incubated at 42C for 1 hour then 55C for 1 hour. TRIzol (Invitrogen) and chloroform, followed by RNeasy Plus Mini Kit (Qiagen), were used to isolate RNAs.
Sequencing libraries were generated using customized primers that anneal to the universal priming sites on the oligos and attach Illumina-compatible sequencing adapters: reverse primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), forward primer (caagcagaagacggcatacgagatCGTGATgtgactggagttcagacgtgtgctcttccgatctACTGGCCGCTTCACTG, CGTGAT is a Illumina truseq index and can be variable).
Amplicon sequencing was performed with a single-end run.

treatment_protocol: Oligo pools were transfected into HEK293T cells using X-tremeGENE HP DNA Transfection Reagent (Roche) according to manufacturer’s instruction. Cells were harvested 48 hours post-transfection by scraping, collected by centrifugation at 500 x g for 5 minutes at 4C, and washed once with cold PBS. Cells were cross-linked in cold PBS resuspension (~5 million cells/mL) with 0.1% formaldehyde for 10 minutes on a nutator at room temperature. To cease the reaction, glycine was added to cells with a final concentration of 125 mM followed by incubation for 5 minutes on a nutator at room temperature. Cross-linked cells were centrifuged at 500 x g for 5 minutes at 4C. Cross-linked cell pellets were washed twice with PBS including cOmplete Protease Inhibitor Cocktail (Roche), flash-frozen and stored at -80C until use.

tag: frip antibody

value: FLAG

tag: overexpression

value: FLAG-GFP-CTCF


title: TPS236_002


title: C2C12 cells, lenvatinib-treated-1

value: differentiation; lenvatinib 1μM


title: C2C12 cells, lenvatinib-untreated-1


title: Mesenchymal Stem Cells, porous, day 3, biol rep 3


title: WRAP53_Rep2_IP


title: TPS236_001


title: Mesenchymal Stem Cells, porous, day 3, biol rep 2


title: LPMC, ATAC

city: Beijing

first: Liu

last: Yang

address: Qinghuayuan street

institute: Tsinghua University

data_processing:
FastQC was used to analyze the quality of the raw reads obtained after sequencing.
Fastp software was used for trimming raw data.
BWA (Burrows Wheeler Aligner) was employed for aligning ATAC-Seq data to the reference genome.
The peak calling analysis was performed using the MACS2 software.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: BigWig

source_name: Intestine

extract_protocol:
Sorted IEMCs and LPMCs were lysed using lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, and 0.5% IGEPAL CA-630). Nuclei were pelleted by centrifugation (4 °C, 500g, 30 minutes) and resuspended in 50-μL reaction mix (Vazyme). DNA fragments were purified using a purification kit (QIAGEN, Hilden, Germany).
The libraries of DNA fragments were amplified by PCR (Vazyme) and  purified using 0.5×/1.2× DNA clean beads (Vazyme). The quality of libraries was evaluated by Agilent 2100 Bioanalyzer.

value: Intestine

value: lamina propria mast cells

value: H. polygyrus infected


title: Mesenchymal Stem Cells, porous, day 3, biol rep 1


title: IEMC, ATAC

value: intraepithelial mast cells


title: WRAP53_Rep2_Input

value: Input


title: WRAP53_Rep1_IP