title: 1/7MC+Pyr+FGF-F7-1

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

institute: Inner Mongolia University

data_processing:
Sequence reads were trimmed using fastp(0.19.7) for adaptor sequence/low-quality sequence(Discard a paired reads if more than 10% of bases are uncertain in either one read/Discard a paired reads if the proportion of low quality (Phred quality <5) bases is   over 50% in either one read).
Trimmed sequence reads were mapped to ucsc-bosTau9 using hisat2(2.1.0) with default parameters.
Read count extraction were performed using subread(2.0)-featureCounts
Assembly: bosTau9
Supplementary files format and content: tab-delimited text files include count values and TPM values for each Sample

organism: Bos taurus

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Total mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size_x0002_selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: embryonic stem cells

value: WT


title: 1/7MC-F7-2

status: Public on Sep 22 2022

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 1/7MC+Pyr-F7-1


title: 1/7MC+Pyr-F7-2


title: 1/7MC+Pyr-F7-3


title: 1/7MC-F7-3


title: 1/7MC-F7-1


title: 1/7MC+Pyr+FGF-F7-3


title: 1/7MC+Pyr+FGF-F7-2


title: ScrAbeta42_3448

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Salmon was used to map reads to the transcriptome
Assembly: Ensembl Mus musculus GRCm38.99 transcriptome
Supplementary files format and content: Count matrix

organism: Mus musculus

source_name: left ventricle

growth_protocol: Male C57BL6 mice were obtained from the Animal Resources Centre (Perth, WA, Australia) and were group housed with a 12 hr light/dark cycle at 22oC. Animals had ad libitum access to food and water. All procedures involving animals were approved by The Deakin University Animal Welfare Committee (A58-2010, G15-2017 and G08-2020), which is subject to the Australian Code for the Responsible Conduct of Research.  High fat feeding: At 12 weeks of age, mice were randomly assigned to regular chow or high fat diet (HFD; 43% digestible energy from fat, 20% from sucrose; SF04-001 Specialty Feeds). Throughout the diet period, mice were weight weekly. After three months of the diet period, mice underwent body composition assessment using EchoMRI. Two days later, mice were fasted for 5 hrs before being humanely killed by cervical dislocation. Epididymal and inguinal adipose tissues were carefully excised and weighted and were either immediately frozen and stored at -80oC for later analysis or were used for ex vivo adipose explant experiments.

extract_protocol:
Bulk RNA was isolated from LV tissue by homogenisation using a hand-held homogeniser in Trizol and RNA was isolated using RNeasy kits (Qiagen), according to manufacturer’s instructions.
Sequencing libraries were generated from 0.5 µg of total RNA using TruSeq Stranded Total RNA preparation kit (Illumina) as per manufacturer’s instructions.

treatment_protocol: Ab peptide administration: Lyophilised recombinant Aβ42 (#AG912, Millipore) and scrambled control peptide (ScrAβ42; #AG916, Millipore) were resuspended in 1% NH4OH and aliquoted at 200ng/ml in H2O and stored at -80◦C for no longer than 4 weeks. Recombinant human Aβ42 was used as it has a greater propensity to aggregate than the mouse sequence65 and peptides appeared as low molecular weight aggregates of Aβ42 by SDS-PAGE (data not shown). Peptide administration began when male C57BL6J mice were 12 weeks of age and involved daily i.p. injection of 1mg of peptide. Throughout the peptide administration period, body weight was measured daily and food intake was measured twice weekly, and body composition was measured weekly by EchoMRI. After two weeks, plasma Aβ42 was determined from samples collected 5 hr after recombinant ScrAβ42 or Aβ42 administration. After 3 weeks, an insulin tolerance test (ITT; i.p. 0.75U/kg) was performed following a 5 hr fast. Blood glucose was measured at baseline and after 20, 40, 60, 90 and 120 min after glucose administration. One week later, a glucose tolerance test (GTT; i.p 2g/kg with 5μCi 3H-2-deoxyglucose and 5μCi 14C-glucose) was performed. Blood glucose was measured at baseline and after 15, 30, 45, 60 and 90 min after glucose administration. Plasma was obtained at 0, 15, 30, 60 and 90 min for insulin determination and the measurement of tracer specific activity. Mice were humanely killed by cervical dislocation immediately after the GTT. Blood was collected for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis. Another cohort of mice were administered ScrAβ42 or Aβ42 for four weeks, as described above. After four weeks of peptide administration, mice were anaesthesia by isoflurane inhalation before undergoing echocardiography. Two days later, mice were humanely killed by cervical dislocation and blood was obtained for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis. Another cohort of mice were administered ScrAβ40 or Aβ40 (Millipore) for four weeks, as described above. After four weeks of peptide administration, mice were anaesthesia by isoflurane inhalation before undergoing echocardiography. Two days later, mice were humanely killed by cervical dislocation and blood was obtained for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis.  3D6 administration: For the 3D6 prevention study, 12-week-old mice were assessed for baseline cardiac structure and function by echocardiography and were assigned to one of two groups such that deceleration time was matched. One week later, mice were fed a high fat diet (as described above) and then received control antibody (IgG2a isotype antibody, #BE-0085 BioXCell) or 3D6 antibody (#TAB-0809CLV, Creative Biolabs) weekly via i.p. injection (0.75mg/kg). Body weight was measured twice per weekly, while body composition was measured every two weeks throughout the study. After 10 weeks of high fat feeding, mice underwent an ITT and a GTT after 11 weeks of high fat feeding. After 12 weeks of high fat feeding mice underwent echocardiography and two weeks later were humanely killed by cervical dislocation following a 5 hr fast.  Blood was collected for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis. In the 3D6 reversal study, 12-week-old mice were assessed for baseline cardiac structure and function by echocardiography and were assigned to one of three groups such that deceleration time was matched. One week later, one group of mice remained on standard chow, while the other two groups were fed a high fat diet. Body weight was measured twice per week throughout the study. After 13 weeks of high fat feeding, mice underwent echocardiography for pre-treatment assessment of cardiac function and morphology. Mice were then administered control antibody or 3D6 antibody weekly via i.p. injection (0.75mg/kg) for the remainder of the study. Four weeks later, mice underwent pre-treatment assessment of cardiac function and morphology, followed by assessment of body composition by EchoMRI two days later. One week later, mice were humanely killed by cervical dislocation following a 5 hr fast.  Blood was collected for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis.

tag: tissue

value: left ventricle

value: wild type

value: Ab42 scrambled control


title: SJLB46

city: Chapel Hill

first: Federico

last: Innocenti

state: North Carolina

address: 120 Mason Farm  Road, CB7361

department: Eshelman School of Pharmacy

country: USA

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-Seq reads were trimmed of adapter and for quality using Trimmomatic v0.35 leaving paired reads with a minimum length of 20 bp
Trimmed RNA-Seq reads were mapped to the human genome reference hg19/GRCh37 via HiSat2
Alignment files were sorted and converted into bam files and Picard Tools used to mark duplicates in the alignments
Counts for exons, genes and TPMs (Transcripts per Kilobase Million) were generated with RNASeqC v2.1 in “legacy” mode with the Gencode.v19.gene.v7.patched_contigs.gtf annotation file as a guide.  The 29,245 gene transcripts with expression thresholds of >0.1 TPM and ≥6 reads in at least ten individuals were selected for analysis.
The distribution of TPMs in each sample was quantile normalized to the average empirical distribution observed across all samples.  The normalized TPMs for each gene were subsequently transformed to the quantiles of the standard normal distribution.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: gene_reads.txt.gz - gene read counts
Supplementary_files_format_and_content: gene_tpm_normalized.txt.gz - normalized TPM counts
Supplementary_files_format_and_content: exon_reads.txt.gz - exon fractional read counts (These are NOT integers. Counts are distributed based on the mappings to exons such that if a read maps to more than one exon, a fractional value is assigned to that exon equal to the percentage of the read contained within that exon); subset of exons within the 29,245 genes

organism: Homo sapiens

source_name: liver tissue

extract_protocol:
 Total RNA was extracted from tissue homogenized in TRIzol reagent, followed by Qiagen RNAeasy cleanup
mRNA libraries were prepared using the Illuminia TruSeq Stranded Total RNA with Ribo-Zero protocol

value: liver

tag: Sex

value: female

tag: age


title: S855Nr42_CAPAN2_C3

city: Warszawa

first: AKANKSHA

last: JAISWAR

address: ul. Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Institute

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.19).
Quality check of the reads has been performed by FastQC and adapters were trimmed with trimmomatic toolkit,then trimmed raw reads were aligned to the human reference genome (hg38) using HISAT2.
Differential Gene Expression Analysis were performed with DESeq2 also we calculate exon gene sizes with the GenomicFeatures Package in R and FeaturesCount which are required to calculate FPKM values in DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic Cancer

growth_protocol: Standard, ATCC-derived protocls for 2D in vitro growth for each cell line.

extract_protocol:
Qiazol reagent extraction from PBS-washed cell line pellets, followed by an isopropanol RNA precipitation and RNA quality control.
RNA libraries were prepared for sequencing using TruSeq Stranded TotalRNA (Illumina) protocols

treatment_protocol: Cell lines indicated in the file names were either treated with carfilzomib (C) for 24h at concentrations at the IC50 of proteasome activity (see the associated manuscript for exact carfilzomib concentrations for each cell line), or with DMSO (D) as a control, in biological triplicates (numbers 1-3).

value: Carfilzomib

value: Pancreatic Cancer


title: Sfmbt RNAi replicate 2

city: Caparica

first: Daniel

last: Sobral

address: Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa, Campus de Caparica

department: Life Sciences

country: Portugal

institute: UCIBIO - FCT NOVA

data_processing:
RNA sequencing reads were aligned against the Drosophila melanogaster BDGP release 6 genome using the STAR aligner (2.7.2a)
Gene-level counts were obtained using featureCounts (v1.6.3); parameters: -s 2 -p -B -P -C
bigWig files were obtained from the RNA-Seq alignments transformed with the deeptools (3.5.0) bamcoverage tool with CPM normalization
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovaries from 2 days old females (after pupae eclosion)

growth_protocol: Ovaries from 2 days old females (after pupae eclosion) were isolated

extract_protocol:
Total RNA was extracted using standard procedures
The cDNA library was made using the TruSeq Stranded mRNA sample prep kit for Illumina

treatment_protocol: For negative control or Sfmbt depleted ovaries, we used the nanos-Gal4 driver for germ line-specific expression of, respectively, UAS-mCherry RNAi (negative control) or UAS-Sfmbt RNAi (Sfmbt RNAi-1)

value: Sfmbt RNAi

tag: replicate


title: SJLB1

value: male


title: Sfmbt RNAi replicate 1


title: S855Nr41_CAPAN2_C2


title: SJLB39


title: S855Nr40_CAPAN2_C1


title: S855Nr39_CAPAN2_D3

value: DMSO


title: HMVEC-L of uninfected airway-on-a-chips rep3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq550 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TPM for every gene and every sample

source_name: human lung microvascular endothelial cells (HMVEC-L)

growth_protocol: Human lung microvascular endothelial cells (HMVEC-L) were obtained from Lonza and maintained in the EGM-2-MV medium (Lonza). To prepare airway-on-a-chip, first, a bottom channel of the Polydimethylsiloxane (PDMS) device was pre-coated with fibronectin (3 μg/mL, Sigma). HMVEC-L were suspended at 5×106 cells/mL in EGM2-MV medium. Ten μL suspension medium was injected into the fibronectin-coated bottom channel of the PDMS device. Then, the PDMS device was turned upside down, and incubated for 1 h. After 1 h, the device was turned over, and EGM2-MV medium was added into the bottom channel of the device. After 4 days, human airway organoids were dissociated and seeded into the top channel of the device. Airway organoids (AO) were dissociated into single cells and then suspended at 5×106 cells/mL in AO differentiation medium. Ten μL suspension medium was injected into a top channel of the PDMS device. After 1 h, AO differentiation medium was added into the top channel. The cells were cultured under a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from HMVEC-L of uninfected or infected airway-on-a-chips using ISOGENE (NIPPON GENE).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: SARS-CoV-2 (0.1 MOI) containing AO differentiation medium was injected into the top channel (airway channel) of airway-on-a-chip. After 120 min, the culture medium containing SARS-CoV-2 was replaced with a fresh medium.

tag: cell source

value: HMVEC-L of airway-on-a-chips

tag: infection

value: control


title: HaCaT cells, shIQGAP2, biol rep 3

city: Guangzhou

first: Guibin

last: Li

address: No. 10 Luoxuan 3rd Road, Guangzhou International Biotech Island

institute: KingMed Diagnostics

data_processing:
Clean reads were aligned to the human reference genome (Ensembl, GRCh38 v104.38) by HISAT2 (2.2.1) with default parameters
Read count of each gene was generated by HTSeq29, and FPKM (Fragments Per Kilo bases per Million fragments) were calculated as the gene expression.
Assembly: GRCh38 v104.38
Supplementary files format and content: A tab-delimited matrix text file includes gene ID and corresponding FPKM values for each sample

source_name: skin

growth_protocol: Cells were cultured with DMEM (Corning) supplemented with 10% (vol/vol) FBS (Gibco) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific,15596026)
The RNA-seq libraries were prepared with TruSeq RNA Sample Preparation Kit (Illumina, USA)

value: skin

value: HaCaT

value: aneuploid immortal keratinocyte cell

value: IQGAP2 knockdown


title: HaCaT cells, shIQGAP2, biol rep 1


title: HMVEC-L of uninfected airway-on-a-chips rep1

value: human lung microvascular endothelial cells (HMVEC-L)


title: S855Nr38_CAPAN2_D2


title: ScrAbeta42_3447

value: left ventricle


title: ScrAbeta42_3445

value: wild type


title: HaCaT cells, shIQGAP2, biol rep 2


title: HaCaT cells, normal control, biol rep 3

value: WT


title: ScrAbeta42_3443

value: Ab42 scrambled control


title: HaCaT cells, normal control, biol rep 2


title: S855Nr37_CAPAN2_D1


title: ScrAbeta42_3442


title: Abeta42_3460


title: ScrAbeta42_3441


title: S855Nr36_H1299_C3

source_name: Lung Cancer

value: Lung Cancer


title: HMVEC-L of uninfected airway-on-a-chips rep2


title: HMVEC-L of SARS-CoV-2 infected airway-on-a-chips rep1


title: HMVEC-L of SARS-CoV-2 infected airway-on-a-chips rep3


title: HMVEC-L of SARS-CoV-2 infected airway-on-a-chips rep2


title: S855Nr35_H1299_C2

value: Carfilzomib


title: HaCaT cells, normal control, biol rep 1


title: S855Nr34_H1299_C1


title: S855Nr33_H1299_D3


title: S855Nr30_H23_C3


title: S855Nr31_H1299_D1


title: S855Nr32_H1299_D2


title: MC-F7-1

value: embryonic stem cells

value: NC


title: MC-F7-3


title: S855Nr29_H23_C2


title: Abeta42_3458


title: MC-F7-2


title: HepG2 cells, Sorafenib resistance 3

city: Chengdu

first: Jiayin

last: Yang

state: Sichuan

address: 37 Guoxue Alley, Wuhou District

department: Department of Liver Surgery and Liver Transplantation Center

institute: West China Hospital of Sichuan University

data_processing:
bcl2fastq software
Evaluate raw data to check the quality control effect
Filter the original data, delete reads that do not meet the analysis criteria, and obtain clean reads that can be used for subsequent alignment, statistics, and subsequent analysis.
Evaluate clean data to check the quality control effect
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HepG2 cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingNEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Cells were inoculated into 6-well plates and grown to approximately 80% confluence, and then the first dose of sorafenib was then applied at a concentration of 10 μmol. The medium was changed after 24 h of drug exposure, and the cells that were survived and proliferated stably after the drug removal were considered sorafenib resistant cells. Then continue to cultivate resistance according to the above process and gradually increase the concentration of the drug for 8 months.

value: HepG2 cells

value: hepatocellular carcinoma cells

value: Sorafenib

tag: time

value: eight months


title: HepG2 cells, Sorafenib resistance 1


title: HepG2 cells, Sorafenib sensitive 2


title: HepG2 cells, Sorafenib sensitive 3


title: HepG2 cells, Sorafenib sensitive 1


title: Huh7 cells, Sorafenib sensitive 3

source_name: Huh7 cells

value: Huh7 cells


title: S855Nr28_H23_C1


title: Ly6Clo-MHCIIhi-ko-8-2

city: Planegg

first: Rebecca

last: Metzger

address: Großhaderner Strasse 9

country: Germany

institute: LMU

description:
sample name in processed data file:
GGGGAC

data_processing:
Raw sequencing data were processed with DropSeq-tools version 1.12 using gene annotations from the Ensembl GRCm38.87 database to generate sample- and gene-wise UMI tables. Downstream analysis was conducted with R v3.4.4 and DESeq2 v1.18.1.
Assembly: GRCm38.87
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol: Library preparation for bulk 3′-sequencing of poly(A)-RNA was performed as described by Parekh et al.  with minor modifications

value: sorted intratumoral immune cells

value: ko

value: AOM DSS


title: Ly6Clo-MHCIIhi-ko-4-2

description:
sample name in processed data file:
GTACCG


title: Ly6Clo-MHCIIhi-ko-7-2

description:
sample name in processed data file:
GCACGG


title: Ly6Clo-MHCIIhi-ctrl-7-2

description:
sample name in processed data file:
TAGTAA

value: ctrl


title: Ly6Clo-MHCIIhi-ctrl-8-2

description:
sample name in processed data file:
TTTACA


title: Ly6Clo-MHCIIhi-ko-5-2

description:
sample name in processed data file:
CCTGGC


title: Ly6Clo-MHCIIhi-ctrl-6-2

description:
sample name in processed data file:
ATTTCA


title: Ly6Clo-MHCIIhi-ctrl-5-2

description:
sample name in processed data file:
AATCTT


title: HepG2 cells, Sorafenib resistance 2


title: S855Nr27_H23_D3

value: DMSO


title: WT2

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.19.1.403 pipeline was used to generate the sequence data.
Skewer v0.2.2 was used to remove low quality bases from the paired fastq files.
Kallisto v0.46.0 was used to map the trimmed reads to the Gencode (v24) mouse transcriptome.
Assembly: GENCODE v24 transcriptome (gencode.vM24.transcripts.fa.gz)
Supplementary files format and content: count matrix

growth_protocol: The Mst1 transgenic strain was previously generated by overexpression of Mst1 transgene driven by the cardiomyocyte-restricted alpha-myosin heavy chain promoter (alpha-MHC)[1]. DCM phenotype in this strain has been well documented by our previous studies[1,2,3]. Genotyping was performed and male DCM and littermate non-transgenic (nTG) mice were used at a young (3-week) and adult (5.5 months) ages. DCM phenotype was similarly present in male and female transgenic mice and in the present study, only male mice were used. As we described previously[3]. Gal-3 gene deletion in DCM mice was achieved by cross-breeding to generate genotypes of nTG, Gal3-KO, DCM and DCM/Gal3-KO, respectively. Gal3-KO mice were obtained from Jackson Laboratories and both Gal3-KO and DCM strains were on the same C57BL/6 background. Animals were housed in a standard temperature-controlled environment under a 12-h light-dark cycle. All protocols and procedures used in this study were approved by local animal ethics committee and conformed to the Guide for the Care and Use of Laboratory Animals published by the National Institutes of Health.    REFERENCES:  1. Yamamoto S, Yang G, Zablocki D, Liu J, Hong C, Kim SJ, Soler S, Odashima M, Thaisz J, Yehia G, Molina CA, Yatani A, Vatner DE, Vatner SF and Sadoshima J. Activation of Mst1 causes dilated cardiomyopathy by stimulating apoptosis without compensatory ventricular myocyte hypertrophy. J Clin Invest. 2003;111:1463-74.   2. Wu W, Ziemann M, Huynh K, She G, Pang ZD, Zhang Y, Duong T, Kiriazis H, Pu TT, Bai RY, Li JJ, Zhang Y, Chen MX, Sadoshima J, Deng XL, Meikle PJ and Du XJ. Activation of Hippo signaling pathway mediates mitochondria dysfunction and dilated cardiomyopathy in mice. Theranostics. 2021;11:8993-9008.   3. Nguyen MN, Ziemann M, Kiriazis H, Su Y, Thomas Z, Lu Q, Donner DG, Zhao WB, Rafehi H, Sadoshima J, McMullen JR, El-Osta A and Du XJ. Galectin-3 deficiency ameliorates fibrosis and remodeling in dilated cardiomyopathy mice with enhanced Mst1 signaling. Am J Physiol Heart Circ Physiol. 2019;316:H45-H60.

extract_protocol:
LV tissues of nTG, KO, TG, and TG/KO mice (3 mo of age) were homogenized in TRIzol for RNA isolation with the Direct-zol RNA Miniprep Kit (Zymo Research).
Total RNA (200 ng) underwent rRNA depletion with the NEBNext rRNA Depletion Kit followed by library construction with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: left ventricle

tag: strain

value: male

tag: disease

value: control


title: Abeta42_3456

value: wild type


title: Abeta42_3451


title: Abeta42_3455


title: WT1

value: WT


title: Abeta42_3452


title: Abeta42_3457


title: WT3


title: WT4


title: Huh7 cells, Sorafenib sensitive 2


title: Ly6Clo-MHCIIhi-ko-8-1

description:
sample name in processed data file:
GGGCAG


title: S855Nr25_H23_D1

value: Lung Cancer


title: Ly6Clo-MHCIIhi-ko-6-1

description:
sample name in processed data file:
CCGTCG


title: Huh7 cells, Sorafenib sensitive 1


title: Ly6Clo-MHCIIhi-ko-7-1

description:
sample name in processed data file:
GAGCGG


title: Huh7 cells, Sorafenib resistance 3


title: S855Nr26_H23_D2


title: Mst1-TG3

value: experimental dilated cardiomyopathy


title: Huh7 cells, Sorafenib resistance 1


title: S855Nr43_PANC1_D1

value: Pancreatic Cancer


title: Mst1-TG2


title: S855Nr24_DLD1_C3

source_name: Colon Cancer

value: Carfilzomib

value: Colon Cancer


title: Ly6Clo-MHCIIhi-ko-5-1

description:
sample name in processed data file:
CCAACC


title: 12984_AM

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

data_processing:
Reads quality filtered and trimmed with Bbtools.
Adaptor removed with Bbtools.
Genome alignment with Hisat2.
Counts generated using StringTie.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: gene_count_matrix.csv: Gene count matrix, comma-separated file.

organism: Sus scrofa

source_name: lung macrophage

extract_protocol:
For microglia and macrophages, cell suspensions were homogenised in 2ml lysing matrix D tubes (MP Biomedicals) on a FastPrep 24 at 6.5m/s for 50 seconds. After 5 minutes incubation at room temperature, an equal volume of chloroform was added to the homogenate, samples placed on a shaker at room temperature for 5 minutes, and then centrifuged at 12000rmp, 4°C for 15minutes. The 100μl of the resulting aqueous phase was transferred to a 96 well plate and 60μl isopropanol added. The plate was placed on an orbital shaker at medium speed for 1 minute. 20μl MagMaxTM beads were added to each well and plate returned to orbital shaker for 3 minutes. The 96 well plate was placed onto a magnetic separation rack and supernatant removed without disturbing the magnetic beads. This was repeated until all the aqueous phase had been used. The remaining extraction was performed as per the MagMaxTM -96 total RNA isolation manufacturers protocol, including a TURBOTM DNase clean up step, with a final total RNA elution volume of 40μl. For tissues, RNAlater stabilised tissues were homogenised in 1ml QIAzol reagent using a Qiagen TissueRuptor II on a medium speed setting for 40seconds, or until the lysate was uniformly homogeneous. Total RNA extraction was performed as per the Qiagen RNeasy Lipid tissue mini kit product guidelines, to a final elution volume of 40μl.
Takara SMARTer stranded total RNA-Seq vs2 library prep protocol.

treatment_protocol: Microglia and macrophages were FACs sorted. Samples were identified as microglia if they were both CD11bhigh/CD45-ve/low. Samples from the alveolar lavage were identified as macrophage if they were F4/80+ve/CD163low/-ve.

value: macrophage

tag: origin

value: lung


title: S855Nr23_DLD1_C2


title: Ly6Clo-MHCIIhi-ko-4-1

description:
sample name in processed data file:
TTGAAA

value: sorted intratumoral immune cells


title: Mst1-TG4


title: Ly6Clo-MHCIIhi-ko-3-1

description:
sample name in processed data file:
TACTAT

value: ko


title: 12902_fc_cell

source_name: frontal cortex microglia

value: microglia


title: S855Nr22_DLD1_C1


title: S855Nr20_DLD1_D2


title: S855Nr21_DLD1_D3


title: Ly6Clo-MHCIIhi-ko-2-1

description:
sample name in processed data file:
ATTCTA

value: AOM DSS


title: apoOBs OLD 3

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

data_processing:
After sequencing, raw reads were filtered using fastp software to remove low quality reads and residual Illumina adapters.
Filtered reads were aligned to mm10 reference genome by STAR.
The quantitative analysis of RNA-seq data were used by HTSeq software and differential gene expression was determined by edgeR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: apoptotic osteoblasts (apoOBs)  from old  mice

growth_protocol: For mouse apoptotic osteoblasts (apoOBs) culture, the bone tissue was cut into about 0.5mm pieces, and then cultured with complete medium (DMEM, 100 U/mL penicillin and 100 μg/mL streptomycin, 10% FBS) for 3 days, at which point nonadherent cells were removed by replenishing culture medium. Adherent cells were passaged once reaching 80%–90% confluence and after three passages, the purified bone marrow mesenchymal stem cells (BMSCs) were obtained and then cultured in osteogenic medium for 3 days to induce into osteoblasts. We obtained apoOBs by introducing osteoblasts under ultraviolet light for 0.5h (>90% Trypan Blue+).

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
RNA libraries for RNA-seq were prepared using U-mRNASeq Library Prep Kit following manufacturer's protocols.

value: primary cell

value: apoptotic osteoblasts

tag: developmental stage

value: old


title: 12902_cereb_cell

source_name: cerebellum microglia

value: cerebellum


title: Ly6Clo-MHCIIhi-ko-1-1

description:
sample name in processed data file:
AATACA


title: apoOBs OLD 1


title: Ly6Clo-MHCIIhi-ctrl-8-1

description:
sample name in processed data file:
GGCGTC

value: ctrl


title: 12872_hipp_tissue

source_name: hippocampus tissue

value: tissue

value: hippocampus


title: Huh7 cells, Sorafenib resistance 2

value: Huh7 cells

value: hepatocellular carcinoma cells

value: WT

value: Sorafenib

value: eight months


title: apoOBs YOUNG 3

source_name: apoptotic osteoblasts (apoOBs)  from young  mice

value: young


title: Ly6Clo-MHCIIhi-ctrl-6-1

description:
sample name in processed data file:
CCGGAC

value: sorted intratumoral immune cells


title: Mst1-TG1

value: left ventricle

value: male

value: experimental dilated cardiomyopathy


title: apoOBs OLD 2

value: primary cell


title: S855Nr19_DLD1_D1

value: DMSO

value: Colon Cancer


title: S855Nr17_RPMI_C2

source_name: Multiple Myeloma

value: Carfilzomib

value: RPMI

value: Multiple Myeloma


title: apoOBs YOUNG 1

value: apoptotic osteoblasts


title: Ly6Clo-MHCIIhi-ctrl-7-1

description:
sample name in processed data file:
GACCGC

value: ctrl

value: AOM DSS


title: Ly6Clo-MHCIIhi-ctrl-5-1

description:
sample name in processed data file:
TCTGCA


title: 12891_fc_cell

value: microglia


title: apoOBs YOUNG 2


title: OSS_128167 treated osteoblasts,Input

library_source: genomic

data_processing:
After sequencing, raw reads were filtered using fastp software to remove low quality reads and residual Illumina adapters.
ChIP-seq reads were aligned to the mm10 genome using bwa. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

molecule: genomic DNA

source_name: primary osteoblasts

growth_protocol: For mouse osteoblasts culture, the bone tissue was cut into about 0.5mm pieces, and then cultured with complete medium (DMEM, 100 U/mL penicillin and 100 μg/mL streptomycin, 10% FBS) for 3 days, at which point nonadherent cells were removed by replenishing culture medium. Adherent cells were passaged once reaching 80%–90% confluence and after three passages, the purified bone marrow mesenchymal stem cells (BMSCs) were obtained and then cultured in osteogenic medium for 3 days to induce into osteoblasts.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: OSS_128167 (SIRT6 inhibitor)

value: primary osteoblasts

tag: chip antibody


title: S855Nr16_RPMI_C1


title: 12847_hipp_tissue

value: tissue

value: hippocampus


title: Ly6Clo-MHCIIhi-ctrl-4-1

description:
sample name in processed data file:
TTATTG

value: sorted intratumoral immune cells


title: 12847_hipp_cell

source_name: hippocampus microglia


title: OSS_128167 treated osteoblasts

value: young

value: Pol II (CST, #2629)


title: 12872_hipp_cell


title: WT Osteoblasts,Input


title: S855Nr15_RPMI_D3


title: 12847_fc_cell


title: S855Nr14_RPMI_D2


title: S855Nr18_RPMI_C3


title: Ly6Clo-MHCIIhi-ctrl-3-1

description:
sample name in processed data file:
TAATGA


title: 12891_cereb_cell

value: cerebellum


title: S855Nr13_RPMI_D1


title: Ly6Clo-MHCIIhi-ctrl-2-1

description:
sample name in processed data file:
ATTACT


title: S855Nr12_H929_C3


title: 12829_hipp_tissue


title: S855Nr11_H929_C2


title: Ly6Chi-MHCIIlo-ko-4-1

description:
sample name in processed data file:
GGCCAC

value: ko


title: 12847_cereb_cell


title: 12829_hipp_cell


title: Ly6Chi-MHCIIlo-ko-3-1

description:
sample name in processed data file:
CTGCGG


title: Ly6Clo-MHCIIhi-ctrl-1-1

description:
sample name in processed data file:
AAGATT


title: Ly6Chi-MHCIIlo-ko-2-1

description:
sample name in processed data file:
CCCTGG


title: S855Nr9_H929_D3

value: DMSO


title: 12829_AM

value: macrophage

value: lung


title: S855Nr10_H929_C1

value: Carfilzomib


title: Ly6Chi-MHCIIlo-ko-1-1

description:
sample name in processed data file:
GTTCGA


title: S855Nr8_H929_D2

value: Multiple Myeloma


title: 4ivd1

city: Cologne

first: Thorsten

last: Hoppe

state: NRW

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

institute: Universität zu Köln

data_processing:
Illumina Casava software used for basecalling.
RNA-Seq data were processed through the QuickNGS analysis pipeline version 1.2.7, based on Ensembl 93.
Sequenced reads mapped to C. elegans.
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks.
Genome_build: Ensembl version 93
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Caenorhabditis elegans

source_name: Whole worm lysate, Mutant

growth_protocol: Worms were cultured in standard conditions: 20°C, on nematode growth medium (NGM) agar plates seeded with OP50 E. coli as food source.

extract_protocol:
TRIzol (Ambion) was added to the worm pellets, together with 200µl zirconia beads and homogenization was conducted with Precellys 24-Dual cell homogenizer (Peqlab). After addition of 1-bromo-3-chloropropane, mixing and phase separation by centrifugation, aqueous supernatant was mixed with the same volume of 70% ethanol and total RNA was isolated with Qiagen RNeasy Mini kit following the manufacturer’s instructions.
Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation Kit. Library preparation started with 2µg total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This was followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent 2100 Bioanalyzer), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced Illumina NovaSeq6000 sequencing instrument with an PE100 protocol.

treatment_protocol: Synchronized worms by egg-prep were harvested at day 1 of adulthood after washing with M9 at least twice to remove bacteria and flash frozen with liquid nitrogen before storing at -80°C.

value: Whole body

tag: Stage

value: Day 1 adulthood


title: S855Nr7_H929_D1

tag: cell line


title: 4WT

source_name: Whole worm lysate, WT

value: wild-type


title: 12821_hipp_cell

tag: cell type

value: microglia


title: WT Osteoblasts

value: primary osteoblasts


title: 3bcat1ivd1

source_name: Whole worm lysate, Double mutant

tag: genotype


title: 12821_hipp_tissue

value: tissue


title: 4hecd1


title: S855Nr6_RKO_C3

tag: treatment

value: RKO

value: Colon Cancer


title: 4bcat1ivd1

tag: tissue


title: 4bcat1


title: Ly6Chi-MHCIIlo-ctrl-4-1

description:
sample name in processed data file:
TTAGTT

value: sorted intratumoral immune cells

value: ctrl

value: AOM DSS


title: Ly6Chi-MHCIIlo-ctrl-3-1

description:
sample name in processed data file:
TAAGAT


title: 3bcat1


title: 12821_AM


title: 12821_cereb_cell

value: cerebellum


title: S855Nr5_RKO_C2


title: S855Nr4_RKO_C1


title: 3hecd1


title: 12817_hipp_cell

value: hippocampus


title: 3ivd1


title: 12781_hipp_cell


title: 3WT


title: 12758_hipp_cell


title: Ly6Clo-MHCIIlo-ko-3-1

description:
sample name in processed data file:
CGTGGG

value: ko


title: 2bcat1ivd1


title: 12758_fc_cell


title: S855Nr1_RKO_D1

value: DMSO


title: Ly6Chi-MHCIIlo-ctrl-2-1

description:
sample name in processed data file:
ATGAAT


title: 2bcat1


title: Ly6Clo-MHCIIlo-ko-1-1

description:
sample name in processed data file:
GGGATT


title: 12758_cereb_cell


title: CRPC-HOXB13-C5K13A

city: St. Louis

first: Kiran

last: Mahajan

state: Missouri

address: CB 8242 600 South Euclid Ave

department: Surgery

institute: Washington University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  R
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Genome_build: Ensemble  R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: cell line

growth_protocol: Parental and HOXB13-K13A mutant C4-2B were grown in C4-2B media.

extract_protocol:
Total RNA was extracted and purified using QIAshredder and RNeasy Plus Mini kits. After RNA purification,  it was treated with DNAse I to remove DNA contaminants, purified again on Qiagen RNA easy. Sample was anayzed on bioanlyzer, concentration and purity determined before proceeding with RNA -sequencing.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.
RiboErase method  was used for sequencing

value: C4-2B media

value: Metastatic CRPC cell line

tag: disease state

value: prostate cancer

tag: sample type


title: S855Nr3_RKO_D3


title: CRPC-HOXB13-C4K13A - 2


title: 2ivd1

value: Whole body

value: Day 1 adulthood

tag: replicate


title: Ly6Clo-MHCIIlo-ctrl-4-1

description:
sample name in processed data file:
TTAATC


title: Ly6Chi-MHCIIlo-ctrl-1-1

description:
sample name in processed data file:
AAATTG


title: CRPC-HOXB13-C4K13A - 1


title: 2WT

value: wild-type


title: 12750_cereb_cell

value: microglia


title: S855Nr2_RKO_D2


title: 12750_fc_cell


title: CRPC cell line-Parental - 2


title: 1bcat1ivd1


title: 12750_hipp_cell


title: 12720_fc_cell


title: CRPC cell line-Parental - 1


title: Ly6Clo-MHCIIlo-ko-2-1

description:
sample name in processed data file:
CCCCGT


title: Ly6Clo-MHCIIlo-ctrl-3-1

description:
sample name in processed data file:
TAAAGT


title: 2hecd1


title: Ly6Clo-MHCIIlo-ctrl-1-1

description:
sample name in processed data file:
AAAGTT


title: Ly6Clo-MHCIIlo-ctrl-2-1

description:
sample name in processed data file:
ATCAAA


title: 12707_fc_cell


title: Ly6Chi-MHCIIhi-ko-4-1

description:
sample name in processed data file:
GCTCGC


title: MG10084 - UT

data_processing: Cell Ranger version 3.1.0

source_name: Human prostate Organoid Single cell

growth_protocol: Fresh normal prostate tissues were directly put in a sterile 60 mm dishes and washed twice with 1X PBS and minced by a disposable sterile surgical scalpel blades into approximately 0.1-0.5 mm diameter pieces and were transferred to 1-2 ml of collagenase containing cell dissociation media (Drost et al., 2016) and incubated at 37 °C for 45 min to 1 h with continuous gentle rotation. The dissociated tissues were trypsinized in 5 ml of TrypLE (Gibco, no. 12605-028) with ROCK inhibitor (Y27632) for 20 minutes with intermittent pipetting every 10 min. About 10 ml of ice-cold human prostate organoids culture media was added and centrifuged at 500 g for 5 minutes at 4 °C, and then the supernatant was removed. The dissociated cell suspension was filtered with a 40-μm mesh filter. Cells were counted and a 1x104 cells were resuspended in 75% Matrigel human prostate organoid culture media and plated in a 40 ul drop in the middle of one well of a 24 well plate to create dome shape. A 0.5 ml of complete human prostate organoids culture media culture media was added after the matrigel solidification and maintained under this condition till the patient derived tumor organoids (PDTOs) achieved 300-micron size and processed for single cell analysis.

extract_protocol:
Samples were prepared as 10X genomics protocol
Single cell suspension was processed for library preparation as described in the 10X Genomics single cell suspension protocol. All samples were quantitated  twice on the bioanalyzer and checked to ensure integrity.  10x Single Cell/Nuclei RNAseq  Library and Sequencing Targeting 25K read pairs/cell.  The samples amplified well for adequate libraries set up as per the 10X Genomics protocol.
During library preparation a unique sequence tag called an index was added onto individual samples. This allows multiplexing  all the samples together into a sequencing lane.

value: Normal Prostate

value: Organoid


title: 1hecd1


title: 12599_cereb_cell


title: 12599_fc_cell


title: Ly6Clo-MHCIIlo-ko-4-1

description:
sample name in processed data file:
GGAGCC


title: 1WT


title: 12583_cereb_cell


title: 1ivd1


title: Ly6Chi-MHCIIhi-ko-2-1

description:
sample name in processed data file:
CCCACG


title: Ly6Chi-MHCIIhi-ko-1-1

description:
sample name in processed data file:
GCTAGA


title: 3047_input91919

description:
Chromatin
C4-2B_input Rep 2

data_processing:
Basecalls performed using CASAVA version 1.4.
Reads were demultiplexed and mapped to hg19 using BWA. Potential PCR duplicates have been removed. The corresponding IgG and/or input datasets have been used as background controls. Peaks were identified by MACS2 using the ENCODE-DCC/chip-seq-pipeline2.
Sequencing reads were demultiplexed and processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with the “histone” option (https://github.com/ENCODE-DCC/chip-seq-pipeline2, version v1.1.6-10-gd4f6442) (Roadmap Epigenomics et al., 2015), which aligns reads to human genome (hg19) by bowtie2, generates signal strength relative to the control samples and creates the optimal set of peaks using MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files were generated by converting MACS2 output from bedGraph format; Scores represent normalized signal strength.
Supplementary_files_format_and_content: MACS2 peaks in narrowPeak format.

source_name: Prostate Cancer

growth_protocol: C4-2B cells were grown in DMEM media with charcoal stripped fetal bovine serum.

extract_protocol:
Chromatin immunoprecipitation was performed using the ChIP-IT Express (Active Motif) in accordance to the manufacturer’s protocol. For cell lines, cells were grown in T-150 flasks and crosslinked with formaldehyde at 70–80% confluency. Frozen cells were lysed using a Dounce homogenizer, and their chromatin was sheared by sonication to 1-kb fragments. Per IP reaction, up to 25 μg of sheared chromatin was incubated with 4 μg of antibodies and 25 μl of protein G magnetic beads at 4°C overnight. The captured antibody-bound protein/DNA complexes were extensively washed, and chromatin was eluted, reverse-crosslinked, and digested with proteinase K. The collected DNA was purified using a PCR purification kit (Qiagen) followed by qPCR analysis or high-throughput sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.
During library preparation a unique sequence tag called an index was added onto individual samples. This allows multiplexing all the samples together into a sequencing lane. Samples are run either as a single lane or multiple lanes of either type depending on the number of reads per sample required for your analysis. To maximize for HOXB13 Transcription Factor binding sites in the ChIP sequencing we performed HiSeq3000 which obtains ~350M reads/lane at 1x50 read length. The DNA sequencing data was processed through a new pipeline that was generated and used for the ENCODE project.

value: Prostate cancer cell line

value: Charcoal stripped FBS


title: 1bcat1


title: 3047_hoxb13k13ac

description:
Chromatin
C4-2B _hoxb13k13ac Rep3
hoxb13k13ac


title: Ly6Chi-MHCIIhi-ctrl-4-1

description:
sample name in processed data file:
TGTTTA

value: sorted intratumoral immune cells

value: ctrl


title: Ly6Chi-MHCIIhi-ctrl-3-1

description:
sample name in processed data file:
GTTTAT

value: AOM DSS


title: Ly6Chi-MHCIIhi-ko-3-1

description:
sample name in processed data file:
CGGTGG


title: Myocaritids heart 5692-MA-1 VDJ

city: Nashville

first: Margaret

middle: L

last: Axelrod

state: TN

address: 2200 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt University

description:
Myocaritids heart
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
CD45+ cells were FACS sorted and prepapred as single cell suspensions
Library was performed according to the manufacter’s instructions (single cell 5’ RNA + VDJ protocol, 10x Genomics).
scRNA-seq and scTCR-seq

value: Heart

tag: age

value: 4 weeks old


title: Myocaritids heart 5692-MA-1 FB

description:
Myocaritids heart
10x Genomics


title: Ly6Chi-MHCIIhi-ctrl-2-1

description:
sample name in processed data file:
ATATAG


title: Ly6Chi-MHCIIhi-ctrl-1-1

description:
sample name in processed data file:
AAAACT


title: 2898_input

description:
Chromatin
C4-2B _input Rep 1


title: 3047_igg

description:
Chromatin
C4-2B _igg Rep 2

value: IgG Control


title: 3047_hoxb13k13ac91919

description:
Chromatin
C4-2B _hoxb13k13ac Rep 2
hoxb13k13ac91919


title: Interface mycelium, infected, 72h, rep1

city: Jülich

first: Tom

last: Luthe

address: Wilhelm-Johnen-Strasse

institute: Forschungszentrum Jülich

data_processing:
CLC Genomics Workbench v 20.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the combined S. venezuelae and Alderaan genomes using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.9 similarity fraction: 0.9)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NZ_CP018074.1 + MT711975.1
Supplementary files format and content: tab-delimited txt file includes TPM values for each sample

organism: Streptomyces venezuelae

source_name: mycelium

growth_protocol: S. venezuelae was grown on a filter disk on a GYM agar plate at 30 °C for 24 h or 72 h.

extract_protocol:
RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB).
Library was constructed by Genewiz, Germany.

treatment_protocol: Alderaan or, as a control, SM buffer were spotted in the middle of the filter disk 1 h after inoculation of S. venezuelae.

value: mycelium

value: WT

tag: infection

value: Alderaan


title: Interface mycelium, infected, 72h, rep2

tag: time


title: Interface mycelium, control, 72h, rep2

value: uninfected


title: Interface mycelium, control, 24h, rep2


title: Interface mycelium, control, 72h, rep1


title: Interface mycelium, control, 24h, rep1


title: Myocaritids heart 5692-MA-1

description:
Myocaritids heart
10x Genomics

library_source: transcriptomic single cell

tag: strain


title: Interface mycelium, infected, 24h, rep1


title: Interface mycelium, infected, 24h, rep2


title: 2937_hoxb13-2

description: Chromatin

data_processing:
Basecalls performed using CASAVA version 1.4.
Sequencing reads were demultiplexed and processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with the “histone” option (https://github.com/ENCODE-DCC/chip-seq-pipeline2, version v1.1.6-10-gd4f6442) (Roadmap Epigenomics et al., 2015), which aligns reads to human genome (hg19) by bowtie2, generates signal strength relative to the control samples and creates the optimal set of peaks using MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files were generated by converting MACS2 output from bedGraph format; Scores represent normalized signal strength.
Supplementary_files_format_and_content: MACS2 peaks in narrowPeak format.

extract_protocol:
Chromatin immunoprecipitation was performed using the ChIP-IT Express or ChIP-IT High Sensitivity kit (Active Motif) in accordance to the manufacturer’s protocol. For prostate tissues, fresh normal or tumor specimens were cut into small pieces on dry ice and immediately crosslinked with 1% paraformaldehyde for 10 minutes. For cell lines, cells were grown in T-150 flasks and crosslinked with 1% paraformaldehyde at 70–80% confluency. Frozen cells or tissues were lysed using a Dounce homogenizer, and their chromatin was sheared by sonication to 1-kb fragments. Per IP reaction, up to 25 μg of sheared chromatin was incubated with 4 μg of antibodies and 25 μl of protein G magnetic beads at 4°C overnight. The captured antibody-bound protein/DNA complexes were extensively washed, and chromatin was eluted, reverse-crosslinked, and digested with proteinase K. The collected DNA was purified using a PCR purification kit (Qiagen) followed by qPCR analysis or high-throughput sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.
During library preparation a unique sequence tag called an index was added onto individual samples. This allows multiplexing all the samples together into a sequencing lane. Samples are run either as a single lane or multiple lanes of either type depending on the number of reads per sample required for analysis. To maximize for HOXB13 Transcription Factor binding sites in the ChIP sequencing we performed HiSeq3000 which obtains ~350M reads/lane at 1x50 read length. The DNA sequencing data was processed through a new pipeline that was generated and used for the ENCODE project.

value: Prostate Cancer Cell Line

value: pan HOXB13


title: 2937_rna_pol_ii

description: Chromatin

value: RNA Pol II


title: 2898_hoxb13_k13ac

description:
Chromatin
C4-2B_hoxb13_k13ac Rep 1
hoxb13_k13ac


title: 2898_igg

description:
Chromatin
C4-2B _igg Rep 1


title: 2937_input

description: Chromatin


title: 2937_hoxb13-1

description: Chromatin


title: CD47KO CD3+CD28 Activated Replicate 3 [CD47KO_CD3_CD28_3]

status: Public on Sep 21 2022

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: ~6w old mouse; spleen; CD8 T cells plated for 6h

data_processing:
Sixteen mRNA-seq libraries were pooled and sequenced on two lanes of the HiSeq3000 with Illumina v4 chemistry.
Samples were trimmed for adapters and low quality bases using Trimmomatic software and aligned with reference mouse mm10 genome using STAR software.
Quantification was carried out with RSEM using the transcriptome bam file created by STAR.
Basecalling was performed by RTA (version 1.18.66.3).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality with 89-94% of pass filter reads having Q30 or above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.36).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.1) with parameters: STAR --genomeDir $star_genome --readFilesIn R1_trimmed.fastq R2_trimmed.fastq --outTmpDir /logs/star --outSAMunmapped Within -- outFilterType BySJout --outFilterMultimapNmax 20 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 -- alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- sjdbScore 1 --runThreadN 8 --genomeLoad NoSharedMemory -- outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.2.22).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Assembly: mm10
Supplementary files format and content: Comma-Separated Values (.csv) file containing filtered raw counts produced by RSEM

source_name: Spleen

growth_protocol: Breeding pairs of WT and B6.129S7-Cd47tm1Fpl/J (Cd47−/−) C57BL/6J mice were purchased from the Jackson Laboratory Cd47−/− mice were backcrossed to minimize genetic drift. Mice were maintained and bred under specific pathogen-free conditions under protocol NCI/LP-012. Littermate and sex-matched mice were used between 6 and 12 weeks of age for experiments. LCMV infection of mice was done under NIAID/LI-5E protocol.

extract_protocol:
Total RNA of untreated and activated CD8+T cells was isolated using the TRIzol RNA extraction protocol using manufacturer's instructions.
Illumina TruSeq® Stranded mRNA Library Prep (Illumina Inc., CA)

treatment_protocol: A total peripheral T cell population was isolated from mouse spleens by negative selection using Pan T cell Isolation Kit II (MACS, Miltenyi Biotec) to deplete cells expressing CD11b, CD11c, CD19, CD45R, CD49b, CD105, MHC class II, and Ter-119. CD8+ cells from the isolated Pan T cells were further sorted using FACSAria II (BD Biosciences). Total CD8+ T cells and untouched naïve CD8+ T Cells from WT and Cd47 null mice were extracted using the mouse CD8a+ T Cell Isolation Kit (Order no. 130-104-075) and mouse Naive CD8a+ T Cell Isolation Kit (Order no. 130-096-543), respectively, from Miltenyi Biotec according to the manufacturer’s instructions. Purified Hamster Anti-Mouse CD28 (BD PharmingenTM) and CD3 Monoclonal Antibody (17A2), Functional Grade (eBioscienceTM) were used to coat 12 well plates (Corning, USA) with anti-CD28 (4 ug/ml) and anti-CD3 (2 ug/ml) overnight at 4°C. The freshly isolated CD8+ T cells (mouse CD8a+ T Cell Isolation Kit, Miltenyi Biotec) were plated on anti-CD3 plus anti-CD28 coated plates for 6h. Untreated CD8+ T cells were used as control.

value: CD3+CD28 activated

value: Spleen


title: Amygdala Control 4 ATAC-seq

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

data_processing:
Reads were aligned to the Rattus norvegicus Rnor_6.0 genome using BWA MEM (Burrows-Wheeler Aligner) (v0.7.15) and alignments were adjusted to account for transposon binding: + strand alignments by +4bp, - strand alignments by -5bp.
Peak calling was performed using Macs2 (v2.1.1). Peaks were filtered at a score threshold >5.
Prior to differential analysis, peaks were merged into a union set using bedtools (v2.27.1) merge and peak abundance was quantified as raw counts based on read alignments using featureCounts (v1.5.0).
Normalization was performed and reads expressed as CPM (counts per million) and additionally, TMM normalization and differential statistics were computed with edgeR. We adjusted p-values for multiple testing using the false discovery rate (FDR) correction.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: '.bed' file format. Files contain peak calls from Macs2 at a p-value threshold of 1e-5.

organism: Rattus norvegicus

source_name: Saline injected

extract_protocol: Frozen amygdala samples (6 controls and 6 ethanol treated) were processed for ATAC-seq. They were tagmented with Illumina’s Nextera DNA sample prep kit and amplified using custom Nextera library specific primers. The resulting libraries were QC checked and paired-end sequenced using the Illumina® platform.

treatment_protocol: Adult male Sprague Dawley rats received either saline or ethanol (1g/kg) intraperitoneal injections and after 1 h animals were sacrificed and amygdala tissue collected for ATAC-seq. This protocol has been described in "Pandey et al., 2008, Journal of Neuroscience 28 (14), 3729-3737".

value: Sprague Dawley/WT

value: Amygdala

tag: treatment group

value: Control


title: Amygdala Control 6 ATAC-seq


title: Amygdala Control 5 ATAC-seq


title: Amygdala Ethanol 3 ATAC-seq

source_name: Ethanol injected (i.p 1g/kg)

value: Acute Ethanol


title: CD47KO CD3+CD28 Activated Replicate 4 [CD47KO_CD3_CD28_4]


title: Amygdala Ethanol 1 ATAC-seq


title: Amygdala Ethanol 2 ATAC-seq


title: Amygdala Ethanol 5 ATAC-seq


title: Amygdala Ethanol 4 ATAC-seq


title: Amygdala Ethanol 6 ATAC-seq


title: CD47KO CD3+CD28 Activated Replicate 1 [CD47KO_CD3_CD28_1]


title: WT CD3+CD28 Activated Replicate 4 [WT_CD3_CD28_4]


title: Amygdala Control 3 ATAC-seq


title: Amygdala Control 2 ATAC-seq


title: WT CD3+CD28 Activated Replicate 3 [WT_CD3_CD28_3]


title: CD47KO Untreated Replicate 2 [CD47KO_UT_2]

value: Untreated


title: CD47KO CD3+CD28 Activated Replicate 2 [CD47KO_CD3_CD28_2]


title: WT CD3+CD28 Activated Replicate 2 [WT_CD3_CD28_2]


title: CD47KO Untreated Replicate 4 [CD47KO_UT_4]


title: WT CD3+CD28 Activated Replicate 1 [WT_CD3_CD28_1]


title: CD47KO Untreated Replicate 3 [CD47KO_UT_3]


title: WT Untreated Replicate 4 [WT_UT_4]


title: WT Untreated Replicate 3 [WT_UT_3]


title: MAP, control, 2

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
For the processing of bacterial transcriptome profile, sequence reads were mapped onto the reference genome of MAP (NC_002944.2) using Bowtie (v1.2.2) with a maximum insert size of 1000 bp and two maximum mismatches after trimming 3 bp at the 3’ ends. Subsequently, SAM output files generated from Bowtie were transformed to BAM format using SAMtools (http://samtools.sourceforge.net/). The differential gene expression was analyzed using the DESeq2 R package.
For the processing of human transcriptome profile, the relative abundances of genes were measured in Read Count using StringTie.
Statistical analysis was performed to find DEGs using the estimates of abundances for each gene in samples. Data were then log2-transformed and subjected to TMM normalization. Statistical significance of the differential expression data was determined using exactTest using edgeR and fold change in which the null hypothesis was that no difference exists among groups.
False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.
Assembly: GRCh37/hg19, NC_002944.2
Supplementary files format and content: Text files include FPKM values for each Sample

organism: Mycobacterium avium subsp. paratuberculosis K-10

source_name: Bacterial broth culture

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Briefly, removal of rRNA in the total RNA was conducted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, Inc., San Diego, CA, USA) and the NEBNext rRNA Depletion kit (Bacteria) (NEB). After the depletion of rRNA, the remaining RNA was fragmented into small pieces. The cleaved RNA fragments were copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen) and random primers, followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. After the ligation of adapters to the cDNA, the products are then purified and enriched with PCR.
Dual RNA-seq

value: Bacterial broth culture


title: WT Untreated Replicate 2 [WT_UT_2]


title: WT Untreated Replicate 1 [WT_UT_1]


title: MAP, control, 1


title: W.MP332F

type: genomic

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

description: Bisulfite treated

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking.
Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with 0 indicating full lack of methylation and 1 full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.

label: Cy3, Cy5

source_name: uterus

label_protocol: Standard Illumina Protocol

extract_protocol: DNeasy Blood and Tissue kit (QIAGEN)

tag: race

value: white

tag: tissue type

value: Fibroid


title: ISREINFECTG10

type: RNA

city: Frederiksberg

first: Per

middle: Walter

last: Kania

address: Stigbojlen 7

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

description:
2
Gill-180

data_processing:
All q-PCR assays exhibited efficiencies within 100% ± 5% so the simplified 2^-ΔΔCq method was used for analysing data (Livak and Schmittgen, 2001). For normalization and as internal calibrator the average of three genes (ARP, ELF1α and β-actin) was chosen by using NormFinder (Andersen et al., 2004). For gene expression analyses, all challenged groups were compared to non-exposed time point controls using Student’s t-test. We considered differences to be significant when regulations were at least two-fold and p < 0.05.
Target gene signals were normalized using the average of 3 housekeeping genes (ARP, b-actin and ELF 1a) as2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_ average of 3 HKGs). Folds were calculated as  2^-ΔΔCt, where -ΔΔCt = -[ΔCt_infected -ΔCt_control].  First case of folds describes infected groups relative to the uninfected groups at the timepoints.  Second case  of folds describes non-QTL groups relative to the QTL groups at the timepoints.  Third case of folds (only relevant at day 20) describes 1x infected groups relative to the 2x infected groups  in both cases of non-QTL and QTL.

label: FAM

organism: Oncorhynchus mykiss

label_protocol: cDNA synthesis was performed in T100 thermocycler, Biorad, Denmark, using Oligo d(T)16 primer and TaqMan® Reverse Transcription Reagents (cat.no. N8080234, Thermo Fischer Scientific, Denmark). Finally, cDNA was stored at −20°C until further use. Quantitative PCR assays were performed using an AriaMx Real-Time PCR machine (cat.no.G8830A-04R-010, AH diagnostics AS, Denmark). The cycling conditions were one cycle of predenaturation at 95°C for 3 min. This was followed by 40 cycles of denaturation at 94°C for 5 sec with a combined annealing/elongation process at 60°C for 15 sec with endpoint measurement. Primers and Taq-Man probes targeting immune-relevant rainbow trout genes were synthesized at TAG Copenhagen AS, Denmark. Reaction volumes were 12.5 μl (2.5 μl cDNA, 6.25 μl Brilliant III Ultra-Fast QPCR Master Mix (600881, AH Diagnostics AS, Denmark), 1.0 μl primer-probe mixture (forward primer, 10 μM and reverse primer, 10 μM), Taq-Man probe (5 μM), and 2.75 μl RNase-free water. Reverse transcriptase minus and negative controls were used for every plate setup. . NormFinder (Andersen et al., 2004) was applied to evaluate all combinations of three reference genes (Elongation factor (ELF) 1-α, β-actin and acidic ribosomal phosphoprotein P0 (ARP)) as endogenous control; the average of the three genes was chosen and stability values were 0.002, 0.005 and 0.002 for liver, spleen and gills, respectively. In order to quantify the bacterial load in different organs at the different time points we measured the gene expression level of the bacterial gene recA, which was described as a household gene in V.anguillarum  (GenBank ass.no. LC370212) by Crisafi et al. (2014).  Bacterial transcript level was estimated as 2^-ΔCq . It should be noted that dead or inactive bacteria may not be detected by this method.

growth_protocol: Fish were maintained in plastic tanks with low density. Water was recycled (20 L/min) by internal biofilters (EHEIM, Germany) applying 30% water replenishment daily. Water quality was monitored and kept constant at pH 7.6, nitrite < 0.01 mg/l, nitrate < 50 mg/l (TetraTest 6in1, cat.no. T704154, Eldorado A/S, Denmark) and ammonia < 0.5 mg/l (API Ammonia Test Strips, VioVet Ltd, UK). During the 14 days acclimation and 14 days experimental infection period, fish received commercial pelleted feed (1.5% biomass per day, INICIO 917, BioMar A/S, Denmark). After the pathogen exposure fish with clinical signs were euthanized with overdose (300 mg/L) of ethyl-3-aminobenzoate methanesulfonate (MS222) (cat.no. A5040, Sigma-Aldrich, Denmark)

extract_protocol: RNAlater fixed samples from fish (gills, liver and spleen) were homogenized (Tissue-lyser II, Qiagen, Denmark) using a homogenization buffer with 2-mercaptoethanol (Sigma-Aldrich). RNA was extracted using the GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). Liver samples were pre-treated by Proteinase K (cat.no.P4850, Sigma-Aldrich, Denmark). DNase I (AMPD1, Sigma-Aldrich, Denmark) treatment was applied to remove genomic DNA. The concentration of RNA was determined in a NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark). Quality of RNA was evaluated by agarose (cat.no. 16500100, ThermoFisher Scientific, Denmark) gel electrophoresis. RNA was kept at −80°C until cDNA synthesis.

treatment_protocol: Tissue  spleen, gills) samples were fixed in RNAlater (cat.no R0901, Sigma-Aldrich, Denmark), placed at 4°C for 24 h and subsequently stored at -20°C until further processing.

tag: organ

tag: genotype omy16

value: G

tag: genotype omy17

value: R

tag: status

value: QTL

tag: timepoint

value: Day 20

tag: no. of exposures

value: 1x infected


title: W.MP332N

description: Bisulfite treated

value: Myometrium


title: pig_2

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

institute: Helmholtz Zentrum Munich

data_processing:
The 10X Genomics core computational software Cellranger v.2.0 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment.
For QC, filtering, normalization and batch correction the scanpy python package v.1.4-1.6 and anndata v0.6-0.7, a python implementation of Combat and the R package scran were used. Scripts for preprocessing with detailed descriptions are available here: https://github.com/theislab/2022_Tritschler_pancreas_cross_species
Assembly: hg19, susscrofa
Supplementary files format and content: anndata (annotated data matrix) object saved in h5ad-file format. Raw file contains raw count data for all cells. Processed file contains raw and normalized count data of filtered and annotated cells.

source_name: Single cells of pig pancreatic islets

extract_protocol:
For single-cell suspension of human and pig islets, 60 islets were hand-picked into a 1.5 ml Eppendorf tube, pelleted (280g, 1 min), washed with PBS (minus Mg or Ca, Gibco) and digested with Tryp-LE (Gibco) at 37 °C for 12 min. During the incubation step with Tryp-LE, islets were mechanically disaggregated with a 1ml pipet tip every 2–3 min. The digestive reaction was then stopped by adding FACS-buffer (PBS, 2% FCS, 2mM EDTA) and cells were pelleted (280g, 3 min). Cells were stained with trypan blue to visualize dead cells and counted with a hemocytometer.
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing of read2.
RNA Seq (10X Genomics)

tag: source tissue

value: pancreas

tag: developmental day

value: adult

tag: treatment


title: ISREINFECTG9

description:
2
Gill-179

value: Spleen


title: ISREINFECTG8

description:
2
Gill-178

value: K

value: Excluded


title: ISREINFECTG7

description:
2
Gill-177


title: 2937_igg

description: Chromatin

tag: cell line

tag: cell type

value: Prostate Cancer Cell Line

value: Charcoal stripped FBS

tag: chip antibody

value: IgG


title: ISREINFECTG5

description:
1
Gill-175

value: A


title: CD47KO Untreated Replicate 1 [CD47KO_UT_1]

tag: genotype

value: Untreated

tag: tissue


title: ISREINFECTG4

description:
1
Gill-174


title: Amygdala Control 1 ATAC-seq

tag: strain

value: Sprague Dawley/WT

value: Amygdala

tag: treatment group

value: Control


title: ISREINFECTG1

description:
1
Gill-171

value: G

value: R

value: QTL


title: IS1WG10

description:
2
Gill-170

value: Day 20

value: 2x infected


title: ISREINFECTG2

description:
1
Gill-172

value: 1x infected


title: pig_1

value: pancreas

value: adult


title: IS1WG9

description:
2
Gill-169

value: Spleen

value: K

value: Excluded


title: ISREINFECTG6

description:
2
Gill-176


title: IS1WG7

description:
2
Gill-167


title: D3

city: Beijing

first: Jiao

last: Shen

address: #15 Datun Rd., Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
The clean reads were mapped to the genome using HISAT2
The expression level of a gene was calculated by RSEM
The mRNA expression level (calculated from transcripts per million, or log10(TPM+1)) was calculated, and the heat map was generated in R using pheatmap
Supplementary files format and content: The mRNA expression level was calculated from transcripts per million, or log10(TPM+1)

source_name: Tumor inflitrating CD8+T cells

growth_protocol: MC38 was inoculated on C57/B6J mice

extract_protocol:
Tumor inflitrating CD8+T cells were isolated on BD AriaIII. Total RNA extraction was accomplished by BGI (Beijing, China).
Library construction was accomplished by BGI (Beijing, China).

treatment_protocol: 30μg αPD-1-IL-15-R was i.p. treated on day 14 and 17

value: Tumor inflitrating CD8+T cells

value: WT


title: C1

value: PBS


title: ISREINFECTG3

description:
1
Gill-173


title: C2


title: D2


title: C3


title: IS1WG6

description:
2
Gill-166


title: e12.5_wt1_input.fq.gz

first: Zhang

last: shuangfeng

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: Institute of Zoology, Chinese Academy of Sciences

description: X-ChIP

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 (v.2.4.1).
MACS2 (v.2.2.7.1) was used to call peaks (-g mm -q 0.01 -f BAM) relative to input sample. MAnorm (v.1.2.0) was then used for quantitative comparison of ChIP-Seq data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: wig files were generated using bamcoverage function of DeepTools (v.3.4.0).
Supplementary_files_format_and_content: tab-delimited text files. Peak annotation was performed using ChIPseeker (v.1.22.1) at gene level and promoter regions was defined as +/- 3000bp of TSS

source_name: Forebrain tissue

extract_protocol: EED DNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. Other DNA libraries were prepared from CUT&Tag protocol and using standard NovaSeq protocols.

value: wild type

value: forebrain

value: untreated


title: IS1WG5

description:
1
Gill-165

value: G

value: A


title: D1


title: IS1WG4

description:
1
Gill-164

value: R


title: e12.5_wt1_eed.fq.gz

description: X-ChIP


title: IS1WG3

description:
1
Gill-163

value: QTL

value: Day 20


title: IS1WG8

description:
2
Gill-168

value: 2x infected


title: e12.5_cko1_input.fq.gz

description: X-ChIP

value: EedcKO


title: IS1WG2

description:
1
Gill-162


title: IS1WG1

description:
1
Gill-161


title: e12.5_cko1_eed.fq.gz

description: X-ChIP


title: E12.5_WT1

data_processing:
Fundamental integrated software inside the BGISEQ-500 sequencing platform was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 2.2.0 with default parameters.
Transcripts per million (TPM) were calculated using a standard protocol. In short, Transcripts Per Kilobase of exon model per Million mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: Raw_gene_tpm_matrix.txt  (tab-delimited text file includes TPM values for each Sample)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt  (Matrix table with raw gene counts for every gene and every sample)

extract_protocol:
Forebrains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Use Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to detect the concentration of total RNA, RIN value, 28S/18S and fragment size.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols.


title: E12.5_cKO3


title: CIS1WG10

description:
2
Gill-160

value: Uninfected


title: E12.5_WT2


title: E12.5_cKO2


title: CIS1WG8

description:
2
Gill-158

value: Spleen


title: CIS1WG9

description:
2
Gill-159


title: CIS1WG7

description:
2
Gill-157

value: K


title: CIS1WG6

description:
2
Gill-156


title: E12.5_cKO1


title: CIS1WG5

description:
1
Gill-155


title: CIS1WG1

description:
1
Gill-151

value: Excluded


title: CIS1WG4

description:
1
Gill-154


title: CIS1WG2

description:
1
Gill-152


title: IS4DG10

description:
2
Gill-150

value: Day 7

value: 1x infected


title: CIS1WG3

description:
1
Gill-153


title: IS4DG9

description:
2
Gill-149


title: IS4DG8

description:
2
Gill-148


title: IS4DG7

description:
2
Gill-147


title: IS4DG6

description:
2
Gill-146


title: IS4DG5

description:
1
Gill-145


title: IS4DG4

description:
1
Gill-144


title: IS4DG3

description:
1
Gill-143


title: IS4DG2

description:
1
Gill-142


title: B.NW1F

description: Bisulfite treated

data_processing:
Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking.
Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating full lack of methylation and “1” full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.

tag: race

value: Black

tag: tissue type

value: Fibroid


title: B.NW166F2

description: Bisulfite treated


title: IS4DG1

description:
1
Gill-141

tag: organ

tag: genotype omy16


title: B.NW166F1

description: Bisulfite treated


title: B.NW63F2

description: Bisulfite treated


title: CIS4DG8

description:
2
Gill-138

tag: genotype omy17

tag: status


title: Caco2_WT-4, RNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

description: 2 X 75 bp

data_processing:
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) or mouse genome (GRCm38) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Assembly: GRCh38 (gencode version 25) and GRCm38
Supplementary files format and content: tab-delimited text files include feature counts

growth_protocol: Caco-2 cells were maintained in MEM medium containing 20% (vol/vol) FCS at 37 °C with 5 % CO2.

extract_protocol:
RNA was isolated from Caco-2 cells and purified IECs using RNeasy kit (Qiagen) according to manufacturer´s instructions.
RNA samples from Caco-2 cells were sequenced on HiSeq3000 (Illumina, San Diego, United States) (2 X 75 bp) while that from mice IECs were sequenced NovaSeq 6000 (2 X 50 bp) using Illumina total RNA stranded TruSeq protocol.

treatment_protocol: Mice were provided with food and water ad libitum and maintained in conformity to national and international laws and policies and with appropriate permissions,

tag: disease state

value: colorectal adenocarcinoma

value: colorectal adenocarcinoma cells

value: WT


title: Caco2_3AKO-4, RNA

description: 2 X 75 bp


title: Caco2_3A1-4, RNA

description: 2 X 75 bp

value: {delta}DNMT3A + DNMT3A1


title: CIS4DG9

description:
2
Gill-139

value: G

value: A

tag: timepoint

tag: no. of exposures


title: B.MP423F

description: Bisulfite treated


title: CIS4DG7

description:
2
Gill-137

value: R


title: B.MP419F

description: Bisulfite treated


title: Caco2_3A2-3, RNA

description: 2 X 75 bp

value: {delta}DNMT3A + DNMT3A2


title: CIS4DG10

description:
2
Gill-140

value: QTL


title: Caco2_3A2-4, RNA

description: 2 X 75 bp


title: Caco2_3AKO-3, RNA

description: 2 X 75 bp


title: CIS4DG4

description:
1
Gill-134

value: Uninfected


title: CIS4DG6

description:
2
Gill-136

value: Spleen


title: B.MP381F

description: Bisulfite treated


title: Caco2_WT-3, RNA

description: 2 X 75 bp


title: B.MP416F

description: Bisulfite treated


title: CIS4DG5

description:
1
Gill-135


title: CIS4DG1

description:
1
Gill-131


title: B.MP380F

description: Bisulfite treated


title: Caco2_3A2-2, RNA

description: 2 X 75 bp


title: IS24HG10

description:
2
Gill-130

value: Day 4


title: Caco2_3A1-2, RNA

description: 2 X 75 bp


title: B.MP366F2

description: Bisulfite treated


title: IS24HG9

description:
2
Gill-129


title: IS24HG8

description:
2
Gill-128


title: IS24HG7

description:
2
Gill-127

value: K


title: Caco2_3AKO-2, RNA

description: 2 X 75 bp


title: B.MP366F1

description: Bisulfite treated


title: CIS4DG3

description:
1
Gill-133

value: Day 7


title: Caco2_WT-2, RNA

description: 2 X 75 bp


title: Caco2_3A1-3, RNA

description: 2 X 75 bp


title: IS24HG5

description:
1
Gill-125

value: 1x infected


title: CIS4DG2

description:
1
Gill-132


title: B.MP357F2

description: Bisulfite treated

value: Black


title: IS24HG6

description:
2
Gill-126

value: Excluded


title: IS24HG4

description:
1
Gill-124


title: IS24HG3

description:
1
Gill-123


title: IS24HG2

description:
1
Gill-122


title: Caco2_3A2-1, RNA

description: 2 X 75 bp

value: colorectal adenocarcinoma


title: Caco2_3A1-1, RNA

description: 2 X 75 bp

value: colorectal adenocarcinoma cells


title: IS24HG1

description:
1
Gill-121


title: CIS24HG10

description:
2
Gill-120


title: B.MP348F1

description: Bisulfite treated

value: Fibroid


title: B.MP344F

description: Bisulfite treated


title: CIS24HG9

description:
2
Gill-119


title: Caco2, WT-2, DNA

hyb_protocol: For Caco-2 cells, bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Infinium Methylation EPIC Beadchip using standard Illumina protocol: For mice tissue, bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation-12v1-0 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
DNA methylation data was analyzed using the Bioconductor package RnBeads (version 1.12.1) with human reference genome version hg19.
The signal intensity values were normalized using the dasen method. The human and mouse data were normalized separately.

source_name: Caco2 cell line

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from Caco-2 cells, purified IECs and intestinal crypts using DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer´s instructions.

treatment_protocol: For DSS experiments, mice were treated with 2%DSS for 5 days followed by 7 days of normal drinking water.

value: WT

tag: treatment

value: No treatment


title: Caco2_3AKO-1, RNA

description: 2 X 75 bp

tag: cell line


title: CIS24HG8

description:
2
Gill-117


title: Caco2, WT-3, DNA

tag: cell type


title: B.MP357F1

description: Bisulfite treated


title: Caco2, 3A2-4, DNA


title: B.MP321F

description: Bisulfite treated


title: Caco2_WT-1, RNA

description: 2 X 75 bp


title: CIS24HG6

description:
2
Gill-116

value: G

value: A


title: H3K27Ac_CIN_d35_rep3

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: H3K27Ac CIN ChIP replicate 3

data_processing:
Raw reads were processed using AIAP (v1.1) to peform QC, alignment, bigwig file generation, and peak calling
Genome_build: hg38
Supplementary_files_format_and_content: bigwig signal density and macs2 peak calls

source_name: embryonic stem cells

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Matrigel coated cultureware

extract_protocol:
For CUT and TAG genomic DNA was amplified after tagmentation and purified using AMPure XP beads. For ChIP DNA was purified using AMPure XP beads.
For CUT and TAG samples with unique dual-end indexes were pooled in equimolar concentrations and were sequenced on the NovaSeq-6000 sequencer with the S4 flow cell as 2 x 150 bp paired-end reads at a depth of 10 million. For ChIP library preparation and sequencing were performed using the HiSeq3000 sequencer to obtain at least 30 M single end 50 base pair reads per sample reads per sample

treatment_protocol: Embryonic stem cells were specified as medial ganglionic eminence (hMGE) progenitor and then further differentiated into human cortical interneurons (hcIN)

value: cortical interneuron

tag: stem cell source

value: H9 hESC

tag: passage


title: Caco2, 3AKO-3, DNA

tag: genotype


title: CIS24HG4

description:
1
Gill-115

value: R

value: Uninfected


title: H3K27Ac_CIN_d35_rep2

description: H3K27Ac CIN ChIP replicate 2


title: CIS24HG5

description:
1
Gill-114

value: Spleen

value: QTL

value: Day 4


title: CIS24HG3

description:
1
Gill-113


title: W.MP364F2

description: Bisulfite treated

value: White


title: W.MP364F1

description: Bisulfite treated


title: ISG10

description:
2
Gill-110

value: 5 hpe

value: 1x infected


title: CIS24HG2

description:
1
Gill-112

value: K

value: Excluded


title: Caco2, 3A1-4, DNA

value: colorectal adenocarcinoma

value: colorectal adenocarcinoma cells

value: {delta}DNMT3A + DNMT3A1


title: Caco2, WT-4, DNA

value: WT

value: No treatment


title: W.MP369F

description: Bisulfite treated

value: Fibroid


title: W.MP359F2

description: Bisulfite treated


title: Caco2, 3A2-2, DNA

value: {delta}DNMT3A + DNMT3A2


title: Caco2, WT-1, DNA


title: Caco2, 3AKO-4, DNA


title: ISG7

description:
2
Gill-107

value: G

value: R


title: Caco2, 3AKO-1, DNA


title: ISG9

description:
2
Gill-109

value: Spleen

value: A


title: H3K27Ac_CIN_d35_rep1

description: H3K27Ac CIN ChIP replicate 1

value: cortical interneuron

value: H9 hESC


title: CIS24HG7

description:
2
Gill-118

value: QTL

value: Day 4

value: Uninfected


title: Caco2, 3AKO-2, DNA


title: W.MP359F1

description: Bisulfite treated

value: White


title: Caco2, 3A1-3, DNA

value: colorectal adenocarcinoma


title: ISG8

description:
2
Gill-108

value: 5 hpe

value: 1x infected


title: Caco2, 3A1-2, DNA

value: colorectal adenocarcinoma cells

value: {delta}DNMT3A + DNMT3A1


title: ISG5

description:
1
Gill-105


title: W.MP355F

description: Bisulfite treated

value: Fibroid


title: ISG4

description:
1
Gill-104

value: K

value: Excluded


title: H3K27Ac_NPC_d15_rep1

description: H3K27Ac NPC ChIP replicate 1

value: medial ganglionic eminence neuronal precursor


title: Caco2, 3A2-1, DNA

value: {delta}DNMT3A + DNMT3A2

value: No treatment


title: H3K27Ac_NPC_d15_rep2

description: H3K27Ac NPC ChIP replicate 2


title: ISG3

description:
1
Gill-103

value: Spleen

value: G

value: R


title: W.MP351F5

description: Bisulfite treated


title: ISG2

description:
1
Gill-102

value: QTL


title: H3K27Ac_ESC_d0_rep3

description: H3K27Ac ESC ChIP replicate 3

value: embryonic stem cells

value: H9 hESC


title: ISG6

description:
2
Gill-106


title: H3K27Ac_NPC_d15_rep3

description: H3K27Ac NPC ChIP replicate 3


title: ISG1

description:
1
Gill-101

value: A


title: W.MP351F3

description: Bisulfite treated

value: White


title: Caco2, 3A1-1, DNA

value: colorectal adenocarcinoma


title: Caco2, 3A2-3, DNA

value: colorectal adenocarcinoma cells


title: CIS5HG10

description:
2
Gill-100

value: 5 hpe

value: Uninfected


title: CIS5HG9

description:
2
Gill-099


title: CIS24HG1

description:
1
Gill-111

value: K

value: Day 4


title: H3K27Ac_ESC_d0_rep1

description: H3K27Ac ESC ChIP replicate 1


title: W.MP351F2

description: Bisulfite treated

value: Fibroid


title: CIS5HG8

description:
2
Gill-098


title: H3K4me3_CIN_d35_rep3

description: H3K4me3 CIN ChIP replicate 3

value: cortical interneuron


title: CIS5HG7

description:
2
Gill-097


title: CIS5HG6

description:
2
Gill-096


title: W.MP346F2

description: Bisulfite treated


title: H3K4me3_CIN_d35_rep2

description: H3K4me3 CIN ChIP replicate 2


title: CIS5HG4

description:
1
Gill-094

value: Excluded


title: H3K4me3_CIN_d35_rep1

description: H3K4me3 CIN ChIP replicate 1


title: W.MP345F

description: Bisulfite treated


title: W.MP346F1

description: Bisulfite treated


title: CIS5HG2

description:
1
Gill-092

value: Spleen


title: W.MP342F1

description: Bisulfite treated


title: H3K4me3_NPC_d15_rep2

description: H3K4me3 NPC ChIP replicate 2

value: medial ganglionic eminence neuronal precursor


title: IRREINFG9

description:
2
Gill-089

value: G

value: non-QTL

value: Day 20

value: 1x infected


title: IRREINFG7

description:
2
Gill-087


title: IRREINFG10

description:
2
Gill-090

value: T


title: IRREINFG8

description:
2
Gill-088

value: R


title: W.MP330F

description: Bisulfite treated

value: White


title: IRREINFG6

description:
2
Gill-086


title: IRREINFG5

description:
1
Gill-085


title: H3K4me3_NPC_d15_rep3

description: H3K4me3 NPC ChIP replicate 3

value: H9 hESC


title: H3K4me3_ESC_d0_rep3

description: H3K4me3 ESC ChIP replicate 3

value: embryonic stem cells


title: H3K4me3_NPC_d15_rep1

description: H3K4me3 NPC ChIP replicate 1


title: IRREINFG4

description:
1
Gill-084


title: W.MP342F2

description: Bisulfite treated


title: H3K4me3_ESC_d0_rep2

description: H3K4me3 ESC ChIP replicate 2


title: CIS5HG5

description:
1
Gill-095

value: QTL

value: 5 hpe

value: Uninfected


title: IRREINFG2

description:
1
Gill-082


title: H3K27Ac_ESC_d0_rep2

description: H3K27Ac ESC ChIP replicate 2


title: IRREINFG1

description:
1
Gill-081


title: W.MP317F

description: Bisulfite treated

value: Fibroid


title: IR1WG9

description:
2
Gill-079

value: 2x infected


title: IR1WG8

description:
2
Gill-078

value: K


title: W.MP315F

description: Bisulfite treated


title: W.MP313F

description: Bisulfite treated


title: W.MP308F

description: Bisulfite treated


title: IR1WG7

description:
2
Gill-077

value: Spleen


title: IR1WG4

description:
1
Gill-074


title: IR1WG5

description:
1
Gill-075


title: IR1WG3

description:
1
Gill-073

value: Excluded


title: W.MP306F

description: Bisulfite treated


title: DSS_LI_ILC2_1

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

institute: Keio University School of Medicine

description: gene expression

data_processing:
Real Time Analysis 2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using kallisto v0.44.0 with parameters -b 100; pachterlab.github.io/kallisto/
Transcripts Per Kilobase Million (TPM) were calculated using sleuth.
Assembly: mm10
Supplementary files format and content: tab-separated values files includes pseudocount matrix for each sample.

extract_protocol:
RNA was harvested using Trizol reagent. RNA was prepared from approximately 10,000–50,000 cells by using TRIzol (Thermo Fisher Scientific Inc.). Total RNAs were subsequently processed to generate an mRNA-seq library using a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB, E7765S) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (NEB, E7335S and E7550S).
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: Colitis was induced in mice by 2.5% DSS solution in drinking water for 7 days. Colons from mice with DSS colitis and control mice were dissected and lamina propria mononuclear cells (LPMC) isolation was performed as previously described.

tag: tissue

value: WT

value: DSS


title: IR1WG2

description:
1
Gill-072

value: G

value: non-QTL

value: Day 20


title: NT_LI_ILC2_r3

description: gene expression

value: NT


title: IRREINFG3

description:
1
Gill-083

value: T

value: 1x infected


title: DSS_LI_ILC2_3

description: gene expression


title: NT_LI_ILC2_r2

description: gene expression


title: W.MP319F

description: Bisulfite treated

value: White


title: IR1WG1

description:
1
Gill-071

value: R


title: W.MP305F

description: Bisulfite treated


title: CIR1WG10

description:
2
Gill-070


title: DSS_LI_ILC2_2

description: gene expression


title: H3K4me3_ESC_d0_rep1

description: H3K4me3 ESC ChIP replicate 1

value: embryonic stem cells

value: H9 hESC


title: IR1WG10

description:
2
Gill-080


title: NT_LI_ILC2_r1

description: gene expression


title: IR1WG6

description:
2
Gill-076


title: CIR1WG9

description:
2
Gill-069

value: Uninfected


title: CIR1WG8

description:
2
Gill-068


title: CIR1WG7

description:
2
Gill-067


title: B.NW63N

description: Bisulfite treated

value: Black

value: Myometrium


title: B.NW1N

description: Bisulfite treated


title: CIR1WG6

description:
2
Gill-066

value: Spleen

value: K


title: B.NW166N

description: Bisulfite treated


title: B.MP423N

description: Bisulfite treated


title: CIS5HG1

description:
1
Gill-091

value: A

value: QTL

value: 5 hpe


title: B.MP419N

description: Bisulfite treated


title: WT_S4h_1

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including RPKM for each sample.

organism: Thermothelomyces thermophilus

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel or 2% starch as the carbon source for an additional 4 h or 6 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

value: mycelia cells


title: WT_S4h_2


title: WT_S4h_3


title: WT_A6h_1


title: W.MP100F

description: Bisulfite treated

tag: race

value: Fibroid


title: WT_A6h_3


title: IR4DG10

description:
2
Gill-060

value: G

value: non-QTL

value: Day 7


title: IR4DG9

description:
2
Gill-059

value: T

value: 1x infected


title: CIR1WG4

description:
1
Gill-064

value: Day 20


title: CIR1WG5

description:
1
Gill-065


title: CIR1WG1

description:
1
Gill-061


title: CIR1WG3

description:
1
Gill-063

value: R


title: CIR1WG2

description:
1
Gill-062

value: Uninfected


title: IR4DG6

description:
2
Gill-056


title: B.MP381N

description: Bisulfite treated

value: Black

tag: tissue type


title: IR4DG7

description:
2
Gill-057

tag: organ


title: WT_A6h_2


title: IR4DG8

description:
2
Gill-058

tag: genotype omy16

value: Excluded


title: WT_A4h_3


title: WT_A4h_2


title: B.MP416N

description: Bisulfite treated

value: Myometrium


title: WT_A4h_1


title: B.MP366N

description: Bisulfite treated


title: B.MP357N

description: Bisulfite treated


title: IR4DG3

description:
1
Gill-053

value: Spleen

tag: genotype omy17


title: CIR4DG10

description:
2
Gill-050

value: K

tag: status


title: IR4DG5

description:
1
Gill-055


title: IR4DG2

description:
1
Gill-052


title: IR4DG4

description:
1
Gill-054


title: CIR4DG9

description:
2
Gill-049


title: CIR4DG6

description:
2
Gill-046


title: CIR4DG5

description:
1
Gill-045


title: B.MP348N

description: Bisulfite treated


title: Mycth_90344_S4h_2


title: CIR4DG8

description:
2
Gill-048


title: B.MP344N

description: Bisulfite treated


title: CIR4DG7

description:
2
Gill-047


title: Mycth_90344_S4h_1


title: Mycth_90344_A6h_3


title: CIR4DG4

description:
1
Gill-044


title: B.MP380N

description: Bisulfite treated


title: B.MP321N

description: Bisulfite treated


title: Mycth_90344_A6h_2


title: W.MP369N

description: Bisulfite treated

value: White


title: CIR4DG2

description:
1
Gill-042


title: CIR4DG3

description:
1
Gill-043


title: IR4DG1

description:
1
Gill-051


title: CIR4DG1

description:
1
Gill-041


title: Mycth_90344_S4h_3


title: IR24HG10

description:
2
Gill-040

value: Day 4


title: IR24HG9

description:
2
Gill-039


title: IR24HG8

description:
2
Gill-038


title: W.MP364N

description: Bisulfite treated


title: Mycth_90344_A4h_3

value: mycelia cells


title: W.MP359N

description: Bisulfite treated